Tools for Ecological Niche Evolution Assessment Considering Uncertainty
Helper function to prepare bin tables
Maximum likelihood reconstruction of ancestral character states
Maximum parsimony reconstruction of ancestral character states
Bin table of environmental conditions in M and for occurrences
Bin tables of environmental conditions in M and for occurrences from o...
Bin tables of environmental conditions in M and for occurrences from d...
Histograms of environmental conditions in M and for occurrences (one s...
Histograms of environmental conditions in M and for occurrences
Example of accessible areas for a species
Maps of niche reconstructions and changes detected
PNG bar figures to represent ecological niches of distinct taxa
Labels to represent niches of tips and ancestors
Legends for niche labels in phylogenetic trees
nichevol: Assessment of Species’ Ecological Niche Evolution Considerin...
PNG bar figures for representing niche evolution
Labels to represent changes of niche characteristics between ancestors...
Legends for niche evolution labels in phylogenetic trees
Helper function to create PDF files with histograms
Read tables of binary niche characters from directory
Helper function to rename tips of trees for simulations
Helper function to calculate the median bin score for a given species
Helper function to assign bin scores to every tip in a given tree
Set values of uncertainty towards one or both ends of the variable
Helper function to get sigma squared values for a given dataset
Smooth character table values resulted from ancestral character state ...
Statistics of environmental conditions in M and for occurrences (one v...
Statistics of environmental conditions in M and for occurrences (multi...
Example of an environmental variable used in analysis
A collection of tools that allow users to perform critical steps in the process of assessing ecological niche evolution over phylogenies, with uncertainty incorporated explicitly in reconstructions. The method proposed here for ancestral reconstruction of ecological niches characterizes species' niches using a bin-based approach that incorporates uncertainty in estimations. Compared to other existing methods, the approaches presented here reduce risk of overestimation of amounts and rates of ecological niche evolution. The main analyses include: initial exploration of environmental data in occurrence records and accessible areas, preparation of data for phylogenetic analyses, executing comparative phylogenetic analyses of ecological niches, and plotting for interpretations. Details on the theoretical background and methods used can be found in: Owens et al. (2020) <doi:10.1002/ece3.6359>, Peterson et al. (1999) <doi:10.1126/science.285.5431.1265>, Soberón and Peterson (2005) <doi:10.17161/bi.v2i0.4>, Peterson (2011) <doi:10.1111/j.1365-2699.2010.02456.x>, Barve et al. (2011) <doi:10.1111/ecog.02671>, Machado-Stredel et al. (2021) <doi:10.21425/F5FBG48814>, Owens et al. (2013) <doi:10.1016/j.ecolmodel.2013.04.011>, Saupe et al. (2018) <doi:10.1093/sysbio/syx084>, and Cobos et al. (2021) <doi:10.1111/jav.02868>.
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