add option to allow asapretro results to be plotted

Author: cmlegault

DESCRIPTION

@@ -1,21 +1,21 @@
-Package: simASAP
-Title: Simulate ASAP Data Sets and Optionally Run Them
-Version: 0.0.0.9009
-Authors@R: 
-    person(given = "Chris",
-           family = "Legault",
-           role = c("aut", "cre"),
-           email = "[email protected]")
-Description: Starting with a successfully run ASAP data file, conduct self-test 
-  by generating data with measurement errors that follow the prescribed distribution 
-  type and level of uncertainty. Can optionally run ASAP on each created data set. 
-  Can plot Freport, recruitment, and spawning stock biomass time series estimates from
-  each simulated data set and compare to true values. Includes example script showing
-  how to use functions and sample ASAP data files.
-License: MIT + file LICENSE
-Encoding: UTF-8
-LazyData: true
-RoxygenNote: 6.1.1
-Imports: 
-    dplyr,
-    ggplot2
+Package: simASAP
+Title: Simulate ASAP Data Sets and Optionally Run Them
+Version: 0.0.0.9010
+Authors@R: 
+    person(given = "Chris",
+           family = "Legault",
+           role = c("aut", "cre"),
+           email = "[email protected]")
+Description: Starting with a successfully run ASAP data file, conduct self-test 
+  by generating data with measurement errors that follow the prescribed distribution 
+  type and level of uncertainty. Can optionally run ASAP on each created data set. 
+  Can plot Freport, recruitment, and spawning stock biomass time series estimates from
+  each simulated data set and compare to true values. Includes example script showing
+  how to use functions and sample ASAP data files.
+License: MIT + file LICENSE
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 6.1.1
+Imports: 
+    dplyr,
+    ggplot2

NAMESPACE

@@ -1,6 +1,6 @@
-# Generated by roxygen2: do not edit by hand
-
-export(PlotSimASAP)
-export(ReadASAP3DatFile)
-export(SimASAP)
-export(WriteASAP3DatFile)
+# Generated by roxygen2: do not edit by hand
+
+export(PlotSimASAP)
+export(ReadASAP3DatFile)
+export(SimASAP)
+export(WriteASAP3DatFile)

R/plot_sim_ASAP.R

@@ -1,85 +1,88 @@
-#' PlotSimASAP
-#'
-#' Comparison plots of SSB, Freport, and Recruitment from SimASAP runs with true values.
-#'
-#' @param wd directory where original ASAP run is located
-#' @param asap.name base name of original dat file (without the .dat extension)
-#' @param whichsim vector of numbers for which simulated data sets to plot
-#' @param od location where new data sets are saved (defaults to sim subdirectory of wd)
-#' @param save.plots will save png files if TRUE (default = FALSE)
-#' @param returnwhat valid options are "results", "plot", "both", "nothing" (default="nothing")
-#' @export
-
-PlotSimASAP <- function(wd, asap.name, whichsim, od=file.path(wd, "sim"), save.plots=FALSE, returnwhat="nothing"){
-
-  # check for valid returnwhat value
-  validoptions <- c("results", "plot", "both", "nothing")
-  if (!(returnwhat %in% validoptions)){
-    return(paste("Error: returnwhat must be one of:", paste(validoptions, collapse = ", ")))
-  }
-
-  # check for files
-  if (!file.exists(file.path(wd, paste0(asap.name, ".rdat")))){
-    return(paste0("Error: ", asap.name, ".rdat not located in ", wd))
-  }
-
-  simrdats <- FALSE
-  for (isim in 1:length(whichsim)){
-    if(file.exists(file.path(od, paste0(asap.name, "_sim", isim, ".rdat")))){
-      simrdats <- TRUE
-    }
-  }
-  if (simrdats == FALSE){
-    return(paste0("Error: no files ", asap.name, "_sim(whichsim).rdat located in ", od))
-  }
-
-  # get true values
-  asap <- dget(file.path(wd, paste0(asap.name, ".rdat")))
-  years <- seq(asap$parms$styr, asap$parms$endyr)
-  nyears <- length(years)
-  res <- data.frame(Source = "True",
-                    metric = rep(c("SSB", "Freport", "Recruits"), each=nyears),
-                    Year = rep(years, 3),
-                    value = c(asap$SSB, asap$F.report, asap$N.age[,1]))
-
-  # get simulated values
-  for (isim in 1:length(whichsim)){
-    mysim <- whichsim[isim]
-    fname <- file.path(od, paste0(asap.name, "_sim", mysim, ".rdat"))
-    if (file.exists(fname)){
-      asap <- dget(fname)
-      simres <- data.frame(Source = paste0("Sim", mysim),
-                           metric = rep(c("SSB", "Freport", "Recruits"), each=nyears),
-                           Year = rep(years, 3),
-                           value = c(asap$SSB, asap$F.report, asap$N.age[,1]))
-      res <- rbind(res, simres)
-    }
-  }
-
-  # make plot and optionally save
-  p <- ggplot2::ggplot(res, aes(x=Year, y=value, color=Source)) +
-    geom_line() +
-    geom_point(data=dplyr::filter(res, Source == "True")) +
-    facet_wrap(~metric, ncol = 1, scales = "free_y") +
-    expand_limits(y=0) +
-    theme_bw()
-
-  if (length(unique(res$Source)) > 5){
-    p <- p + theme(legend.position = "none")
-  }
-
-  print(p)
-  if (save.plots == TRUE){
-    ggplot2::ggsave(filename = file.path(od, "comparisonplots.png"), p)
-  }
-
-  myreturn <- NULL
-  if (returnwhat == "results"){
-    myreturn <- res
-  } else if (returnwhat == "plot"){
-    myreturn <- p
-  } else if (returnwhat == "both"){
-    myreturn <- list(res = res, p = p)
-  }
-  return(myreturn)
-}
+#' PlotSimASAP
+#'
+#' Comparison plots of SSB, Freport, and Recruitment from SimASAP runs with true values.
+#'
+#' @param wd directory where original ASAP run is located
+#' @param asap.name base name of original dat file (without the .dat extension)
+#' @param whichsim vector of numbers for which simulated data sets to plot
+#' @param od location where new data sets are saved (defaults to sim subdirectory of wd)
+#' @param asapretro logical flag for whether to add "_000" before ".rdat" when selecting files (default=FALSE)
+#' @param save.plots will save png files if TRUE (default = FALSE)
+#' @param returnwhat valid options are "results", "plot", "both", "nothing" (default="nothing")
+#' @export
+
+PlotSimASAP <- function(wd, asap.name, whichsim, od=file.path(wd, "sim"), asapretro=FALSE, save.plots=FALSE, returnwhat="nothing"){
+
+  # check for valid returnwhat value
+  validoptions <- c("results", "plot", "both", "nothing")
+  if (!(returnwhat %in% validoptions)) {
+    return(paste("Error: returnwhat must be one of:", paste(validoptions, collapse = ", ")))
+  }
+
+  # check for files
+  rdat_ext <- ifelse(asapretro == FALSE, ".rdat", "_000.rdat")
+  
+  if (!file.exists(file.path(wd, paste0(asap.name, rdat_ext)))) {
+    return(paste0("Error: ", asap.name, rdat_ext, " not located in ", wd))
+  }
+
+  simrdats <- FALSE
+  for (isim in 1:length(whichsim)) {
+    if(file.exists(file.path(od, paste0(asap.name, "_sim", isim, rdat_ext)))) {
+      simrdats <- TRUE
+    }
+  }
+  if (simrdats == FALSE) {
+    return(paste0("Error: no files ", asap.name, "_sim(whichsim)", rdat_ext," located in ", od))
+  }
+
+  # get true values
+  asap <- dget(file.path(wd, paste0(asap.name, rdat_ext)))
+  years <- seq(asap$parms$styr, asap$parms$endyr)
+  nyears <- length(years)
+  res <- data.frame(Source = "True",
+                    metric = rep(c("SSB", "Freport", "Recruits"), each=nyears),
+                    Year = rep(years, 3),
+                    value = c(asap$SSB, asap$F.report, asap$N.age[,1]))
+
+  # get simulated values
+  for (isim in 1:length(whichsim)) {
+    mysim <- whichsim[isim]
+    fname <- file.path(od, paste0(asap.name, "_sim", mysim, rdat_ext))
+    if (file.exists(fname)) {
+      asap <- dget(fname)
+      simres <- data.frame(Source = paste0("Sim", mysim),
+                           metric = rep(c("SSB", "Freport", "Recruits"), each=nyears),
+                           Year = rep(years, 3),
+                           value = c(asap$SSB, asap$F.report, asap$N.age[,1]))
+      res <- rbind(res, simres)
+    }
+  }
+
+  # make plot and optionally save
+  p <- ggplot2::ggplot(res, aes(x=Year, y=value, color=Source)) +
+    geom_line() +
+    geom_point(data=dplyr::filter(res, Source == "True")) +
+    facet_wrap(~metric, ncol = 1, scales = "free_y") +
+    expand_limits(y=0) +
+    theme_bw()
+
+  if (length(unique(res$Source)) > 5){
+    p <- p + theme(legend.position = "none")
+  }
+
+  print(p)
+  if (save.plots == TRUE){
+    ggplot2::ggsave(filename = file.path(od, "comparisonplots.png"), p)
+  }
+
+  myreturn <- NULL
+  if (returnwhat == "results"){
+    myreturn <- res
+  } else if (returnwhat == "plot"){
+    myreturn <- p
+  } else if (returnwhat == "both"){
+    myreturn <- list(res = res, p = p)
+  }
+  return(myreturn)
+}