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#' Get a Summary Table of Historical Stock Size
#'
#' Get summary results of historical stock size, recruitment, and fishing
#' pressure.
#'
#' @param assessmentKey the unique identifier of the stock assessment
#' @param ... arguments passed to \code{\link{sag_get}}.
#'
#' @return A data frame.
#'
#' @seealso
#' \code{\link{getSAG}} supports querying many years and quarters in one
#' function call.
#'
#' \code{\link{getListStocks}} and \code{\link{getFishStockReferencePoints}} get
#' a list of stocks and reference points.
#'
#' \code{\link{icesSAG-package}} gives an overview of the package.
#'
#' @author Colin Millar.
#'
#' @examples
#' \dontrun{
#' assessmentKey <- findAssessmentKey("had.27.46a20", year = 2022)
#' sumtab <- getSummaryTable(assessmentKey)
#' head(sumtab)
#' }
#' @export
getSummaryTable <- function(assessmentKey, ...) {
# call webservice for all supplied keys
out <-
lapply(
assessmentKey,
function(i) {
x <-
sag_get(
sag_api("SummaryTable", assessmentKey = i), ...
)
# format into a data.frame
cbind(
lapply(x[names(x) != "Lines"], function(y) if (is.null(y)) NA else y),
x$Lines
)
}
)
# rbind output
out <- do.call(rbind, out)
# temporary fix, untill webservice is reverted
new_names <-
c(
"Year", "Recruitment", "High_Recruitment", "Low_Recruitment",
"Low_SSB", "SSB", "High_SSB",
"Low_F", "F", "High_F",
"Catches", "Landings", "Discards",
"IBC", "Unallocated_Removals",
"LandingsBMS", "TBiomass", "LogbookRegisteredDiscards",
"StockPublishNote", "Purpose", "FAge",
"FishStock", "RecruitmentAge", "AssessmentYear",
"Units", "StockSizeDescription", "StockSizeUnits",
"FishingPressureDescription", "FishingPressureUnits",
"AssessmentKey", "AssessmentComponent"
)
old_names <-
c(
"Year", "recruitment", "high_recruitment", "low_recruitment",
"low_SSB", "SSB", "high_SSB",
"low_F", "F", "high_F",
"catches", "landings", "discards",
"IBC", "Unallocated_Removals",
"LandingsBMS", "TBiomass", "LogbookRegisteredDiscards",
"StockPublishNote", "Purpose", "Fage",
"fishstock", "recruitment_age", "AssessmentYear",
"units", "stockSizeDescription", "stockSizeUnits",
"fishingPressureDescription", "fishingPressureUnits",
"AssessmentKey", "AssessmentComponent"
)
out <- out[new_names]
names(out) <- old_names
sag_clean(out)
}
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