R/tables_cpue.R

In iantaylor-NOAA/Lingcod_2021: Estimate the Status of Lingcod off the US West Coast in 2021

#' Read in OR index table information
#'
#' @param grep A regex for the file names in `data-raw`
#' that will pick up all three files.
#' @param fleet The fleet name from [get_fleet].
#'
#' @examples
#' \dontrun{
#' unlink(file.path(dirname(system.file(package=utils_name())),
#'   "tables", "tables_cpue.csv")
#' )
#' unlink(file.path(dirname(system.file(package=utils_name())),
#'   "figures", "figures_cpue.csv")
#' )
#' cpue_output(
#'   grep = "OR_COMM_NSLOG_CPUE", fleet = "Fix"
#' )
#' cpue_output(
#'   grep = "OR_ORBS_CPUE", fleet = "OR"
#' )
#' }
cpue_output <- function(grep, fleet) {
  stopifnot(dir.exists("data-raw"))
  files <- dir(path = "data-raw", pattern = grep, full.names = TRUE)
  data <- mapply(
    FUN = readxl::read_excel,
    path = files
  )

  surveyname <- get_fleet(fleet, col = "label_long")
  labelhead <-  gsub("_| ", "", surveyname)
  labels <- paste0("cpue-", labelhead,
    "-", c("filter", "ts", "aic")
  )
  out <- data.frame(
    caption = c(
      paste0(
        "Filtering criteria for ", surveyname,
        " data and the resulting number (N) and percent positive (pos) ",
        "records remaining after filtering."
      ),
      paste0(
        "Estimates of the index and associated log standard error ",
        "for the ", surveyname, " index."
      ),
      paste0(
        "Model-selection results."
      )
    ),
    altcaption = rep(" ", length(data)),
    label = labels,
    filename = paste0(labels, ".tex"),
    loc = file.path("..", "tables")
  )[1, ]

  masterfn <- file.path("tables", "tables_cpue.csv")
  if (file.exists(masterfn)) {
    master <- rbind(
      utils::read.csv(masterfn),
      out
    )
  } else {
    master <- out
  }

  dir.create("tables", showWarnings = FALSE)
  utils::write.csv(
    master,
    row.names = FALSE,
    file = file.path("tables", "tables_cpue.csv")
  )

  t <- kableExtra::kbl(data[[1]] %>%
    dplyr::select(-dplyr::matches("RECORDS")) %>%
    dplyr::rename_with(stringr::str_to_sentence) %>%
    dplyr::rename_with(~ gsub("No\\. Pos.+", "N pos", .)) %>%
    dplyr::rename_with(~ gsub("Pos[\\.]*", "pos", .)) %>%
    dplyr::rename_with(~ gsub("Perc.", "%", .)) %>%
    dplyr::mutate(`% pos` = round(`% pos` * 100, 2)),
      booktabs = TRUE,
      format = "latex",
      longtable = TRUE,
      caption = out[["caption"]][1],
      label = out[["label"]][1]
    ) %>%
    # kableExtra::kable_styling(full_width = TRUE) %>%
    kableExtra::column_spec(2, width = "6cm")
  kableExtra::save_kable(t,
    file = file.path("tables", out[["filename"]][1]))

  # Figures
  filesbase <- dir("figures", pattern = grep)
  labelsnew <- paste0("cpue-", labelhead, c("qqbin", "qqpos"))
  filesnew <- file.path("figures", paste0(labelsnew, ".png"))
  file.copy(
    file.path("figures", filesbase,
      c("ScaledQQplot_bin.png", "ScaledQQplot_pos.png")
    ),
    filesnew
  )

  out <- data.frame(
    caption = c(
      paste0(
        "Scaled quantile-quantile plot (left) and ",
        "rank-transformed versus standardized residuals (right) for the ",
        c("binomial", "positive"), " model of the ", surveyname, " index."
      )
    ),
    alt_caption = c(
      paste0(
        "Residuals follow one to one line for the ",
        c("binomial", "positive"), " model of the ", surveyname, " index."
      )
    ),
    label = labelsnew,
    filein = file.path("..", filesnew)
  )
  masterfn <- file.path("figures", "figures_cpue.csv")
  if (file.exists(masterfn)) {
    master <- rbind(
      utils::read.csv(masterfn),
      out
    )
  } else {
    master <- out
  }
  dir.create("figures", showWarnings = FALSE)
  utils::write.csv(
    master,
    row.names = FALSE,
    file = file.path("figures", "figures_cpue.csv")
  )
}