The goal of tidysdm is to implement Species Distribution Models using the
tidymodels framework. The advantage of tidymodels is that the model syntax and the results
returned to the user are standardised, thus providing a coherent interface to
modelling. Given the variety of models required for SDM, tidymodels is an
ideal framework. tidysdm provides a number of wrappers and specialised
functions to facilitate the fitting of SDM with tidymodels.
Besides modelling contemporary species, tidysdm has a number of functions
specifically designed to work with palaeontological data.
Whilst users are free
to use their own environmental data, the articles showcase the potential integration
with pastclim,
which helps downloading and manipulating present day data,
future predictions, and palaeoclimate reconstructions.
An overview of the capabilities of tidysdm is given in Leonardi et al.
(2023).
tidysdm is on CRAN, and the easiest way to install it is with:
install.packages("tidysdm")
The version on CRAN is recommended for every day use. New features and
bug fixes appear first on the dev branch on GitHub, before they make
their way to CRAN. If you need to have early access to these new
features, you can install tidysdm directly from GitHub. To install
from GitHub, you will need to use devtools; if you haven't done so
already, get it from CRAN with install.packages("devtools").
You can install the latest dev version of tidysdm from GitHub with:
# install.packages("devtools")
devtools::install_github("EvolEcolGroup/tidysdm", ref = "dev")On its dedicated website, you can find Articles giving you a step-by-step overview of the fitting SDMs to contemporary species, as well as an equivalent tutorial for using palaeontological data. Furthermore, there is an Article with examples of how to leverage various features of tidymodels that are not commonly adopted in SDM pipelines
There is also a dev
version of the site
updated for the dev branch of tidysdm (on the top left of the dev
website, the version number is in red and in the format x.x.x.9xxx,
indicating it is a development version). If you want to contribute, make
sure to read our contributing guide.
What should you do if you get an error when trying to fit a model? tidysdm
is a relatively new package, so it might well be that, when you get an
error, you might have encountered a bug. However, it is also possible that you
have misspecified your model (and so the error comes from tidymodels, because
your model is not valid). We have prepared an Article on how to diagnose failing
models.
It is not a fully comprehensive list of everything that could go wrong, but it will
hopefully give you ideas on how to dig deeper in what is wrong. You should also
check the issues on
GitHub to see whether
the problem has already been reported.
If you are convinced
that the problem is a bug in tidysdm, feel free to create an
new issue. Please make sure you have updated to the latest version of
tidysdm, as well as updating all other packages on your
system, and provide a reproducible
example
for the developers to investigate the problem. If you think you can help
with fixing that bug, read our contributing guide.