Description Usage Arguments Value
fit.bugs.env
fits a spatial GLM with plateau envelope on the climate
covariates via MCMC in WinBUGS.
1 2 3 4 5 6 7 8 9 10 | fit.bugs.env(data, y, x.clim, x.nonclim = NULL, x.factor = NULL,
car.sigma = 0.1, num, adj, u, prior.ax, prior.beta, prior.beta0.difference,
constrain.beta, initial.pars.input, informative.priors = list(beta = FALSE,
beta0 = FALSE, ax = FALSE), burnin = 5000, post.burnin = 1000,
chains = 2, thin = 1, working.directory = NULL, silent = TRUE,
bugs.directory = "C:/Program Files (x86)/WinBUGS14/",
WinBUGS.debug = FALSE, WinBUGS.code = NULL,
WinBUGS.code.location = NULL, no.starting.value = NULL,
estimate.p = FALSE, estimate.u = FALSE, u.clique.start, u.clique.end,
adj.clique.start, adj.clique.end, clique, clique.i)
|
data |
The data frame (with n rows) containing all the variables for analysis. |
y |
A string denoting the binary response variable (taking values 0 or 1 for absence and
presence respectively); must correspond to a column name in the data frame
specied at |
x.clim |
A vector (length p) of strings denoting which columns in the supplied data
frame correspond to the climate covariates; must correspond to column names in the data frame
specied at |
x.nonclim |
A vector (length p2) of strings denoting which columns in the supplied data
frame correspond to the non-climate covariates; must correspond to column names in the data frame
specied at |
x.factor |
A vector (length p3) of strings denoting which columns in the supplied data
frame correspond to the non-climate factors; must correspond to column names in the data frame
specied at |
car.sigma |
Standard deviation of the WinBUGS |
num |
A vector (length n) of the numbers of neighbours of each cell, in order (but see later comment on cliques). |
adj |
A vector of adjacencies, length 2*number of neighbourhood pairs. |
u |
Vector of spatial random effects to be supplied as data, of length
n; mostly The next four inputs are used to set identifiability constraints on the modelling. |
prior.ax |
A list of up to two p-vector objects, |
prior.beta |
A list of two p by 2 matrix objects, |
prior.beta0.difference |
A list of two scalar objects, |
constrain.beta |
A p by 2 matrix of logicals in order to indicate
which beta parameters should be constrained to not vary too
much from its pair - set at most only one of these to |
initial.pars.input |
Vector of length 2p+p+2+p(p-1)/2 containing
starting values for each parameter; if missing, the code
works out its own starting value. If |
informative.priors |
List of logical scalars for which informative
priors should be used (from: beta, beta0, ax);
this option uses the function |
burnin |
Scalar specifying the number of "burn-in" iterations to be discarded (default 5000). |
post.burnin |
Scalar specifying the number of subsequent iterations to be retained (default 1000). |
chains |
Scalar, number of parallel chains to run (default 2). |
thin |
Scalar, the thinning to apply to the MCMC iterations (default 1). |
working.directory |
String containing the location of the WinBUGS code file; default NULL, in which case a temporary folder is used. |
silent |
Logical flag denoting whether the function runs silently or
not. Default is The final inputs are optional and will be ignored otherwise. Specifically,
you have the option of setting up more than one |
bugs.directory |
String containing location of WinBUGS installation; default "C:/Program Files (x86)/WinBUGS14/" is for Windows 64-bit machines. |
WinBUGS.debug |
Logical flag as to whether to close WinBUGS after
running (default |
WinBUGS.code |
You can supply your own code file, especially useful if
you want to use informative priors for external information. The default
value is |
WinBUGS.code.location |
If |
no.starting.value |
A list of strings denoting the objects we should
not initialise, usually because we set them or calculate them in a bespoke
WinBUGS code file. These objects will be set to |
estimate.p |
Logical flag specifying whether or not to retain samples
for the posterior probabilities of presence for each cell,
default |
estimate.u |
Logical flag specifying whether or not to retain samples
for the spatial random effects of presence for each cell,
default |
u.clique.start |
Vector of length |
u.clique.end |
Vector of length |
adj.clique.start |
Where each clique starts in |
adj.clique.end |
Where each clique ends in |
clique |
Vector to say which clique each observation is in, length n. |
clique.i |
Vector to say which element each observation is of its clique, length n. If none of these six are supplied, they will be set in the code to enable a "standard" (single clique) analysis. |
A list object as returned by the bugs()
function in
R2WinBUGS; see the help file for that function for further details.
The list is augmented by the response y
and the climate variables
x.clim
, primarily to aid the plotting functions, and by
the vector which.beta, of length p, which contains 1's and
2's to signify which set of beta parameters to use; see
the description of beta below.
The variables in WinBUGS are (i indexes the climate variable):
beta[which.beta[i],i,1/2]
which.beta
(see above)
specifies which of two sets of beta
parameters to use.
There are two betas
in order to facilitate constraining
either the beta[i,1]
(up-slope) or beta[i,2]
(down-slope)
is to be constrained to be close to its opposite. If
beta[i,2]
is constrained, we'll use the first set (i.e.
which.beta[i]==1
) as this models beta[i,1]
directly and
the multiplicative difference between that and beta[i,2]
;
if beta[i,1]
is constrained (which.beta[i]==2
) then we
model beta[i,2]
directly.
ax
The x-coordinate of the apex for each climate variable.
beta0
Scalar suggesting where the top-slicing should be applied.
az
Scalar coordinate on the logit scale of the response axis apex.
gamma
(Upper triangle) matrix of pairwise interaction parameters
between the climate variables; these are constrained
relative to the betas
in order not to break the geometric
formula for a cone.
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