R/tableSample.R

In nwfsc-assess/PacFIN.Utilities: Generate fishery composition data from PacFIN data for the NWFSC

#' Table of Sample Size By Fleet and Year
#'
#' Create a table of samples by fleet and year to
#' be included in an assessment document.
#'
#' @inheritParams cleanPacFIN
#' @inheritParams writeComps
#' @param strat A vector of column names to stratify the output over. For
#'   example, if you wish to summarize by ageing method, then the argument
#'   would look like `strat = "agemethod"` or, if you want to look at fleets
#'   and gear, `strat = c("fleet", "usegear")`.
#' @param comps Specify whether to calculate the length or Age samples.
#' The default is to calculate the number of length samples.
#' @param remove_yrs A vector of years to remove from the data before
#' summarizing sample sizes. The default of \code{NULL} leads to no
#' sub setting of the data.
#'
#' @return
#' A table is written to a csv file as specified in \code{fname} and the data frame
#' is also returned as an object invisibly.

#' @author Chantel R. Wetzel
#' @export

tableSample <- function(Pdata,
                        fname = paste0("fishery_", comps, "_samples.csv"),
                        strat = "SOURCE_AGID",
                        comps = c("LEN", "AGE"), remove_yrs = NULL) {
  Pdata$strat <- apply(Pdata[, strat, drop = FALSE], 1, paste0, collapse = ".")
  comps <- match.arg(comps, several.ok = FALSE)
  if (comps == "LEN") {
    temp <- Pdata[!is.na(Pdata$FISH_LENGTH), ]
  }

  if (comps == "AGE") {
    temp <- Pdata[!is.na(Pdata$Age), ]
  }

  if (!is.null(remove_yrs)) {
    temp <- temp[!temp$SAMPLE_YEAR %in% remove_yrs, ]
  }

  Ntow <- table(temp$SAMPLE_YEAR, temp$strat, !duplicated(as.character(temp$SAMPLE_NO)))[, , "TRUE"]
  Nfish <- table(temp$SAMPLE_YEAR, temp$strat)

  samples <- rownames(Ntow)
  names <- "Year"
  for (a in colnames(Ntow)) {
    get <- cbind(Ntow[, a], Nfish[, a])
    samples <- cbind(samples, get)
    names <- c(names, paste0(a, ".tows"), paste0(a, ".fish"))
  }
  colnames(samples) <- names

  utils::write.csv(samples, file = fname, row.names = FALSE)
  return(invisible(samples))
}