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SDMTools specifications

Information


Unique identifier OMICS_33018
Name SDMTools
Alternative name Species Distribution Modelling Tools
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 1.1-221
Stability Stable
Source code URL https://cran.r-project.org/src/contrib/SDMTools_1.1-221.tar.gz
Maintained Yes

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Versioning


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Documentation


Maintainer


  • person_outline Jeremy VanDerWal

SDMTools citations

 (56)
call_split

Genetic structure of wild pea (Pisum sativum subsp. elatius) populations in the northern part of the Fertile Crescent reflects moderate cross pollination and strong effect of geographic but not environmental distance

2018
PLoS One
PMCID: 5868773
PMID: 29579076
DOI: 10.1371/journal.pone.0194056
call_split See protocol

[…] the studied populations have been estimated in the current and future projected climatic niche. For the manipulation of GIS data, as well as the creation of figures, the packages Sp [], Raster [] and SDMTools [] were employed. […]

call_split

Flow Management to Control Excessive Growth of Macrophytes – An Assessment Based on Habitat Suitability Modeling

2018
Front Plant Sci
PMCID: 5868135
PMID: 29616067
DOI: 10.3389/fpls.2018.00356
call_split See protocol

[…] used the “True Skill Statistic” (TSS; sensitivity + specificity – 1), because it accounts for the effect of the species prevalence (). All accuracy measurements were carried out using the R package “SDMtools” ().In order to investigate whether our models accounted for all the factors causing the species’ distributional pattern, we checked the observed species occurrence in the model reach for spa […]

library_books

Species Distribution Modelling: Contrasting presence only models with plot abundance data

2018
Sci Rep
PMCID: 5772443
PMID: 29343741
DOI: 10.1038/s41598-017-18927-1

[…] the median predicted area of occupancy for IDW.All calculations and analyses were performed with R version 3.0.33, including the R packages raster, rgdal, gstat, dismo, vegan, quantreg, sp, rJava and SDMTools. […]

library_books

Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high latitude adaptation

2018
PLoS Biol
PMCID: 5760011
PMID: 29315301
DOI: 10.1371/journal.pbio.2003703

[…] al clusters from K = 2 to K = 20. Common signals between independent runs for each K were identified using the LargeKGreedy algorithm of CLUMPP []. Clustering was visualized using rworldmap, ggplot2, SDMTools, and RColorBrewer packages of GNU R version 3.3.0. Starting from K = 3, when the modern samples split up into an African and eastern and western Eurasian clusters, the Mesolithic Scandinavian […]

call_split

Westwards and northwards dispersal of Triosteum himalayanum (Caprifoliaceae) from the Hengduan Mountains region based on chloroplast DNA phylogeography

2018
PeerJ
PMCID: 5951126
PMID: 29770273
DOI: 10.7717/peerj.4748
call_split See protocol

[…] iscriminant analysis; ), MARS (multivariate adaptive regression splines; ), RF (random forests; ), and MAXENT (maximum entropy; ) in R packages “Biomod 2” (), supported with rworld map, rgdal, dismo, SDMTools. The effectiveness of all the models were evaluated using TSS (true skill statistics) and AUC (area under curve; curve-receiver operating characteristic curve) values >0.7. A total of nine bi […]

library_books

On the absence of the Green tailed Trainbearer Lesbia nuna (Trochilidae) from Venezuela: an analysis based on environmental niche modelling

2017
Biodivers Data J
PMCID: 5742234
PMID: 29308047
DOI: 10.3897/BDJ.5.e22092

[…] ollected over a long period in a region characterised by high habitat transformation rates ().The grids of variables used in this study were processed using the libraries “raster” version 2.3-12 (), “SDMTools” version 1.1-221 (), “maptools” version 0.8-30 () and “rgdal” version 0.9-1 (), projected to the same coordinate system (EPSG:4248).To remove the effects of multi-collinearity, Pearson's corr […]

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