From 4c830bd3f7845e40c6e28320b29dec0e965416f9 Mon Sep 17 00:00:00 2001
From: Kelli Johnson <kelli.johnson@noaa.gov>
Date: Thu, 17 Nov 2022 15:37:02 -0800
Subject: [PATCH] deprecate(dopng=)

Deprecates `dopng =` because dir = NULL can serve as FALSE.

* Remove importsFrom for two functions with ::
* Uses ifelse to create main_ to remove
  so many if statements with duplicated code.
* Uses on.exit to call dev.off() in case the function fails, then the
  device is not left on.
*  fix(PlotPresenceAbsence.fn):
  * dim: `match.arg` allows you to list all of the possible options in
    the function call so users know what is available. Then, `match.arg`
    will use the first listed as the default.
  * Uses dontrun plot b/c the figures and download take too long and
    `check()` complains. So, I wrapped them in dontrun{} and I added an
    example with the package data where you do not have to download
    anything.
  * Checked spelling in documentation and wrapped at 80 characters.

Part of #31

TODO:
* Use `ggplot2::ggsave()`
* Remove the call to windows() which only works on windows machines and
  will cause GitHub actions to fail if there was a test.
---
 DESCRIPTION                 |  3 +-
 Examples/example_code_pop.R | 11 ++---
 R/PlotMap.fn.R              | 87 +++++++++++++++++--------------------
 R/PlotPresenceAbsence.fn.R  | 74 ++++++++++++++++++-------------
 R/PlotSexRatioStrata.fn.R   | 54 +++++++++++------------
 R/plotBio.fn.R              | 54 ++++++++++++-----------
 R/plotBioStrata.fn.R        | 62 +++++++++++++-------------
 R/plotFreqData.fn.R         | 52 ++++++++++++----------
 R/plotSexRatio.fn.R         | 52 +++++++++++++---------
 R/plotVarLengthAtAge.fn.R   | 52 ++++++++++++----------
 R/plot_proportion.R         | 73 +++++++++++++------------------
 vignettes/nwfscSurvey.Rmd   | 12 +++--
 12 files changed, 303 insertions(+), 283 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index b65c257..19e2478 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: nwfscSurvey
 Type: Package
 Title: Northwest Fisheries Science Center Survey
-Version: 2.0
+Version: 2.1
 Authors@R:
     c(person(given = c("Chantel", "R."),
              family = "Wetzel",
@@ -26,6 +26,7 @@ Imports:
     httr,
     jsonlite,
     kableExtra,
+    lifecycle,
     reshape2,
     ggplot2 (>= 3.0.0),
     xtable,
diff --git a/Examples/example_code_pop.R b/Examples/example_code_pop.R
index 832f963..f01f5e0 100644
--- a/Examples/example_code_pop.R
+++ b/Examples/example_code_pop.R
@@ -51,8 +51,8 @@ biomass = Biomass.fn(dir = getwd(), dat = catch,  strat.df = strata, printfolder
 # Creates a csv file within the "printfolder" that will be saved within the directory location (dir).
 
 # Plot the biomass index
-PlotBio.fn(dir = getwd(), dat = biomass, main = "NWFSC WCBBT Survey", dopng = TRUE)
-PlotBioStrata.fn(dir = getwd(), survey.name = "NWFSC_WCGBT_Survey", dat = biomass, mfrow.in = c(3,2), sameylim = TRUE, ylim = c(0, 22), dopng = TRUE)
+PlotBio.fn(dir = getwd(), dat = biomass, main = "NWFSC WCBBT Survey")
+PlotBioStrata.fn(dir = getwd(), survey.name = "NWFSC_WCGBT_Survey", dat = biomass, mfrow.in = c(3,2), sameylim = TRUE, ylim = c(0, 22))
 
 # Plot the CPUE
 plot_cpue(dir = getwd(), catch = catch)
@@ -116,7 +116,8 @@ LFs <- SurveyLFs.fn(dir = getwd(), datL = len, datTows = catch,
 # NWFSC combo survey data in the past).
 
 plot_comps(data = LFs, dir = getwd())
-PlotSexRatio.fn(dir = getwd(), dat = len, data.type = "length", dopng = TRUE, main = "NWFSC WCGBT Survey")
+PlotSexRatio.fn(dir = getwd(), dat = len, data.type = "length", main = "NWFSC WCGBT Survey")
+
 
 #============================================================================================
 #Length Biological Data without expansion 
@@ -148,8 +149,8 @@ AFs <- SurveyAFs.fn(dir = getwd(), datA = age, datTows = catch,
                      sex = 3, nSamps = n, fleet = 7)
 
 plot_comps(data = AFs, dir = getwd())
-PlotVarLengthAtAge.fn(dir = getwd(), dat = age, main = "NWFSC WCGBT Survey", dopng = TRUE) 
-PlotSexRatio.fn(dir = getwd(), dat = age, data.type = "age", dopng = TRUE, main = "NWFSC WCGBT Survey")
+PlotVarLengthAtAge.fn(dir = getwd(), dat = age, main = "NWFSC WCGBT Survey") 
+PlotSexRatio.fn(dir = getwd(), dat = age, data.type = "age", main = "NWFSC WCGBT Survey")
 
 #============================================================================================
 #Age Biological Data without Expansion
diff --git a/R/PlotMap.fn.R b/R/PlotMap.fn.R
index 0358703..6ce6545 100644
--- a/R/PlotMap.fn.R
+++ b/R/PlotMap.fn.R
@@ -1,21 +1,37 @@
-#' #This function will create two plots
-#' 1. CPUE from survey data across all years, and
-#' 2. CPUE plot of the survey data by year.
+#' Create maps with catch-per-unit-effort
 #'
-#' @param dir directory
-#' @param dat object created by the PullCatch.fn function
-#' @param main name that will be used to name the saved png (i.e., "NWFSC" results in a file called "NWFSC_CPUE_Map.png")
-#' @param dopng save the plot as a png inside plots folder
-#' @param plot select a subset of plots: 1 = coastwide across all years, 2 = coastwide by year
+#' Create the following figures:
+#' 1. CPUE plot of the data across all years and/or
+#' 2. CPUE plot of the data by year.
 #'
-#' @author Chantel Wetzel
+#' @template dir
+#' @param dat An object created by [PullCatch.fn()].
+#' @param main A string that will be prepended to the name of the saved png
+#'   (i.e., "NWFSC" results in a file called "NWFSC_CPUE_Map.png").
+#' @param dopng Deprecated with {nwfscSurvey} 2.1 because providing a non-NULL
+#'   value to `dir` can serve the same purpose as `dopng = TRUE` without the
+#'   potential for errors when `dopng = TRUE` and `dir = NULL`. Thus, users
+#'   no longer have to specify `dopng` to save the plot as a png.
+#' @param plot A vector of integers specifying the selection of a subset of
+#'   plots: 1 = coastwide across all years, 2 = coastwide by year.
+#'
+#' @author Chantel R. Wetzel
 #' @export
 #'
 #' @import ggplot2
-#' @importFrom rnaturalearth ne_states
-#' @importFrom stats quantile
 
-PlotMap.fn <- function(dir = NULL, dat, main = NULL, dopng = FALSE, plot = 1:2) {
+PlotMap.fn <- function(dir = NULL,
+                       dat,
+                       main = NULL,
+                       dopng = lifecycle::deprecated(),
+                       plot = 1:2) {
+
+  if (lifecycle::is_present(dopng)) {
+    lifecycle::deprecate_warn(
+      when = "2.1",
+      what = "nwfscSurvey::PlotMap.fn(dopng =)"
+    )
+  }
 
   # Create specialized plots
   pngfun <- function(dir, file, w = 7, h = 7, pt = 12) {
@@ -28,28 +44,15 @@ PlotMap.fn <- function(dir = NULL, dat, main = NULL, dopng = FALSE, plot = 1:2)
     )
   }
 
+  plotdir <- file.path(dir, "map_plots")
+  check_dir(dir = plotdir)
+  main_ <- ifelse(is.null(main), "", paste0(main, "_"))
 
-  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("map_plots", sep = ""))
-    plotdir.isdir <- file.info(plotdir)$isdir
-    if (is.na(plotdir.isdir) | !plotdir.isdir) {
-      dir.create(plotdir)
-    }
-  }
-
-  if (!dopng) {
+  if (!is.null(dir)) {
     windows(width = 5, height = 7, record = TRUE)
   }
 
-
-  map.hires <- ne_states(country = c(
+  map.hires <- rnaturalearth::ne_states(country = c(
     "United States of America",
     "Mexico",
     "Canada"
@@ -59,7 +62,7 @@ PlotMap.fn <- function(dir = NULL, dat, main = NULL, dopng = FALSE, plot = 1:2)
   ind <- dat$cpue_kg_km2 > 0
   pos.cat <- dat[ind, ]
   neg <- dat[dat$cpue_kg_km2 == 0, ]
-  mid <- as.numeric(quantile(pos.cat$cpue_kg_km2, 0.50))
+  mid <- as.numeric(stats::quantile(pos.cat$cpue_kg_km2, 0.50))
   max.size <- 12
 
   plot_format <- theme(
@@ -71,13 +74,8 @@ PlotMap.fn <- function(dir = NULL, dat, main = NULL, dopng = FALSE, plot = 1:2)
 
   igroup <- 1
   if (igroup %in% plot) {
-    if (dopng) {
-      if (is.null(main)) {
-        pngfun(dir = plotdir, file = "CPUE_Map.png", h = 7, w = 5)
-      }
-      if (!is.null(main)) {
-        pngfun(dir = plotdir, file = paste0(main, "_CPUE_Map.png"), h = 7, w = 5)
-      }
+    if (!is.null(dir)) {
+      pngfun(dir = plotdir, file = paste0(main_, "_CPUE_Map.png"), w = 5)
     }
 
     g <- ggplot(dat) +
@@ -97,7 +95,7 @@ PlotMap.fn <- function(dir = NULL, dat, main = NULL, dopng = FALSE, plot = 1:2)
       theme(legend.position = "right")
     print(g)
 
-    if (dopng) {
+    if (!is.null(dir)) {
       dev.off()
     }
   }
@@ -113,13 +111,8 @@ PlotMap.fn <- function(dir = NULL, dat, main = NULL, dopng = FALSE, plot = 1:2)
       axis.ticks.x = element_blank()
     )
 
-    if (dopng) {
-      if (is.null(main)) {
-        pngfun(dir = plotdir, file = "CPUE_Map_Year.png", h = 7, w = 7)
-      }
-      if (!is.null(main)) {
-        pngfun(dir = plotdir, file = paste0(main, "_CPUE_Map_Year.png"), h = 7, w = 7)
-      }
+    if (!is.null(dir)) {
+      pngfun(dir = plotdir, file = paste0(main_, "_CPUE_Map_Year.png"))
     }
 
     h <- ggplot(dat) +
@@ -141,7 +134,7 @@ PlotMap.fn <- function(dir = NULL, dat, main = NULL, dopng = FALSE, plot = 1:2)
     # coord_fixed(1.3)
     print(h)
 
-    if (dopng) {
+    if (!is.null(dir)) {
       dev.off()
     }
   }
diff --git a/R/PlotPresenceAbsence.fn.R b/R/PlotPresenceAbsence.fn.R
index caeec14..d751bd5 100644
--- a/R/PlotPresenceAbsence.fn.R
+++ b/R/PlotPresenceAbsence.fn.R
@@ -1,37 +1,39 @@
-#' Plot showing presence and absence per haul by depth or latitute bin
+#' Plot showing presence and absence per haul by depth, latitude, or sex bin
 #'
-#' Uses the data.frame of data values extracted from the data warehouse
-#' by either [PullCatch.fn()] or [PullBio.fn()] to make a table of 
-#' proportion by depth or latitude bins. If biological data are passed
-#' to the function then there is a single option to plot the sex 
-#' ratio by depth.
+#' This function was deprecated in {nwfsc} version 2.1. Please use
+#' [plot_proportion()] instead.
 #'
-#' @param data data.frame containing data per haul created by
-#' PullCatch.fn() or biological data created by PullBio.fn() where the
-#' dim input must be "sex". 
-#' @param dim Dimension of interest, either "depth", "lat", or "sex"
-#' @param dir The directory name to print to
-#' @param plot_type Two options area avialable "proportion" or "total" where
-#' the default, "proportion", plot the proportion by depth/latitude with equal
-#' bar widths and the "total" option plot the numbers by depth/latitude were
-#' the bar widths in a production of sampling by depth/latitude.
-#' @param depth_min Minimum depth (in meters)
+#' @param data data.frame containing data per haul created by [PullCatch.fn()]
+#'   or biological data created by [PullBio.fn()] where the `dim = "sex"` must
+#'   be true for the latter.
+#' @param dim Dimension of interest, either "depth", "lat", or "sex".
+#' @template dir
+#' @param plot_type Two options area available "proportion" or "total" where the
+#'   default, "proportion", plot the proportion by depth/latitude with equal bar
+#'   widths and the "total" option plot the numbers by depth/latitude were the
+#'   bar widths in a production of sampling by depth/latitude.
+#' @param dopng Deprecated with {nwfscSurvey} 2.1 because providing a non-NULL
+#'   value to `dir` can serve the same purpose as `dopng = TRUE` without the
+#'   potential for errors when `dopng = TRUE` and `dir = NULL`. Thus, users
+#'   no longer have to specify `dopng` to save the plot as a png.
+#' @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)
+#'   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
+#' are filtered.
 #' @param xlab Label for x-axis. A NULL value will cause the function
-#' to choose either "Depth (m)" or "Latitude (°N)"
+#' to choose either "Depth (m)" or "Latitude (°N)".
 #'
 #' @author Ian G. Taylor and Chantel Wetzel
 #' @importFrom grDevices gray
 #' @export
 #' @examples
+#' \dontrun{
 #' # load WCGBTS data data
 #' data.WCGBTS.ling <- nwfscSurvey::PullCatch.fn(
 #'   Name = "lingcod",
@@ -44,11 +46,15 @@
 #' PlotPresenceAbsence.fn(data = data.WCGBTS.ling, dim = "lat")
 #' PlotPresenceAbsence.fn(data = data.WCGBTS.ling, dim = "depth")
 #' PlotPresenceAbsence.fn(data = bio.WCGBTS.ling, dim = "sex")
-#' 
+#'
+#' # Plot with package data
+#' PlotPresenceAbsence.fn(catch_nwfsc_combo)
+#' }
 PlotPresenceAbsence.fn <- function(data,
-                                   dim = c("depth", "lat", "sex")[1],
+                                   dim = c("depth", "lat", "sex"),
                                    dir = NULL,
-                                   plot_type = c('proportion', 'total')[1],
+                                   dopng = lifecycle::deprecated(),
+                                   plot_type = c("proportion", "total"),
                                    depth_min = 50,
                                    depth_max = NULL,
                                    depth_bin_width = 25,
@@ -57,8 +63,17 @@ PlotPresenceAbsence.fn <- function(data,
                                    lat_bin_width = 1.0,
                                    add_range_to_main = TRUE,
                                    xlab = NULL) {
+  lifecycle::deprecate_soft(
+    when = "2.1",
+    what = "PlotPresenceAbsence.fn()",
+    with = "plot_proportion()"
+  )
+
+  dim <- match.arg(dim)
+  plot_type <- match.arg(plot_type)
 
-  plot_proportion(data = data,
+  plot_proportion(
+    data = data,
     dim = dim,
     dir = dir,
     plot_type = plot_type,
@@ -69,6 +84,7 @@ PlotPresenceAbsence.fn <- function(data,
     lat_max = lat_max,
     lat_bin_width = lat_bin_width,
     add_range_to_main = add_range_to_main,
-    xlab = xlab)
+    xlab = xlab
+  )
 
 }
diff --git a/R/PlotSexRatioStrata.fn.R b/R/PlotSexRatioStrata.fn.R
index 77cbcc6..bad6d3d 100644
--- a/R/PlotSexRatioStrata.fn.R
+++ b/R/PlotSexRatioStrata.fn.R
@@ -6,32 +6,38 @@
 #' @param strat.vars the parameters to stratify the data
 #' @param strat.df the created strata matrix with the calculated areas by the createStrataDF.fn function
 #' @param circleSize circle size
-#' @param dopng TRUE/FALSE whether to save a png file
+#' @param dopng Deprecated with {nwfscSurvey} 2.1 because providing a non-NULL
+#'   value to `dir` can serve the same purpose as `dopng = TRUE` without the
+#'   potential for errors when `dopng = TRUE` and `dir = NULL`. Thus, users
+#'   no longer have to specify `dopng` to save the plot as a png.
 #' @param ...      Additional arguments for the plots
 #'
 #' @author Allan Hicks and Chantel Wetzel
 #' @export
 #' @seealso \code{\link{StrataFactors.fn}}
 
-PlotSexRatioStrata.fn <- function(dir = NULL, dat, type = "length", strat.vars = c("Depth_m", "Latitude_dd"), strat.df = NULL, circleSize = 0.05, dopng = FALSE, ...) {
-  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)
-    }
-    if (is.null(main)) {
-      png(file.path(dir, paste("plots/fraction_female.png", sep = "")), height = 7, width = 7, units = "in", res = 300)
-    }
-    if (!is.null(main)) {
-      png(file.path(dir, paste("plots/", main, "_fraction_female.png", sep = "")), height = 7, width = 7, units = "in", res = 300)
-    }
+PlotSexRatioStrata.fn <- function(dir = NULL, dat, type = "length", strat.vars = c("Depth_m", "Latitude_dd"), strat.df = NULL, circleSize = 0.05, dopng = lifecycle::deprecated(), ...) {
+  if (lifecycle::is_present(dopng)) {
+    lifecycle::deprecate_warn(
+      when = "2.1",
+      what = "nwfscSurvey::PlotMap.fn(dopng =)"
+    )
+  }
+  plotdir <- file.path(dir, "plots")
+  check_dir(dir = plotdir)
+  main_ <- ifelse(is.null(main), "", paste0(main, "_"))
+  if (!is.null(dir)) {
+    png(
+      filename = file.path(
+        plotdir,
+        paste0(main_, "fraction_female.png")
+      ),
+      height = 7,
+      width = 7,
+      units = "in",
+      res = 300
+    )
+    on.exit(dev.off(), add = TRUE)
   }
 
   row.names(strat.df) <- strat.df[, 1] # put in rownames to make easier to index later
@@ -41,13 +47,9 @@ PlotSexRatioStrata.fn <- function(dir = NULL, dat, type = "length", strat.vars =
 
   datB <- data.frame(datB, stratum = StrataFactors.fn(datB, strat.vars, strat.df)) # create a new column for the stratum factor
 
-  # if (dopng) { png(paste0(dir, "/plots/", survey,"_fraction_female.png") ) }
-  # if (dopng) { png(file.path(dir, paste("plots/", survey,"_fraction_female.png", sep ="")), height=7, width=7, units="in",res=300) }
   par(mfrow = c(3, 3))
 
   for (i in 1:length(row.names(strat.df))) {
-    # if (dopng) { png(paste0(dir, "/plots/", survey,"_", row.names(strat.df)[i], "_fraction_female.png"), height=7, width=7, units="in",res=300) }
-    # par(mfrow = c(5,3))
     z <- which(datB$stratum == row.names(strat.df)[i])
     subDF <- datB[z, ]
 
@@ -64,9 +66,5 @@ PlotSexRatioStrata.fn <- function(dir = NULL, dat, type = "length", strat.vars =
     nobs <- temp[, "F"] + temp[, "M"]
     plot(ratioF, type = "l", col = "red", xlab = axis.name, ylab = "Fraction female", main = row.names(strat.df)[i], ylim = c(0, 1)) # ,...)
     symbols(ratioF, circles = nobs, inches = circleSize, fg = "red", bg = rgb(1, 0, 0, alpha = 0.5), add = T)
-    # if (dopng) {dev.off()}
-  }
-  if (dopng) {
-    dev.off()
   }
 }
diff --git a/R/plotBio.fn.R b/R/plotBio.fn.R
index 87a9093..678b0f1 100644
--- a/R/plotBio.fn.R
+++ b/R/plotBio.fn.R
@@ -11,34 +11,42 @@
 #' @param add add additional line to plot
 #' @param col color
 #' @param main plot label
-#' @param dopng save the plot as a png inside plots folder
+#' @param dopng Deprecated with {nwfscSurvey} 2.1 because providing a non-NULL
+#'   value to `dir` can serve the same purpose as `dopng = TRUE` without the
+#'   potential for errors when `dopng = TRUE` and `dir = NULL`. Thus, users
+#'   no longer have to specify `dopng` to save the plot as a png.
 #' @param ...      Additional arguments for the plots
 #'
 #' @author Allan Hicks and John Wallace
 #' @export
 
 PlotBio.fn <- function(dir = NULL, dat, CI = 0.95, scalar = 1e6, gap = 0.03, ylab = "Biomass ('000 mt)", xlab = "Year",
-                       main = NULL, ylim = NULL, add = FALSE, col = "black", dopng = FALSE, ...) {
+                       main = NULL, ylim = NULL, add = FALSE, col = "black", dopng = lifecycle::deprecated(), ...) {
+
+  if (lifecycle::is_present(dopng)) {
+    lifecycle::deprecate_warn(
+      when = "2.1",
+      what = "nwfscSurvey::PlotMap.fn(dopng =)"
+    )
+  }
+
   bio <- dat$Bio
 
-  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)
-    }
-    if (is.null(main)) {
-      png(paste0(dir, "/plots/designed_based_index.png"), height = 7, width = 7, units = "in", res = 300)
-    }
-    if (!is.null(main)) {
-      png(paste0(dir, "/plots/", main, "_designed_based_index.png"), height = 7, width = 7, units = "in", res = 300)
-    }
+  plotdir <- file.path(dir, "plots")
+  check_dir(plotdir)
+  main_ <- ifelse(is.null(main), "", paste0(main, "_"))
+  if (!is.null(dir)) {
+    png(
+      filename = file.path(
+        plotdir,
+        paste0(main_, "_designed_based_index.png")
+      ),
+      height = 7,
+      width = 7,
+      units = "in",
+      res = 300
+    )
+    on.exit(dev.off(), add = TRUE)
   }
 
   par(mfrow = c(1, 1))
@@ -56,13 +64,9 @@ PlotBio.fn <- function(dir = NULL, dat, CI = 0.95, scalar = 1e6, gap = 0.03, yla
   gap <- gap * max(y)
   if (add) {
     points(x, y, col = col)
-  }
-  else {
+  } else {
     plot(x, y, ylab = ylab, xlab = xlab, ylim = ylim, main = main, col = col, ...)
   }
   segments(x, y + gap, x, ci[1, ], col = col)
   segments(x, y - gap, x, ci[2, ], col = col)
-  if (dopng) {
-    dev.off()
-  }
 }
diff --git a/R/plotBioStrata.fn.R b/R/plotBioStrata.fn.R
index aae12d5..7a13c9e 100644
--- a/R/plotBioStrata.fn.R
+++ b/R/plotBioStrata.fn.R
@@ -16,7 +16,10 @@
 #' @param strata.names custom strata names, if not specified will use the defined names from CreateStrataDF.fn
 #' @param pch.col Color as string, defaults to "black"
 #' @param pch.type Numeric pch type, defaults to 16
-#' @param dopng save the plot as a png inside plots folder
+#' @param dopng Deprecated with {nwfscSurvey} 2.1 because providing a non-NULL
+#'   value to `dir` can serve the same purpose as `dopng = TRUE` without the
+#'   potential for errors when `dopng = TRUE` and `dir = NULL`. Thus, users
+#'   no longer have to specify `dopng` to save the plot as a png.
 #' @param ...      Additional arguments for the plots
 #'
 #' @author Allan Hicks and John Wallace
@@ -24,41 +27,41 @@
 
 PlotBioStrata.fn <- function(dir = NULL, dat, CI = 0.95, scalar = 1e6, gap = 0.03, ylab = "Biomass ('000 mt)", xlab = "Year",
                              survey.name = NULL, strata.names = NULL, ylim = NULL, sameylim = FALSE, add = FALSE, mfrow.in = NULL, col = "black",
-                             pch.col = "black", pch.type = 16, dopng = FALSE, ...) {
+                             pch.col = "black", pch.type = 16, dopng = lifecycle::deprecated(), ...) {
+
+  if (lifecycle::is_present(dopng)) {
+    lifecycle::deprecate_warn(
+      when = "2.1",
+      what = "nwfscSurvey::PlotMap.fn(dopng =)"
+    )
+  }
+
   bio_strat <- dat$StrataEsts
 
-  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)
-    }
-    if (is.null(survey.name)) {
-      png(paste0(dir, "/plots/designed_based_by_strata_index.png"), height = 7, width = 7, units = "in", res = 300)
-    }
-    if (!is.null(survey.name)) {
-      png(paste0(dir, "/plots/", survey.name, "_designed_based_by_strata_index.png"), height = 7, width = 7, units = "in", res = 300)
-    }
+  plotdir <- file.path(dir, "plots")
+  check_dir(dir = plotdir)
+  main_ <- ifelse(is.null(survey.name), "", paste0(survey.name, "_"))
+  if (!is.null(dir)) {
+    png(
+      filename = file.path(
+        plotdir,
+        paste0(main_, "designed_based_by_strata_index.png")
+      ),
+      height = 7,
+      width = 7,
+      units = "in",
+      res = 300
+    )
+    on.exit(dev.off(), add = TRUE)
   }
+
   if (is.null(strata.names)) {
     strata.names <- names(bio_strat)
   }
 
   if (!is.null(mfrow.in)) {
-    if (length(mfrow.in) == 1) {
-      par(mfrow = c(mfrow.in[1], mfrow.in[1]))
-    }
-    if (length(mfrow.in) != 1) {
-      par(mfrow = c(mfrow.in[1], mfrow.in[2]))
-    }
-  }
-  if (is.null(mfrow.in)) {
+    par(mfrow = c(mfrow.in[1], mfrow.in[length(mfrow.in)]))
+  } else {
     par(mfrow = c(length(bio_strat) / 2, 2))
   }
 
@@ -99,7 +102,4 @@ PlotBioStrata.fn <- function(dir = NULL, dat, CI = 0.95, scalar = 1e6, gap = 0.0
     segments(x0 = x, y0 = y - gap, x1 = x, y1 = ci[2, ], col = col)
   }
 
-  if (dopng) {
-    dev.off()
-  }
 }
diff --git a/R/plotFreqData.fn.R b/R/plotFreqData.fn.R
index f222b3f..b860b36 100644
--- a/R/plotFreqData.fn.R
+++ b/R/plotFreqData.fn.R
@@ -11,7 +11,10 @@
 #' @param main main plot text
 #' @param xlim x-limit values
 #' @param ymax Value used to truncate y-axis, defaults to NULL
-#' @param dopng save the plot as a png inside plots folder
+#' @param dopng Deprecated with {nwfscSurvey} 2.1 because providing a non-NULL
+#'   value to `dir` can serve the same purpose as `dopng = TRUE` without the
+#'   potential for errors when `dopng = TRUE` and `dir = NULL`. Thus, users
+#'   no longer have to specify `dopng` to save the plot as a png.
 #' @param w Numeric figure width, defaults to 7
 #' @param h Numeric figure height, defaults to 7
 #' @param ...      Additional arguments for the plots
@@ -20,29 +23,33 @@
 #' @export
 
 PlotFreqData.fn <- function(dir = NULL, dat, inch = 0.15, ylab = "Bins", xlab = "Year", zero2NAs = T, main = NULL,
-                            xlim = NULL, ymax = NULL, dopng = FALSE, w = 7, h = 7, ...) {
+                            xlim = NULL, ymax = NULL, dopng = lifecycle::deprecated(), w = 7, h = 7, ...) {
+
+  if (lifecycle::is_present(dopng)) {
+    lifecycle::deprecate_warn(
+      when = "2.1",
+      what = "nwfscSurvey::PlotMap.fn(dopng =)"
+    )
+  }
+
   dataType <- sum(names(dat) == "ageErr")
   dataType <- ifelse(dataType == 0, "Length", "Age")
 
-  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)
-    }
-    if (is.null(main)) {
-      png(file.path(dir, paste("plots/", dataType, "_Frequency.png", sep = "")), height = h, width = w, units = "in", res = 300)
-    }
-    if (!is.null(main)) {
-      png(file.path(dir, paste("plots/", main, "_", dataType, "_Frequency.png", sep = "")), height = h, width = w, units = "in", res = 300)
-    }
+  plotdir <- file.path(dir, "plots")
+  check_dir(dir = plotdir)
+  main_ <- ifelse(is.null(main), "", paste0(main, "_"))
+  if (!is.null(dir)) {
+    png(
+      filename = file.path(
+        plotdir,
+        paste0(main_, dataType, "_Frequency.png")
+      ),
+      height = h,
+      width = w,
+      units = "in",
+      res = 300
+    )
+    on.exit(dev.off(), add = TRUE)
   }
 
   x <- as.numeric(as.character(dat$year))
@@ -115,7 +122,4 @@ PlotFreqData.fn <- function(dir = NULL, dat, inch = 0.15, ylab = "Bins", xlab =
     z <- c(unlist(dat[, (numLens + 1):ncol(dat)]), min(dat, na.rm = TRUE))
     symbols(c(rep(x, length(y)), 0), c(rep(y, each = length(x)), 0), circles = z, main = name, inches = inch, xlab = xlab, ylab = ylab, xlim = xlim, ...)
   }
-  if (dopng) {
-    dev.off()
-  }
 }
diff --git a/R/plotSexRatio.fn.R b/R/plotSexRatio.fn.R
index 0ee00bf..79e1520 100644
--- a/R/plotSexRatio.fn.R
+++ b/R/plotSexRatio.fn.R
@@ -5,29 +5,45 @@
 #' @param data.type "length" or "age"
 #' @param main ame that will be used to name the saved png
 #' @param circleSize circle size
+#' @param dopng Deprecated with {nwfscSurvey} 2.1 because providing a non-NULL
+#'   value to `dir` can serve the same purpose as `dopng = TRUE` without the
+#'   potential for errors when `dopng = TRUE` and `dir = NULL`. Thus, users
+#'   no longer have to specify `dopng` to save the plot as a png.
 #' @param ...      Additional arguments for the plots
 #'
 #' @author Allan Hicks and Chantel Wetzel
 #' @importFrom graphics abline
 #' @export
 
-PlotSexRatio.fn <- function(dir, dat, data.type = "length", main = NULL, circleSize = 0.1,  ...) {
+PlotSexRatio.fn <- function(dir,
+                            dat,
+                            data.type = "length",
+                            main = NULL,
+                            circleSize = 0.1,
+                            dopng = lifecycle::deprecated(),
+                            ...) {
+  if (lifecycle::is_present(dopng)) {
+    lifecycle::deprecate_warn(
+      when = "2.1",
+      what = "nwfscSurvey::PlotMap.fn(dopng =)"
+    )
+  }
 
-  if(!is.null(dir)) {
-    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)
-    }
-    if (is.null(main)) {
-      png(file.path(dir, "plots", paste(data.type, "_fraction_female.png", sep = "")), height = 7, width = 7, units = "in", res = 300)
-    }
-    if (!is.null(main)) {
-      png(file.path(dir, "plots", paste(main, "_", data.type, "_fraction_female.png", sep = "")), height = 7, width = 7, units = "in", res = 300)
-    }
+  plotdir <- file.path(dir, "plots")
+  check_dir(dir = plotdir)
+  main_ <- ifelse(is.null(main), "", paste0(main, "_"))
+  if (!is.null(dir)) {
+    png(
+      filename = file.path(
+        plotdir,
+        paste0(main_, data.type, "_fraction_female.png")
+      ),
+      height = 7,
+      width = 7,
+      units = "in",
+      res = 300
+    )
+    on.exit(dev.off(), add = TRUE)
   }
 
   round_any <- function(x, accuracy, f = round) {
@@ -57,10 +73,6 @@ PlotSexRatio.fn <- function(dir, dat, data.type = "length", main = NULL, circleS
     inches = circleSize, fg = "red", bg = rgb(1, 0, 0, alpha = 0.5), 
     add = TRUE)
 
-  if (!is.null(dir)) {
-    dev.off()
-  }
-
   test <- dplyr::count(dat, bin, Sex) %>%
     mutate(Proportion = n / sum(n))
 
diff --git a/R/plotVarLengthAtAge.fn.R b/R/plotVarLengthAtAge.fn.R
index efcfaf0..bf36832 100644
--- a/R/plotVarLengthAtAge.fn.R
+++ b/R/plotVarLengthAtAge.fn.R
@@ -13,13 +13,24 @@
 #' @param bins     The bins to put ages into. If NULL then simply uses the ages as recorded.
 #' @param legX legend location for x axis, defaults to "bottomleft"
 #' @param legY legend location for y axis, defaults to NULL
-#' @param dopng TRUE/FALSE whether to save a png file
+#' @param dopng Deprecated with {nwfscSurvey} 2.1 because providing a non-NULL
+#'   value to `dir` can serve the same purpose as `dopng = TRUE` without the
+#'   potential for errors when `dopng = TRUE` and `dir = NULL`. Thus, users
+#'   no longer have to specify `dopng` to save the plot as a png.
 #' @param ...      Additional arguments for the plots
 #'
 #' @author Allan Hicks and Chantel Wetzel
 #' @export
 
-PlotVarLengthAtAge.fn <- function(dir = NULL, dat, main = NULL, ageBin = 1, bySex = T, parStart = c(52, 0.09, 1), estVB = T, bins = NULL, legX = "bottomleft", legY = NULL, dopng = FALSE, ...) {
+PlotVarLengthAtAge.fn <- function(dir = NULL, dat, main = NULL, ageBin = 1, bySex = T, parStart = c(52, 0.09, 1), estVB = T, bins = NULL, legX = "bottomleft", legY = NULL, dopng = lifecycle::deprecated(), ...) {
+
+  if (lifecycle::is_present(dopng)) {
+    lifecycle::deprecate_warn(
+      when = "2.1",
+      what = "nwfscSurvey::PlotMap.fn(dopng =)"
+    )
+  }
+
   # calculate and plot the sd and cv for length at age
   # if you enter estVB=F, then it uses the parStart as the VB parameters
 
@@ -57,24 +68,21 @@ PlotVarLengthAtAge.fn <- function(dir = NULL, dat, main = NULL, ageBin = 1, bySe
     nn <- 2
   }
 
-  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)
-    }
-    if (is.null(main)) {
-      png(file.path(dir, paste("plots/VarLengthAtAge.png", sep = "")), height = 7, width = 7, units = "in", res = 300)
-    }
-    if (!is.null(main)) {
-      png(file.path(dir, paste("plots/", main, "_VarLengthAtAge.png", sep = "")), height = 7, width = 7, units = "in", res = 300)
-    }
+  plotdir <- file.path(dir, "plots")
+  check_dir(dir = plotdir)
+  main_ <- ifelse(is.null(main), "", paste0(main, "_"))
+  if (!is.null(dir)) {
+    png(
+      filename = file.path(
+        plotdir,
+        paste0(main_, "VarLengthAtAge.png")
+      ),
+      height = 7,
+      width = 7,
+      units = "in",
+      res = 300
+    )
+    on.exit(dev.off(), add = TRUE)
   }
 
   par(mfcol = c(2, nn), mar = c(3, 5, 3, 5))
@@ -117,8 +125,6 @@ PlotVarLengthAtAge.fn <- function(dir = NULL, dat, main = NULL, ageBin = 1, bySe
     mtext("CV", side = 4, line = 2.6)
     legend(x = legX, y = legY, c("SD", "CV"), pch = c(16, 3), lty = c(1, 2))
   }
-  if (dopng) {
-    dev.off()
-  }
+
   return(out)
 }
diff --git a/R/plot_proportion.R b/R/plot_proportion.R
index 602237d..39e9a66 100644
--- a/R/plot_proportion.R
+++ b/R/plot_proportion.R
@@ -1,38 +1,39 @@
-#' Plot showing presence and absence per haul by depth or latitute bin
+#' Plot showing presence and absence per haul by depth, latitude, or sex bin
 #'
-#' Uses the data.frame of data values extracted from the data warehouse
-#' by either [PullCatch.fn()] or [PullBio.fn()] to make a table of 
+#' Uses the `data.frame` of data values extracted from the data warehouse
+#' by either [PullCatch.fn()] or [PullBio.fn()] to make a table of
 #' proportion by depth or latitude bins. If biological data are passed
-#' to the function then there is a single option to plot the sex 
+#' to the function then there is a single option to plot the sex
 #' ratio by depth.
 #'
-#' @param data data.frame containing data per haul created by
-#' PullCatch.fn() or biological data created by PullBio.fn() where the
-#' dim input must be "sex". 
+#' @param data `data.frame` containing data per haul created by
+#' [PullCatch.fn()] or biological data created by [PullBio.fn()] where
+#' `dim` must be `dim = "sex"`.
 #' @param dim Dimension of interest, either "depth", "lat", or "sex".
-#' @param dir The directory name to save figures to where they will be save
-#' via file.path(dir, "plots").
-#' @param plot_type Two options area avialable "proportion" or "total" where
-#' the default, "proportion", plot the proportion by depth/latitude with equal
-#' bar widths and the "total" option plot the numbers by depth/latitude were
-#' the bar widths in a production of sampling by depth/latitude.
-#' @param depth_min Minimum depth (in meters)
+#' @dir dir The directory name to save figures to where they will be save
+#' via `file.path(dir, "plots")`.
+#' @param plot_type Two options area available, `"proportion"` or `"total"` where
+#' the default, `"proportion"`, plots the proportion by depth/latitude with equal
+#' bar widths and the `"total"` option plots the numbers by depth/latitude with
+#' the bar widths in relation to sampling by depth/latitude.
+#' @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 depth_bin_width Width of each depth bin (in meters).
+#' @param lat_min Minimum latitude (in decimal degrees).
+#' @param lat_max Maximum latitude (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
+#' are filtered.
 #' @param xlab Label for x-axis. A NULL value will cause the function
-#' to choose either "Depth (m)" or "Latitude (°N)"
+#' to choose either "Depth (m)" or "Latitude (°N)".
 #'
 #' @author Ian G. Taylor and Chantel Wetzel
 #' @importFrom grDevices gray
 #' @export
 #' @examples
+#' \dontrun{
 #' # load WCGBTS data data
 #' data.WCGBTS.ling <- nwfscSurvey::PullCatch.fn(
 #'   Name = "lingcod",
@@ -45,11 +46,11 @@
 #' plot_proportion(data = data.WCGBTS.ling, dim = "lat")
 #' plot_proportion(data = data.WCGBTS.ling, dim = "depth")
 #' plot_proportion(data = bio.WCGBTS.ling, dim = "sex")
-#' 
+#' }
 plot_proportion <- function(data,
-  dim = c("depth", "lat", "sex")[1],
+  dim = c("depth", "lat", "sex"),
   dir = NULL,
-  plot_type = c('proportion', 'total')[1],
+  plot_type = c("proportion", "total"),
   depth_min = 50,
   depth_max = NULL,
   depth_bin_width = 25,
@@ -60,17 +61,12 @@ plot_proportion <- function(data,
   xlab = NULL) {
 
   # check inputs
-  if (!dim %in% c("depth", "lat", "sex")) {
-    message(
-      "The dim function input needs to be either depth, lat, or sex.")
-    break()
-  }
+  dim <- match.arg(dim)
+  dim <- match.arg(plot_type)
 
   if (dim == "sex"){
     if (sum(colnames(data) == "Sex") != 1) {
-      message(
-        "The data function input needs to be a biological data file.")
-      break()
+      stop("The data function input needs to be a biological data file.")
     }
   }
 
@@ -149,18 +145,13 @@ plot_proportion <- function(data,
     filename <- paste0("sex_", plot_type, "_by_depth.png")
   }
 
-  if (!is.null(dir)) {     
-    if (!file.exists(dir)) {
-      stop("The dir argument leads to a location", ",\ni.e., ", dir, ", that doesn't exist.")
-    }
+  if (!is.null(dir)) {
     plotdir <- file.path(dir, paste("plots", sep = ""))
-    plotdir.isdir <- file.info(plotdir)$isdir
-    if (is.na(plotdir.isdir) | !plotdir.isdir) {
-      dir.create(plotdir)
-    }
+    check_dir(plotdir)
     png(file.path(dir, "plots", filename),
       height = 7, width = 7, units = "in", res = 300
     )
+    on.exit(dev.off())
   }
   
   # make table
@@ -201,8 +192,4 @@ plot_proportion <- function(data,
   }
   abline(h = 0.5, col = 'white', lty = 1, lwd = 4)
 
-  # close PNG if it was used
-  if (!is.null(dir)) {
-    dev.off()
-  }
 }
diff --git a/vignettes/nwfscSurvey.Rmd b/vignettes/nwfscSurvey.Rmd
index 4ae45cb..410c709 100644
--- a/vignettes/nwfscSurvey.Rmd
+++ b/vignettes/nwfscSurvey.Rmd
@@ -107,7 +107,7 @@ PlotBio.fn(dir = getwd(),
            main = "NWFSC shelf-slope bottom trawl survey",
            ...)
 ```
-The Biomass.fn returns a list with the second element containing the design-based index of abundance. The design based index is calculated based on the defined stratas. The function writes a csv file inside the dir input location to a "forSS" folder. The PlotBio.fn plots the calculated design based index from the Biomass.fn. If the dopng is set to true a "plot" folder will be created in the directory location and a png of the plot will be saved.
+The Biomass.fn returns a list with the second element containing the design-based index of abundance. The design based index is calculated based on the defined stratas. The function writes a csv file inside the dir input location to a "forSS" folder. The PlotBio.fn plots the calculated design based index from the Biomass.fn. If `dir` does not equal `NULL`, then a "plot" folder will be created in the directory location and a png of the plot will be saved.
 
 
 #### Length composition data
@@ -141,12 +141,11 @@ PlotFreqData.fn(dir = getwd(),
                 dat = Lengths, 
                 ylim = c(0,50), 
                 yaxs = "i",
-                ylab = "Length (cm)", 
-                dopng = TRUE,
+                ylab = "Length (cm)",
                 ...)
 
 ```
-If the dopng is set to true a "plot" folder will be created in the directory location and a png of the plot will be saved. 
+If `dir` does not equal `NULL`, then a "plot" folder will be created in the directory location and a png of the plot will be saved. 
 
 
 #### Marginal age composition data
@@ -176,11 +175,10 @@ To plot the age frequency data:
 PlotFreqData.fn(dir = getwd(), 
                 dat = Ages, 
                 ylim = c(0,100),
-                ylab = "Age", 
-                dopng = TRUE,
+                ylab = "Age",
                 ...)
 ```
-If the dopng is set to true a "plot" folder will be created in the directory location and a png of the plot will be saved.
+If `dir` is not `NULL`, then a "plot" folder will be created in the directory location and a png of the plot will be saved.
 
 #### Conditional-age-at-length data
 To calculate conditional-age-at-length data formatted for SS: