eems.posterior.draws: Plotting smoothed Voronoi diagrams of effective migration and...

In reems: Estimating Effective Migration Surfaces from Single Nucleotide Polymorphism Data

Plotting smoothed Voronoi diagrams of effective migration and diversity rates

Description

Given a set of EEMS output directories, this function takes random draws from the posterior distribution of the migration and diversity rate parameters. Each draw is visualized as two smoothed Voronoi diagrams; the migration diagram is saved to a file ending in mvoronoiXX, the diversity diagram is saved to a file ending in qvoronoiXX where XX is a numeric id. Specify the number of times to draw from the posterior with the argument post.draws. If post.draws = 10, then eems.posterior.draws will generate plots with id XX = 1 to XX = 10. This function differs from eems.voronoi.samples() by plotting smoothed contour diagrams rather than raw Voronoi plots.

Usage

eems.posterior.draws(
  mcmcpath,
  plotpath,
  longlat,
  post.draws = 1,
  plot.width = 10,
  plot.height = 10,
  out.png = TRUE,
  res = 600,
  xpd = TRUE,
  add.grid = FALSE,
  col.grid = "gray80",
  lwd.grid = 1,
  add.demes = FALSE,
  col.demes = "black",
  pch.demes = 19,
  min.cex.demes = 1,
  max.cex.demes = 3,
  add.outline = FALSE,
  col.outline = "gray90",
  lwd.outline = 2,
  projection.in = NULL,
  projection.out = NULL,
  add.map = FALSE,
  col.map = "gray60",
  lwd.map = 2,
  eems.colors = NULL,
  add.colbar = FALSE,
  m.colscale = NULL,
  q.colscale = NULL,
  add.title = FALSE,
  m.plot.xy = NULL,
  q.plot.xy = NULL
)

Arguments

mcmcpath	A vector of EEMS output directories, for the same dataset. Warning: There is minimal checking that the given directories are for the same dataset.
plotpath	The full path and the file name for the graphics to be generated.
longlat	A logical value indicating whether the coordinates are given as pairs (longitude, latitude) or (latitude, longitude).
post.draws	Number of times to sample from the posterior. The default is 1.
plot.width	The width of the graphics region for the two rate contour plots, in inches. The default value is 10.
plot.height	The height of the graphics region, in inches. The default value is 10.
out.png	A logical value which, if set, forces output graphics to be generated as PNGs (if TRUE) or PDFs (if FALSE). Defaults to TRUE.
res	Resolution, in dots per inch; used only for PNG images. The default is 600.
xpd	A logical value indicating whether to clip plotting to the figure region (xpd = TRUE, which is the default) or clip plotting to the plot region (xpd = FALSE).
add.grid	A logical value indicating whether to add the population grid or not.
col.grid	The color of the population grid. Defaults to gray80.
lwd.grid	The line width of the population grid. Defaults to 1.
add.demes	A logical value indicating whether to add the observed demes or not.
col.demes	The color of the demes. Defaults to black.
pch.demes	The symbol, specified as an integer, or the character to be used for plotting the demes. Defaults to 19.
min.cex.demes	The minimum size of the deme symbol/character.
max.cex.demes	The maximum size of the deme symbol/character. Defaults to 1 and 3, respectively. If max.cex.demes > min.cex.demes, then demes with more samples also have bigger size: the deme with the fewest samples has size min.cex.demes and the deme with the most samples has size max.cex.demes.
add.outline	A logical value indicating whether to add the habitat outline or not.
col.outline	The color of the habitat outline. Defaults to white.
lwd.outline	The line width of the habitat outline. Defaults to 2.
projection.in	The input cartographic projection, specified as a PROJ.4 string.
projection.out	The output cartographic projection, specified as a PROJ.4 string.
add.map	A logical value indicating whether to add a high-resolution geographic map. Requires the rworldmap and rworldxtra packages. It also requires that projection.in is specified.
col.map	The color of the geographic map. Default is gray60.
lwd.map	The line width of the geographic map. Defaults to 2.
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.
add.colbar	A logical value indicating whether to add the color bar (the key that shows how colors map to rates) to the right of the plot. Defaults to TRUE.
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. By default, no range is specified for either type of rates.
q.colscale	A fixed range for log10-transformed diversity rates.
add.title	A logical value indicating whether to add the main title in the contour plots. Defaults to TRUE.
m.plot.xy	Statements which add graphical elements (e.g. points) on top of the migration sufrace.
q.plot.xy	Statements which add graphical elements (e.g. points) on top of the diversity surface.

Details

Note about the implementation: eems.voronoi.samples samples randomly from the posterior draws saved during the execution of EEMS, after burn-in and thinning.

Value

None

References

Light A and Bartlein PJ (2004). The End of the Rainbow? Color Schemes for Improved Data Graphics. EOS Transactions of the American Geophysical Union, 85(40), 385.

See Also

eems.voronoi.samples

Examples

# Use the provided example or supply the path to your own EEMS run.
extdata_path <- system.file("extdata", package = "reems")
eems_results <- file.path(extdata_path, "EEMS-example")
# Create a temporary output directory for this example 
outdir <- file.path(tempdir(), "path_out")
dir.create(outdir, showWarnings = FALSE)
name_figures <- file.path(outdir, "EEMS-example")

# Plot a series of Voronoi diagrams for the EEMS model parameters:
# the effective migration rates (m) and the effective diversity rates (q).
eems.posterior.draws(
  mcmcpath = eems_results,
  plotpath = paste0(name_figures, "-posterior-draws"),
  longlat = TRUE,
  post.draws = 2,
  out.png = FALSE
)
# Delete the output directory to tidy up. 
unlink(outdir, recursive = TRUE, force = TRUE)

reems documentation built on May 6, 2026, 1:07 a.m.