plot_col_vs_unobsSpp: Plot colonizers and unobserved species

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

Description

Colonizers from data this year versus MSOM estimates of last year's unobserved species

Usage

plot_col_vs_unobsSpp(prn, Figures, 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
FUN	graphical device function
...	arguments passed to plot_device

Details

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.

I'm not sure how valuable this figure is. But the original idea was that if the survey didn't detect a species last year (but it was present), maybe the MSOM would have estimated it as a present but unobserved species. And if that unobserved species was observed this year, it could look like a colonization. In that case, observed colonizations might just be correlated with the number of unobserved species from last year. Obviously unobserved species from last year could have gone extinct, and, more importantly, the MSOM isn't perfect. So I'm hesitant to read too far into the results of this figure. However, I do think it is useful to note the relative magnitude of unobserved species in a given year, and the number of colonizers in a given year.

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.