This repository contains data and code used to investigate relationships among inflorescence architecture, diversification, and elevation in Bomarea (Alstroemeriaceae). Analyses include state-dependent diversification models (HiSSE), correlated trait evolution models, latent liability analyses, and ancestral state estimation analyses. Scripts not used in the final manuscript are labeled with _not_used.
data/
cleaned trait datasets in .nexus format for each trait
trimmed phylogenetic trees
data_prep/
raw trait dataset
raw phylogenetic tree
raw *Bomarea* occurrence data downloaded from GBIF
scripts used to calculate traits and generate .nexus files
scripts used to integrate trait datasets into a single dataframe
shared function file used across trait scripts
scripts/
latent_liability/
subfolders correspond to the traits included in each analysis
.xml files used in latent liability analyses
latent_liability.R and print_latent_liability_functions.R generate .xml files
latent_liability_figs.R and latent_liability_figs_functions.R generate figures from .log files
README.md documents manual edits made to final .xml files
plotting/
scripts for geographic distribution maps, trait correlation heat maps,
elevation and inflorescence-type correlations, and HiSSE visualizations
rb/
RevBayes scripts for elevation and inflorescence-type correlation analyses,
HiSSE analyses, and All Rates Different (ARD) ancestral state estimation
Analyses were conducted in R 4.4.2, RevBayes, BEAST.