deac232bf2b946031e655018bbbb7292 *DESCRIPTION
2618ca8244f9f1af51d07df82160ab71 *NAMESPACE
135d98a0ccacc02e10f3965caf8c6019 *R/are_beast2_input_lines.R
07e522ed885e675b1069fca4f463d6c8 *R/are_identical_alignments.R
05a40830bb502e7d50b216ca8e224129 *R/beast2_internal_filenames_to_table.R
7813f23352a7840f669f92ee60be067a *R/beast2_options_to_table.R
b2258137e5115a378f9b8fba2eec8b81 *R/beastier.R
dc23b080900c7bc7bb4a4ec2f1c7fedc *R/beastier_report.R
89e24768d8cb2e3ada4352599cd8fa2e *R/check_beast2.R
b720f722a6e46c332450bd15a5d5b9f8 *R/check_beast2_internal_filenames.R
7d1796dfca6918880de8c9ede6276a89 *R/check_beast2_options.R
f60a6b2fcc486715c9883f786f056c11 *R/check_beast2_options_do_not_overwrite_existing_files.R
02e2c4e20cdd203a0a7a3de9f9305893 *R/check_beast2_optionses.R
c27aa47b6e33e05f86663a4bd7bd48b5 *R/check_beast2_path.R
43ae5520cd3c5c7b11268c84e955244f *R/check_can_create_file.R
6899b286e585d3f68e75405ac4385062 *R/check_input_filename.R
197d62ba1e6ee65918d5f2ba32620143 *R/check_n_threads.R
603f5787f4392dbe42223a72338c6c3c *R/check_os.R
9a3be2e1f5d5560e0f5a607bc2810275 *R/check_rng_seed.R
0e0b988d205fd49f07922a45cb5e609c *R/create_beast2_internal_filenames.R
cf6efb17833beab858b6900ddf581b0c *R/create_beast2_options.R
b53dd59773f545631dcfd07b89be6589 *R/create_beast2_run_cmd.R
77aea7c17dd9da962d9339b769fca94c *R/create_beast2_validate_cmd.R
30a8a387f59a80219a30c7991e02afbd *R/create_beast2_version_cmd.R
3624fd828ec440a15c7be58641778977 *R/create_random_alignment.R
710b6799b96939879d96378f849e17a0 *R/create_random_fasta.R
28c15f484b3876c99eb7c0a0c800ae0c *R/create_random_phylogeny.R
23b5a8889fe74975499d92ab3f31930b *R/create_temp_input_filename.R
e57ba54bf9fbf082b22704bdc6566522 *R/create_temp_state_filename.R
ebfbac6e883fba0bf38fd1f219524442 *R/default_params_doc.R
cd2d5b0e169b4f9bc543483c9eb80114 *R/do_minimal_run.R
39f02e44dd5130658a243b4a2e685795 *R/get_alignment_ids.R
204137e1601d47e7eb9375eb1231f834 *R/get_beast2_example_filename.R
639ec19f1860a1aa4dc5881085b10124 *R/get_beast2_example_filenames.R
bbb607cebc98c74d0be46ca69c246c63 *R/get_beast2_main_class_name.R
c0d55084f8fa899c4cef8a04ec343113 *R/get_beast2_options_filenames.R
253f2b38cd3c90df3e2469a06d4a1381 *R/get_beast2_version.R
ba59dbd9bd3bf634e0f369d0cd89bf80 *R/get_default_beast2_bin_path.R
52780cddebf9c2db4a1e6718bf2014c8 *R/get_default_beast2_download_url.R
a2e617ab0dae7dbd6a8e68cd900a6c5c *R/get_default_beast2_folder.R
a74d8397c42c34c5b31e29e8b727e928 *R/get_default_beast2_jar_path.R
14218030d7b436c10b5e3179c7efe099 *R/get_default_beast2_path.R
d015d5a062572175b0d35d261eabb75e *R/get_default_beast2_version.R
96985a5ac7e438cce1b39aa6501b1f26 *R/get_default_java_path.R
4c2e0985aca200d44b98fde6cea2d4cb *R/get_duplicate_param_ids.R
cc3a29c083a164a20526fa7125d858ef *R/get_java_version.R
4660761297b2179b0c2d8545def67b50 *R/get_path.R
a2f7376ad5e606add36be2c10a8afe61 *R/get_paths.R
fccd68c91873e482426fb0f5b6060c0b *R/get_trees_filenames.R
4b72eab02c7a4260ec198a18fa279cdd *R/gives_beast2_warning.R
ed5e7c6147e98f3173b7a24ec77428c4 *R/has_unique_ids.R
2ef4a54aa6ecaa1b0d264c68e46a4154 *R/install_beast2.R
5faee41cf340b076cf1d4e7216931db0 *R/is_alignment.R
85a257da14bba76c8db306b0055f83cf *R/is_beast2_input_file.R
83d1ed711c0c89d4ffa0a911b44cba1a *R/is_beast2_installed.R
535ee235daefffbae62a45e08cb83a8d *R/is_bin_path.R
0d10a89b077826a59b5e02711770e977 *R/is_jar_path.R
a9acc7076e6ec73c01c675e46c1212c0 *R/is_on_ci.R
cc3eec95277c438067023ce7657de32e *R/print_beast2_internal_filenames.R
20760b745ee7f4b55c3c7922d3ef02eb *R/print_beast2_options.R
af8ea4189862ea88869c983dfcabecb1 *R/remove_file_if_present.R
fb3d889cb272314fd924394301f02e57 *R/rename_beast2_options_filenames.R
525bf86999cc9cea41fca01966ad1c6e *R/run_beast2.R
a7df91d83104ae2b314ab17bdaa2883d *R/run_beast2_from_options.R
266d8d105c0605191a32414e74ec5ad7 *R/save_lines.R
3cfef14ec72d624446aebcc87377b4b0 *R/save_nexus_as_fasta.R
161c3d5f62eddecfc999372c6ced93f4 *R/uninstall_beast2.R
2c48f049a80164f86faaec7b39ed0f9b *R/update_beastier.R
a3c7f7c5749062fc4bbfbb6c40211542 *R/upgrade_beast2.R
2fc53baa82648fdf69caab43842884c7 *build/vignette.rds
604d69ff7d5954219736e01c41d18e48 *inst/CITATION
0efe7ad8f0e51b1754add0539df18d8a *inst/WORDLIST
61987cfa13b217b2a1ca2816156ff19f *inst/doc/demo.R
0628d2da61ef30ea7fc8beba876e5e5b *inst/doc/demo.Rmd
bb4f8585de79940e5456325869c80a92 *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
2136162ef6e2c998ffc177fc82d4153b *man/are_beast2_input_lines.Rd
85203f9afe984e5894026f0e909e5edd *man/are_beast2_input_lines_deep.Rd
8fb75e3bfe78a3a3e8afc29dada47c66 *man/are_beast2_input_lines_fast.Rd
8e2402770e7727e23e878a49068bab43 *man/are_identical_alignments.Rd
17d8840b889decc45fc65dec73187ca7 *man/beast2_internal_filenames_to_table.Rd
94256909affcfeb7a26025a676b82d6e *man/beast2_options_to_table.Rd
a8654ed5d23aa9075d0cdbabb5ccc804 *man/beastier.Rd
2aadfe2c5f6e48bb3dc934f57a60f936 *man/beastier_report.Rd
02e6a6eb2f6d720ed137c287ca8f7275 *man/check_beast2.Rd
c4de33500b34e8cec5a7cfec051496ff *man/check_beast2_internal_filenames.Rd
695beffbcd5c6af38d0939a75badf536 *man/check_beast2_internal_filenames_data_types.Rd
c9d502407c64e6a5606ab8330ab190c2 *man/check_beast2_internal_filenames_filenames_differ.Rd
c54c9e43a74eb0ca3f871695510e350f *man/check_beast2_internal_filenames_names.Rd
4fc2534282cf0dc5d141ce4a7af16847 *man/check_beast2_options.Rd
6401225185e55b902bab940bf41a3c42 *man/check_beast2_options_data_types.Rd
b241a75b20e3ced400a3cc00576d0815 *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
390d3c3a824465d85891407f15523ace *man/check_beast2_optionses.Rd
c265634dd0e57879bdf8052662dd806e *man/check_beast2_path.Rd
41f695cb1ca18038b8deef529eec0b6c *man/check_can_create_file.Rd
09ccf0804bd05575e3368a09446f5eb9 *man/check_input_filename.Rd
dea892717a8a523e4adf9ab1eab4321a *man/check_n_threads.Rd
f6ef1cba350f5dd5f2285b5023ce89b1 *man/check_os.Rd
ddc1d95368965611911f3bff725a87c8 *man/check_rng_seed.Rd
e68c8536b177619d5492fc3174ceb806 *man/create_beast2_internal_filenames.Rd
742108c83797433aa9b572959bb16f56 *man/create_beast2_options.Rd
c270b84118e6fd287e909552a464d51e *man/create_beast2_run_cmd.Rd
30608aca336668865f0181e8cf9aac7a *man/create_beast2_validate_cmd.Rd
7b9ef91d2647516e26e2637f8bfc361a *man/create_beast2_validate_cmd_bin.Rd
702c14f03c4f95cdb2eeade1067836ca *man/create_beast2_validate_cmd_jar.Rd
5eb0fc8ba58b005e4c57b6b001ef6216 *man/create_beast2_version_cmd.Rd
d66692c32441dc98fa617139511b9b3e *man/create_beast2_version_cmd_bin.Rd
9937aa416c995a7050f78dacd779b4c1 *man/create_beast2_version_cmd_jar.Rd
6663201713762b46f15d7f58c1ab543b *man/create_temp_input_filename.Rd
9ad9ae5956d3cecca9d492cdc77b3e4b *man/create_temp_state_filename.Rd
9b96ecb1e7137e9cf84be239c2cb66b4 *man/default_params_doc.Rd
952fd1ec6715daf3709644481ae173c8 *man/do_minimal_run.Rd
f7de71e5ff24145a37bf281e4d155cfa *man/figures/AppVeyor.png
3f25ab37a1f6270f76c025cf6eda5421 *man/figures/Codecov.png
4f9bce317a2b82518737a7ee7381c2ec *man/figures/TravisCI.png
57002b68e0eb59e211c93d40911ba46e *man/figures/beastier_logo.png
6a3b550c34217a5f0d08c74dfaefbbce *man/get_alignment_ids_from_xml_filename.Rd
a1aa4700e9c45cbc51c6d669cc383c6b *man/get_beast2_example_filename.Rd
63badddaa8c39f9e83a8c0dae990bf60 *man/get_beast2_example_filenames.Rd
cdc57960f595ccf7b69356e9c40686a1 *man/get_beast2_main_class_name.Rd
7f24958a4b365289e8caeec024eca0fe *man/get_beast2_options_filenames.Rd
8e743d2208fce0760d11687a3a952f53 *man/get_beast2_version.Rd
700960db63ab1aed428eeb0b2102f30d *man/get_beastier_path.Rd
b46ec448014e88a1ff5d318888d054d8 *man/get_beastier_paths.Rd
e38daacb654b69e99261da0d71ed74d8 *man/get_default_beast2_bin_path.Rd
454f72a7489e1255913e2ff71274cbd2 *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
610bfb7738454cf59d34a89dd7d75f0c *man/get_default_beast2_folder.Rd
6d2ccfcb5c245e5cd97bc8dcb76cdca1 *man/get_default_beast2_jar_path.Rd
146c4b1b89db541c72a11f1730df30d5 *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
fbc32fdb19460a20f4b60291566b5eee *man/get_java_version.Rd
d46a979098b7383eb7563695eed2d0cd *man/get_trees_filenames.Rd
e97e740c5235cde8fca5cccc7f55e969 *man/gives_beast2_warning.Rd
3aa587e8b26d962682928ffc35af6f74 *man/has_unique_ids.Rd
59615ccd3515c898d09bf7ab9cd26615 *man/install_beast2.Rd
3a57a66697d32afaabd8212857047251 *man/is_alignment.Rd
25d54588f64d59381742b1c14df51883 *man/is_beast2_input_file.Rd
c298b17645ab6610dbbd26ed0c3ac99e *man/is_beast2_installed.Rd
10b312bcf284be4d202fe8dcb0ce5d67 *man/is_bin_path.Rd
c66db63bf482a4f60b002d55449b34ab *man/is_jar_path.Rd
b428bc38d93cc19e9e1f2b95a868ce18 *man/is_on_appveyor.Rd
1a6e9b7e9ff758f9ec39798eb0ac26b7 *man/is_on_ci.Rd
1bd58c528cd6ae013e927953fd44e41d *man/is_on_travis.Rd
b0199eb036bfcd3a60dda83e7335c6e1 *man/print_beast2_internal_filenames.Rd
60cc25781098592a4964e4f59281c526 *man/print_beast2_options.Rd
8a7e299bd999ec0d2847bc8a68b6cfc7 *man/remove_file_if_present.Rd
db679f0600f487b9ec7fe0a4250025d0 *man/rename_beast2_options_filenames.Rd
c916f985810375b0555b4f88c15390f6 *man/run_beast2.Rd
d3bc4c9c16fac2e117d0c92062d5ba72 *man/run_beast2_from_options.Rd
3296d46966c6b7defd69ce4e07353e79 *man/save_lines.Rd
a6ebcdff48e0e2ece773481ca367e00e *man/save_nexus_as_fasta.Rd
f6c03784547494c89974a1a1a41dea74 *man/uninstall_beast2.Rd
94e1539756bcca2f027d2151755d391e *man/update_beastier.Rd
bc8614d7f04d8c76e7a544a0b1d455df *man/upgrade_beast2.Rd
57002b68e0eb59e211c93d40911ba46e *vignettes/beastier_logo.png
0628d2da61ef30ea7fc8beba876e5e5b *vignettes/demo.Rmd
