Package: gdm 1.6.0-3

gdm: Generalized Dissimilarity Modeling

A toolkit with functions to fit, plot, summarize, and apply Generalized Dissimilarity Models. Mokany K, Ware C, Woolley SNC, Ferrier S, Fitzpatrick MC (2022) <doi:10.1111/geb.13459> Ferrier S, Manion G, Elith J, Richardson K (2007) <doi:10.1111/j.1472-4642.2007.00341.x>.

Authors:Matt Fitzpatrick [aut, cre], Karel Mokany [aut], Glenn Manion [aut], Diego Nieto-Lugilde [aut], Simon Ferrier [aut], Roozbeh Valavi [ctb], Matthew Lisk [ctb], Chris Ware [ctb], Skip Woolley [ctb], Tom Harwood [ctb]

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gdm.pdf |gdm.html✨
gdm/json (API)
NEWS

# Install 'gdm' in R:

install.packages('gdm', repos = c('https://fitzlab-al.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/fitzlab-al/gdm/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

gdmDissim - An example biological dissimilarity matrix
southwest - Species and Environmental Data from Southwestern Australia.

On CRAN:

7.86 score 33 stars 122 scripts 1.2k downloads 16 mentions 10 exports 24 dependencies

Last updated 4 days agofrom:7164734afa. Checks:OK: 9. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 19 2024
R-4.5-win-x86_64	OK	Nov 19 2024
R-4.5-linux-x86_64	OK	Nov 19 2024
R-4.4-win-x86_64	OK	Nov 19 2024
R-4.4-mac-x86_64	OK	Nov 19 2024
R-4.4-mac-aarch64	OK	Nov 19 2024
R-4.3-win-x86_64	OK	Nov 19 2024
R-4.3-mac-x86_64	OK	Nov 19 2024
R-4.3-mac-aarch64	OK	Nov 19 2024

Exports:calculate.gdm.deviance formatsitepair gdm gdm.crossvalidation gdm.partition.deviance gdm.transform gdm.varImp isplineExtract plotUncertainty subsample.sitepair

Dependencies:cli cluster codetools doParallel foreach glue iterators lattice lifecycle magrittr MASS Matrix mgcv nlme pbapply permute plyr Rcpp reshape2 rlang stringi stringr vctrs vegan

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Overview of the functions in the gdm package	gdm-package
Calculate GDM Deviance for Observed & Predicted Dissimilarities	calculate.gdm.deviance
Combines Biological and Environmental Data to Produce a GDM-formatted Site-Pair Table	formatsitepair
Fit a Generalized Dissimilarity Model to Tabular Site-Pair Data	gdm
Cross-Validation Assessment of a Fitted GDM	gdm.crossvalidation
Perform Deviance Partitioning of a Fitted GDM	gdm.partition.deviance
Transform Environmental Data Using a Fitted Generalized Dissimilarity Model	gdm.transform
Assess Predictor Importance and Quantify Model Significance in a Fitted Generalized Dissimilarity Model.	gdm.varImp
An example biological dissimilarity matrix	gdmDissim
Extract I-spline Values From a Fitted Generalized Dissimilarity Model.	isplineExtract
Plot Model Fit and I-splines from a Fitted Generalized Dissimilarity Model.	plot.gdm
Plot I-splines With Error Bands Using Bootstrapping.	plotUncertainty
Predict Biological Dissimilarities Between Sites or Times Using a Fitted Generalized Dissimilarity Model	predict.gdm
Species and Environmental Data from Southwestern Australia.	southwest
Remove Sites at Random from a Site-Pair Table	subsample.sitepair
Summarize a Fitted Generalized Dissimilarity Model	summary.gdm