R/plotRawData.R

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

#############################################################################
#'
#' Diagnostic plots and summaries for a raw PacFIN dataset pre-filtering.
#'
#' \code{plotRawData} creates a set of diagnostic plots and summaries, writing
#' pdfs and a text file in addition to plotting onscreen and console.
#'
#' \subsection{Workflow}{
#' Run \code{plotRawData} to visualize and summarize the PacFIN data prior to
#' running \code{\link{cleanPacFIN}}.
#' }
#'
#' @param rawData an unfiltered PacFIN dataset
#' @template fname
#'
#' @export
#'
#' @details
#' Will create a filename from the species ID if one is not provided.
#'
##############################################################################

plotRawData <- function(rawData,
                        fname = NULL) {
  cat("\nRunning diagnostics\n\n")

  if (is.null(fname)) {
    # Set up filenames for txt, pdf

    species <- sort(unique(rawData$SPID))
    pdffile <- paste("Diags.", species, ".pdf", sep = "")
    txtfile <- paste("Diags.", species, ".txt", sep = "")
  } else {
    # Remove the extension
    fname <- gsub("\\.[a-zA-Z]{3}$", "", fname)
    pdffile <- paste(fname, ".pdf", sep = "")
    txtfile <- paste(fname, ".txt", sep = "")
  } # End ifelse

  cat("Plots will be written to", pdffile, "\n")
  cat("Summaries will be written to", txtfile, "\n")

  sink(file = txtfile, split = T, append = T)

  # Develop statistics of interest

  len <- rawData[!is.na(rawData$FISH_LENGTH), ]
  len$len <- floor(len$FISH_LENGTH / 10)
  len$depth_mid <- (len$DEPTH_MIN + len$DEPTH_MAX) / 2
  ltows <- len[!duplicated(len$SAMPLE_NO), ]

  meanLen.yr <- tapply(len$len, list(len$SAMPLE_YEAR), mean)
  meanLen <- tapply(len$len, list(len$SAMPLE_NO, len$SAMPLE_YEAR), mean)

  age <- rawData[!is.na(rawData$FISH_AGE_YEARS_FINAL), ]
  age$Age <- age$FISH_AGE_YEARS_FINAL
  atows <- age[!duplicated(age$SAMPLE_NO), ]
  meanAge <- tapply(age$Age, list(age$SAMPLE_NO, age$SAMPLE_YEAR), mean)

  # Print tables

  # cat("Lengths for which FISH_LENGTH_TYPE is T:  ")
  # print(len[len$FISH_LENGTH_TYPE=="T",])
  # cat("\n\n")

  cat("Records per SAMPLE_YEAR\n\n")
  print(table(rawData$SAMPLE_YEAR, useNA = "ifany"))
  cat("\n\n")

  cat("FISH_LENGTH_TYPE\n")
  print(table(rawData$FISH_LENGTH_TYPE, useNA = "ifany"))
  cat("\n\n")

  cat("FISH_LENGTH\n")
  print(table(rawData$FISH_LENGTH, useNA = "ifany"))
  cat("\n\n")

  cat("GEAR vs GRID\n")
  print(table(len$GEAR, len$GRID))
  cat("\n\n")

  cat("FISH_LENGTH for lengthed fish\n")
  print(table(len$FISH_LENGTH_TYPE, useNA = "ifany"))
  cat("\n\n")

  cat("SAMPLE_YEAR vs SOURCE_AGID for lengthed fish\n")
  print(table(len$SAMPLE_YEAR, len$SOURCE_AGID))
  cat("\n\n")

  cat("Difference between FISH_LENGTH and floor(FISH_LENGTH)\n")
  print(table(len$FISH_LENGTH - floor(len$FISH_LENGTH)))
  cat("\n\n")

  cat("Difference between FISH_LENGTH/10 and floor(FISH_LENGTH/10)\n")
  print(table(round(len$FISH_LENGTH / 10 - floor(len$FISH_LENGTH / 10), 1)))
  cat("\n\n")

  cat("DEPTH_AVG for lengthed fish\n")
  print(table(is.na(len$DEPTH_AVG)))
  cat("\n\n")

  cat("SAMPLE_YEAR vs. SOURCE_AGID for SAMPLE_NOs with lengthed fish\n")
  print(table(ltows$SAMPLE_YEAR, ltows$SOURCE_AGID))
  cat("\n\n")

  cat("DEPTH_AVG for SAMPLE_NOs with lengthed fish\n")
  print(table(is.na(ltows$DEPTH_AVG), useNA = "ifany"))
  cat("\n\n")

  cat("Number of aged fish\n")
  print(nrow(age))
  cat("\n\n")

  cat("SAMPLE_YEAR vs. SOURCE_AGID for SAMPLE_NOs with aged fish\n")
  print(table(atows$SAMPLE_YEAR, atows$SOURCE_AGID))
  cat("\n\n")

  cat("SAMPLE_YEAR vs. SOURCE_AGID for aged fish\n")
  print(table(age$SAMPLE_YEAR, age$SOURCE_AGID))
  cat("\n\n")

  cat("age vs. ageX for aged fish\n")
  print(table(age[, grep("^age[0-9]*$", colnames(age))], useNA = "ifany"))
  cat("\n\n")

  sink()

  # Plots

  # Fingers crossed, works the same for Mac and PC

  # Set up device for pdf

  grDevices::graphics.off()

  grDevices::pdf(pdffile)

  graphics::par(mfrow = c(2, 2))

  graphics::hist(len$len, nclass = 30, xlab = "", main = "FISH_LENGTH")

  graphics::barplot(table(10 * round(len$FISH_LENGTH / 10 - floor(len$FISH_LENGTH / 10), 1)),
    xlab = "Difference in rounded and floored lengths"
  )

  plot(len$FISH_LENGTH, len$FORK_LENGTH, pch = 16, xlab = "FISH_LENGTH", ylab = "FORK_LENGTH")

  plot(len$DEPTH_AVG, len$depth_mid, xlim = c(0, 400), ylim = c(0, 400), xlab = "DEPTH_AVG", ylab = "Depth_mid")
  graphics::abline(a = 0, b = 1)

  graphics::hist(ltows$DEPTH_AVG, xlab = "", main = "DEPTH_AVG")

  graphics::hist(age$Age, nclass = 30, xlab = "", main = "Age")

  graphics::par(mfrow = c(2, 1))
  graphics::boxplot(as.list(as.data.frame(meanLen)), varwidth = T, main = "Mean length")
  graphics::boxplot(as.list(as.data.frame(meanAge)), varwidth = T, main = "Mean age")

  grDevices::dev.off()
} # End plotRawData