tidysdm
R package to fit species distribution models (SDMs) using the 'tidymodels' framework
Science Score: 57.0%
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 2 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
3 of 11 committers (27.3%) from academic institutions -
✓Institutional organization owner
Organization evolecolgroup has institutional domain (www.eeg.zoo.cam.ac.uk) -
○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (18.5%) to scientific vocabulary
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Repository
R package to fit species distribution models (SDMs) using the 'tidymodels' framework
Basic Info
- Host: GitHub
- Owner: EvolEcolGroup
- License: agpl-3.0
- Language: R
- Default Branch: main
- Homepage: https://evolecolgroup.github.io/tidysdm/
- Size: 45.5 MB
Statistics
- Stars: 34
- Watchers: 3
- Forks: 10
- Open Issues: 7
- Releases: 4
Topics
Metadata Files
README.md
tidysdm 
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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:
r
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:
``` r
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
- Name: Evolutionary Ecology Group at University of Cambridge
- Login: EvolEcolGroup
- Kind: organization
- Website: http://www.eeg.zoo.cam.ac.uk/
- Repositories: 3
- Profile: https://github.com/EvolEcolGroup
GitHub Events
Total
- Create event: 17
- Release event: 1
- Issues event: 33
- Watch event: 9
- Delete event: 12
- Issue comment event: 90
- Push event: 157
- Pull request review comment event: 21
- Pull request review event: 10
- Pull request event: 24
- Fork event: 3
Last Year
- Create event: 17
- Release event: 1
- Issues event: 33
- Watch event: 9
- Delete event: 12
- Issue comment event: 90
- Push event: 157
- Pull request review comment event: 21
- Pull request review event: 10
- Pull request event: 24
- Fork event: 3
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Andrea Manica | a****5@c****k | 331 |
| 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 (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 32
- Total pull requests: 88
- Average time to close issues: 16 days
- Average time to close pull requests: 1 day
- Total issue authors: 21
- Total pull request authors: 12
- Average comments per issue: 1.94
- Average comments per pull request: 0.94
- Merged pull requests: 66
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 20
- Pull requests: 29
- Average time to close issues: 7 days
- Average time to close pull requests: 2 days
- Issue authors: 13
- Pull request authors: 5
- Average comments per issue: 2.25
- Average comments per pull request: 1.69
- Merged pull requests: 21
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- dramanica (4)
- ramiromagno (3)
- kolive4 (3)
- jmburgos (2)
- ManuelSpinola (2)
- jlapaijmans (2)
- btupper (2)
- hpilat (1)
- OndraPelanek (1)
- EmilHvitfeldt (1)
- djensing (1)
- evhersh (1)
- piabenaud (1)
- zpmdal (1)
- topepo (1)
Pull Request Authors
- dramanica (60)
- m-colucci (7)
- avpozzi (4)
- japilo (4)
- EmilHvitfeldt (2)
- btupper (2)
- barnabasharris (2)
- MichaelChirico (2)
- topepo (2)
- jlapaijmans (1)
- simonpcouch (1)
- mikleonardi (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 3
-
Total downloads:
- cran 412 last-month
-
Total dependent packages: 0
(may contain duplicates) -
Total dependent repositories: 1
(may contain duplicates) - Total versions: 15
- Total maintainers: 1
proxy.golang.org: github.com/EvolEcolGroup/tidysdm
- Documentation: https://pkg.go.dev/github.com/EvolEcolGroup/tidysdm#section-documentation
- License: agpl-3.0
-
Latest release: v1.0.3
published 6 months ago
Rankings
proxy.golang.org: github.com/evolecolgroup/tidysdm
- Documentation: https://pkg.go.dev/github.com/evolecolgroup/tidysdm#section-documentation
- License: agpl-3.0
-
Latest release: v1.0.3
published 6 months ago
Rankings
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
- License: AGPL (≥ 3)
-
Latest release: 1.0.3
published 6 months ago
Rankings
Maintainers (1)
Dependencies
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- r-lib/actions/setup-r-dependencies v2 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
- 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
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- knitr * suggests
- pastclim * suggests
- ranger * suggests
- readr * suggests
- rmarkdown * suggests
- stacks * suggests
- testthat >= 3.0.0 suggests
- tidyterra * suggests
- xgboost * suggests