Man pages for richelbilderbeek/wiritttea
WIRITTTE analysis
| a2i | Convert an alignment position to an index |
| are_from_same_distribution | Checks if two samples are from the same distribution with a... |
| calc_dmid | Calculates the Distance Matrix Information Density, which is... |
| collect_all | Performs the full analysis on all the .RDa files present in a... |
| collect_file_esses | Collects the ESSes of all phylogenies belonging to a... |
| collect_file_n_alignments | Collect the number of alignments in a parameter file |
| collect_file_nltts | Collects the nLTTs of all phylogenies belonging to a... |
| collect_file_nltt_stats | Calculates the nLTT statistics from a file |
| collect_file_n_posteriors | Collect the number of posteriors in a parameter file |
| collect_file_nrbss | Collects the NRBS values between species trees and posteriors... |
| collect_file_posterior_gammas | Collect the gamma statistics of the BEAST2 posteriors |
| collect_file_posterior_nltts | Collect the nLTT values of the BEAST2 posteriors |
| collect_file_pstr_crown_ages | Collect the crown ages of the BEAST2 posteriors |
| collect_file_pstr_likelihoods | Collect the tree likelihoods of the BEAST2 posteriors |
| collect_files_alignments | Collects the quality of the alignments of the files |
| collect_files_alignments_dmid | Collect the alignments' DMIDs |
| collect_files_esses | Collects the ESSes of all phylogenies belonging to the .RDa... |
| collect_files_esses_from_logs | Collects the ESSes of all phylogenies belonging to the... |
| collect_files_n_alignments | Collects the number of alignments of all phylogenies... |
| collect_files_nltt_stats | Calculates the nLTT statistics from multiple clean files |
| collect_files_nltt_stats_dirty | Calculates the nLTT statistics from multiple files that may... |
| collect_files_n_posteriors | Collects the number of posteriors of all phylogenies... |
| collect_files_nrbss | Collects the NRBS values of all phylogenies belonging to a... |
| collect_files_n_species_trees | Collects the number of sampled species trees of all... |
| collect_files_n_taxa | Collects the number of taxa of all phylogenies belonging to a... |
| collect_files_operators | Calculates the BEAST2 operators from multiple files |
| collect_files_parameters | Collects the parameters of its input files |
| collect_files_posterior_gammas | Collects the gamma statistics of all phylogenies belonging to... |
| collect_files_posterior_nltts | Collects the nLTT statistics of all phylogenies belonging to... |
| collect_files_pstr_crown_ages | Collects the tree crown_ages of all phylogenies belonging to... |
| collect_files_pstr_likelihoods | Collects the tree likelihoods of all phylogenies belonging to... |
| collect_files_stree_gammas | Collects the gamma statistics of all phylogenies belonging to... |
| collect_files_stree_nltts | Collects the nLTT statistics of all phylogenies belonging to... |
| collect_files_strees_identical | Collects if the two sampled species trees (from the same... |
| collect_file_stree_gammas | Collect the gamma statistics of the species trees with... |
| collect_file_stree_nltts | Collect the nLTT values of the species trees with outgroup |
| collect_gamma_statistics | Collects the gamma statistics of all phylogenies in the... |
| collect_log_file_info | Collects information of a log file in the melted/uncast/long... |
| collect_log_files_info | Collects log file information in the melted/uncast/long form |
| collect_nltt_stats | Calculate the nLTT statistic between a focal phylogeny and... |
| collect_n_species_trees | Collect the number of sampled species trees in a parameter... |
| collect_n_taxa | Collects the number of taxa of all phylogenies in the... |
| collect_species_tree_n_taxa | Collect the number of taxa of the species trees |
| convert_alignment_to_fasta | Convert an alignment (of type DNAbin) to a FASTA file |
| create_figure_acceptance_mcmc_operators | Create the figure 'Operator acceptances' |
| create_figure_alignment_qualities | Create figure 'alignment_qualities' |
| create_figure_error | Creates figure 'figure_error.svg', showing the complete... |
| create_figure_error_alignment_length | Create figure 'error_alignment_length' |
| create_figure_error_alignment_length_mean | Create figure 'figure_error_alignment_length_mean' |
| create_figure_error_alignment_length_median | Create figure 'figure_error_alignment_length_median' |
| create_figure_error_bd | Create figure create_figure_error_bd |
| create_figure_error_bd_mean | Create figure create_figure_error_bd_mean |
| create_figure_error_for_scr | Create figure create_figure_error_for_scr |
| create_figure_error_low_high_ess | Create figure 'figure_error_low_high_ess' |
| create_figure_error_low_high_ess_mean | Create figure 'figure_error_low_high_ess' using mean nLTT... |
| create_figure_error_max | Create 'figure_error_max', showing the phylogeny with the... |
| create_figure_error_mean_dur_spec | Create 'figure_error_mean_dur_spec' |
| create_figure_error_mean_dur_spec_alignment_length | Create 'figure_error_expected_mean_dur_spec_alignment_length' |
| create_figure_error_mean_dur_spec_mean | Create 'figure_error_expected_mean_dur_spec_mean' (tailing... |
| create_figure_error_mean_dur_spec_mean_alignment_length | Create 'figure_error_expected_mean_dur_spec_alignment_length' |
| create_figure_error_mean_dur_spec_mean_sampling | Create 'figure_error_expected_mean_dur_spec_mean_sampling' |
| create_figure_error_mean_dur_spec_median | Create 'figure_error_expected_mean_dur_spec_median' (tailing... |
| create_figure_error_mean_dur_spec_sampling | Create 'figure_error_expected_mean_dur_spec_sampling' |
| create_figure_error_posterior_nltt_si | Create 'figure_error_posterior_nltt_si', showing phylogenies... |
| create_figure_error_sampling_representative | Create figure figure_error_sampling_representative |
| create_figure_error_tree_size | Create figure 'figure_error_tree_size' |
| create_figure_ess_distribution | Create 'figure_ess_distribution' |
| create_figure_ess_distribution_likelihood | Create 'figure_ess_distribution_likelihood' |
| create_figure_ess_expected_mean_dur_spec_alignment_length | Create 'figure_ess_expected_mean_dur_spec_alignment_length' |
| create_figure_exit_statuses | Create figure 'figure_exit_statuses' |
| create_figure_exit_statuses_posteriors | Create figure_exit_statuses_posteriors: How many parameter... |
| create_figure_lowest_ess | Create figure_lowest_ess: Which estimated parameter has the... |
| create_figure_posterior_bd | Create 'figure_posterior_distributions_bd' |
| create_figure_posterior_crown_ages | Create 'figure_posterior_distributions_crown_age' |
| create_figure_posterior_likelihoods | Create 'figure_posterior_distributions_likelihood' and... |
| create_figure_posterior_nltts | Create 'figure_posterior_distributions_nltts' |
| create_figure_run_times | figure_run_times: distribution of runtimes |
| create_figure_strees_different | Create figure_strees_different Analyse if the two sampled... |
| create_log_filenames | Creates the filenames of the log files |
| create_table_109 | Table 109: Successes and reasons of failures |
| create_table_111 | Table 111: How many parameter estimates are OK? |
| create_table_112 | Table 112: Which estimated parameter has the lowest ESS? |
| file_to_lines | Read a file and convert it to a vector of strings, in... |
| find_path | Finds the full path of a file |
| find_paths | Finds the full path of files |
| get_phylogeny_crown_age | Obtain the crown age of a phylony |
| has_alignments | Checks if alignments are present |
| have_same_strees | See if a file its two species trees have different branch... |
| is_distributed_normally | Sees if the values of a distribution are normally distributed... |
| is_good_alignment | Checks if an alignment is good enough |
| is_whole_number | Checks if x is a single, whole-number variable |
| nrbs | Calculates the Normalized Rooted Branch Score (NRBS) |
| p2i | Convert a posterior position to an index |
| postrs_same_distr_nltt_stat | Tests if the nLTT statistics between posteriors are of the... |
| read_collected_alignments | Reads the file with the collected alignments' qualities |
| read_collected_esses | Read all the collected ESSes of all simulations' posteriors |
| read_collected_gammas_postrs | Read all the collected gamma statistics of all posteriors |
| read_collected_gammas_strees | Read all the collected nLTT values of all species trees |
| read_collected_log_files_info | Reads the file with the collected log files info |
| read_collected_nltts_postrs | Read all the collected nLTT values of all posteriors |
| read_collected_nltts_strees | Read all the collected nLTT values of all species trees |
| read_collected_nltt_stats | Read all the collected nLTT statistics of all simulations |
| read_collected_n_taxa | Reads the file with the collected number of taxa |
| read_collected_operators | Reads the file with the collected BEAST2 operators'... |
| read_collected_parameters | Reads the file with the collected parameters |
| read_collected_posterior_nltts | Read all the collected nLTT statistics of all posteriors |
| read_collected_pstr_crown_ages | Read all the collected tree crown_ages of all posteriors |
| read_collected_pstr_liks | Read all the collected tree likelihoods of all posteriors |
| read_collected_strees_identical | Reads the file with the collected species trees being... |
