7f97edb526b6bf0146eb994848b04406 *DESCRIPTION
2f4a1a615f25c9f309d8c4de6fac1e9b *NAMESPACE
bf9ba6b3c01e1c9d57225802b4852a73 *R/add_quotes_if_has_spaces.R
07a3ebcdc1bc24a3509d16959081ee27 *R/are_beast2_input_lines.R
cbdc7cbd570215fa1c87c1ce61f29247 *R/are_identical_alignments.R
ea7b4779479ff409a5074da9b14b0ab9 *R/beast2_options_to_table.R
0f8343222a61dd3e9e154368d438fdf8 *R/beastier.R
fe07bc040a248b061a10000079132ea1 *R/beastier_report.R
598fb09c229cf9b71d2f4d327589eee4 *R/check_beast2.R
45e6b555ade9b0b12f70157c01024f30 *R/check_beast2_options.R
ccc80c01b70fec0bb4d5729acddf8672 *R/check_beast2_options_do_not_overwrite_existing_files.R
d2b2e0683e0d117206bf4c0853e817dc *R/check_beast2_optionses.R
ff900d2cb3b7b3da1311772ea27e7982 *R/check_beast2_path.R
841d45a98ea4c27f31bfcdf1636b18bf *R/check_can_create_dir_for_state_output_file.R
7019c3d7ba5a3f255a8e6962a83299fd *R/check_can_create_file.R
3d04d5ada4872ea9d2240dc65946cd50 *R/check_can_create_screenlog_file.R
4511ffd503ca085d60614b250a32da53 *R/check_can_create_state_output_file.R
d6da062ba8d94ba674055caeae81b336 *R/check_can_create_tracelog_file.R
5058c3079425d0b0263bea93f0199bfb *R/check_can_create_treelog_file.R
8d8b20c0b7dadd9b0e689703df44d8ce *R/check_empty_beastier_folder.R
74f89bf0dd27ef5dec6d83fa5622a6c1 *R/check_empty_beaustier_folders.R
30f5788f70e1800d25081ade3ff27a73 *R/check_input_filename.R
771b020b831ef6307ce627b3a153a221 *R/check_n_threads.R
50075fb3515c8e716491c704f8a5c28f *R/check_os.R
d1b6023495294e2fd2756acffbeba8cc *R/check_rng_seed.R
b14f9967898e702c5619de311ba6957e *R/continue_beast2.R
f95f9a2ce4e61c5f84e317d27ad26fda *R/create_beast2_continue_cmd_from_options.R
ec21e74700c3e280e924484a66daafe3 *R/create_beast2_input_file_folder.R
67ff8fce4ae2ddcc6f50d4cf442e0000 *R/create_beast2_options.R
fd4ad075d4066ccdb040aac108c3bea0 *R/create_beast2_run_cmd.R
d64ac2f577f8519b9e6ebba5d90ba3b5 *R/create_beast2_run_cmd_from_options.R
760ad6db2eb80ec2fa7ce0748707a40f *R/create_beast2_screenlog_folder.R
3b494a7a1b612a6d9ee4b58eb0809d5d *R/create_beast2_state_output_file_folder.R
e4405dc1b02ae9536527781d07b56f32 *R/create_beast2_tracelog_folder.R
23016c82742c0650ed24839f3d9afd0a *R/create_beast2_treelog_folder.R
55d645398a989f54a98d0e74690f7974 *R/create_beast2_validate_cmd.R
9eb74b60cdd1e47a24873ae522c18201 *R/create_beast2_version_cmd.R
b800c3242c32fc396472a8cb66b99c66 *R/create_beastier_tempfolder.R
67d869b108cfab8ce33679e7e95d4da5 *R/create_mcbette_beast2_options.R
a56f940b99d3de64eaba7b816c573512 *R/create_random_alignment.R
207dc5a6a8804be6b34b168fb8d9c761 *R/create_random_fasta.R
b3e2228d074e27964311136a6f24d8d0 *R/create_random_phylogeny.R
1fe112df16af41052024783ddea45030 *R/create_temp_input_filename.R
7810b8b7583e92413eec570509ff150d *R/create_temp_state_filename.R
beedb12ee549921d6f74045ad4bbceb2 *R/default_params_doc.R
bd75543aabf9c0dcc3f879c1b39a44d7 *R/do_minimal_run.R
f19cd743689413131b8b259aa8a5b420 *R/extract_screenlog_filename_from_beast2_input_file.R
dd48ca70fff280f5178f8147629270de *R/extract_tracelog_filename_from_beast2_input_file.R
649abcfc365151213ca427e24ddd9bc1 *R/extract_treelog_filename_from_beast2_input_file.R
7f3e00f9625a31a49c09c68ea74e56f7 *R/get_alignment_ids.R
d9b0231e194df902cfd18e3ced903822 *R/get_beast2_example_filename.R
c753e2ba414bfe483dc4d0187ad45b30 *R/get_beast2_example_filenames.R
e622a41355dc6f6aeea72c5e20f49857 *R/get_beast2_main_class_name.R
cb04f885251b000bb6e41cfe4c43c8dd *R/get_beast2_options_filenames.R
a2af5e9236a0c6fb9d4fed37d24a989a *R/get_beast2_version.R
a1a3b68874b97e003917103791564703 *R/get_beastier_folder.R
7c9a9ccf6836681708c2d09a5fae9abd *R/get_beastier_tempfilename.R
995686766eb58c8dab8e89204aae1d11 *R/get_default_beast2_bin_path.R
53aa4602d3704a63ee3dea4c48096c4f *R/get_default_beast2_download_url.R
a33ebb3d5f898e4cfc45823366dbe374 *R/get_default_beast2_folder.R
9076e75bf5674a2807d001282da39ab8 *R/get_default_beast2_jar_path.R
7f34282e7b45d1f80edf99da2a07bf40 *R/get_default_beast2_path.R
100266cb13d61748727d70ebb21b67e1 *R/get_default_beast2_version.R
465418f6e651bd5ad8be4fa6ba56c550 *R/get_default_java_path.R
3d6e571f342dd3c3686b90289b3af445 *R/get_duplicate_param_ids.R
91002d8833ac0994a966b517fdbaacbf *R/get_java_version.R
a08f6f49471d12f10ab686ad41336f07 *R/get_path.R
6faa062f278b3c9b8147031d3352dceb *R/get_paths.R
bc5e748876ab6bfecdd956745d6167c1 *R/get_trees_filenames.R
5a657757b1f65bd75f2dccb280403c30 *R/gives_beast2_warning.R
d02abf545a28581b51842e755f38a98c *R/has_unique_ids.R
d9965f6fb5a3f66aa9202f9cf960d4b1 *R/install_beast2.R
5faee41cf340b076cf1d4e7216931db0 *R/is_alignment.R
06699eb453a5eabfee67fa3c67f56d1f *R/is_beast2_input_file.R
74f7417c4b791e7ecc8015958b047ce7 *R/is_beast2_installed.R
4f669f709ccca252d85d185c16338678 *R/is_bin_path.R
4c1e058e045285f709e2dc3df5fd09ce *R/is_jar_path.R
2c101c0cf61de8149ae1b747220edef0 *R/is_on_ci.R
dcd0066c875ff49826fccd095c3b22b9 *R/print_beast2_options.R
bf63eddf36b1faf8734d680ddce43870 *R/remove_beastier_folder.R
e3dd27be69816fc43a403dd87c3aadfb *R/remove_beaustier_folders.R
5fddfd3a5a2510eb580a9f2a9c856117 *R/remove_file_if_present.R
0f6216e8bbac3d96c9c9f5056f5d3727 *R/rename_beast2_options_filenames.R
b7ee22c6dcc96168098735832782d945 *R/run_beast2.R
217b69072a19fa695743f78a004329fa *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
2bfbeda85feb007dccc0d4f0fe3afdbe *build/vignette.rds
d5d08093170334ef5651f86d4f732f7f *inst/CITATION
3575a41c8a8a39ce5bc8591a97fe5445 *inst/WORDLIST
fd14e86faf17da2dbd67ee14bf0757da *inst/doc/demo.R
5ba2200b15caa67ab83af72a7af5b537 *inst/doc/demo.Rmd
eb03144c78c16b2b09c0c102622b743a *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
2f8293badcf5e9b19aa200d472cbd9a0 *man/beastier.Rd
90a2515141ab128553833590788d3e56 *man/beastier_report.Rd
676b712095b9d5175891e770e5628cdf *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
3ca7f0038092802d9de73ffb80bebac0 *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
9f054aec9d521ac1964cbc2406e776d1 *man/create_mcbette_beast2_options.Rd
e7a076ca1667197fbd96e91fbaa8d4c1 *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
f7de71e5ff24145a37bf281e4d155cfa *man/figures/AppVeyor.png
3f25ab37a1f6270f76c025cf6eda5421 *man/figures/Codecov.png
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4f9bce317a2b82518737a7ee7381c2ec *man/figures/TravisCI.png
57002b68e0eb59e211c93d40911ba46e *man/figures/beastier_logo.png
37203e0325e108cb3b8904316e327d3c *man/get_alignment_ids_from_xml_filename.Rd
f1e67a5c83acebaf6880a0453f3a37d2 *man/get_beast2_example_filename.Rd
e587beb58e4cc1b0bbe91ee18d4ae8b9 *man/get_beast2_example_filenames.Rd
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
afcb5e8466b0d620935252b345cfbb41 *man/get_beastier_tempfilename.Rd
b4fc09784233e439fe4eee5d6157d093 *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
14ec80b33e5b733140c616d8d15bbb08 *man/get_default_beast2_folder.Rd
fff9d85f9ee28e4c2dfc0676db462308 *man/get_default_beast2_jar_path.Rd
c5125872c20a6b00063717049b897794 *man/get_default_beast2_path.Rd
af66c4a1849205dfe90a974d91ba6333 *man/get_default_beast2_version.Rd
8a2d89c99fcea1f70f201fb7a5c3fa04 *man/get_default_java_path.Rd
f52bd7ef03cf5040c3ca34380cc40e93 *man/get_duplicate_param_ids.Rd
c04ee0efaa9372a7b0cd685982814354 *man/get_java_version.Rd
81d05a11b9f38c25db0a9fc4c293b483 *man/get_trees_filenames.Rd
bd597500b1e48b6eafd31f1f73986d06 *man/gives_beast2_warning.Rd
2b6ef7c1ab45f3b80ba163997b3ac71b *man/has_unique_ids.Rd
dacf9f13ea51e42467104b2ba15633bd *man/install_beast2.Rd
3a57a66697d32afaabd8212857047251 *man/is_alignment.Rd
fb020d7922615bb0ce7d7c1669f3530c *man/is_beast2_input_file.Rd
a03e38d5bf267cbe69d1010707cff518 *man/is_beast2_installed.Rd
00f75bc16ed40adfc36d971c7d720f5d *man/is_bin_path.Rd
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
