1b09ef4b12261e4992bbfa2e64c95bf7 *DESCRIPTION
0f900ec6bb44080324d0270a51d0ddae *NAMESPACE
cdae93f0a10ae4b580279b8a1c1a9a47 *R/add_quotes_if_has_spaces.R
9dd76df203e35c37da231db9e81946f0 *R/are_beast2_input_lines.R
cbdc7cbd570215fa1c87c1ce61f29247 *R/are_identical_alignments.R
7813f23352a7840f669f92ee60be067a *R/beast2_options_to_table.R
b65621203edcc98f723093b8a11c4f07 *R/beastier.R
045d14fb2b3752ba60b282b1b51674a9 *R/beastier_report.R
07ab45354ff32cc68d970cd94426193c *R/check_beast2.R
50c2d29c65a155a0f6654eac07fc4192 *R/check_beast2_options.R
4b8eafd951c9dd80b0d613781efc2f9a *R/check_beast2_options_do_not_overwrite_existing_files.R
339fe10d05eef396e6c8c1596a92f95a *R/check_beast2_optionses.R
696a0810ed98ff7e41c6d345420f4334 *R/check_beast2_path.R
4ed095dd20485c9ed2802fe792c07269 *R/check_can_create_dir_for_state_output_file.R
43ae5520cd3c5c7b11268c84e955244f *R/check_can_create_file.R
a4bc64bebc749e0be5fdceb8d42dcdaf *R/check_can_create_screenlog_file.R
7c37e3a4bcc64fea158d7bca2c8ad875 *R/check_can_create_state_output_file.R
6970b832583f6d1fd245bf1bf3f4265e *R/check_can_create_tracelog_file.R
85d74aeb5db669c30c7cd72f11a0392a *R/check_can_create_treelog_file.R
9814ce566561896eaa17c0934f5e851d *R/check_input_filename.R
bc4d8f756fa548ea474feb8396e34ad2 *R/check_n_threads.R
2950400ae1b3cd1f09deae828d60632b *R/check_os.R
d1aff39220feae4de559079d3243b630 *R/check_rng_seed.R
2023d0599a3ddf9972bae81388915376 *R/continue_beast2.R
f95f9a2ce4e61c5f84e317d27ad26fda *R/create_beast2_continue_cmd_from_options.R
c176a0736481a4742f640d000dbb63ae *R/create_beast2_options.R
97ccaf9cec4c144dfaf5971ebcb928d9 *R/create_beast2_run_cmd.R
51492f91ab0bc3d0ac617dd0e1579325 *R/create_beast2_run_cmd_from_options.R
649981b4f9af987351f93df0aee2463c *R/create_beast2_validate_cmd.R
6a059ec77933933662ba4be37ab26735 *R/create_beast2_version_cmd.R
e796d55a6f2383a129ffcda095904eb1 *R/create_mcbette_beast2_options.R
c732f359a67d24d21ff12452147199e2 *R/create_random_alignment.R
e92f46e4f31c29eafcfcd60cbb68db43 *R/create_random_fasta.R
5b575dbc519571e1e248b69c0e5780a0 *R/create_random_phylogeny.R
2167e02639f67a925c2e29d296a699f5 *R/create_temp_input_filename.R
5141b2c9daa8430d6464edcd44bb8126 *R/create_temp_state_filename.R
1a5a465d04441f52e9f47f2317564ed0 *R/default_params_doc.R
8e6c2f205785d0de785706cc82e98f51 *R/do_minimal_run.R
d9d918b61a4a031be91aa139d1a80c99 *R/get_alignment_ids.R
b9909236dabdfb8e3259c0b0f01f42d5 *R/get_beast2_example_filename.R
b41892120ce388882ef0583465f767a4 *R/get_beast2_example_filenames.R
bbb607cebc98c74d0be46ca69c246c63 *R/get_beast2_main_class_name.R
5edffadbf8b7ee92d88069a23691003a *R/get_beast2_options_filenames.R
0344db25abf1f27f2dad300dce47699e *R/get_beast2_version.R
0351672c83c159375662c020f848f4ae *R/get_beastier_tempfilename.R
ba59dbd9bd3bf634e0f369d0cd89bf80 *R/get_default_beast2_bin_path.R
53aa4602d3704a63ee3dea4c48096c4f *R/get_default_beast2_download_url.R
d68da0452ffbb1b2770c0d0bf13bcc6a *R/get_default_beast2_folder.R
df7e641cabc28a5e2f241835b2e55f0e *R/get_default_beast2_jar_path.R
1d6772291421524e6092f9beec74e653 *R/get_default_beast2_path.R
d015d5a062572175b0d35d261eabb75e *R/get_default_beast2_version.R
465418f6e651bd5ad8be4fa6ba56c550 *R/get_default_java_path.R
4c2e0985aca200d44b98fde6cea2d4cb *R/get_duplicate_param_ids.R
c0dd55f0bdf87df25273af04689ccb26 *R/get_java_version.R
a08f6f49471d12f10ab686ad41336f07 *R/get_path.R
6faa062f278b3c9b8147031d3352dceb *R/get_paths.R
e46159592b5fad1a9d6ab952584ffdea *R/get_trees_filenames.R
ee7d2473ea81460a7151f1730bf56484 *R/gives_beast2_warning.R
2c960c558826ff9a88d21d6995b8ae36 *R/has_unique_ids.R
a18913ca72818424b1371fa5e8e0ab94 *R/install_beast2.R
5faee41cf340b076cf1d4e7216931db0 *R/is_alignment.R
eac4bbf80c015921c93d6d23451bc329 *R/is_beast2_input_file.R
2d5e278eea6ccc6c966d569618f99e02 *R/is_beast2_installed.R
753b8ce89ef656d18d7ccedabae47310 *R/is_bin_path.R
4c1e058e045285f709e2dc3df5fd09ce *R/is_jar_path.R
d167e749bfe33235fb786ef278799617 *R/is_on_ci.R
20760b745ee7f4b55c3c7922d3ef02eb *R/print_beast2_options.R
af8ea4189862ea88869c983dfcabecb1 *R/remove_file_if_present.R
fb3d889cb272314fd924394301f02e57 *R/rename_beast2_options_filenames.R
dc545f2c7650fb4899a11f2a7d79d211 *R/run_beast2.R
50b6d4914c7fee9a8ee29921fd15c097 *R/run_beast2_from_options.R
5e3ccdca7e67b61efc7a163cc88fdb73 *R/save_lines.R
3cfef14ec72d624446aebcc87377b4b0 *R/save_nexus_as_fasta.R
3c9620ae9072aa2703e6a937f9749a04 *R/uninstall_beast2.R
745438b487f77337931c9611f39e0dd6 *R/upgrade_beast2.R
217087027299f1cb803d5e179352f1cd *build/vignette.rds
604d69ff7d5954219736e01c41d18e48 *inst/CITATION
c2522f2adc8fd86f713338e61982ab4a *inst/WORDLIST
2ea03aa4e76af0d2460b5bc4072c972e *inst/doc/demo.R
1dbece8586f0f731ad997c4358c96cac *inst/doc/demo.Rmd
43dc2219bb31003a525acbba7577b8da *inst/doc/demo.html
59dc5020cc76a70d138c1465d93c5b12 *inst/extdata/2_4.xml
69ae9f49cd0d6f81d75e6a10d284fd15 *inst/extdata/README.md
0f10b2e8a0c32ae1593678977e71d909 *inst/extdata/anthus_15_15.xml
e448411f3b6ecbf4d2304a23fabcb788 *inst/extdata/anthus_15_15_long.xml
a5b87ff2e286d857fa94735b096f69e4 *inst/extdata/anthus_15_26.xml
ff3ce7acb6c88f7c8cbedce5274f64a5 *inst/extdata/anthus_15_na.xml
a75c01a5ea48922948f932b39597be48 *inst/extdata/anthus_2_4.xml
0eedfd95a1fff834d513246b4e4624e2 *inst/extdata/anthus_aco.fas
e39a06790872a8429c306e0d0ac4a080 *inst/extdata/anthus_na_15.xml
4f47d3dda06c4ad6605b84cf43579113 *inst/extdata/anthus_na_na.xml
93d45a2f0c0145ebfebdedeb073025f1 *inst/extdata/anthus_nd2.fas
4ce27062dcd961771b12dd9adfcdd946 *inst/extdata/beast2_error.xml
b8231c2de96de5d0c4ab0082a38c41d5 *inst/extdata/beast2_example_output.log
f83191933040361f729577af64c44110 *inst/extdata/beast2_example_output.trees
346226afa164793704af01106aa3b2d8 *inst/extdata/beast2_example_output.xml
5ac7281e62e96d3c330bb6072aa6096d *inst/extdata/beast2_example_output.xml.state
f175cffff0c68f238ea16652fe6456ea *inst/extdata/beast2_warning.xml
4ce27062dcd961771b12dd9adfcdd946 *inst/extdata/nested_sampling.xml
b2681db80ca3445eea3fcb15dff6124a *inst/extdata/read_beast2_trees_example.trees
a7ce1f2ed7f9b7bae358166c0528f30a *inst/extdata/test_output_2.fas
96b0de13446d005fdaf3fcfee81f67e3 *man/add_quotes_if_has_spaces.Rd
6ef1fb085eacc4f7caf64749fadd62fa *man/are_beast2_input_lines.Rd
04f6943c5ccc78c046c11f447929fcca *man/are_beast2_input_lines_deep.Rd
bfd6d3a2e5d114a8b5da2a06858a21b9 *man/are_beast2_input_lines_fast.Rd
8e2402770e7727e23e878a49068bab43 *man/are_identical_alignments.Rd
94256909affcfeb7a26025a676b82d6e *man/beast2_options_to_table.Rd
fcf652a2bef26e9c4a7f186e13609099 *man/beastier.Rd
2aadfe2c5f6e48bb3dc934f57a60f936 *man/beastier_report.Rd
547da38d9200709e99f053f44845637a *man/check_beast2.Rd
43b33f35255d6a9548c072d4c2f3b8de *man/check_beast2_options.Rd
6401225185e55b902bab940bf41a3c42 *man/check_beast2_options_data_types.Rd
5e38e041d4ad89e96e1b153a8c64287f *man/check_beast2_options_do_not_overwrite_existing_files.Rd
7dbee06fc56915db3c94a456bf1e2add *man/check_beast2_options_filenames_differ.Rd
39aec4d2b69a712dcea61fa167a279a5 *man/check_beast2_options_names.Rd
278bbd8181aebbf0cd22a488cb7acc31 *man/check_beast2_optionses.Rd
0bee46ecd4247d3ef7ede2c04b33155f *man/check_beast2_path.Rd
ac5518f43c9e3902942cba67fac36c60 *man/check_can_create_dir_for_state_output_file.Rd
41f695cb1ca18038b8deef529eec0b6c *man/check_can_create_file.Rd
0dae73aa4c1aa61edefcce35ef08d511 *man/check_can_create_screenlog_file.Rd
4b952b778275d498c4c28457ed80626b *man/check_can_create_state_output_file.Rd
9eaaf75e0657c3c26162117a4368897c *man/check_can_create_tracelog_file.Rd
fa47df4fdcb4520567d6642d4b7b27f4 *man/check_can_create_treelog_file.Rd
bc08033e379b14aa8c4ae669dc9906ee *man/check_input_filename.Rd
23631744b0b9d7d195f2d97b13a07ccf *man/check_input_filename_validity.Rd
9b72b0819066e16ec8079ab7f4c7ed63 *man/check_n_threads.Rd
0e3d2d1f589aa79e810d1ef7184b757f *man/check_os.Rd
88d157897c3fcae04b5a5b06fdf34e39 *man/check_rng_seed.Rd
c8fd2b4b153ca14175262eaeb3a069fe *man/continue_beast2.Rd
86200ce44d53719d901ac2e1b335e4ea *man/create_beast2_continue_cmd_from_options.Rd
c73b7d0f768f496893fe075d79c7046c *man/create_beast2_options.Rd
1048c3161eed201fad826f9e73c9daa6 *man/create_beast2_run_cmd.Rd
3de947c4e52c3a0e339808a91b3babed *man/create_beast2_run_cmd_from_options.Rd
465fb3d53daae711d01863640399d6ae *man/create_beast2_validate_cmd.Rd
df66da67b2e2297de9b6ea76d9adace0 *man/create_beast2_validate_cmd_bin.Rd
2e2552912f6001a0bc2cc509a8e2b0e0 *man/create_beast2_validate_cmd_jar.Rd
05a02ca2450caf2c8ce40d57d136dd25 *man/create_beast2_version_cmd.Rd
c58139a662a66d2141963706f5d3ae8f *man/create_beast2_version_cmd_bin.Rd
b3c50ee23ad3d728214f062f4aef20e9 *man/create_beast2_version_cmd_jar.Rd
1f28e45776654a0ba61aef273aba65a6 *man/create_mcbette_beast2_options.Rd
9fffbb927c43fa67db036d61fc016dae *man/create_random_alignment.Rd
ad1fa9ff8476dd85e2a433de6539353b *man/create_random_fasta.Rd
db76f39c855e86aa1320e7886911a22b *man/create_random_phylogeny.Rd
6663201713762b46f15d7f58c1ab543b *man/create_temp_input_filename.Rd
9ad9ae5956d3cecca9d492cdc77b3e4b *man/create_temp_state_filename.Rd
559a8f52400026a2462fffc1eb26a877 *man/default_params_doc.Rd
e43a2f30c7c71ddae9b11d316e40d63d *man/do_minimal_run.Rd
f7de71e5ff24145a37bf281e4d155cfa *man/figures/AppVeyor.png
3f25ab37a1f6270f76c025cf6eda5421 *man/figures/Codecov.png
b55c56f3943a394162527954ca4a3009 *man/figures/GitHubActions.png
4f9bce317a2b82518737a7ee7381c2ec *man/figures/TravisCI.png
57002b68e0eb59e211c93d40911ba46e *man/figures/beastier_logo.png
5c903eae532ccc2c0aff2a981c0eb6f6 *man/get_alignment_ids_from_xml_filename.Rd
f07af9f4e37e4210f6a5b7874e49d041 *man/get_beast2_example_filename.Rd
63badddaa8c39f9e83a8c0dae990bf60 *man/get_beast2_example_filenames.Rd
cdc57960f595ccf7b69356e9c40686a1 *man/get_beast2_main_class_name.Rd
fc049cda0bbc42dc275a3987c34517bb *man/get_beast2_options_filenames.Rd
a1412fcae28e0bd4750d88c790f5ac79 *man/get_beast2_version.Rd
0ef44cbe9d661df40a665e40d405f406 *man/get_beastier_path.Rd
ba8b927e0737b8ea5487e5de62da2ebd *man/get_beastier_paths.Rd
b4bbeab25a6a18c0a47a152d59198c27 *man/get_beastier_tempfilename.Rd
e38daacb654b69e99261da0d71ed74d8 *man/get_default_beast2_bin_path.Rd
d52b41a14208ca3529f672d934497242 *man/get_default_beast2_download_url.Rd
4dad387ad43f0e926691b99340de744b *man/get_default_beast2_download_url_linux.Rd
ba10b92e1757f725204383c82ea2f1c4 *man/get_default_beast2_download_url_win.Rd
05cc258b0b0f88c438904a12cdde9890 *man/get_default_beast2_folder.Rd
2f2a80070613f2e955df299a95d1e2b3 *man/get_default_beast2_jar_path.Rd
47e92a993c2e39e49845f8dd0df011ba *man/get_default_beast2_path.Rd
18137cc85d3ed3a5ebe146d9c41d3723 *man/get_default_beast2_version.Rd
8a2d89c99fcea1f70f201fb7a5c3fa04 *man/get_default_java_path.Rd
2abc83fbb98844fedc6a25b1a9ff3bff *man/get_duplicate_param_ids.Rd
fdc387a0b2fdd9af1dbbdc1f1a93311f *man/get_java_version.Rd
1e960f3aee707c7f9de444f9406a12b4 *man/get_trees_filenames.Rd
166a361c55742e142a9ad4742573ff94 *man/gives_beast2_warning.Rd
0330385ff697702f931ebf4f5fc79584 *man/has_unique_ids.Rd
c7ded23acd602acf2b22b2548492c4e5 *man/install_beast2.Rd
3a57a66697d32afaabd8212857047251 *man/is_alignment.Rd
d78a68aea3f6cfe1707218de76180a2c *man/is_beast2_input_file.Rd
d2fa01e1e90941c9fc9cac197ecc6434 *man/is_beast2_installed.Rd
9ca3b9ce4c34a95ba08c68f62e91fa0a *man/is_bin_path.Rd
0f82066d2cdc11eb7ee3c79129a570e6 *man/is_jar_path.Rd
0ce1e3e13462deca28b89f095e6f2b27 *man/is_on_appveyor.Rd
6aabe3407ce8c98f2116d52317563b74 *man/is_on_ci.Rd
49beaacb245bb72f17883d5a2934b517 *man/is_on_travis.Rd
a4cc177374c04ebd46509c3af243bfc4 *man/is_win_bin_path.Rd
60cc25781098592a4964e4f59281c526 *man/print_beast2_options.Rd
8a7e299bd999ec0d2847bc8a68b6cfc7 *man/remove_file_if_present.Rd
db679f0600f487b9ec7fe0a4250025d0 *man/rename_beast2_options_filenames.Rd
f1c29992e1e1f12f3f96b1326532125f *man/run_beast2.Rd
8d9e0ee11dba05cd6a651368597b1ec6 *man/run_beast2_from_options.Rd
60ce3217c1baa51d3721d0fc9be69b76 *man/save_lines.Rd
a6ebcdff48e0e2ece773481ca367e00e *man/save_nexus_as_fasta.Rd
b012b92a0792e2e3a8da84c82623a4d9 *man/uninstall_beast2.Rd
9f20aa53fb51102ac016d2f416a393ef *man/upgrade_beast2.Rd
57002b68e0eb59e211c93d40911ba46e *vignettes/beastier_logo.png
1dbece8586f0f731ad997c4358c96cac *vignettes/demo.Rmd
