Files in richelbilderbeek/rbeast2
Control 'BEAST2'
.Rbuildignore
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/custom.md
.github/ISSUE_TEMPLATE/feature_request.md
.github/pull_request_template.md
.github/workflows/R-CMD-check.yaml
.github/workflows/build_singularity.yaml
.github/workflows/check_bash_style.yaml
.github/workflows/check_links.yaml
.gitignore
CODE_OF_CONDUCT.md
CONTRIBUTING.md
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
R/babette-package.R
R/bbt_continue.R
R/bbt_delete_temp_files.R
R/bbt_run.R
R/bbt_run_from_model.R
R/bbt_self_test.R
R/check_beast2_pkgs.R
R/create_test_bbt_run_output.R
R/create_test_ns_output.R
R/default_params_doc.R
R/get_alignment_ids_from_xml.R
R/get_babette_path.R
R/get_babette_paths.R
R/parse_beast2_output.R
R/parse_beast2_output_to_ns.R
R/plot_densitree.R
R/prepare_file_creation.R
R/update_babette.R
README.md
Singularity
appveyor.yml
babette.Rproj
codemeta.json
doc/README.md
doc/beast_cannot_find_java.png
doc/code_of_conduct.md
doc/dependencies.dot
doc/dependencies.png
doc/dependencies.ps
doc/download_oracle_java_sdk.png
doc/examples.md
doc/faq.md
doc/install.md
doc/install_oracle_java_sdk.png
doc/open_oracle_java_sdk.png
doc/rjava.md
inst/CITATION
inst/WORDLIST
inst/extdata/2_4.xml
inst/extdata/Felinecoronavirus_Envelope_1.fas
inst/extdata/Felinecoronavirus_Envelope_1.trees
inst/extdata/Felinecoronavirus_Envelope_1.txt
inst/extdata/Felinecoronavirus_Envelope_1_no_quotes.txt
inst/extdata/anthus_2_4.xml
inst/extdata/anthus_aco.fas
inst/extdata/anthus_aco_sub.fas
inst/extdata/anthus_aco_sub.posterior.log
inst/extdata/anthus_aco_sub.posterior.trees
inst/extdata/anthus_nd2.fas
inst/extdata/anthus_nd2_sub.fas
inst/extdata/beautier_issue_135.xml
inst/extdata/nested_sampling.xml
man/babette-package.Rd
man/bbt_continue.Rd
man/bbt_delete_temp_files.Rd
man/bbt_run.Rd
man/bbt_run_from_model.Rd
man/bbt_self_test.Rd
man/check_beast2_pkgs.Rd
man/create_test_bbt_run_output.Rd
man/create_test_ns_output.Rd
man/default_params_doc.Rd
man/figures/AppVeyor.png
man/figures/Codecov.png
man/figures/GitHubActions.png
man/figures/babette_logo.png
man/figures/example_birth_rate.png
man/figures/example_ess.png
man/figures/r_logo.png
man/figures/swan.png
man/figures/swan_mono_background.png
man/figures/swan_mono_background_2.png
man/get_alignment_ids_from_xml.Rd
man/get_babette_path.Rd
man/get_babette_paths.Rd
man/parse_beast2_output.Rd
man/parse_beast2_output_to_ns.Rd
man/plot_densitree.Rd
man/prepare_file_creation.Rd
man/update_babette.Rd
mlc_config.json
pics/AppVeyor.png
pics/Capitosquamatus.jpg
pics/Codecov.png
pics/GitHubActions.png
pics/README.md
pics/babette_logo.png
pics/example_birth_rate.png
pics/example_ess.png
pics/r_logo.png
pics/swan.png
pics/swan_mono_background.png
pics/swan_mono_background_2.png
scripts/build_cran.sh
scripts/build_singularity_container.sh
scripts/check_no_local_files
scripts/create_imports.R
scripts/demo_container.R
scripts/install_bab_deps_cran.sh
scripts/install_bab_deps_github.sh
scripts/install_beast2
scripts/issue_101.r
scripts/merge
scripts/push
scripts/ropensci_create_figs_blog_post.R
scripts/run_container.sh
scripts/run_r_script
tests/spelling.R
tests/testthat.R
tests/testthat/test-bbt_continue.R
tests/testthat/test-bbt_delete_temp_files.R
tests/testthat/test-bbt_run.R
tests/testthat/test-bbt_run_from_model.R
tests/testthat/test-bbt_run_ns.R
tests/testthat/test-bbt_self_test.R
tests/testthat/test-check_beast2_pkgs.R
tests/testthat/test-create_test_bbt_run_output.R
tests/testthat/test-create_test_ns_output.R
tests/testthat/test-get_alignment_ids_from_xml.R
tests/testthat/test-get_path.R
tests/testthat/test-get_paths.R
tests/testthat/test-issues.R
tests/testthat/test-nested_sampling.R
tests/testthat/test-parse_beast2_output.R
tests/testthat/test-parse_beast2_output_to_ns.R
tests/testthat/test-plot_densitree.R
tests/testthat/test-prepare_file_creation.R
tests/testthat/test-update_babette.R
vignettes/.gitignore
vignettes/aco_hky_nd2_tn93.png
vignettes/all_default.png
vignettes/anthus_2_4.png
vignettes/babette_logo.png
vignettes/bd_2_4.png
vignettes/birth_rate_normal_2_4.png
vignettes/demo.Rmd
vignettes/examples.Rmd
vignettes/hky_prop_invariant_0_5_2_4.png
vignettes/jc69_2_4.png
vignettes/mrca_crown_age.png
vignettes/nested_sampling.Rmd
vignettes/rln_2_4.png
vignettes/step_by_step.Rmd
vignettes/strict_clock_rate_0_5_2_4.png
vignettes/tutorial.Rmd
