machu.plotmap: Map model output from machu.3.anc.niche()

In wxguillo/machuruku: Ancestral niche reconstruction

Map model output from machu.3.anc.niche()

Description

Plot one or more niche models using model output from machu.3.anc.niche(). User can specify color ramps inspired by the viridis package and plot maps in various configurations.

Usage

machu.plotmap(
  model,
  col = 1,
  axes = T,
  title = T,
  title.cex = 1,
  to.scale = F,
  plot = "separately",
  plot.asp = 16/9
)

Arguments

model	Output from machu.3.anc.niche(), a list of lists of SpatRasters, generally one per taxon per timeslice. Subsettable, though this may interfere with the format of titles.
col	Desired color ramp, usually a numeric value from 1 to 6. 1 = base; 2 = plasma; 3 = viridis; 4 = l17 pure white; 5 = r3 pure blue; 6 = black and white. Ramps can also be specified with strings, e.g. "viridis" or "v". Custom color ramps (character vectors with length > 1) can also be supplied, for example by the colorRampPalette function. Default = 1 ("base").
axes	Whether to display axes (lat/long). Default = T.
title	Whether to display titles. These are supposed to take the format "timeslice, taxon", but certain input formats from machu.3.anc.niche, or subsetting the input, may interfere with this. Default = T.
title.cex	Specify size of titles. Default = 1.
to.scale	Whether to color each raster according to the same scale (i.e., the min and max value among all rasters) so that they can be directly compared. Default = F.
plot	How to arrange plots of multiple climate variables. When "separate", plot each in its own window. When "together", plot all in the same window, using n2mfrow to calculate the best arrangement given a specified aspect ratio ('plot.asp'). Default = "separately".
plot.asp	Aspect ratio used to calculate the best arrangement of plots when plot="together". Default = 16/9.

Details

Titles may not display properly (timeslice, taxon) depending on the input format from machu.3.anc.niche and the amount of subsetting of the input.

Implementing scale bars was more trouble than I wanted to deal with so currently they are not supported with this function. Using the plot() function will automatically generate one for your raster though.

When to.scale=T, the function calculates the minimum and maximum suitability value among all the input rasters, and scales the color for each one using this range. This enables the rasters to be directly compared; as such, when to.scale=F, comparing the rasters can be misleading.

Value

Plots of niche models in various configurations.

Examples

# plot all models, separately, with default color ramp, axes, and titles
machu.plotmap(model)
# together
machu.plotmap(model, plot="t")
# no axes or titles
machu.plotmap(model, plot="t", axes=F, title=F)
# plot all rasters on the same color scale
machu.plotmap(model, plot="t", axes=F, title=F, to.scale=T)

# plot only the first raster, using the "viridis" color ramp
machu.plotmap(model[[1]][[1]], col=3)

# plot only rasters from the first timeslice/scenario, using a custom "Mardi Gras" color ramp
mardi.gras <- colorRampPalette(c("purple", "forestgreen", "gold"))(256)
machu.plotmap(model[[1]], col=mardi.gras, plot="t")

wxguillo/machuruku documentation built on Jan. 23, 2025, 3:25 p.m.