Files in richelbilderbeek/wiritttes

WIRITTE simulation

.Rbuildignore

.Rprofile

.gitignore

.travis.yml

Codecov.png

DESCRIPTION

FAQ.md

LICENSE

NAMESPACE

R/add_alignments.R R/add_pbd_output.R R/add_posteriors.R R/add_species_trees.R R/alignment_to_beast_input_file.R R/alignment_to_beast_posterior.R R/are_identical_posteriors.R R/are_identical_trees_posteriors.R R/are_valid_files.R R/convert_alignment_to_fasta.R R/convert_indices.R R/convert_phylogeny_to_alignment.R R/create_parameter_files_article.R R/create_parameter_files_timings.R R/create_test_parameter_files.R R/do_simulation.R R/do_test_simulations.R R/extract_parameters.R R/file_has_valid_parameters.R R/find_paths.R R/get_alignment.R R/get_alignments.R R/get_pbd_output.R R/get_phylogeny_crown_age.R R/get_posterior.R R/get_posterior_tree.R R/get_posteriors.R R/get_species_tree.R R/has_alignments.R R/has_beast2.R R/has_species_trees.R R/is_valid_file.R R/nrbs.R R/read_file.R R/read_files.R R/save_parameters_to_file.R R/set_alignment.R R/set_posterior.R R/set_species_tree.R README.md

TravisCI.png

inst/extdata/article_0_3_0_3_0_472.RDa

inst/extdata/beast2_example_output.log

inst/extdata/beast2_example_output.trees

inst/extdata/beast2_example_output.xml

inst/extdata/beast2_example_output.xml.state

inst/extdata/is_trees_posterior.trees

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/add_alignments.Rd man/add_pbd_output.Rd man/add_pbd_output_iff_absent.Rd man/add_posteriors.Rd man/add_species_trees.Rd man/alignment_to_beast_input_file.Rd man/alignment_to_beast_posterior.Rd man/are_identical_posteriors.Rd man/are_identical_trees_posteriors.Rd man/are_valid_files.Rd man/convert_alignment_to_fasta.Rd man/convert_phylogeny_to_alignment.Rd man/create_parameter_files_article.Rd man/create_parameter_files_timings.Rd man/create_test_parameter_files.Rd man/do_simulation.Rd man/do_test_simulations.Rd man/extract_age.Rd man/extract_crown_age.Rd man/extract_erg.Rd man/extract_eri.Rd man/extract_fixed_crown_age.Rd man/extract_mutation_rate.Rd man/extract_napst.Rd man/extract_nppa.Rd man/extract_nspp.Rd man/extract_parameters.Rd man/extract_scr.Rd man/extract_seed.Rd man/extract_sequence_length.Rd man/extract_sirg.Rd man/extract_siri.Rd man/file_has_valid_parameters.Rd man/find_beast_jar_path.Rd man/find_path.Rd man/find_paths.Rd man/get_alignment.Rd man/get_alignment_by_index.Rd man/get_alignments.Rd man/get_pbd_output.Rd man/get_phylogeny_crown_age.Rd man/get_posterior.Rd man/get_posterior_by_index.Rd man/get_posterior_tree.Rd man/get_posteriors.Rd man/get_species_tree_by_index.Rd man/get_species_tree_oldest.Rd man/get_species_tree_youngest.Rd man/has_alignments.Rd man/has_beast2.Rd man/has_species_trees.Rd man/is_valid_file.Rd man/nrbs.Rd man/p2i.Rd man/read_file.Rd man/read_files.Rd man/save_parameters_to_file.Rd man/set_alignment.Rd man/set_alignment_by_index.Rd man/set_posterior.Rd man/set_posterior_by_index.Rd man/set_species_tree_by_index.Rd

scripts/add_alignments.sh

scripts/add_pbd_output.sh

scripts/add_pbd_output_iff_absent.sh

scripts/add_posteriors.sh

scripts/add_species_trees.sh

scripts/analyse_time.R

scripts/analyse_time.sh

scripts/clean.sh

scripts/create_parameter_files_article.sh

scripts/create_parameter_files_timings.sh

scripts/create_test_parameter_files.sh

scripts/ifluatex.sty

scripts/ifxetex.sty

scripts/install_r_packages.R

scripts/install_r_packages.sh

scripts/install_this_r_package.R

scripts/install_this_r_package.sh

scripts/run.sh

scripts/run_0.sh

scripts/run_1.sh

scripts/run_2.sh

scripts/run_3.sh

scripts/run_4.sh

scripts/sbatch_me.sh

scripts/send_me_an_email.sh

scripts/show_parameters.sh

scripts/test_beast2.R

scripts/test_beast2.sh

scripts/test_package.sh

scripts/test_pdf.R

scripts/test_pdf.sh

tests/testthat-a2i.R tests/testthat-add.R tests/testthat-alignment.R tests/testthat-are.R tests/testthat-convert.R tests/testthat-create.R tests/testthat-do.R tests/testthat-extract.R tests/testthat-find.R tests/testthat-get.R tests/testthat-has.R tests/testthat-is.R tests/testthat-nrbs.R tests/testthat-p2i.R tests/testthat-posterior.R tests/testthat-read.R tests/testthat-save.R tests/testthat-set.R tests/testthat/test-a2i.R tests/testthat/test-add_alignments.R tests/testthat/test-add_pbd_output.R tests/testthat/test-add_posteriors.R tests/testthat/test-add_species_trees.R tests/testthat/test-alignment_to_beast_input_file.R tests/testthat/test-alignment_to_beast_posterior.R tests/testthat/test-are_identical_posteriors.R tests/testthat/test-are_identical_trees_posteriors.R tests/testthat/test-are_valid_filenames.R tests/testthat/test-convert_alignment_to_fasta.R tests/testthat/test-convert_phylogeny_to_alignment.R tests/testthat/test-create_parameter_files_article.R tests/testthat/test-create_parameter_files_timings.R tests/testthat/test-create_parameter_files_toy_examples.R tests/testthat/test-do_simulation.R tests/testthat/test-do_test_simulations.R tests/testthat/test-extract_parameters.R tests/testthat/test-file_has_valid_parameters.R tests/testthat/test-find_path.R tests/testthat/test-get_alignment.R tests/testthat/test-get_alignment_by_index.R tests/testthat/test-get_alignments.R tests/testthat/test-get_phylogeny_crown_age.R tests/testthat/test-get_posterior.R tests/testthat/test-get_posterior_by_index.R tests/testthat/test-get_posterior_tree.R tests/testthat/test-get_posteriors.R tests/testthat/test-get_species_tree.R tests/testthat/test-has_alignments.R tests/testthat/test-has_beast2.R

tests/testthat/test-has_species_trees

tests/testthat/test-has_species_trees.R

tests/testthat/test-is_posterior.R

tests/testthat/test-is_valid_file.R tests/testthat/test-nrbs.R tests/testthat/test-p2i.R tests/testthat/test-read_file.R tests/testthat/test-read_files.R tests/testthat/test-save_parameters_to_file.R tests/testthat/test-set_alignment.R tests/testthat/test-set_alignment_by_index.R tests/testthat/test-set_posterior.R tests/testthat/test-set_posterior_by_index.R tests/testthat/test-set_species_tree.R vignettes/add_posteriors_demo.Rmd vignettes/convert_alignment_to_beast_posterior_demo.Rmd vignettes/convert_phylogeny_to_alignment_demo.Rmd vignettes/demo.Rmd vignettes/investigate_posteriors.Rmd vignettes/sample_species_trees_demo.Rmd

wiritttes.Rproj

richelbilderbeek/wiritttes documentation built on May 27, 2019, 8:14 a.m.