Man pages for richelbilderbeek/wiritttes
WIRITTE simulation

a2iConvert an alignment position to an index
add_alignmentsAdd an alignment to a file
add_pbd_outputAdds a pbd_sim result to a file
add_pbd_output_iff_absentAdds a pbd_sim result to a file, if and only if it is absent
add_posteriorsAdd BEAST2 posteriors to a file
add_species_treesAdd two reconstructed species trees to a file that already...
alignment_to_beast_input_fileConvert an alignment and parameters to a BEAST XML input file
alignment_to_beast_posteriorConvert an alignment to a BEAST2 XML input file
are_identical_posteriorsDetermines if the input is a wiritttes posterior,
are_identical_trees_posteriorsDetermines if the input is a BEAST2 posterior, as parsed by...
are_valid_filesChecks if files are valid parameter files
convert_alignment_to_fastaConvert an alignment (of type DNAbin) to a FASTA file
convert_phylogeny_to_alignmentConverts a phylogeny to a random DNA alignment
create_parameter_files_articleCreates the parameter files in the article Now every...
create_parameter_files_timingsCreates the parameter files in the article, but slimmed down...
create_test_parameter_filesCreates the parameter files for the toy examples
do_simulationRun the full simulation pipeline on a parameter file on a...
do_test_simulationsRun the full simulation pipeline on the test parameters
extract_ageExtract the crown age from a file
extract_crown_ageExtract the crown age from a file
extract_ergExtract the ERG ('Extinction Rate of a Good species')...
extract_eriExtract the ERI ('Extinction Rate of an Incipient species')...
extract_fixed_crown_ageExtract if the crown age is fixed from a file
extract_mutation_rateExtract the mutation rate parameter value from a file
extract_napstExtract the number of alignments per species tree parameter...
extract_nppaExtract the number of posteriors per alignment parameter...
extract_nsppExtract the number of states per posterior parameter value...
extract_parametersExtract the parameters from a file created by...
extract_scrExtract the SCR ('Speciation Completion Rate') parameter...
extract_seedExtract the RNG seed parameter value from a file
extract_sequence_lengthExtract the DNA aligment sequence length parameter value from...
extract_sirgExtract the SIRG ('Speciation Initial Rate of a Good...
extract_siriExtract the SIRI ('Speciation Initial Rate of an Incipient...
file_has_valid_parametersChecks if a file is a valid parameter file
find_beast_jar_pathFind the path of the BEAST2 jar file
find_pathFinds the full path of a file
find_pathsFinds the full path of files
get_alignmentExtract an alignment from an index from a file
get_alignment_by_indexExtract an alignment from an index from a file
get_alignmentsExtract the alignments from a file
get_pbd_outputGet the PBD simulation output
get_phylogeny_crown_ageObtain the crown age of a phylony
get_posteriorExtract a BEAST2 posterior from a file
get_posterior_by_indexExtract a BEAST2 posterior phyogenies from a file
get_posteriorsExtract the BEAST2 posterior phyogenies from a file
get_posterior_treeExtract a BEAST2 posterior tree from a file
get_species_tree_by_indexExtract an species_tree from an index from a file
get_species_tree_oldestGet the species tree with oldest subspecies representing each...
get_species_tree_youngestGet the species tree with youngest subspecies representing...
has_alignmentsChecks if alignments are present
has_beast2Determines if BEAST2 is installed
has_species_treesSees if a the sampled species tree are present in the file
is_valid_fileChecks if one or more files are valid parameter files
nrbsCalculates the Normalized Rooted Branch Score (NRBS)
p2iConvert a posterior position to an index
read_fileRead a parameter (.RDa) file
read_filesRead multiple parameter (.RDa) files
save_parameters_to_fileCreates a valid parameter file
set_alignmentSet an alignment from an index from a file
set_alignment_by_indexSet an alignment of a file
set_posteriorSet an posterior to a file
set_posterior_by_indexSet a BEAST2 posterior of a file
set_species_tree_by_indexSet an species_tree of a file
richelbilderbeek/wiritttes documentation built on May 27, 2019, 8:14 a.m.