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.
pfmc-assessments · Nov 22, 2022 · 4c830bd · 4c830bd
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diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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()
   }
 }