Monday, February 18, 2019

Low memory options for rangebreak tests are now available on develop branch

There are now options available for writing replicate models to disk for the rangebreak tests, instead of storing them in the output object.  This works in exactly the same way as it does for the identity and background tests, as outlined here:

http://enmtools.blogspot.com/2019/02/low-memory-usage-options-for.html

Again it's currently only on the develop branch, but we'll move it to main before too terribly long.

RWTY 1.0.2 now on CRAN

The newest version of RWTY, version 1.0.2 is now on CRAN.  This is a relatively minor release except for one significant bug fix: there was an issue causing one of the plotting functions to fail when it was called with a single MCMC chain (as opposed to multiple MCMC chains).  That's fixed now, and all is well.

The other major change (for the worse, IMO) is that we had to remove the "Plot Comparisons" vignette to get the package in under CRAN's size restrictions.  That's a really useful vignette, so it sucks to have to remove it.  There are just too many images to make it fit the size requirements, though, and since the entire point of that vignette is comparing those images it doesn't make sense to remove them.  You can still get the vignette installed with RWTY by installing from GitHub or just check it out here: http://danwarren.net/plot-comparisons.html

Wednesday, February 13, 2019

Low memory usage options for identity.test and background.test

This is something I've been meaning to do for a while, but just finally got around to because it was screwing someone's analysis up. 

Originally, the ENMTools R package was designed to store all replicate models in the output object for the identity and background tests.  While that's fine for low resolution or small extent studies, it got to be a real problem for people working with high-resolution data over larger geographic extents.

To deal with this, I've created options for background.test and identity.test that allow you to save the replicate models to .Rda files instead of storing them in the output object.  When called using this option, the replicate.models entries in the identity.test and background.test objects contain paths to the saved model files instead of containing the models themselves.

By default these functions just store models in the working directory, but you can specify a directory to save them to instead if you prefer. 

To run these tests using the low memory options, just pass the argument low.memory = TRUE.  If you want to pass it a directory to save to, just add rep.dir = "PATH", where PATH is your directory name.

Be warned that replicate models WILL be overwritten if they exist.  It's a good idea to make a separate directory for the reps from each analysis.

This new functionality is currently only implemented on the "develop" branch, but we'll move it over to the main branch soon.

Monday, January 21, 2019

Fun fact: you can run a whole bunch of models at once using ENMTools quite easily

The ENMTools R package contains a function called "species.from.file". This takes a .csv file and creates a list of species objects, one for each value in the "species" column in your .csv file. So you can do:

species.list <- species.from.file("myspecies.csv")

and you'll get back a list with ENMTools species in it. If you wanted to run a bunch of models using those species with the same settings, you could then do:

my.models <- lapply(species.list, function(x) enmtools.gam(x, climate.layers, test.prop = 0.3))

where "climate.layers" is your raster stack. That would create a list of ENMTools GAM objects, setting aside 30% of the data from each for testing.