Supplementary Data and Code: Different traits dominate evolution at early and late stages of adaptive radiation

Supplementary Data and R code for phylogenetic analyses for manuscript entitled Different traits dominate evolution at early and late stages of adaptive radiation. 

Code.zip contains all R scripts and data needed for analyses in the paper. It is divided in two parts, DECOUPLED DIVERSIFICATION (folder 1) and STATES-DEPENDENT SPECIATION AND EXTINCTION (folder 2).

1) DECOUPLED DIVERSIFICATION

"data" folder contains phyogeny, morpho and eco data, species by clades, and RDS with imputed values for missing traits.

Niphargus_trait_evolution.rmd file runs neccessary packages and scripts and outputs results. Note that working directory and "result" folder need to be defined before you run the script.

00_data.R: import and data manipulation, including imputation of missing values to morpho ds. All variables needed in later analyses are defined here, including subsets, subclades, etc.
00_functions.R: all custom functions
01_figure1_phylogeny.R: plots half-circle phylogeny
02_regression_PCA.R: runs phylogenetic regression and PCA, and saves results
03_kmeans.R: calculates k-means and saves results
04_modeling.R: runs modeling, ancestral trait reconstruction and morphospace expansion through time, simulations and comparison of morphospace expansion of real and simulated data.

2) STATES-DEPENDENT SPECIATION AND EXTINCTION

This folder includes data and code used for sec_sse analysis. The analysis was run on whole genus and three major clades. Additionally, trophic trait classes were compared with habitat trait class (trophicD and trophicP), so overall, 8 combinations of model comparisons were performed. The folder is thus divided into "clades" and "whole_genus" subfolders. Data and R scripts for model setup, launching the analysis and calculation of AIC values are provided.