R/PlotStackedBarChart.R

In bmcnellis/RSFIA: FIA Tree Mortality Analysis

#' @title Plots a stacked barchart
#' @description TODO: this
#'
#' @param by X-variable, either 'section' or 'ftype'
#' @param mort_df data to plot, can be NULL for package data
#' @param drop_no_mort Flag to drop 'no mortality' plots
#' @param split Split plot into background/outlier
#' @param clear_plots Flag to clear previous plots
#' @param excl_dom_ftype Flag to drop 'dominant' ftypes, see details
#'
#' @details
#'
#' Dominant ftypes (n plots > 400):
#'
#' Douglas-fir, Ponderosa pine, Lodgepole pine, Pinyon / juniper woodland,
#' California mixed conifer, Engelmann spruce / subalpine fir, Aspen
#'
#'
#' @export
#' @examples PlotStackedBarChart()
PlotStackedBarChart <- function(by, mort_df = NULL,
                                drop_no_mort = F, split = F, clear_plots = F,
                                excl_dom_ftype = F) {
  if (!(by %in% c('ftype', 'section'))) stop ('by must be ftype or section')
  # Setup
  if (is.null(mort_df)) {
    pkg_df <- PrepPlotEnvir(ret = 'plots', clear = clear_plots)
  } else {
    pkg_df <- mort_df
    PrepPlotEnvir(ret = F, clear = clear_plots)
  }
  ytag <- '10 Year Mortality Rate'
  if (by == 'section') {
    by_var <- 'Section'
    FUN_df <- pkg_df[, c('Cleland_section', 'dominant_AGENTCD', 'percent_AGENTCD',
                         'mort_outlier')]
    FUN_df[, 5] <- as.factor(KeyClelandCode(FUN_df$Cleland_section, lvl = 'section'))
    if (excl_dom_ftype) warning('Ignoring excl_dom_ftype flag')
  } else if (by == 'ftype') {
    by_var <- 'Forest_Type'
    mod_df <- BinUncommonForestType(mort_df = pkg_df)
    message('Forest types binned into Other:')
    print(names(mod_df[[2]]))
    cat('\n')
    message('Total counts:')
    cat(sum(mod_df[[2]]), '\n')
    pkg_df <- mod_df[[1]]
    FUN_df <- pkg_df[, c('forest_type', 'dominant_AGENTCD', 'percent_AGENTCD',
                         'mort_outlier')]
    #FUN_df <- SubDominantForestType(mort_df = FUN_df, sub = F, n_plot_cutoff = 400)
    FUN_df[, 5] <- FUN_df[, 1]
  }
  colnames(FUN_df)[5] <- c(by_var)
  if (drop_no_mort) {
    FUN_df <- FUN_df[-which(FUN_df$dominant_AGENTCD == 'No Mortality'), ]
  }

  full_df <- FUN_df
  high_df <- FUN_df[FUN_df$mort_outlier, ]
  back_df <- FUN_df[!FUN_df$mort_outlier, ]

  # Return code:
  if (split) {
    lab1 <- "Dominant\nBackground\nMortality\nAgent"
    lab2 <- "Dominant\nOutlier\nMortality\nAgent"
    s1 <- PlotStacked(back_df, by = by_var,
                      llab = lab1, bar_fill = 'dominant_AGENTCD',
                      yylab = '')
    s2 <- PlotStacked(high_df, by = by_var,
                      llab = lab2, bar_fill = 'dominant_AGENTCD',
                      yylab = 'Number of plots')
    Multiplot(s1, s2)
  } else {
    lab0 <- "Dominant\nMortality\nAgent"
    s0 <- PlotStacked(full_df, by = by_var,
                      llab = lab0, bar_fill = 'dominant_AGENTCD',
                      yylab = 'Number of plots')
    print(s0)
  }
  invisible()
}
#' @describeIn PlotStackedBarChart Wrapper for dominant ftype stacked bar
#' @family plot_wrappers
#' @export
PlotStackedDomForType <- function() {
  mort_df <- SubDominantForestType(sub = T)
  PlotStackedBarChart(by = 'ftype', mort_df = mort_df,
                      drop_no_mort = T, split = T, clear_plots = T)
  invisible()
}
#' @describeIn PlotStackedBarChart Wrapper for non-dominant ftype stacked bar
#' @family plot_wrappers
#' @export
PlotStackedUncommForType <- function() {
  mort_df <- SubDominantForestType(sub = F)
  PlotStackedBarChart(mort_df = mort_df, by = 'ftype',
                      drop_no_mort = T, split = T, clear_plots = T)
  invisible()
}