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Mapper for concatenated variables

Source: R/mappers.R
bru_mapper_collect.Rd

Constructs a concatenated collection mapping

Usage

bru_mapper_collect(mappers, hidden = FALSE)

# S3 method for class 'bru_mapper_collect'
ibm_n(mapper, inla_f = FALSE, multi = FALSE, ...)

# S3 method for class 'bru_mapper_collect'
ibm_n_output(mapper, input, state = NULL, inla_f = FALSE, multi = FALSE, ...)

# S3 method for class 'bru_mapper_collect'
ibm_values(mapper, inla_f = FALSE, multi = FALSE, ...)

# S3 method for class 'bru_mapper_collect'
ibm_is_linear(mapper, inla_f = FALSE, multi = FALSE, ...)

# S3 method for class 'bru_mapper_collect'
ibm_jacobian(
  mapper,
  input,
  state = NULL,
  inla_f = FALSE,
  multi = FALSE,
  ...,
  sub_lin = NULL
)

# S3 method for class 'bru_mapper_collect'
ibm_eval(
  mapper,
  input,
  state,
  inla_f = FALSE,
  multi = FALSE,
  ...,
  sub_lin = NULL
)

# S3 method for class 'bru_mapper_collect'
ibm_linear(mapper, input, state, inla_f = FALSE, ...)

# S3 method for class 'bru_mapper_collect'
ibm_invalid_output(mapper, input, state, inla_f = FALSE, multi = FALSE, ...)

# S3 method for class 'bru_mapper_collect'
x[i, drop = TRUE]

# S3 method for class 'bru_mapper_collect'
ibm_names(mapper)

# S3 method for class 'bru_mapper_collect'
ibm_names(mapper) <- value

Arguments

mappers

A list of bru_mapper objects

hidden

logical, set to TRUE to flag that the mapper is to be used as a first level input mapper for INLA::f() in a model that requires making only the first mapper visible to INLA::f() and INLA::inla.stack(), such as for "bym2" models, as activated by the inla_f argument to ibm_n, ibm_values, and ibm_jacobian. Set to FALSE to always access the full mapper, e.g. for rgeneric models

mapper

A mapper S3 object, inheriting from bru_mapper.

inla_f

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.

multi

logical; If TRUE (or positive), recurse one level into sub-mappers

...

Arguments passed on to other methods

input

Data input for the mapper.

state

A vector of latent state values for the mapping, of length ibm_n(mapper, inla_f = FALSE)

sub_lin

Internal, optional pre-computed sub-mapper information

x

object from which to extract element(s)

i

indices specifying element(s) to extract

drop

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

value

a character vector of the same length as the number of sub-mappers in the mapper

Value

  • [-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

Methods (by generic)

  • ibm_jacobian(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(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.

See also

bru_mapper, bru_mapper_generics

Other mappers: bru_get_mapper(), bru_mapper(), bru_mapper.fm_mesh_1d(), bru_mapper.fm_mesh_2d(), bru_mapper_aggregate(), bru_mapper_const(), bru_mapper_factor(), bru_mapper_fmesher(), bru_mapper_generics, bru_mapper_harmonics(), bru_mapper_index(), bru_mapper_linear(), bru_mapper_logsumexp(), bru_mapper_marginal(), bru_mapper_matrix(), bru_mapper_mesh_B(), bru_mapper_multi(), bru_mapper_pipe(), bru_mapper_repeat(), bru_mapper_scale(), bru_mapper_shift(), bru_mapper_taylor()

Examples

(m <- bru_mapper_collect(list(
  a = bru_mapper_index(2),
  b = bru_mapper_index(3)
), hidden = FALSE))
#> collect(a = index, b = index)
ibm_eval2(m, list(a = c(1, 2), b = c(1, 3, 2)), 1:5)
#> $offset
#> [1] 1 2 3 5 4
#> 
#> $jacobian
#> 5 x 5 sparse Matrix of class "dgTMatrix"
#>               
#> [1,] 1 . . . .
#> [2,] . 1 . . .
#> [3,] . . 1 . .
#> [4,] . . . . 1
#> [5,] . . . 1 .
#>