#' Create an `n2kImport` object
#' @inheritParams n2k_inla
#' @template analysis_metadata
#' @details
#' - `formula`: a string holding the model formula.
#' - `dataset`: A `data.frame` with `filename`, `fingerprint` and `import_date`.
#' @name n2k_import
#' @rdname n2k_import
#' @exportMethod n2k_import
#' @docType methods
#' @importFrom methods setGeneric
setGeneric(
name = "n2k_import",
def = function(
...
) {
standardGeneric("n2k_import") # nocov
}
)
#' @description A new `n2kImport` model.
#' @rdname n2k_import
#' @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_import_class.R
setMethod(
f = "n2k_import",
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$integer.max, 1)
} else {
assert_that(is.count(dots$seed))
dots$seed <- as.integer(dots$seed)
}
assert_that(is.string(dots$result_datasource_id))
assert_that(is.string(dots$scheme_id))
assert_that(is.string(dots$species_group_id))
assert_that(is.string(dots$location_group_id))
assert_that(is.string(dots$model_type))
assert_that(is.string(dots$formula))
assert_that(is.count(dots$first_imported_year))
dots$first_imported_year <- as.integer(dots$first_imported_year)
assert_that(is.count(dots$last_imported_year))
dots$last_imported_year <- as.integer(dots$last_imported_year)
if (is.null(dots$duration)) {
dots$duration <- dots$last_imported_year - dots$first_imported_year + 1L
} else {
assert_that(is.count(dots$duration))
dots$duration <- as.integer(dots$duration)
}
if (is.null(dots$last_analysed_year)) {
dots$last_analysed_year <- dots$last_imported_year
} else {
assert_that(is.count(dots$last_analysed_year))
dots$last_analysed_year <- as.integer(dots$last_analysed_year)
}
assert_that(is.time(dots$analysis_date))
assert_that(inherits(dots$dataset, "data.frame"))
file_fingerprint <- sha1(
list(
dots$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$seed, character(0)
),
environment = FALSE
)
version <- get_analysis_version(sessionInfo())
status_fingerprint <- sha1(
list(
file_fingerprint, dots$status, version@AnalysisVersion$fingerprint,
version@AnalysisVersion, version@RPackage,
version@AnalysisVersionRPackage, dots$dataset
),
digits = 6L
)
new(
"n2kImport",
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$formula)),
Dataset = dots$dataset
)
}
)
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