R code for the analyses from "Evolutionary and environmental drivers of species richness in poeciliid fishes across the Americas" by García-Andrade et al. 2021. Global Ecology and Biogeography, 30:1245–1257.
R code to replicate all data treatment and analyses from the paper
(1) Extents of occurrence: This section generates the species' extents of occurrence (EOO, range maps) using alpha convex hull polygons overlapped on sub-basins, and/or the sub-basin distribution of each species.
(2) Presence-absence matrix: This section creates the presence-absence matrix (PAM) that will be used to calculate all modeled variables (response and predictors), using the species' extents of occurrence.
(3) Evolutionary time: This section calculates the maximum branch length (MBL) across a multiphylo object
(4) Speciation rates: This section calculates the mean diversification rate (mDR)
(5) Environmental variables: This section prepares all environmental variables to the resolution of 50x50 km, Mollweide projection and the extent of study area
(6) Piecewise structural equation modeling: This code section fits a series of spatial autoregressive models, using different neighbour distances and weights scheme to find the best fit for each pathway. Also, it runs and fits a piecewise structural equation model (pSEM) for the data.
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