R/models.R
In INBO-BMK/INLA: Full Bayesian Analysis of Latent Gaussian Models using Integrated Nested Laplace Approximations
Defines functions
`inla.models.section.latent`
`inla.models.section.group`
`inla.models.section.mix`
`inla.models.section.link`
`inla.models.section.predictor`
`inla.models.section.hazard`
`inla.models.section.likelihood`
`inla.models.section.prior`
`inla.models.section.wrapper`
`inla.models`
`inla.is.model`
`inla.model.properties`
`inla.model.properties.generic`
`inla.model.validate.link.function`
## Export: inla.models
## this is how to define a must-be-enabled...
## status = "changed:Oct.25.2017",
`inla.models.section.latent` = function()
{
return
list(latent =
list(
linear = list(
doc = "Alternative interface to an fixed effect",
hyper = list(
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
pdf = "linear"
),
iid = list(
doc = "Gaussian random effects in dim=1",
hyper = list(
theta = list(
hyperid = 1001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.00005),
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
pdf = "indep"
),
mec = list(
doc = "Classical measurement error model",
hyper = list(
theta1 = list(
hyperid = 2001,
name = "beta",
short.name = "b",
prior = "gaussian",
param = c(1, 0.001),
initial = 1,
fixed = FALSE,
to.theta = function(x) x,
from.theta = function(x) x
),
theta2 = list(
hyperid = 2002,
name = "prec.u",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.0001),
initial = log(1/0.0001),
fixed = TRUE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta3 = list(
hyperid = 2003,
name = "mean.x",
short.name = "mu.x",
prior = "gaussian",
param = c(0, 0.0001),
initial = 0,
fixed = TRUE,
to.theta = function(x) x,
from.theta = function(x) x
),
theta4 = list(
hyperid = 2004,
name = "prec.x",
short.name = "prec.x",
prior = "loggamma",
param = c(1, 10000),
initial = log(1/10000),
fixed = TRUE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
pdf = "mec"
),
meb = list(
doc = "Berkson measurement error model",
hyper = list(
theta1 = list(
hyperid = 3001,
name = "beta",
short.name = "b",
prior = "gaussian",
param = c(1, 0.001),
initial = 1,
fixed = FALSE,
to.theta = function(x) x,
from.theta = function(x) x
),
theta2 = list(
hyperid = 3002,
name = "prec.u",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.0001),
initial = log(1000),
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
pdf = "meb"
),
rgeneric = list(
doc = "Generic latent model spesified using R",
hyper = list(),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = TRUE,
set.default.values = TRUE,
status = "experimental",
pdf = "rgeneric"
),
rw1 = list(
doc = "Random walk of order 1",
hyper = list(
theta = list(
hyperid = 4001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.00005),
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = TRUE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
min.diff = 1E-5,
pdf = "rw1"
),
rw2 = list(
doc = "Random walk of order 2",
hyper = list(
theta = list(
hyperid = 5001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.00005),
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = TRUE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
min.diff = 1E-3,
pdf = "rw2"
),
crw2 = list(
doc = "Exact solution to the random walk of order 2",
hyper = list(
theta = list(
hyperid = 6001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.00005),
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = TRUE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 2L,
aug.constr = 1L,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
min.diff = 1E-3,
pdf = "crw2"
),
seasonal = list(
doc = "Seasonal model for time series",
hyper = list(
theta = list(
hyperid = 7001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.00005),
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
pdf = "seasonal"
),
besag = list(
doc = "The Besag area model (CAR-model)",
hyper = list(
theta = list(
hyperid = 8001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.00005),
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = TRUE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = TRUE,
set.default.values = TRUE,
pdf = "besag"
),
besag2 = list(
doc = "The shared Besag model",
hyper = list(
theta1 = list(
hyperid = 9001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.00005),
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 9002,
name = "scaling parameter",
short.name = "a",
prior = "loggamma",
param = c(10, 10),
initial = 0,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = c(1L, 2L),
n.div.by = 2L,
n.required = TRUE,
set.default.values = TRUE,
pdf = "besag2"
),
bym = list(
doc = "The BYM-model (Besag-York-Mollier model)",
hyper = list(
theta1 = list(
hyperid = 10001,
name = "log unstructured precision",
short.name = "prec.unstruct",
prior = "loggamma",
param = c(1, 0.0005),
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 10002,
name = "log spatial precision",
short.name = "prec.spatial",
prior = "loggamma",
param = c(1, 0.0005),
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = TRUE,
nrow.ncol = FALSE,
augmented = TRUE,
aug.factor = 2L,
aug.constr = 2L,
n.div.by = NULL,
n.required = TRUE,
set.default.values = TRUE,
pdf = "bym"
),
bym2 = list(
doc = "The BYM-model with the PC priors",
hyper = list(
theta1 = list(
hyperid = 11001,
name = "log precision",
short.name = "prec",
prior = "pc.prec",
param = c(1, .01),
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 11002,
name = "logit phi",
short.name = "phi",
prior = "pc",
param = c(0.5, 0.5),
initial = -3,
fixed = FALSE,
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
constr = TRUE,
nrow.ncol = FALSE,
augmented = TRUE,
aug.factor = 2L,
aug.constr = 2L,
n.div.by = NULL,
n.required = TRUE,
set.default.values = TRUE,
status = "experimental",
pdf = "bym2"
),
besagproper = list(
doc = "A proper version of the Besag model",
hyper = list(
theta1 = list(
hyperid = 12001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.0005),
initial = 2,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 12002,
name = "log diagonal",
short.name = "diag",
prior = "loggamma",
param = c(1, 1),
initial = 1,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = TRUE,
set.default.values = TRUE,
status = "experimental",
pdf = "besagproper"
),
besagproper2 = list(
doc = "An alternative proper version of the Besag model",
hyper = list(
theta1 = list(
hyperid = 13001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.0005),
initial = 2,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 13002,
name = "logit lambda",
short.name = "lambda",
prior = "gaussian",
param = c(0, 0.45),
initial = 3,
fixed = FALSE,
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = TRUE,
set.default.values = TRUE,
status = "experimental",
pdf = "besagproper2"
),
fgn = list(
doc = "Fractional Gaussian noise model",
hyper = list(
theta1 = list(
hyperid = 13101,
name = "log precision",
short.name = "prec",
prior = "pc.prec",
param = c(3, 0.01),
initial = 1,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 13102,
name = "logit H",
short.name = "H",
prior = "pcfgnh",
param = c(0.9, 0.1),
initial = 2,
fixed = FALSE,
to.theta = function(x) log((2*x-1)/(2*(1-x))),
from.theta = function(x) 0.5 + 0.5*exp(x)/(1+exp(x))
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = TRUE,
aug.factor = 5L,
aug.constr = 1L,
n.div.by = NULL,
n.required = FALSE,
set.default.values = TRUE,
order.default = 4L, ## default order for approximation
order.defined = 3L:4L, ## the list of orders which are implemented
pdf = "fgn"
),
fgn2 = list(
doc = "Fractional Gaussian noise model (alt 2)",
hyper = list(
theta1 = list(
hyperid = 13111,
name = "log precision",
short.name = "prec",
prior = "pc.prec",
param = c(3, 0.01),
initial = 1,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 13112,
name = "logit H",
short.name = "H",
prior = "pcfgnh",
param = c(0.9, 0.1),
initial = 2,
fixed = FALSE,
to.theta = function(x) log((2*x-1)/(2*(1-x))),
from.theta = function(x) 0.5 + 0.5*exp(x)/(1+exp(x))
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = TRUE,
aug.factor = 4L,
aug.constr = 1L,
n.div.by = NULL,
n.required = FALSE,
set.default.values = TRUE,
order.default = 4L, ## default order for approximation
order.defined = 3L:4L, ## the list of orders which are implemented
pdf = "fgn"
),
ar1 = list(
doc = "Auto-regressive model of order 1 (AR(1))",
hyper = list(
theta1 = list(
hyperid = 14001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.00005),
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 14002,
name = "logit lag one correlation",
short.name = "rho",
prior = "normal",
param = c(0, 0.15),
initial = 2,
fixed = FALSE,
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta3 = list(
hyperid = 14003,
name = "mean",
short.name = "mean",
prior = "normal",
param = c(0, 1),
initial = 0,
fixed = TRUE,
to.theta = function(x) x,
from.theta = function(x) x
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
pdf = "ar1"
),
ar1c = list(
doc = "Auto-regressive model of order 1 w/covariates",
hyper = list(
theta1 = list(
hyperid = 14101,
name = "log precision",
short.name = "prec",
prior = "pc.prec",
param = c(1, 0.01),
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 14102,
name = "logit lag one correlation",
short.name = "rho",
prior = "pc.cor0",
param = c(0.5, 0.5),
initial = 2,
fixed = FALSE,
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = TRUE,
status = "experimental",
pdf = "ar1c"
),
ar = list(
doc = "Auto-regressive model of order p (AR(p))",
## to many parameters here, but ...
hyper = list(
theta1 = list(
hyperid = 15001,
name = "log precision",
short.name = "prec",
initial = 4,
fixed = FALSE,
prior = "pc.prec",
param = c(3, 0.01),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 15002,
name = "pacf1",
short.name = "pacf1",
initial = 1,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.5),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta3 = list(
hyperid = 15003,
name = "pacf2",
short.name = "pacf2",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.4),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta4 = list(
hyperid = 15004,
name = "pacf3",
short.name = "pacf3",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.3),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta5 = list(
hyperid = 15005,
name = "pacf4",
short.name = "pacf4",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.2),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta6 = list(
hyperid = 15006,
name = "pacf5",
short.name = "pacf5",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.1),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta7 = list(
hyperid = 15007,
name = "pacf6",
short.name = "pacf6",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.1),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta8 = list(
hyperid = 15008,
name = "pacf7",
short.name = "pacf7",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.1),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta9 = list(
hyperid = 15009,
name = "pacf8",
short.name = "pacf8",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.1),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta10 = list(
hyperid = 15010,
name = "pacf9",
short.name = "pacf9",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.1),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta11 = list(
hyperid = 15011,
name = "pacf10",
short.name = "pacf10",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.1),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
pdf = "ar"
),
ou = list(
doc = "The Ornstein-Uhlenbeck process",
hyper = list(
theta1 = list(
hyperid = 16001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.00005),
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 16002,
name = "log phi",
short.name = "phi",
prior = "normal",
param = c(0, .2),
initial = -1,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
pdf = "ou"
),
intslope = list(
doc = "Intecept-slope model with Wishart-prior",
hyper = list(
theta1 = list(
hyperid = 16101,
name = "log precision1",
short.name = "prec1",
initial = 4,
fixed = FALSE,
prior = "wishart2d",
param = c(4, 1, 1, 0),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 16102,
name = "log precision2",
short.name = "prec2",
initial = 4,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta3 = list(
hyperid = 16103,
name = "logit correlation",
short.name = "cor",
initial = 4,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta4 = list(
hyperid = 16104,
name = "gamma1",
short.name = "g1",
initial = 1,
fixed = TRUE, ## YES.
prior = "normal",
param = c(1, 36),
to.theta = function(x) x,
from.theta = function(x) x
),
theta5 = list(
hyperid = 16105,
name = "gamma2",
short.name = "g2",
initial = 1,
fixed = FALSE,
prior = "normal",
param = c(1, 36),
to.theta = function(x) x,
from.theta = function(x) x
),
theta6 = list(
hyperid = 16106,
name = "gamma3",
short.name = "g3",
initial = 1,
fixed = FALSE,
prior = "normal",
param = c(1, 36),
to.theta = function(x) x,
from.theta = function(x) x
),
theta7 = list(
hyperid = 16107,
name = "gamma4",
short.name = "g4",
initial = 1,
fixed = FALSE,
prior = "normal",
param = c(1, 36),
to.theta = function(x) x,
from.theta = function(x) x
),
theta8 = list(
hyperid = 16108,
name = "gamma5",
short.name = "g5",
initial = 1,
fixed = FALSE,
prior = "normal",
param = c(1, 36),
to.theta = function(x) x,
from.theta = function(x) x
),
theta9 = list(
hyperid = 16109,
name = "gamma6",
short.name = "g6",
initial = 1,
fixed = FALSE,
prior = "normal",
param = c(1, 36),
to.theta = function(x) x,
from.theta = function(x) x
),
theta10 = list(
hyperid = 16110,
name = "gamma7",
short.name = "g7",
initial = 1,
fixed = FALSE,
prior = "normal",
param = c(1, 36),
to.theta = function(x) x,
from.theta = function(x) x
),
theta11 = list(
hyperid = 16111,
name = "gamma8",
short.name = "g8",
initial = 1,
fixed = FALSE,
prior = "normal",
param = c(1, 36),
to.theta = function(x) x,
from.theta = function(x) x
),
theta12 = list(
hyperid = 16112,
name = "gamma9",
short.name = "g9",
initial = 1,
fixed = FALSE,
prior = "normal",
param = c(1, 36),
to.theta = function(x) x,
from.theta = function(x) x
),
theta13 = list(
hyperid = 16113,
name = "gamma10",
short.name = "g10",
initial = 1,
fixed = FALSE,
prior = "normal",
param = c(1, 36),
to.theta = function(x) x,
from.theta = function(x) x
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = TRUE,
status = "experimental",
pdf = "intslope"
),
generic = list(
doc = "A generic model",
hyper = list(
theta = list(
hyperid = 17001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.00005),
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = TRUE,
set.default.values = TRUE,
pdf = "generic0"
),
generic0 = list(
doc = "A generic model (type 0)",
hyper = list(
theta = list(
hyperid = 18001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.00005),
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = TRUE,
set.default.values = TRUE,
pdf = "generic0"
),
generic1 = list(
doc = "A generic model (type 1)",
hyper = list(
theta1 = list(
hyperid = 19001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.00005),
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 19002,
name = "beta",
short.name = "beta",
initial = 2,
fixed = FALSE,
prior = "gaussian",
param = c(0, 0.1),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = TRUE,
set.default.values = TRUE,
pdf = "generic1"
),
generic2 = list(
doc = "A generic model (type 2)",
hyper = list(
theta1 = list(
hyperid = 20001,
name = "log precision cmatrix",
short.name = "prec",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 20002,
name = "log precision random",
short.name = "prec.random",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.001),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 2L,
aug.constr = 2L,
n.div.by = NULL,
n.required = TRUE,
set.default.values = TRUE,
pdf = "generic2"
),
generic3 = list(
doc = "A generic model (type 3)",
hyper = list(
theta1 = list(
hyperid = 21001,
name = "log precision1",
short.name = "prec1",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 21002,
name = "log precision2",
short.name = "prec2",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta3 = list(
hyperid = 21003,
name = "log precision3",
short.name = "prec3",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta4 = list(
hyperid = 21004,
name = "log precision4",
short.name = "prec4",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta5 = list(
hyperid = 21005,
name = "log precision5",
short.name = "prec5",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta6 = list(
hyperid = 21006,
name = "log precision6",
short.name = "prec6",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta7 = list(
hyperid = 21007,
name = "log precision7",
short.name = "prec7",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta8 = list(
hyperid = 21008,
name = "log precision8",
short.name = "prec8",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta9 = list(
hyperid = 21009,
name = "log precision9",
short.name = "prec9",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta10 = list(
hyperid = 21010,
name = "log precision10",
short.name = "prec10",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta11 = list(
hyperid = 21011,
name = "log precision common",
short.name = "prec.common",
initial = 0, ## yes!
fixed = TRUE, ## yes!
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = TRUE,
set.default.values = TRUE,
status = "experimental",
pdf = "generic3"
),
spde = list(
doc = "A SPDE model",
## this will be redone anyway soon....
hyper = list(
theta1 = list(
hyperid = 22001,
name = "theta.T",
short.name = "T",
initial = 2,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta2 = list(
hyperid = 22002,
name = "theta.K",
short.name = "K",
initial = -2,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta3 = list(
hyperid = 22003,
name = "theta.KT",
short.name = "KT",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta4 = list(
hyperid = 22004,
name = "theta.OC",
short.name = "OC",
initial = -20,
fixed = TRUE,
prior = "normal",
param = c(0, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = TRUE,
set.default.values = TRUE,
pdf = "spde"
),
spde2 = list(
doc = "A SPDE2 model",
## to many parameters here, but ...
hyper = list(
theta1 = list(
hyperid = 23001,
name = "theta1",
short.name = "t1",
initial = 0,
fixed = FALSE,
prior = "mvnorm",
param = c(1, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta2 = list(
hyperid = 23002,
name = "theta2",
short.name = "t2",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta3 = list(
hyperid = 23003,
name = "theta3",
short.name = "t3",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta4 = list(
hyperid = 23004,
name = "theta4",
short.name = "t4",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta5 = list(
hyperid = 23005,
name = "theta5",
short.name = "t5",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta6 = list(
hyperid = 23006,
name = "theta6",
short.name = "t6",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta7 = list(
hyperid = 23007,
name = "theta7",
short.name = "t7",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta8 = list(
hyperid = 23008,
name = "theta8",
short.name = "t8",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta9 = list(
hyperid = 23009,
name = "theta9",
short.name = "t9",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta10 = list(
hyperid = 23010,
name = "theta10",
short.name = "t10",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta11 = list(
hyperid = 23011,
name = "theta11",
short.name = "t11",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta12 = list(
hyperid = 23012,
name = "theta12",
short.name = "t12",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta13 = list(
hyperid = 23013,
name = "theta13",
short.name = "t13",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta14 = list(
hyperid = 23014,
name = "theta14",
short.name = "t14",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta15 = list(
hyperid = 23015,
name = "theta15",
short.name = "t15",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta16 = list(
hyperid = 23016,
name = "theta16",
short.name = "t16",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta17 = list(
hyperid = 23017,
name = "theta17",
short.name = "t17",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta18 = list(
hyperid = 23018,
name = "theta18",
short.name = "t18",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta19 = list(
hyperid = 23019,
name = "theta19",
short.name = "t19",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta20 = list(
hyperid = 23020,
name = "theta20",
short.name = "t20",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta21 = list(
hyperid = 23021,
name = "theta21",
short.name = "t21",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta22 = list(
hyperid = 23022,
name = "theta22",
short.name = "t22",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta23 = list(
hyperid = 23023,
name = "theta23",
short.name = "t23",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta24 = list(
hyperid = 23024,
name = "theta24",
short.name = "t24",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta25 = list(
hyperid = 23025,
name = "theta25",
short.name = "t25",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta26 = list(
hyperid = 23026,
name = "theta26",
short.name = "t26",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta27 = list(
hyperid = 23027,
name = "theta27",
short.name = "t27",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta28 = list(
hyperid = 23028,
name = "theta28",
short.name = "t28",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta29 = list(
hyperid = 23029,
name = "theta29",
short.name = "t29",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta30 = list(
hyperid = 23030,
name = "theta30",
short.name = "t30",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta31 = list(
hyperid = 23031,
name = "theta31",
short.name = "t31",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta32 = list(
hyperid = 23032,
name = "theta32",
short.name = "t32",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta33 = list(
hyperid = 23033,
name = "theta33",
short.name = "t33",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta34 = list(
hyperid = 23034,
name = "theta34",
short.name = "t34",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta35 = list(
hyperid = 23035,
name = "theta35",
short.name = "t35",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta36 = list(
hyperid = 23036,
name = "theta36",
short.name = "t36",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta37 = list(
hyperid = 23037,
name = "theta37",
short.name = "t37",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta38 = list(
hyperid = 23038,
name = "theta38",
short.name = "t38",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta39 = list(
hyperid = 23039,
name = "theta39",
short.name = "t39",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta40 = list(
hyperid = 23040,
name = "theta40",
short.name = "t40",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta41 = list(
hyperid = 23041,
name = "theta41",
short.name = "t41",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta42 = list(
hyperid = 23042,
name = "theta42",
short.name = "t42",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta43 = list(
hyperid = 23043,
name = "theta43",
short.name = "t43",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta44 = list(
hyperid = 23044,
name = "theta44",
short.name = "t44",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta45 = list(
hyperid = 23045,
name = "theta45",
short.name = "t45",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta46 = list(
hyperid = 23046,
name = "theta46",
short.name = "t46",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta47 = list(
hyperid = 23047,
name = "theta47",
short.name = "t47",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta48 = list(
hyperid = 23048,
name = "theta48",
short.name = "t48",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta49 = list(
hyperid = 23049,
name = "theta49",
short.name = "t49",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta50 = list(
hyperid = 23050,
name = "theta50",
short.name = "t50",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta51 = list(
hyperid = 23051,
name = "theta51",
short.name = "t51",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta52 = list(
hyperid = 23052,
name = "theta52",
short.name = "t52",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta53 = list(
hyperid = 23053,
name = "theta53",
short.name = "t53",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta54 = list(
hyperid = 23054,
name = "theta54",
short.name = "t54",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta55 = list(
hyperid = 23055,
name = "theta55",
short.name = "t55",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta56 = list(
hyperid = 23056,
name = "theta56",
short.name = "t56",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta57 = list(
hyperid = 23057,
name = "theta57",
short.name = "t57",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta58 = list(
hyperid = 23058,
name = "theta58",
short.name = "t58",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta59 = list(
hyperid = 23059,
name = "theta59",
short.name = "t59",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta60 = list(
hyperid = 23060,
name = "theta60",
short.name = "t60",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta61 = list(
hyperid = 23061,
name = "theta61",
short.name = "t61",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta62 = list(
hyperid = 23062,
name = "theta62",
short.name = "t62",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta63 = list(
hyperid = 23063,
name = "theta63",
short.name = "t63",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta64 = list(
hyperid = 23064,
name = "theta64",
short.name = "t64",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta65 = list(
hyperid = 23065,
name = "theta65",
short.name = "t65",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta66 = list(
hyperid = 23066,
name = "theta66",
short.name = "t66",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta67 = list(
hyperid = 23067,
name = "theta67",
short.name = "t67",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta68 = list(
hyperid = 23068,
name = "theta68",
short.name = "t68",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta69 = list(
hyperid = 23069,
name = "theta69",
short.name = "t69",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta70 = list(
hyperid = 23070,
name = "theta70",
short.name = "t70",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta71 = list(
hyperid = 23071,
name = "theta71",
short.name = "t71",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta72 = list(
hyperid = 23072,
name = "theta72",
short.name = "t72",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta73 = list(
hyperid = 23073,
name = "theta73",
short.name = "t73",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta74 = list(
hyperid = 23074,
name = "theta74",
short.name = "t74",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta75 = list(
hyperid = 23075,
name = "theta75",
short.name = "t75",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta76 = list(
hyperid = 23076,
name = "theta76",
short.name = "t76",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta77 = list(
hyperid = 23077,
name = "theta77",
short.name = "t77",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta78 = list(
hyperid = 23078,
name = "theta78",
short.name = "t78",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta79 = list(
hyperid = 23079,
name = "theta79",
short.name = "t79",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta80 = list(
hyperid = 23080,
name = "theta80",
short.name = "t80",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta81 = list(
hyperid = 23081,
name = "theta81",
short.name = "t81",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta82 = list(
hyperid = 23082,
name = "theta82",
short.name = "t82",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta83 = list(
hyperid = 23083,
name = "theta83",
short.name = "t83",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta84 = list(
hyperid = 23084,
name = "theta84",
short.name = "t84",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta85 = list(
hyperid = 23085,
name = "theta85",
short.name = "t85",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta86 = list(
hyperid = 23086,
name = "theta86",
short.name = "t86",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta87 = list(
hyperid = 23087,
name = "theta87",
short.name = "t87",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta88 = list(
hyperid = 23088,
name = "theta88",
short.name = "t88",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta89 = list(
hyperid = 23089,
name = "theta89",
short.name = "t89",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta90 = list(
hyperid = 23090,
name = "theta90",
short.name = "t90",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta91 = list(
hyperid = 23091,
name = "theta91",
short.name = "t91",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta92 = list(
hyperid = 23092,
name = "theta92",
short.name = "t92",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta93 = list(
hyperid = 23093,
name = "theta93",
short.name = "t93",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta94 = list(
hyperid = 23094,
name = "theta94",
short.name = "t94",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta95 = list(
hyperid = 23095,
name = "theta95",
short.name = "t95",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta96 = list(
hyperid = 23096,
name = "theta96",
short.name = "t96",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta97 = list(
hyperid = 23097,
name = "theta97",
short.name = "t97",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta98 = list(
hyperid = 23098,
name = "theta98",
short.name = "t98",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta99 = list(
hyperid = 23099,
name = "theta99",
short.name = "t99",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta100 = list(
hyperid = 23100,
name = "theta100",
short.name = "t100",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = TRUE,
set.default.values = TRUE,
pdf = "spde2"
),
spde3 = list(
doc = "A SPDE3 model",
## to many parameters here, but ...
hyper = list(
theta1 = list(
hyperid = 24001,
name = "theta1",
short.name = "t1",
initial = 0,
fixed = FALSE,
prior = "mvnorm",
param = c(1, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta2 = list(
hyperid = 24002,
name = "theta2",
short.name = "t2",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta3 = list(
hyperid = 24003,
name = "theta3",
short.name = "t3",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta4 = list(
hyperid = 24004,
name = "theta4",
short.name = "t4",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta5 = list(
hyperid = 24005,
name = "theta5",
short.name = "t5",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta6 = list(
hyperid = 24006,
name = "theta6",
short.name = "t6",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta7 = list(
hyperid = 24007,
name = "theta7",
short.name = "t7",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta8 = list(
hyperid = 24008,
name = "theta8",
short.name = "t8",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta9 = list(
hyperid = 24009,
name = "theta9",
short.name = "t9",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta10 = list(
hyperid = 24010,
name = "theta10",
short.name = "t10",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta11 = list(
hyperid = 24011,
name = "theta11",
short.name = "t11",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta12 = list(
hyperid = 24012,
name = "theta12",
short.name = "t12",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta13 = list(
hyperid = 24013,
name = "theta13",
short.name = "t13",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta14 = list(
hyperid = 24014,
name = "theta14",
short.name = "t14",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta15 = list(
hyperid = 24015,
name = "theta15",
short.name = "t15",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta16 = list(
hyperid = 24016,
name = "theta16",
short.name = "t16",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta17 = list(
hyperid = 24017,
name = "theta17",
short.name = "t17",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta18 = list(
hyperid = 24018,
name = "theta18",
short.name = "t18",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta19 = list(
hyperid = 24019,
name = "theta19",
short.name = "t19",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta20 = list(
hyperid = 24020,
name = "theta20",
short.name = "t20",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta21 = list(
hyperid = 24021,
name = "theta21",
short.name = "t21",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta22 = list(
hyperid = 24022,
name = "theta22",
short.name = "t22",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta23 = list(
hyperid = 24023,
name = "theta23",
short.name = "t23",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta24 = list(
hyperid = 24024,
name = "theta24",
short.name = "t24",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta25 = list(
hyperid = 24025,
name = "theta25",
short.name = "t25",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta26 = list(
hyperid = 24026,
name = "theta26",
short.name = "t26",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta27 = list(
hyperid = 24027,
name = "theta27",
short.name = "t27",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta28 = list(
hyperid = 24028,
name = "theta28",
short.name = "t28",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta29 = list(
hyperid = 24029,
name = "theta29",
short.name = "t29",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta30 = list(
hyperid = 24030,
name = "theta30",
short.name = "t30",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta31 = list(
hyperid = 24031,
name = "theta31",
short.name = "t31",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta32 = list(
hyperid = 24032,
name = "theta32",
short.name = "t32",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta33 = list(
hyperid = 24033,
name = "theta33",
short.name = "t33",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta34 = list(
hyperid = 24034,
name = "theta34",
short.name = "t34",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta35 = list(
hyperid = 24035,
name = "theta35",
short.name = "t35",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta36 = list(
hyperid = 24036,
name = "theta36",
short.name = "t36",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta37 = list(
hyperid = 24037,
name = "theta37",
short.name = "t37",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta38 = list(
hyperid = 24038,
name = "theta38",
short.name = "t38",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta39 = list(
hyperid = 24039,
name = "theta39",
short.name = "t39",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta40 = list(
hyperid = 24040,
name = "theta40",
short.name = "t40",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta41 = list(
hyperid = 24041,
name = "theta41",
short.name = "t41",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta42 = list(
hyperid = 24042,
name = "theta42",
short.name = "t42",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta43 = list(
hyperid = 24043,
name = "theta43",
short.name = "t43",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta44 = list(
hyperid = 24044,
name = "theta44",
short.name = "t44",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta45 = list(
hyperid = 24045,
name = "theta45",
short.name = "t45",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta46 = list(
hyperid = 24046,
name = "theta46",
short.name = "t46",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta47 = list(
hyperid = 24047,
name = "theta47",
short.name = "t47",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta48 = list(
hyperid = 24048,
name = "theta48",
short.name = "t48",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta49 = list(
hyperid = 24049,
name = "theta49",
short.name = "t49",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta50 = list(
hyperid = 24050,
name = "theta50",
short.name = "t50",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta51 = list(
hyperid = 24051,
name = "theta51",
short.name = "t51",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta52 = list(
hyperid = 24052,
name = "theta52",
short.name = "t52",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta53 = list(
hyperid = 24053,
name = "theta53",
short.name = "t53",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta54 = list(
hyperid = 24054,
name = "theta54",
short.name = "t54",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta55 = list(
hyperid = 24055,
name = "theta55",
short.name = "t55",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta56 = list(
hyperid = 24056,
name = "theta56",
short.name = "t56",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta57 = list(
hyperid = 24057,
name = "theta57",
short.name = "t57",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta58 = list(
hyperid = 24058,
name = "theta58",
short.name = "t58",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta59 = list(
hyperid = 24059,
name = "theta59",
short.name = "t59",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta60 = list(
hyperid = 24060,
name = "theta60",
short.name = "t60",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta61 = list(
hyperid = 24061,
name = "theta61",
short.name = "t61",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta62 = list(
hyperid = 24062,
name = "theta62",
short.name = "t62",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta63 = list(
hyperid = 24063,
name = "theta63",
short.name = "t63",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta64 = list(
hyperid = 24064,
name = "theta64",
short.name = "t64",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta65 = list(
hyperid = 24065,
name = "theta65",
short.name = "t65",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta66 = list(
hyperid = 24066,
name = "theta66",
short.name = "t66",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta67 = list(
hyperid = 24067,
name = "theta67",
short.name = "t67",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta68 = list(
hyperid = 24068,
name = "theta68",
short.name = "t68",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta69 = list(
hyperid = 24069,
name = "theta69",
short.name = "t69",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta70 = list(
hyperid = 24070,
name = "theta70",
short.name = "t70",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta71 = list(
hyperid = 24071,
name = "theta71",
short.name = "t71",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta72 = list(
hyperid = 24072,
name = "theta72",
short.name = "t72",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta73 = list(
hyperid = 24073,
name = "theta73",
short.name = "t73",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta74 = list(
hyperid = 24074,
name = "theta74",
short.name = "t74",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta75 = list(
hyperid = 24075,
name = "theta75",
short.name = "t75",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta76 = list(
hyperid = 24076,
name = "theta76",
short.name = "t76",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta77 = list(
hyperid = 24077,
name = "theta77",
short.name = "t77",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta78 = list(
hyperid = 24078,
name = "theta78",
short.name = "t78",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta79 = list(
hyperid = 24079,
name = "theta79",
short.name = "t79",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta80 = list(
hyperid = 24080,
name = "theta80",
short.name = "t80",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta81 = list(
hyperid = 24081,
name = "theta81",
short.name = "t81",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta82 = list(
hyperid = 24082,
name = "theta82",
short.name = "t82",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta83 = list(
hyperid = 24083,
name = "theta83",
short.name = "t83",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta84 = list(
hyperid = 24084,
name = "theta84",
short.name = "t84",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta85 = list(
hyperid = 24085,
name = "theta85",
short.name = "t85",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta86 = list(
hyperid = 24086,
name = "theta86",
short.name = "t86",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta87 = list(
hyperid = 24087,
name = "theta87",
short.name = "t87",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta88 = list(
hyperid = 24088,
name = "theta88",
short.name = "t88",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta89 = list(
hyperid = 24089,
name = "theta89",
short.name = "t89",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta90 = list(
hyperid = 24090,
name = "theta90",
short.name = "t90",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta91 = list(
hyperid = 24091,
name = "theta91",
short.name = "t91",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta92 = list(
hyperid = 24092,
name = "theta92",
short.name = "t92",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta93 = list(
hyperid = 24093,
name = "theta93",
short.name = "t93",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta94 = list(
hyperid = 24094,
name = "theta94",
short.name = "t94",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta95 = list(
hyperid = 24095,
name = "theta95",
short.name = "t95",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta96 = list(
hyperid = 24096,
name = "theta96",
short.name = "t96",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta97 = list(
hyperid = 24097,
name = "theta97",
short.name = "t97",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta98 = list(
hyperid = 24098,
name = "theta98",
short.name = "t98",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta99 = list(
hyperid = 24099,
name = "theta99",
short.name = "t99",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta100 = list(
hyperid = 24100,
name = "theta100",
short.name = "t100",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = TRUE,
set.default.values = TRUE,
pdf = "spde3"
),
iid1d = list(
doc = "Gaussian random effect in dim=1 with Wishart prior",
hyper = list(
theta = list(
hyperid = 25001,
name = "precision",
short.name = "prec",
initial = 4,
fixed = FALSE,
prior = "wishart1d",
## this is the
## corresponding
## wishart prior for
## the (a, b) gamma
## parameters, so
## default we get the
## same.
param = c(2*1, 2*0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE, ## TRUE is not
## needed here.
set.default.values = TRUE,
pdf = "iid123d"
),
iid2d = list(
doc = "Gaussian random effect in dim=2 with Wishart prior",
hyper = list(
theta1 = list(
hyperid = 26001,
name = "log precision1",
short.name = "prec1",
initial = 4,
fixed = FALSE,
prior = "wishart2d",
param = c(4, 1, 1, 0),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 26002,
name = "log precision2",
short.name = "prec2",
initial = 4,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta3 = list(
hyperid = 26003,
name = "logit correlation",
short.name = "cor",
initial = 4,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = TRUE,
aug.factor = 1L,
aug.constr = c(1L, 2L),
n.div.by = 2L,
n.required = TRUE,
set.default.values = TRUE,
pdf = "iid123d"
),
iid3d = list(
doc = "Gaussian random effect in dim=3 with Wishart prior",
hyper = list(
theta1 = list(
hyperid = 27001,
name = "log precision1",
short.name = "prec1",
initial = 4,
fixed = FALSE,
prior = "wishart3d",
param = c(7, 1, 1, 1, 0, 0, 0),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 27002,
name = "log precision2",
short.name = "prec2",
initial = 4,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta3 = list(
hyperid = 27003,
name = "log precision3",
short.name = "prec3",
initial = 4,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta4= list(
hyperid = 27004,
name = "logit correlation12",
short.name = "cor12",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta5 = list(
hyperid = 27005,
name = "logit correlation13",
short.name = "cor13",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta6 = list(
hyperid = 27006,
name = "logit correlation23",
short.name = "cor23",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = TRUE,
aug.factor = 1L,
aug.constr = c(1L, 2L, 3L),
n.div.by = 3L,
n.required = TRUE,
set.default.values = TRUE,
pdf = "iid123d"
),
iid4d = list(
doc = "Gaussian random effect in dim=4 with Wishart prior",
hyper = list(
theta1 = list(
hyperid = 28001,
name = "log precision1",
short.name = "prec1",
initial = 4,
fixed = FALSE,
prior = "wishart4d",
param = c(11, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 28002,
name = "log precision2",
short.name = "prec2",
initial = 4,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta3 = list(
hyperid = 28003,
name = "log precision3",
short.name = "prec3",
initial = 4,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta4 = list(
hyperid = 28004,
name = "log precision4",
short.name = "prec4",
initial = 4,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta5= list(
hyperid = 28005,
name = "logit correlation12",
short.name = "cor12",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta6 = list(
hyperid = 28006,
name = "logit correlation13",
short.name = "cor13",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta7 = list(
hyperid = 28007,
name = "logit correlation14",
short.name = "cor14",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta8 = list(
hyperid = 28008,
name = "logit correlation23",
short.name = "cor23",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta9 = list(
hyperid = 28009,
name = "logit correlation24",
short.name = "cor24",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta10 = list(
hyperid = 28010,
name = "logit correlation34",
short.name = "cor34",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = TRUE,
aug.factor = 1L,
aug.constr = c(1L, 2L, 3L, 4L),
n.div.by = 4L,
n.required = TRUE,
set.default.values = TRUE,
pdf = "iid123d"
),
iid5d = list(
doc = "Gaussian random effect in dim=5 with Wishart prior",
hyper = list(
theta1 = list(
hyperid = 29001,
name = "log precision1",
short.name = "prec1",
initial = 4,
fixed = FALSE,
prior = "wishart5d",
param = c(16, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 29002,
name = "log precision2",
short.name = "prec2",
initial = 4,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta3 = list(
hyperid = 29003,
name = "log precision3",
short.name = "prec3",
initial = 4,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta4 = list(
hyperid = 29004,
name = "log precision4",
short.name = "prec4",
initial = 4,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta5 = list(
hyperid = 29005,
name = "log precision5",
short.name = "prec5",
initial = 4,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta6= list(
hyperid = 29006,
name = "logit correlation12",
short.name = "cor12",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta7 = list(
hyperid = 29007,
name = "logit correlation13",
short.name = "cor13",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta8 = list(
hyperid = 29008,
name = "logit correlation14",
short.name = "cor14",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta9 = list(
hyperid = 29009,
name = "logit correlation15",
short.name = "cor15",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta10 = list(
hyperid = 29010,
name = "logit correlation23",
short.name = "cor23",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta11 = list(
hyperid = 29011,
name = "logit correlation24",
short.name = "cor24",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta12 = list(
hyperid = 29012,
name = "logit correlation25",
short.name = "cor25",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta13 = list(
hyperid = 29013,
name = "logit correlation34",
short.name = "cor34",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta14 = list(
hyperid = 29014,
name = "logit correlation35",
short.name = "cor35",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta15 = list(
hyperid = 29015,
name = "logit correlation45",
short.name = "cor45",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = TRUE,
aug.factor = 1L,
aug.constr = c(1L, 2L, 3L, 4L, 5L),
n.div.by = 5L,
n.required = TRUE,
set.default.values = TRUE,
pdf = "iid123d"
),
"2diid" = list(
doc = "(This model is obsolute)",
hyper = list(
theta1 = list(
hyperid = 30001,
name = "log precision1",
short.name = "prec1",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 30002,
name = "log precision2",
short.name = "prec2",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta3 = list(
hyperid = 30003,
name = "correlation",
short.name = "cor",
initial = 4,
fixed = FALSE,
prior = "normal",
param = c(0, 0.15),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = c(1L, 2L),
n.div.by = 2L,
n.required = TRUE,
set.default.values = TRUE,
pdf = "iid123d"
),
z = list(
doc = "The z-model in a classical mixed model formulation",
hyper = list(
theta = list(
hyperid = 31001,
name = "log precision",
short.name = "prec",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = TRUE,
set.default.values = TRUE,
pdf = "z",
status = "experimental"
),
rw2d = list(
doc = "Thin-plate spline model",
hyper = list(
theta = list(
hyperid = 32001,
name = "log precision",
short.name = "prec",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = TRUE,
nrow.ncol = TRUE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = TRUE,
pdf = "rw2d"
),
rw2diid = list(
doc = "Thin-plate spline with iid noise",
hyper = list(
theta1 = list(
hyperid = 33001,
name = "log precision",
short.name = "prec",
prior = "pc.prec",
param = c(1, .01),
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 33002,
name = "logit phi",
short.name = "phi",
prior = "pc",
param = c(0.5, 0.5),
initial = 3,
fixed = FALSE,
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
constr = TRUE,
nrow.ncol = TRUE,
augmented = TRUE,
aug.factor = 2L,
aug.constr = 2L,
n.div.by = NULL,
n.required = FALSE,
set.default.values = TRUE,
status = "experimental",
pdf = "rw2diid"
),
slm = list(
doc = "Spatial lag model",
hyper = list(
theta1 = list(
hyperid = 34001,
name = "log precision",
short.name = "prec",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 34002,
name = "rho",
short.name = "rho",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 10),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) 1/(1+exp(-x))
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = TRUE,
set.default.values = TRUE,
pdf = "slm",
status = "experimental"
),
matern2d = list(
doc = "Matern covariance function on a regular grid",
hyper = list(
theta1 = list(
hyperid = 35001,
name = "log precision",
short.name = "prec",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 35002,
name = "log range",
short.name = "range",
initial = 2,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.01),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = TRUE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = TRUE,
pdf = "matern2d"
),
dmatern = list(
doc = "Dense Matern field",
hyper = list(
theta1 = list(
hyperid = 35101,
name = "log precision",
short.name = "prec",
initial = 3,
fixed = FALSE,
prior = "pc.prec",
param = c(1, 0.01),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 35102,
name = "log range",
short.name = "range",
initial = 0,
fixed = FALSE,
prior = "pc.range",
param = c(1, 0.5),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta3 = list(
hyperid = 35103,
name = "log nu",
short.name = "nu",
initial = log(0.5),
fixed = TRUE,
prior = "loggamma",
param = c(0.5, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = TRUE,
set.default.values = TRUE,
status = "experimental",
pdf = "dmatern"
),
copy = list(
doc = "Create a copy of a model component",
hyper = list(
theta = list(
hyperid = 36001,
name = "beta",
short.name = "b",
initial = 1,
fixed = TRUE,
prior = "normal",
param = c(1, 10),
to.theta = function(x, REPLACE.ME.low, REPLACE.ME.high) {
if (all(is.infinite(c(low, high))) || low == high) {
return (x)
} else if (all(is.finite(c(low, high)))) {
stopifnot(low < high)
return (log( - (low - x)/(high -x)))
} else if (is.finite(low) && is.infinite(high) && high > low) {
return (log(x-low))
} else {
stop("Condition not yet implemented")
}
},
from.theta = function(x, REPLACE.ME.low, REPLACE.ME.high) {
if (all(is.infinite(c(low, high))) || low == high) {
return (x)
} else if (all(is.finite(c(low, high)))) {
stopifnot(low < high)
return (low + exp(x)/(1+exp(x)) * (high - low))
} else if (is.finite(low) && is.infinite(high) && high > low) {
return (low + exp(x))
} else {
stop("Condition not yet implemented")
}
}
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
pdf = NA
),
clinear = list(
doc = "Constrained linear effect",
hyper = list(
theta = list(
hyperid = 37001,
name = "beta",
short.name = "b",
initial = 1,
fixed = FALSE,
prior = "normal",
param = c(1, 10),
to.theta = function(x, REPLACE.ME.low, REPLACE.ME.high) {
if (all(is.infinite(c(low, high))) || low == high) {
stopifnot(low < high)
return (x)
} else if (all(is.finite(c(low, high)))) {
stopifnot(low < high)
return (log( - (low - x)/(high -x)))
} else if (is.finite(low) && is.infinite(high) && high > low) {
return (log(x-low))
} else {
stop("Condition not yet implemented")
}
},
from.theta = function(x, REPLACE.ME.low, REPLACE.ME.high) {
if (all(is.infinite(c(low, high))) || low == high) {
stopifnot(low < high)
return (x)
} else if (all(is.finite(c(low, high)))) {
stopifnot(low < high)
return (low + exp(x)/(1+exp(x)) * (high - low))
} else if (is.finite(low) && is.infinite(high) && high > low) {
return (low + exp(x))
} else {
stop("Condition not yet implemented")
}
}
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
pdf = "clinear"
),
sigm = list(
doc = "Sigmoidal effect of a covariate",
hyper = list(
theta1 = list(
hyperid = 38001,
name = "beta",
short.name = "b",
initial = 1,
fixed = FALSE,
prior = "normal",
param = c(1, 10),
to.theta = function(x) x,
from.theta = function(x) x
),
theta2 = list(
hyperid = 38002,
name = "loghalflife",
short.name = "halflife",
initial = 3,
fixed = FALSE,
prior = "loggamma",
param = c(3, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta3 = list(
hyperid = 38003,
name = "logshape",
short.name = "shape",
initial = 0,
fixed = FALSE,
prior = "loggamma",
param = c(10, 10),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
status = "experimental",
pdf = "sigm"
),
revsigm = list(
doc = "Reverse sigmoidal effect of a covariate",
hyper = list(
theta1 = list(
hyperid = 39001,
name = "beta",
short.name = "b",
initial = 1,
fixed = FALSE,
prior = "normal",
param = c(1, 10),
to.theta = function(x) x,
from.theta = function(x) x
),
theta2 = list(
hyperid = 39002,
name = "loghalflife",
short.name = "halflife",
initial = 3,
fixed = FALSE,
prior = "loggamma",
param = c(3, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta3 = list(
hyperid = 39003,
name = "logshape",
short.name = "shape",
initial = 0,
fixed = FALSE,
prior = "loggamma",
param = c(10, 10),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
status = "experimental",
pdf = "sigm"
),
log1exp = list(
doc = "A nonlinear model of a covariate",
hyper = list(
theta1 = list(
hyperid = 39011,
name = "beta",
short.name = "b",
initial = 1,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta2 = list(
hyperid = 39012,
name = "alpha",
short.name = "a",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta3 = list(
hyperid = 39013,
name = "gamma",
short.name = "g",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
status = "experimental",
pdf = "log1exp"
),
logdist = list(
doc = "A nonlinear model of a covariate",
hyper = list(
theta1 = list(
hyperid = 39021,
name = "beta",
short.name = "b",
initial = 1,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta2 = list(
hyperid = 39022,
name = "alpha1",
short.name = "a1",
initial = 0,
fixed = FALSE,
prior = "loggamma",
param = c(0.1, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta3 = list(
hyperid = 39023,
name = "alpha2",
short.name = "a2",
initial = 0,
fixed = FALSE,
prior = "loggamma",
param = c(0.1, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
status = "experimental",
pdf = "logdist"
)
##
)
)
}
`inla.models.section.group` = function()
{
## prevent a warning with R CMD check
ngroup = NULL
return
list(group =
list(
exchangeable = list(
doc = "Exchangeable correlations",
hyper = list(
theta = list(
hyperid = 40001,
name = "logit correlation",
short.name = "rho",
initial = 1,
fixed = FALSE,
prior = "normal",
param = c(0, 0.2),
to.theta = function(x, REPLACE.ME.ngroup) log((1+x*(ngroup-1))/(1-x)),
from.theta = function(x, REPLACE.ME.ngroup) (exp(x)-1)/(exp(x) + ngroup -1)
)
)
),
exchangeablepos = list(
doc = "Exchangeable positive correlations",
hyper = list(
theta = list(
hyperid = 40101,
name = "logit correlation",
short.name = "rho",
initial = 1,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.5),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
)
),
ar1 = list(
doc = "AR(1) correlations",
hyper = list(
theta = list(
hyperid = 41001,
name = "logit correlation",
short.name = "rho",
initial = 2,
fixed = FALSE,
prior = "normal",
param = c(0, 0.15),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
)
)
),
ar = list(
doc = "AR(p) correlations",
## to many parameters here, but ...
hyper = list(
theta1 = list(
hyperid = 42001,
name = "log precision",
short.name = "prec",
initial = 0,
fixed = TRUE,
prior = "pc.prec",
param = c(3, 0.01),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 42002,
name = "pacf1",
short.name = "pacf1",
initial = 2,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.5),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta3 = list(
hyperid = 42003,
name = "pacf2",
short.name = "pacf2",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.4),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta4 = list(
hyperid = 42004,
name = "pacf3",
short.name = "pacf3",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.3),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta5 = list(
hyperid = 42005,
name = "pacf4",
short.name = "pacf4",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.2),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta6 = list(
hyperid = 42006,
name = "pacf5",
short.name = "pacf5",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.1),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta7 = list(
hyperid = 42007,
name = "pacf6",
short.name = "pacf6",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.1),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta8 = list(
hyperid = 42008,
name = "pacf7",
short.name = "pacf7",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.1),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta9 = list(
hyperid = 42009,
name = "pacf8",
short.name = "pacf8",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.1),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta10 = list(
hyperid = 42010,
name = "pacf9",
short.name = "pacf9",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.1),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta11 = list(
hyperid = 42011,
name = "pacf10",
short.name = "pacf10",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.1),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
)
)
),
rw1 = list(
doc = "Random walk of order 1",
hyper = list(
theta = list(
hyperid = 43001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.00005),
initial = 0,
fixed = TRUE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
)
),
rw2 = list(
doc = "Random walk of order 2",
hyper = list(
theta = list(
hyperid = 44001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.00005),
initial = 0,
fixed = TRUE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
)
),
besag = list(
doc = "Besag model",
hyper = list(
theta = list(
hyperid = 45001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.00005),
initial = 0,
fixed = TRUE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
)
),
iid = list(
doc = "Independent model",
hyper = list(
theta = list(
hyperid = 46001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.00005),
initial = 0,
fixed = TRUE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
)
)
)
)
}
`inla.models.section.mix` = function()
{
return
list(mix =
list(
gaussian = list(
doc = "Gaussian mixture",
hyper = list(
theta = list(
hyperid = 47001,
name = "log precision",
short.name = "prec",
prior = "pc.prec",
param = c(1, 0.01),
initial = 0,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
)
),
loggamma = list(
## > a = 1/inla.pc.rgamma(100000, lambda = 4.8)
## > x = log(rgamma(length(a), shape=a, rate = a))
## > sd (x)
## [1] 0.3344429082
doc = "LogGamma mixture",
hyper = list(
theta = list(
hyperid = 47101,
name = "log precision",
short.name = "prec",
prior = "pc.mgamma",
param = 4.8,
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
)
),
mloggamma = list(
## > a = 1/inla.pc.rgamma(100000, lambda = 4.8)
## > x = log(rgamma(length(a), shape=a, rate = a))
## > sd (x)
## [1] 0.3344429082
doc = "Minus-LogGamma mixture",
hyper = list(
theta = list(
hyperid = 47201,
name = "log precision",
short.name = "prec",
prior = "pc.mgamma",
param = 4.8,
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
)
)
)
)
}
`inla.models.section.link` = function()
{
return
list(link =
list(
default = list(
doc = "The default link",
hyper = list()
),
cloglog = list(
doc = "The complementary log-log link",
hyper = list()
),
loglog = list(
doc = "The log-log link",
hyper = list()
),
identity = list(
doc = "The identity link",
hyper = list()
),
inverse = list(
doc = "The inverse link",
hyper = list()
),
log = list(
doc = "The log-link",
hyper = list()
),
neglog = list(
doc = "The negative log-link",
hyper = list()
),
logit = list(
doc = "The logit-link",
hyper = list()
),
probit = list(
doc = "The probit-link",
hyper = list()
),
cauchit = list(
doc = "The cauchit-link",
hyper = list()
),
tan = list(
doc = "The tan-link",
hyper = list()
),
quantile = list(
doc = "The quantile-link",
hyper = list()
),
pquantile = list(
doc = "The population quantile-link",
hyper = list()
),
sslogit = list(
doc = "Logit link with sensitivity and specificity",
hyper = list(
theta1 = list(
hyperid = 48001,
name = "sensitivity",
short.name = "sens",
prior = "logitbeta",
param = c(10, 5),
initial = 1,
fixed = FALSE,
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
),
theta2 = list(
hyperid = 48002,
name = "specificity",
short.name = "spec",
prior = "logitbeta",
param = c(10, 5),
initial = 1,
fixed = FALSE,
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)),
pdf = NA
),
logoffset = list(
doc = "Log-link with an offset",
## variant = 0, a+exp(...), a>0
## variant = 1, a-exp(...), a>0
hyper = list(
theta = list(
hyperid = 49001,
name = "beta",
short.name = "b",
prior = "normal",
param = c(0, 100),
initial = 0,
fixed = TRUE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)),
pdf = "logoffset"
),
logitoffset = list(
doc = "Logit-link with an offset",
hyper = list(
theta = list(
hyperid = 49011,
name = "prob",
short.name = "p",
prior = "normal",
param = c(-1, 100),
initial = -1,
fixed = FALSE,
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)),
status = "experimental",
pdf = "logitoffset"
),
robit = list(
doc = "Robit link",
hyper = list(
theta = list(
hyperid = 49021,
name = "log degrees of freedom",
short.name = "dof",
initial = log(5),
fixed = TRUE,
prior = "pc.dof",
param = c(50, 0.5),
to.theta = function(x) log(x-2),
from.theta = function(x) 2+exp(x)
)
),
status = "experimental",
pdf = "robit"
),
test1 = list(
doc = "A test1-link function (experimental)",
hyper = list(
theta = list(
hyperid = 50001,
name = "beta",
short.name = "b",
prior = "normal",
param = c(0, 100),
initial = 0,
fixed = FALSE,
to.theta = function(x) x,
from.theta = function(x) x
)),
pdf = NA
),
special1 = list(
doc = "A special1-link function (experimental)",
hyper = list(
theta1 = list(
hyperid = 51001,
name = "log precision",
short.name = "prec",
initial = 0,
fixed = FALSE,
prior = "loggamma",
param = c(1, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta2 = list(
hyperid = 51002,
name = "beta1",
short.name = "beta1",
initial = 0,
fixed = FALSE,
prior = "mvnorm",
param = c(0, 100),
to.theta = function(x) x,
from.theta = function(x) x
),
theta3 = list(
hyperid = 51003,
name = "beta2",
short.name = "beta2",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta4 = list(
hyperid = 51004,
name = "beta3",
short.name = "beta3",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta5 = list(
hyperid = 51005,
name = "beta4",
short.name = "beta4",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta6 = list(
hyperid = 51006,
name = "beta5",
short.name = "beta5",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta7 = list(
hyperid = 51007,
name = "beta6",
short.name = "beta6",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta8 = list(
hyperid = 51008,
name = "beta7",
short.name = "beta7",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta9 = list(
hyperid = 51009,
name = "beta8",
short.name = "beta8",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta10 = list(
hyperid = 51010,
name = "beta9",
short.name = "beta9",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta11 = list(
hyperid = 51011,
name = "beta10",
short.name = "beta10",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
)
),
pdf = NA
),
special2 = list(
doc = "A special2-link function (experimental)",
hyper = list(
theta = list(
hyperid = 52001,
name = "beta",
short.name = "b",
prior = "normal",
param = c(0, 10),
initial = 0,
fixed = FALSE,
to.theta = function(x) x,
from.theta = function(x) x
)),
pdf = NA
)
)
)
}
`inla.models.section.predictor` = function()
{
return
list(predictor =
list(
predictor = list(
doc = "(not used)",
hyper = list(
theta = list(
hyperid = 53001,
name = "log precision",
short.name = "prec",
initial = 12,
fixed = TRUE,
prior = "loggamma",
param = c(1, 0.00001),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
)
)
)
)
}
`inla.models.section.hazard` = function()
{
return
list(hazard =
list(
rw1 = list(
doc = "A random walk of order 1 for the log-hazard",
hyper = list(
theta = list(
hyperid = 54001,
name = "log precision",
short.name = "prec",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
)
),
rw2 = list(
doc = "A random walk of order 2 for the log-hazard",
hyper = list(
theta = list(
hyperid = 55001,
name = "log precision",
short.name = "prec",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
)
)
)
)
}
`inla.models.section.likelihood` = function()
{
return
list(likelihood =
list(
## the first non-default link-function is the default one.
poisson = list(
doc = "The Poisson likelihood",
hyper = list(
),
survival = FALSE,
discrete = TRUE,
link = c("default", "log", "logoffset", "quantile", "test1", "special1", "special2"),
pdf = "poisson"
),
contpoisson = list(
doc = "The Cont Poisson likelihood",
hyper = list(
),
survival = FALSE,
discrete = TRUE,
link = c("default", "log"),
pdf = "contpoisson"
),
qcontpoisson = list(
doc = "The quantile Cont Poisson likelihood",
hyper = list(
),
survival = FALSE,
discrete = TRUE,
link = c("default", "log"),
pdf = "qcontpoisson"
),
cenpoisson = list(
doc = "Then censored Poisson likelihood",
hyper = list(
),
survival = FALSE,
discrete = TRUE,
link = c("default", "log", "logoffset", "test1", "special1", "special2"),
status = "experimental",
pdf = "cenpoisson"
),
gpoisson = list(
doc = "The generalized Poisson likelihood",
hyper = list(
theta1 = list(
hyperid = 56001,
name = "overdispersion",
short.name = "phi",
initial = 0,
fixed = FALSE,
prior = "loggamma",
param = c(1, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 56002,
name = "p",
short.name = "p",
initial = 1,
fixed = TRUE,
prior = "normal",
## use a tight prior, as this can go very wrong if set to weak
param = c(1, 100),
to.theta = function(x) x,
from.theta = function(x) x
)
),
survival = FALSE,
discrete = TRUE,
link = c("default", "log", "logoffset"),
pdf = "gpoisson",
status = "experimental"
),
binomial = list(
doc = "The Binomial likelihood",
hyper = list(
),
survival = FALSE,
discrete = TRUE,
link = c("default", "logit", "cauchit", "probit", "cloglog", "loglog",
"log", "sslogit", "logitoffset", "quantile", "pquantile", "robit"),
pdf = "binomial"
),
pom = list(
doc = "Likelihood for the proportional odds model",
hyper = list(
theta1 = list(
hyperid = 57101,
name = "theta1",
short.name = "theta1",
initial = NA,
fixed = FALSE,
prior = "dirichlet",
param = 3.0,
to.theta = function(x) x,
from.theta = function(x) x
),
theta2 = list(
hyperid = 57102,
name = "theta2",
short.name = "theta2",
initial = NA,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta3 = list(
hyperid = 57103,
name = "theta3",
short.name = "theta3",
initial = NA,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta4 = list(
hyperid = 57104,
name = "theta4",
short.name = "theta4",
initial = NA,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta5 = list(
hyperid = 57105,
name = "theta5",
short.name = "theta5",
initial = NA,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta6 = list(
hyperid = 57106,
name = "theta6",
short.name = "theta6",
initial = NA,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta7 = list(
hyperid = 57107,
name = "theta7",
short.name = "theta7",
initial = NA,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta8 = list(
hyperid = 57108,
name = "theta8",
short.name = "theta8",
initial = NA,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta9 = list(
hyperid = 57109,
name = "theta9",
short.name = "theta9",
initial = NA,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta10 = list(
hyperid = 57110,
name = "theta10",
short.name = "theta10",
initial = NA,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
status = "experimental",
survival = FALSE,
discrete = TRUE,
link = c("default", "identity"),
pdf = "pom"
),
gev2 = list(
doc = "The Generalized Extreme Value likelihood (2nd variant)",
hyper = list(
theta1 = list(
hyperid = 57201,
name = "spread",
short.name = "sd",
initial = 0,
fixed = FALSE,
prior = "loggamma",
param = c(1, 3),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 57202,
name = "tail",
short.name = "tail",
initial = -4,
fixed = FALSE,
prior = "pc.gevtail",
param = c(7, 0.0, 0.5),
to.theta = function(x, interval = c(REPLACE.ME.low, REPLACE.ME.high)) log(-(interval[1] - x)/(interval[2] - x)),
from.theta = function(x, interval = c(REPLACE.ME.low, REPLACE.ME.high)) interval[1] + (interval[2]-interval[1]) * exp(x)/(1.0 + exp(x))
),
theta3 = list(
hyperid = 57203,
name = "beta1",
short.name = "beta1",
initial = NA,
fixed = FALSE,
prior = "normal",
param = c(0, 300),
to.theta = function(x) x,
from.theta = function(x) x
),
theta4 = list(
hyperid = 57204,
name = "beta2",
short.name = "beta2",
initial = NA,
fixed = FALSE,
prior = "normal",
param = c(0, 300),
to.theta = function(x) x,
from.theta = function(x) x
),
theta5 = list(
hyperid = 57205,
name = "beta3",
short.name = "beta3",
initial = NA,
fixed = FALSE,
prior = "normal",
param = c(0, 300),
to.theta = function(x) x,
from.theta = function(x) x
),
theta6 = list(
hyperid = 57206,
name = "beta4",
short.name = "beta4",
initial = NA,
fixed = FALSE,
prior = "normal",
param = c(0, 300),
to.theta = function(x) x,
from.theta = function(x) x
),
theta7 = list(
hyperid = 57207,
name = "beta5",
short.name = "beta5",
initial = NA,
fixed = FALSE,
prior = "normal",
param = c(0, 300),
to.theta = function(x) x,
from.theta = function(x) x
),
theta8 = list(
hyperid = 57208,
name = "beta6",
short.name = "beta6",
initial = NA,
fixed = FALSE,
prior = "normal",
param = c(0, 300),
to.theta = function(x) x,
from.theta = function(x) x
),
theta9 = list(
hyperid = 57209,
name = "beta7",
short.name = "beta7",
initial = NA,
fixed = FALSE,
prior = "normal",
param = c(0, 300),
to.theta = function(x) x,
from.theta = function(x) x
),
theta10 = list(
hyperid = 57210,
name = "beta8",
short.name = "beta8",
initial = NA,
fixed = FALSE,
prior = "normal",
param = c(0, 300),
to.theta = function(x) x,
from.theta = function(x) x
),
theta11 = list(
hyperid = 57211,
name = "beta9",
short.name = "beta9",
initial = NA,
fixed = FALSE,
prior = "normal",
param = c(0, 300),
to.theta = function(x) x,
from.theta = function(x) x
),
theta12 = list(
hyperid = 57212,
name = "beta10",
short.name = "beta",
initial = NA,
fixed = FALSE,
prior = "normal",
param = c(0, 300),
to.theta = function(x) x,
from.theta = function(x) x
)
),
status = "experimental",
survival = FALSE,
discrete = FALSE,
link = c("default", "identity"),
pdf = "gev2"
),
gamma = list(
doc = "The Gamma likelihood",
hyper = list(
theta = list(
hyperid = 58001,
name = "precision parameter",
short.name = "prec",
initial = log(100),
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.01),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "log", "quantile"),
pdf = "gamma"
),
gammasurv = list(
doc = "The Gamma likelihood (survival)",
hyper = list(
theta = list(
hyperid = 58101,
name = "precision parameter",
short.name = "prec",
initial = log(1),
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.01),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = TRUE,
discrete = FALSE,
status = "experimental",
link = c("default", "log", "quantile"),
pdf = "gammasurv"
),
gammacount = list(
doc = "A Gamma generalisation of the Poisson likelihood",
hyper = list(
theta = list(
hyperid = 59001,
name = "log alpha",
short.name = "alpha",
initial = log(1.0),
fixed = FALSE,
prior = "pc.gammacount",
param = 3,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "log"),
status = "experimental",
pdf = "gammacount"
),
qkumar = list(
doc = "A quantile version of the Kumar likelihood",
hyper = list(
theta = list(
hyperid = 60001,
name = "precision parameter",
short.name = "prec",
initial = 0,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.001),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "logit", "cauchit"),
pdf = "qkumar"
),
qloglogistic = list(
doc = "A quantile loglogistic likelihood",
hyper = list(
theta = list(
hyperid = 60011,
name = "log alpha",
short.name = "alpha",
initial = 1,
fixed = FALSE,
prior = "loggamma",
param = c(25, 25),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "log", "neglog"),
pdf = "qloglogistic"
),
qloglogisticsurv = list(
doc = "A quantile loglogistic likelihood (survival)",
hyper = list(
theta = list(
hyperid = 60021,
name = "log alpha",
short.name = "alpha",
initial = 1,
fixed = FALSE,
prior = "loggamma",
param = c(25, 25),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = TRUE,
discrete = FALSE,
link = c("default", "log", "neglog"),
pdf = "qloglogistic"
),
beta = list(
doc = "The Beta likelihood",
hyper = list(
theta = list(
hyperid = 61001,
name = "precision parameter",
short.name = "phi",
initial = log(10),
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "logit", "cauchit", "probit", "cloglog", "loglog"),
pdf = "beta"
),
betabinomial = list(
doc = "The Beta-Binomial likelihood",
hyper = list(
theta = list(
hyperid = 62001,
name = "overdispersion",
short.name = "rho",
initial = 0,
fixed = FALSE,
prior = "gaussian",
param = c(0.0, 0.4),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
survival = FALSE,
discrete = TRUE,
link = c("default", "logit", "cauchit", "probit", "cloglog", "loglog", "robit"),
pdf = "betabinomial"
),
cbinomial = list(
doc = "The clustered Binomial likelihood",
hyper = list(),
survival = FALSE,
discrete = TRUE,
link = c("default", "logit", "cauchit", "probit", "cloglog", "loglog", "robit"),
status = "experimental",
pdf = "cbinomial"
),
nbinomial = list(
doc = "The negBinomial likelihood",
hyper = list(
theta = list(
hyperid = 63001,
name = "size",
short.name = "size",
initial = log(10),
fixed = FALSE,
prior = "pc.mgamma",
param = 7,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = TRUE,
link = c("default", "log", "logoffset", "quantile"),
pdf = "nbinomial"
),
nbinomial2 = list(
doc = "The negBinomial2 likelihood",
hyper = list(),
survival = FALSE,
discrete = TRUE,
link = c("default", "logit", "cauchit", "probit", "cloglog", "loglog"),
pdf = "nbinomial"
),
simplex = list(
doc = "The simplex likelihood",
hyper = list(
theta = list(
hyperid = 64001,
name = "log precision",
short.name = "prec",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "logit", "cauchit", "probit", "cloglog", "loglog"),
pdf = "simplex"
),
gaussian = list(
doc = "The Gaussian likelihoood",
hyper = list(
theta1 = list(
hyperid = 65001,
name = "log precision",
short.name = "prec",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 65002,
name = "log precision offset",
short.name = "precoffset",
initial = (-2.0 * log(.Machine$double.eps)),
fixed = TRUE,
prior = "none",
param = numeric(),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "identity", "logit", "cauchit", "log", "logoffset"),
pdf = "gaussian"
),
circularnormal = list(
doc = "The circular Gaussian likelihoood",
hyper = list(
theta = list(
hyperid = 67001,
name = "log precision parameter",
short.name = "prec",
initial = 2,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.01),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "tan"),
pdf = "circular-normal",
status = "experimental"
),
wrappedcauchy = list(
doc = "The wrapped Cauchy likelihoood",
hyper = list(
theta = list(
hyperid = 68001,
name = "log precision parameter",
short.name = "prec",
initial = 2,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.005),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "tan"),
pdf = "wrapped-cauchy",
status = "disabled"
),
iidgamma = list(
doc = "(experimental)",
hyper = list(
theta1 = list(
hyperid = 69001,
name = "logshape",
short.name = "shape",
initial = 0,
fixed = FALSE,
prior = "loggamma",
param = c(100, 100),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 69002,
name = "lograte",
short.name = "rate",
initial = 0,
fixed = FALSE,
prior = "loggamma",
param = c(100, 100),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "identity"),
pdf = "iidgamma",
status = "experimental"
),
iidlogitbeta = list(
doc = "(experimental)",
hyper = list(
theta1 = list(
hyperid = 70001,
name = "log.a",
short.name = "a",
initial = 1,
fixed = FALSE,
prior = "loggamma",
param = c(1, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 70002,
name = "log.b",
short.name = "b",
initial = 1,
fixed = FALSE,
prior = "loggamma",
param = c(1, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "logit"),
pdf = "iidlogitbeta",
status = "experimental"
),
loggammafrailty = list(
doc = "(experimental)",
hyper = list(
theta = list(
hyperid = 71001,
name = "log precision",
short.name = "prec",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "identity"),
pdf = "loggammafrailty",
status = "experimental"
),
logistic = list(
doc = "The Logistic likelihoood",
hyper = list(
theta = list(
hyperid = 72001,
name = "log precision",
short.name = "prec",
initial = 1,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "identity"),
pdf = "logistic"
),
skewnormal = list(
doc = "The Skew-Normal likelihoood",
hyper = list(
theta1 = list(
hyperid = 73001,
name = "log inverse scale",
short.name = "iscale",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 73002,
name = "logit skewness",
short.name = "skew",
initial = 4,
fixed = FALSE,
prior = "gaussian",
param = c(0, 10),
to.theta = function(x, shape.max = 1) log((1+x/shape.max)/(1-x/shape.max)),
from.theta = function(x, shape.max = 1) shape.max*(2*exp(x)/(1+exp(x))-1)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "identity"),
pdf = "sn"
),
sn = list(
doc = "The Skew-Normal likelihoood",
hyper = list(
theta1 = list(
hyperid = 74001,
name = "log inverse scale",
short.name = "iscale",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 74002,
name = "logit skewness",
short.name = "skew",
initial = 0,
fixed = FALSE,
prior = "gaussian",
param = c(0, 10),
to.theta = function(x, shape.max = 1) log((1+x/shape.max)/(1-x/shape.max)),
from.theta = function(x, shape.max = 1) shape.max*(2*exp(x)/(1+exp(x))-1)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "identity"),
pdf = "sn"
),
sn2 = list(
doc = "The Skew-Normal likelihoood (alt param)",
hyper = list(
theta1 = list(
hyperid = 75001,
name = "log precision",
short.name = "prec",
initial = 1,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 75002,
name = "logit skewness",
short.name = "skew",
initial = 0,
fixed = FALSE,
prior = "gaussian",
param = c(0, 10),
to.theta = function(x, shape.max = 1) log((1+x/shape.max)/(1-x/shape.max)),
from.theta = function(x, shape.max = 1) shape.max*(2*exp(x)/(1+exp(x))-1)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "identity"),
status = "experimental",
pdf = "sn2"
),
gev = list(
doc = "The Generalized Extreme Value likelihood",
hyper = list(
theta1 = list(
hyperid = 76001,
name = "log precision",
short.name = "prec",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 76002,
name = "tail parameter",
short.name = "tail",
initial = 0,
fixed = FALSE,
prior = "gaussian",
param = c(0, 25),
to.theta = function(x) x,
from.theta = function(x) x
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "identity"),
status = "experimental",
pdf = "gev"
),
lognormal = list(
doc = "The log-Normal likelihood",
hyper = list(
theta = list(
hyperid = 77101,
name = "log precision",
short.name = "prec",
initial = 0,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "identity"),
pdf = "lognormal"
),
lognormalsurv = list(
doc = "The log-Normal likelihood (survival)",
hyper = list(
theta = list(
hyperid = 78001,
name = "log precision",
short.name = "prec",
initial = 0,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = TRUE,
discrete = FALSE,
link = c("default", "identity"),
pdf = "lognormal"
),
exponential = list(
doc = "The Exponential likelihood",
hyper = list(
),
survival = FALSE,
discrete = FALSE,
link = c("default", "log"),
pdf = "exponential"
),
exponentialsurv = list(
doc = "The Exponential likelihood (survival)",
hyper = list(
),
survival = TRUE,
discrete = FALSE,
link = c("default", "log", "neglog"),
pdf = "exponential"
),
coxph = list(
doc = "Cox-proportional hazard likelihood",
hyper = list(
),
survival = TRUE,
discrete = TRUE,
link = c("default", "log", "neglog"),
pdf = "coxph"
),
weibull = list(
doc = "The Weibull likelihood",
## variant=0: lambda*y^alpha
## variant=1: (lambda*y)^alpha
hyper = list(
theta = list(
hyperid = 79001,
name = "log alpha",
short.name = "alpha",
initial = 0.1,
fixed = FALSE,
prior = "pc.alphaw",
param = c(5),
## the 'sc' constant is defined in inla.h, and must be the same.
## I know, this is hard-coded for the moment. Should be a generic
## way of doing this...
to.theta = function(x, sc = 0.1) log(x)/sc,
from.theta = function(x, sc = 0.1) exp(sc*x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "log", "neglog", "quantile"),
pdf = "weibull"
),
weibullsurv = list(
doc = "The Weibull likelihood (survival)",
## variant=0: lambda*y^alpha
## variant=1: (lambda*y)^alpha
hyper = list(
theta = list(
hyperid = 79101,
name = "log alpha",
short.name = "alpha",
initial = 0.1,
fixed = FALSE,
prior = "pc.alphaw",
param = c(5),
## the 'sc' constant is defined in inla.h, and must be the same.
## I know, this is hard-coded for the moment. Should be a generic
## way of doing this...
to.theta = function(x, sc = 0.1) log(x)/sc,
from.theta = function(x, sc = 0.1) exp(sc*x)
)
),
survival = TRUE,
discrete = FALSE,
link = c("default", "log", "neglog", "quantile"),
pdf = "weibull"
),
loglogistic = list(
doc = "The loglogistic likelihood",
hyper = list(
theta = list(
hyperid = 80001,
name = "log alpha",
short.name = "alpha",
initial = 1,
fixed = FALSE,
prior = "loggamma",
param = c(25, 25),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "log", "neglog"),
pdf = "loglogistic"
),
loglogisticsurv = list(
doc = "The loglogistic likelihood (survival)",
hyper = list(
theta = list(
hyperid = 80011,
name = "log alpha",
short.name = "alpha",
initial = 1,
fixed = FALSE,
prior = "loggamma",
param = c(25, 25),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = TRUE,
discrete = FALSE,
link = c("default", "log", "neglog"),
pdf = "loglogistic"
),
weibullcure = list(
doc = "The Weibull-cure likelihood (survival)",
hyper = list(
theta1 = list(
hyperid = 81001,
name = "log alpha",
short.name = "a",
initial = 0.1,
fixed = FALSE,
prior = "pc.alphaw",
param = c(5),
## the 'sc' constant is defined in inla.h, and must be the same.
## I know, this is hard-coded for the moment. Should be a generic
## way of doing this...
to.theta = function(x, sc = 0.1) log(x)/sc,
from.theta = function(x, sc = 0.1) exp(sc*x)
),
theta2 = list(
hyperid = 81002,
name = "logit probability",
short.name = "prob",
initial = -1,
fixed = FALSE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
survival = TRUE,
discrete = FALSE,
link = c("default", "log", "neglog"),
pdf = "weibullcure"
),
stochvol = list(
doc = "The Gaussian stochvol likelihood",
hyper = list(
theta = list(
hyperid = 82001,
name = "log precision",
short.name = "prec",
initial = 500, ## yes, this is correct
fixed = TRUE, ## yes, this is correct
prior = "loggamma",
param = c(1, 0.005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "log"),
pdf = "stochvolgaussian"
),
stochvolt = list(
doc = "The Student-t stochvol likelihood",
hyper = list(
theta = list(
hyperid = 83001,
name = "log degrees of freedom",
short.name = "dof",
initial = 4,
fixed = FALSE,
prior = "pc.dof",
param = c(15, 0.5),
to.theta = function(x) log(x-2),
from.theta = function(x) 2+exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "log"),
pdf = "stochvolt"
),
stochvolnig = list(
doc = "The Normal inverse Gaussian stochvol likelihood",
hyper = list(
theta1 = list(
hyperid = 84001,
name = "skewness",
short.name = "skew",
initial = 0,
fixed = FALSE,
prior = "gaussian",
param = c(0, 10),
to.theta = function(x) x,
from.theta = function(x) x
),
theta2 = list(
hyperid = 84002,
name = "shape",
short.name = "shape",
initial = 0,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.5),
to.theta = function(x) log(x-1),
from.theta = function(x) 1+exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "log"),
pdf = "stochvolnig"
),
zeroinflatedpoisson0 = list(
doc = "Zero-inflated Poisson, type 0",
hyper = list(
theta = list(
hyperid = 85001,
name = "logit probability",
short.name = "prob",
initial = -1,
fixed = FALSE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "log"),
pdf = "zeroinflated"
),
zeroinflatedpoisson1 = list(
doc = "Zero-inflated Poisson, type 1",
hyper = list(
theta = list(
hyperid = 86001,
name = "logit probability",
short.name = "prob",
initial = -1,
fixed = FALSE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "log"),
pdf = "zeroinflated"
),
zeroinflatedpoisson2 = list(
doc = "Zero-inflated Poisson, type 2",
hyper = list(
theta = list(
hyperid = 87001,
name = "log alpha",
short.name = "a",
initial = log(2),
fixed = FALSE,
prior = "gaussian",
param = c(log(2), 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "log"),
pdf = "zeroinflated"
),
zeroinflatedbetabinomial0 = list(
doc = "Zero-inflated Beta-Binomial, type 0",
hyper = list(
theta1 = list(
hyperid = 88001,
name = "overdispersion",
short.name = "rho",
initial = 0,
fixed = FALSE,
prior = "gaussian",
param = c(0.0, 0.4),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
),
theta2 = list(
hyperid = 88002,
name = "logit probability",
short.name = "prob",
initial = -1,
fixed = FALSE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
survival = FALSE,
discrete = TRUE,
link = c("default", "logit", "cauchit", "probit", "cloglog", "loglog", "robit"),
pdf = "zeroinflated"
),
zeroinflatedbetabinomial1 = list(
doc = "Zero-inflated Beta-Binomial, type 1",
hyper = list(
theta1 = list(
hyperid = 89001,
name = "overdispersion",
short.name = "rho",
initial = 0,
fixed = FALSE,
prior = "gaussian",
param = c(0.0, 0.4),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
),
theta2 = list(
hyperid = 89002,
name = "logit probability",
short.name = "prob",
initial = -1,
fixed = FALSE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
survival = FALSE,
discrete = TRUE,
link = c("default", "logit", "cauchit", "probit", "cloglog", "loglog", "robit"),
pdf = "zeroinflated"
),
zeroinflatedbinomial0 = list(
doc = "Zero-inflated Binomial, type 0",
hyper = list(
theta = list(
hyperid = 90001,
name = "logit probability",
short.name = "prob",
initial = -1,
fixed = FALSE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "logit", "cauchit", "probit", "cloglog", "loglog", "robit"),
pdf = "zeroinflated"
),
zeroinflatedbinomial1 = list(
doc = "Zero-inflated Binomial, type 1",
hyper = list(
theta = list(
hyperid = 91001,
name = "logit probability",
short.name = "prob",
initial = -1,
fixed = FALSE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "logit", "cauchit", "probit", "cloglog", "loglog", "robit"),
pdf = "zeroinflated"
),
zeroinflatedbinomial2 = list(
doc = "Zero-inflated Binomial, type 2",
hyper = list(
theta = list(
hyperid = 92001,
name = "alpha",
short.name = "alpha",
initial = -1,
fixed = FALSE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "logit", "cauchit", "probit", "cloglog", "loglog", "robit"),
pdf = "zeroinflated"
),
zeroninflatedbinomial2 = list(
doc = "Zero and N inflated binomial, type 2",
hyper = list(
theta1 = list(
hyperid = 93001,
name = "alpha1",
short.name = "alpha1",
initial = -1,
fixed = FALSE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 93002,
name = "alpha2",
short.name = "alpha2",
initial = -1,
fixed = FALSE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "logit", "cauchit", "probit", "cloglog", "loglog", "robit"),
pdf = NA
),
zeroninflatedbinomial3 = list(
doc = "Zero and N inflated binomial, type 3",
hyper = list(
theta1 = list(
hyperid = 93101,
name = "alpha0",
short.name = "alpha0",
initial = 1,
fixed = FALSE,
prior = "loggamma",
param = c(1, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 93102,
name = "alphaN",
short.name = "alphaN",
initial = 1,
fixed = FALSE,
prior = "loggamma",
param = c(1, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
status = "experimental",
survival = FALSE,
discrete = FALSE,
link = c("default", "logit", "cauchit", "probit", "cloglog", "loglog", "robit"),
pdf = "zeroinflated"
),
zeroinflatedbetabinomial2 = list(
doc = "Zero inflated Beta-Binomial, type 2",
hyper = list(
theta1 = list(
hyperid = 94001,
name = "log alpha",
short.name = "a",
initial = log(2),
fixed = FALSE,
prior = "gaussian",
param = c(log(2), 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 94002,
name = "beta",
short.name = "b",
initial = log(1),
fixed = FALSE,
prior = "gaussian",
param = c(0, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "logit", "cauchit", "probit", "cloglog", "loglog", "robit"),
pdf = "zeroinflated"
),
zeroinflatednbinomial0 = list(
doc = "Zero inflated negBinomial, type 0",
hyper = list(
theta1 = list(
hyperid = 95001,
name = "log size",
short.name = "size",
initial = log(10),
fixed = FALSE,
prior = "pc.mgamma",
param = 7,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 95002,
name = "logit probability",
short.name = "prob",
initial = -1,
fixed = FALSE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "log"),
pdf = "zeroinflated"
),
zeroinflatednbinomial1 = list(
doc = "Zero inflated negBinomial, type 1",
hyper = list(
theta1 = list(
hyperid = 96001,
name = "log size",
short.name = "size",
initial = log(10),
fixed = FALSE,
prior = "pc.mgamma",
param = 7,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 96002,
name = "logit probability",
short.name = "prob",
initial = -1,
fixed = FALSE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "log"),
pdf = "zeroinflated"
),
zeroinflatednbinomial1strata2 = list(
doc = "Zero inflated negBinomial, type 1, strata 2",
hyper = list(
theta1 = list(
hyperid = 97001,
name = "log size",
short.name = "size",
initial = log(10),
fixed = FALSE,
prior = "pc.mgamma",
param = 7,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 97002,
name = "logit probability 1",
short.name = "prob1",
initial = -1,
fixed = FALSE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
),
theta3 = list(
hyperid = 97003,
name = "logit probability 2",
short.name = "prob2",
initial = -1,
fixed = FALSE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
),
theta4 = list(
hyperid = 97004,
name = "logit probability 3",
short.name = "prob3",
initial = -1,
fixed = TRUE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
),
theta5 = list(
hyperid = 97005,
name = "logit probability 4",
short.name = "prob4",
initial = -1,
fixed = TRUE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
),
theta6 = list(
hyperid = 97006,
name = "logit probability 5",
short.name = "prob5",
initial = -1,
fixed = TRUE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
),
theta7 = list(
hyperid = 97007,
name = "logit probability 6",
short.name = "prob6",
initial = -1,
fixed = TRUE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
),
theta8 = list(
hyperid = 97008,
name = "logit probability 7",
short.name = "prob7",
initial = -1,
fixed = TRUE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
),
theta9 = list(
hyperid = 97009,
name = "logit probability 8",
short.name = "prob8",
initial = -1,
fixed = TRUE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
),
theta10 = list(
hyperid = 97010,
name = "logit probability 9",
short.name = "prob9",
initial = -1,
fixed = TRUE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
),
theta11 = list(
hyperid = 97011,
name = "logit probability 10",
short.name = "prob10",
initial = -1,
fixed = TRUE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
status = "experimental",
survival = FALSE,
discrete = FALSE,
link = c("default", "log"),
pdf = "zeroinflated"
),
zeroinflatednbinomial1strata3 = list(
doc = "Zero inflated negBinomial, type 1, strata 3",
hyper = list(
theta1 = list(
hyperid = 98001,
name = "logit probability",
short.name = "prob",
initial = -1,
fixed = FALSE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
),
theta2 = list(
hyperid = 98002,
name = "log size 1",
short.name = "size1",
initial = log(10),
fixed = FALSE,
prior = "pc.mgamma",
param = 7,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta3 = list(
hyperid = 98003,
name = "log size 2",
short.name = "size2",
initial = log(10),
fixed = FALSE,
prior = "pc.mgamma",
param = 7,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta4 = list(
hyperid = 98004,
name = "log size 3",
short.name = "size3",
initial = log(10),
fixed = TRUE,
prior = "pc.mgamma",
param = 7,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta5 = list(
hyperid = 98005,
name = "log size 4",
short.name = "size4",
initial = log(10),
fixed = TRUE,
prior = "pc.mgamma",
param = 7,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta6 = list(
hyperid = 98006,
name = "log size 5",
short.name = "size5",
initial = log(10),
fixed = TRUE,
prior = "pc.mgamma",
param = 7,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta7 = list(
hyperid = 98007,
name = "log size 6",
short.name = "size6",
initial = log(10),
fixed = TRUE,
prior = "pc.mgamma",
param = 7,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta8 = list(
hyperid = 98008,
name = "log size 7",
short.name = "size7",
initial = log(10),
fixed = TRUE,
prior = "pc.mgamma",
param = 7,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta9 = list(
hyperid = 98009,
name = "log size 8",
short.name = "size8",
initial = log(10),
fixed = TRUE,
prior = "pc.mgamma",
param = 7,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta10 = list(
hyperid = 98010,
name = "log size 9",
short.name = "size9",
initial = log(10),
fixed = TRUE,
prior = "pc.mgamma",
param = 7,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta11 = list(
hyperid = 98011,
name = "log size 10",
short.name = "size10",
initial = log(10),
fixed = TRUE,
prior = "pc.mgamma",
param = 7,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
status = "experimental",
survival = FALSE,
discrete = FALSE,
link = c("default", "log"),
pdf = "zeroinflated"
),
zeroinflatednbinomial2 = list(
doc = "Zero inflated negBinomial, type 2",
hyper = list(
theta1 = list(
hyperid = 99001,
name = "log size",
short.name = "size",
initial = log(10),
fixed = FALSE,
prior = "pc.mgamma",
param = 7,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 99002,
name = "log alpha",
short.name = "a",
initial = log(2),
fixed = FALSE,
prior = "gaussian",
param = c(2, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "log"),
pdf = "zeroinflated"
),
t = list(
doc = "Student-t likelihood",
hyper = list(
theta1 = list(
hyperid = 100001,
name = "log precision",
short.name = "prec",
initial = 0,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 100002,
name = "log degrees of freedom",
short.name = "dof",
initial = 5,
fixed = FALSE,
prior = "pc.dof",
param = c(15, 0.5),
to.theta = function(x) log(x-2),
from.theta = function(x) 2+exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "identity"),
pdf = "student-t"
),
tstrata = list(
doc = "A stratified version of the Student-t likelihood",
hyper = list(
theta1 = list(
hyperid = 101001,
name = "log degrees of freedom",
short.name = "dof",
initial = 4,
fixed = FALSE,
prior = "pc.dof",
param = c(15, 0.5),
to.theta = function(x) log(x-5),
from.theta = function(x) 5+exp(x)
),
theta2 = list(
hyperid = 101002,
name = "log precision1",
short.name = "prec1",
initial = 2,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta3 = list(
hyperid = 101003,
name = "log precision2",
short.name = "prec2",
initial = 2,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta4 = list(
hyperid = 101004,
name = "log precision3",
short.name = "prec3",
initial = 2,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta5 = list(
hyperid = 101005,
name = "log precision4",
short.name = "prec4",
initial = 2,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta6 = list(
hyperid = 101006,
name = "log precision5",
short.name = "prec5",
initial = 2,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta7 = list(
hyperid = 101007,
name = "log precision6",
short.name = "prec6",
initial = 2,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta8 = list(
hyperid = 101008,
name = "log precision7",
short.name = "prec7",
initial = 2,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta9 = list(
hyperid = 101009,
name = "log precision8",
short.name = "prec8",
initial = 2,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta10 = list(
hyperid = 101010,
name = "log precision9",
short.name = "prec9",
initial = 2,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta11 = list(
hyperid = 101011,
name = "log precision10",
short.name = "prec10",
initial = 2,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "identity"),
pdf = "tstrata"
),
nmix = list(
doc = "Binomial-Poisson mixture",
hyper = list(
theta1 = list(
hyperid = 101101,
name = "beta1",
short.name = "beta1",
initial = log(10),
fixed = FALSE,
prior = "normal",
param = c(0, 0.5),
to.theta = function(x) x,
from.theta = function(x) x
),
theta2 = list(
hyperid = 101102,
name = "beta2",
short.name = "beta2",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta3 = list(
hyperid = 101103,
name = "beta3",
short.name = "beta3",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta4 = list(
hyperid = 101104,
name = "beta4",
short.name = "beta4",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta5 = list(
hyperid = 101105,
name = "beta5",
short.name = "beta5",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta6 = list(
hyperid = 101106,
name = "beta6",
short.name = "beta6",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta7 = list(
hyperid = 101107,
name = "beta7",
short.name = "beta7",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta8 = list(
hyperid = 101108,
name = "beta8",
short.name = "beta8",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta9 = list(
hyperid = 101109,
name = "beta9",
short.name = "beta9",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta10 = list(
hyperid = 101110,
name = "beta10",
short.name = "beta10",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta11 = list(
hyperid = 101111,
name = "beta11",
short.name = "beta11",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta12 = list(
hyperid = 101112,
name = "beta12",
short.name = "beta12",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta13 = list(
hyperid = 101113,
name = "beta13",
short.name = "beta13",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta14 = list(
hyperid = 101114,
name = "beta14",
short.name = "beta14",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta15 = list(
hyperid = 101115,
name = "beta15",
short.name = "beta15",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
)
),
status = "experimental",
survival = FALSE,
discrete = TRUE,
link = c("default", "logit", "probit"),
pdf = "nmix"
),
nmixnb = list(
doc = "NegBinomial-Poisson mixture",
hyper = list(
theta1 = list(
hyperid = 101121,
name = "beta1",
short.name = "beta1",
initial = log(10),
fixed = FALSE,
prior = "normal",
param = c(0, 0.5),
to.theta = function(x) x,
from.theta = function(x) x
),
theta2 = list(
hyperid = 101122,
name = "beta2",
short.name = "beta2",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta3 = list(
hyperid = 101123,
name = "beta3",
short.name = "beta3",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta4 = list(
hyperid = 101124,
name = "beta4",
short.name = "beta4",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta5 = list(
hyperid = 101125,
name = "beta5",
short.name = "beta5",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta6 = list(
hyperid = 101126,
name = "beta6",
short.name = "beta6",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta7 = list(
hyperid = 101127,
name = "beta7",
short.name = "beta7",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta8 = list(
hyperid = 101128,
name = "beta8",
short.name = "beta8",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta9 = list(
hyperid = 101129,
name = "beta9",
short.name = "beta9",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta10 = list(
hyperid = 101130,
name = "beta10",
short.name = "beta10",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta11 = list(
hyperid = 101131,
name = "beta11",
short.name = "beta11",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta12 = list(
hyperid = 101132,
name = "beta12",
short.name = "beta12",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta13 = list(
hyperid = 101133,
name = "beta13",
short.name = "beta13",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta14 = list(
hyperid = 101134,
name = "beta14",
short.name = "beta14",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta15 = list(
hyperid = 101135,
name = "beta15",
short.name = "beta15",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta16 = list(
hyperid = 101136,
name = "overdispersion",
short.name = "overdispersion",
initial = 0,
fixed = FALSE,
prior = "pc.gamma",
param = 7,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
status = "experimental",
survival = FALSE,
discrete = TRUE,
link = c("default", "logit", "probit"),
pdf = "nmixnb"
),
gp = list(
doc = "Generalized Pareto likelihood",
hyper = list(
theta = list(
hyperid = 101201,
name = "shape",
short.name = "xi",
initial = log(0.1),
fixed = FALSE,
prior = "loggamma",
param = c(1, 15),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
status = "experimental",
survival = FALSE,
discrete = TRUE,
link = c("default", "quantile"),
pdf = "genPareto"
),
logperiodogram = list(
doc = "Likelihood for the log-periodogram",
hyper = list(
),
survival = FALSE,
discrete = FALSE,
link = c("default", "identity"),
pdf = NA
)
)
)
}
`inla.models.section.prior` = function()
{
return
list(prior =
list(
normal = list(
doc = "Normal prior",
nparameters = 2L,
pdf = "gaussian"
),
gaussian = list(
doc = "Gaussian prior",
nparameters = 2L,
pdf = "gaussian"
),
wishart1d = list(
doc = "Wishart prior dim=1",
nparameters = 2L,
pdf = "iid123d"
),
wishart2d = list(
doc = "Wishart prior dim=2",
nparameters = 4L,
pdf = "iid123d"
),
wishart3d = list(
doc = "Wishart prior dim=3",
nparameters = 7L,
pdf = "iid123d"
),
wishart4d = list(
doc = "Wishart prior dim=4",
nparameters = 11L,
pdf = "iid123d"
),
wishart5d = list(
doc = "Wishart prior dim=5",
nparameters = 16L,
pdf = "iid123d"
),
loggamma = list(
doc = "Log-Gamma prior",
nparameters = 2L,
pdf = "prior-loggamma"
),
gamma = list(
doc = "Gamma prior",
nparameters = 2L,
pdf = "prior-loggamma"
),
minuslogsqrtruncnormal = list(
doc = "(obsolete)",
nparameters = 2L,
pdf = "prior-logtnorm"
),
logtnormal = list(
doc = "Truncated Normal prior",
nparameters = 2L,
pdf = "prior-logtnorm"
),
logtgaussian = list(
doc = "Truncated Gaussian prior",
nparameters = 2L,
pdf = "prior-logtnorm"
),
flat=list(
doc = "A constant prior",
nparameters = 0L,
pdf = "various-flat"
),
logflat=list(
doc = "A constant prior for log(theta)",
nparameters = 0L,
pdf = "various-flat"
),
logiflat=list(
doc = "A constant prior for log(1/theta)",
nparameters = 0L,
pdf = "various-flat"
),
mvnorm = list(
doc = "A multivariate Normal prior",
nparameters = -1L,
pdf = "mvnorm"
),
pc.alphaw = list(
doc = "PC prior for alpha in Weibull",
nparameters = 1L,
pdf = "pc.alphaw"
),
pc.ar = list(
doc = "PC prior for the AR(p) model",
nparameters = 1L,
pdf = "pc.ar"
),
dirichlet = list(
doc ="Dirichlet prior",
nparameters = 1L,
pdf = "dirichlet"
),
## this is the 'no prior needed' prior
none = list(
doc = "No prior",
nparameters = 0L),
## this is the 'flag an error if used' prior
invalid = list(
doc = "Void prior",
nparameters = 0L),
betacorrelation = list(
doc = "Beta prior for the correlation",
nparameters = 2L,
pdf = "betacorrelation"
),
logitbeta = list(
doc = "Logit prior for a probability",
nparameters = 2L,
pdf = "logitbeta"
),
pc.prec = list(
doc = "PC prior for log(precision)",
nparameters = 2L,
pdf = "pc.prec"
),
pc.dof = list(
doc = "PC prior for log(dof-2)",
nparameters = 2L,
pdf = "pc.dof"
),
pc.cor0 = list(
doc = "PC prior correlation, basemodel cor=0",
nparameters = 2L,
pdf = "pc.cor0"
),
pc.cor1 = list(
doc = "PC prior correlation, basemodel cor=1",
nparameters = 2L,
pdf = "pc.cor1"
),
pc.fgnh = list(
doc = "PC prior for the Hurst parameter in FGN",
nparameters = 2L,
pdf = "pc.fgnh"
),
## experimental prior from GA
pc.spde.GA = list(
doc = "(experimental)",
nparameters = 4L,
pdf = NA
),
pc.matern = list(
doc = "PC prior for the Matern SPDE",
nparameters = 3L,
pdf = NA
),
pc.range = list(
doc = "PC prior for the range in the Matern SPDE",
nparameters = 2L,
pdf = NA
),
pc.gamma = list(
doc = "PC prior for a Gamma parameter",
nparameters = 1L,
pdf = "pc.gamma"
),
pc.mgamma = list(
doc = "PC prior for a Gamma parameter",
nparameters = 1L,
pdf = "pc.gamma"
),
pc.gammacount = list(
doc = "PC prior for the GammaCount likelihood",
nparameters = 1L,
pdf = "pc.gammacount"
),
pc.gevtail = list(
doc = "PC prior for the tail in the GEV likelihood",
nparameters = 3L,
pdf = "pc.gevtail"
),
## this is the generic one, which is case-spesific and possibly adaptive
pc = list(
doc = "Generic PC prior",
nparameters = 2L,
pdf = NA
),
ref.ar = list(
doc = "Reference prior for the AR(p) model, p<=3",
nparameters = 0L,
pdf = NA
),
pom = list(
doc = "#classes-dependent prior for the POM model",
nparameters = 0L,
pdf = "pom"
),
jeffreystdf = list(
doc = "Jeffreys prior for the doc",
nparameters = 0L,
pdf = "jeffreystdf"
),
"expression:" = list(
doc = "A generic prior defined using expressions",
nparameters = -1L,
pdf = "expression"
),
"table:" = list(
doc = "A generic tabulated prior",
nparameters = -1L,
pdf = "table"
)
)
)
}
`inla.models.section.wrapper` = function()
{
return
list(wrapper =
list(
joint = list(
doc = "(experimental)",
hyper = list(
theta = list(
hyperid = 102001,
name = "log precision",
short.name = "prec",
initial = 0,
fixed = TRUE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
pdf = NA
)
)
)
}
`inla.models` = function()
{
## this is not very clean solution, but for the moment is ok. the
## inla.models() function takes just to much time!!!
envir = inla.get.inlaEnv()
if (exists("inla.models", envir = envir) &&
exists("hgid", envir = envir) &&
get("hgid", envir = envir) == inla.version("hgid")) {
return (get("inla.models", envir = envir))
} else {
## have to split it, as option keep.source has an upper limit...
models = c(
inla.models.section.latent(),
inla.models.section.group(),
inla.models.section.mix(),
inla.models.section.link(),
inla.models.section.predictor(),
inla.models.section.hazard(),
inla.models.section.likelihood(),
inla.models.section.prior(),
inla.models.section.wrapper())
## set "read.only" attribute for the `hyper' at those elements
## that cannot be changed.
for (section in names(models)) {
for (model in names(models[[section]])) {
a = models[[section]][[model]]
if (!is.null(a$hyper) && length(a$hyper) > 0) {
for (theta in names(a$hyper)) {
for (elm in names(a$hyper[[theta]])) {
val = FALSE
if (elm == "prior") {
if (a$hyper[[theta]][[elm]] == "none" ||
a$hyper[[theta]][[elm]] == "wishart1d" ||
a$hyper[[theta]][[elm]] == "wishart2d" ||
a$hyper[[theta]][[elm]] == "wishart3d" ||
a$hyper[[theta]][[elm]] == "wishart4d" ||
a$hyper[[theta]][[elm]] == "wishart5d") {
val = TRUE
}
}
if (elm == "to.theta" || elm == "from.theta")
val = TRUE
## append the new attribute, so the code
## depends on if the object has an attribute
## from before or not.
if (is.null(attributes(models[[section]][[model]]$hyper[[theta]][[elm]]))) {
attributes(models[[section]][[model]]$hyper[[theta]][[elm]]) =
list("inla.read.only" = val)
} else {
attributes(models[[section]][[model]]$hyper[[theta]][[elm]]) =
c("inla.read.only" = val,
attributes(models[[section]][[model]]$hyper[[theta]][[elm]]))
}
}
}
}
}
}
assign("inla.models", models, envir = envir)
assign("hgid", inla.version("hgid"), envir = envir)
return (models)
}
stop("This should not happen")
}
`inla.is.model` = function(model, section = NULL,
stop.on.error = TRUE, ignore.case = FALSE)
{
mm = inla.models()
if (is.null(section)) {
stop("No section given; please fix...")
}
section = match.arg(section, names(mm))
models = names((mm[ names(mm) == section ])[[1]])
if (is.character(model) && length(model) > 0) {
if (ignore.case) {
m = tolower(model)
ms = tolower(models)
} else {
m = model
ms = models
}
ret = c()
for(i in 1L:length(m)) {
if (is.element(m[i], ms)) {
ret[i] = TRUE
} else {
if (stop.on.error) {
print("Valid models are:")
print(models)
stop(paste(c("\n\tUnknown name [", model[i], "]\n", "\tValid choices are: ",
models), sep=" ", collapse=" "))
} else {
ret[i] = FALSE
}
}
}
} else {
if (stop.on.error)
stop(paste("\n\tModel [", model, "] is not of type character()\n", sep=""))
}
return (ret)
}
`inla.model.properties` = function(
model,
section = NULL,
stop.on.error = TRUE,
ignore.case = FALSE)
{
if (is.null(section)) {
stop("No section given; please fix...")
}
mm = inla.models()
section = match.arg(section, names(mm))
m = inla.model.properties.generic(inla.trim.family(model),
(mm[names(mm) == section])[[1]],
stop.on.error, ignore.case,
## would like to know the section for a possible warning/error if the status says so.
section = section)
if (is.null(m)) {
return (NULL)
}
return (m)
}
`inla.model.properties.generic` = function(model, models, stop.on.error = TRUE, ignore.case = TRUE, section = "UKNOWN")
{
## argument 'section' is for 'status' only...
m = ifelse(ignore.case, tolower(model), model)
if (ignore.case) {
ms = tolower(names(models))
} else {
ms = names(models)
}
ms = inla.trim.family(ms)
k = grep(paste("^", m, "$", sep=""), ms)
if (length(k) == 0L) {
if (stop.on.error) {
stop(paste("Name '", model, "' is unknown. Valid choices are: ", inla.paste(ms), ".", sep=""))
}
return (NULL)
} else {
## if 'status' is set, then issue a warning/error depending on
## 'status'. do this the first time only if status is
## 'experimental'.
status = models[[k]]$status
if (is.null(status)) {
## do nothing; all ok.
} else {
status.core = strsplit(status, ":")[[1]][1]
stopifnot(any(inla.strcasecmp(status.core, c("experimental", "disabled", "changed"))))
envir = inla.get.inlaEnv()
var = paste("processed.status.for.model.", model, ".in.section.", section, sep="")
if (inla.strcasecmp(status.core, "experimental")) {
if (!(exists(var, envir = envir) && get(var, envir = envir))) {
assign(var, TRUE, envir = envir)
msg = paste0("Model '", model, "' in section '", section, "' is marked as '", status,
"'; changes may appear at any time.",
"\n ",
"Use this model with extra care!!! Further warnings are disabled.")
warning(msg)
} else {
## the warning is already given; do nothing
}
} else if (inla.strcasecmp(status.core, "disabled")) {
assign(var, TRUE, envir = envir)
msg = paste("Model '", model, "' in section '", section, "' is marked as '",
status, ".\n",
"Usage is either not recommended and unsupported.",
"\n", sep="")
var = paste("enable.model.", section, ".", model, sep="")
if (!(exists(var, envir = envir) && get(var, envir = envir))) {
msg = paste0(c(msg, paste(" You can enable this model setting variable '", var,
"'\n to 'TRUE' in environment INLA:::inla.get.inlaEnv().\n",
" If you chose to do so, you are on your own.")))
stop(msg)
}
} else if (inla.strcasecmp(status.core, "changed")) {
assign(var, TRUE, envir = envir)
msg = paste0("Model '", model, "' in section '", section, "' is marked as '",
status, ".\n",
" There have been a change in the model definition, which is not backward compatible.\n",
" Please refer to the documentation before proceeeding.")
var = paste("enable.model.", section, ".", model, sep="")
if (!(exists(var, envir = envir) && get(var, envir = envir))) {
msg = paste0(c(msg, paste0("\n You can bypass this check setting variable '", var,
"'\n to 'TRUE' in environment INLA:::inla.get.inlaEnv().\n")))
stop(msg)
}
}
}
return (models[[k]])
}
}
`inla.model.validate.link.function` = function(model, link)
{
valid.links = inla.model.properties(model, "likelihood")$link
stopifnot(!is.null(valid.links))
stopifnot(length(valid.links) >= 2L)
stopifnot(valid.links[1L] == "default")
link = tolower(link)
if (is.element(link, valid.links)) {
## this is the convention: the default link is the second
## entry in the list. the first entry is always "default"
if (link == "default") {
link = valid.links[2L]
}
} else {
stop(inla.paste(c("Link function `", link, "' is not valid or yet implemented.",
"\n",
"Valid ones are: ", inla.paste(valid.links), "\n"), sep=""))
}
return (link)
}
INBO-BMK/INLA documentation built on Dec. 4, 2019, 11:43 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions `inla.models.section.latent` `inla.models.section.group` `inla.models.section.mix` `inla.models.section.link` `inla.models.section.predictor` `inla.models.section.hazard` `inla.models.section.likelihood` `inla.models.section.prior` `inla.models.section.wrapper` `inla.models` `inla.is.model` `inla.model.properties` `inla.model.properties.generic` `inla.model.validate.link.function`
## Export: inla.models
## this is how to define a must-be-enabled...
## status = "changed:Oct.25.2017",
`inla.models.section.latent` = function()
{
return
list(latent =
list(
linear = list(
doc = "Alternative interface to an fixed effect",
hyper = list(
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
pdf = "linear"
),
iid = list(
doc = "Gaussian random effects in dim=1",
hyper = list(
theta = list(
hyperid = 1001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.00005),
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
pdf = "indep"
),
mec = list(
doc = "Classical measurement error model",
hyper = list(
theta1 = list(
hyperid = 2001,
name = "beta",
short.name = "b",
prior = "gaussian",
param = c(1, 0.001),
initial = 1,
fixed = FALSE,
to.theta = function(x) x,
from.theta = function(x) x
),
theta2 = list(
hyperid = 2002,
name = "prec.u",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.0001),
initial = log(1/0.0001),
fixed = TRUE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta3 = list(
hyperid = 2003,
name = "mean.x",
short.name = "mu.x",
prior = "gaussian",
param = c(0, 0.0001),
initial = 0,
fixed = TRUE,
to.theta = function(x) x,
from.theta = function(x) x
),
theta4 = list(
hyperid = 2004,
name = "prec.x",
short.name = "prec.x",
prior = "loggamma",
param = c(1, 10000),
initial = log(1/10000),
fixed = TRUE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
pdf = "mec"
),
meb = list(
doc = "Berkson measurement error model",
hyper = list(
theta1 = list(
hyperid = 3001,
name = "beta",
short.name = "b",
prior = "gaussian",
param = c(1, 0.001),
initial = 1,
fixed = FALSE,
to.theta = function(x) x,
from.theta = function(x) x
),
theta2 = list(
hyperid = 3002,
name = "prec.u",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.0001),
initial = log(1000),
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
pdf = "meb"
),
rgeneric = list(
doc = "Generic latent model spesified using R",
hyper = list(),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = TRUE,
set.default.values = TRUE,
status = "experimental",
pdf = "rgeneric"
),
rw1 = list(
doc = "Random walk of order 1",
hyper = list(
theta = list(
hyperid = 4001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.00005),
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = TRUE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
min.diff = 1E-5,
pdf = "rw1"
),
rw2 = list(
doc = "Random walk of order 2",
hyper = list(
theta = list(
hyperid = 5001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.00005),
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = TRUE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
min.diff = 1E-3,
pdf = "rw2"
),
crw2 = list(
doc = "Exact solution to the random walk of order 2",
hyper = list(
theta = list(
hyperid = 6001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.00005),
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = TRUE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 2L,
aug.constr = 1L,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
min.diff = 1E-3,
pdf = "crw2"
),
seasonal = list(
doc = "Seasonal model for time series",
hyper = list(
theta = list(
hyperid = 7001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.00005),
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
pdf = "seasonal"
),
besag = list(
doc = "The Besag area model (CAR-model)",
hyper = list(
theta = list(
hyperid = 8001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.00005),
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = TRUE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = TRUE,
set.default.values = TRUE,
pdf = "besag"
),
besag2 = list(
doc = "The shared Besag model",
hyper = list(
theta1 = list(
hyperid = 9001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.00005),
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 9002,
name = "scaling parameter",
short.name = "a",
prior = "loggamma",
param = c(10, 10),
initial = 0,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = c(1L, 2L),
n.div.by = 2L,
n.required = TRUE,
set.default.values = TRUE,
pdf = "besag2"
),
bym = list(
doc = "The BYM-model (Besag-York-Mollier model)",
hyper = list(
theta1 = list(
hyperid = 10001,
name = "log unstructured precision",
short.name = "prec.unstruct",
prior = "loggamma",
param = c(1, 0.0005),
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 10002,
name = "log spatial precision",
short.name = "prec.spatial",
prior = "loggamma",
param = c(1, 0.0005),
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = TRUE,
nrow.ncol = FALSE,
augmented = TRUE,
aug.factor = 2L,
aug.constr = 2L,
n.div.by = NULL,
n.required = TRUE,
set.default.values = TRUE,
pdf = "bym"
),
bym2 = list(
doc = "The BYM-model with the PC priors",
hyper = list(
theta1 = list(
hyperid = 11001,
name = "log precision",
short.name = "prec",
prior = "pc.prec",
param = c(1, .01),
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 11002,
name = "logit phi",
short.name = "phi",
prior = "pc",
param = c(0.5, 0.5),
initial = -3,
fixed = FALSE,
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
constr = TRUE,
nrow.ncol = FALSE,
augmented = TRUE,
aug.factor = 2L,
aug.constr = 2L,
n.div.by = NULL,
n.required = TRUE,
set.default.values = TRUE,
status = "experimental",
pdf = "bym2"
),
besagproper = list(
doc = "A proper version of the Besag model",
hyper = list(
theta1 = list(
hyperid = 12001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.0005),
initial = 2,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 12002,
name = "log diagonal",
short.name = "diag",
prior = "loggamma",
param = c(1, 1),
initial = 1,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = TRUE,
set.default.values = TRUE,
status = "experimental",
pdf = "besagproper"
),
besagproper2 = list(
doc = "An alternative proper version of the Besag model",
hyper = list(
theta1 = list(
hyperid = 13001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.0005),
initial = 2,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 13002,
name = "logit lambda",
short.name = "lambda",
prior = "gaussian",
param = c(0, 0.45),
initial = 3,
fixed = FALSE,
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = TRUE,
set.default.values = TRUE,
status = "experimental",
pdf = "besagproper2"
),
fgn = list(
doc = "Fractional Gaussian noise model",
hyper = list(
theta1 = list(
hyperid = 13101,
name = "log precision",
short.name = "prec",
prior = "pc.prec",
param = c(3, 0.01),
initial = 1,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 13102,
name = "logit H",
short.name = "H",
prior = "pcfgnh",
param = c(0.9, 0.1),
initial = 2,
fixed = FALSE,
to.theta = function(x) log((2*x-1)/(2*(1-x))),
from.theta = function(x) 0.5 + 0.5*exp(x)/(1+exp(x))
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = TRUE,
aug.factor = 5L,
aug.constr = 1L,
n.div.by = NULL,
n.required = FALSE,
set.default.values = TRUE,
order.default = 4L, ## default order for approximation
order.defined = 3L:4L, ## the list of orders which are implemented
pdf = "fgn"
),
fgn2 = list(
doc = "Fractional Gaussian noise model (alt 2)",
hyper = list(
theta1 = list(
hyperid = 13111,
name = "log precision",
short.name = "prec",
prior = "pc.prec",
param = c(3, 0.01),
initial = 1,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 13112,
name = "logit H",
short.name = "H",
prior = "pcfgnh",
param = c(0.9, 0.1),
initial = 2,
fixed = FALSE,
to.theta = function(x) log((2*x-1)/(2*(1-x))),
from.theta = function(x) 0.5 + 0.5*exp(x)/(1+exp(x))
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = TRUE,
aug.factor = 4L,
aug.constr = 1L,
n.div.by = NULL,
n.required = FALSE,
set.default.values = TRUE,
order.default = 4L, ## default order for approximation
order.defined = 3L:4L, ## the list of orders which are implemented
pdf = "fgn"
),
ar1 = list(
doc = "Auto-regressive model of order 1 (AR(1))",
hyper = list(
theta1 = list(
hyperid = 14001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.00005),
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 14002,
name = "logit lag one correlation",
short.name = "rho",
prior = "normal",
param = c(0, 0.15),
initial = 2,
fixed = FALSE,
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta3 = list(
hyperid = 14003,
name = "mean",
short.name = "mean",
prior = "normal",
param = c(0, 1),
initial = 0,
fixed = TRUE,
to.theta = function(x) x,
from.theta = function(x) x
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
pdf = "ar1"
),
ar1c = list(
doc = "Auto-regressive model of order 1 w/covariates",
hyper = list(
theta1 = list(
hyperid = 14101,
name = "log precision",
short.name = "prec",
prior = "pc.prec",
param = c(1, 0.01),
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 14102,
name = "logit lag one correlation",
short.name = "rho",
prior = "pc.cor0",
param = c(0.5, 0.5),
initial = 2,
fixed = FALSE,
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = TRUE,
status = "experimental",
pdf = "ar1c"
),
ar = list(
doc = "Auto-regressive model of order p (AR(p))",
## to many parameters here, but ...
hyper = list(
theta1 = list(
hyperid = 15001,
name = "log precision",
short.name = "prec",
initial = 4,
fixed = FALSE,
prior = "pc.prec",
param = c(3, 0.01),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 15002,
name = "pacf1",
short.name = "pacf1",
initial = 1,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.5),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta3 = list(
hyperid = 15003,
name = "pacf2",
short.name = "pacf2",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.4),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta4 = list(
hyperid = 15004,
name = "pacf3",
short.name = "pacf3",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.3),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta5 = list(
hyperid = 15005,
name = "pacf4",
short.name = "pacf4",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.2),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta6 = list(
hyperid = 15006,
name = "pacf5",
short.name = "pacf5",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.1),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta7 = list(
hyperid = 15007,
name = "pacf6",
short.name = "pacf6",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.1),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta8 = list(
hyperid = 15008,
name = "pacf7",
short.name = "pacf7",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.1),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta9 = list(
hyperid = 15009,
name = "pacf8",
short.name = "pacf8",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.1),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta10 = list(
hyperid = 15010,
name = "pacf9",
short.name = "pacf9",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.1),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta11 = list(
hyperid = 15011,
name = "pacf10",
short.name = "pacf10",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.1),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
pdf = "ar"
),
ou = list(
doc = "The Ornstein-Uhlenbeck process",
hyper = list(
theta1 = list(
hyperid = 16001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.00005),
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 16002,
name = "log phi",
short.name = "phi",
prior = "normal",
param = c(0, .2),
initial = -1,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
pdf = "ou"
),
intslope = list(
doc = "Intecept-slope model with Wishart-prior",
hyper = list(
theta1 = list(
hyperid = 16101,
name = "log precision1",
short.name = "prec1",
initial = 4,
fixed = FALSE,
prior = "wishart2d",
param = c(4, 1, 1, 0),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 16102,
name = "log precision2",
short.name = "prec2",
initial = 4,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta3 = list(
hyperid = 16103,
name = "logit correlation",
short.name = "cor",
initial = 4,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta4 = list(
hyperid = 16104,
name = "gamma1",
short.name = "g1",
initial = 1,
fixed = TRUE, ## YES.
prior = "normal",
param = c(1, 36),
to.theta = function(x) x,
from.theta = function(x) x
),
theta5 = list(
hyperid = 16105,
name = "gamma2",
short.name = "g2",
initial = 1,
fixed = FALSE,
prior = "normal",
param = c(1, 36),
to.theta = function(x) x,
from.theta = function(x) x
),
theta6 = list(
hyperid = 16106,
name = "gamma3",
short.name = "g3",
initial = 1,
fixed = FALSE,
prior = "normal",
param = c(1, 36),
to.theta = function(x) x,
from.theta = function(x) x
),
theta7 = list(
hyperid = 16107,
name = "gamma4",
short.name = "g4",
initial = 1,
fixed = FALSE,
prior = "normal",
param = c(1, 36),
to.theta = function(x) x,
from.theta = function(x) x
),
theta8 = list(
hyperid = 16108,
name = "gamma5",
short.name = "g5",
initial = 1,
fixed = FALSE,
prior = "normal",
param = c(1, 36),
to.theta = function(x) x,
from.theta = function(x) x
),
theta9 = list(
hyperid = 16109,
name = "gamma6",
short.name = "g6",
initial = 1,
fixed = FALSE,
prior = "normal",
param = c(1, 36),
to.theta = function(x) x,
from.theta = function(x) x
),
theta10 = list(
hyperid = 16110,
name = "gamma7",
short.name = "g7",
initial = 1,
fixed = FALSE,
prior = "normal",
param = c(1, 36),
to.theta = function(x) x,
from.theta = function(x) x
),
theta11 = list(
hyperid = 16111,
name = "gamma8",
short.name = "g8",
initial = 1,
fixed = FALSE,
prior = "normal",
param = c(1, 36),
to.theta = function(x) x,
from.theta = function(x) x
),
theta12 = list(
hyperid = 16112,
name = "gamma9",
short.name = "g9",
initial = 1,
fixed = FALSE,
prior = "normal",
param = c(1, 36),
to.theta = function(x) x,
from.theta = function(x) x
),
theta13 = list(
hyperid = 16113,
name = "gamma10",
short.name = "g10",
initial = 1,
fixed = FALSE,
prior = "normal",
param = c(1, 36),
to.theta = function(x) x,
from.theta = function(x) x
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = TRUE,
status = "experimental",
pdf = "intslope"
),
generic = list(
doc = "A generic model",
hyper = list(
theta = list(
hyperid = 17001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.00005),
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = TRUE,
set.default.values = TRUE,
pdf = "generic0"
),
generic0 = list(
doc = "A generic model (type 0)",
hyper = list(
theta = list(
hyperid = 18001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.00005),
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = TRUE,
set.default.values = TRUE,
pdf = "generic0"
),
generic1 = list(
doc = "A generic model (type 1)",
hyper = list(
theta1 = list(
hyperid = 19001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.00005),
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 19002,
name = "beta",
short.name = "beta",
initial = 2,
fixed = FALSE,
prior = "gaussian",
param = c(0, 0.1),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = TRUE,
set.default.values = TRUE,
pdf = "generic1"
),
generic2 = list(
doc = "A generic model (type 2)",
hyper = list(
theta1 = list(
hyperid = 20001,
name = "log precision cmatrix",
short.name = "prec",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 20002,
name = "log precision random",
short.name = "prec.random",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.001),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 2L,
aug.constr = 2L,
n.div.by = NULL,
n.required = TRUE,
set.default.values = TRUE,
pdf = "generic2"
),
generic3 = list(
doc = "A generic model (type 3)",
hyper = list(
theta1 = list(
hyperid = 21001,
name = "log precision1",
short.name = "prec1",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 21002,
name = "log precision2",
short.name = "prec2",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta3 = list(
hyperid = 21003,
name = "log precision3",
short.name = "prec3",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta4 = list(
hyperid = 21004,
name = "log precision4",
short.name = "prec4",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta5 = list(
hyperid = 21005,
name = "log precision5",
short.name = "prec5",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta6 = list(
hyperid = 21006,
name = "log precision6",
short.name = "prec6",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta7 = list(
hyperid = 21007,
name = "log precision7",
short.name = "prec7",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta8 = list(
hyperid = 21008,
name = "log precision8",
short.name = "prec8",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta9 = list(
hyperid = 21009,
name = "log precision9",
short.name = "prec9",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta10 = list(
hyperid = 21010,
name = "log precision10",
short.name = "prec10",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta11 = list(
hyperid = 21011,
name = "log precision common",
short.name = "prec.common",
initial = 0, ## yes!
fixed = TRUE, ## yes!
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = TRUE,
set.default.values = TRUE,
status = "experimental",
pdf = "generic3"
),
spde = list(
doc = "A SPDE model",
## this will be redone anyway soon....
hyper = list(
theta1 = list(
hyperid = 22001,
name = "theta.T",
short.name = "T",
initial = 2,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta2 = list(
hyperid = 22002,
name = "theta.K",
short.name = "K",
initial = -2,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta3 = list(
hyperid = 22003,
name = "theta.KT",
short.name = "KT",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta4 = list(
hyperid = 22004,
name = "theta.OC",
short.name = "OC",
initial = -20,
fixed = TRUE,
prior = "normal",
param = c(0, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = TRUE,
set.default.values = TRUE,
pdf = "spde"
),
spde2 = list(
doc = "A SPDE2 model",
## to many parameters here, but ...
hyper = list(
theta1 = list(
hyperid = 23001,
name = "theta1",
short.name = "t1",
initial = 0,
fixed = FALSE,
prior = "mvnorm",
param = c(1, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta2 = list(
hyperid = 23002,
name = "theta2",
short.name = "t2",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta3 = list(
hyperid = 23003,
name = "theta3",
short.name = "t3",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta4 = list(
hyperid = 23004,
name = "theta4",
short.name = "t4",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta5 = list(
hyperid = 23005,
name = "theta5",
short.name = "t5",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta6 = list(
hyperid = 23006,
name = "theta6",
short.name = "t6",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta7 = list(
hyperid = 23007,
name = "theta7",
short.name = "t7",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta8 = list(
hyperid = 23008,
name = "theta8",
short.name = "t8",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta9 = list(
hyperid = 23009,
name = "theta9",
short.name = "t9",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta10 = list(
hyperid = 23010,
name = "theta10",
short.name = "t10",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta11 = list(
hyperid = 23011,
name = "theta11",
short.name = "t11",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta12 = list(
hyperid = 23012,
name = "theta12",
short.name = "t12",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta13 = list(
hyperid = 23013,
name = "theta13",
short.name = "t13",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta14 = list(
hyperid = 23014,
name = "theta14",
short.name = "t14",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta15 = list(
hyperid = 23015,
name = "theta15",
short.name = "t15",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta16 = list(
hyperid = 23016,
name = "theta16",
short.name = "t16",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta17 = list(
hyperid = 23017,
name = "theta17",
short.name = "t17",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta18 = list(
hyperid = 23018,
name = "theta18",
short.name = "t18",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta19 = list(
hyperid = 23019,
name = "theta19",
short.name = "t19",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta20 = list(
hyperid = 23020,
name = "theta20",
short.name = "t20",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta21 = list(
hyperid = 23021,
name = "theta21",
short.name = "t21",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta22 = list(
hyperid = 23022,
name = "theta22",
short.name = "t22",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta23 = list(
hyperid = 23023,
name = "theta23",
short.name = "t23",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta24 = list(
hyperid = 23024,
name = "theta24",
short.name = "t24",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta25 = list(
hyperid = 23025,
name = "theta25",
short.name = "t25",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta26 = list(
hyperid = 23026,
name = "theta26",
short.name = "t26",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta27 = list(
hyperid = 23027,
name = "theta27",
short.name = "t27",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta28 = list(
hyperid = 23028,
name = "theta28",
short.name = "t28",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta29 = list(
hyperid = 23029,
name = "theta29",
short.name = "t29",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta30 = list(
hyperid = 23030,
name = "theta30",
short.name = "t30",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta31 = list(
hyperid = 23031,
name = "theta31",
short.name = "t31",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta32 = list(
hyperid = 23032,
name = "theta32",
short.name = "t32",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta33 = list(
hyperid = 23033,
name = "theta33",
short.name = "t33",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta34 = list(
hyperid = 23034,
name = "theta34",
short.name = "t34",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta35 = list(
hyperid = 23035,
name = "theta35",
short.name = "t35",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta36 = list(
hyperid = 23036,
name = "theta36",
short.name = "t36",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta37 = list(
hyperid = 23037,
name = "theta37",
short.name = "t37",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta38 = list(
hyperid = 23038,
name = "theta38",
short.name = "t38",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta39 = list(
hyperid = 23039,
name = "theta39",
short.name = "t39",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta40 = list(
hyperid = 23040,
name = "theta40",
short.name = "t40",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta41 = list(
hyperid = 23041,
name = "theta41",
short.name = "t41",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta42 = list(
hyperid = 23042,
name = "theta42",
short.name = "t42",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta43 = list(
hyperid = 23043,
name = "theta43",
short.name = "t43",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta44 = list(
hyperid = 23044,
name = "theta44",
short.name = "t44",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta45 = list(
hyperid = 23045,
name = "theta45",
short.name = "t45",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta46 = list(
hyperid = 23046,
name = "theta46",
short.name = "t46",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta47 = list(
hyperid = 23047,
name = "theta47",
short.name = "t47",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta48 = list(
hyperid = 23048,
name = "theta48",
short.name = "t48",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta49 = list(
hyperid = 23049,
name = "theta49",
short.name = "t49",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta50 = list(
hyperid = 23050,
name = "theta50",
short.name = "t50",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta51 = list(
hyperid = 23051,
name = "theta51",
short.name = "t51",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta52 = list(
hyperid = 23052,
name = "theta52",
short.name = "t52",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta53 = list(
hyperid = 23053,
name = "theta53",
short.name = "t53",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta54 = list(
hyperid = 23054,
name = "theta54",
short.name = "t54",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta55 = list(
hyperid = 23055,
name = "theta55",
short.name = "t55",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta56 = list(
hyperid = 23056,
name = "theta56",
short.name = "t56",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta57 = list(
hyperid = 23057,
name = "theta57",
short.name = "t57",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta58 = list(
hyperid = 23058,
name = "theta58",
short.name = "t58",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta59 = list(
hyperid = 23059,
name = "theta59",
short.name = "t59",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta60 = list(
hyperid = 23060,
name = "theta60",
short.name = "t60",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta61 = list(
hyperid = 23061,
name = "theta61",
short.name = "t61",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta62 = list(
hyperid = 23062,
name = "theta62",
short.name = "t62",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta63 = list(
hyperid = 23063,
name = "theta63",
short.name = "t63",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta64 = list(
hyperid = 23064,
name = "theta64",
short.name = "t64",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta65 = list(
hyperid = 23065,
name = "theta65",
short.name = "t65",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta66 = list(
hyperid = 23066,
name = "theta66",
short.name = "t66",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta67 = list(
hyperid = 23067,
name = "theta67",
short.name = "t67",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta68 = list(
hyperid = 23068,
name = "theta68",
short.name = "t68",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta69 = list(
hyperid = 23069,
name = "theta69",
short.name = "t69",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta70 = list(
hyperid = 23070,
name = "theta70",
short.name = "t70",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta71 = list(
hyperid = 23071,
name = "theta71",
short.name = "t71",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta72 = list(
hyperid = 23072,
name = "theta72",
short.name = "t72",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta73 = list(
hyperid = 23073,
name = "theta73",
short.name = "t73",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta74 = list(
hyperid = 23074,
name = "theta74",
short.name = "t74",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta75 = list(
hyperid = 23075,
name = "theta75",
short.name = "t75",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta76 = list(
hyperid = 23076,
name = "theta76",
short.name = "t76",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta77 = list(
hyperid = 23077,
name = "theta77",
short.name = "t77",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta78 = list(
hyperid = 23078,
name = "theta78",
short.name = "t78",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta79 = list(
hyperid = 23079,
name = "theta79",
short.name = "t79",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta80 = list(
hyperid = 23080,
name = "theta80",
short.name = "t80",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta81 = list(
hyperid = 23081,
name = "theta81",
short.name = "t81",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta82 = list(
hyperid = 23082,
name = "theta82",
short.name = "t82",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta83 = list(
hyperid = 23083,
name = "theta83",
short.name = "t83",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta84 = list(
hyperid = 23084,
name = "theta84",
short.name = "t84",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta85 = list(
hyperid = 23085,
name = "theta85",
short.name = "t85",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta86 = list(
hyperid = 23086,
name = "theta86",
short.name = "t86",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta87 = list(
hyperid = 23087,
name = "theta87",
short.name = "t87",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta88 = list(
hyperid = 23088,
name = "theta88",
short.name = "t88",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta89 = list(
hyperid = 23089,
name = "theta89",
short.name = "t89",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta90 = list(
hyperid = 23090,
name = "theta90",
short.name = "t90",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta91 = list(
hyperid = 23091,
name = "theta91",
short.name = "t91",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta92 = list(
hyperid = 23092,
name = "theta92",
short.name = "t92",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta93 = list(
hyperid = 23093,
name = "theta93",
short.name = "t93",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta94 = list(
hyperid = 23094,
name = "theta94",
short.name = "t94",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta95 = list(
hyperid = 23095,
name = "theta95",
short.name = "t95",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta96 = list(
hyperid = 23096,
name = "theta96",
short.name = "t96",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta97 = list(
hyperid = 23097,
name = "theta97",
short.name = "t97",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta98 = list(
hyperid = 23098,
name = "theta98",
short.name = "t98",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta99 = list(
hyperid = 23099,
name = "theta99",
short.name = "t99",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta100 = list(
hyperid = 23100,
name = "theta100",
short.name = "t100",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = TRUE,
set.default.values = TRUE,
pdf = "spde2"
),
spde3 = list(
doc = "A SPDE3 model",
## to many parameters here, but ...
hyper = list(
theta1 = list(
hyperid = 24001,
name = "theta1",
short.name = "t1",
initial = 0,
fixed = FALSE,
prior = "mvnorm",
param = c(1, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta2 = list(
hyperid = 24002,
name = "theta2",
short.name = "t2",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta3 = list(
hyperid = 24003,
name = "theta3",
short.name = "t3",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta4 = list(
hyperid = 24004,
name = "theta4",
short.name = "t4",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta5 = list(
hyperid = 24005,
name = "theta5",
short.name = "t5",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta6 = list(
hyperid = 24006,
name = "theta6",
short.name = "t6",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta7 = list(
hyperid = 24007,
name = "theta7",
short.name = "t7",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta8 = list(
hyperid = 24008,
name = "theta8",
short.name = "t8",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta9 = list(
hyperid = 24009,
name = "theta9",
short.name = "t9",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta10 = list(
hyperid = 24010,
name = "theta10",
short.name = "t10",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta11 = list(
hyperid = 24011,
name = "theta11",
short.name = "t11",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta12 = list(
hyperid = 24012,
name = "theta12",
short.name = "t12",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta13 = list(
hyperid = 24013,
name = "theta13",
short.name = "t13",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta14 = list(
hyperid = 24014,
name = "theta14",
short.name = "t14",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta15 = list(
hyperid = 24015,
name = "theta15",
short.name = "t15",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta16 = list(
hyperid = 24016,
name = "theta16",
short.name = "t16",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta17 = list(
hyperid = 24017,
name = "theta17",
short.name = "t17",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta18 = list(
hyperid = 24018,
name = "theta18",
short.name = "t18",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta19 = list(
hyperid = 24019,
name = "theta19",
short.name = "t19",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta20 = list(
hyperid = 24020,
name = "theta20",
short.name = "t20",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta21 = list(
hyperid = 24021,
name = "theta21",
short.name = "t21",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta22 = list(
hyperid = 24022,
name = "theta22",
short.name = "t22",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta23 = list(
hyperid = 24023,
name = "theta23",
short.name = "t23",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta24 = list(
hyperid = 24024,
name = "theta24",
short.name = "t24",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta25 = list(
hyperid = 24025,
name = "theta25",
short.name = "t25",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta26 = list(
hyperid = 24026,
name = "theta26",
short.name = "t26",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta27 = list(
hyperid = 24027,
name = "theta27",
short.name = "t27",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta28 = list(
hyperid = 24028,
name = "theta28",
short.name = "t28",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta29 = list(
hyperid = 24029,
name = "theta29",
short.name = "t29",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta30 = list(
hyperid = 24030,
name = "theta30",
short.name = "t30",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta31 = list(
hyperid = 24031,
name = "theta31",
short.name = "t31",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta32 = list(
hyperid = 24032,
name = "theta32",
short.name = "t32",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta33 = list(
hyperid = 24033,
name = "theta33",
short.name = "t33",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta34 = list(
hyperid = 24034,
name = "theta34",
short.name = "t34",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta35 = list(
hyperid = 24035,
name = "theta35",
short.name = "t35",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta36 = list(
hyperid = 24036,
name = "theta36",
short.name = "t36",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta37 = list(
hyperid = 24037,
name = "theta37",
short.name = "t37",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta38 = list(
hyperid = 24038,
name = "theta38",
short.name = "t38",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta39 = list(
hyperid = 24039,
name = "theta39",
short.name = "t39",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta40 = list(
hyperid = 24040,
name = "theta40",
short.name = "t40",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta41 = list(
hyperid = 24041,
name = "theta41",
short.name = "t41",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta42 = list(
hyperid = 24042,
name = "theta42",
short.name = "t42",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta43 = list(
hyperid = 24043,
name = "theta43",
short.name = "t43",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta44 = list(
hyperid = 24044,
name = "theta44",
short.name = "t44",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta45 = list(
hyperid = 24045,
name = "theta45",
short.name = "t45",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta46 = list(
hyperid = 24046,
name = "theta46",
short.name = "t46",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta47 = list(
hyperid = 24047,
name = "theta47",
short.name = "t47",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta48 = list(
hyperid = 24048,
name = "theta48",
short.name = "t48",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta49 = list(
hyperid = 24049,
name = "theta49",
short.name = "t49",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta50 = list(
hyperid = 24050,
name = "theta50",
short.name = "t50",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta51 = list(
hyperid = 24051,
name = "theta51",
short.name = "t51",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta52 = list(
hyperid = 24052,
name = "theta52",
short.name = "t52",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta53 = list(
hyperid = 24053,
name = "theta53",
short.name = "t53",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta54 = list(
hyperid = 24054,
name = "theta54",
short.name = "t54",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta55 = list(
hyperid = 24055,
name = "theta55",
short.name = "t55",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta56 = list(
hyperid = 24056,
name = "theta56",
short.name = "t56",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta57 = list(
hyperid = 24057,
name = "theta57",
short.name = "t57",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta58 = list(
hyperid = 24058,
name = "theta58",
short.name = "t58",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta59 = list(
hyperid = 24059,
name = "theta59",
short.name = "t59",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta60 = list(
hyperid = 24060,
name = "theta60",
short.name = "t60",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta61 = list(
hyperid = 24061,
name = "theta61",
short.name = "t61",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta62 = list(
hyperid = 24062,
name = "theta62",
short.name = "t62",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta63 = list(
hyperid = 24063,
name = "theta63",
short.name = "t63",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta64 = list(
hyperid = 24064,
name = "theta64",
short.name = "t64",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta65 = list(
hyperid = 24065,
name = "theta65",
short.name = "t65",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta66 = list(
hyperid = 24066,
name = "theta66",
short.name = "t66",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta67 = list(
hyperid = 24067,
name = "theta67",
short.name = "t67",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta68 = list(
hyperid = 24068,
name = "theta68",
short.name = "t68",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta69 = list(
hyperid = 24069,
name = "theta69",
short.name = "t69",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta70 = list(
hyperid = 24070,
name = "theta70",
short.name = "t70",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta71 = list(
hyperid = 24071,
name = "theta71",
short.name = "t71",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta72 = list(
hyperid = 24072,
name = "theta72",
short.name = "t72",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta73 = list(
hyperid = 24073,
name = "theta73",
short.name = "t73",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta74 = list(
hyperid = 24074,
name = "theta74",
short.name = "t74",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta75 = list(
hyperid = 24075,
name = "theta75",
short.name = "t75",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta76 = list(
hyperid = 24076,
name = "theta76",
short.name = "t76",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta77 = list(
hyperid = 24077,
name = "theta77",
short.name = "t77",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta78 = list(
hyperid = 24078,
name = "theta78",
short.name = "t78",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta79 = list(
hyperid = 24079,
name = "theta79",
short.name = "t79",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta80 = list(
hyperid = 24080,
name = "theta80",
short.name = "t80",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta81 = list(
hyperid = 24081,
name = "theta81",
short.name = "t81",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta82 = list(
hyperid = 24082,
name = "theta82",
short.name = "t82",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta83 = list(
hyperid = 24083,
name = "theta83",
short.name = "t83",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta84 = list(
hyperid = 24084,
name = "theta84",
short.name = "t84",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta85 = list(
hyperid = 24085,
name = "theta85",
short.name = "t85",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta86 = list(
hyperid = 24086,
name = "theta86",
short.name = "t86",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta87 = list(
hyperid = 24087,
name = "theta87",
short.name = "t87",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta88 = list(
hyperid = 24088,
name = "theta88",
short.name = "t88",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta89 = list(
hyperid = 24089,
name = "theta89",
short.name = "t89",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta90 = list(
hyperid = 24090,
name = "theta90",
short.name = "t90",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta91 = list(
hyperid = 24091,
name = "theta91",
short.name = "t91",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta92 = list(
hyperid = 24092,
name = "theta92",
short.name = "t92",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta93 = list(
hyperid = 24093,
name = "theta93",
short.name = "t93",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta94 = list(
hyperid = 24094,
name = "theta94",
short.name = "t94",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta95 = list(
hyperid = 24095,
name = "theta95",
short.name = "t95",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta96 = list(
hyperid = 24096,
name = "theta96",
short.name = "t96",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta97 = list(
hyperid = 24097,
name = "theta97",
short.name = "t97",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta98 = list(
hyperid = 24098,
name = "theta98",
short.name = "t98",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta99 = list(
hyperid = 24099,
name = "theta99",
short.name = "t99",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta100 = list(
hyperid = 24100,
name = "theta100",
short.name = "t100",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = TRUE,
set.default.values = TRUE,
pdf = "spde3"
),
iid1d = list(
doc = "Gaussian random effect in dim=1 with Wishart prior",
hyper = list(
theta = list(
hyperid = 25001,
name = "precision",
short.name = "prec",
initial = 4,
fixed = FALSE,
prior = "wishart1d",
## this is the
## corresponding
## wishart prior for
## the (a, b) gamma
## parameters, so
## default we get the
## same.
param = c(2*1, 2*0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE, ## TRUE is not
## needed here.
set.default.values = TRUE,
pdf = "iid123d"
),
iid2d = list(
doc = "Gaussian random effect in dim=2 with Wishart prior",
hyper = list(
theta1 = list(
hyperid = 26001,
name = "log precision1",
short.name = "prec1",
initial = 4,
fixed = FALSE,
prior = "wishart2d",
param = c(4, 1, 1, 0),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 26002,
name = "log precision2",
short.name = "prec2",
initial = 4,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta3 = list(
hyperid = 26003,
name = "logit correlation",
short.name = "cor",
initial = 4,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = TRUE,
aug.factor = 1L,
aug.constr = c(1L, 2L),
n.div.by = 2L,
n.required = TRUE,
set.default.values = TRUE,
pdf = "iid123d"
),
iid3d = list(
doc = "Gaussian random effect in dim=3 with Wishart prior",
hyper = list(
theta1 = list(
hyperid = 27001,
name = "log precision1",
short.name = "prec1",
initial = 4,
fixed = FALSE,
prior = "wishart3d",
param = c(7, 1, 1, 1, 0, 0, 0),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 27002,
name = "log precision2",
short.name = "prec2",
initial = 4,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta3 = list(
hyperid = 27003,
name = "log precision3",
short.name = "prec3",
initial = 4,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta4= list(
hyperid = 27004,
name = "logit correlation12",
short.name = "cor12",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta5 = list(
hyperid = 27005,
name = "logit correlation13",
short.name = "cor13",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta6 = list(
hyperid = 27006,
name = "logit correlation23",
short.name = "cor23",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = TRUE,
aug.factor = 1L,
aug.constr = c(1L, 2L, 3L),
n.div.by = 3L,
n.required = TRUE,
set.default.values = TRUE,
pdf = "iid123d"
),
iid4d = list(
doc = "Gaussian random effect in dim=4 with Wishart prior",
hyper = list(
theta1 = list(
hyperid = 28001,
name = "log precision1",
short.name = "prec1",
initial = 4,
fixed = FALSE,
prior = "wishart4d",
param = c(11, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 28002,
name = "log precision2",
short.name = "prec2",
initial = 4,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta3 = list(
hyperid = 28003,
name = "log precision3",
short.name = "prec3",
initial = 4,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta4 = list(
hyperid = 28004,
name = "log precision4",
short.name = "prec4",
initial = 4,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta5= list(
hyperid = 28005,
name = "logit correlation12",
short.name = "cor12",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta6 = list(
hyperid = 28006,
name = "logit correlation13",
short.name = "cor13",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta7 = list(
hyperid = 28007,
name = "logit correlation14",
short.name = "cor14",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta8 = list(
hyperid = 28008,
name = "logit correlation23",
short.name = "cor23",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta9 = list(
hyperid = 28009,
name = "logit correlation24",
short.name = "cor24",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta10 = list(
hyperid = 28010,
name = "logit correlation34",
short.name = "cor34",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = TRUE,
aug.factor = 1L,
aug.constr = c(1L, 2L, 3L, 4L),
n.div.by = 4L,
n.required = TRUE,
set.default.values = TRUE,
pdf = "iid123d"
),
iid5d = list(
doc = "Gaussian random effect in dim=5 with Wishart prior",
hyper = list(
theta1 = list(
hyperid = 29001,
name = "log precision1",
short.name = "prec1",
initial = 4,
fixed = FALSE,
prior = "wishart5d",
param = c(16, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 29002,
name = "log precision2",
short.name = "prec2",
initial = 4,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta3 = list(
hyperid = 29003,
name = "log precision3",
short.name = "prec3",
initial = 4,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta4 = list(
hyperid = 29004,
name = "log precision4",
short.name = "prec4",
initial = 4,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta5 = list(
hyperid = 29005,
name = "log precision5",
short.name = "prec5",
initial = 4,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta6= list(
hyperid = 29006,
name = "logit correlation12",
short.name = "cor12",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta7 = list(
hyperid = 29007,
name = "logit correlation13",
short.name = "cor13",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta8 = list(
hyperid = 29008,
name = "logit correlation14",
short.name = "cor14",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta9 = list(
hyperid = 29009,
name = "logit correlation15",
short.name = "cor15",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta10 = list(
hyperid = 29010,
name = "logit correlation23",
short.name = "cor23",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta11 = list(
hyperid = 29011,
name = "logit correlation24",
short.name = "cor24",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta12 = list(
hyperid = 29012,
name = "logit correlation25",
short.name = "cor25",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta13 = list(
hyperid = 29013,
name = "logit correlation34",
short.name = "cor34",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta14 = list(
hyperid = 29014,
name = "logit correlation35",
short.name = "cor35",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta15 = list(
hyperid = 29015,
name = "logit correlation45",
short.name = "cor45",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = TRUE,
aug.factor = 1L,
aug.constr = c(1L, 2L, 3L, 4L, 5L),
n.div.by = 5L,
n.required = TRUE,
set.default.values = TRUE,
pdf = "iid123d"
),
"2diid" = list(
doc = "(This model is obsolute)",
hyper = list(
theta1 = list(
hyperid = 30001,
name = "log precision1",
short.name = "prec1",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 30002,
name = "log precision2",
short.name = "prec2",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta3 = list(
hyperid = 30003,
name = "correlation",
short.name = "cor",
initial = 4,
fixed = FALSE,
prior = "normal",
param = c(0, 0.15),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = c(1L, 2L),
n.div.by = 2L,
n.required = TRUE,
set.default.values = TRUE,
pdf = "iid123d"
),
z = list(
doc = "The z-model in a classical mixed model formulation",
hyper = list(
theta = list(
hyperid = 31001,
name = "log precision",
short.name = "prec",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = TRUE,
set.default.values = TRUE,
pdf = "z",
status = "experimental"
),
rw2d = list(
doc = "Thin-plate spline model",
hyper = list(
theta = list(
hyperid = 32001,
name = "log precision",
short.name = "prec",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = TRUE,
nrow.ncol = TRUE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = TRUE,
pdf = "rw2d"
),
rw2diid = list(
doc = "Thin-plate spline with iid noise",
hyper = list(
theta1 = list(
hyperid = 33001,
name = "log precision",
short.name = "prec",
prior = "pc.prec",
param = c(1, .01),
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 33002,
name = "logit phi",
short.name = "phi",
prior = "pc",
param = c(0.5, 0.5),
initial = 3,
fixed = FALSE,
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
constr = TRUE,
nrow.ncol = TRUE,
augmented = TRUE,
aug.factor = 2L,
aug.constr = 2L,
n.div.by = NULL,
n.required = FALSE,
set.default.values = TRUE,
status = "experimental",
pdf = "rw2diid"
),
slm = list(
doc = "Spatial lag model",
hyper = list(
theta1 = list(
hyperid = 34001,
name = "log precision",
short.name = "prec",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 34002,
name = "rho",
short.name = "rho",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 10),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) 1/(1+exp(-x))
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = TRUE,
set.default.values = TRUE,
pdf = "slm",
status = "experimental"
),
matern2d = list(
doc = "Matern covariance function on a regular grid",
hyper = list(
theta1 = list(
hyperid = 35001,
name = "log precision",
short.name = "prec",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 35002,
name = "log range",
short.name = "range",
initial = 2,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.01),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = TRUE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = TRUE,
pdf = "matern2d"
),
dmatern = list(
doc = "Dense Matern field",
hyper = list(
theta1 = list(
hyperid = 35101,
name = "log precision",
short.name = "prec",
initial = 3,
fixed = FALSE,
prior = "pc.prec",
param = c(1, 0.01),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 35102,
name = "log range",
short.name = "range",
initial = 0,
fixed = FALSE,
prior = "pc.range",
param = c(1, 0.5),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta3 = list(
hyperid = 35103,
name = "log nu",
short.name = "nu",
initial = log(0.5),
fixed = TRUE,
prior = "loggamma",
param = c(0.5, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = TRUE,
set.default.values = TRUE,
status = "experimental",
pdf = "dmatern"
),
copy = list(
doc = "Create a copy of a model component",
hyper = list(
theta = list(
hyperid = 36001,
name = "beta",
short.name = "b",
initial = 1,
fixed = TRUE,
prior = "normal",
param = c(1, 10),
to.theta = function(x, REPLACE.ME.low, REPLACE.ME.high) {
if (all(is.infinite(c(low, high))) || low == high) {
return (x)
} else if (all(is.finite(c(low, high)))) {
stopifnot(low < high)
return (log( - (low - x)/(high -x)))
} else if (is.finite(low) && is.infinite(high) && high > low) {
return (log(x-low))
} else {
stop("Condition not yet implemented")
}
},
from.theta = function(x, REPLACE.ME.low, REPLACE.ME.high) {
if (all(is.infinite(c(low, high))) || low == high) {
return (x)
} else if (all(is.finite(c(low, high)))) {
stopifnot(low < high)
return (low + exp(x)/(1+exp(x)) * (high - low))
} else if (is.finite(low) && is.infinite(high) && high > low) {
return (low + exp(x))
} else {
stop("Condition not yet implemented")
}
}
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
pdf = NA
),
clinear = list(
doc = "Constrained linear effect",
hyper = list(
theta = list(
hyperid = 37001,
name = "beta",
short.name = "b",
initial = 1,
fixed = FALSE,
prior = "normal",
param = c(1, 10),
to.theta = function(x, REPLACE.ME.low, REPLACE.ME.high) {
if (all(is.infinite(c(low, high))) || low == high) {
stopifnot(low < high)
return (x)
} else if (all(is.finite(c(low, high)))) {
stopifnot(low < high)
return (log( - (low - x)/(high -x)))
} else if (is.finite(low) && is.infinite(high) && high > low) {
return (log(x-low))
} else {
stop("Condition not yet implemented")
}
},
from.theta = function(x, REPLACE.ME.low, REPLACE.ME.high) {
if (all(is.infinite(c(low, high))) || low == high) {
stopifnot(low < high)
return (x)
} else if (all(is.finite(c(low, high)))) {
stopifnot(low < high)
return (low + exp(x)/(1+exp(x)) * (high - low))
} else if (is.finite(low) && is.infinite(high) && high > low) {
return (low + exp(x))
} else {
stop("Condition not yet implemented")
}
}
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
pdf = "clinear"
),
sigm = list(
doc = "Sigmoidal effect of a covariate",
hyper = list(
theta1 = list(
hyperid = 38001,
name = "beta",
short.name = "b",
initial = 1,
fixed = FALSE,
prior = "normal",
param = c(1, 10),
to.theta = function(x) x,
from.theta = function(x) x
),
theta2 = list(
hyperid = 38002,
name = "loghalflife",
short.name = "halflife",
initial = 3,
fixed = FALSE,
prior = "loggamma",
param = c(3, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta3 = list(
hyperid = 38003,
name = "logshape",
short.name = "shape",
initial = 0,
fixed = FALSE,
prior = "loggamma",
param = c(10, 10),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
status = "experimental",
pdf = "sigm"
),
revsigm = list(
doc = "Reverse sigmoidal effect of a covariate",
hyper = list(
theta1 = list(
hyperid = 39001,
name = "beta",
short.name = "b",
initial = 1,
fixed = FALSE,
prior = "normal",
param = c(1, 10),
to.theta = function(x) x,
from.theta = function(x) x
),
theta2 = list(
hyperid = 39002,
name = "loghalflife",
short.name = "halflife",
initial = 3,
fixed = FALSE,
prior = "loggamma",
param = c(3, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta3 = list(
hyperid = 39003,
name = "logshape",
short.name = "shape",
initial = 0,
fixed = FALSE,
prior = "loggamma",
param = c(10, 10),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
status = "experimental",
pdf = "sigm"
),
log1exp = list(
doc = "A nonlinear model of a covariate",
hyper = list(
theta1 = list(
hyperid = 39011,
name = "beta",
short.name = "b",
initial = 1,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta2 = list(
hyperid = 39012,
name = "alpha",
short.name = "a",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta3 = list(
hyperid = 39013,
name = "gamma",
short.name = "g",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
status = "experimental",
pdf = "log1exp"
),
logdist = list(
doc = "A nonlinear model of a covariate",
hyper = list(
theta1 = list(
hyperid = 39021,
name = "beta",
short.name = "b",
initial = 1,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta2 = list(
hyperid = 39022,
name = "alpha1",
short.name = "a1",
initial = 0,
fixed = FALSE,
prior = "loggamma",
param = c(0.1, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta3 = list(
hyperid = 39023,
name = "alpha2",
short.name = "a2",
initial = 0,
fixed = FALSE,
prior = "loggamma",
param = c(0.1, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
status = "experimental",
pdf = "logdist"
)
##
)
)
}
`inla.models.section.group` = function()
{
## prevent a warning with R CMD check
ngroup = NULL
return
list(group =
list(
exchangeable = list(
doc = "Exchangeable correlations",
hyper = list(
theta = list(
hyperid = 40001,
name = "logit correlation",
short.name = "rho",
initial = 1,
fixed = FALSE,
prior = "normal",
param = c(0, 0.2),
to.theta = function(x, REPLACE.ME.ngroup) log((1+x*(ngroup-1))/(1-x)),
from.theta = function(x, REPLACE.ME.ngroup) (exp(x)-1)/(exp(x) + ngroup -1)
)
)
),
exchangeablepos = list(
doc = "Exchangeable positive correlations",
hyper = list(
theta = list(
hyperid = 40101,
name = "logit correlation",
short.name = "rho",
initial = 1,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.5),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
)
),
ar1 = list(
doc = "AR(1) correlations",
hyper = list(
theta = list(
hyperid = 41001,
name = "logit correlation",
short.name = "rho",
initial = 2,
fixed = FALSE,
prior = "normal",
param = c(0, 0.15),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
)
)
),
ar = list(
doc = "AR(p) correlations",
## to many parameters here, but ...
hyper = list(
theta1 = list(
hyperid = 42001,
name = "log precision",
short.name = "prec",
initial = 0,
fixed = TRUE,
prior = "pc.prec",
param = c(3, 0.01),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 42002,
name = "pacf1",
short.name = "pacf1",
initial = 2,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.5),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta3 = list(
hyperid = 42003,
name = "pacf2",
short.name = "pacf2",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.4),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta4 = list(
hyperid = 42004,
name = "pacf3",
short.name = "pacf3",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.3),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta5 = list(
hyperid = 42005,
name = "pacf4",
short.name = "pacf4",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.2),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta6 = list(
hyperid = 42006,
name = "pacf5",
short.name = "pacf5",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.1),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta7 = list(
hyperid = 42007,
name = "pacf6",
short.name = "pacf6",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.1),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta8 = list(
hyperid = 42008,
name = "pacf7",
short.name = "pacf7",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.1),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta9 = list(
hyperid = 42009,
name = "pacf8",
short.name = "pacf8",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.1),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta10 = list(
hyperid = 42010,
name = "pacf9",
short.name = "pacf9",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.1),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta11 = list(
hyperid = 42011,
name = "pacf10",
short.name = "pacf10",
initial = 0,
fixed = FALSE,
prior = "pc.cor0",
param = c(0.5, 0.1),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
)
)
),
rw1 = list(
doc = "Random walk of order 1",
hyper = list(
theta = list(
hyperid = 43001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.00005),
initial = 0,
fixed = TRUE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
)
),
rw2 = list(
doc = "Random walk of order 2",
hyper = list(
theta = list(
hyperid = 44001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.00005),
initial = 0,
fixed = TRUE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
)
),
besag = list(
doc = "Besag model",
hyper = list(
theta = list(
hyperid = 45001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.00005),
initial = 0,
fixed = TRUE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
)
),
iid = list(
doc = "Independent model",
hyper = list(
theta = list(
hyperid = 46001,
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.00005),
initial = 0,
fixed = TRUE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
)
)
)
)
}
`inla.models.section.mix` = function()
{
return
list(mix =
list(
gaussian = list(
doc = "Gaussian mixture",
hyper = list(
theta = list(
hyperid = 47001,
name = "log precision",
short.name = "prec",
prior = "pc.prec",
param = c(1, 0.01),
initial = 0,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
)
),
loggamma = list(
## > a = 1/inla.pc.rgamma(100000, lambda = 4.8)
## > x = log(rgamma(length(a), shape=a, rate = a))
## > sd (x)
## [1] 0.3344429082
doc = "LogGamma mixture",
hyper = list(
theta = list(
hyperid = 47101,
name = "log precision",
short.name = "prec",
prior = "pc.mgamma",
param = 4.8,
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
)
),
mloggamma = list(
## > a = 1/inla.pc.rgamma(100000, lambda = 4.8)
## > x = log(rgamma(length(a), shape=a, rate = a))
## > sd (x)
## [1] 0.3344429082
doc = "Minus-LogGamma mixture",
hyper = list(
theta = list(
hyperid = 47201,
name = "log precision",
short.name = "prec",
prior = "pc.mgamma",
param = 4.8,
initial = 4,
fixed = FALSE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
)
)
)
)
}
`inla.models.section.link` = function()
{
return
list(link =
list(
default = list(
doc = "The default link",
hyper = list()
),
cloglog = list(
doc = "The complementary log-log link",
hyper = list()
),
loglog = list(
doc = "The log-log link",
hyper = list()
),
identity = list(
doc = "The identity link",
hyper = list()
),
inverse = list(
doc = "The inverse link",
hyper = list()
),
log = list(
doc = "The log-link",
hyper = list()
),
neglog = list(
doc = "The negative log-link",
hyper = list()
),
logit = list(
doc = "The logit-link",
hyper = list()
),
probit = list(
doc = "The probit-link",
hyper = list()
),
cauchit = list(
doc = "The cauchit-link",
hyper = list()
),
tan = list(
doc = "The tan-link",
hyper = list()
),
quantile = list(
doc = "The quantile-link",
hyper = list()
),
pquantile = list(
doc = "The population quantile-link",
hyper = list()
),
sslogit = list(
doc = "Logit link with sensitivity and specificity",
hyper = list(
theta1 = list(
hyperid = 48001,
name = "sensitivity",
short.name = "sens",
prior = "logitbeta",
param = c(10, 5),
initial = 1,
fixed = FALSE,
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
),
theta2 = list(
hyperid = 48002,
name = "specificity",
short.name = "spec",
prior = "logitbeta",
param = c(10, 5),
initial = 1,
fixed = FALSE,
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)),
pdf = NA
),
logoffset = list(
doc = "Log-link with an offset",
## variant = 0, a+exp(...), a>0
## variant = 1, a-exp(...), a>0
hyper = list(
theta = list(
hyperid = 49001,
name = "beta",
short.name = "b",
prior = "normal",
param = c(0, 100),
initial = 0,
fixed = TRUE,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)),
pdf = "logoffset"
),
logitoffset = list(
doc = "Logit-link with an offset",
hyper = list(
theta = list(
hyperid = 49011,
name = "prob",
short.name = "p",
prior = "normal",
param = c(-1, 100),
initial = -1,
fixed = FALSE,
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)),
status = "experimental",
pdf = "logitoffset"
),
robit = list(
doc = "Robit link",
hyper = list(
theta = list(
hyperid = 49021,
name = "log degrees of freedom",
short.name = "dof",
initial = log(5),
fixed = TRUE,
prior = "pc.dof",
param = c(50, 0.5),
to.theta = function(x) log(x-2),
from.theta = function(x) 2+exp(x)
)
),
status = "experimental",
pdf = "robit"
),
test1 = list(
doc = "A test1-link function (experimental)",
hyper = list(
theta = list(
hyperid = 50001,
name = "beta",
short.name = "b",
prior = "normal",
param = c(0, 100),
initial = 0,
fixed = FALSE,
to.theta = function(x) x,
from.theta = function(x) x
)),
pdf = NA
),
special1 = list(
doc = "A special1-link function (experimental)",
hyper = list(
theta1 = list(
hyperid = 51001,
name = "log precision",
short.name = "prec",
initial = 0,
fixed = FALSE,
prior = "loggamma",
param = c(1, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta2 = list(
hyperid = 51002,
name = "beta1",
short.name = "beta1",
initial = 0,
fixed = FALSE,
prior = "mvnorm",
param = c(0, 100),
to.theta = function(x) x,
from.theta = function(x) x
),
theta3 = list(
hyperid = 51003,
name = "beta2",
short.name = "beta2",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta4 = list(
hyperid = 51004,
name = "beta3",
short.name = "beta3",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta5 = list(
hyperid = 51005,
name = "beta4",
short.name = "beta4",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta6 = list(
hyperid = 51006,
name = "beta5",
short.name = "beta5",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta7 = list(
hyperid = 51007,
name = "beta6",
short.name = "beta6",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta8 = list(
hyperid = 51008,
name = "beta7",
short.name = "beta7",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta9 = list(
hyperid = 51009,
name = "beta8",
short.name = "beta8",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta10 = list(
hyperid = 51010,
name = "beta9",
short.name = "beta9",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
),
theta11 = list(
hyperid = 51011,
name = "beta10",
short.name = "beta10",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
)
),
pdf = NA
),
special2 = list(
doc = "A special2-link function (experimental)",
hyper = list(
theta = list(
hyperid = 52001,
name = "beta",
short.name = "b",
prior = "normal",
param = c(0, 10),
initial = 0,
fixed = FALSE,
to.theta = function(x) x,
from.theta = function(x) x
)),
pdf = NA
)
)
)
}
`inla.models.section.predictor` = function()
{
return
list(predictor =
list(
predictor = list(
doc = "(not used)",
hyper = list(
theta = list(
hyperid = 53001,
name = "log precision",
short.name = "prec",
initial = 12,
fixed = TRUE,
prior = "loggamma",
param = c(1, 0.00001),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
)
)
)
)
}
`inla.models.section.hazard` = function()
{
return
list(hazard =
list(
rw1 = list(
doc = "A random walk of order 1 for the log-hazard",
hyper = list(
theta = list(
hyperid = 54001,
name = "log precision",
short.name = "prec",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
)
),
rw2 = list(
doc = "A random walk of order 2 for the log-hazard",
hyper = list(
theta = list(
hyperid = 55001,
name = "log precision",
short.name = "prec",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
)
)
)
)
}
`inla.models.section.likelihood` = function()
{
return
list(likelihood =
list(
## the first non-default link-function is the default one.
poisson = list(
doc = "The Poisson likelihood",
hyper = list(
),
survival = FALSE,
discrete = TRUE,
link = c("default", "log", "logoffset", "quantile", "test1", "special1", "special2"),
pdf = "poisson"
),
contpoisson = list(
doc = "The Cont Poisson likelihood",
hyper = list(
),
survival = FALSE,
discrete = TRUE,
link = c("default", "log"),
pdf = "contpoisson"
),
qcontpoisson = list(
doc = "The quantile Cont Poisson likelihood",
hyper = list(
),
survival = FALSE,
discrete = TRUE,
link = c("default", "log"),
pdf = "qcontpoisson"
),
cenpoisson = list(
doc = "Then censored Poisson likelihood",
hyper = list(
),
survival = FALSE,
discrete = TRUE,
link = c("default", "log", "logoffset", "test1", "special1", "special2"),
status = "experimental",
pdf = "cenpoisson"
),
gpoisson = list(
doc = "The generalized Poisson likelihood",
hyper = list(
theta1 = list(
hyperid = 56001,
name = "overdispersion",
short.name = "phi",
initial = 0,
fixed = FALSE,
prior = "loggamma",
param = c(1, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 56002,
name = "p",
short.name = "p",
initial = 1,
fixed = TRUE,
prior = "normal",
## use a tight prior, as this can go very wrong if set to weak
param = c(1, 100),
to.theta = function(x) x,
from.theta = function(x) x
)
),
survival = FALSE,
discrete = TRUE,
link = c("default", "log", "logoffset"),
pdf = "gpoisson",
status = "experimental"
),
binomial = list(
doc = "The Binomial likelihood",
hyper = list(
),
survival = FALSE,
discrete = TRUE,
link = c("default", "logit", "cauchit", "probit", "cloglog", "loglog",
"log", "sslogit", "logitoffset", "quantile", "pquantile", "robit"),
pdf = "binomial"
),
pom = list(
doc = "Likelihood for the proportional odds model",
hyper = list(
theta1 = list(
hyperid = 57101,
name = "theta1",
short.name = "theta1",
initial = NA,
fixed = FALSE,
prior = "dirichlet",
param = 3.0,
to.theta = function(x) x,
from.theta = function(x) x
),
theta2 = list(
hyperid = 57102,
name = "theta2",
short.name = "theta2",
initial = NA,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta3 = list(
hyperid = 57103,
name = "theta3",
short.name = "theta3",
initial = NA,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta4 = list(
hyperid = 57104,
name = "theta4",
short.name = "theta4",
initial = NA,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta5 = list(
hyperid = 57105,
name = "theta5",
short.name = "theta5",
initial = NA,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta6 = list(
hyperid = 57106,
name = "theta6",
short.name = "theta6",
initial = NA,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta7 = list(
hyperid = 57107,
name = "theta7",
short.name = "theta7",
initial = NA,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta8 = list(
hyperid = 57108,
name = "theta8",
short.name = "theta8",
initial = NA,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta9 = list(
hyperid = 57109,
name = "theta9",
short.name = "theta9",
initial = NA,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta10 = list(
hyperid = 57110,
name = "theta10",
short.name = "theta10",
initial = NA,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
status = "experimental",
survival = FALSE,
discrete = TRUE,
link = c("default", "identity"),
pdf = "pom"
),
gev2 = list(
doc = "The Generalized Extreme Value likelihood (2nd variant)",
hyper = list(
theta1 = list(
hyperid = 57201,
name = "spread",
short.name = "sd",
initial = 0,
fixed = FALSE,
prior = "loggamma",
param = c(1, 3),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 57202,
name = "tail",
short.name = "tail",
initial = -4,
fixed = FALSE,
prior = "pc.gevtail",
param = c(7, 0.0, 0.5),
to.theta = function(x, interval = c(REPLACE.ME.low, REPLACE.ME.high)) log(-(interval[1] - x)/(interval[2] - x)),
from.theta = function(x, interval = c(REPLACE.ME.low, REPLACE.ME.high)) interval[1] + (interval[2]-interval[1]) * exp(x)/(1.0 + exp(x))
),
theta3 = list(
hyperid = 57203,
name = "beta1",
short.name = "beta1",
initial = NA,
fixed = FALSE,
prior = "normal",
param = c(0, 300),
to.theta = function(x) x,
from.theta = function(x) x
),
theta4 = list(
hyperid = 57204,
name = "beta2",
short.name = "beta2",
initial = NA,
fixed = FALSE,
prior = "normal",
param = c(0, 300),
to.theta = function(x) x,
from.theta = function(x) x
),
theta5 = list(
hyperid = 57205,
name = "beta3",
short.name = "beta3",
initial = NA,
fixed = FALSE,
prior = "normal",
param = c(0, 300),
to.theta = function(x) x,
from.theta = function(x) x
),
theta6 = list(
hyperid = 57206,
name = "beta4",
short.name = "beta4",
initial = NA,
fixed = FALSE,
prior = "normal",
param = c(0, 300),
to.theta = function(x) x,
from.theta = function(x) x
),
theta7 = list(
hyperid = 57207,
name = "beta5",
short.name = "beta5",
initial = NA,
fixed = FALSE,
prior = "normal",
param = c(0, 300),
to.theta = function(x) x,
from.theta = function(x) x
),
theta8 = list(
hyperid = 57208,
name = "beta6",
short.name = "beta6",
initial = NA,
fixed = FALSE,
prior = "normal",
param = c(0, 300),
to.theta = function(x) x,
from.theta = function(x) x
),
theta9 = list(
hyperid = 57209,
name = "beta7",
short.name = "beta7",
initial = NA,
fixed = FALSE,
prior = "normal",
param = c(0, 300),
to.theta = function(x) x,
from.theta = function(x) x
),
theta10 = list(
hyperid = 57210,
name = "beta8",
short.name = "beta8",
initial = NA,
fixed = FALSE,
prior = "normal",
param = c(0, 300),
to.theta = function(x) x,
from.theta = function(x) x
),
theta11 = list(
hyperid = 57211,
name = "beta9",
short.name = "beta9",
initial = NA,
fixed = FALSE,
prior = "normal",
param = c(0, 300),
to.theta = function(x) x,
from.theta = function(x) x
),
theta12 = list(
hyperid = 57212,
name = "beta10",
short.name = "beta",
initial = NA,
fixed = FALSE,
prior = "normal",
param = c(0, 300),
to.theta = function(x) x,
from.theta = function(x) x
)
),
status = "experimental",
survival = FALSE,
discrete = FALSE,
link = c("default", "identity"),
pdf = "gev2"
),
gamma = list(
doc = "The Gamma likelihood",
hyper = list(
theta = list(
hyperid = 58001,
name = "precision parameter",
short.name = "prec",
initial = log(100),
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.01),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "log", "quantile"),
pdf = "gamma"
),
gammasurv = list(
doc = "The Gamma likelihood (survival)",
hyper = list(
theta = list(
hyperid = 58101,
name = "precision parameter",
short.name = "prec",
initial = log(1),
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.01),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = TRUE,
discrete = FALSE,
status = "experimental",
link = c("default", "log", "quantile"),
pdf = "gammasurv"
),
gammacount = list(
doc = "A Gamma generalisation of the Poisson likelihood",
hyper = list(
theta = list(
hyperid = 59001,
name = "log alpha",
short.name = "alpha",
initial = log(1.0),
fixed = FALSE,
prior = "pc.gammacount",
param = 3,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "log"),
status = "experimental",
pdf = "gammacount"
),
qkumar = list(
doc = "A quantile version of the Kumar likelihood",
hyper = list(
theta = list(
hyperid = 60001,
name = "precision parameter",
short.name = "prec",
initial = 0,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.001),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "logit", "cauchit"),
pdf = "qkumar"
),
qloglogistic = list(
doc = "A quantile loglogistic likelihood",
hyper = list(
theta = list(
hyperid = 60011,
name = "log alpha",
short.name = "alpha",
initial = 1,
fixed = FALSE,
prior = "loggamma",
param = c(25, 25),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "log", "neglog"),
pdf = "qloglogistic"
),
qloglogisticsurv = list(
doc = "A quantile loglogistic likelihood (survival)",
hyper = list(
theta = list(
hyperid = 60021,
name = "log alpha",
short.name = "alpha",
initial = 1,
fixed = FALSE,
prior = "loggamma",
param = c(25, 25),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = TRUE,
discrete = FALSE,
link = c("default", "log", "neglog"),
pdf = "qloglogistic"
),
beta = list(
doc = "The Beta likelihood",
hyper = list(
theta = list(
hyperid = 61001,
name = "precision parameter",
short.name = "phi",
initial = log(10),
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "logit", "cauchit", "probit", "cloglog", "loglog"),
pdf = "beta"
),
betabinomial = list(
doc = "The Beta-Binomial likelihood",
hyper = list(
theta = list(
hyperid = 62001,
name = "overdispersion",
short.name = "rho",
initial = 0,
fixed = FALSE,
prior = "gaussian",
param = c(0.0, 0.4),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
survival = FALSE,
discrete = TRUE,
link = c("default", "logit", "cauchit", "probit", "cloglog", "loglog", "robit"),
pdf = "betabinomial"
),
cbinomial = list(
doc = "The clustered Binomial likelihood",
hyper = list(),
survival = FALSE,
discrete = TRUE,
link = c("default", "logit", "cauchit", "probit", "cloglog", "loglog", "robit"),
status = "experimental",
pdf = "cbinomial"
),
nbinomial = list(
doc = "The negBinomial likelihood",
hyper = list(
theta = list(
hyperid = 63001,
name = "size",
short.name = "size",
initial = log(10),
fixed = FALSE,
prior = "pc.mgamma",
param = 7,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = TRUE,
link = c("default", "log", "logoffset", "quantile"),
pdf = "nbinomial"
),
nbinomial2 = list(
doc = "The negBinomial2 likelihood",
hyper = list(),
survival = FALSE,
discrete = TRUE,
link = c("default", "logit", "cauchit", "probit", "cloglog", "loglog"),
pdf = "nbinomial"
),
simplex = list(
doc = "The simplex likelihood",
hyper = list(
theta = list(
hyperid = 64001,
name = "log precision",
short.name = "prec",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "logit", "cauchit", "probit", "cloglog", "loglog"),
pdf = "simplex"
),
gaussian = list(
doc = "The Gaussian likelihoood",
hyper = list(
theta1 = list(
hyperid = 65001,
name = "log precision",
short.name = "prec",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 65002,
name = "log precision offset",
short.name = "precoffset",
initial = (-2.0 * log(.Machine$double.eps)),
fixed = TRUE,
prior = "none",
param = numeric(),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "identity", "logit", "cauchit", "log", "logoffset"),
pdf = "gaussian"
),
circularnormal = list(
doc = "The circular Gaussian likelihoood",
hyper = list(
theta = list(
hyperid = 67001,
name = "log precision parameter",
short.name = "prec",
initial = 2,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.01),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "tan"),
pdf = "circular-normal",
status = "experimental"
),
wrappedcauchy = list(
doc = "The wrapped Cauchy likelihoood",
hyper = list(
theta = list(
hyperid = 68001,
name = "log precision parameter",
short.name = "prec",
initial = 2,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.005),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "tan"),
pdf = "wrapped-cauchy",
status = "disabled"
),
iidgamma = list(
doc = "(experimental)",
hyper = list(
theta1 = list(
hyperid = 69001,
name = "logshape",
short.name = "shape",
initial = 0,
fixed = FALSE,
prior = "loggamma",
param = c(100, 100),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 69002,
name = "lograte",
short.name = "rate",
initial = 0,
fixed = FALSE,
prior = "loggamma",
param = c(100, 100),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "identity"),
pdf = "iidgamma",
status = "experimental"
),
iidlogitbeta = list(
doc = "(experimental)",
hyper = list(
theta1 = list(
hyperid = 70001,
name = "log.a",
short.name = "a",
initial = 1,
fixed = FALSE,
prior = "loggamma",
param = c(1, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 70002,
name = "log.b",
short.name = "b",
initial = 1,
fixed = FALSE,
prior = "loggamma",
param = c(1, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "logit"),
pdf = "iidlogitbeta",
status = "experimental"
),
loggammafrailty = list(
doc = "(experimental)",
hyper = list(
theta = list(
hyperid = 71001,
name = "log precision",
short.name = "prec",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "identity"),
pdf = "loggammafrailty",
status = "experimental"
),
logistic = list(
doc = "The Logistic likelihoood",
hyper = list(
theta = list(
hyperid = 72001,
name = "log precision",
short.name = "prec",
initial = 1,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "identity"),
pdf = "logistic"
),
skewnormal = list(
doc = "The Skew-Normal likelihoood",
hyper = list(
theta1 = list(
hyperid = 73001,
name = "log inverse scale",
short.name = "iscale",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 73002,
name = "logit skewness",
short.name = "skew",
initial = 4,
fixed = FALSE,
prior = "gaussian",
param = c(0, 10),
to.theta = function(x, shape.max = 1) log((1+x/shape.max)/(1-x/shape.max)),
from.theta = function(x, shape.max = 1) shape.max*(2*exp(x)/(1+exp(x))-1)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "identity"),
pdf = "sn"
),
sn = list(
doc = "The Skew-Normal likelihoood",
hyper = list(
theta1 = list(
hyperid = 74001,
name = "log inverse scale",
short.name = "iscale",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 74002,
name = "logit skewness",
short.name = "skew",
initial = 0,
fixed = FALSE,
prior = "gaussian",
param = c(0, 10),
to.theta = function(x, shape.max = 1) log((1+x/shape.max)/(1-x/shape.max)),
from.theta = function(x, shape.max = 1) shape.max*(2*exp(x)/(1+exp(x))-1)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "identity"),
pdf = "sn"
),
sn2 = list(
doc = "The Skew-Normal likelihoood (alt param)",
hyper = list(
theta1 = list(
hyperid = 75001,
name = "log precision",
short.name = "prec",
initial = 1,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 75002,
name = "logit skewness",
short.name = "skew",
initial = 0,
fixed = FALSE,
prior = "gaussian",
param = c(0, 10),
to.theta = function(x, shape.max = 1) log((1+x/shape.max)/(1-x/shape.max)),
from.theta = function(x, shape.max = 1) shape.max*(2*exp(x)/(1+exp(x))-1)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "identity"),
status = "experimental",
pdf = "sn2"
),
gev = list(
doc = "The Generalized Extreme Value likelihood",
hyper = list(
theta1 = list(
hyperid = 76001,
name = "log precision",
short.name = "prec",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 76002,
name = "tail parameter",
short.name = "tail",
initial = 0,
fixed = FALSE,
prior = "gaussian",
param = c(0, 25),
to.theta = function(x) x,
from.theta = function(x) x
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "identity"),
status = "experimental",
pdf = "gev"
),
lognormal = list(
doc = "The log-Normal likelihood",
hyper = list(
theta = list(
hyperid = 77101,
name = "log precision",
short.name = "prec",
initial = 0,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "identity"),
pdf = "lognormal"
),
lognormalsurv = list(
doc = "The log-Normal likelihood (survival)",
hyper = list(
theta = list(
hyperid = 78001,
name = "log precision",
short.name = "prec",
initial = 0,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = TRUE,
discrete = FALSE,
link = c("default", "identity"),
pdf = "lognormal"
),
exponential = list(
doc = "The Exponential likelihood",
hyper = list(
),
survival = FALSE,
discrete = FALSE,
link = c("default", "log"),
pdf = "exponential"
),
exponentialsurv = list(
doc = "The Exponential likelihood (survival)",
hyper = list(
),
survival = TRUE,
discrete = FALSE,
link = c("default", "log", "neglog"),
pdf = "exponential"
),
coxph = list(
doc = "Cox-proportional hazard likelihood",
hyper = list(
),
survival = TRUE,
discrete = TRUE,
link = c("default", "log", "neglog"),
pdf = "coxph"
),
weibull = list(
doc = "The Weibull likelihood",
## variant=0: lambda*y^alpha
## variant=1: (lambda*y)^alpha
hyper = list(
theta = list(
hyperid = 79001,
name = "log alpha",
short.name = "alpha",
initial = 0.1,
fixed = FALSE,
prior = "pc.alphaw",
param = c(5),
## the 'sc' constant is defined in inla.h, and must be the same.
## I know, this is hard-coded for the moment. Should be a generic
## way of doing this...
to.theta = function(x, sc = 0.1) log(x)/sc,
from.theta = function(x, sc = 0.1) exp(sc*x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "log", "neglog", "quantile"),
pdf = "weibull"
),
weibullsurv = list(
doc = "The Weibull likelihood (survival)",
## variant=0: lambda*y^alpha
## variant=1: (lambda*y)^alpha
hyper = list(
theta = list(
hyperid = 79101,
name = "log alpha",
short.name = "alpha",
initial = 0.1,
fixed = FALSE,
prior = "pc.alphaw",
param = c(5),
## the 'sc' constant is defined in inla.h, and must be the same.
## I know, this is hard-coded for the moment. Should be a generic
## way of doing this...
to.theta = function(x, sc = 0.1) log(x)/sc,
from.theta = function(x, sc = 0.1) exp(sc*x)
)
),
survival = TRUE,
discrete = FALSE,
link = c("default", "log", "neglog", "quantile"),
pdf = "weibull"
),
loglogistic = list(
doc = "The loglogistic likelihood",
hyper = list(
theta = list(
hyperid = 80001,
name = "log alpha",
short.name = "alpha",
initial = 1,
fixed = FALSE,
prior = "loggamma",
param = c(25, 25),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "log", "neglog"),
pdf = "loglogistic"
),
loglogisticsurv = list(
doc = "The loglogistic likelihood (survival)",
hyper = list(
theta = list(
hyperid = 80011,
name = "log alpha",
short.name = "alpha",
initial = 1,
fixed = FALSE,
prior = "loggamma",
param = c(25, 25),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = TRUE,
discrete = FALSE,
link = c("default", "log", "neglog"),
pdf = "loglogistic"
),
weibullcure = list(
doc = "The Weibull-cure likelihood (survival)",
hyper = list(
theta1 = list(
hyperid = 81001,
name = "log alpha",
short.name = "a",
initial = 0.1,
fixed = FALSE,
prior = "pc.alphaw",
param = c(5),
## the 'sc' constant is defined in inla.h, and must be the same.
## I know, this is hard-coded for the moment. Should be a generic
## way of doing this...
to.theta = function(x, sc = 0.1) log(x)/sc,
from.theta = function(x, sc = 0.1) exp(sc*x)
),
theta2 = list(
hyperid = 81002,
name = "logit probability",
short.name = "prob",
initial = -1,
fixed = FALSE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
survival = TRUE,
discrete = FALSE,
link = c("default", "log", "neglog"),
pdf = "weibullcure"
),
stochvol = list(
doc = "The Gaussian stochvol likelihood",
hyper = list(
theta = list(
hyperid = 82001,
name = "log precision",
short.name = "prec",
initial = 500, ## yes, this is correct
fixed = TRUE, ## yes, this is correct
prior = "loggamma",
param = c(1, 0.005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "log"),
pdf = "stochvolgaussian"
),
stochvolt = list(
doc = "The Student-t stochvol likelihood",
hyper = list(
theta = list(
hyperid = 83001,
name = "log degrees of freedom",
short.name = "dof",
initial = 4,
fixed = FALSE,
prior = "pc.dof",
param = c(15, 0.5),
to.theta = function(x) log(x-2),
from.theta = function(x) 2+exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "log"),
pdf = "stochvolt"
),
stochvolnig = list(
doc = "The Normal inverse Gaussian stochvol likelihood",
hyper = list(
theta1 = list(
hyperid = 84001,
name = "skewness",
short.name = "skew",
initial = 0,
fixed = FALSE,
prior = "gaussian",
param = c(0, 10),
to.theta = function(x) x,
from.theta = function(x) x
),
theta2 = list(
hyperid = 84002,
name = "shape",
short.name = "shape",
initial = 0,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.5),
to.theta = function(x) log(x-1),
from.theta = function(x) 1+exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "log"),
pdf = "stochvolnig"
),
zeroinflatedpoisson0 = list(
doc = "Zero-inflated Poisson, type 0",
hyper = list(
theta = list(
hyperid = 85001,
name = "logit probability",
short.name = "prob",
initial = -1,
fixed = FALSE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "log"),
pdf = "zeroinflated"
),
zeroinflatedpoisson1 = list(
doc = "Zero-inflated Poisson, type 1",
hyper = list(
theta = list(
hyperid = 86001,
name = "logit probability",
short.name = "prob",
initial = -1,
fixed = FALSE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "log"),
pdf = "zeroinflated"
),
zeroinflatedpoisson2 = list(
doc = "Zero-inflated Poisson, type 2",
hyper = list(
theta = list(
hyperid = 87001,
name = "log alpha",
short.name = "a",
initial = log(2),
fixed = FALSE,
prior = "gaussian",
param = c(log(2), 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "log"),
pdf = "zeroinflated"
),
zeroinflatedbetabinomial0 = list(
doc = "Zero-inflated Beta-Binomial, type 0",
hyper = list(
theta1 = list(
hyperid = 88001,
name = "overdispersion",
short.name = "rho",
initial = 0,
fixed = FALSE,
prior = "gaussian",
param = c(0.0, 0.4),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
),
theta2 = list(
hyperid = 88002,
name = "logit probability",
short.name = "prob",
initial = -1,
fixed = FALSE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
survival = FALSE,
discrete = TRUE,
link = c("default", "logit", "cauchit", "probit", "cloglog", "loglog", "robit"),
pdf = "zeroinflated"
),
zeroinflatedbetabinomial1 = list(
doc = "Zero-inflated Beta-Binomial, type 1",
hyper = list(
theta1 = list(
hyperid = 89001,
name = "overdispersion",
short.name = "rho",
initial = 0,
fixed = FALSE,
prior = "gaussian",
param = c(0.0, 0.4),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
),
theta2 = list(
hyperid = 89002,
name = "logit probability",
short.name = "prob",
initial = -1,
fixed = FALSE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
survival = FALSE,
discrete = TRUE,
link = c("default", "logit", "cauchit", "probit", "cloglog", "loglog", "robit"),
pdf = "zeroinflated"
),
zeroinflatedbinomial0 = list(
doc = "Zero-inflated Binomial, type 0",
hyper = list(
theta = list(
hyperid = 90001,
name = "logit probability",
short.name = "prob",
initial = -1,
fixed = FALSE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "logit", "cauchit", "probit", "cloglog", "loglog", "robit"),
pdf = "zeroinflated"
),
zeroinflatedbinomial1 = list(
doc = "Zero-inflated Binomial, type 1",
hyper = list(
theta = list(
hyperid = 91001,
name = "logit probability",
short.name = "prob",
initial = -1,
fixed = FALSE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "logit", "cauchit", "probit", "cloglog", "loglog", "robit"),
pdf = "zeroinflated"
),
zeroinflatedbinomial2 = list(
doc = "Zero-inflated Binomial, type 2",
hyper = list(
theta = list(
hyperid = 92001,
name = "alpha",
short.name = "alpha",
initial = -1,
fixed = FALSE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "logit", "cauchit", "probit", "cloglog", "loglog", "robit"),
pdf = "zeroinflated"
),
zeroninflatedbinomial2 = list(
doc = "Zero and N inflated binomial, type 2",
hyper = list(
theta1 = list(
hyperid = 93001,
name = "alpha1",
short.name = "alpha1",
initial = -1,
fixed = FALSE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 93002,
name = "alpha2",
short.name = "alpha2",
initial = -1,
fixed = FALSE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "logit", "cauchit", "probit", "cloglog", "loglog", "robit"),
pdf = NA
),
zeroninflatedbinomial3 = list(
doc = "Zero and N inflated binomial, type 3",
hyper = list(
theta1 = list(
hyperid = 93101,
name = "alpha0",
short.name = "alpha0",
initial = 1,
fixed = FALSE,
prior = "loggamma",
param = c(1, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 93102,
name = "alphaN",
short.name = "alphaN",
initial = 1,
fixed = FALSE,
prior = "loggamma",
param = c(1, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
status = "experimental",
survival = FALSE,
discrete = FALSE,
link = c("default", "logit", "cauchit", "probit", "cloglog", "loglog", "robit"),
pdf = "zeroinflated"
),
zeroinflatedbetabinomial2 = list(
doc = "Zero inflated Beta-Binomial, type 2",
hyper = list(
theta1 = list(
hyperid = 94001,
name = "log alpha",
short.name = "a",
initial = log(2),
fixed = FALSE,
prior = "gaussian",
param = c(log(2), 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 94002,
name = "beta",
short.name = "b",
initial = log(1),
fixed = FALSE,
prior = "gaussian",
param = c(0, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "logit", "cauchit", "probit", "cloglog", "loglog", "robit"),
pdf = "zeroinflated"
),
zeroinflatednbinomial0 = list(
doc = "Zero inflated negBinomial, type 0",
hyper = list(
theta1 = list(
hyperid = 95001,
name = "log size",
short.name = "size",
initial = log(10),
fixed = FALSE,
prior = "pc.mgamma",
param = 7,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 95002,
name = "logit probability",
short.name = "prob",
initial = -1,
fixed = FALSE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "log"),
pdf = "zeroinflated"
),
zeroinflatednbinomial1 = list(
doc = "Zero inflated negBinomial, type 1",
hyper = list(
theta1 = list(
hyperid = 96001,
name = "log size",
short.name = "size",
initial = log(10),
fixed = FALSE,
prior = "pc.mgamma",
param = 7,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 96002,
name = "logit probability",
short.name = "prob",
initial = -1,
fixed = FALSE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "log"),
pdf = "zeroinflated"
),
zeroinflatednbinomial1strata2 = list(
doc = "Zero inflated negBinomial, type 1, strata 2",
hyper = list(
theta1 = list(
hyperid = 97001,
name = "log size",
short.name = "size",
initial = log(10),
fixed = FALSE,
prior = "pc.mgamma",
param = 7,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 97002,
name = "logit probability 1",
short.name = "prob1",
initial = -1,
fixed = FALSE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
),
theta3 = list(
hyperid = 97003,
name = "logit probability 2",
short.name = "prob2",
initial = -1,
fixed = FALSE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
),
theta4 = list(
hyperid = 97004,
name = "logit probability 3",
short.name = "prob3",
initial = -1,
fixed = TRUE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
),
theta5 = list(
hyperid = 97005,
name = "logit probability 4",
short.name = "prob4",
initial = -1,
fixed = TRUE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
),
theta6 = list(
hyperid = 97006,
name = "logit probability 5",
short.name = "prob5",
initial = -1,
fixed = TRUE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
),
theta7 = list(
hyperid = 97007,
name = "logit probability 6",
short.name = "prob6",
initial = -1,
fixed = TRUE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
),
theta8 = list(
hyperid = 97008,
name = "logit probability 7",
short.name = "prob7",
initial = -1,
fixed = TRUE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
),
theta9 = list(
hyperid = 97009,
name = "logit probability 8",
short.name = "prob8",
initial = -1,
fixed = TRUE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
),
theta10 = list(
hyperid = 97010,
name = "logit probability 9",
short.name = "prob9",
initial = -1,
fixed = TRUE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
),
theta11 = list(
hyperid = 97011,
name = "logit probability 10",
short.name = "prob10",
initial = -1,
fixed = TRUE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
status = "experimental",
survival = FALSE,
discrete = FALSE,
link = c("default", "log"),
pdf = "zeroinflated"
),
zeroinflatednbinomial1strata3 = list(
doc = "Zero inflated negBinomial, type 1, strata 3",
hyper = list(
theta1 = list(
hyperid = 98001,
name = "logit probability",
short.name = "prob",
initial = -1,
fixed = FALSE,
prior = "gaussian",
param = c(-1, 0.2),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
),
theta2 = list(
hyperid = 98002,
name = "log size 1",
short.name = "size1",
initial = log(10),
fixed = FALSE,
prior = "pc.mgamma",
param = 7,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta3 = list(
hyperid = 98003,
name = "log size 2",
short.name = "size2",
initial = log(10),
fixed = FALSE,
prior = "pc.mgamma",
param = 7,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta4 = list(
hyperid = 98004,
name = "log size 3",
short.name = "size3",
initial = log(10),
fixed = TRUE,
prior = "pc.mgamma",
param = 7,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta5 = list(
hyperid = 98005,
name = "log size 4",
short.name = "size4",
initial = log(10),
fixed = TRUE,
prior = "pc.mgamma",
param = 7,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta6 = list(
hyperid = 98006,
name = "log size 5",
short.name = "size5",
initial = log(10),
fixed = TRUE,
prior = "pc.mgamma",
param = 7,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta7 = list(
hyperid = 98007,
name = "log size 6",
short.name = "size6",
initial = log(10),
fixed = TRUE,
prior = "pc.mgamma",
param = 7,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta8 = list(
hyperid = 98008,
name = "log size 7",
short.name = "size7",
initial = log(10),
fixed = TRUE,
prior = "pc.mgamma",
param = 7,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta9 = list(
hyperid = 98009,
name = "log size 8",
short.name = "size8",
initial = log(10),
fixed = TRUE,
prior = "pc.mgamma",
param = 7,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta10 = list(
hyperid = 98010,
name = "log size 9",
short.name = "size9",
initial = log(10),
fixed = TRUE,
prior = "pc.mgamma",
param = 7,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta11 = list(
hyperid = 98011,
name = "log size 10",
short.name = "size10",
initial = log(10),
fixed = TRUE,
prior = "pc.mgamma",
param = 7,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
status = "experimental",
survival = FALSE,
discrete = FALSE,
link = c("default", "log"),
pdf = "zeroinflated"
),
zeroinflatednbinomial2 = list(
doc = "Zero inflated negBinomial, type 2",
hyper = list(
theta1 = list(
hyperid = 99001,
name = "log size",
short.name = "size",
initial = log(10),
fixed = FALSE,
prior = "pc.mgamma",
param = 7,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 99002,
name = "log alpha",
short.name = "a",
initial = log(2),
fixed = FALSE,
prior = "gaussian",
param = c(2, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "log"),
pdf = "zeroinflated"
),
t = list(
doc = "Student-t likelihood",
hyper = list(
theta1 = list(
hyperid = 100001,
name = "log precision",
short.name = "prec",
initial = 0,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
hyperid = 100002,
name = "log degrees of freedom",
short.name = "dof",
initial = 5,
fixed = FALSE,
prior = "pc.dof",
param = c(15, 0.5),
to.theta = function(x) log(x-2),
from.theta = function(x) 2+exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "identity"),
pdf = "student-t"
),
tstrata = list(
doc = "A stratified version of the Student-t likelihood",
hyper = list(
theta1 = list(
hyperid = 101001,
name = "log degrees of freedom",
short.name = "dof",
initial = 4,
fixed = FALSE,
prior = "pc.dof",
param = c(15, 0.5),
to.theta = function(x) log(x-5),
from.theta = function(x) 5+exp(x)
),
theta2 = list(
hyperid = 101002,
name = "log precision1",
short.name = "prec1",
initial = 2,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta3 = list(
hyperid = 101003,
name = "log precision2",
short.name = "prec2",
initial = 2,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta4 = list(
hyperid = 101004,
name = "log precision3",
short.name = "prec3",
initial = 2,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta5 = list(
hyperid = 101005,
name = "log precision4",
short.name = "prec4",
initial = 2,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta6 = list(
hyperid = 101006,
name = "log precision5",
short.name = "prec5",
initial = 2,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta7 = list(
hyperid = 101007,
name = "log precision6",
short.name = "prec6",
initial = 2,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta8 = list(
hyperid = 101008,
name = "log precision7",
short.name = "prec7",
initial = 2,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta9 = list(
hyperid = 101009,
name = "log precision8",
short.name = "prec8",
initial = 2,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta10 = list(
hyperid = 101010,
name = "log precision9",
short.name = "prec9",
initial = 2,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta11 = list(
hyperid = 101011,
name = "log precision10",
short.name = "prec10",
initial = 2,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "identity"),
pdf = "tstrata"
),
nmix = list(
doc = "Binomial-Poisson mixture",
hyper = list(
theta1 = list(
hyperid = 101101,
name = "beta1",
short.name = "beta1",
initial = log(10),
fixed = FALSE,
prior = "normal",
param = c(0, 0.5),
to.theta = function(x) x,
from.theta = function(x) x
),
theta2 = list(
hyperid = 101102,
name = "beta2",
short.name = "beta2",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta3 = list(
hyperid = 101103,
name = "beta3",
short.name = "beta3",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta4 = list(
hyperid = 101104,
name = "beta4",
short.name = "beta4",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta5 = list(
hyperid = 101105,
name = "beta5",
short.name = "beta5",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta6 = list(
hyperid = 101106,
name = "beta6",
short.name = "beta6",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta7 = list(
hyperid = 101107,
name = "beta7",
short.name = "beta7",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta8 = list(
hyperid = 101108,
name = "beta8",
short.name = "beta8",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta9 = list(
hyperid = 101109,
name = "beta9",
short.name = "beta9",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta10 = list(
hyperid = 101110,
name = "beta10",
short.name = "beta10",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta11 = list(
hyperid = 101111,
name = "beta11",
short.name = "beta11",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta12 = list(
hyperid = 101112,
name = "beta12",
short.name = "beta12",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta13 = list(
hyperid = 101113,
name = "beta13",
short.name = "beta13",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta14 = list(
hyperid = 101114,
name = "beta14",
short.name = "beta14",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta15 = list(
hyperid = 101115,
name = "beta15",
short.name = "beta15",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
)
),
status = "experimental",
survival = FALSE,
discrete = TRUE,
link = c("default", "logit", "probit"),
pdf = "nmix"
),
nmixnb = list(
doc = "NegBinomial-Poisson mixture",
hyper = list(
theta1 = list(
hyperid = 101121,
name = "beta1",
short.name = "beta1",
initial = log(10),
fixed = FALSE,
prior = "normal",
param = c(0, 0.5),
to.theta = function(x) x,
from.theta = function(x) x
),
theta2 = list(
hyperid = 101122,
name = "beta2",
short.name = "beta2",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta3 = list(
hyperid = 101123,
name = "beta3",
short.name = "beta3",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta4 = list(
hyperid = 101124,
name = "beta4",
short.name = "beta4",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta5 = list(
hyperid = 101125,
name = "beta5",
short.name = "beta5",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta6 = list(
hyperid = 101126,
name = "beta6",
short.name = "beta6",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta7 = list(
hyperid = 101127,
name = "beta7",
short.name = "beta7",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta8 = list(
hyperid = 101128,
name = "beta8",
short.name = "beta8",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta9 = list(
hyperid = 101129,
name = "beta9",
short.name = "beta9",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta10 = list(
hyperid = 101130,
name = "beta10",
short.name = "beta10",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta11 = list(
hyperid = 101131,
name = "beta11",
short.name = "beta11",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta12 = list(
hyperid = 101132,
name = "beta12",
short.name = "beta12",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta13 = list(
hyperid = 101133,
name = "beta13",
short.name = "beta13",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta14 = list(
hyperid = 101134,
name = "beta14",
short.name = "beta14",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta15 = list(
hyperid = 101135,
name = "beta15",
short.name = "beta15",
initial = 0,
fixed = FALSE,
prior = "normal",
param = c(0, 1),
to.theta = function(x) x,
from.theta = function(x) x
),
theta16 = list(
hyperid = 101136,
name = "overdispersion",
short.name = "overdispersion",
initial = 0,
fixed = FALSE,
prior = "pc.gamma",
param = 7,
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
status = "experimental",
survival = FALSE,
discrete = TRUE,
link = c("default", "logit", "probit"),
pdf = "nmixnb"
),
gp = list(
doc = "Generalized Pareto likelihood",
hyper = list(
theta = list(
hyperid = 101201,
name = "shape",
short.name = "xi",
initial = log(0.1),
fixed = FALSE,
prior = "loggamma",
param = c(1, 15),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
status = "experimental",
survival = FALSE,
discrete = TRUE,
link = c("default", "quantile"),
pdf = "genPareto"
),
logperiodogram = list(
doc = "Likelihood for the log-periodogram",
hyper = list(
),
survival = FALSE,
discrete = FALSE,
link = c("default", "identity"),
pdf = NA
)
)
)
}
`inla.models.section.prior` = function()
{
return
list(prior =
list(
normal = list(
doc = "Normal prior",
nparameters = 2L,
pdf = "gaussian"
),
gaussian = list(
doc = "Gaussian prior",
nparameters = 2L,
pdf = "gaussian"
),
wishart1d = list(
doc = "Wishart prior dim=1",
nparameters = 2L,
pdf = "iid123d"
),
wishart2d = list(
doc = "Wishart prior dim=2",
nparameters = 4L,
pdf = "iid123d"
),
wishart3d = list(
doc = "Wishart prior dim=3",
nparameters = 7L,
pdf = "iid123d"
),
wishart4d = list(
doc = "Wishart prior dim=4",
nparameters = 11L,
pdf = "iid123d"
),
wishart5d = list(
doc = "Wishart prior dim=5",
nparameters = 16L,
pdf = "iid123d"
),
loggamma = list(
doc = "Log-Gamma prior",
nparameters = 2L,
pdf = "prior-loggamma"
),
gamma = list(
doc = "Gamma prior",
nparameters = 2L,
pdf = "prior-loggamma"
),
minuslogsqrtruncnormal = list(
doc = "(obsolete)",
nparameters = 2L,
pdf = "prior-logtnorm"
),
logtnormal = list(
doc = "Truncated Normal prior",
nparameters = 2L,
pdf = "prior-logtnorm"
),
logtgaussian = list(
doc = "Truncated Gaussian prior",
nparameters = 2L,
pdf = "prior-logtnorm"
),
flat=list(
doc = "A constant prior",
nparameters = 0L,
pdf = "various-flat"
),
logflat=list(
doc = "A constant prior for log(theta)",
nparameters = 0L,
pdf = "various-flat"
),
logiflat=list(
doc = "A constant prior for log(1/theta)",
nparameters = 0L,
pdf = "various-flat"
),
mvnorm = list(
doc = "A multivariate Normal prior",
nparameters = -1L,
pdf = "mvnorm"
),
pc.alphaw = list(
doc = "PC prior for alpha in Weibull",
nparameters = 1L,
pdf = "pc.alphaw"
),
pc.ar = list(
doc = "PC prior for the AR(p) model",
nparameters = 1L,
pdf = "pc.ar"
),
dirichlet = list(
doc ="Dirichlet prior",
nparameters = 1L,
pdf = "dirichlet"
),
## this is the 'no prior needed' prior
none = list(
doc = "No prior",
nparameters = 0L),
## this is the 'flag an error if used' prior
invalid = list(
doc = "Void prior",
nparameters = 0L),
betacorrelation = list(
doc = "Beta prior for the correlation",
nparameters = 2L,
pdf = "betacorrelation"
),
logitbeta = list(
doc = "Logit prior for a probability",
nparameters = 2L,
pdf = "logitbeta"
),
pc.prec = list(
doc = "PC prior for log(precision)",
nparameters = 2L,
pdf = "pc.prec"
),
pc.dof = list(
doc = "PC prior for log(dof-2)",
nparameters = 2L,
pdf = "pc.dof"
),
pc.cor0 = list(
doc = "PC prior correlation, basemodel cor=0",
nparameters = 2L,
pdf = "pc.cor0"
),
pc.cor1 = list(
doc = "PC prior correlation, basemodel cor=1",
nparameters = 2L,
pdf = "pc.cor1"
),
pc.fgnh = list(
doc = "PC prior for the Hurst parameter in FGN",
nparameters = 2L,
pdf = "pc.fgnh"
),
## experimental prior from GA
pc.spde.GA = list(
doc = "(experimental)",
nparameters = 4L,
pdf = NA
),
pc.matern = list(
doc = "PC prior for the Matern SPDE",
nparameters = 3L,
pdf = NA
),
pc.range = list(
doc = "PC prior for the range in the Matern SPDE",
nparameters = 2L,
pdf = NA
),
pc.gamma = list(
doc = "PC prior for a Gamma parameter",
nparameters = 1L,
pdf = "pc.gamma"
),
pc.mgamma = list(
doc = "PC prior for a Gamma parameter",
nparameters = 1L,
pdf = "pc.gamma"
),
pc.gammacount = list(
doc = "PC prior for the GammaCount likelihood",
nparameters = 1L,
pdf = "pc.gammacount"
),
pc.gevtail = list(
doc = "PC prior for the tail in the GEV likelihood",
nparameters = 3L,
pdf = "pc.gevtail"
),
## this is the generic one, which is case-spesific and possibly adaptive
pc = list(
doc = "Generic PC prior",
nparameters = 2L,
pdf = NA
),
ref.ar = list(
doc = "Reference prior for the AR(p) model, p<=3",
nparameters = 0L,
pdf = NA
),
pom = list(
doc = "#classes-dependent prior for the POM model",
nparameters = 0L,
pdf = "pom"
),
jeffreystdf = list(
doc = "Jeffreys prior for the doc",
nparameters = 0L,
pdf = "jeffreystdf"
),
"expression:" = list(
doc = "A generic prior defined using expressions",
nparameters = -1L,
pdf = "expression"
),
"table:" = list(
doc = "A generic tabulated prior",
nparameters = -1L,
pdf = "table"
)
)
)
}
`inla.models.section.wrapper` = function()
{
return
list(wrapper =
list(
joint = list(
doc = "(experimental)",
hyper = list(
theta = list(
hyperid = 102001,
name = "log precision",
short.name = "prec",
initial = 0,
fixed = TRUE,
prior = "loggamma",
param = c(1, 0.00005),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
constr = FALSE,
nrow.ncol = FALSE,
augmented = FALSE,
aug.factor = 1L,
aug.constr = NULL,
n.div.by = NULL,
n.required = FALSE,
set.default.values = FALSE,
pdf = NA
)
)
)
}
`inla.models` = function()
{
## this is not very clean solution, but for the moment is ok. the
## inla.models() function takes just to much time!!!
envir = inla.get.inlaEnv()
if (exists("inla.models", envir = envir) &&
exists("hgid", envir = envir) &&
get("hgid", envir = envir) == inla.version("hgid")) {
return (get("inla.models", envir = envir))
} else {
## have to split it, as option keep.source has an upper limit...
models = c(
inla.models.section.latent(),
inla.models.section.group(),
inla.models.section.mix(),
inla.models.section.link(),
inla.models.section.predictor(),
inla.models.section.hazard(),
inla.models.section.likelihood(),
inla.models.section.prior(),
inla.models.section.wrapper())
## set "read.only" attribute for the `hyper' at those elements
## that cannot be changed.
for (section in names(models)) {
for (model in names(models[[section]])) {
a = models[[section]][[model]]
if (!is.null(a$hyper) && length(a$hyper) > 0) {
for (theta in names(a$hyper)) {
for (elm in names(a$hyper[[theta]])) {
val = FALSE
if (elm == "prior") {
if (a$hyper[[theta]][[elm]] == "none" ||
a$hyper[[theta]][[elm]] == "wishart1d" ||
a$hyper[[theta]][[elm]] == "wishart2d" ||
a$hyper[[theta]][[elm]] == "wishart3d" ||
a$hyper[[theta]][[elm]] == "wishart4d" ||
a$hyper[[theta]][[elm]] == "wishart5d") {
val = TRUE
}
}
if (elm == "to.theta" || elm == "from.theta")
val = TRUE
## append the new attribute, so the code
## depends on if the object has an attribute
## from before or not.
if (is.null(attributes(models[[section]][[model]]$hyper[[theta]][[elm]]))) {
attributes(models[[section]][[model]]$hyper[[theta]][[elm]]) =
list("inla.read.only" = val)
} else {
attributes(models[[section]][[model]]$hyper[[theta]][[elm]]) =
c("inla.read.only" = val,
attributes(models[[section]][[model]]$hyper[[theta]][[elm]]))
}
}
}
}
}
}
assign("inla.models", models, envir = envir)
assign("hgid", inla.version("hgid"), envir = envir)
return (models)
}
stop("This should not happen")
}
`inla.is.model` = function(model, section = NULL,
stop.on.error = TRUE, ignore.case = FALSE)
{
mm = inla.models()
if (is.null(section)) {
stop("No section given; please fix...")
}
section = match.arg(section, names(mm))
models = names((mm[ names(mm) == section ])[[1]])
if (is.character(model) && length(model) > 0) {
if (ignore.case) {
m = tolower(model)
ms = tolower(models)
} else {
m = model
ms = models
}
ret = c()
for(i in 1L:length(m)) {
if (is.element(m[i], ms)) {
ret[i] = TRUE
} else {
if (stop.on.error) {
print("Valid models are:")
print(models)
stop(paste(c("\n\tUnknown name [", model[i], "]\n", "\tValid choices are: ",
models), sep=" ", collapse=" "))
} else {
ret[i] = FALSE
}
}
}
} else {
if (stop.on.error)
stop(paste("\n\tModel [", model, "] is not of type character()\n", sep=""))
}
return (ret)
}
`inla.model.properties` = function(
model,
section = NULL,
stop.on.error = TRUE,
ignore.case = FALSE)
{
if (is.null(section)) {
stop("No section given; please fix...")
}
mm = inla.models()
section = match.arg(section, names(mm))
m = inla.model.properties.generic(inla.trim.family(model),
(mm[names(mm) == section])[[1]],
stop.on.error, ignore.case,
## would like to know the section for a possible warning/error if the status says so.
section = section)
if (is.null(m)) {
return (NULL)
}
return (m)
}
`inla.model.properties.generic` = function(model, models, stop.on.error = TRUE, ignore.case = TRUE, section = "UKNOWN")
{
## argument 'section' is for 'status' only...
m = ifelse(ignore.case, tolower(model), model)
if (ignore.case) {
ms = tolower(names(models))
} else {
ms = names(models)
}
ms = inla.trim.family(ms)
k = grep(paste("^", m, "$", sep=""), ms)
if (length(k) == 0L) {
if (stop.on.error) {
stop(paste("Name '", model, "' is unknown. Valid choices are: ", inla.paste(ms), ".", sep=""))
}
return (NULL)
} else {
## if 'status' is set, then issue a warning/error depending on
## 'status'. do this the first time only if status is
## 'experimental'.
status = models[[k]]$status
if (is.null(status)) {
## do nothing; all ok.
} else {
status.core = strsplit(status, ":")[[1]][1]
stopifnot(any(inla.strcasecmp(status.core, c("experimental", "disabled", "changed"))))
envir = inla.get.inlaEnv()
var = paste("processed.status.for.model.", model, ".in.section.", section, sep="")
if (inla.strcasecmp(status.core, "experimental")) {
if (!(exists(var, envir = envir) && get(var, envir = envir))) {
assign(var, TRUE, envir = envir)
msg = paste0("Model '", model, "' in section '", section, "' is marked as '", status,
"'; changes may appear at any time.",
"\n ",
"Use this model with extra care!!! Further warnings are disabled.")
warning(msg)
} else {
## the warning is already given; do nothing
}
} else if (inla.strcasecmp(status.core, "disabled")) {
assign(var, TRUE, envir = envir)
msg = paste("Model '", model, "' in section '", section, "' is marked as '",
status, ".\n",
"Usage is either not recommended and unsupported.",
"\n", sep="")
var = paste("enable.model.", section, ".", model, sep="")
if (!(exists(var, envir = envir) && get(var, envir = envir))) {
msg = paste0(c(msg, paste(" You can enable this model setting variable '", var,
"'\n to 'TRUE' in environment INLA:::inla.get.inlaEnv().\n",
" If you chose to do so, you are on your own.")))
stop(msg)
}
} else if (inla.strcasecmp(status.core, "changed")) {
assign(var, TRUE, envir = envir)
msg = paste0("Model '", model, "' in section '", section, "' is marked as '",
status, ".\n",
" There have been a change in the model definition, which is not backward compatible.\n",
" Please refer to the documentation before proceeeding.")
var = paste("enable.model.", section, ".", model, sep="")
if (!(exists(var, envir = envir) && get(var, envir = envir))) {
msg = paste0(c(msg, paste0("\n You can bypass this check setting variable '", var,
"'\n to 'TRUE' in environment INLA:::inla.get.inlaEnv().\n")))
stop(msg)
}
}
}
return (models[[k]])
}
}
`inla.model.validate.link.function` = function(model, link)
{
valid.links = inla.model.properties(model, "likelihood")$link
stopifnot(!is.null(valid.links))
stopifnot(length(valid.links) >= 2L)
stopifnot(valid.links[1L] == "default")
link = tolower(link)
if (is.element(link, valid.links)) {
## this is the convention: the default link is the second
## entry in the list. the first entry is always "default"
if (link == "default") {
link = valid.links[2L]
}
} else {
stop(inla.paste(c("Link function `", link, "' is not valid or yet implemented.",
"\n",
"Valid ones are: ", inla.paste(valid.links), "\n"), sep=""))
}
return (link)
}
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