#' Create an `n2kModelImputed` object
#' @inheritParams n2k_inla
#' @template analysis_metadata
#' @details
#' - `model_fun`: The `model_fun` argument of [multimput::model_impute()].
#' - `package`: A character vector of package names which must be loaded for
#' `model_fun`.
#' - `model_args`: An optional list for the `model_args` argument of
#' [multimput::model_impute()].
#' - `extractor`: An optional list for the `extractor` argument of
#' [multimput::model_impute()].
#' - `extractor_args`: An optional list for the `extractor_args` argument of
#' [multimput::model_impute()].
#' - `filter`: An optional list for the `filter` argument of
#' [multimput::model_impute()].
#' - `mutate`: An optional list for the `mutate`` argument of
#' [multimput::model_impute()].
#' @name n2k_model_imputed
#' @rdname n2k_model_imputed
#' @exportMethod n2k_model_imputed
#' @docType methods
#' @importFrom methods setGeneric
setGeneric(
name = "n2k_model_imputed",
def = function(
...
) {
standardGeneric("n2k_model_imputed") # nocov
}
)
#' @description A new `n2kModelImputed` model.
#' @rdname n2k_model_imputed
#' @aliases n2k_model_imputed,n2kModelImputed-methods
#' @importFrom methods setMethod new
#' @importFrom assertthat assert_that is.count is.string is.time
#' @importFrom digest sha1
#' @importFrom stats as.formula
#' @importFrom utils sessionInfo
#' @include n2k_model_imputed_class.R
setMethod(
f = "n2k_model_imputed",
signature = signature("ANY"),
definition = function(
...
) {
dots <- list(...)
#set the defaults for missing arguments in dots
if (is.null(dots$status)) {
dots$status <- "waiting"
}
if (is.null(dots$seed)) {
dots$seed <- sample(.Machine$integer.max, 1)
}
assert_that(
is.count(dots$seed), is.string(dots$result_datasource_id),
is.string(dots$scheme_id), is.string(dots$species_group_id),
is.string(dots$location_group_id), is.string(dots$model_type),
is.string(dots$formula), is.count(dots$first_imported_year),
is.count(dots$last_imported_year), is.time(dots$analysis_date)
)
dots$seed <- as.integer(dots$seed)
dots$first_imported_year <- as.integer(dots$first_imported_year)
dots$last_imported_year <- as.integer(dots$last_imported_year)
dots$duration <- coalesce(
dots$duration, dots$last_imported_year - dots$first_imported_year + 1L
)
dots$last_analysed_year <- coalesce(
dots$last_analysed_year, dots$last_imported_year
)
dots$filter <- c(dots$filter, list())
dots$mutate <- c(dots$mutate, list())
dots$model_args <- c(dots$model_args, list())
dots$prepare_model_args <- c(dots$prepare_model_args, list())
dots$extractor_args <- c(dots$extractor_args, list())
dots$package <- c(dots$package, character(0))
assert_that(
is.count(dots$duration), is.count(dots$last_analysed_year),
is.list(dots$filter), is.list(dots$mutate), is.list(dots$model_args),
is.function(dots$model_fun) || is.string(dots$model_fun),
is.function(dots$extractor), is.list(dots$prepare_model_args),
length(dots$prepare_model_args) <= 1, is.list(dots$extractor_args),
is.character(dots$package), is.string(dots$parent)
)
dots$duration <- as.integer(dots$duration)
dots$last_analysed_year <- as.integer(dots$last_analysed_year)
if (length(dots$prepare_model_args)) {
assert_that(is.function(dots$prepare_model_args[[1]]))
}
file_fingerprint <- sha1(
list(
dots$result_datasource_id,
dots$scheme_id, dots$species_group_id, dots$location_group_id,
dots$model_type, dots$formula, dots$first_imported_year,
dots$last_imported_year, dots$duration, dots$last_analysed_year,
format(dots$analysis_date, tz = "UTC"),
dots$seed, dots$parent, dots$model_fun, dots$filter,
dots$mutate, dots$model_args, dots$prepare_model_args, dots$extractor,
dots$extractor_args, dots$package
),
environment = FALSE
)
if (is.null(dots$parent_statusfingerprint)) {
dots$parent_status <- coalesce(dots$parent_status, "waiting")
dots$parent_statusfingerprint <- sha1(dots$parent_status)
}
stopifnot(
"'parent_status' is required when 'parent_statusfingerprint' is provided" =
!is.null(dots[["parent_status"]])
)
analysis_relation <- data.frame(
analysis = file_fingerprint, parent_analysis = dots$parent,
parentstatus_fingerprint = dots$parent_statusfingerprint,
parent_status = dots$parent_status, stringsAsFactors = FALSE
)
version <- get_analysis_version(sessionInfo())
status_fingerprint <- sha1(
list(
file_fingerprint, dots$status, version@AnalysisVersion$fingerprint,
version@AnalysisVersion, version@RPackage,
version@AnalysisVersionRPackage, analysis_relation, NULL, NULL
),
digits = 6L
)
new(
"n2kModelImputed",
AnalysisVersion = version@AnalysisVersion,
RPackage = version@RPackage,
AnalysisVersionRPackage = version@AnalysisVersionRPackage,
AnalysisMetadata = data.frame(
result_datasource_id = dots$result_datasource_id,
scheme_id = dots$scheme_id,
species_group_id = dots$species_group_id,
location_group_id = dots$location_group_id,
model_type = dots$model_type,
formula = dots$formula,
first_imported_year = dots$first_imported_year,
last_imported_year = dots$last_imported_year,
duration = dots$duration,
last_analysed_year = dots$last_analysed_year,
analysis_date = dots$analysis_date,
seed = dots$seed,
status = dots$status,
analysis_version = version@AnalysisVersion$fingerprint,
file_fingerprint = file_fingerprint,
status_fingerprint = status_fingerprint,
stringsAsFactors = FALSE
),
AnalysisFormula = list(as.formula(dots$formula)),
AnalysisRelation = analysis_relation,
Function = dots$model_fun,
Package = dots$package,
Filter = dots$filter,
Mutate = dots$mutate,
ModelArgs = dots$model_args,
PrepareModelArgs = dots$prepare_model_args,
Extractor = dots$extractor,
ExtractorArgs = dots$extractor_args,
AggregatedImputed = NULL,
Results = NULL
)
}
)
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