SSDM

A package to map species richness and endemism based on stacked species distribution models.
https://github.com/sylvainschmitt/ssdm

Category: Biosphere
Sub Category: Species Distribution Modeling

Keywords from Contributors

ecology forest distribution species

Last synced: about 8 hours ago
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Repository metadata

Stacked Species Distribution Modelling R package

Host: GitHub
URL: https://github.com/sylvainschmitt/ssdm
Owner: sylvainschmitt
License: other
Created: 2015-12-17T04:24:52.000Z (over 9 years ago)
Default Branch: master
Last Pushed: 2025-04-11T08:54:30.000Z (17 days ago)
Last Synced: 2025-04-20T06:30:25.996Z (8 days ago)
Language: HTML
Size: 5.39 MB
Stars: 44
Watchers: 3
Forks: 18
Open Issues: 14
Releases: 7
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- License: LICENSE

SSDM: Stacked species distribution modelling

SSDM is a package to map species richness and endemism based on stacked species distribution models (SSDM). Individual SDMs can be created using a single or multiple algorithms (ensemble SDMs). For each species, an SDM can yield a habitat suitability map, a binary map, a between-algorithm variance map, and can assess variable importance, algorithm accuracy, and between-algorithm correlation. Methods to stack individual SDMs include summing individual probabilities and thresholding then summing. Thresholding can be based on a specific evaluation metric or by drawing repeatedly from a Bernouilli distribution. The SSDM package also provides a user-friendly interface gui.

For a full list of changes see NEWS.

Installation

Please be aware that SSDM package use a lot of dependencies (see DESCRIPTION)

Install from Github

You can install the latest version of SSDM from Github using the devtools package:

if (!requireNamespace("devtools", quietly = TRUE))
  install.packages("devtools")

devtools::install_github("sylvainschmitt/SSDM")

Install from CRAN

The stable version of SSDM, is available on CRAN:

install.packages("SSDM")

We advise users to install from github. Due to CRAN policies and the development of SSDM, many new features and bugfixes may be available on CRAN later.

Usage

After installing, SSDM package, you can launch the graphical user interface by typing gui() in the console.

Click to enlarge

Screenshot

Functionnalities

SSDM provides five categories of functions (that you can find in details below): Data preparation, Modelling main functions, Model main methods, Model classes, and Miscellaneous.

Data preparation

load_occ: Load occurrence data
load_var: Load environmental variables

Modelling main functions

modelling: Build an SDM using a single algorithm
ensemble_modelling: Build an SDM that assembles multiple algorithms
stack_modelling: Build an SSDMs that assembles multiple algorithms and species

Model main methods

ensemble,Algorithm.SDM-method: Build an ensemble SDM
stacking,Ensemble.SDM-method: Build an SSDM
update,Stacked.SDM-method: Update a previous SSDM with new occurrence data

Model classes

Algorithm.SDM: S4 class to represent SDMs
Ensemble.SDM: S4 class to represent ensemble SDMs
Stacked.SDM: S4 class to represent SSDMs

Miscellanous

gui: user-friendly interface for SSDM package
plot.model: Plot SDMs
save.model: Save SDMs
load.model: Load SDMs

Owner metadata

Name: Sylvain SCHMITT
Login: sylvainschmitt
Email:
Kind: user
Description: Postdoctoral researcher in tropical tree ecology and evolution
Website: https://sylvainschmitt.netlify.com/
Location: French Guiana
Twitter:
Company: @EcoFoG
Icon url: https://avatars.githubusercontent.com/u/16331085?u=36154e83a7d475f777d9b396ade2527664c97ae7&v=4
Repositories: 7
Last ynced at: 2023-02-26T08:52:15.344Z
Profile URL: https://github.com/sylvainschmitt

GitHub Events

Total

Issues event: 4
Watch event: 4
Issue comment event: 3
Push event: 1
Fork event: 1

Last Year

Issues event: 4
Watch event: 4
Issue comment event: 3
Push event: 1
Fork event: 1

Committers metadata

Last synced: 6 days ago

Total Commits: 189
Total Committers: 8
Avg Commits per committer: 23.625
Development Distribution Score (DDS): 0.37

Commits in past year: 3
Committers in past year: 1
Avg Commits per committer in past year: 3.0
Development Distribution Score (DDS) in past year: 0.0

Name	Email	Commits
sylvain.schmitt	s**t@a**r	119
Lukas Baumbach	l**h@y**e	46
Sylvain Schmitt	s**t@g**m	16
Rekyt	m**e@e**r	3
Florian de Boissieu	f**s@g**m	2
pritchardtom	4****m	1
Dimitri Justeau	d**u@g**m	1
Darío Hereñú	m**a@g**m	1

Committer domains:

Issue and Pull Request metadata

Last synced: 1 day ago

Total issues: 123
Total pull requests: 18
Average time to close issues: 8 months
Average time to close pull requests: about 2 months
Total issue authors: 60
Total pull request authors: 4
Average comments per issue: 4.41
Average comments per pull request: 2.39
Merged pull request: 17
Bot issues: 0
Bot pull requests: 0

Past year issues: 7
Past year pull requests: 0
Past year average time to close issues: 12 minutes
Past year average time to close pull requests: N/A
Past year issue authors: 3
Past year pull request authors: 0
Past year average comments per issue: 0.57
Past year average comments per pull request: 0
Past year merged pull request: 0
Past year bot issues: 0
Past year bot pull requests: 0

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

Top Issue Authors

BettyBoyse (10)
lukasbaumbach (10)
sylvainschmitt (6)
preuss96 (4)
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Otoliths (4)
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mathildehure (3)
magdaresende (3)
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AJ-KBA (3)
RafP2021 (3)
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Top Pull Request Authors

lukasbaumbach (9)
sylvainschmitt (7)
pritchardtom (1)
kant (1)

Top Issue Labels

question (19)
enhancement (16)
bug (13)
user issue? (10)

Top Pull Request Labels

enhancement (1)

Package metadata

Total packages: 1
Total downloads:
- cran: 443 last-month
Total dependent packages: 1
Total dependent repositories: 1
Total versions: 13
Total maintainers: 1

cran.r-project.org: SSDM

Stacked Species Distribution Modelling

Homepage: https://github.com/sylvainschmitt/SSDM
Documentation: http://cran.r-project.org/web/packages/SSDM/SSDM.pdf
Licenses: GPL (≥ 3) | file LICENSE
Latest release: 0.2.10 (published 14 days ago)
Last Synced: 2025-04-26T12:33:16.151Z (1 day ago)
Versions: 13
Dependent Packages: 1
Dependent Repositories: 1
Downloads: 443 Last month
Rankings:
- Forks count: 4.36%
- Stargazers count: 8.164%
- Average: 14.346%
- Downloads: 17.2%
- Dependent packages count: 18.142%
- Dependent repos count: 23.862%
Maintainers (1)
- [email protected]

Dependencies

DESCRIPTION cran

R >= 3.2.2 depends
dismo >= 1.0.12 imports
doParallel >= 1.0.14 imports
e1071 >= 1.6.7 imports
earth >= 4.4.3 imports
foreach >= 1.4.4 imports
gbm >= 2.1.1 imports
ggplot2 >= 3.1.1 imports
iterators >= 1.0.10 imports
itertools >= 0.1 imports
methods >= 3.2.2 imports
mgcv >= 1.8.7 imports
nnet >= 7.3.10 imports
parallel >= 3.5.2 imports
poibin >= 1.3.0 imports
randomForest >= 4.6.10 imports
raster >= 2.9 imports
reshape2 >= 1.4.3 imports
rpart >= 4.1.10 imports
scales >= 1.0.0 imports
shiny >= 0.12.2 imports
shinyFiles >= 0.7.0 imports
shinydashboard >= 0.5.1 imports
snow >= 0.4 imports
sp >= 1.2.0 imports
spThin >= 0.1.0 imports
fasterize * suggests
geobuffer * suggests
knitr * suggests
rgdal * suggests
rmarkdown * suggests
sdm * suggests
testthat * suggests

Score: 12.240203504246319

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