Coding Characters From Scratch

This section offers tips on how to start coding taxa for which there are no prior phylogenetic studies. This also is intended to offer tips on how to mentor someone attempting such a project. This might also be useful for groups that have existing phylogenetic studies but for which additional comparative anatomy in the “traditional” literature might provide further characters & states.

Some R Code Example

common_source_folder <- "~/Documents/R_Projects/Common_R_Source_Files/";    # directory to folder where you keep common source
source(paste(common_source_folder,"RevBayes_Setup.r",sep=""));

analysis_name <- "Cinctanmania_2019";
mesquite_to_RevBayes <- diffindo_character_matrix_by_state_numbers_and_other_partitions(analysis_name);

set_wdir <- "/Users/bilbo_baggins/Documents/RevBayes_Projects/";   # set directory for folder where you want the output to go.
scribio_RevBayes_scripts_from_chosen_nexus_file_and_existing_FBD_script_and_data(analysis_name=analysis_name,set_wdir=set_wdir);

end()