A bru_mapper sub-class implementation must provide an
ibm_jacobian() method. If the model size 'n' and definition
values 'values' are stored in the object itself, default methods are
available (see Details). Otherwise the
ibm_n() and ibm_values() methods also need to be provided.
# S3 method for bru_mapper_inla_mesh_2d
ibm_n(mapper, ...)# S3 method for bru_mapper_inla_mesh_2d
ibm_values(mapper, ...)
# S3 method for bru_mapper_inla_mesh_2d
ibm_jacobian(mapper, input, ...)
# S3 method for bru_mapper_inla_mesh_1d
ibm_n(mapper, ...)
# S3 method for bru_mapper_inla_mesh_1d
ibm_values(mapper, ...)
# S3 method for bru_mapper_inla_mesh_1d
ibm_jacobian(mapper, input, ...)
# S3 method for bru_mapper_index
ibm_invalid_output(mapper, input, state, ...)
# S3 method for bru_mapper_index
ibm_jacobian(mapper, input, state, ...)
# S3 method for bru_mapper_taylor
ibm_n(mapper, inla_f = FALSE, multi = FALSE, ...)
# S3 method for bru_mapper_taylor
ibm_n_output(mapper, input, ...)
# S3 method for bru_mapper_taylor
ibm_values(mapper, inla_f = FALSE, multi = FALSE, ...)
# S3 method for bru_mapper_taylor
ibm_jacobian(mapper, ..., multi = FALSE)
# S3 method for bru_mapper_taylor
ibm_eval(mapper, input = NULL, state = NULL, ...)
# S3 method for bru_mapper_linear
ibm_n(mapper, ...)
# S3 method for bru_mapper_linear
ibm_values(mapper, ...)
# S3 method for bru_mapper_linear
ibm_jacobian(mapper, input, ...)
# S3 method for bru_mapper_matrix
ibm_n(mapper, ...)
# S3 method for bru_mapper_matrix
ibm_values(mapper, ...)
# S3 method for bru_mapper_matrix
ibm_jacobian(mapper, input, state = NULL, inla_f = FALSE, ...)
# S3 method for bru_mapper_factor
ibm_n(mapper, ...)
# S3 method for bru_mapper_factor
ibm_values(mapper, ...)
# S3 method for bru_mapper_factor
ibm_jacobian(mapper, input, ...)
# S3 method for bru_mapper_const
ibm_n(mapper, ...)
# S3 method for bru_mapper_const
ibm_values(mapper, ...)
# S3 method for bru_mapper_const
ibm_jacobian(mapper, input, ...)
# S3 method for bru_mapper_const
ibm_eval(mapper, input, state = NULL, ...)
# S3 method for bru_mapper_scale
ibm_n(mapper, ..., state = NULL, n_state = NULL)
# S3 method for bru_mapper_scale
ibm_n_output(mapper, input, state = NULL, ..., n_state = NULL)
# S3 method for bru_mapper_scale
ibm_values(mapper, ..., state = NULL, n_state = NULL)
# S3 method for bru_mapper_scale
ibm_jacobian(mapper, input, state = NULL, ..., sub_lin = NULL)
# S3 method for bru_mapper_scale
ibm_linear(mapper, input, state, ...)
# S3 method for bru_mapper_scale
ibm_eval(mapper, input, state = NULL, ..., sub_lin = NULL)
# S3 method for bru_mapper_aggregate
ibm_n(mapper, ..., input = NULL, state = NULL, n_state = NULL)
# S3 method for bru_mapper_aggregate
ibm_n_output(mapper, input = NULL, ...)
# S3 method for bru_mapper_aggregate
ibm_values(mapper, ..., state = NULL, n_state = NULL)
# S3 method for bru_mapper_aggregate
ibm_jacobian(mapper, input, state = NULL, ...)
# S3 method for bru_mapper_aggregate
ibm_eval(mapper, input, state = NULL, ..., sub_lin = NULL)
# S3 method for bru_mapper_aggregate
ibm_linear(mapper, input, state, ...)
# S3 method for bru_mapper_logsumexp
ibm_jacobian(mapper, input, state = NULL, ...)
# S3 method for bru_mapper_logsumexp
ibm_eval(mapper, input, state = NULL, ..., sub_lin = NULL)
# S3 method for bru_mapper_logsumexp
ibm_linear(mapper, input, state, ...)
# S3 method for bru_mapper_pipe
ibm_n(mapper, ..., state = NULL)
# S3 method for bru_mapper_pipe
ibm_n_output(mapper, input, state = NULL, ...)
# S3 method for bru_mapper_pipe
ibm_values(mapper, ...)
# S3 method for bru_mapper_pipe
ibm_jacobian(mapper, input, state = NULL, ...)
# S3 method for bru_mapper_pipe
ibm_linear(mapper, input, state, ...)
# S3 method for bru_mapper_pipe
ibm_eval(mapper, input, state = NULL, ...)
# S3 method for bru_mapper_multi
ibm_n(mapper, inla_f = FALSE, multi = FALSE, ...)
# S3 method for bru_mapper_multi
ibm_n_output(mapper, input, ...)
# S3 method for bru_mapper_multi
ibm_values(mapper, inla_f = FALSE, multi = FALSE, ...)
# S3 method for bru_mapper_multi
ibm_is_linear(mapper, multi = FALSE, ...)
# S3 method for bru_mapper_multi
ibm_jacobian(
mapper,
input,
state = NULL,
inla_f = FALSE,
multi = FALSE,
...,
sub_A = NULL
)
# S3 method for bru_mapper_multi
ibm_linear(mapper, input, state, inla_f = FALSE, ...)
# S3 method for bru_mapper_multi
ibm_eval(mapper, input, state = NULL, inla_f = FALSE, ..., pre_A = NULL)
# S3 method for bru_mapper_multi
ibm_invalid_output(mapper, input, state, inla_f = FALSE, multi = FALSE, ...)
# S3 method for bru_mapper_multi
[(x, i, drop = TRUE)
# S3 method for bru_mapper_multi
ibm_names(mapper)
# S3 method for bru_mapper_multi
ibm_names(mapper) <- value
# S3 method for bru_mapper_collect
ibm_n(mapper, inla_f = FALSE, multi = FALSE, ...)
# S3 method for bru_mapper_collect
ibm_n_output(mapper, input, state = NULL, inla_f = FALSE, multi = FALSE, ...)
# S3 method for bru_mapper_collect
ibm_values(mapper, inla_f = FALSE, multi = FALSE, ...)
# S3 method for bru_mapper_collect
ibm_is_linear(mapper, inla_f = FALSE, multi = FALSE, ...)
# S3 method for bru_mapper_collect
ibm_jacobian(
mapper,
input,
state = NULL,
inla_f = FALSE,
multi = FALSE,
...,
sub_lin = NULL
)
# S3 method for bru_mapper_collect
ibm_eval(
mapper,
input,
state,
inla_f = FALSE,
multi = FALSE,
...,
sub_lin = NULL
)
# S3 method for bru_mapper_collect
ibm_linear(mapper, input, state, inla_f = FALSE, ...)
# S3 method for bru_mapper_collect
ibm_invalid_output(mapper, input, state, inla_f = FALSE, multi = FALSE, ...)
# S3 method for bru_mapper_collect
[(x, i, drop = TRUE)
# S3 method for bru_mapper_collect
ibm_names(mapper)
# S3 method for bru_mapper_collect
ibm_names(mapper) <- value
# S3 method for bru_mapper_harmonics
ibm_n(mapper, inla_f = FALSE, ...)
# S3 method for bru_mapper_harmonics
ibm_jacobian(mapper, input, state = NULL, inla_f = FALSE, ...)
[-indexing a bru_mapper_multi extracts a subset
bru_mapper_multi object (for drop FALSE) or an individual sub-mapper
(for drop TRUE, and i identifies a single element)
[-indexing a bru_mapper_collect extracts a subset
bru_mapper_collect object (for drop FALSE) or an individual sub-mapper
(for drop TRUE, and i identifies a single element)
The names() method for bru_mapper_collect returns the names from the
sub-mappers list
A mapper S3 object, inheriting from bru_mapper.
Arguments passed on to other methods
Data input for the mapper.
A vector of latent state values for the mapping,
of length ibm_n(mapper, inla_f = FALSE)
logical; when TRUE for ibm_n() and ibm_values(), the
result must be compatible with the INLA::f(...) and corresponding
INLA::inla.stack(...) constructions. For ibm_{eval,jacobian,linear},
the input interpretation may be different.
Implementations do not normally need to do anything different, except
for mappers of the type needed for hidden multicomponent models such
as "bym2", which can be handled by bru_mapper_collect.
logical;
If TRUE (or positive), recurse one level into sub-mappers
integer giving the length of the state vector for mappers that have state dependent output size.
Internal, optional pre-computed sub-mapper information
Internal; precomputed Jacobian matrices.
Internal; precomputed Jacobian matrix
object from which to extract element(s)
indices specifying element(s) to extract
logical;
For [.bru_mapper_collect, whether to extract an individual mapper when
i identifies a single element. If FALSE, a list of sub-mappers is
returned (suitable e.g. for creating a new bru_mapper_collect object).
Default: TRUE
a character vector of up to the same length as the number of mappers in the multi-mapper x
ibm_names(bru_mapper_multi): Returns the names from the sub-mappers list
The ibm_eval.bru_mapper_taylor() evaluates linearised
mapper information at the given state. The input argument is ignored,
so that the usual argument order
ibm_eval(mapper, input, state) syntax can be used, but also
ibm_eval(mapper, state = state). For a mapper with a named jacobian list,
the state argument must also be a named list. If state is NULL,
all-zero is assumed.
For bru_mapper_scale, input values without a scale element
are interpreted as no scaling.
For bru_mapper_aggregate, input should be a list with elements block
and weights. block
should be a vector of the same length as the state, or NULL, with NULL
equivalent to all-1.
If weights is NULL, it's interpreted as all-1.
For bru_mapper_logsumexp, input should be a list with elements block
and weights. block
should be a vector of the same length as the state, or NULL, with NULL
equivalent to all-1.
If weights is NULL, it's interpreted as all-1.
ibm_jacobian for bru_mapper_multi accepts a list with
named entries, or a list with unnamed but ordered elements.
The names must match the sub-mappers, see ibm_names.bru_mapper_multi().
Each list element should take a format accepted by the corresponding
sub-mapper. In case each element is a vector, the input can be given as a
data.frame with named columns, a matrix with named columns, or a matrix
with unnamed but ordered columns.
ibm_invalid_output for bru_mapper_multi accepts a list with
named entries, or a list with unnamed but ordered elements.
The names must match the sub-mappers, see ibm_names.bru_mapper_multi().
Each list element should take a format accepted by the corresponding
sub-mapper. In case each element is a vector, the input can be given as a
data.frame with named columns, a matrix with named columns, or a matrix
with unnamed but ordered columns.
ibm_jacobian for bru_mapper_collect accepts a list with
named entries, or a list with unnamed but ordered elements.
The names must match the sub-mappers, see ibm_names.bru_mapper_collect().
Each list element should take a format accepted by the corresponding
sub-mapper. In case each element is a vector, the input can be given as a
data.frame with named columns, a matrix with named columns, or a matrix
with unnamed but ordered columns. When inla_f=TRUE and hidden=TRUE in
the mapper definition, the input format should instead match that of
the first, non-hidden, sub-mapper.
ibm_invalid_output for bru_mapper_collect accepts a list with
named entries, or a list with unnamed but ordered elements.
The names must match the sub-mappers, see ibm_names.bru_mapper_collect().
Each list element should take a format accepted by the corresponding
sub-mapper. In case each element is a vector, the input can be given as a
data.frame with named columns, a matrix with named columns, or a matrix
with unnamed but ordered columns.
bru_mapper for constructor methods, and bru_get_mapper for hooks to extract mappers from latent model object class objects.
bru_mapper, bru_mapper_generics