Files in richelbilderbeek/razzo
The Error if Nature is MBD

.Rbuildignore
.github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/custom.md .github/ISSUE_TEMPLATE/feature_request.md .github/pull_request_template.md
.gitignore
.travis.yml
CODE_OF_CONDUCT.md
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md R/calc_n_taxas.R R/check_mbd_paramses.R R/check_params_mbd.R R/check_params_misc.R R/check_params_razzo.R R/check_razzo_experiments.R R/check_razzo_params_filenames.R R/check_traces_in_df.R R/collect_all_data.R R/collect_esses.R R/collect_marg_liks.R R/collect_mbd_params.R R/collect_n_mb_species.R R/collect_n_mutations.R R/collect_n_taxa.R R/collect_nltt_stats.R R/collect_run_times.R R/create_all_data_file.R R/create_fig_1.R R/create_file_esses.R R/create_file_fig_1.R R/create_file_marg_liks.R R/create_file_mbd_params.R R/create_file_n_taxa.R R/create_file_nltt_stats.R R/create_file_run_times.R R/create_mbd_params_table.R R/create_mbd_paramses.R R/create_n_mb_species_file.R R/create_n_mutations_file.R R/create_parameters_files.R R/create_params_mbd.R R/create_params_misc.R R/create_params_razzo.R R/create_razzo_alignment_params.R R/create_razzo_beast2_options.R R/create_razzo_cand_experiments.R R/create_razzo_experiments.R R/create_razzo_gen_experiment.R R/create_razzo_mrca_prior.R R/create_razzo_ns_mcmc.R R/create_razzo_paramses.R R/create_razzo_pir_params.R R/create_razzo_twinning_params.R R/create_test_mbd_paramses.R R/create_test_razzo_experiments.R R/create_test_razzo_paramses.R R/create_test_razzo_pir_params.R R/default_params_doc.R R/get_razzo_crown_age.R R/get_razzo_dna_alignment_length.R R/get_razzo_filenames.R R/get_razzo_lambdas.R R/get_razzo_mcmc.R R/get_razzo_mcmc_chain_length.R R/get_razzo_mcmc_store_every.R R/get_razzo_mus.R R/get_razzo_mutation_rate.R R/get_razzo_n_replicates.R R/get_razzo_nus.R R/get_razzo_qs.R R/path_functions.R R/razzo.R R/remove_cbs_exps.R R/run_razzo.R R/run_razzo_from_file.R R/save_razzo_paramses.R R/update_razzo.R R/utils-pipe.R R/utils.R README.md
appveyor.yml
doc/README.md
doc/alignment.png
doc/choices.odp
doc/choices.pdf
doc/densitree.png
doc/dependencies.dot
doc/dependencies.png
doc/dependencies.ps
doc/install.md
doc/obsolete_overview.dia
doc/obsolete_overview.png
doc/overview.dia
doc/overview.png
doc/pipeline.png
inst/extdata/mbd.fasta
inst/extdata/mbd.tree
inst/extdata/mbd_marg_lik.csv
inst/extdata/mbd_marg_lik_twin.csv
inst/extdata/mbd_nltts_best.csv
inst/extdata/mbd_nltts_best_twin.csv
inst/extdata/mbd_nltts_gen.csv
inst/extdata/mbd_nltts_gen_twin.csv
inst/extdata/mbd_twin.tree
inst/extdata/parameters.RDa
inst/extdata/razzo_project/data/0.2-0.15-1-0.1/1/mbd.fasta
inst/extdata/razzo_project/data/0.2-0.15-1-0.1/1/mbd.tree
inst/extdata/razzo_project/data/0.2-0.15-1-0.1/1/parameters.RDa
inst/extdata/razzo_project/data/0.2-0.15-1-0.1/2/mbd.fasta
inst/extdata/razzo_project/data/0.2-0.15-1-0.1/2/mbd.tree
inst/extdata/razzo_project/data/0.2-0.15-1-0.1/2/parameters.RDa
inst/extdata/razzo_project/results/esses.csv
man/calc_n_taxas.Rd man/check_mbd_params.Rd man/check_mbd_paramses.Rd man/check_misc_params.Rd man/check_project_folder_name.Rd man/check_razzo_experiments.Rd man/check_razzo_params.Rd man/check_razzo_params_filenames.Rd man/check_razzo_params_names.Rd man/check_traces_in_df.Rd man/clean_path.Rd man/clean_paths.Rd man/collect_all_data.Rd man/collect_esses.Rd man/collect_evidences.Rd man/collect_mbd_params.Rd man/collect_n_mb_species.Rd man/collect_n_mutations.Rd man/collect_n_taxa.Rd man/collect_nltt_stats.Rd man/collect_run_times.Rd man/create_fig_1.Rd man/create_file_all_data.Rd man/create_file_esses.Rd man/create_file_fig_1.Rd man/create_file_marg_liks.Rd man/create_file_mbd_params.Rd man/create_file_n_mutations.Rd man/create_file_n_taxa.Rd man/create_file_nltt_stats.Rd man/create_file_run_times.Rd man/create_mbd_params_table.Rd man/create_mbd_paramses.Rd man/create_misc_params.Rd man/create_n_mb_species_file.Rd man/create_parameters_files.Rd man/create_params_mbd.Rd man/create_params_razzo.Rd man/create_razzo_alignment_params.Rd man/create_razzo_beast2_options.Rd man/create_razzo_cand_experiments.Rd man/create_razzo_experiments.Rd man/create_razzo_gen_experiment.Rd man/create_razzo_mrca_prior.Rd man/create_razzo_ns_mcmc.Rd man/create_razzo_paramses.Rd man/create_razzo_pir_params.Rd man/create_razzo_twinning_params.Rd man/create_test_mbd_params.Rd man/create_test_mbd_paramses.Rd man/create_test_razzo_experiments.Rd man/create_test_razzo_params.Rd man/create_test_razzo_paramses.Rd man/create_test_razzo_pir_params.Rd man/default_params_doc.Rd man/get_alignment_filename.Rd man/get_best_model.Rd man/get_data_paths.Rd man/get_errors_filename.Rd man/get_evidence_filename.Rd man/get_gen_models.Rd man/get_generative_model.Rd man/get_input_filename.Rd man/get_output_log_filename.Rd man/get_output_state_filename.Rd man/get_output_trees_filenames.Rd man/get_razzo_crown_age.Rd man/get_razzo_dna_alignment_length.Rd man/get_razzo_lambdas.Rd man/get_razzo_mcmc.Rd man/get_razzo_mcmc_chain_length.Rd man/get_razzo_mcmc_store_every.Rd man/get_razzo_mus.Rd man/get_razzo_mutation_rate.Rd man/get_razzo_n_replicates.Rd man/get_razzo_nus.Rd man/get_razzo_qs.Rd man/get_results_path.Rd man/get_seed_folder_name.Rd man/get_tracelog_filename.Rd man/get_tree_filename.Rd man/get_treelog_filename.Rd man/open_parameters_file.Rd man/pipe.Rd man/razzo.Rd man/remove_cbs_exps.Rd man/run_razzo.Rd man/run_razzo_from_file.Rd man/save_razzo_paramses.Rd man/update_razzo.Rd
pics/AppVeyor.png
pics/Codecov.png
pics/Pippo_Baudo_1975.jpg
pics/TravisCI.png
pics/pippo_baudo_as_cannonball.png
pics/razzo_logo.png
pics/razzo_logo_2.png
pics/rocket.png
razzo.Rproj
scripts/.gitignore
scripts/10_create_fig_1_file.sh
scripts/11_create_n_taxa_file.sh
scripts/12_create_run_times_file.sh
scripts/1_install_razzo.sh
scripts/2_create_parameter_files.sh
scripts/3_run_razzo.sh
scripts/7_create_nltt_stats_file.sh
scripts/8_create_esses_files.sh
scripts/90_collect_run_times.R
scripts/9_create_marg_liks_file.sh
scripts/build_cran
scripts/check_dead_links
scripts/install_r_packages.R
scripts/install_r_packages.sh
scripts/issue_228.R scripts/issue_230.R scripts/issue_242.R scripts/issue_260.R scripts/issue_294.R scripts/issue_294.md scripts/issue_299.R scripts/issue_326.R scripts/issue_327.R
scripts/regen_data.sh
scripts/rerun_failed.sh
scripts/run_r_cmd
scripts/run_r_script
scripts/sim_alignments.R
scripts/test_detect_env
tests/testthat.R tests/testthat/test-calc_n_taxas.R tests/testthat/test-check_mbd_params.R tests/testthat/test-check_mbd_paramses.R tests/testthat/test-check_misc_params.R tests/testthat/test-check_project_folder_name.R tests/testthat/test-check_razzo_params.R tests/testthat/test-check_traces_in_df.R tests/testthat/test-clean_path.R tests/testthat/test-clean_paths.R tests/testthat/test-collect_all_data.R tests/testthat/test-collect_esses.R tests/testthat/test-collect_marg_liks.R tests/testthat/test-collect_mbd_params.R tests/testthat/test-collect_n_mb_species.R tests/testthat/test-collect_n_mutations.R tests/testthat/test-collect_n_taxa.R tests/testthat/test-collect_nltt_stats.R tests/testthat/test-collect_run_times.R tests/testthat/test-create_all_data_file.R tests/testthat/test-create_esses_file.R tests/testthat/test-create_fig_1.R tests/testthat/test-create_fig_1_file.R tests/testthat/test-create_marg_liks_file.R tests/testthat/test-create_mbd_params.R tests/testthat/test-create_mbd_params_file.R tests/testthat/test-create_mbd_params_table.R tests/testthat/test-create_mbd_paramses.R tests/testthat/test-create_misc_params.R tests/testthat/test-create_n_mb_species_file.R tests/testthat/test-create_n_mutations_file.R tests/testthat/test-create_n_taxa_file.R tests/testthat/test-create_nltt_stats_file.R tests/testthat/test-create_parameters_files.R tests/testthat/test-create_razzo_alignment_params.R tests/testthat/test-create_razzo_beast2_options.R tests/testthat/test-create_razzo_cand_experiments.R tests/testthat/test-create_razzo_experiments.R tests/testthat/test-create_razzo_gen_experiment.R tests/testthat/test-create_razzo_mcmc.R tests/testthat/test-create_razzo_mrca_prior.R tests/testthat/test-create_razzo_ns_mcmc.R tests/testthat/test-create_razzo_params.R tests/testthat/test-create_razzo_paramses.R tests/testthat/test-create_razzo_pir_params.R tests/testthat/test-create_razzo_twinning_params.R tests/testthat/test-create_run_times_file.R tests/testthat/test-create_test_mbd_paramses.R tests/testthat/test-create_test_razzo_experiments.R tests/testthat/test-create_test_razzo_paramses.R tests/testthat/test-create_test_razzo_pir_params.R tests/testthat/test-get_data_paths.R tests/testthat/test-get_path.R tests/testthat/test-get_razzo_crown_age.R tests/testthat/test-get_razzo_dna_alignment_length.R tests/testthat/test-get_razzo_lambdas.R tests/testthat/test-get_razzo_mcmc.R tests/testthat/test-get_razzo_mcmc_chain_length.R tests/testthat/test-get_razzo_mcmc_store_every.R tests/testthat/test-get_razzo_mus.R tests/testthat/test-get_razzo_mutation_rate.R tests/testthat/test-get_razzo_n_replicates.R tests/testthat/test-get_razzo_nus.R tests/testthat/test-get_razzo_qs.R tests/testthat/test-get_results_paths.R tests/testthat/test-get_tree_filename.R tests/testthat/test-open_parameters_file.R tests/testthat/test-remove_cbs_exps.R tests/testthat/test-run_razzo.R tests/testthat/test-run_razzo_from_file.R tests/testthat/test-save_razzo_paramses.R tests/testthat/test-style.R
vignettes/.gitignore
vignettes/mbd.tree
vignettes/parameters.Rmd
vignettes/parameters_q.png
vignettes/razzo_pipeline.Rmd
vignettes/test_tree
richelbilderbeek/razzo documentation built on March 28, 2020, 9:32 p.m.