Code for revisiting the biogeography of SoutEast Asia while accounting for extinction. In this repository I show the code used to call the main function of R package lemad to reconstruct the distribution of ancestors. In this code, several models will be fitted to data with different fixed rates of species extinction. I also include a code for plotting the output from lemad. Notice that lemad package now includes a function that does that.
The data used for the analysis was kindly provided by the authors of the revisited papers. I therefore have no the rights to make them available to the public, except for two datasets: Pseuduvaria treelets and Paphiopedilum orchids. For those two datasets, I provide the data (phylogenetic tree and geographic distribution) to replicate the analysis. This can be done with the function at main_paphiopedilum.R and main_pseuduvaria.R files.