e5be741635f86fb41ccfd7b9c16223d3 *DESCRIPTION
eb08d7dceded5601bef9c80121fa8244 *NAMESPACE
bf9ba6b3c01e1c9d57225802b4852a73 *R/add_quotes_if_has_spaces.R
24d9588fbe61c1e745344430be95d0fb *R/are_beast2_input_lines.R
07e522ed885e675b1069fca4f463d6c8 *R/are_identical_alignments.R
5fd37c58f6a8a4469162beb32d415f04 *R/beast2_options_to_table.R
42825a4731b0b26fc7220603497552d8 *R/beastier-package.R
865758338e335c9612ba77ab99e441be *R/beastier_report.R
c420545cdb658d936b5b76ea0d9bf3df *R/check_beast2.R
d2d71db90d0182cfa3777f0fe532cc94 *R/check_beast2_options.R
f8c189f5652f83c394b6aaf541bc0eee *R/check_beast2_options_do_not_overwrite_existing_files.R
83b856ad3f28f627f173f0fb6c6ada8f *R/check_beast2_optionses.R
ff900d2cb3b7b3da1311772ea27e7982 *R/check_beast2_path.R
b0799eccf9bb40e1daf840d15d4304e4 *R/check_can_create_dir_for_state_output_file.R
37f4ca6aa2e000c10e8091f344f0eb12 *R/check_can_create_file.R
3f935b225c235da33b85522c32021800 *R/check_can_create_screenlog_file.R
f8dc93290f410dcd45b5afc83dc1429e *R/check_can_create_state_output_file.R
cdb588c0f41fa0c82b0321713fffcb63 *R/check_can_create_tracelog_file.R
8b5a5433dffe72c8c71b844414bf4225 *R/check_can_create_treelog_file.R
8d8b20c0b7dadd9b0e689703df44d8ce *R/check_empty_beastier_folder.R
74f89bf0dd27ef5dec6d83fa5622a6c1 *R/check_empty_beaustier_folders.R
9f0587948f5517ac28473983e9fa715e *R/check_input_filename.R
771b020b831ef6307ce627b3a153a221 *R/check_n_threads.R
50075fb3515c8e716491c704f8a5c28f *R/check_os.R
5ab4ff6cfde7fc55247fdb5aa8104a7a *R/check_rng_seed.R
8fd1c69e6d2c28b9cb8f832c8e78812e *R/check_true_false.R
1c04828a492750bc6f13113bb8b5d3eb *R/continue_beast2.R
a22219cc0046161cd62788093669ef18 *R/create_beast2_continue_cmd_from_options.R
77603bf114dad3d00cdb06b9c4e808fe *R/create_beast2_input_file_folder.R
f2efdf55500f57a2e78bfbb2c14c2dd1 *R/create_beast2_options.R
44353b13df45d9a653f3b51c661e21e6 *R/create_beast2_run_cmd.R
4cd433d76bbccadf66dbb0e8ebcf1e7c *R/create_beast2_run_cmd_from_options.R
00a5e731ca6c8ace1b0377053d677666 *R/create_beast2_screenlog_folder.R
b6470fdd28b632b2741986f74cb8f070 *R/create_beast2_state_output_file_folder.R
6a7a621abea390818c3f3194ab3b88aa *R/create_beast2_tracelog_folder.R
37bbeffa03d92c0faa9ff78dca30aecf *R/create_beast2_treelog_folder.R
1bd205b24eb9474fd296270ca1fe2fdf *R/create_beast2_validate_cmd.R
0bc2272ddbaa1fc990a44dbabd088001 *R/create_beast2_version_cmd.R
ad8f100def2a874b6f876a58fff1d900 *R/create_beastier_tempfolder.R
5d9333007908e7dd88c1f110a9411785 *R/create_mcbette_beast2_options.R
95675ec7398d86c7bc225c2e63a77572 *R/create_random_alignment.R
5dd90637674b6d42bb86e847dd9b2ca7 *R/create_random_fasta.R
b3e2228d074e27964311136a6f24d8d0 *R/create_random_phylogeny.R
44c4cdea3be69e9ffe05ec1461043079 *R/create_temp_input_filename.R
101154aa441fe75fa232f35f2d6eac30 *R/create_temp_state_filename.R
beedb12ee549921d6f74045ad4bbceb2 *R/default_params_doc.R
1b1c20d1d38f94b48a49b74dfb259aa7 *R/do_minimal_run.R
0c01ab7a03318517f4f963cc2e9a9f89 *R/extract_screenlog_filename_from_beast2_input_file.R
11c63f9571fb785678bebbe8e31a7a84 *R/extract_tracelog_filename_from_beast2_input_file.R
4f6b93644321c549a88a491cafa00180 *R/extract_treelog_filename_from_beast2_input_file.R
7f3e00f9625a31a49c09c68ea74e56f7 *R/get_alignment_ids.R
d7dddc626e91d1c7ca46fdaa92ff03a8 *R/get_beast2_example_filename.R
d77e1da67f12eb8f705f96d11a21567b *R/get_beast2_example_filenames.R
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0bd0f58545627a0d3c0be6a3215a92ca *R/get_beast2_options_filenames.R
0d143ac1de890202e87c80c0b934ea35 *R/get_beast2_version.R
a1a3b68874b97e003917103791564703 *R/get_beastier_folder.R
479b5e1b3a39262dd143022c4462045a *R/get_beastier_tempfilename.R
d9c0f22fc5df02a87189f7d82c118224 *R/get_default_beast2_bin_path.R
16cbc8ee0af1096b5a37f382dfd33971 *R/get_default_beast2_download_url.R
a33ebb3d5f898e4cfc45823366dbe374 *R/get_default_beast2_folder.R
28163a9aeaabf6448d266a17b95d5647 *R/get_default_beast2_jar_path.R
20822f6dac611a201ea49f3f0403e628 *R/get_default_beast2_path.R
100266cb13d61748727d70ebb21b67e1 *R/get_default_beast2_version.R
256dd759de714897320a271e6945f35e *R/get_default_java_path.R
3d6e571f342dd3c3686b90289b3af445 *R/get_duplicate_param_ids.R
91002d8833ac0994a966b517fdbaacbf *R/get_java_version.R
a08f6f49471d12f10ab686ad41336f07 *R/get_path.R
051c29bf0691fc61ca8b3b433d279cc7 *R/get_paths.R
6f820043c9f8415369570cb137fc5f0f *R/get_trees_filenames.R
ac76b7173707ad024554670f074f1ea9 *R/gives_beast2_warning.R
d48c298585c3ef6a4d24499db6464196 *R/has_unique_ids.R
c80a9eb1427c585807cecf618b6f3870 *R/import-standalone-obj-type.R
c40f882046a958444c6058a9e2cb9a3b *R/import-standalone-types-check.R
10f37317b0815d4f464891fbea743135 *R/install_beast2.R
5faee41cf340b076cf1d4e7216931db0 *R/is_alignment.R
10277ddd17200d9cae8181a6853832ca *R/is_beast2_input_file.R
91f6d80ccc3e07bff19184a2157c3d18 *R/is_beast2_installed.R
4f669f709ccca252d85d185c16338678 *R/is_bin_path.R
4c1e058e045285f709e2dc3df5fd09ce *R/is_jar_path.R
2c101c0cf61de8149ae1b747220edef0 *R/is_on_ci.R
9a61bfa9eeb6cf49c528dd014b8c8602 *R/print_beast2_options.R
c206ea0f26fb0c6c09b0e090a7e3ce59 *R/remove_beastier_folder.R
bd989b101c1225c1a99dd4845d621961 *R/remove_beaustier_folders.R
2febf0e1864024dc7d2aabd31563024a *R/remove_file_if_present.R
8e7ba85955b44a3ae82d927f6ea4c888 *R/rename_beast2_options_filenames.R
53a6101d785f5c740cae32eae3cea989 *R/run_beast2.R
fe103ad2024323808e2a97ba874ea7fd *R/run_beast2_from_options.R
d66f8085b50cc2798d59dd74d58dfd81 *R/save_lines.R
3048320fe0fe596d19dedbb49996ff27 *R/save_nexus_as_fasta.R
3cffccf15ff6afec63f59003cb996603 *R/uninstall_beast2.R
19b19ebb2b040f217eb10a286c7d452d *R/upgrade_beast2.R
d4123e5df4c6d1d8192987e456861a53 *build/vignette.rds
fbf1b7cb8e1e4bd94845c6b29b206273 *inst/CITATION
894885c41448c74e2582733bbe627d2a *inst/WORDLIST
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5ba2200b15caa67ab83af72a7af5b537 *inst/doc/demo.Rmd
98559fedee1d52e4a99256a9c4b77fe7 *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
8a2468cfc8816a3cc479bf37c5091b34 *man/add_quotes_if_has_spaces.Rd
ddaf12e30f3c027c37f0ceb9c49d7062 *man/are_beast2_input_lines.Rd
9ee0fc880230c59df4c3a5b6f56d5230 *man/are_beast2_input_lines_deep.Rd
e2801b443742c38e89f80c397598b053 *man/are_beast2_input_lines_fast.Rd
8e2402770e7727e23e878a49068bab43 *man/are_identical_alignments.Rd
3a514e7f52613046edc7e423cbd32a80 *man/beast2_options_to_table.Rd
20b5c1a9b72d5e7b2d3beacd1879c387 *man/beastier-package.Rd
90a2515141ab128553833590788d3e56 *man/beastier_report.Rd
2c6f2fc8ab2d7fd971dae98c6491e4df *man/check_beast2.Rd
d2c3cdccd9036a807edd58c4b9aa1588 *man/check_beast2_options.Rd
6401225185e55b902bab940bf41a3c42 *man/check_beast2_options_data_types.Rd
d03c3aa518c906c6bd36acff87209697 *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
0fe2729211b6becfbae74acf96939d99 *man/check_beast2_optionses.Rd
ca766c46e6b174a1392027c23a5c2c0d *man/check_beast2_path.Rd
5b5b79e3437770c8978c00bf04335daf *man/check_can_create_dir_for_state_output_file.Rd
081baf8ca5783d8b9bcb5938c9cf7387 *man/check_can_create_file.Rd
eca1088b29936725fc619aa7f1cf6eca *man/check_can_create_screenlog_file.Rd
cab84d99b40db1c318a9895e118a5809 *man/check_can_create_state_output_file.Rd
ba6304a0e6af5f51ef8885d09c7dd391 *man/check_can_create_tracelog_file.Rd
5471d9c6532b7c87745d56b736cbc136 *man/check_can_create_treelog_file.Rd
151dca4d74f00f637f8c58dcf166fb99 *man/check_empty_beastier_folder.Rd
7d63c09bac70bd31147c0c62d188cab2 *man/check_empty_beaustier_folders.Rd
c8bf7398e7d7b062b9d6cf548df52a92 *man/check_input_filename.Rd
8ad7a36cb8583689c22f1d956a1c69f1 *man/check_input_filename_validity.Rd
ad1bb1305b958b20fafe9195c244d7a4 *man/check_n_threads.Rd
d9107c754a96e28b85a478cd4f85f75c *man/check_os.Rd
ff4162d84e67780a9a6ceea56160f940 *man/check_rng_seed.Rd
fada4e287c59b8d8df35ba758b2c7c0c *man/continue_beast2.Rd
86200ce44d53719d901ac2e1b335e4ea *man/create_beast2_continue_cmd_from_options.Rd
9725f5b8a24b9c6b230104a10135611b *man/create_beast2_input_file_folder.Rd
acb8e0ab1bbd629e4adf0097afbd056a *man/create_beast2_options.Rd
222dd45bc8144ac686def59192cecba7 *man/create_beast2_run_cmd.Rd
5431299cac7d49776b736e897d7ace90 *man/create_beast2_run_cmd_from_options.Rd
f1afb2b3695c58308b6f9f1d463c9641 *man/create_beast2_screenlog_folder.Rd
aaa6e9c861f3d03d0a6a5beb1b95f4d6 *man/create_beast2_state_output_file_folder.Rd
22620ccf26e25ee77bccdbd5e9a7f301 *man/create_beast2_tracelog_folder.Rd
b4cf4db2a8b4777ff46f17cf6da1c4a7 *man/create_beast2_treelog_folder.Rd
02f258282e614cb3de597111e77767fa *man/create_beast2_validate_cmd.Rd
506ba8f9225432af1d371f8c8fa9f938 *man/create_beast2_validate_cmd_bin.Rd
a44c152662dba2c080336459c3c10242 *man/create_beast2_validate_cmd_jar.Rd
4aa361176878f579ec48f29e3106c434 *man/create_beast2_version_cmd.Rd
dab11972dc89bbb71425abf09a718dc0 *man/create_beast2_version_cmd_bin.Rd
b3c50ee23ad3d728214f062f4aef20e9 *man/create_beast2_version_cmd_jar.Rd
1348a75934d72f1402202e22e73520fa *man/create_beastier_tempfolder.Rd
e741508c8cfd945b0cbc85b39b9fcdce *man/create_mcbette_beast2_options.Rd
e7b5984bbc7bcfdd1de0cf5222b9e1d9 *man/create_random_alignment.Rd
8489503da6227ad5d5558e3ac6e41ec2 *man/create_random_fasta.Rd
bef0f9706c861aba55c8b6d5ee476026 *man/create_random_phylogeny.Rd
810caa3ba913eee18c223d131d65f5a6 *man/create_temp_input_filename.Rd
a6c64c9663c561ff7a0a384a0d60e312 *man/create_temp_state_filename.Rd
0b68a0dce5178b0d67507feb660a6de5 *man/default_params_doc.Rd
81b99828a5a6baaa63740dd13913d4b7 *man/do_minimal_run.Rd
74822b9c14a71ceed48e5e7b093c9d74 *man/extract_screenlog_filename_from_beast2_input_file.Rd
e46f7a2cc5b9f2bc882ee1808b012317 *man/extract_tracelog_filename_from_beast2_input_file.Rd
ea189271c4aeeb3dde14ac3222051263 *man/extract_treelog_filename_from_beast2_input_file.Rd
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3f25ab37a1f6270f76c025cf6eda5421 *man/figures/Codecov.png
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37203e0325e108cb3b8904316e327d3c *man/get_alignment_ids_from_xml_filename.Rd
f1e67a5c83acebaf6880a0453f3a37d2 *man/get_beast2_example_filename.Rd
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48b02b48d1da24aea945952f9db01040 *man/get_beast2_main_class_name.Rd
58467b250392197e68af05478b187d5e *man/get_beast2_options_filenames.Rd
ea425c03ffa312b3e252a96913e9137b *man/get_beast2_version.Rd
bfb70adc7a1b9a085d1af46ab54a8892 *man/get_beastier_folder.Rd
0ef44cbe9d661df40a665e40d405f406 *man/get_beastier_path.Rd
ba8b927e0737b8ea5487e5de62da2ebd *man/get_beastier_paths.Rd
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b4fc09784233e439fe4eee5d6157d093 *man/get_default_beast2_bin_path.Rd
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90848fb837d0a1e6cb9e46640e50c3d2 *man/get_default_beast2_download_url_linux.Rd
637ba5cf3c462792741d84f00282077b *man/get_default_beast2_download_url_win.Rd
14ec80b33e5b733140c616d8d15bbb08 *man/get_default_beast2_folder.Rd
c88d1f0c3964ab17f49858f29e743430 *man/get_default_beast2_jar_path.Rd
4ea0eb7fa9d4f3998de9c1af0d834ed9 *man/get_default_beast2_path.Rd
af66c4a1849205dfe90a974d91ba6333 *man/get_default_beast2_version.Rd
8a2d89c99fcea1f70f201fb7a5c3fa04 *man/get_default_java_path.Rd
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c04ee0efaa9372a7b0cd685982814354 *man/get_java_version.Rd
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47a62cc7be58613000f937816e2505e4 *man/gives_beast2_warning.Rd
2b6ef7c1ab45f3b80ba163997b3ac71b *man/has_unique_ids.Rd
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3a57a66697d32afaabd8212857047251 *man/is_alignment.Rd
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a03e38d5bf267cbe69d1010707cff518 *man/is_beast2_installed.Rd
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0f82066d2cdc11eb7ee3c79129a570e6 *man/is_jar_path.Rd
2c82cc9a3703e7f4f0f9dfa9136bfaa6 *man/is_on_appveyor.Rd
40f7353bccb46484b31abe6a62f830bb *man/is_on_ci.Rd
7f02cc911f63ab5dd6074440ce943700 *man/is_on_travis.Rd
846a3f714e5b73a14af941ad166a380d *man/is_win_bin_path.Rd
2211027f1b76c51d1938ac129963db8b *man/print_beast2_options.Rd
a97b330e1dca15c1a1abd9cc37d73230 *man/remove_beastier_folder.Rd
6ab719b6f171593c45d61b7564d47b8b *man/remove_beaustier_folders.Rd
ee6cf8e748bce879a10894eee2624fc5 *man/remove_file_if_present.Rd
13710215eaddda1c32c43cc2b3a3c846 *man/rename_beast2_options_filenames.Rd
9e28ef77fcd4f9aef2835b7ea544f3b9 *man/run_beast2.Rd
a4ea41b1242899fe4ba01806b3aa5167 *man/run_beast2_from_options.Rd
dcccdba8eb89ab0058055d409b4f5e1d *man/save_lines.Rd
926c0f586ed62136f90535b10296384b *man/save_nexus_as_fasta.Rd
874bb2fe6364e7d3173efe2ae352a1ec *man/uninstall_beast2.Rd
c3b981f69c2cd2263c28ee10af21c959 *man/upgrade_beast2.Rd
57002b68e0eb59e211c93d40911ba46e *vignettes/beastier_logo.png
5ba2200b15caa67ab83af72a7af5b537 *vignettes/demo.Rmd
