SDMtoolbox 2.0: the next generation Python-based GIS toolkit for landscape genetic, biogeographic and species distribution model analyses

SDMtoolbox 2.0 is a software package for spatial studies of ecology, evolution, and genetics. The release of SDMtoolbox 2.0 allows researchers to use the most current ArcGIS software and MaxEnt software, and reduces the amount of time that would be spent developing common solutions. The central aim...

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Bibliographic Details
Published in:PeerJ (San Francisco, CA) Vol. 5; p. e4095
Main Authors: Brown, Jason L., Bennett, Joseph R., French, Connor M.
Format: Journal Article
Language:English
Published: United States PeerJ. Ltd 05.12.2017
PeerJ Inc
Subjects:
Analysis
Animal behavior
Animal populations
ArcGIS
Biodiversity
Biogeography
Bioinformatics
Conservation Biology
Ecological niche models
Geographic information systems
Graphical user interfaces
MaxEnt bias files
Python (Programming language)
Rarefy occurrences
Spatial jackknifing
Technology application
ArcGIS
CANAPE categorization
Ecological niche models
Rarefy occurrences
Spatial jackknifing
MaxEnt bias files
Geographic information systems
ISSN:2167-8359, 2167-8359
Online Access:Get full text
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Summary:SDMtoolbox 2.0 is a software package for spatial studies of ecology, evolution, and genetics. The release of SDMtoolbox 2.0 allows researchers to use the most current ArcGIS software and MaxEnt software, and reduces the amount of time that would be spent developing common solutions. The central aim of this software is to automate complicated and repetitive spatial analyses in an intuitive graphical user interface. One core tenant facilitates careful parameterization of species distribution models (SDMs) to maximize each model’s discriminatory ability and minimize overfitting. This includes carefully processing of occurrence data, environmental data, and model parameterization. This program directly interfaces with MaxEnt, one of the most powerful and widely used species distribution modeling software programs, although SDMtoolbox 2.0 is not limited to species distribution modeling or restricted to modeling in MaxEnt. Many of the SDM pre- and post-processing tools have ‘universal’ analogs for use with any modeling software. The current version contains a total of 79 scripts that harness the power of ArcGIS for macroecology, landscape genetics, and evolutionary studies. For example, these tools allow for biodiversity quantification (such as species richness or corrected weighted endemism), generation of least-cost paths and corridors among shared haplotypes, assessment of the significance of spatial randomizations, and enforcement of dispersal limitations of SDMs projected into future climates—to only name a few functions contained in SDMtoolbox 2.0. Lastly, dozens of generalized tools exists for batch processing and conversion of GIS data types or formats, which are broadly useful to any ArcMap user.
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ISSN:2167-8359
2167-8359
DOI:10.7717/peerj.4095