f {INLA} | R Documentation |
Function used for defining of smooth and spatial terms within inla
model
formulae. The function does not evaluate anything - it
exists purely to help set up a model. The function specifies one
smooth function in the linear predictor (see inla.list.models
) as
weight*f(var)
f(..., model = "iid", copy=NULL, same.as = NULL, n=NULL, nrep = NULL, replicate = NULL, ngroup = NULL, group = NULL, control.group = inla.set.control.group.default(), hyper = NULL, initial=NULL, prior=NULL, param = NULL, fixed = NULL, season.length=NULL, constr = NULL, extraconstr=list(A=NULL, e=NULL), values=NULL, cyclic = NULL, diagonal = NULL, graph=NULL, graph.file=NULL, cdf=NULL, quantiles=NULL, Cmatrix=NULL, rankdef=NULL, Z = NULL, nrow = NULL, ncol = NULL, nu = NULL, bvalue = NULL, spde.prefix = NULL, spde2.prefix = NULL, spde2.transform = c("logit", "log", "identity"), spde3.prefix = NULL, spde3.transform = c("logit", "log", "identity"), mean.linear = inla.set.control.fixed.default()$mean, prec.linear = inla.set.control.fixed.default()$prec, compute = TRUE, of=NULL, precision = exp(14), range = NULL, adjust.for.con.comp = TRUE, order = NULL, scale = NULL, strata = NULL, rgeneric = NULL, scale.model = NULL, args.slm = list(rho.min = NULL, rho.max = NULL, X = NULL, W = NULL, Q.beta = NULL), args.ar1c = list(Z = NULL, Q.beta = NULL), args.intslope = list(subject = NULL, strata = NULL, covariates = NULL), vb.correct = NULL, locations = NULL, debug = FALSE)
... |
Name of the covariate and, possibly of the weights vector. NB: order counts!!!! The first specified term is the covariate and the second one is the vector of weights (which can be negative). |
model |
A string indicating the choosen model. The
default is |
copy |
TODO |
same.as |
TODO |
n |
An optional argument which defines the dimension
of the model if this is different from
|
nrep |
TODO |
replicate |
We need to write documentation here |
ngroup |
TODO |
group |
TODO |
control.group |
TODO |
hyper |
Specification of the hyperparameter, fixed or
random, initial values, priors and its parameters. See
|
initial |
THIS OPTION IS OBSOLETE; use
|
prior |
THIS OPTION IS OBSOLETE; use |
param |
THIS OPTION IS OBSOLETE; use |
fixed |
THIS OPTION IS OBSOLETE; use |
season.length |
Lenght of the seasonal compoment
(ONLY if |
constr |
A boolean variable indicating whater to set a sum to 0 constraint on the term. By default the sum to 0 constraint is imposed on all intrinsic models ("iid","rw1","rw1","besag", etc..). |
extraconstr |
This argument defines extra linear
constraints. The argument is a list with two elements, a
matrix |
values |
An optional vector giving all values
assumed by the covariate for which we want estimated the
effect. It must be a numeric vector, a vector of factors
or |
cyclic |
A boolean specifying wheather the model is cyclical. Only valid for "rw1" and "rw2" models, is cyclic=T then the sum to 0 constraint is removed. For the correct form of the grah file see Martino and Rue (2008). |
diagonal |
An extra constant added to the diagonal of the precision matrix. |
graph |
Defines the graph-object either as a file with
a graph-description, an |
graph.file |
THIS OPTION IS OBSOLETE AND REPLACED BY
THE MORE GENERAL ARGUMENT |
cdf |
A vector of maximum 10 values between 0 and 1 x(0), x(1),…. The function returns, for each posterior marginal the probabilities Prob(X<x(p)) |
quantiles |
A vector of maximum 10 quantiles, p(0), p(1),… to compute for each posterior marginal. The function returns, for each posterior marginal, the values x(0), x(1),… such that Prob(X<x)=p |
Cmatrix |
The specification of the precision matrix
for the generic, generic3 or z models (up to a scaling constant).
|
rankdef |
A number defining the rank deficiency of the model, with sum-to-zero constraint and possible extra-constraints taken into account. See details. |
Z |
The matrix for the z-model |
nrow |
Number of rows for 2d-models |
ncol |
Number of columns for 2d-models |
nu |
Smoothing parameter for the Matern2d-model,
possible values are |
bvalue |
TODO |
spde.prefix |
TODO |
spde2.prefix |
TODO |
spde2.transform |
TODO |
spde3.prefix |
TODO |
spde3.transform |
TODO |
mean.linear |
Prior mean for the linear component,
only used if |
prec.linear |
Prior precision for the linear
component, only used if |
compute |
A boolean variable indicating wheather the
marginal posterior distribution for the nodes in the
|
of |
TODO |
precision |
The precision for the artifical noise added when creating a copy of a model and others. |
range |
A vector of size two giving the lower and
upper range for the scaling parameter |
adjust.for.con.comp |
If TRUE (default), adjust some of the models (currently: besag, bym, bym2 and besag2) if the number of connected components in graph is larger than 1. If FALSE, do nothing. |
order |
Defines the |
scale |
A scaling vector. Its meaning depends on the model. |
strata |
Currently not in use |
rgeneric |
A object of class |
scale.model |
Logical. If |
args.slm |
Required arguments to the model="slm"; see the documentation for further details. |
,
args.ar1c |
Required arguments to the model="ar1c"; see the documentation for further details. |
,
args.intslope |
A list with the |
,
vb.correct |
Add this model component to the list of variables to be used for the vb corrected Laplace approximation? If |
,
locations |
A matrix with locations for the model |
debug |
Enable local debug output |
There is no default value for rankdef
, if it
is not defined by the user then it is computed by the rank
deficiency of the prior model (for the generic model, the
default is zero), plus 1 for the sum-to-zero constraint if the
prior model is proper, plus the number of extra
constraints. Oops: This can be wrong, and then the user
must define the rankdef
explicitely.
TODO
Havard Rue hrue@r-inla.org