plot_ce_wrap: Colonization and Extinction Plotting Wrapper

In rBatt/trawlDiversity: Long-term changes in species richness along the North American coastline

Description

Creates 3 plots for each species involved in some combination of colonization and extinction

Usage

plot_ce_wrap(prn, Figures, spp_cat = c("col", "ext", "both", "neither"),
  width.max = 12, height.max = 7, max_spp_columns = 15, nPlots = 3,
  FUN = "dev.new", ...)

Arguments

prn	the p object (processed msom; output from process_msomStatic)
Figures	option list to which the figure and its information should be added
spp_cat	Category for colonization/ extinction to be chosen
width.max	max width of figure in inches
height.max	max height of figure in inches
max_spp_columns	max number of columns
nPlots	max number of plots per species
FUN	the graphical device function
...	arguments passed to plot_device

Details

This figure is rather complicated, and is divided into 3 parts. This function is the piece that should be interacted with. The core piece of the function is plot_ce, which creates 3 core plots.

The function uses unpack_p to get much of the information it needs. The Figures object is a list whose first level is intended to be the region. The second level is specific to each figure. The third level has 3 elements: 'figure', 'name', and 'dim'. The 'figure' element is the result of using recordPlot on what is plotted. The name of the figure is, e.g., what the saved figure would be called. The dim is the width and height (in that order) in inches.

Value

Returns the Figure object

See Also

There are several functions that are run through the process_msom_figures script. Richness and temperature plots are plot_btemp_map, plot_rich_bt_scatter, and plot_rich_bt_ts. Figures for colonization, extinction, and the species and places associated with those processes are plot_ce_wrap, plot_col_vs_unobsSpp, plot_colExt_perStrat, and plot_rank_temp. Figures for diagnostics are plot_traceplot and plot_post_corr.

rBatt/trawlDiversity documentation built on Aug. 14, 2021, 1:01 p.m.