R/compareResults.ManagementQuantities.R

In wStockhausen/rCompTCMs: Package to compare TCSAM02, rsimTCSAM, and TCSAM2013 model runs

#'
#' @title Compare management quantities among model scenarios
#'
#' @description Function to compare management quantities among model scenarios.
#'
#'@param objs - single model resLst object, or named list of them
#' @param base - name or index of base case for difference calculations
#'@param colour_scale - ggplot2 colour scale to substitute for default (if not NULL)
#'@param fill_scale - ggplot2 fill scale to substitute for default (if not NULL)
#'@param verbose - flag (T/F) to print diagnostic info
#'
#'@return a list of ggplot2 plot objects
#'
#'@details Uses [rTCSAM02::getMDFR.ManagementQuantities()] to get the management quantities calculated
#'in each model case. Uses [computeDiffs()] with \code{sense=1} to compute differences with base case.
#'
#' @importFrom cowplot get_legend plot_grid
#' @importFrom dplyr filter mutate
#' @importFrom stringr str_replace
#' @importFrom tibble tribble
#' @importFrom tidyr pivot_longer
#' @importFrom tidyselect matches
#'
#' @importFrom rTCSAM02 getMDFR.ManagementQuantities
#'
#' @import ggplot2
#'
#' @md
#'
#'@export
#'
compareResults.ManagementQuantities<-function(objs,
                                              base=1,
                                              colour_scale=NULL,
                                              fill_scale=NULL,
                                              verbose=FALSE){
  plots = list();

  mdfr = rTCSAM02::getMDFR.ManagementQuantities(objs,verbose=verbose);

  #--plot values
  categories = tibble::tribble(~category,~label,
                               "recruitment", "Millions",
                               "biomass",     "1,000's t",
                               "fishing rate",expression(yr^{-1}),
                               "catch",       "1,000's t")
  ps=list();
  for (ic in 1:nrow(categories)){
    dfr = mdfr %>% dplyr::filter(category==categories$category[ic]);
    p = ggplot(dfr,aes(x=type,y=val,colour=case,fill=case))+
                    geom_col(position="dodge") +
                    facet_grid(.~category,scales="free") +
                    scale_colour_viridis_d(aesthetics=c("colour","fill"))+
                    labs(y=categories$label[[ic]]);
    if (!is.null(colour_scale)) p = p + colour_scale
    if (!is.null(fill_scale))   p = p + fill_scale;
    if (ic==1) lgnd = cowplot::get_legend(p);
    p = p + theme(panel.background=element_rect(colour="black",fill="white"),
                  legend.position="none",
                  axis.title.x=element_blank());
    ps[[ic]] = p;
    rm(dfr,p)
  }
  pg1 = cowplot::plot_grid(plotlist=ps,nrow=2,byrow=TRUE)
  pg2 = cowplot::plot_grid(pg1,lgnd,nrow=1,rel_widths=c(4,1))
  cap1<-paste0("\n  \nFigure &&figno. Comparison of management quantities among model scenarios.  \n  \n");
  plots[[cap1]] = pg2;
  rm(categories,ps,lgnd,pg1,pg2)

  #--calculate % differences relative to the base case,
  #--pivot back to long form,
  #--revert "case" names to original names
  mdfr1 = computeDiffs(mdfr,
                       base=base,
                       cast="process+fleet+category+type",
                       type="percent",
                       sense=1) %>%
           tidyr::pivot_longer(cols=tidyselect::matches("^.*-"),names_to="case",values_to="val") %>%
           dplyr::mutate(case=stringr::str_replace(case,pattern="^.*-",""));

  base = attr(mdfr1,"base",exact=TRUE);#--name of base case
  #--plot % differences relative to the base case
  categories = tibble::tribble(~category,~label,
                               "recruitment", "% difference from base",
                               "biomass",     "% difference from base",
                               "fishing rate","% difference from base",
                               "catch",       "% difference from base")
  ps=list();
  for (ic in 1:nrow(categories)){
    dfr = mdfr1 %>% dplyr::filter(category==categories$category[ic]);
    p = ggplot(dfr,aes(x=type,y=val,colour=case,fill=case))+
                    geom_col(position="dodge") +
                    facet_grid(.~category,scales="free") +
                    scale_colour_viridis_d(aesthetics=c("colour","fill"))+
                    labs(y=categories$label[[ic]]);
    if (!is.null(colour_scale)) p = p + colour_scale
    if (!is.null(fill_scale))   p = p + fill_scale;
    if (ic==1) lgnd = cowplot::get_legend(p);
    p = p + theme(panel.background=element_rect(colour="black",fill="white"),
                  legend.position="none",
                  axis.title.x=element_blank());
    ps[[ic]] = p;
  }
  pg1 = cowplot::plot_grid(plotlist=ps,nrow=2,byrow=TRUE)
  pg2 = cowplot::plot_grid(pg1,lgnd,nrow=1,rel_widths=c(4,1))
  cap2<-paste0("\n  \nFigure &&figno. Comparison of differences in management quantities among model scenarios, relative to the base case (",base,").  \n  \n")
  plots[[cap2]] = pg2;

  return(plots);
}