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 the latest dev version
of tidysdm from r-universe with:
install.packages("tidysdm", repos = c("https://evolecolgroup.r-universe.dev",
"https://cloud.r-project.org"))Alternatively, you can also use devtools and install the
package from source directly from GitHub, but you might need to set up
your development environment first:
# install.packages("devtools") # if you haven't installed devtools yet
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.
If some of your models are failing, first look at our 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.
If after reading the article you are still unsure what is going
wrong, there are two places to get help with tidysdm:
If you are unsure how to do something, go to StackOverflow and, after checking
that a similar question has not been asked yet, tag your question with
tidymodels and r (there is no
tidysdm tag yet, as there aren’t enough questions), and
make sure tidysdm is in the title. This will ensure that
the developers see your question and can help you. If you have not
received an answer after a couple of days, feel free to drop us an email
in case we missed your post.
If you think you have found a bug, or have a feature request,
open an issue on our [GitHub
repository]((https://github.com/EvolEcolGroup/tidysdm/issues). Before
doing so, please make sure that you have installed the latest
development version of tidysdm (as the bug
might have already been fixed), as well as updating all other packages
on your system. If the problem persists, and there is no issue already
opened that deals with your bug, file a new issue
providing a reproducible example for the
developers to investigate the problem. A small reproducible
example is crucial in allowing us to understand the problem and
fix it, so please do your best to come up with the shortest bit of code
needed to show the bug.