R/treeMap.R

In KateMMiller/forestMIDNarch: Package for importing, joining and querying MS Access based MIDN forest database tables.

#' @include treeMapPrep.R
#' @title treeMap: creates plot of trees by status and size
#'
#' @importFrom dplyr select filter arrange mutate summarise group_by
#' @importFrom magrittr %>%
#' @import ggplot2
#'
#' @description This function converts tree distance and azimuth values to coordinates and plots the coordinates
#' of live or dead trees. Trees are color coded by status, and size is relative to DBH. Works best with data.frame
#' derived from joinLocEvent and joinTreeData, then cleaned up with treeMapPrep(). Requires a data.frame with the
#' following fields: Plot_Name, Tree_Number_MIDN, Distance, Azimuth, Orientation, Status_ID (n=7), DBH, x, and y.
#'
#' @return Returns a map of trees on a given plot. Trees are color coded by status, with AB= Alive Broken,
#' AF= Alive Fallen, AL= Alive Leaning, AS= Alive Standing, DB= Dead Broken, DL= Dead Leaning, and DS= Dead Standing.
#' The size of the circle is relative to the DBH of the tree. The plot is relative to the plot Orientation, which
#' is North (360 degrees) on flat lands, and upslope on slopes.
#'
#' @examples
#' importData()
#' # Compile data to have the fields that feed into the treeMap and treeMapPrep functions
#' park_plots<-joinLocEvent(from=2015, to=2015, output='verbose')[,c('Event_ID','Orientation')]
#' tree_data<-joinTreeData(from=2015, to=2015)
#' tree_data2<-merge(tree_data,park_plots,by="Event_ID",all.x=T)
#'
#' # Select a plot to map
#' tree_plot<-tree_data2 %>% filter(Plot_Name=='RICH-064') %>% droplevels()
#' treeMap(tree_plot)
#'
#' # Or create a list of plots to iterate through and save each to a .pdf file
#' #--- Create function for plotting and saving maps
#' saveTreeMaps<-function(path,df){
#'   plotname<-as.character(unique(df$Plot_Name))
#'   pdf(file=paste0(path, plotname,".pdf"))
#'   treeMap(df)
#'   dev.off()
#' }
#'
#' #--- Create list of plots to iterate through
#' plots<-as.character(unique(tree_data2$Plot_Name)) #list of plots to iterate
#' filepath = c('./treeMap_output/')
#'
#' #--- Loop through list of plots
#' for (i in 1:length(plots)){
#'   df <- tree_data2 %>% filter(Plot_Name==plots[[i]]) %>% droplevels()
#'   saveTreeMaps(path=filepath,df=df)
#' }
#'
#' @export
#'
#------------------------
# Plots tree map by status and size
#------------------------
treeMap<-function(df){

  if(!requireNamespace("ggrepel", quietly = TRUE)){
    stop("Package 'ggrepel' needed for this function to work. Please install it.", call. = FALSE)
  }

  if(!requireNamespace("cowplot", quietly = TRUE)){
    stop("Package 'cowplot' needed for this function to work. Please install it.", call. = FALSE)
  }

  df<-treeMapPrep(df)

  status_cols<-c("#d9f008","#a6db12","#73c71c","#009900", "#00f2ff", "#0066ff", "#3300CC")
  names(status_cols)<-as.character(c('AB','AF','AL','AS','DB','DL','DS'))

  orient<-paste0(unique(df$Plot_Name),' Orientation: ',unique(df$Orientation))

  p<-ggplot(data=df,aes(x=x, y=y, group=Status_ID, fill=Status_ID, size=DBH, label=Tree_Number_MIDN))+
    geom_rect(aes(xmin=-10.5, xmax=10.5, ymin=-10.5, ymax=10.5),
              color='black', fill="lightgrey", alpha=0.1, size=0.1)+
    geom_segment(aes(x=-10.2, xend=10.2, y=0, yend=0), lwd=1, color='DimGrey')+
    geom_segment(aes(x=0, xend=0, y=-10.5, yend=10.5), lwd=1, color='DimGrey')+
    geom_jitter(aes(fill=Status_ID),shape=21, width=0.25)+ xlim(-14.14,14.14)+ylim(-14.14,14.14)+
    scale_fill_manual(values=status_cols)+
    theme_bw()+
    theme(panel.background=element_blank(), panel.grid.major=element_blank(),plot.background=element_blank(),
          panel.border=element_blank(),axis.ticks=element_blank(),
          panel.grid.minor=element_blank(), axis.text=element_blank(),
          plot.margin=unit(c(1,0.5,1,1), 'lines'), legend.position='none',
          legend.spacing.y=unit(0.05,'cm'), legend.text=element_text(size=10))+
    guides(shape=T, size=F)+
    scale_size_continuous(range=c(2,10))+
    ggrepel::geom_text_repel(aes(x=x,y=y,label=Tree_Number_MIDN), direction='both', size=5, nudge_x=0.2,nudge_y=0.2)+
    coord_cartesian(xlim=c(-14.14,14.14), clip='off')+
    labs(x=NULL,y=NULL, fill='Status')+
    geom_text(x=0, y=11.5, size=5, label='UP')+ geom_text(x=11.5,y=11.5,size=5,label='UR')+
    geom_text(x=11.5,y=-11.5,size=5,label='BR')+ geom_text(x=-11.5,y=-11.5,size=5,label='BL')+
    geom_text(x=-11.5,y=11.5, size=5, label='UL')+
    geom_text(x=0, y=12.3, label=orient, size=5, col='red')

  leg<-cowplot::get_legend(ggplot(data=df, aes(x=x, y=y, group=Status_ID, fill=Status_ID))+
                    geom_point(aes(fill=Status_ID),shape=21, size=6)+labs(fill='Status')+
                    scale_fill_manual(values=status_cols)+
                    guides(shape=T))

  print(cowplot::plot_grid(p,leg,rel_widths=c(1.1,0.2)))

} # end of function