Files in richelbilderbeek/wiritttea

WIRITTTE analysis

.Rbuildignore

.Rprofile

.gitignore

.travis.yml

Codecov.png

DESCRIPTION

FAQ.md

LICENSE

NAMESPACE

R/are_from_same_distribution.R R/calc_dmid.R R/collect_all.R R/collect_file_esses.R R/collect_file_n_alignments.R R/collect_file_n_posteriors.R R/collect_file_nltt_stats.R R/collect_file_nltts.R R/collect_file_nrbss.R R/collect_file_posterior_crown_ages.R R/collect_file_posterior_gammas.R R/collect_file_posterior_likelihoods.R R/collect_file_posterior_nllts.R R/collect_file_stree_gammas.R R/collect_file_stree_nltts.R R/collect_files_alignments.R R/collect_files_alignments_dmid.R R/collect_files_esses.R R/collect_files_n_alignments.R R/collect_files_n_posteriors.R R/collect_files_n_species_trees.R R/collect_files_n_taxa.R R/collect_files_nltt_stats.R R/collect_files_nrbss.R R/collect_files_operators.R R/collect_files_parameters.R R/collect_files_posterior_crown_ages.R R/collect_files_posterior_gammas.R R/collect_files_posterior_likelihoods.R R/collect_files_posterior_nltt_stats.R R/collect_files_posterior_nltts.R R/collect_files_species_tree_gammas.R R/collect_files_species_tree_nltt_stats.R R/collect_files_species_tree_nltts.R R/collect_files_strees_identical.R R/collect_gamma_statistics.R R/collect_log_file_info.R R/collect_log_files_info.R R/collect_n_species_trees.R R/collect_n_taxa.R R/collect_nltt_stats.R R/collect_species_tree_n_taxa.R R/convert_alignment_to_fasta.R R/convert_indices.R R/create_figure_acceptance_mcmc_operators.R R/create_figure_alignment_qualities.R R/create_figure_error.R R/create_figure_error_alignment_length.R R/create_figure_error_alignment_length_mean.R R/create_figure_error_alignment_length_median.R R/create_figure_error_bd.R R/create_figure_error_bd_mean.R R/create_figure_error_for_scr.R R/create_figure_error_low_high_ess.R R/create_figure_error_low_high_ess_mean.R R/create_figure_error_max.R R/create_figure_error_mean_dur_spec.R R/create_figure_error_mean_dur_spec_alignment_length.R R/create_figure_error_mean_dur_spec_mean.R R/create_figure_error_mean_dur_spec_mean_alignment_length.R R/create_figure_error_mean_dur_spec_mean_sampling.R R/create_figure_error_mean_dur_spec_median.R R/create_figure_error_mean_dur_spec_sampling.R R/create_figure_error_posterior_nltt_si.R R/create_figure_error_sampling_representative.R R/create_figure_error_tree_size.R R/create_figure_ess_distribution.R R/create_figure_ess_distribution_likelihood.R R/create_figure_ess_expected_mean_dur_spec_alignment_length.R R/create_figure_exit_statuses.R R/create_figure_exit_statuses_posteriors.R R/create_figure_lowest_ess.R R/create_figure_posterior_bd.R R/create_figure_posterior_crown_ages.R R/create_figure_posterior_likelihoods.R R/create_figure_posterior_nltts.R R/create_figure_run_times.R R/create_figure_strees_different.R R/create_log_filenames.R R/create_table_109.R R/create_table_111.R R/create_table_112.R

R/file_has_valid_parameters.R

R/file_to_lines.R R/find_paths.R R/get_phylogeny_crown_age.R R/has_alignments.R R/have_same_strees.R R/is_distributed_normally.R R/is_good_alignment.R R/is_whole_number.R R/nrbs.R R/postrs_same_distr_nltt_stat.R R/read_collected_alignments.R R/read_collected_esses.R R/read_collected_gammas_postrs.R R/read_collected_gammas_strees.R R/read_collected_log_files_info.R R/read_collected_n_taxa.R R/read_collected_nltt_stats.R R/read_collected_nltts_postrs.R R/read_collected_nltts_strees.R R/read_collected_operators.R R/read_collected_parameters.R R/read_collected_postr_cas.R R/read_collected_postr_liks.R R/read_collected_postr_nltts.R R/read_collected_strees_identical.R R/zzz.R README.md

TravisCI.png

demo/00Index

demo/create_figure_error_bd.R demo/create_figure_error_bd_mean.R demo/create_figure_error_for_scr.R demo/create_figure_error_low_high_ess.R demo/create_figure_error_max.R demo/create_figure_error_mean_dur_spec.R demo/create_figure_error_mean_dur_spec_alignment_length.R demo/create_figure_error_mean_dur_spec_mean.R demo/create_figure_error_mean_dur_spec_mean_sampling.R demo/create_figure_error_mean_dur_spec_sampling.R demo/create_figure_error_sampling_representative.R demo/create_figure_error_tree_size.R demo/create_figure_ess_distribution.R demo/create_figure_ess_expected_mean_dur_spec_alignment_length.R demo/create_figure_exit_statuses.R demo/create_figure_exit_statuses_posteriors.R demo/create_figure_lowest_ess.R demo/create_figure_posterior_bd.R demo/create_figure_posterior_crown_ages.R demo/create_figure_posterior_likelihoods.R demo/create_figure_posterior_nltts.R demo/create_figure_run_times.R demo/create_figure_strees_different.R demo/create_table_109.R demo/create_table_111.R demo/create_table_112.R demo/src/README.md

demo/src/build_and_analyse_peregrine

demo/src/ess.cpp

demo/src/ess.h

demo/src/esses.cpp

demo/src/esses.h

demo/src/helper.cpp

demo/src/helper.h

demo/src/main.cpp

demo/src/nltt_stat.cpp

demo/src/nltt_stat.h

demo/src/nltt_stats.cpp

demo/src/nltt_stats.h

demo/src/parameters.cpp

demo/src/parameters.h

demo/src/posterior.cpp

demo/src/posterior.h

demo/src/posterior_row.cpp

demo/src/posterior_row.h

demo/src/r_helper.cpp

demo/src/r_helper.h

demo/src/state.cpp

demo/src/state.h

demo/src/wiritttea.R

demo/src/wiritttea.cpp

demo/src/wiritttea.h

demo/src/wiritttea.pri

demo/src/wiritttea.pro

demo/src/wiritttea_peregrine.pro

download_data.sh

inst/extdata/add_alignments_exceeded_memory.log

inst/extdata/add_alignments_ok.log

inst/extdata/add_posteriors_cannot_read_fasta.log

inst/extdata/add_posteriors_died_by_signal.log

inst/extdata/add_posteriors_fasta_io_error.log

inst/extdata/add_posteriors_incorrect_alignment.log

inst/extdata/add_posteriors_invalid_file.log

inst/extdata/add_posteriors_save_posterior_failed.log

inst/extdata/add_posteriors_sequence_no_dnabin.log

inst/extdata/add_posteriors_trees_file_absent.log

inst/extdata/article_no_newline.log

inst/extdata/collect_files_alignments.csv

inst/extdata/collect_files_esses.csv

inst/extdata/collect_files_esses_from_log_files.csv

inst/extdata/collect_files_esses_invalid.RDa

inst/extdata/collect_files_n_alignments.csv

inst/extdata/collect_files_n_posteriors.csv

inst/extdata/collect_files_n_species_trees.csv

inst/extdata/collect_files_n_taxa.csv

inst/extdata/collect_files_nltt_stats.csv

inst/extdata/collect_files_nrbss.csv

inst/extdata/collect_files_operators.xml.state

inst/extdata/collect_files_operators_empty.xml.state

inst/extdata/collect_files_parameters.csv

inst/extdata/collect_files_posterior_crown_ages.csv

inst/extdata/collect_files_posterior_gammas.csv

inst/extdata/collect_files_posterior_likelihoods.csv

inst/extdata/collect_files_posterior_nltts.csv

inst/extdata/collect_files_species_tree_nltts.csv

inst/extdata/collect_files_stree_gammas.csv

inst/extdata/collect_files_stree_nltts.csv

inst/extdata/collect_files_strees_gammas.csv

inst/extdata/collect_files_strees_identical.csv

inst/extdata/read_collected_alignments.csv

inst/extdata/read_collected_operators.csv

inst/extdata/toy_example_1.RDa

inst/extdata/toy_example_2.RDa

inst/extdata/toy_example_3.RDa

inst/extdata/toy_example_4.RDa

install_beast2

man/a2i.Rd man/are_from_same_distribution.Rd man/calc_dmid.Rd man/collect_all.Rd man/collect_file_esses.Rd man/collect_file_n_alignments.Rd man/collect_file_n_posteriors.Rd man/collect_file_nltt_stats.Rd man/collect_file_nltts.Rd man/collect_file_nrbss.Rd man/collect_file_posterior_gammas.Rd man/collect_file_posterior_nltts.Rd man/collect_file_pstr_crown_ages.Rd man/collect_file_pstr_likelihoods.Rd man/collect_file_stree_gammas.Rd man/collect_file_stree_nltts.Rd man/collect_files_alignments.Rd man/collect_files_alignments_dmid.Rd man/collect_files_esses.Rd man/collect_files_esses_from_logs.Rd man/collect_files_n_alignments.Rd man/collect_files_n_posteriors.Rd man/collect_files_n_species_trees.Rd man/collect_files_n_taxa.Rd man/collect_files_nltt_stats.Rd man/collect_files_nltt_stats_dirty.Rd man/collect_files_nrbss.Rd man/collect_files_operators.Rd man/collect_files_parameters.Rd man/collect_files_posterior_gammas.Rd man/collect_files_posterior_nltts.Rd man/collect_files_pstr_crown_ages.Rd man/collect_files_pstr_likelihoods.Rd man/collect_files_stree_gammas.Rd man/collect_files_stree_nltts.Rd man/collect_files_strees_identical.Rd man/collect_gamma_statistics.Rd man/collect_log_file_info.Rd man/collect_log_files_info.Rd man/collect_n_species_trees.Rd man/collect_n_taxa.Rd man/collect_nltt_stats.Rd man/collect_species_tree_n_taxa.Rd man/convert_alignment_to_fasta.Rd man/create_figure_acceptance_mcmc_operators.Rd man/create_figure_alignment_qualities.Rd man/create_figure_error.Rd man/create_figure_error_alignment_length.Rd man/create_figure_error_alignment_length_mean.Rd man/create_figure_error_alignment_length_median.Rd man/create_figure_error_bd.Rd man/create_figure_error_bd_mean.Rd man/create_figure_error_for_scr.Rd man/create_figure_error_low_high_ess.Rd man/create_figure_error_low_high_ess_mean.Rd man/create_figure_error_max.Rd man/create_figure_error_mean_dur_spec.Rd man/create_figure_error_mean_dur_spec_alignment_length.Rd man/create_figure_error_mean_dur_spec_mean.Rd man/create_figure_error_mean_dur_spec_mean_alignment_length.Rd man/create_figure_error_mean_dur_spec_mean_sampling.Rd man/create_figure_error_mean_dur_spec_median.Rd man/create_figure_error_mean_dur_spec_sampling.Rd man/create_figure_error_posterior_nltt_si.Rd man/create_figure_error_sampling_representative.Rd man/create_figure_error_tree_size.Rd man/create_figure_ess_distribution.Rd man/create_figure_ess_distribution_likelihood.Rd man/create_figure_ess_expected_mean_dur_spec_alignment_length.Rd man/create_figure_exit_statuses.Rd man/create_figure_exit_statuses_posteriors.Rd man/create_figure_lowest_ess.Rd man/create_figure_posterior_bd.Rd man/create_figure_posterior_crown_ages.Rd man/create_figure_posterior_likelihoods.Rd man/create_figure_posterior_nltts.Rd man/create_figure_run_times.Rd man/create_figure_strees_different.Rd man/create_log_filenames.Rd man/create_table_109.Rd man/create_table_111.Rd man/create_table_112.Rd man/file_to_lines.Rd man/find_path.Rd man/find_paths.Rd man/get_phylogeny_crown_age.Rd man/has_alignments.Rd man/have_same_strees.Rd man/is_distributed_normally.Rd man/is_good_alignment.Rd man/is_whole_number.Rd man/nrbs.Rd man/p2i.Rd man/postrs_same_distr_nltt_stat.Rd man/read_collected_alignments.Rd man/read_collected_esses.Rd man/read_collected_gammas_postrs.Rd man/read_collected_gammas_strees.Rd man/read_collected_log_files_info.Rd man/read_collected_n_taxa.Rd man/read_collected_nltt_stats.Rd man/read_collected_nltts_postrs.Rd man/read_collected_nltts_strees.Rd man/read_collected_operators.Rd man/read_collected_parameters.Rd man/read_collected_posterior_nltts.Rd man/read_collected_pstr_crown_ages.Rd man/read_collected_pstr_liks.Rd man/read_collected_strees_identical.Rd

ql.sh

scripts/clean.sh

scripts/collect

scripts/collect.R

scripts/collect_alignments

scripts/collect_alignments.R

scripts/collect_alignments_dmid

scripts/collect_alignments_dmid.R

scripts/collect_esses

scripts/collect_esses.R scripts/collect_gammas.R

scripts/collect_gammas.sh

scripts/collect_log_files

scripts/collect_log_files.R

scripts/collect_n_alignments

scripts/collect_n_alignments.R

scripts/collect_n_posteriors

scripts/collect_n_posteriors.R

scripts/collect_n_species_trees

scripts/collect_n_species_trees.R

scripts/collect_n_taxa

scripts/collect_n_taxa.R

scripts/collect_nltt_stats

scripts/collect_nltt_stats.R scripts/collect_nrbss.R

scripts/collect_nrbss.sh

scripts/collect_obsolete

scripts/collect_operators

scripts/collect_operators.R

scripts/collect_parameters

scripts/collect_parameters.R

scripts/collect_posterior_crown_ages

scripts/collect_posterior_crown_ages.R

scripts/collect_posterior_likelihoods

scripts/collect_posterior_likelihoods.R

scripts/collect_strees_identical

scripts/collect_strees_identical.R scripts/collect_times.R

scripts/collect_times.sh

scripts/create_figures

scripts/create_figures.R scripts/do_analysis.R

scripts/ifluatex.sty

scripts/ifxetex.sty

scripts/install_r_packages

scripts/install_r_packages.R

scripts/install_this_r_package

scripts/install_this_r_package.R

scripts/is_peregrine

scripts/is_peregrine.R

scripts/run

scripts/run_parallel.sh

scripts/run_stub

scripts/send_me_an_email.sh

scripts/test_beast2.sh

scripts/test_package.sh

scripts/test_pdf.R

scripts/test_pdf.sh

tests/testthat-alignment.R tests/testthat-are.R tests/testthat-calc.R tests/testthat-collect.R tests/testthat-convert.R tests/testthat-create.R tests/testthat-find.R tests/testthat-is.R tests/testthat-nrbs.R tests/testthat-read.R tests/testthat/test-are_from_same_distribution.R tests/testthat/test-calc_dmid.R tests/testthat/test-calc_nltt_stats.R tests/testthat/test-calc_nltt_stats_from_file.R tests/testthat/test-calc_nltt_stats_from_files.R tests/testthat/test-collect_file_esses.R tests/testthat/test-collect_file_n_alignments.R tests/testthat/test-collect_file_n_posteriors.R tests/testthat/test-collect_file_nltts.R tests/testthat/test-collect_file_nrbss.R tests/testthat/test-collect_file_posterior_crown_ages.R tests/testthat/test-collect_file_posterior_gammas.R tests/testthat/test-collect_file_posterior_likelihoods.R tests/testthat/test-collect_file_posterior_nltts.R tests/testthat/test-collect_file_stree_gammas.R tests/testthat/test-collect_file_stree_nltts.R tests/testthat/test-collect_files_alignments.R tests/testthat/test-collect_files_esses.R tests/testthat/test-collect_files_n_alignments.R tests/testthat/test-collect_files_n_posteriors.R tests/testthat/test-collect_files_n_species_trees.R tests/testthat/test-collect_files_n_taxa.R tests/testthat/test-collect_files_nrbss.R tests/testthat/test-collect_files_operators.R tests/testthat/test-collect_files_parameters.R tests/testthat/test-collect_files_posterior_crown_ages.R tests/testthat/test-collect_files_posterior_gammas.R tests/testthat/test-collect_files_posterior_likelihoods.R tests/testthat/test-collect_files_posterior_nltts.R tests/testthat/test-collect_files_species_tree_gammas.R tests/testthat/test-collect_files_species_tree_nltts.R tests/testthat/test-collect_files_strees_identical.R tests/testthat/test-collect_gamma_statistics.R tests/testthat/test-collect_log_file_info.R tests/testthat/test-collect_log_files_info.R tests/testthat/test-collect_n_species_trees.R tests/testthat/test-collect_n_taxa.R tests/testthat/test-collect_species_tree_n_taxa.R tests/testthat/test-convert_alignment_to_fasta.R tests/testthat/test-create_figure_acceptance_mcmc_operators.R tests/testthat/test-create_figure_alignment_qualities.R tests/testthat/test-create_figure_error.R tests/testthat/test-create_figure_error_alignment_length.R tests/testthat/test-create_figure_error_alignment_length_mean.R tests/testthat/test-create_figure_error_alignment_length_median.R tests/testthat/test-create_figure_error_bd.R tests/testthat/test-create_figure_error_bd_mean.R tests/testthat/test-create_figure_error_for_scr.R tests/testthat/test-create_figure_error_low_high_ess.R tests/testthat/test-create_figure_error_low_high_ess_mean.R tests/testthat/test-create_figure_error_max.R tests/testthat/test-create_figure_error_mean_dur_spec.R tests/testthat/test-create_figure_error_mean_dur_spec_alignment_length.R tests/testthat/test-create_figure_error_mean_dur_spec_mean.R tests/testthat/test-create_figure_error_mean_dur_spec_mean_alignment_length.R tests/testthat/test-create_figure_error_mean_dur_spec_mean_sampling.R tests/testthat/test-create_figure_error_mean_dur_spec_sampling.R tests/testthat/test-create_figure_error_posterior_nltt_si.R tests/testthat/test-create_figure_error_sampling_representative.R tests/testthat/test-create_figure_error_tree_size.R tests/testthat/test-create_figure_ess_distribution.R tests/testthat/test-create_figure_ess_distribution_likelihood.R tests/testthat/test-create_figure_ess_expected_mean_dur_spec_alignment_length.R tests/testthat/test-create_figure_exit_statuses.R tests/testthat/test-create_figure_exit_statuses_posteriors.R tests/testthat/test-create_figure_lowest_ess.R tests/testthat/test-create_figure_posterior_bd.R tests/testthat/test-create_figure_posterior_crown_ages.R tests/testthat/test-create_figure_posterior_likelihoods.R tests/testthat/test-create_figure_posterior_nltts.R tests/testthat/test-create_figure_run_times.R tests/testthat/test-create_figure_strees_different.R tests/testthat/test-create_log_filenames.R tests/testthat/test-create_table_109.R tests/testthat/test-create_table_111.R tests/testthat/test-create_table_112.R

tests/testthat/test-file_has_valid_parameters.R

tests/testthat/test-file_to_lines.R tests/testthat/test-find_path.R tests/testthat/test-have_same_strees.R tests/testthat/test-is_distributed_normally.R tests/testthat/test-is_good_alignment.R tests/testthat/test-nrbs.R tests/testthat/test-read_collected_alignments.R tests/testthat/test-read_collected_esses.R tests/testthat/test-read_collected_n_taxa.R tests/testthat/test-read_collected_nltts_postrs.R tests/testthat/test-read_collected_nltts_strees.R tests/testthat/test-read_collected_operators.R tests/testthat/test-read_collected_parameters.R tests/testthat/test-read_collected_strees_identical.R

wiritttea.Rproj

richelbilderbeek/wiritttea documentation built on May 27, 2019, 8:02 a.m.