R/raster_plot_species_by_stake.R

# # Script for producing "heatmap" of capture history of selected species (or individuals)
# # EMC 1/2017
#
#
# raster_of_plot_captures = function(path, group_or_individual, year){
#   # load latest version of rodent data
#   data = loadData(path)
#   rdat = data[[1]]
#
#   # table of adjustments to x and y coords to put plots in approximate locations
#   plotcoords = data.frame(plot=seq(1,24),
#                         x_adj = c(0,10,20,30,40,50, 0,10,20,30,40,50,
#                                   0,10,20,30,40,50,60,30,40,50,60,60),
#                         y_adj = c(0, 0, 0, 0, 0, 0,10,10,10,10,10,10,20,
#                                   20,20,20,20,20,15,30,30,30,25,5))
#
#   # select group (species) or individual to plot.  also time period
#   group_or_individual = dplyr::filter(rdat,species==group_or_individual,yr==year)
#
#   df = capture_history_coordinates(group_or_individual,plotcoords)
#
#   ggplot2::ggplot(df,ggplot2::aes(x_position,y_position,fill=z)) +
#     ggplot2::scale_y_continuous(trans = "reverse") +
#     ggplot2::geom_raster()
# }
#
# capture_history_coordinates = function(group_or_individual,plotcoords) {
#   # function takes selected data and counts number of captures at each stake on each plot
#
#   # count number of captures at each stake / plot
#   counts = aggregate(group_or_individual$stake,
#                      by=list(stake=group_or_individual$stake,plot=group_or_individual$plot),
#                      FUN=length)
#   names(counts) = c('stake','plot','z')
#   counts$x = as.numeric(substr(counts$stake,2,2))
#   counts$y = as.numeric(substr(counts$stake,1,1))
#
#   # merge with full 7x7 grid
#   g = expand.grid(x=1:7, y=1:7, plot=1:24)
#   df = merge(g,counts,by=c('plot','x','y'),all=T)
#
#   # merge with plot-location adjustments
#   df = merge(df,plotcoords,all=T)
#   df$x_position = df$x+df$x_adj
#   df$y_position = df$y+df$y_adj
#
#   # replace NAs with 0s
#   df$z[is.na(df$z)]=0
#
#   return(df)
# }
weecology/portalr documentation built on Feb. 29, 2024, 3:34 a.m.