plot_voronoi_tiles: Sample Voronoi diagrams from the posterior of m and q

In dipetkov/reemsplots2: Generate plots to inspect and visualize the results of EEMS

Description

Given a set of EEMS output directories, this function takes random samples from the posterior distribution of the migration rates m and the diversity rates q. Each draw is visualized as a Voronoi diagram with the help of the deldir package.

Usage

plot_voronoi_tiles(mcmcpath, longlat, num_draws = 1, add_seeds = TRUE,
  eems_colors = NULL, m_colscale = NULL, q_colscale = NULL)

Arguments

mcmcpath	A vector of EEMS output directories, for the same dataset. Warning: There is minimal checking that the directories all correspond to the same dataset.
longlat	A logical value indicating whether the coordinates are given as pairs (longitude, latitude) or (latitude, longitude).
num_draws	Number of times to sample from the posterior. The default is 1.
add_seeds	A logical value indicating whether to add the Voronoi centers or not.
eems_colors	The EEMS color scheme as a vector of colors, ordered from low to high. Defaults to a DarkOrange to Blue divergent palette with six orange shades, white in the middle, six blue shades. Acknowledgement: The default color scheme is adapted from the dichromat package.
m_colscale	A fixed range for log10-transformed migration rates. If the estimated rates fall outside the specified range, then the color scale is ignored. The default range is [-2.5, +2.5].
q_colscale	A fixed range for log10-transformed diversity rates. The default range is -0.1, +0.1.

See Also

deldir, make_eems_plots, plot_population_grid, plot_resid_heatmap

Examples

# Use the provided example or supply the path to your own EEMS run
mcmcpath <- system.file("extdata", "EEMS-example", package = "reemsplots2")

# Plot a series of Voronoi diagrams for the EEMS model parameters:
# the effective migration rates (m) and the effective diversity rates (q).
plots <- plot_voronoi_tiles(mcmcpath, longlat = TRUE, num_draws = 2)
plots

dipetkov/reemsplots2 documentation built on May 15, 2019, 8:47 a.m.