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Now on biorXiv: Evaluating species distribution models with discrimination...
I've just recently posted a new paper to biorXiv entitled "Evaluating species distribution models with discrimination accuracy is uninformative for many applications", which I did in collaboration with...
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ENMTools R package now has a DOI
I finally got some time to put together the first real beta release of ENMTools, and got a doi number for it. If you're using the R version of ENMTools, please cite it as follows for now:Warren, D.L.,...
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Calibration metrics added to ENMTools R package
Given our recent paper on how badly discrimination accuracy performs at selecting models that estimate ecological phenomena, the obvious next question is whether there are existing alternatives that do...
View ArticleCode 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...
View ArticleIntroductory 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...
View Articleinstall.packages("ENMTools") - ENMTools is now on CRAN!
Hey everybody! I'm happy to announce that we've finally put ENMTools onto CRAN! It took a while, but everything seems to be working. From now on you can install ENMTools just by...
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Hacking together the Bohl et al. test
A recent paper by Bohl et al. suggested a new method for testing statistical significance of ENM predictions. It's similar to a test by Raes and ter Steege and existing tests in ENMTools, but as I...
View ArticleHow do deal with recalibration errors
Due to changes to the CalibratR package, some of the recalibration methods don't work properly on some systems. This is due to the way CalibratR is addressing the parallel package, which Mac OS (and...
View ArticleENMTools version 1.0.1 is on CRAN! Clamping, variable importance, and...
EnhancementsAdded variable importance tests via interface with the vip packageAdded clamping for the predict functions, including plots of where clamping is happeningAdded clamping for model...
View ArticleApplication note for ENMTools R package is out today!
Hooray, it's finally out!https://onlinelibrary.wiley.com/doi/10.1111/ecog.05485This is the culmination of a lot of work by a lot of people, and I just wanted to take this opportunity to express my...
View ArticleDoing replicates of ENMTools models
This is coming from a question on the maxent google group. Someone wanted to know how to do multiple replicates of an ENMTools model. At some point we need to create some code for that, but for now...
View ArticleCRAN version of ENMTools is currently not working for some people
Due to updates with the spatstat package, the CRAN version of ENMTools is currently not working for some people. We've got a develop version on github that seems to be doing okay, though, so you can...
View ArticleENMTools currently unavailable on CRAN
Due to some changes to the spatstat package, quite a few packages were kicked off CRAN today including ENMTools. We have submitted a version that (we think) fixes these issues, but it's currently...
View ArticleSpecifying regularization multiplier for maxent from ENMTools
I just got a question about this and I figured I should post about it, since it's quite counterintuitive. If you need to specify a regularization multiplier in ENMTools for Maxent to use, you need to...
View ArticleENMTools is back on CRAN, minus ppmlasso models
We've finished the changes necessary to come up to date with the changes to the spatstat package, and ENMTools is now back on CRAN. Unfortunately one of the changes we had to make was to disable...
View ArticleThe "block" crossvalidation feature is currently broken on CRAN
As part of fixing the recent spatstat-related issues, I somehow managed to roll back some much older changes and as a result broke the block crossvalidation features on the CRAN version of ENMTools....
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Estimating bias in transferring species distribution models
As some of you may have seen, I had a recent paper come out with Alex Dornburg, Teresa Iglesias, and Katerina Zapfe on the effects of climate change on Australia's only endemic Pokémon, kangaskhan....
View ArticleFixing bugs, adding the ability to use bias layers
Version 1.0.4 of ENMTools is now on GitHub. It fixes some issues with the permutation tests for model fit, and just a few other minor usability fixes. It also adds two important things:A check.env()...
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Removing points from suitability plots
This is a question I got via email: how do you remove occurrence points from the suitability plots that are spit out by ENMTools modeling functions?Luckily this is quite easy, as these are just ggplot...
View ArticleProblems with background test in ENMTools R package
At some point, I think fairly recently, something got messed up in the background tests of the ENMTools R package and it is building the models for the permutation tests using incorrect presence...
View ArticleYoutube tutorial on implementing the bias test from Warren et al. 2021
I've just posted a Youtube tutorial on how to implement the bias test from last year's paper "The effects of climate change on Australia’s only endemic Pokémon: Measuring bias in species distribution...
View ArticleNew preprint out: Incorporating sampling bias into permutation tests for...
I'm happy to announce that I have a new preprint out in collaboration with Jamie Kass, Ale Casadei-Ferreira, and Evan Economo. I think this one is pretty important for anyone who's using ENMTools for...
View ArticleENMTools is temporarily off of CRAN
ENMTools has been temporarily removed from CRAN due to an issue with another package. The other package has now been fixed, but we have to re-upload ENMTools as a result. We're going to take that...
View ArticleBig Changes in ENMTools 1.1.0!
ENMTools version 1.1.0 is now on the master branch on github. We're working on getting ENMTools back on CRAN, but it has necessitated some big changes. A lot of stuff has had to change under the hood...
View ArticleBug fix: plots for RTS-style tests
In the midst of doing some modeling work I discovered that the plots for the RTS-style tests were incorrect - the training AUC was used for the vertical dashed line instead of the metric that was...
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