- formula
a formula
where the right hand side is a general R
expression defines the predictor used in the model.
- family
A string identifying a valid INLA::inla
likelihood family.
The default is
gaussian
with identity link. In addition to the likelihoods provided
by inla (see names(INLA::inla.models()$likelihood)
)
inlabru supports fitting latent Gaussian Cox
processes via family = "cp"
.
As an alternative to bru()
, the lgcp()
function provides
a convenient interface to fitting Cox processes.
- data
Likelihood-specific data, as a data.frame
or
SpatialPoints[DataFrame]
object.
- response_data
Likelihood-specific data for models that need different
size/format for inputs and response variables, as a data.frame
or
SpatialPoints[DataFrame]
object.
- mesh
Deprecated.
- E
Exposure parameter for family = 'poisson' passed on to
INLA::inla
. Special case if family is 'cp': rescale all integration
weights by a scalar E. For sampler specific reweighting/effort, use a weight
column in the samplers
object, see fmesher::fm_int()
.
Default taken from options$E
, normally 1
.
- Ntrials
A vector containing the number of trials for the 'binomial'
likelihood. Default taken from options$Ntrials
, normally 1
.
- weights
Fixed (optional) weights parameters of the likelihood,
so the log-likelihood[i]
is changed into weights[i] * log_likelihood[i]
.
Default value is 1
. WARNING: The normalizing constant for the likelihood
is NOT recomputed, so ALL marginals (and the marginal likelihood) must be
interpreted with great care.
- scale
Fixed (optional) scale parameters of the precision for several
models, such as Gaussian and student-t response models.
- samplers
Integration domain for 'cp' family.
- ips
Integration points for 'cp' family. Overrides samplers
.
- domain
Named list of domain definitions.
- include
Character vector of component labels that are used as effects
by the
predictor expression; Default: the result of [all.vars()]
on the
predictor expression, unless the expression is not ".", in which case
include=NULL
, to include all components that are not
explicitly excluded. The bru_used()
methods are used
to extract the variable names, followed by removal of non-component names
when the components are available.
- exclude
Character vector of component labels that are not used by the
predictor expression. The exclusion list is applied to the list
as determined by the include
parameter; Default: NULL (do not remove
any components from the inclusion list)
- include_latent
character vector.
Specifies which the latent state variables are
directly available to the predictor expression, with a _latent
suffix.
This also makes evaluator functions with suffix _eval
available, taking
parameters main
, group
, and replicate
, taking values for where to
evaluate the component effect that are different than those defined in the
component definition itself (see component_eval()
). Default NULL
auto-detects use of _latent
and _eval
in the predictor expression.
- used
Either NULL
or a bru_used()
object, overriding include
,
exclude
, and include_latent
.
- allow_latent
logical, deprecated.
Use include_latent
instead.
- allow_combine
logical; If TRUE
, the predictor expression may involve
several rows of the input data to influence the same row. Default FALSE
,
but forced to TRUE
if response_data
is non-NULL
, data
is a list
,
or the likelihood construction requires it.
- control.family
A optional list
of INLA::control.family
options
- options
A bru_options options object or a list of options passed
on to bru_options()
- .envir
The evaluation environment to use for special arguments (E
,
Ntrials
, weights
, and scale
) if not found in response_data
or data
.
Defaults to the calling environment.
- ...
For like_list.bru_like
, one or more bru_like
objects
- object
A list of bru_like
objects
- envir
An optional environment for the new bru_like_list
object
- x
bru_like_list
object from which to extract element(s)
- i
indices specifying elements to extract