biomod2

A computer platform for ensemble forecasting of species distributions, enabling the treatment of a range of methodological uncertainties in models and the examination of species-environment relationships.
https://github.com/biomodhub/biomod2

Category: Biosphere
Sub Category: Species Distribution Modeling

Keywords from Contributors

species ecological-modelling ecology species-distribution-modelling

Last synced: about 8 hours ago
JSON representation

Repository metadata

BIOMOD is a computer platform for ensemble forecasting of species distributions, enabling the treatment of a range of methodological uncertainties in models and the examination of species-environment relationships.

Host: GitHub
URL: https://github.com/biomodhub/biomod2
Owner: biomodhub
Created: 2018-02-26T15:55:28.000Z (about 7 years ago)
Default Branch: master
Last Pushed: 2025-04-18T07:35:37.000Z (10 days ago)
Last Synced: 2025-04-25T12:09:51.246Z (2 days ago)
Language: R
Size: 28 MB
Stars: 96
Watchers: 6
Forks: 26
Open Issues: 29
Releases: 9
Metadata Files:
- Readme: README.md

README.md

------------------------------------------------------------
Species distribution modeling,
calibration and evaluation,
ensemble modeling
------------------------------------------------------------

https://biomodhub.github.io/biomod2/

Installation

Stable version from cran :

install.packages("biomod2", dependencies = TRUE)

Development version from biomodhub :

library(devtools)
devtools::install_github("biomodhub/biomod2", dependencies = TRUE)

All changes between versions are detailed in News.

NEW video tutorial in Videos !

`biomod 4.3-1` - Abundance modelling

Please feel free to indicate if you notice some strange new behaviors !

What is changed ?

Nothing for presences/absences (or presence-only) modelling.
BIOMOD_RangeSize becomes bm_RangeSize and the new BIOMOD_RangeSize accepts BIOMOD.projection.out objects. See News for more information.

What is new ?

You can now use non-binary data four your modelling. All the information can be found in the Abundance Vignette.

`biomod 4.2-6` - Improved OptionsBigBoss and new model

What is changed ?

To improve the models, we made some change in the options for OptionsBigboss. (This only affects the ANN, CTA and RF models.) You can check all your options with the get_options() function.
To reduce the tuning calculation time, we update the tuning ranges for ANN, FDA and MARS models.

What is new ?

biomod2 has a new model: RFd. It's a Random Forest model with a down-sampling method.
You can now define seed.val for bm_PseudoAbsences() and BIOMOD_FormatingData().
New fact.aggr argument, for pseudo-absences selection with the random and disk methods, allows to reduce the resolution of the environment.
Possibility to give the same options for all datasets with "for_all_datasets" in bm_ModelingOptions().

`biomod 4.2-5` - Modeling options & Tuning Update

What is changed ?

modeling options are now automatically retrieved from single models functions, normally allowing the use of all arguments taken into account by these functions
tuning has been cleaned up, but keep in mind that it is still a quite long running process
in consequence, BIOMOD_ModelingOptions and BIOMOD_Tuning functions become secondary functions (bm_ModelingOptions and bm_Tuning), and modeling options can be directly built through BIOMOD_Modeling function

What is new ?

ModelsTable and OptionsBigboss datasets (note that improvement of bigboss modeling options is planned in near future)
3 new vignettes have been created :
- data preparation (questions you should ask yourself before modeling)
- cross-validation (to prepare your own calibration / validation datasets)
- modeling options (to help you navigate through the new way of parametrizing single models)

`biomod 4.2` - Terra Update

What is changed ?

biomod2 now relies on the new terra package that aims at replacing rasterand sp.
biomod2 is still compatible with old format such as RasterStackand SpatialPointsDataFrame.
biomod2 function will sometimes return SpatRaster from package terra that you can always convert into RasterStack using function stack in raster.

`biomod 4.1` is now available

/!\ Package fresh start... meaning some changes in function names and parameters. We apologize for the trouble >{o.o}<
Sorry for the inconvenience, and please feel free to indicate if you notice some strange new behaviors !

What is changed ?

all code functions have been cleaned, and old / unused functions have been removed
function names have been standardized (BIOMOD_ for main functions, bm_ for secondary functions)
parameter names have been standardized (same typo, same names for similar parameters across functions)
all documentation and examples have been cleaned up

What is new ?

plot functions have been re-written with ggplot2
biomod2 website has been created, with proper roxygen2 documentation and help vignettes

But... why ?

“For every minute spent on organizing, an hour is earned.” — Benjamin Franklin
- better documentation, better formation, better help provided
- new improvements to come (update of single models, implementation of abundance models, etc)

Owner metadata

Name: biomod2 package, tools and scripts
Login: biomodhub
Email:
Kind: organization
Description:
Website:
Location:
Twitter:
Company:
Icon url: https://avatars.githubusercontent.com/u/36854792?v=4
Repositories: 2
Last ynced at: 2023-03-05T19:50:51.371Z
Profile URL: https://github.com/biomodhub

GitHub Events

Total

Create event: 1
Release event: 1
Issues event: 194
Watch event: 10
Issue comment event: 390
Push event: 55
Pull request event: 3
Fork event: 4

Last Year

Create event: 1
Release event: 1
Issues event: 194
Watch event: 10
Issue comment event: 390
Push event: 55
Pull request event: 3
Fork event: 4

Committers metadata

Last synced: 5 days ago

Total Commits: 1,088
Total Committers: 13
Avg Commits per committer: 83.692
Development Distribution Score (DDS): 0.563

Commits in past year: 172
Committers in past year: 4
Avg Commits per committer in past year: 43.0
Development Distribution Score (DDS) in past year: 0.355

Name	Email	Commits
MayaGueguen	m**n@g**m	475
Rémi Patin	r**n@n**r	210
rpatin	r**n@g**m	199
HeleneBlt	h**u@f**r	127
Unknown	d**2@g**m	40
rpatin	r**n@f**r	16
Rekyt	m**e@e**r	8
fbreiner	f**r@u**h	5
jamiemkass	j**s@g**m	4
rhijmans	r**s@g**m	1
olivroy	5****y	1
magn4304	m**4@g**m	1
HÉLÈNE BLANCHETEAU	b**e@a**r	1

Committer domains:

Issue and Pull Request metadata

Last synced: 1 day ago

Total issues: 585
Total pull requests: 16
Average time to close issues: about 2 months
Average time to close pull requests: 2 days
Total issue authors: 236
Total pull request authors: 8
Average comments per issue: 4.03
Average comments per pull request: 0.38
Merged pull request: 13
Bot issues: 0
Bot pull requests: 0

Past year issues: 192
Past year pull requests: 4
Past year average time to close issues: about 1 month
Past year average time to close pull requests: 2 days
Past year issue authors: 94
Past year pull request authors: 3
Past year average comments per issue: 4.22
Past year average comments per pull request: 0.25
Past year merged pull request: 4
Past year bot issues: 0
Past year bot pull requests: 0

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/biomodhub/biomod2

Top Issue Authors

yuliaUU (20)
LorenzoBernicchi (15)
ShreePoudel0 (14)
tongruiju (14)
675979649 (11)
chenyongpeng1 (10)
carlosbedson (10)
GitBen01 (10)
luispedrosantiago (10)
zali37 (9)
Farewe (9)
CatherineBuckland (9)
basille (9)
mula-jpg (8)
guimaricato (7)

Top Pull Request Authors

rpatin (5)
CeresBarros (3)
HeleneBlt (2)
MayaGueguen (2)
magn4304 (1)
rhijmans (1)
Rekyt (1)
olivroy (1)

Top Issue Labels

help wanted (225)
bug (171)
modeling question (123)
outdated (44)
version 3.x.x or older (27)
enhancement (19)
external problem (13)
devel (4)

Top Pull Request Labels

Package metadata

Total packages: 2
Total downloads:
- cran: 4,455 last-month
Total docker downloads: 1,430
Total dependent packages: 7 (may contain duplicates)
Total dependent repositories: 11 (may contain duplicates)
Total versions: 24
Total maintainers: 1

cran.r-project.org: biomod2

Ensemble Platform for Species Distribution Modeling

Homepage: https://biomodhub.github.io/biomod2/
Documentation: http://cran.r-project.org/web/packages/biomod2/biomod2.pdf
Licenses: GPL-3
Latest release: 3.5.1 (published almost 4 years ago)
Last Synced: 2025-04-26T12:35:31.335Z (1 day ago)
Versions: 21
Dependent Packages: 6
Dependent Repositories: 10
Downloads: 4,455 Last month
Docker Downloads: 1,430
Rankings:
- Forks count: 3.929%
- Stargazers count: 5.838%
- Dependent packages count: 7.259%
- Downloads: 8.164%
- Dependent repos count: 9.23%
- Average: 9.879%
- Docker downloads count: 24.857%
Maintainers (1)
- [email protected]

conda-forge.org: r-biomod2

Homepage: https://CRAN.R-project.org/package=biomod2
Licenses: GPL-3.0-only
Latest release: 3.5.1 (published almost 4 years ago)
Last Synced: 2025-04-01T02:11:26.532Z (27 days ago)
Versions: 3
Dependent Packages: 1
Dependent Repositories: 1
Rankings:
- Dependent repos count: 24.367%
- Dependent packages count: 28.978%
- Average: 32.699%
- Forks count: 36.713%
- Stargazers count: 40.736%

Dependencies

DESCRIPTION cran

R >= 4.1 depends
ENMeval * imports
MASS * imports
PresenceAbsence * imports
abind * imports
dismo * imports
dplyr * imports
earth * imports
foreach * imports
gbm >= 2.1.3 imports
ggplot2 * imports
maxnet * imports
mda * imports
methods * imports
nnet * imports
pROC >= 1.15.0 imports
randomForest * imports
raster * imports
reshape * imports
reshape2 * imports
rpart * imports
sp * imports
stats * imports
utils * imports
Hmisc * suggests
car * suggests
caret * suggests
doParallel * suggests
ecospat * suggests
gam * suggests
ggpubr * suggests
mgcv * suggests
rasterVis * suggests
testthat * suggests

.github/workflows/R-CMD-check.yml actions

actions/cache v3 composite
actions/checkout v3 composite
actions/upload-artifact main composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite

Score: 16.078171690584668

biomod2

Keywords from Contributors

Repository metadata

README.md

Installation

biomod 4.3-1 - Abundance modelling

What is changed ?

What is new ?

biomod 4.2-6 - Improved OptionsBigBoss and new model

What is changed ?

What is new ?

biomod 4.2-5 - Modeling options & Tuning Update

What is changed ?

What is new ?

biomod 4.2 - Terra Update

What is changed ?

biomod 4.1 is now available

What is changed ?

What is new ?

But... why ?

Owner metadata

GitHub Events

Total

Last Year

Committers metadata

Committer domains:

Issue and Pull Request metadata

Top Issue Authors

Top Pull Request Authors

Top Issue Labels

Top Pull Request Labels

Package metadata

cran.r-project.org: biomod2

conda-forge.org: r-biomod2

Dependencies

`biomod 4.3-1` - Abundance modelling

`biomod 4.2-6` - Improved OptionsBigBoss and new model

`biomod 4.2-5` - Modeling options & Tuning Update

`biomod 4.2` - Terra Update

`biomod 4.1` is now available