@MOshima-PIFSC requested changes #94

R/SSplotEnsemble.R

@@ -1,6 +1,6 @@
 #' Model ensemble plots
 #'
-#' Plots model ensembles and forecasts with uncertainty represented by MVLN or 
+#' Plots model ensembles and forecasts with uncertainty represented by MVLN or
 #' MCMC posteriors
 #'
 #' @param kb `kb` type output created by `SSdeltaMVLN()`
@@ -9,19 +9,19 @@
 #'  \item `"stock"` Fish Population
 #'  \item `"harvest"` Harvest Rate
 #'  \item `"SSB"` Spawning Stock Biomass
-#'  \item `"F"` Fishing Mortality 
+#'  \item `"F"` Fishing Mortality
 #'  \item `"Recr"` Recruitment
 #'  \item `"Catch"` Total Catch
-#' } 
+#' }
 #' @param models option to manually subset the models in `kb[["run"]]`
-#' @param quantiles quantiles for uncertainty in plots. Input as a list, 
+#' @param quantiles quantiles for uncertainty in plots. Input as a list,
 #' default is the 95TH percentile: `list(c(0.025, 0.975))`
 #' @param ylabs y-axis labels for quants
-#' @param shadealpha Transparency adjustment used to make uncertainty regions, 
+#' @param shadealpha Transparency adjustment used to make uncertainty regions,
 #' default is 0.3
-#' @param indexQlabel TRUE/FALSE include labels for indices. Default is TRUE 
+#' @param indexQlabel TRUE/FALSE include labels for indices. Default is TRUE
 #' (currently not used)
-#' @param indexQdigits Number of significant digits for catchability in legend. 
+#' @param indexQdigits Number of significant digits for catchability in legend.
 #' Default is 4
 #' @param endyrvec Optional single year or vector of years representing the
 #' final year of values to show for each model. By `"default"` it is set to the
@@ -97,8 +97,7 @@ SSplotEnsemble <- function(kb,
                            mcmcVec = FALSE,
                            indexQlabel = TRUE,
                            indexQdigits = 4,
-                           legendindex = NULL) { 
-
+                           legendindex = NULL) {
   # plot different fits to a single index of abundance
 
   # Parameter DEPRECATION checks

R/SSplotGeneric.R

@@ -1,84 +1,82 @@
-
-
 #' Generic SSplot function
-#' 
-#' Generalized version of ss3diags SSplots functions. Not intended for 
+#'
+#' Generalized version of ss3diags SSplots functions. Not intended for
 #' production
-#' 
-#' @param pwidth 
+#'
+#' @param pwidth
 #' Default width of plot printed to plot in units of `punits`
-#' 
-#' @param pheight 
+#'
+#' @param pheight
 #' Height of plot printed to plot in units of `punits `
-#' 
-#' @param punits 
+#'
+#' @param punits
 #' Measurement units for `pwidth` and `pheight`. Default is `"in"`.
 #' \itemize{
 #'  \item `"px"` (pixels)
 #'  \item `"in"` (inches)
 #'  \item `"cm"` (centimeters)
 #'  \item `"mm"` (millimeters)
 #' }
-#' 
-#' @param res 
+#'
+#' @param res
 #' Resolution for plots printed to files.
-#' 
-#' @param ptsize 
+#'
+#' @param ptsize
 #' Point size for plotted text in plots printed in files. See `help("png")`
 #' for more details
-#' 
-#' @param cex.main 
+#'
+#' @param cex.main
 #' Character expansion for plot titles.
-#' 
-#' @param plotdir 
-#' Directory where output plot file will be written. By default, 
+#'
+#' @param plotdir
+#' Directory where output plot file will be written. By default,
 #' it will be the directory where the model was run.
-#' 
-#' @param filenameprefix 
+#'
+#' @param filenameprefix
 #' Additional text to append to output plot file name.
 #' It will be separated from default name by an underscore.
-#' 
-#' @param par 
-#' A numerical vector of the form c(bottom, left, top, right) which 
-#' gives the number of lines of margin to be specified on the four sides of 
-#' the plot,which is passed to `par()`. Entering `NULL` passes plot's default 
+#'
+#' @param par
+#' A numerical vector of the form c(bottom, left, top, right) which
+#' gives the number of lines of margin to be specified on the four sides of
+#' the plot,which is passed to `par()`. Entering `NULL` passes plot's default
 #' `par()` values (which depends on whether the main title is included or not)
-#' 
-#' @param verbose 
+#'
+#' @param verbose
 #' Flag to print additional diagnostic messages to R console
-#' 
-#' @param plot 
-#' DEPRECATED. By default, TRUE, Plots (and subplots) are drawn to the 
-#' plot device. The option to explicitly disable this option (FALSE), is not 
+#'
+#' @param plot
+#' DEPRECATED. By default, TRUE, Plots (and subplots) are drawn to the
+#' plot device. The option to explicitly disable this option (FALSE), is not
 #' implemented. This option flag will be defunct in a future version
-#' 
-#' @param print 
+#'
+#' @param print
 #' DEPRECATED, please use `print_plot`.
-#' 
-#' @param print_plot 
+#'
+#' @param print_plot
 #' Flag to enable plot graphic device to print to PNG or PNG files.
-#' 
-#' @param png 
+#'
+#' @param png
 #' DEPRECATED. Please use `use_png`.
-#' 
-#' @param use_png 
+#'
+#' @param use_png
 #' Enables plots to be generated to PNG files. Defaults to print value
-#' 
-#' @param pdf 
+#'
+#' @param pdf
 #' DEPRECATED. Please use `use_pdf`.
-#' 
-#' @param use_pdf 
+#'
+#' @param use_pdf
 #' Enables plots to be generated to pdf file.
-#' 
-#' @param new 
+#'
+#' @param new
 #' Deprecated. New plot windows are created by default (TRUE), and the
 #' option to disable this, via FALSE, is unused.
-#' 
-#' @param add 
+#'
+#' @param add
 #' suppresses `par()` to create multiplot figs
-#' 
+#'
 #' @keywords internal
-#' 
+#'
 SSplotGeneric <- function(pwidth = 6.5,
                           pheight = 5.0,
                           punits = "in",
@@ -98,45 +96,44 @@ SSplotGeneric <- function(pwidth = 6.5,
                           use_pdf = FALSE,
                           new = TRUE,
                           add = FALSE) {
-
   stop("SSplotGeneric not implemented")
 }
 
 
-#' Legend parameters for Generic SSplot 
+#' Legend parameters for Generic SSplot
 #'
-#' Generalized version of ss3diags SSplots functions specfic to plot legend 
+#' Generalized version of ss3diags SSplots functions specfic to plot legend
 #' parameters. Not intended for production.
 #'
-#' @param legend 
+#' @param legend
 #' Flag to enable legend to plot. TRUE by default.
-#' 
-#' @param legendlabels 
+#'
+#' @param legendlabels
 #' Optional vector of labels to include in legend.
-#' 
-#' @param legendloc 
-#' Location of legend. Either a string like "topleft" or a vector of two 
+#'
+#' @param legendloc
+#' Location of legend. Either a string like "topleft" or a vector of two
 #' numeric values representing the fraction of the maximum in the x and y
-#' dimensions, respectively. See `help("legend")` for more info on the 
+#' dimensions, respectively. See `help("legend")` for more info on the
 #' string options.
-#' 
-#' @param legendorder 
-#' Optional vector of model numbers that can be used to have the legend 
+#'
+#' @param legendorder
+#' Optional vector of model numbers that can be used to have the legend
 #' display the model names in an order that is different than that
 #' which is represented in the summary input object.
-#' 
-#' @param legendncol 
+#'
+#' @param legendncol
 #' Number of columns for the legend.
-#' 
-#' @param legendcex 
+#'
+#' @param legendcex
 #' Allows to adjust legend cex
-#' 
-#' @param legendsp 
+#'
+#' @param legendsp
 #' Space between legend labels
-#' 
-#' @param legendindex 
+#'
+#' @param legendindex
 #' Allows to add legend for selected indices (plots)
-#' 
+#'
 #' @keywords internal
 #'
 SSplotGenericLegend <- function(legend = TRUE,
@@ -147,7 +144,6 @@ SSplotGenericLegend <- function(legend = TRUE,
                                 legendcex = 1,
                                 legendsp = 0.9,
                                 legendindex = NULL) {
-
   stop("SSplotGenericLegend not implemented")
 }
 
@@ -157,44 +153,44 @@ SSplotGenericLegend <- function(legend = TRUE,
 #' Generalized version of ss3diags SSplots functions to specify to `par()` or
 #' to pass plot attributes. Not intended for production.
 #'
-#' @param col 
+#' @param col
 #' Optional vector of colors to be used for lines. Input NULL
-#' 
-#' @param pch 
+#'
+#' @param pch
 #' Optional vector of plot character values
-#' 
-#' @param lty 
+#'
+#' @param lty
 #' Optional vector of line types
-#' 
-#' @param lwd 
+#'
+#' @param lwd
 #' Optional vector of line widths
-#' 
-#' @param tickEndYr 
-#' [Logical][base::logical] flag: set TRUE or FALSE to switch to turn 
+#'
+#' @param tickEndYr
+#' [Logical][base::logical] flag: set TRUE or FALSE to switch to turn
 #' on/off extra axis mark at final year in timeseries plots.
-#' 
-#' @param ylimAdj 
+#'
+#' @param ylimAdj
 #' Multiplier for ylim parameter. Allows additional white space.
-#' 
-#' @param xlim 
-#' Optional, years to use for x-axis. Default value NULL (or "default"), 
+#'
+#' @param xlim
+#' Optional, years to use for x-axis. Default value NULL (or "default"),
 #' uses all years available.
-#' 
-#' @param xaxs 
+#'
+#' @param xaxs
 #' Choice of xaxs parameter See `?par` for more info.
-#' 
-#' @param yaxs 
+#'
+#' @param yaxs
 #' Choice of yaxs parameter. See `?par` for more info.
-#' 
-#' @param xylabs 
-#' [Logical][base::logical] flag: set TRUE or FALSE to include x- and 
+#'
+#' @param xylabs
+#' [Logical][base::logical] flag: set TRUE or FALSE to include x- and
 #' y-axis labels to the plot. Defaults to TRUE
-#' 
-#' @param type 
+#'
+#' @param type
 #' The type of plot to be drawn. For more details, see [`plot`][base::plot].
-#' 
+#'
 #' @keywords internal
-#' 
+#'
 SSplotGenericPar <- function(col = NULL,
                              pch = NULL,
                              lty = 1,
@@ -215,27 +211,26 @@ SSplotGenericPar <- function(col = NULL,
 #' Generalized version of ss3diags SSplots functions to specify uncertainty.
 #' Not intended for production.
 #'
-#' @param uncertainty 
+#' @param uncertainty
 #' Logical flag to enable plots with uncertainty intervals. Either a single
-#' TRUE/FALSE value, or a vector of TRUE/FALSE values around SSB or F 
-#' estimated timeseries, or a set of integers corresponding to 
+#' TRUE/FALSE value, or a vector of TRUE/FALSE values around SSB or F
+#' estimated timeseries, or a set of integers corresponding to
 #' the choice of models.
-#' 
-#' @param mcmcVec 
+#'
+#' @param mcmcVec
 #' Logical vector of TRUE/FALSE values (or single value) indicating
 #' whether input values are from MCMC or to use normal distribution around
 #' MLE.
-#' 
+#'
 #' @param models Optional subset of the models of `summaryoutput` (or a similar
-#' field with a different name): a list created by the function 
-#' [r4ss::SSsummarize]. Either `"all"` or a vector of numbers indicating 
+#' field with a different name): a list created by the function
+#' [r4ss::SSsummarize]. Either `"all"` or a vector of numbers indicating
 #' columns in summary tables.
-#' 
+#'
 #' @keywords internal
 #'
-SSplotGenericUncertainty <- function (uncertainty = TRUE,
-                                      mcmcVec = FALSE,
-                                      models = "all") {
-
+SSplotGenericUncertainty <- function(uncertainty = TRUE,
+                                     mcmcVec = FALSE,
+                                     models = "all") {
   stop("SSplotGenericUncertainty not implemented")
-}
+}