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Marlon E. Cobos, Hannah L. Owens, and A. Townsend Peterson
- nichevol is now on CRAN, you can find it here.
- Check our User Guide for further details on how to install and use nichevol.
nichevol is an R package that helps users to perform critical steps in the process of assessment of species’ ecological niche evolution, with uncertainty incorporated explicitly in evolutionary reconstructions. The method proposed here for ancestral reconstruction of ecological niches characterizes species’ niches using a bin-based approach that incorporates uncertainty directly in estimations. Compared to other existing methods, the approaches presented here reduce risks of overestimation of amounts or rates of ecological niche evolution. The main analyses include: initial exploration of environmental data in species records and accessible areas, preparation of data for phylogenetic analyses, comparative phylogenetic analyses, and plotting for interpretations.
Four main types of functions are included in nichevol: (1) the ones that help in preparing data (exploration plots and tables of characters) for ancestral reconstruction; (2) the ones that perform the ancestral reconstructions (Maximum Parsimony and Maximum Likelihood); (3) some complementary functions that help in performing post-reconstruction steps (reconstruction smoothing, and niche and niche evolution representations); and (4) the ones that help in producing virtual species for exploring hypothesis. Of course, other helper functions are used in the package, but they won’t be used as commonly.
These functions are used to explore numerically and graphically how environments in the areas accessible to the species (M) and in their occurrences look like. They also help to prepare tables of characters that represent species ecological niches considering used and non-used conditions, as well as conditions where the use is uncertain. Most of the functions in this module can be used to consider all species of interest and multiple environmental variables at the time. For that reason, they read data from a local directory and have the option to write results in such directories as well. The functions that work with data from the R environment are the ones specifically designed to work with multiple species but only one variable. These last functions do not write results in local directories. We have intentionally designed some of our functions to work interacting with local directories to avoid RAM-related limitations (especially when working with multiple environmental raster layers at high resolution).
This module contains functions that help in performing ancestral reconstruction of species ecological niches. These functions use as inputs the results of the ones from the previous module (tables of characters) and phylogenetic trees as in objects of class “phylo” (see the package ape). There are two types of reconstructions available to date (Maximum Likelihood and Maximum Parsimony), but at least other type will be included. All these functions use inputs and produce outputs in the R environment.
Functions in this module are intended to help with two main processes. First, one of these functions helps in smoothing results from ancestral reconstructions. This is necessary to prevent misinterpretations of results from comparing reconstructed niches of ancestors with niches of descendants (younger ancestors or taxa of interest). Second, other functions help in representing results of previous analyses. For instance, they help in producing bar-like labels that represent the niche of a species, or, they can also be used to represent how niches have evolved across the phylogeny.
This module is still under development, but it is intended to help in creating a suit of virtual species’ niches and their phylogenetic relationships to explore hypothesis of niche evolution.