Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/EvolEcolGroup/tidysdm
R package to fit species distribution models (SDMs) using the 'tidymodels' framework
https://github.com/EvolEcolGroup/tidysdm
Last synced: about 2 months ago
JSON representation
R package to fit species distribution models (SDMs) using the 'tidymodels' framework
- Host: GitHub
- URL: https://github.com/EvolEcolGroup/tidysdm
- Owner: EvolEcolGroup
- License: agpl-3.0
- Created: 2023-07-14T09:50:27.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2024-10-26T09:42:57.000Z (2 months ago)
- Last Synced: 2024-10-29T22:31:49.280Z (2 months ago)
- Language: R
- Homepage: https://evolecolgroup.github.io/tidysdm/
- Size: 32.6 MB
- Stars: 27
- Watchers: 3
- Forks: 8
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE.md
- Code of conduct: .github/CODE_OF_CONDUCT.md
Awesome Lists containing this project
- open-sustainable-technology - tidysdm - A Species Distribution Models in R. (Biosphere / Species Distribution Modeling)
README
# tidysdm 
[](https://github.com/EvolEcolGroup/tidysdm/actions/workflows/R-CMD-check.yaml)
[](https://app.codecov.io/gh/EvolEcolGroup/tidysdm)
[](https://CRAN.R-project.org/package=tidysdm)
[](https://github.com/r-hub/cranlogs.app)
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`](https://evolecolgroup.github.io/pastclim/dev/index.html),
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)](https://doi.org/10.1101/2023.07.24.550358).
## Installation
`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](https://github.com/) with:
``` r
# install.packages("devtools")
devtools::install_github("EvolEcolGroup/tidysdm", ref = "dev")
```
## Overview of functionality
On its dedicated [website](https://evolecolgroup.github.io/tidysdm/),
you can find Articles giving you a step-by-step [overview of the
fitting SDMs to contemporary species](https://evolecolgroup.github.io/tidysdm/articles/a0_tidysdm_overview.html),
as well as an equivalent [tutorial for using palaeontological data](https://evolecolgroup.github.io/tidysdm/articles/a1_palaeodata_application.html).
Furthermore, there is an [Article with examples of how to leverage various
features of tidymodels](https://evolecolgroup.github.io/tidysdm/dev/articles/a2_tidymodels_additions.html) that are not commonly adopted in SDM pipelines
There is also a [dev
version](https://evolecolgroup.github.io/tidysdm/dev/) 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](https://evolecolgroup.github.io/tidysdm/CONTRIBUTING.html).
## When something does not work
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](https://evolecolgroup.github.io/tidysdm/dev/articles/a3_troubleshooting.html).
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](https://github.com/EvolEcolGroup/tidysdm/issues) 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](https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example)
for the developers to investigate the problem. If you think you can help
with fixing that bug, read our [contributing guide](https://evolecolgroup.github.io/tidysdm/CONTRIBUTING.html).