nichevol {nichevol}

nichevol: Assessment of Species’ Ecological Niche Evolution Considering Uncertainty in Reconstructions

Description

nichevol is 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.

Main functions in nichevol

bin_ml_rec, bin_par_rec, bin_table, bin_tables, bin_tables0, hist_evalues, histograms_env, map_nichevol, niche_bars, nichevol_bars, niche_labels, nichevol_labels, niche_legend, nichevol_legend, set_uncertainty, smooth_rec, stats_eval, stats_evalues

Other functions (important helpers)

bin_env, pdf_histograms, rename_tips, score_tip, score_tree, sig_sq