R/q_ts_length_comp.R

In BenWilliams-NOAA/gfdata: Data queries for accessing the AKFIN and AFSC databases.

#' trawl survey length comp data query
#'
#' @param year assessment year
#' @param area default is "goa"
#' @param afsc_species afsc species code(s)
#' @param afsc  the database to query
#' @param save save the file in designated folder
#'
#' @return
#' @export
#'
#' @examples
#'
q_ts_length_comp <- function(year, area = "goa", afsc_species, afsc, save = TRUE){

  area = tolower(area)

  files <- grep(paste0(area,"_ts_length"),
                list.files(system.file("sql", package = "gfdata")), value=TRUE)

  # if(afsc_species == 20510){
  #   # sablefish are different...
  #   .one = sql_read(files[1])
  #   .two = sql_read(files[3])
  # } else {
    .one = sql_read(files[2])
    .two = sql_read(files[3])
  # }

  if(length(afsc_species) == 1){
    .one = sql_filter(x = afsc_species, sql_code = .one, flag = "-- insert species")
    .two = sql_filter(x = afsc_species, sql_code = .two, flag = "-- insert species")

  } else {
    .one = sql_filter(sql_precode = "IN", x = afsc_species,
                      sql_code = .one, flag = "-- insert species")
    .two = sql_filter(sql_precode = "IN", x = afsc_species,
                      sql_code = .two, flag = "-- insert species")
  }

  if(isTRUE(save)){
    sql_run(afsc, .one) %>%
      write.csv(here::here(year, "data", "raw", paste0(area, "_ts_length_data.csv")),
                row.names = FALSE)
    sql_run(afsc, .two) %>%
      write.csv(here::here(year, "data", "raw", paste0(area, "_ts_length_specimen_data.csv")),
                row.names = FALSE)
  } else{
    list(sql_run(afsc, .one),
         sql_run(afsc, .two))
  }

}