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Open Sustainable Technology

A curated list of open technology projects to sustain a stable climate, energy supply, biodiversity and natural resources.

tidysdm

A Species Distribution Models in R.
https://github.com/evolecolgroup/tidysdm

Category: Biosphere
Sub Category: Species Distribution Modeling

Keywords

r species-distribution-modelling tidymodels

Keywords from Contributors

tidy-data shiny tidyverse setup

Last synced: about 10 hours ago
JSON representation

Repository metadata

R package to fit species distribution models (SDMs) using the 'tidymodels' framework

README.md

tidysdm

R-CMD-check
codecov
CRAN status
CRAN downloads

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).

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 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")

Overview of functionality

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.

Getting help

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:

  1. 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.

  2. If you think you have found a bug, or have a feature request, open an issue on our
    GitHub repository. 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.

Owner metadata

GitHub Events

Total
Last Year

Committers metadata

Last synced: 7 days ago

Total Commits: 369
Total Committers: 11
Avg Commits per committer: 33.545
Development Distribution Score (DDS): 0.206

Commits in past year: 158
Committers in past year: 7
Avg Commits per committer in past year: 22.571
Development Distribution Score (DDS) in past year: 0.297

Name Email Commits
Andrea Manica a****5@c****k 293
m-colucci m****l@g****m 34
avpozzi a****6@c****k 12
July Pilowsky j****o 11
Johanna Paijmans p****a@g****m 7
Ben Tupper b****r@b****g 5
topepo m****n@g****m 2
Michela Leonardi m****7@c****k 2
simonpcouch s****h@g****m 1
Michael Chirico m****4@g****m 1
Emil Hvitfeldt e****t@g****m 1

Committer domains:

Issue and Pull Request metadata

Last synced: 1 day ago

Total issues: 29
Total pull requests: 54
Average time to close issues: 19 days
Average time to close pull requests: 1 day
Total issue authors: 20
Total pull request authors: 11
Average comments per issue: 3.52
Average comments per pull request: 1.15
Merged pull request: 46
Bot issues: 0
Bot pull requests: 0

Past year issues: 17
Past year pull requests: 21
Past year average time to close issues: 8 days
Past year average time to close pull requests: 3 days
Past year issue authors: 12
Past year pull request authors: 6
Past year average comments per issue: 4.41
Past year average comments per pull request: 1.76
Past year merged pull request: 17
Past year bot issues: 0
Past year bot pull requests: 0

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/evolecolgroup/tidysdm

Top Issue Authors

  • kolive4 (3)
  • ramiromagno (3)
  • btupper (2)
  • jlapaijmans (2)
  • ManuelSpinola (2)
  • dramanica (2)
  • Aguncan (2)
  • whisnuafrianto (1)
  • rylielrobinson (1)
  • simonpcouch (1)
  • pitherj (1)
  • avpozzi (1)
  • japilo (1)
  • topepo (1)
  • zpmdal (1)

Top Pull Request Authors

  • dramanica (35)
  • m-colucci (5)
  • japilo (4)
  • avpozzi (2)
  • btupper (2)
  • jlapaijmans (1)
  • EmilHvitfeldt (1)
  • simonpcouch (1)
  • MichaelChirico (1)
  • mikleonardi (1)
  • topepo (1)

Top Issue Labels

  • enhancement (2)
  • wontfix (1)

Top Pull Request Labels

Package metadata

cran.r-project.org: tidysdm

Species Distribution Models with Tidymodels

  • Homepage: https://github.com/EvolEcolGroup/tidysdm
  • Documentation: http://cran.r-project.org/web/packages/tidysdm/tidysdm.pdf
  • Licenses: AGPL (≥ 3)
  • Latest release: 1.0.0 (published about 2 months ago)
  • Last Synced: 2025-04-26T14:03:34.932Z (1 day ago)
  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 471 Last month
  • Rankings:
    • Stargazers count: 20.576%
    • Forks count: 20.992%
    • Dependent repos count: 23.802%
    • Average: 25.282%
    • Dependent packages count: 28.642%
    • Downloads: 32.399%
  • Maintainers (1)

Dependencies

.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.4.1 composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/test-coverage.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION cran
  • R >= 2.10 depends
  • spatialsample * depends
  • tidymodels * depends
  • dials * imports
  • dplyr * imports
  • ggplot2 * imports
  • lubridate * imports
  • magrittr * imports
  • maxnet * imports
  • overlapping * imports
  • parsnip * imports
  • patchwork * imports
  • recipes * imports
  • rlang >= 1.0.0 imports
  • rsample * imports
  • sf * imports
  • stats * imports
  • terra * imports
  • tibble * imports
  • tune * imports
  • workflows * imports
  • workflowsets * imports
  • yardstick * imports
  • doParallel * suggests
  • earth * suggests
  • knitr * suggests
  • pastclim * suggests
  • ranger * suggests
  • readr * suggests
  • rmarkdown * suggests
  • stacks * suggests
  • testthat >= 3.0.0 suggests
  • tidyterra * suggests
  • xgboost * suggests

Score: 11.990977865775449