Tuesday, June 2, 2020

Introductory tutorials for the R version of ENMTools

Hey everybody!  I've started recording quick tutorials on the most important bits of ENMTools.  Here's one on how to install ENMTools and all of its dependencies:



And here's one on how to build ENMTools species objects and some quick models:





Sunday, May 24, 2020

Code snippet from Tyler Smith for fast plotting of ENMTools models

Over on the ENMTools GitHub page, Tyler Smith asked a question about plotting ENMTools models.  He pointed out that large models are very slow to plot, largely because of our use of ggplot2.  We like ggplot for this because it allows us to store plots in objects easily, and makes it possible for users to modify plots after the fact using all of the features of ggplot and the extensions people have written for it.  That said, it's probably frustrating to have a long draw time if you just want to take a quick peek at your model's predictions.  Tyler provided a code chunk that does a nice quick plot using base graphics.  The end result looks a lot like the standard ggplot plots we've been returning, but takes a fraction of the time to display.  Here's that code:

library(viridis) # to match ENMTools color palette

plotTWS <- ...="" function="" p="" x="">  plot(x$suitability, col = viridis(100, option = "B" ),
       xlab =  "Longitude", ylab = "Latitude",
       main = paste("Maxent model for", x$species.name),
       bty = 'l', box = FALSE)
  points(subset(x$analysis.df, presence == 1), pch = 21,
       bg = "white")
  points(x$test.data, pch = 21, bg = "green")
}

We're going to see if we can work out a quicker way to do our built-in plots using ggplot, but for now this is a nice workaround!