R/models.R
In andrewzm/INLA: Functions which allow to perform full Bayesian analysis of latent Gaussian models using Integrated Nested Laplace Approximaxion
## Export: inla.models
`inla.models.section.latent` = function()
{
return
list(latent =
list(
linear = list(
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(
hyper = list(
theta = list(
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(
hyper = list(
theta1 = list(
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(
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(
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(
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,
status = "experimental",
pdf = "mec"
),
meb = list(
hyper = list(
theta1 = list(
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(
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,
status = "experimental",
pdf = "meb"
),
rgeneric = list(
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,
status = "experimental",
pdf = "rgeneric"
),
rw1 = list(
hyper = list(
theta = list(
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,
pdf = "rw1"
),
rw2 = list(
hyper = list(
theta = list(
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,
pdf = "rw2"
),
crw2 = list(
hyper = list(
theta = list(
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,
pdf = "crw2"
),
seasonal = list(
hyper = list(
theta = list(
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(
hyper = list(
theta = list(
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(
hyper = list(
theta1 = list(
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(
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(
hyper = list(
theta1 = list(
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(
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(
hyper = list(
theta1 = list(
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(
name = "logit phi",
short.name = "phi",
prior = "pc",
param = c(0.5, -1),
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(
hyper = list(
theta1 = list(
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(
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(
hyper = list(
theta1 = list(
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(
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"
),
ar1 = list(
hyper = list(
theta1 = list(
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(
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
)
),
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"
),
ar = list(
## to many parameters here, but ...
hyper = list(
theta1 = list(
name = "log precision",
short.name = "prec",
initial = 4,
fixed = FALSE,
prior = "pc.prec",
param = c(1, 0.01),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
name = "pacf1",
short.name = "pacf1",
initial = 1,
fixed = FALSE,
prior = "pc.ar",
param = 1.0, ## lambda
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta3 = list(
name = "pacf2",
short.name = "pacf2",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta4 = list(
name = "pacf3",
short.name = "pacf3",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta5 = list(
name = "pacf4",
short.name = "pacf4",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta6 = list(
name = "pacf5",
short.name = "pacf5",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta7 = list(
name = "pacf6",
short.name = "pacf6",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta8 = list(
name = "pacf7",
short.name = "pacf7",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta9 = list(
name = "pacf8",
short.name = "pacf8",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta10 = list(
name = "pacf9",
short.name = "pacf9",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta11 = list(
name = "pacf10",
short.name = "pacf10",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
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,
status = "experimental",
pdf = "ar"
),
ou = list(
hyper = list(
theta1 = list(
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(
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"
),
generic = list(
hyper = list(
theta = list(
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(
hyper = list(
theta = list(
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(
hyper = list(
theta1 = list(
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(
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(
hyper = list(
theta1 = list(
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(
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(
hyper = list(
theta1 = list(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
## this will be redone anyway soon....
hyper = list(
theta1 = list(
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(
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(
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(
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(
## to many parameters here, but ...
hyper = list(
theta1 = list(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
## to many parameters here, but ...
hyper = list(
theta1 = list(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
hyper = list(
theta = list(
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(
hyper = list(
theta1 = list(
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(
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(
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(
hyper = list(
theta1 = list(
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(
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(
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(
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(
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(
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(
hyper = list(
theta1 = list(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
hyper = list(
theta1 = list(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
hyper = list(
theta1 = list(
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(
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(
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(
hyper = list(
theta = list(
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(
hyper = list(
theta = list(
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(
hyper = list(
theta1 = list(
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(
name = "logit phi",
short.name = "phi",
prior = "pc",
param = c(0.5, -1),
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(
hyper = list(
theta1 = list(
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(
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(
hyper = list(
theta1 = list(
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(
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"
),
copy = list(
hyper = list(
theta = list(
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(
hyper = list(
theta = list(
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(
hyper = list(
theta1 = list(
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(
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(
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(
hyper = list(
theta1 = list(
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(
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(
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"
)
##
)
)
}
`inla.models.section.group` = function()
{
## prevent a warning with R CMD check
ngroup = NULL
return
list(group =
list(
exchangeable = list(
hyper = list(
theta = list(
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)
)
)
),
ar1 = list(
hyper = list(
theta = list(
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(
## to many parameters here, but ...
hyper = list(
theta1 = list(
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)
),
theta2 = list(
name = "pacf1",
short.name = "pacf1",
initial = 2,
fixed = FALSE,
prior = "mvnorm",
param = c(0, 0.15), ## same as for AR1
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta3 = list(
name = "pacf2",
short.name = "pacf2",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta4 = list(
name = "pacf3",
short.name = "pacf3",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta5 = list(
name = "pacf4",
short.name = "pacf4",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta6 = list(
name = "pacf5",
short.name = "pacf5",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta7 = list(
name = "pacf6",
short.name = "pacf6",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta8 = list(
name = "pacf7",
short.name = "pacf7",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta9 = list(
name = "pacf8",
short.name = "pacf8",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta10 = list(
name = "pacf9",
short.name = "pacf9",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta11 = list(
name = "pacf10",
short.name = "pacf10",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
)
)
),
rw1 = list(
hyper = list(
theta = list(
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(
hyper = list(
theta = list(
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(
hyper = list(
theta = list(
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)
)
)
),
I = list(
hyper = list(
theta = list(
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(
hyper = list(
theta = list(
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.01),
initial = 0,
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(hyper = list()),
cloglog = list(hyper = list()),
identity = list(hyper = list()),
log = list(hyper = list()),
logit = list(hyper = list()),
probit = list(hyper = list()),
tan = list(hyper = list()),
sslogit = list(
hyper = list(
theta1 = list(
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(
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(
hyper = list(
theta = list(
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"
),
test1 = list(
hyper = list(
theta = list(
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
),
special2 = list(
hyper = list(
theta = list(
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
),
special1 = list(
hyper = list(
theta1 = list(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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
)
)
)
}
`inla.models.section.predictor` = function()
{
return
list(predictor =
list(
predictor = list(
hyper = list(
theta = list(
name = "log precision",
short.name = "prec",
initial = 11,
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(
hyper = list(
theta = list(
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(
hyper = list(
theta = list(
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(
hyper = list(
),
survival = FALSE,
discrete = TRUE,
link = c("default", "log", "logoffset", "test1", "special1", "special2"),
pdf = "poisson"
),
gpoisson = list(
hyper = list(
theta1 = list(
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(
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(
hyper = list(
),
survival = FALSE,
discrete = TRUE,
link = c("default", "logit", "probit", "cloglog", "log", "sslogit"),
pdf = "binomial"
),
testbinomial1 = list(
hyper = list(
theta1 = list(
name = "sensitivity",
short.name = "s",
initial = 3,
fixed = FALSE,
prior = "logitbeta",
param = c(2, 1),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
),
theta2 = list(
name = "specificity",
short.name = "e",
initial = 3,
fixed = FALSE,
prior = "logitbeta",
param = c(2, 1),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
status = "experimental",
survival = FALSE,
discrete = TRUE,
link = c("default", "logit", "probit", "cloglog", "log"),
pdf = "testbinomial1"
),
gamma = list(
hyper = list(
theta = list(
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"),
pdf = "gamma"
),
gammacount = list(
hyper = list(
theta = list(
name = "log alpha",
short.name = "alpha",
initial = log(1),
fixed = FALSE,
prior = "loggamma",
param = c(10, 10),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "log"),
status = "experimental",
pdf = "gammacount"
),
kumar = list(
hyper = list(
theta1 = list(
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)
),
theta2 = list(
name = "quantile",
short.name = "q",
initial = 0.5,
fixed = TRUE,
prior = "invalid",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "logit"),
pdf = "kumar"
),
beta = list(
hyper = list(
theta = list(
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", "probit", "cloglog"),
pdf = "beta"
),
betabinomial = list(
hyper = list(
theta = list(
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", "probit", "cloglog"),
pdf = "betabinomial"
),
cbinomial = list(
hyper = list(
),
survival = FALSE,
discrete = TRUE,
link = c("default", "logit", "probit", "cloglog"),
status = "experimental",
pdf = "cbinomial"
),
nbinomial = list(
hyper = list(
theta = list(
name = "size",
short.name = "size",
initial = log(10),
fixed = FALSE,
prior = "loggamma",
param = c(1, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = TRUE,
link = c("default", "log", "logoffset"),
pdf = "nbinomial"
),
simplex = list(
hyper = list(
theta = list(
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", "probit", "cloglog"),
pdf = "simplex"
),
gaussian = list(
hyper = list(
theta = list(
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", "logit", "log"),
pdf = "gaussian"
),
normal = list(
hyper = list(
theta = list(
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 = "gaussian"
),
circularnormal = list(
hyper = list(
theta = list(
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(
hyper = list(
theta = list(
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(
hyper = list(
theta1 = list(
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(
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(
hyper = list(
theta1 = list(
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(
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(
hyper = list(
theta = list(
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"
),
logistic = list(
hyper = list(
theta = list(
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(
hyper = list(
theta1 = list(
name = "inverse.scale",
short.name = "iscale",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005)
),
theta2 = list(
name = "skewness",
short.name = "skew",
initial = 4,
fixed = FALSE,
prior = "gaussian",
param = c(0, 10)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "identity"),
pdf = "sn"
),
sn = list(
hyper = list(
theta1 = list(
name = "log inverse scale",
short.name = "iscale",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005)
),
theta2 = list(
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(
hyper = list(
theta1 = list(
name = "log precision",
short.name = "prec",
initial = 1,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005)
),
theta2 = list(
name = "logit skewness",
short.name = "skew",
initial = 0,
fixed = FALSE,
prior = "gaussian",
param = c(0, 10),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) (2*exp(x)/(1+exp(x))-1)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "identity"),
status = "experimental",
pdf = "sn2"
),
gev = list(
hyper = list(
theta1 = list(
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(
name = "gev parameter",
short.name = "gev",
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"
),
laplace = list(
hyper = list(
theta = list(
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"),
status = "disabled",
pdf = "laplace"
),
lognormal = list(
hyper = list(
theta = list(
name = "log precision",
short.name = "prec",
initial = 2,
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(
hyper = list(
),
survival = TRUE,
discrete = FALSE,
link = c("default", "log"),
pdf = "exponential"
),
coxph = list(
hyper = list(
),
survival = TRUE,
discrete = TRUE,
link = c("default", "log"),
pdf = "coxph"
),
weibull = list(
hyper = list(
theta = list(
name = "log alpha",
short.name = "a",
initial = 0,
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"),
pdf = "weibull"
),
loglogistic = list(
hyper = list(
theta = list(
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"),
pdf = "loglogistic"
),
weibullcure = list(
hyper = list(
theta1 = list(
name = "log alpha",
short.name = "a",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(25, 25),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
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"),
pdf = NA
),
stochvol = list(
hyper = list(
theta = list(
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(
hyper = list(
theta = list(
name = "log degrees of freedom",
short.name = "dof",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 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(
hyper = list(
theta1 = list(
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(
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(
hyper = list(
theta = list(
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(
hyper = list(
theta = list(
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(
hyper = list(
theta = list(
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(
hyper = list(
theta1 = list(
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(
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", "probit", "cloglog"),
pdf = "zeroinflated"
),
zeroinflatedbetabinomial1 = list(
hyper = list(
theta1 = list(
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(
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", "probit", "cloglog"),
pdf = "zeroinflated"
),
zeroinflatedbinomial0 = list(
hyper = list(
theta = list(
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", "probit", "cloglog"),
pdf = "zeroinflated"
),
zeroinflatedbinomial1 = list(
hyper = list(
theta = list(
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", "probit", "cloglog"),
pdf = "zeroinflated"
),
zeroinflatedbinomial2 = list(
hyper = list(
theta = list(
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", "probit", "cloglog"),
pdf = "zeroinflated"
),
zeroninflatedbinomial2 = list(
hyper = list(
theta1 = list(
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(
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", "probit", "cloglog"),
pdf = NA
),
zeroinflatedbetabinomial2 = list(
hyper = list(
theta1 = list(
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(
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", "probit", "cloglog"),
pdf = "zeroinflated"
),
zeroinflatednbinomial0 = list(
hyper = list(
theta1 = list(
name = "log size",
short.name = "size",
initial = log(10),
fixed = FALSE,
prior = "loggamma",
param = c(1, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
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(
hyper = list(
theta1 = list(
name = "log size",
short.name = "size",
initial = log(10),
fixed = FALSE,
prior = "loggamma",
param = c(1, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
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(
hyper = list(
theta1 = list(
name = "log size",
short.name = "size",
initial = log(10),
fixed = FALSE,
prior = "loggamma",
param = c(1, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
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(
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))
)
),
status = "experimental",
survival = FALSE,
discrete = FALSE,
link = c("default", "log"),
pdf = "zeroinflated"
),
zeroinflatednbinomial1strata3 = list(
hyper = list(
theta1 = list(
name = "log size 1",
short.name = "size1",
initial = log(10),
fixed = FALSE,
prior = "loggamma",
param = c(1, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
name = "log size 2",
short.name = "size2",
initial = log(10),
fixed = FALSE,
prior = "loggamma",
param = c(1, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta3 = list(
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))
)
),
status = "experimental",
survival = FALSE,
discrete = FALSE,
link = c("default", "log"),
pdf = "zeroinflated"
),
zeroinflatednbinomial2 = list(
hyper = list(
theta1 = list(
name = "log size",
short.name = "size",
initial = log(10),
fixed = FALSE,
prior = "loggamma",
param = c(1, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
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(
hyper = list(
theta1 = list(
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(
name = "log degrees of freedom",
short.name = "dof",
initial = 5,
fixed = FALSE,
prior = "loggamma",
param = c(1, 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(
hyper = list(
theta1 = list(
name = "log degrees of freedom",
short.name = "dof",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.01),
to.theta = function(x) log(x-5),
from.theta = function(x) 5+exp(x)
),
theta2 = list(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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"
),
logperiodogram = list(
hyper = list(
),
survival = FALSE,
discrete = FALSE,
link = c("default", "identity"),
pdf = NA
)
)
)
}
`inla.models.section.prior` = function()
{
return
list(prior =
list(
normal = list(
nparameters = 2L,
pdf = "gaussian"
),
gaussian = list(
nparameters = 2L,
pdf = "gaussian"
),
wishart1d = list(
nparameters = 2L,
pdf = "iid123d"
),
wishart2d = list(
nparameters = 4L,
pdf = "iid123d"
),
wishart3d = list(
nparameters = 7L,
pdf = "iid123d"
),
wishart4d = list(
nparameters = 11L,
pdf = "iid123d"
),
wishart5d = list(
nparameters = 16L,
pdf = "iid123d"
),
loggamma = list(
nparameters = 2L,
pdf = "prior-loggamma"
),
minuslogsqrtruncnormal = list(
nparameters = 2L,
pdf = "prior-logtnorm"
),
logtnormal = list(
nparameters = 2L,
pdf = "prior-logtnorm"
),
logtgaussian = list(
nparameters = 2L,
pdf = "prior-logtnorm"
),
flat=list(
nparameters = 0L,
pdf = "various-flat"
),
logflat=list(
nparameters = 0L,
pdf = "various-flat"
),
logiflat=list(
nparameters = 0L,
pdf = "various-flat"
),
mvnorm = list(
nparameters = -1L,
pdf = "mvnorm"
),
pc.ar = list(
nparameters = 1L,
pdf = "pc.ar"
),
## this is the 'no prior needed' prior
none = list(nparameters = 0L),
## this is the 'flag an error if used' prior
invalid = list(nparameters = 0L),
betacorrelation = list(
nparameters = 2L,
pdf = "betacorrelation"
),
logitbeta = list(
nparameters = 2L,
pdf = "logitbeta"
),
pc.prec = list(
nparameters = 2L,
pdf = "pc.prec"
),
pc.dof = list(
nparameters = 2L,
pdf = "pc.dof"
),
pc.rho0 = list(
nparameters = 2L,
pdf = "pc.rho0"
),
pc.rho1 = list(
nparameters = 2L,
pdf = "pc.rho1"
),
## experimental prior from GA
pc.spde.GA = list(
nparameters = 4L,
pdf = NA
),
## this is the generic one, which is case-spesific and possibly adaptive
pc = list(
nparameters = 2L,
pdf = NA
),
ref.ar = list(
nparameters = 0L,
pdf = NA
),
jeffreystdf = list(
nparameters = 0L,
pdf = "jeffreystdf"
),
"expression:" = list(
nparameters = -1L,
pdf = "expression"
),
"table:" = list(
nparameters = -1L,
pdf = "table"
)
)
)
}
`inla.models.section.wrapper` = function()
{
return
list(wrapper =
list(
joint = list(
hyper = list(
theta = list(
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 = names(inla.models()),
stop.on.error = TRUE, ignore.case = FALSE)
{
section = match.arg(section)
mm = inla.models()
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 = c("..invalid.model..", names(inla.models())),
stop.on.error = TRUE,
ignore.case = FALSE)
{
section = match.arg(section)
if (section == "..invalid.model..")
stop("No section given; please fix...")
mm = inla.models()
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 {
stopifnot(any(inla.strcasecmp(status, c("experimental", "disabled"))))
envir = inla.get.inlaEnv()
var = paste("processed.status.for.model.", model, ".in.section.", section, sep="")
if (inla.strcasecmp(status, "experimental")) {
if (!(exists(var, envir = envir) && get(var, envir = envir))) {
assign(var, TRUE, envir = envir)
msg = paste("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.", sep="")
warning(msg)
} else {
## the warning is already given; do nothing
}
} else if (inla.strcasecmp(status, "disabled")) {
assign(var, TRUE, envir = envir)
msg = paste("Model '", model, "' in section '", section, "' is marked as '", status,
"'.\n Usage is not recommended and unsupported.\n", sep="")
var = paste("enable.model.", section, ".", model, sep="")
if (!(exists(var, envir = envir) && get(var, envir = envir))) {
msg = paste(c(msg, paste(" You can enable it setting variable '", var,
"'\n to 'TRUE' in environment INLA:::inla.get.inlaEnv().\n",
" If you chose to do so, you are on your own.", sep="")))
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)
}
andrewzm/INLA documentation built on May 10, 2019, 11:12 a.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.
## Export: inla.models
`inla.models.section.latent` = function()
{
return
list(latent =
list(
linear = list(
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(
hyper = list(
theta = list(
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(
hyper = list(
theta1 = list(
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(
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(
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(
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,
status = "experimental",
pdf = "mec"
),
meb = list(
hyper = list(
theta1 = list(
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(
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,
status = "experimental",
pdf = "meb"
),
rgeneric = list(
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,
status = "experimental",
pdf = "rgeneric"
),
rw1 = list(
hyper = list(
theta = list(
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,
pdf = "rw1"
),
rw2 = list(
hyper = list(
theta = list(
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,
pdf = "rw2"
),
crw2 = list(
hyper = list(
theta = list(
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,
pdf = "crw2"
),
seasonal = list(
hyper = list(
theta = list(
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(
hyper = list(
theta = list(
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(
hyper = list(
theta1 = list(
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(
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(
hyper = list(
theta1 = list(
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(
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(
hyper = list(
theta1 = list(
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(
name = "logit phi",
short.name = "phi",
prior = "pc",
param = c(0.5, -1),
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(
hyper = list(
theta1 = list(
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(
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(
hyper = list(
theta1 = list(
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(
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"
),
ar1 = list(
hyper = list(
theta1 = list(
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(
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
)
),
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"
),
ar = list(
## to many parameters here, but ...
hyper = list(
theta1 = list(
name = "log precision",
short.name = "prec",
initial = 4,
fixed = FALSE,
prior = "pc.prec",
param = c(1, 0.01),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
name = "pacf1",
short.name = "pacf1",
initial = 1,
fixed = FALSE,
prior = "pc.ar",
param = 1.0, ## lambda
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta3 = list(
name = "pacf2",
short.name = "pacf2",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta4 = list(
name = "pacf3",
short.name = "pacf3",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta5 = list(
name = "pacf4",
short.name = "pacf4",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta6 = list(
name = "pacf5",
short.name = "pacf5",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta7 = list(
name = "pacf6",
short.name = "pacf6",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta8 = list(
name = "pacf7",
short.name = "pacf7",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta9 = list(
name = "pacf8",
short.name = "pacf8",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta10 = list(
name = "pacf9",
short.name = "pacf9",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta11 = list(
name = "pacf10",
short.name = "pacf10",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
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,
status = "experimental",
pdf = "ar"
),
ou = list(
hyper = list(
theta1 = list(
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(
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"
),
generic = list(
hyper = list(
theta = list(
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(
hyper = list(
theta = list(
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(
hyper = list(
theta1 = list(
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(
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(
hyper = list(
theta1 = list(
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(
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(
hyper = list(
theta1 = list(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
## this will be redone anyway soon....
hyper = list(
theta1 = list(
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(
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(
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(
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(
## to many parameters here, but ...
hyper = list(
theta1 = list(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
## to many parameters here, but ...
hyper = list(
theta1 = list(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
hyper = list(
theta = list(
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(
hyper = list(
theta1 = list(
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(
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(
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(
hyper = list(
theta1 = list(
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(
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(
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(
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(
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(
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(
hyper = list(
theta1 = list(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
hyper = list(
theta1 = list(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
hyper = list(
theta1 = list(
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(
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(
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(
hyper = list(
theta = list(
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(
hyper = list(
theta = list(
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(
hyper = list(
theta1 = list(
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(
name = "logit phi",
short.name = "phi",
prior = "pc",
param = c(0.5, -1),
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(
hyper = list(
theta1 = list(
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(
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(
hyper = list(
theta1 = list(
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(
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"
),
copy = list(
hyper = list(
theta = list(
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(
hyper = list(
theta = list(
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(
hyper = list(
theta1 = list(
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(
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(
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(
hyper = list(
theta1 = list(
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(
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(
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"
)
##
)
)
}
`inla.models.section.group` = function()
{
## prevent a warning with R CMD check
ngroup = NULL
return
list(group =
list(
exchangeable = list(
hyper = list(
theta = list(
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)
)
)
),
ar1 = list(
hyper = list(
theta = list(
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(
## to many parameters here, but ...
hyper = list(
theta1 = list(
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)
),
theta2 = list(
name = "pacf1",
short.name = "pacf1",
initial = 2,
fixed = FALSE,
prior = "mvnorm",
param = c(0, 0.15), ## same as for AR1
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta3 = list(
name = "pacf2",
short.name = "pacf2",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta4 = list(
name = "pacf3",
short.name = "pacf3",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta5 = list(
name = "pacf4",
short.name = "pacf4",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta6 = list(
name = "pacf5",
short.name = "pacf5",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta7 = list(
name = "pacf6",
short.name = "pacf6",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta8 = list(
name = "pacf7",
short.name = "pacf7",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta9 = list(
name = "pacf8",
short.name = "pacf8",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta10 = list(
name = "pacf9",
short.name = "pacf9",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
),
theta11 = list(
name = "pacf10",
short.name = "pacf10",
initial = 0,
fixed = FALSE,
prior = "none",
param = numeric(0),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) 2*exp(x)/(1+exp(x))-1
)
)
),
rw1 = list(
hyper = list(
theta = list(
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(
hyper = list(
theta = list(
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(
hyper = list(
theta = list(
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)
)
)
),
I = list(
hyper = list(
theta = list(
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(
hyper = list(
theta = list(
name = "log precision",
short.name = "prec",
prior = "loggamma",
param = c(1, 0.01),
initial = 0,
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(hyper = list()),
cloglog = list(hyper = list()),
identity = list(hyper = list()),
log = list(hyper = list()),
logit = list(hyper = list()),
probit = list(hyper = list()),
tan = list(hyper = list()),
sslogit = list(
hyper = list(
theta1 = list(
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(
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(
hyper = list(
theta = list(
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"
),
test1 = list(
hyper = list(
theta = list(
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
),
special2 = list(
hyper = list(
theta = list(
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
),
special1 = list(
hyper = list(
theta1 = list(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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
)
)
)
}
`inla.models.section.predictor` = function()
{
return
list(predictor =
list(
predictor = list(
hyper = list(
theta = list(
name = "log precision",
short.name = "prec",
initial = 11,
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(
hyper = list(
theta = list(
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(
hyper = list(
theta = list(
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(
hyper = list(
),
survival = FALSE,
discrete = TRUE,
link = c("default", "log", "logoffset", "test1", "special1", "special2"),
pdf = "poisson"
),
gpoisson = list(
hyper = list(
theta1 = list(
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(
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(
hyper = list(
),
survival = FALSE,
discrete = TRUE,
link = c("default", "logit", "probit", "cloglog", "log", "sslogit"),
pdf = "binomial"
),
testbinomial1 = list(
hyper = list(
theta1 = list(
name = "sensitivity",
short.name = "s",
initial = 3,
fixed = FALSE,
prior = "logitbeta",
param = c(2, 1),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
),
theta2 = list(
name = "specificity",
short.name = "e",
initial = 3,
fixed = FALSE,
prior = "logitbeta",
param = c(2, 1),
to.theta = function(x) log(x/(1-x)),
from.theta = function(x) exp(x)/(1+exp(x))
)
),
status = "experimental",
survival = FALSE,
discrete = TRUE,
link = c("default", "logit", "probit", "cloglog", "log"),
pdf = "testbinomial1"
),
gamma = list(
hyper = list(
theta = list(
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"),
pdf = "gamma"
),
gammacount = list(
hyper = list(
theta = list(
name = "log alpha",
short.name = "alpha",
initial = log(1),
fixed = FALSE,
prior = "loggamma",
param = c(10, 10),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "log"),
status = "experimental",
pdf = "gammacount"
),
kumar = list(
hyper = list(
theta1 = list(
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)
),
theta2 = list(
name = "quantile",
short.name = "q",
initial = 0.5,
fixed = TRUE,
prior = "invalid",
param = numeric(0),
to.theta = function(x) x,
from.theta = function(x) x
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "logit"),
pdf = "kumar"
),
beta = list(
hyper = list(
theta = list(
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", "probit", "cloglog"),
pdf = "beta"
),
betabinomial = list(
hyper = list(
theta = list(
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", "probit", "cloglog"),
pdf = "betabinomial"
),
cbinomial = list(
hyper = list(
),
survival = FALSE,
discrete = TRUE,
link = c("default", "logit", "probit", "cloglog"),
status = "experimental",
pdf = "cbinomial"
),
nbinomial = list(
hyper = list(
theta = list(
name = "size",
short.name = "size",
initial = log(10),
fixed = FALSE,
prior = "loggamma",
param = c(1, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
)
),
survival = FALSE,
discrete = TRUE,
link = c("default", "log", "logoffset"),
pdf = "nbinomial"
),
simplex = list(
hyper = list(
theta = list(
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", "probit", "cloglog"),
pdf = "simplex"
),
gaussian = list(
hyper = list(
theta = list(
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", "logit", "log"),
pdf = "gaussian"
),
normal = list(
hyper = list(
theta = list(
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 = "gaussian"
),
circularnormal = list(
hyper = list(
theta = list(
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(
hyper = list(
theta = list(
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(
hyper = list(
theta1 = list(
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(
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(
hyper = list(
theta1 = list(
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(
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(
hyper = list(
theta = list(
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"
),
logistic = list(
hyper = list(
theta = list(
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(
hyper = list(
theta1 = list(
name = "inverse.scale",
short.name = "iscale",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005)
),
theta2 = list(
name = "skewness",
short.name = "skew",
initial = 4,
fixed = FALSE,
prior = "gaussian",
param = c(0, 10)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "identity"),
pdf = "sn"
),
sn = list(
hyper = list(
theta1 = list(
name = "log inverse scale",
short.name = "iscale",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005)
),
theta2 = list(
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(
hyper = list(
theta1 = list(
name = "log precision",
short.name = "prec",
initial = 1,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.00005)
),
theta2 = list(
name = "logit skewness",
short.name = "skew",
initial = 0,
fixed = FALSE,
prior = "gaussian",
param = c(0, 10),
to.theta = function(x) log((1+x)/(1-x)),
from.theta = function(x) (2*exp(x)/(1+exp(x))-1)
)
),
survival = FALSE,
discrete = FALSE,
link = c("default", "identity"),
status = "experimental",
pdf = "sn2"
),
gev = list(
hyper = list(
theta1 = list(
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(
name = "gev parameter",
short.name = "gev",
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"
),
laplace = list(
hyper = list(
theta = list(
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"),
status = "disabled",
pdf = "laplace"
),
lognormal = list(
hyper = list(
theta = list(
name = "log precision",
short.name = "prec",
initial = 2,
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(
hyper = list(
),
survival = TRUE,
discrete = FALSE,
link = c("default", "log"),
pdf = "exponential"
),
coxph = list(
hyper = list(
),
survival = TRUE,
discrete = TRUE,
link = c("default", "log"),
pdf = "coxph"
),
weibull = list(
hyper = list(
theta = list(
name = "log alpha",
short.name = "a",
initial = 0,
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"),
pdf = "weibull"
),
loglogistic = list(
hyper = list(
theta = list(
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"),
pdf = "loglogistic"
),
weibullcure = list(
hyper = list(
theta1 = list(
name = "log alpha",
short.name = "a",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(25, 25),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
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"),
pdf = NA
),
stochvol = list(
hyper = list(
theta = list(
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(
hyper = list(
theta = list(
name = "log degrees of freedom",
short.name = "dof",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 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(
hyper = list(
theta1 = list(
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(
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(
hyper = list(
theta = list(
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(
hyper = list(
theta = list(
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(
hyper = list(
theta = list(
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(
hyper = list(
theta1 = list(
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(
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", "probit", "cloglog"),
pdf = "zeroinflated"
),
zeroinflatedbetabinomial1 = list(
hyper = list(
theta1 = list(
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(
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", "probit", "cloglog"),
pdf = "zeroinflated"
),
zeroinflatedbinomial0 = list(
hyper = list(
theta = list(
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", "probit", "cloglog"),
pdf = "zeroinflated"
),
zeroinflatedbinomial1 = list(
hyper = list(
theta = list(
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", "probit", "cloglog"),
pdf = "zeroinflated"
),
zeroinflatedbinomial2 = list(
hyper = list(
theta = list(
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", "probit", "cloglog"),
pdf = "zeroinflated"
),
zeroninflatedbinomial2 = list(
hyper = list(
theta1 = list(
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(
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", "probit", "cloglog"),
pdf = NA
),
zeroinflatedbetabinomial2 = list(
hyper = list(
theta1 = list(
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(
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", "probit", "cloglog"),
pdf = "zeroinflated"
),
zeroinflatednbinomial0 = list(
hyper = list(
theta1 = list(
name = "log size",
short.name = "size",
initial = log(10),
fixed = FALSE,
prior = "loggamma",
param = c(1, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
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(
hyper = list(
theta1 = list(
name = "log size",
short.name = "size",
initial = log(10),
fixed = FALSE,
prior = "loggamma",
param = c(1, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
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(
hyper = list(
theta1 = list(
name = "log size",
short.name = "size",
initial = log(10),
fixed = FALSE,
prior = "loggamma",
param = c(1, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
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(
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))
)
),
status = "experimental",
survival = FALSE,
discrete = FALSE,
link = c("default", "log"),
pdf = "zeroinflated"
),
zeroinflatednbinomial1strata3 = list(
hyper = list(
theta1 = list(
name = "log size 1",
short.name = "size1",
initial = log(10),
fixed = FALSE,
prior = "loggamma",
param = c(1, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
name = "log size 2",
short.name = "size2",
initial = log(10),
fixed = FALSE,
prior = "loggamma",
param = c(1, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta3 = list(
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))
)
),
status = "experimental",
survival = FALSE,
discrete = FALSE,
link = c("default", "log"),
pdf = "zeroinflated"
),
zeroinflatednbinomial2 = list(
hyper = list(
theta1 = list(
name = "log size",
short.name = "size",
initial = log(10),
fixed = FALSE,
prior = "loggamma",
param = c(1, 1),
to.theta = function(x) log(x),
from.theta = function(x) exp(x)
),
theta2 = list(
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(
hyper = list(
theta1 = list(
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(
name = "log degrees of freedom",
short.name = "dof",
initial = 5,
fixed = FALSE,
prior = "loggamma",
param = c(1, 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(
hyper = list(
theta1 = list(
name = "log degrees of freedom",
short.name = "dof",
initial = 4,
fixed = FALSE,
prior = "loggamma",
param = c(1, 0.01),
to.theta = function(x) log(x-5),
from.theta = function(x) 5+exp(x)
),
theta2 = list(
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(
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(
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(
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(
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(
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(
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(
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(
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(
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"
),
logperiodogram = list(
hyper = list(
),
survival = FALSE,
discrete = FALSE,
link = c("default", "identity"),
pdf = NA
)
)
)
}
`inla.models.section.prior` = function()
{
return
list(prior =
list(
normal = list(
nparameters = 2L,
pdf = "gaussian"
),
gaussian = list(
nparameters = 2L,
pdf = "gaussian"
),
wishart1d = list(
nparameters = 2L,
pdf = "iid123d"
),
wishart2d = list(
nparameters = 4L,
pdf = "iid123d"
),
wishart3d = list(
nparameters = 7L,
pdf = "iid123d"
),
wishart4d = list(
nparameters = 11L,
pdf = "iid123d"
),
wishart5d = list(
nparameters = 16L,
pdf = "iid123d"
),
loggamma = list(
nparameters = 2L,
pdf = "prior-loggamma"
),
minuslogsqrtruncnormal = list(
nparameters = 2L,
pdf = "prior-logtnorm"
),
logtnormal = list(
nparameters = 2L,
pdf = "prior-logtnorm"
),
logtgaussian = list(
nparameters = 2L,
pdf = "prior-logtnorm"
),
flat=list(
nparameters = 0L,
pdf = "various-flat"
),
logflat=list(
nparameters = 0L,
pdf = "various-flat"
),
logiflat=list(
nparameters = 0L,
pdf = "various-flat"
),
mvnorm = list(
nparameters = -1L,
pdf = "mvnorm"
),
pc.ar = list(
nparameters = 1L,
pdf = "pc.ar"
),
## this is the 'no prior needed' prior
none = list(nparameters = 0L),
## this is the 'flag an error if used' prior
invalid = list(nparameters = 0L),
betacorrelation = list(
nparameters = 2L,
pdf = "betacorrelation"
),
logitbeta = list(
nparameters = 2L,
pdf = "logitbeta"
),
pc.prec = list(
nparameters = 2L,
pdf = "pc.prec"
),
pc.dof = list(
nparameters = 2L,
pdf = "pc.dof"
),
pc.rho0 = list(
nparameters = 2L,
pdf = "pc.rho0"
),
pc.rho1 = list(
nparameters = 2L,
pdf = "pc.rho1"
),
## experimental prior from GA
pc.spde.GA = list(
nparameters = 4L,
pdf = NA
),
## this is the generic one, which is case-spesific and possibly adaptive
pc = list(
nparameters = 2L,
pdf = NA
),
ref.ar = list(
nparameters = 0L,
pdf = NA
),
jeffreystdf = list(
nparameters = 0L,
pdf = "jeffreystdf"
),
"expression:" = list(
nparameters = -1L,
pdf = "expression"
),
"table:" = list(
nparameters = -1L,
pdf = "table"
)
)
)
}
`inla.models.section.wrapper` = function()
{
return
list(wrapper =
list(
joint = list(
hyper = list(
theta = list(
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]]$hyper[[theta]][[elm]]))
}
}
}
}
}
}
assign("inla.models", models, envir = envir)
assign("hgid", inla.version("hgid"), envir = envir)
return (models)
}
stop("This should not happen")
}
`inla.is.model` = function(model, section = names(inla.models()),
stop.on.error = TRUE, ignore.case = FALSE)
{
section = match.arg(section)
mm = inla.models()
models = names((mm[ names(mm) == section ])[[1]])
if (is.character(model) && length(model) > 0) {
if (ignore.case) {
m = tolower(model)
ms = tolower(models)
} else {
m = model
ms = models
}
ret = c()
for(i in 1L:length(m)) {
if (is.element(m[i], ms)) {
ret[i] = TRUE
} else {
if (stop.on.error) {
print("Valid models are:")
print(models)
stop(paste(c("\n\tUnknown name [", model[i], "]\n", "\tValid choices are: ",
models), sep=" ", collapse=" "))
} else {
ret[i] = FALSE
}
}
}
} else {
if (stop.on.error)
stop(paste("\n\tModel [", model, "] is not of type character()\n", sep=""))
}
return (ret)
}
`inla.model.properties` = function(
model,
section = c("..invalid.model..", names(inla.models())),
stop.on.error = TRUE,
ignore.case = FALSE)
{
section = match.arg(section)
if (section == "..invalid.model..")
stop("No section given; please fix...")
mm = inla.models()
m = inla.model.properties.generic(inla.trim.family(model),
(mm[names(mm) == section])[[1]],
stop.on.error, ignore.case,
## would like to know the section for a possible warning/error if the status says so.
section = section)
if (is.null(m)) {
return (NULL)
}
return (m)
}
`inla.model.properties.generic` = function(model, models, stop.on.error = TRUE, ignore.case = TRUE, section = "UKNOWN")
{
## argument 'section' is for 'status' only...
m = ifelse(ignore.case, tolower(model), model)
if (ignore.case) {
ms = tolower(names(models))
} else {
ms = names(models)
}
ms = inla.trim.family(ms)
k = grep(paste("^", m, "$", 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]]$status
if (is.null(status)) {
## do nothing; all ok.
} else {
stopifnot(any(inla.strcasecmp(status, c("experimental", "disabled"))))
envir = inla.get.inlaEnv()
var = paste("processed.status.for.model.", model, ".in.section.", section, sep="")
if (inla.strcasecmp(status, "experimental")) {
if (!(exists(var, envir = envir) && get(var, envir = envir))) {
assign(var, TRUE, envir = envir)
msg = paste("Model '", model, "' in section '", section, "' is marked as '", status,
"'; changes may appear at any time.",
"\n ",
"Use this model with extra care!!! Further warnings are disabled.", sep="")
warning(msg)
} else {
## the warning is already given; do nothing
}
} else if (inla.strcasecmp(status, "disabled")) {
assign(var, TRUE, envir = envir)
msg = paste("Model '", model, "' in section '", section, "' is marked as '", status,
"'.\n Usage is not recommended and unsupported.\n", sep="")
var = paste("enable.model.", section, ".", model, sep="")
if (!(exists(var, envir = envir) && get(var, envir = envir))) {
msg = paste(c(msg, paste(" You can enable it setting variable '", var,
"'\n to 'TRUE' in environment INLA:::inla.get.inlaEnv().\n",
" If you chose to do so, you are on your own.", sep="")))
stop(msg)
}
}
}
return (models[[k]])
}
}
`inla.model.validate.link.function` = function(model, link)
{
valid.links = inla.model.properties(model, "likelihood")$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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