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SSDM

Stacked Species Distribution Modelling R package

https://github.com/sylvainschmitt/ssdm

Science Score: 26.0%

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    CITATION.cff file
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    codemeta.json file
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    DOI references
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    Committers with academic emails
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (16.4%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Stacked Species Distribution Modelling R package

Basic Info
  • Host: GitHub
  • Owner: sylvainschmitt
  • License: other
  • Language: HTML
  • Default Branch: master
  • Size: 5.39 MB
Statistics
  • Stars: 46
  • Watchers: 3
  • Forks: 18
  • Open Issues: 15
  • Releases: 7
Created over 10 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License

README.md

SSDM: Stacked species distribution modelling

R-CMD-check Downloads Codecov test coverage Research software impact

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:

``` r 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:

r 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

  • Name: Sylvain SCHMITT
  • Login: sylvainschmitt
  • Kind: user
  • Location: Montpellier, France
  • Company: CIRAD

Researcher in Ecology and Climate Change

GitHub Events

Total
  • Issues event: 5
  • Watch event: 5
  • Issue comment event: 4
  • Push event: 1
  • Fork event: 1
Last Year
  • Issues event: 5
  • Watch event: 5
  • Issue comment event: 4
  • Push event: 1
  • Fork event: 1

Committers

Last synced: 11 months ago

All Time
  • Total Commits: 189
  • Total Committers: 8
  • Avg Commits per committer: 23.625
  • Development Distribution Score (DDS): 0.37
Past Year
  • Commits: 3
  • Committers: 1
  • Avg Commits per committer: 3.0
  • Development Distribution Score (DDS): 0.0
Top Committers
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 (Top 20 + Academic)
ens-lyon.fr: 1 yahoo.de: 1 agroparistech.fr: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 95
  • Total pull requests: 15
  • Average time to close issues: 10 months
  • Average time to close pull requests: 2 months
  • Total issue authors: 61
  • Total pull request authors: 4
  • Average comments per issue: 4.2
  • Average comments per pull request: 1.93
  • Merged pull requests: 14
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 5
  • Pull requests: 0
  • Average time to close issues: 12 minutes
  • Average time to close pull requests: N/A
  • Issue authors: 4
  • Pull request authors: 0
  • Average comments per issue: 0.6
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • lukasbaumbach (8)
  • BettyBoyse (7)
  • sylvainschmitt (4)
  • RafP2021 (3)
  • Otoliths (3)
  • biswasdibyendu (3)
  • mathildehure (2)
  • CarvalhoResearch (2)
  • rmc2025 (2)
  • magdaresende (2)
  • AJ-KBA (2)
  • dpoursanidis (2)
  • asierrl (2)
  • preuss96 (2)
  • priyamvadazsi (2)
Pull Request Authors
  • sylvainschmitt (7)
  • lukasbaumbach (6)
  • pritchardtom (2)
  • kant (1)
Top Labels
Issue Labels
enhancement (15) question (11) bug (9) user issue? (6)
Pull Request Labels
enhancement (1)

Packages

  • Total packages: 1
  • Total downloads:
    • cran 574 last-month
  • Total dependent packages: 1
  • Total dependent repositories: 1
  • Total versions: 14
  • Total maintainers: 1
cran.r-project.org: SSDM

Stacked Species Distribution Modelling

  • Versions: 14
  • Dependent Packages: 1
  • Dependent Repositories: 1
  • Downloads: 574 Last month
Rankings
Forks count: 4.4%
Stargazers count: 8.2%
Average: 14.3%
Downloads: 17.2%
Dependent packages count: 18.1%
Dependent repos count: 23.9%
Maintainers (1)
sylvain.m.schmitt@gmail.com
Last synced: 10 months ago

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