R/PlotOffset.r

In nwfsc-assess/nwfscDeltaGLM: Bayesian delta-GLM package for constructing indices of CPUE data

#' PlotOffset plots the positive and presence absence offset by strata
#'
#' @param Data The data frame with the raw survey data
#' @param BugsList List of the fitted BUGS / JAGS object
#' @param maxDims Max dimensions of grid (rows, columns). Defaults to 8
#' @param FileName Name of the file(s) created
#' @param Folder Where to put the output is to be stored, defaults to NA
#'
#' @import grDevices
#' @import utils
#' @export
#'
PlotOffset <- function(Data, BugsList, maxDims = 8, FileName, Folder = NA) {
  if (is.na(Folder)) Folder <- paste(getwd(), "/", sep = "")

  # Attach stuff
  attach(BugsList, warn.conflicts = FALSE)
  on.exit(detach(BugsList))
  # attach(Data)
  nonZeros <- which(isNonZeroTrawl == TRUE)

  # Positive offset
  LogEffortRange <- seq(min(logeffort), max(logeffort), length = 1000)
  Nstrat <- length(unique(strataYear[nonZeros]))
  Nplots <- ceiling(Nstrat / maxDims^2)
  for (PlotI in 1:Nplots) {
    ParSet <- (PlotI - 1) * maxDims^2 + 1:min(Nstrat - (PlotI - 1) * maxDims^2, maxDims^2)
    Ncol <- ceiling(sqrt(length(ParSet)))
    Nrow <- ceiling(length(ParSet) / Ncol)
    jpeg(paste(Folder, "/", FileName, "Offset_Positive_by_strata_", PlotI, ".jpg", sep = ""), width = Ncol * 1.5, height = Nrow * 1.5, res = 150, units = "in")
    par(mfrow = c(Nrow, Ncol), mar = c(2, 2, 2, 0), mgp = c(1.25, 0.25, 0), tck = -0.02)
    for (StrataYearI in ParSet) {
      StrataI <- strata[which(strataYear == unique(strataYear)[StrataYearI])[1]]
      YearI <- year[which(strataYear == unique(strataYear)[StrataYearI])[1]]
      Y <- exp(median(cMx(Sdev)[, StrataI]) + median(Ydev[, YearI]) + median(SYdev[, StrataYearI]) + median(B.pos[, 1]) * LogEffortRange + median(B.pos[, 2]) * LogEffortRange)
      plot(x = exp(LogEffortRange), y = Y, ylab = "", xlab = "", main = unique(strataYear[nonZeros])[StrataI], ylim = c(0, max(Y)), xlim = c(0, max(exp(LogEffortRange))), type = "l")
    }
    dev.off()
  }

  # Presence/Absence offset
  LogEffortRange <- seq(min(logeffort), max(logeffort), length = 1000)
  Nstrat <- length(unique(strataYear[nonZeros]))
  Nplots <- ceiling(Nstrat / maxDims^2)
  for (PlotI in 1:Nplots) {
    ParSet <- (PlotI - 1) * maxDims^2 + 1:min(Nstrat - (PlotI - 1) * maxDims^2, maxDims^2)
    Ncol <- ceiling(sqrt(length(ParSet)))
    Nrow <- ceiling(length(ParSet) / Ncol)
    jpeg(paste(Folder, "/", FileName, "Offset_Presence-Absence_by_strata_", PlotI, ".jpg", sep = ""), width = Ncol * 1.5, height = Nrow * 1.5, res = 150, units = "in")
    par(mfrow = c(Nrow, Ncol), mar = c(2, 2, 2, 0), mgp = c(1.25, 0.25, 0), tck = -0.02)
    for (StrataYearI in ParSet) {
      StrataI <- strata[which(strataYear == unique(strataYear)[StrataYearI])[1]]
      YearI <- year[which(strataYear == unique(strataYear)[StrataYearI])[1]]
      Y <- plogis(median(cMx(pSdev)[, StrataI]) + median(pYdev[, YearI]) + median(pSYdev[, StrataYearI]) + median(B.zero[, 1]) * LogEffortRange + median(B.zero[, 2]) * LogEffortRange)
      plot(x = exp(LogEffortRange), y = Y, ylab = "", xlab = "", main = unique(strataYear[nonZeros])[StrataI], ylim = c(0, 1), xlim = c(0, max(exp(LogEffortRange))), type = "l")
    }
    dev.off()
  }
}