Man pages for richelbilderbeek/wiritttea
WIRITTTE analysis

a2iConvert an alignment position to an index
are_from_same_distributionChecks if two samples are from the same distribution with a...
calc_dmidCalculates the Distance Matrix Information Density, which is...
collect_allPerforms the full analysis on all the .RDa files present in a...
collect_file_essesCollects the ESSes of all phylogenies belonging to a...
collect_file_n_alignmentsCollect the number of alignments in a parameter file
collect_file_nlttsCollects the nLTTs of all phylogenies belonging to a...
collect_file_nltt_statsCalculates the nLTT statistics from a file
collect_file_n_posteriorsCollect the number of posteriors in a parameter file
collect_file_nrbssCollects the NRBS values between species trees and posteriors...
collect_file_posterior_gammasCollect the gamma statistics of the BEAST2 posteriors
collect_file_posterior_nlttsCollect the nLTT values of the BEAST2 posteriors
collect_file_pstr_crown_agesCollect the crown ages of the BEAST2 posteriors
collect_file_pstr_likelihoodsCollect the tree likelihoods of the BEAST2 posteriors
collect_files_alignmentsCollects the quality of the alignments of the files
collect_files_alignments_dmidCollect the alignments' DMIDs
collect_files_essesCollects the ESSes of all phylogenies belonging to the .RDa...
collect_files_esses_from_logsCollects the ESSes of all phylogenies belonging to the...
collect_files_n_alignmentsCollects the number of alignments of all phylogenies...
collect_files_nltt_statsCalculates the nLTT statistics from multiple clean files
collect_files_nltt_stats_dirtyCalculates the nLTT statistics from multiple files that may...
collect_files_n_posteriorsCollects the number of posteriors of all phylogenies...
collect_files_nrbssCollects the NRBS values of all phylogenies belonging to a...
collect_files_n_species_treesCollects the number of sampled species trees of all...
collect_files_n_taxaCollects the number of taxa of all phylogenies belonging to a...
collect_files_operatorsCalculates the BEAST2 operators from multiple files
collect_files_parametersCollects the parameters of its input files
collect_files_posterior_gammasCollects the gamma statistics of all phylogenies belonging to...
collect_files_posterior_nlttsCollects the nLTT statistics of all phylogenies belonging to...
collect_files_pstr_crown_agesCollects the tree crown_ages of all phylogenies belonging to...
collect_files_pstr_likelihoodsCollects the tree likelihoods of all phylogenies belonging to...
collect_files_stree_gammasCollects the gamma statistics of all phylogenies belonging to...
collect_files_stree_nlttsCollects the nLTT statistics of all phylogenies belonging to...
collect_files_strees_identicalCollects if the two sampled species trees (from the same...
collect_file_stree_gammasCollect the gamma statistics of the species trees with...
collect_file_stree_nlttsCollect the nLTT values of the species trees with outgroup
collect_gamma_statisticsCollects the gamma statistics of all phylogenies in the...
collect_log_file_infoCollects information of a log file in the melted/uncast/long...
collect_log_files_infoCollects log file information in the melted/uncast/long form
collect_nltt_statsCalculate the nLTT statistic between a focal phylogeny and...
collect_n_species_treesCollect the number of sampled species trees in a parameter...
collect_n_taxaCollects the number of taxa of all phylogenies in the...
collect_species_tree_n_taxaCollect the number of taxa of the species trees
convert_alignment_to_fastaConvert an alignment (of type DNAbin) to a FASTA file
create_figure_acceptance_mcmc_operatorsCreate the figure 'Operator acceptances'
create_figure_alignment_qualitiesCreate figure 'alignment_qualities'
create_figure_errorCreates figure 'figure_error.svg', showing the complete...
create_figure_error_alignment_lengthCreate figure 'error_alignment_length'
create_figure_error_alignment_length_meanCreate figure 'figure_error_alignment_length_mean'
create_figure_error_alignment_length_medianCreate figure 'figure_error_alignment_length_median'
create_figure_error_bdCreate figure create_figure_error_bd
create_figure_error_bd_meanCreate figure create_figure_error_bd_mean
create_figure_error_for_scrCreate figure create_figure_error_for_scr
create_figure_error_low_high_essCreate figure 'figure_error_low_high_ess'
create_figure_error_low_high_ess_meanCreate figure 'figure_error_low_high_ess' using mean nLTT...
create_figure_error_maxCreate 'figure_error_max', showing the phylogeny with the...
create_figure_error_mean_dur_specCreate 'figure_error_mean_dur_spec'
create_figure_error_mean_dur_spec_alignment_lengthCreate 'figure_error_expected_mean_dur_spec_alignment_length'
create_figure_error_mean_dur_spec_meanCreate 'figure_error_expected_mean_dur_spec_mean' (tailing...
create_figure_error_mean_dur_spec_mean_alignment_lengthCreate 'figure_error_expected_mean_dur_spec_alignment_length'
create_figure_error_mean_dur_spec_mean_samplingCreate 'figure_error_expected_mean_dur_spec_mean_sampling'
create_figure_error_mean_dur_spec_medianCreate 'figure_error_expected_mean_dur_spec_median' (tailing...
create_figure_error_mean_dur_spec_samplingCreate 'figure_error_expected_mean_dur_spec_sampling'
create_figure_error_posterior_nltt_siCreate 'figure_error_posterior_nltt_si', showing phylogenies...
create_figure_error_sampling_representativeCreate figure figure_error_sampling_representative
create_figure_error_tree_sizeCreate figure 'figure_error_tree_size'
create_figure_ess_distributionCreate 'figure_ess_distribution'
create_figure_ess_distribution_likelihoodCreate 'figure_ess_distribution_likelihood'
create_figure_ess_expected_mean_dur_spec_alignment_lengthCreate 'figure_ess_expected_mean_dur_spec_alignment_length'
create_figure_exit_statusesCreate figure 'figure_exit_statuses'
create_figure_exit_statuses_posteriorsCreate figure_exit_statuses_posteriors: How many parameter...
create_figure_lowest_essCreate figure_lowest_ess: Which estimated parameter has the...
create_figure_posterior_bdCreate 'figure_posterior_distributions_bd'
create_figure_posterior_crown_agesCreate 'figure_posterior_distributions_crown_age'
create_figure_posterior_likelihoodsCreate 'figure_posterior_distributions_likelihood' and...
create_figure_posterior_nlttsCreate 'figure_posterior_distributions_nltts'
create_figure_run_timesfigure_run_times: distribution of runtimes
create_figure_strees_differentCreate figure_strees_different Analyse if the two sampled...
create_log_filenamesCreates the filenames of the log files
create_table_109Table 109: Successes and reasons of failures
create_table_111Table 111: How many parameter estimates are OK?
create_table_112Table 112: Which estimated parameter has the lowest ESS?
file_to_linesRead a file and convert it to a vector of strings, in...
find_pathFinds the full path of a file
find_pathsFinds the full path of files
get_phylogeny_crown_ageObtain the crown age of a phylony
has_alignmentsChecks if alignments are present
have_same_streesSee if a file its two species trees have different branch...
is_distributed_normallySees if the values of a distribution are normally distributed...
is_good_alignmentChecks if an alignment is good enough
is_whole_numberChecks if x is a single, whole-number variable
nrbsCalculates the Normalized Rooted Branch Score (NRBS)
p2iConvert a posterior position to an index
postrs_same_distr_nltt_statTests if the nLTT statistics between posteriors are of the...
read_collected_alignmentsReads the file with the collected alignments' qualities
read_collected_essesRead all the collected ESSes of all simulations' posteriors
read_collected_gammas_postrsRead all the collected gamma statistics of all posteriors
read_collected_gammas_streesRead all the collected nLTT values of all species trees
read_collected_log_files_infoReads the file with the collected log files info
read_collected_nltts_postrsRead all the collected nLTT values of all posteriors
read_collected_nltts_streesRead all the collected nLTT values of all species trees
read_collected_nltt_statsRead all the collected nLTT statistics of all simulations
read_collected_n_taxaReads the file with the collected number of taxa
read_collected_operatorsReads the file with the collected BEAST2 operators'...
read_collected_parametersReads the file with the collected parameters
read_collected_posterior_nlttsRead all the collected nLTT statistics of all posteriors
read_collected_pstr_crown_agesRead all the collected tree crown_ages of all posteriors
read_collected_pstr_liksRead all the collected tree likelihoods of all posteriors
read_collected_strees_identicalReads the file with the collected species trees being...
richelbilderbeek/wiritttea documentation built on Oct. 17, 2017, 1:34 p.m.