feat: added new PlotPresenceAbsence.fn() #31

NAMESPACE

@@ -13,6 +13,7 @@ export(PlotBio.fn)
 export(PlotBioStrata.fn)
 export(PlotFreqData.fn)
 export(PlotMap.fn)
+export(PlotPresenceAbsence.fn)
 export(PlotSexRatio.fn)
 export(PlotSexRatioStrata.fn)
 export(PlotVarLengthAtAge.fn)

R/PlotPresenceAbsence.fn.R

@@ -0,0 +1,126 @@
+#' Plot showing presence and absence per haul by depth or latitute bin
+#'
+#' Uses the data.frame of catch values extracted from the data warehouse
+#' by [PullCatch.fn()] to make a table of zero and non-zero catch by
+#' depth or latitute bins.
+#'
+#' @param catch data.frame containing catch per haul created by
+#' PullCatch.fn()
+#' @param dim Dimension of interest, either "depth" or "lat"
+#' @param depth_min Minimum depth (in meters)
+#' @param depth_max Maximum depth (in meters). A NULL value will cause the
+#' function to automatically set depth_max to the multiple of depth_bin_width beyond
+#' the 99.9 percentile of the observations.
+#' @param depth_bin_width Width of each depth bin (in meters)
+#' @param lat_min Minimum latitute (in decimal degrees)
+#' @param lat_max Maximum latitute (in decimal degrees)
+#' @param lat_bin_width Width of each latitude bin (in decimal degrees)
+#' @param add_range_to_main Add the range of latitude or depth by which the data
+#' are filtered
+#' @param xlab Label for x-axis. A NULL value will cause the function
+#' to choose either "Depth (m)" or "Latitude (°N)"
+#'
+#' @author Ian G. Taylor
+#' @export
+#' @examples
+#' # load WCGBTS catch data
+#' catch.WCGBTS.ling <- nwfscSurvey::PullCatch.fn(Name = "lingcod",
+#'                                                SurveyName = "NWFSC.Combo")
+#' PlotPresenceAbsence.fn(catch.WCGBTS.ling, dim = "lat")
+#' PlotPresenceAbsence.fn(catch.WCGBTS.ling, dim = "depth")
+
+PlotPresenceAbsence.fn <- function(catch,
+                                   dim = "depth",
+                                   dir = NULL,
+                                   dopng = FALSE,
+                                   depth_min = 50,
+                                   depth_max = NULL,
+                                   depth_bin_width = 25,
+                                   lat_min = 32,
+                                   lat_max = 49,
+                                   lat_bin_width = 1.0,
+                                   main = "Presence/absence in WCGBT Survey",
+                                   add_range_to_main = TRUE,
+                                   xlab = NULL) {
+  # check inputs
+  if (!dim %in% c("depth", "lat")) {
+  }
+
+  # set depth_max if not provided
+  if (is.null(depth_max)) {
+    depth_999 <- quantile(
+      prob = 0.999,
+      x = catch$Depth_m[catch$Latitude_dd > lat_min &
+        catch$Latitude_dd < lat_max &
+        catch$cpue_kg_km2 > 0]
+    )
+    depth_max <- 2 * depth_bin_width + depth_bin_width * floor(depth_999 / depth_bin_width)
+    message(
+      "99.9% of positive hauls are shallower than ", round(depth_999), ".\n",
+      "'depth_max' set to ", depth_max, ". Input alternative value if you wish."
+    )
+  }
+
+  # code in "if (dopng)" section below copied from plotBio.fn()
+  if (dopng) {
+    if (is.null(dir)) {
+      stop("Directory needs to be set.")
+    }
+    if (!file.exists(dir)) {
+      stop("The dir argument leads to a location", ",\ni.e., ", dir, ", that doesn't exist.")
+    }
+    plotdir <- file.path(dir, paste("plots", sep = ""))
+    plotdir.isdir <- file.info(plotdir)$isdir
+    if (is.na(plotdir.isdir) | !plotdir.isdir) {
+      dir.create(plotdir)
+    }
+    png(paste0(dir, "/plots/Presence-absence_in_WCGBT_Survey.png"),
+      height = 7, width = 7, units = "in", res = 300
+    )
+  }
+
+  # filter catch based on input depth and latitute range
+  catch2 <- catch[catch$Depth_m < depth_max &
+    catch$Depth_m > depth_min &
+    catch$Latitude_dd > lat_min &
+    catch$Latitude_dd < lat_max, ]
+
+  # note: \u00B0 is degree symbol and \u2013 is n-dash
+
+  # depth as dimension of interest
+  if (dim == "depth") {
+    # get binned value
+    binned_value <- depth_bin_width * floor(catch2$Depth_m / depth_bin_width)
+    # update xlab and caption
+    if (is.null(xlab)) {
+      xlab <- "Depth (m)"
+    }
+    if (add_range_to_main) {
+      main <- paste0(main, " (", lat_min, "\u00B0N \u2013 ", lat_max, "\u00B0N)")
+    }
+  }
+  # rounded value for latitude
+  if (dim == "lat") {
+    # get binned value
+    binned_value <- lat_bin_width * floor(catch2$Latitude_dd / lat_bin_width)
+    # update xlab and caption
+    if (is.null(xlab)) {
+      xlab <- "Latitude (\u00B0N)"
+    }
+    if (add_range_to_main) {
+      main <- paste0(main, " (", depth_min, " \u2013 ", depth_max, "m)")
+    }
+  }
+
+  # make table
+  tab <- table(binned_value, catch2$cpue_kg_km2 > 0)
+  # add names for the dimensions which get used in the plot
+  dimnames(tab)[[2]] <- c("Absent", "Present")
+  # make plot
+  plot(tab, col = c(gray(.7), "blue3"), cex = 1, main = main, xlab = xlab)
+
+  # close PNG if it was used
+  if (dopng) {
+    dev.off()
+  }
+}