Man pages for richelbilderbeek/wiritttes
WIRITTE simulation

a2i	Convert an alignment position to an index
add_alignments	Add an alignment to a file
add_pbd_output	Adds a pbd_sim result to a file
add_pbd_output_iff_absent	Adds a pbd_sim result to a file, if and only if it is absent
add_posteriors	Add BEAST2 posteriors to a file
add_species_trees	Add two reconstructed species trees to a file that already...
alignment_to_beast_input_file	Convert an alignment and parameters to a BEAST XML input file
alignment_to_beast_posterior	Convert an alignment to a BEAST2 XML input file
are_identical_posteriors	Determines if the input is a wiritttes posterior,
are_identical_trees_posteriors	Determines if the input is a BEAST2 posterior, as parsed by...
are_valid_files	Checks if files are valid parameter files
convert_alignment_to_fasta	Convert an alignment (of type DNAbin) to a FASTA file
convert_phylogeny_to_alignment	Converts a phylogeny to a random DNA alignment
create_parameter_files_article	Creates the parameter files in the article Now every...
create_parameter_files_timings	Creates the parameter files in the article, but slimmed down...
create_test_parameter_files	Creates the parameter files for the toy examples
do_simulation	Run the full simulation pipeline on a parameter file on a...
do_test_simulations	Run the full simulation pipeline on the test parameters
extract_age	Extract the crown age from a file
extract_crown_age	Extract the crown age from a file
extract_erg	Extract the ERG ('Extinction Rate of a Good species')...
extract_eri	Extract the ERI ('Extinction Rate of an Incipient species')...
extract_fixed_crown_age	Extract if the crown age is fixed from a file
extract_mutation_rate	Extract the mutation rate parameter value from a file
extract_napst	Extract the number of alignments per species tree parameter...
extract_nppa	Extract the number of posteriors per alignment parameter...
extract_nspp	Extract the number of states per posterior parameter value...
extract_parameters	Extract the parameters from a file created by...
extract_scr	Extract the SCR ('Speciation Completion Rate') parameter...
extract_seed	Extract the RNG seed parameter value from a file
extract_sequence_length	Extract the DNA aligment sequence length parameter value from...
extract_sirg	Extract the SIRG ('Speciation Initial Rate of a Good...
extract_siri	Extract the SIRI ('Speciation Initial Rate of an Incipient...
file_has_valid_parameters	Checks if a file is a valid parameter file
find_beast_jar_path	Find the path of the BEAST2 jar file
find_path	Finds the full path of a file
find_paths	Finds the full path of files
get_alignment	Extract an alignment from an index from a file
get_alignment_by_index	Extract an alignment from an index from a file
get_alignments	Extract the alignments from a file
get_pbd_output	Get the PBD simulation output
get_phylogeny_crown_age	Obtain the crown age of a phylony
get_posterior	Extract a BEAST2 posterior from a file
get_posterior_by_index	Extract a BEAST2 posterior phyogenies from a file
get_posteriors	Extract the BEAST2 posterior phyogenies from a file
get_posterior_tree	Extract a BEAST2 posterior tree from a file
get_species_tree_by_index	Extract an species_tree from an index from a file
get_species_tree_oldest	Get the species tree with oldest subspecies representing each...
get_species_tree_youngest	Get the species tree with youngest subspecies representing...
has_alignments	Checks if alignments are present
has_beast2	Determines if BEAST2 is installed
has_species_trees	Sees if a the sampled species tree are present in the file
is_valid_file	Checks if one or more files are valid parameter files
nrbs	Calculates the Normalized Rooted Branch Score (NRBS)
p2i	Convert a posterior position to an index
read_file	Read a parameter (.RDa) file
read_files	Read multiple parameter (.RDa) files
save_parameters_to_file	Creates a valid parameter file
set_alignment	Set an alignment from an index from a file
set_alignment_by_index	Set an alignment of a file
set_posterior	Set an posterior to a file
set_posterior_by_index	Set a BEAST2 posterior of a file
set_species_tree_by_index	Set an species_tree of a file