0e08dfe05cb03e44696ba7bc433c64be *DESCRIPTION
c080912ee72f75cefc29dc04b46c1b22 *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
f1067065fb19be58ec73fb1751221d14 *R/beastier.R
89e24768d8cb2e3ada4352599cd8fa2e *R/check_beast2.R
da8ffb954e79efd3350ec6eb5a9ba24b *R/check_beast2_internal_filenames.R
9480bef133e4a5418c08924b9f491012 *R/check_beast2_options.R
cdb7845ba38cb59ec36749fd0476fad8 *R/check_beast2_options_do_not_overwrite_existing_files.R
02e2c4e20cdd203a0a7a3de9f9305893 *R/check_beast2_optionses.R
c27aa47b6e33e05f86663a4bd7bd48b5 *R/check_beast2_path.R
df5892fab569a0233b350c535125e0b8 *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
95701f8fc7e9aaf1026c7b9c76ab49ef *R/create_beast2_validate_cmd.R
37f11a90feb291895d328ae5b8301342 *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
7ad21eed1553ff23ca26324e1b547840 *R/default_params_doc.R
50a9f8eedf1176e03beb7970ef2e929e *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
128d29db3c7944abc7d7aabe805e31d7 *R/get_beast2_version.R
ba59dbd9bd3bf634e0f369d0cd89bf80 *R/get_default_beast2_bin_path.R
d38cb5afc76b2d95dcf1665c737df1f8 *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
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
1a23ea7d76b8d933eb652ed388a50122 *R/get_trees_filenames.R
4b72eab02c7a4260ec198a18fa279cdd *R/gives_beast2_warning.R
ed5e7c6147e98f3173b7a24ec77428c4 *R/has_unique_ids.R
b82180fc0cbfacd319f4e53d19e46705 *R/install_beast2.R
5faee41cf340b076cf1d4e7216931db0 *R/is_alignment.R
14be0c8676ed248013fc010854e2f448 *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
525bf86999cc9cea41fca01966ad1c6e *R/run_beast2.R
6a2fc55530381402d3163ecdaddf64d3 *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
ac2f2a29a649cebc0ab02b28da2b0281 *build/vignette.rds
604d69ff7d5954219736e01c41d18e48 *inst/CITATION
14cb2f6a23cc9c050c9e934ad9e61871 *inst/WORDLIST
61987cfa13b217b2a1ca2816156ff19f *inst/doc/demo.R
0628d2da61ef30ea7fc8beba876e5e5b *inst/doc/demo.Rmd
3aa7e6b615897481b118424b9019d708 *inst/doc/demo.html
59dc5020cc76a70d138c1465d93c5b12 *inst/extdata/2_4.xml
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
cf67cea70b8b6fa59bbd3c07995c052f *man/are_beast2_input_lines.Rd
ff5fc46e361f72c1e33ac4892985bcca *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
6551f8c11e3756052c7fcc4222842cc6 *man/beastier.Rd
02e6a6eb2f6d720ed137c287ca8f7275 *man/check_beast2.Rd
c4de33500b34e8cec5a7cfec051496ff *man/check_beast2_internal_filenames.Rd
6aa11b94dde59476c47aa4849f13a2d5 *man/check_beast2_options.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
08ea9bc1dbaeeef474ed8d6b64bad154 *man/create_beast2_options.Rd
43d6cef7e6b824dc42b8cc6f6456efee *man/create_beast2_run_cmd.Rd
73276051e9fefd9ec1b15dcdc16d096d *man/create_beast2_validate_cmd.Rd
e36d425b9872ca009357185977e77b6b *man/create_beast2_validate_cmd_bin.Rd
40b2d34cc07a2f126a679004617b3d02 *man/create_beast2_validate_cmd_jar.Rd
68558a2fc057b3fb602a1ecec72cd14a *man/create_beast2_version_cmd.Rd
a27f783e33e0b3b33bf918c820047c53 *man/create_beast2_version_cmd_bin.Rd
5bd7b1821990990f1baaa17aa1d89021 *man/create_beast2_version_cmd_jar.Rd
6663201713762b46f15d7f58c1ab543b *man/create_temp_input_filename.Rd
9ad9ae5956d3cecca9d492cdc77b3e4b *man/create_temp_state_filename.Rd
56b14e5e62568d54613c987de5108ec3 *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
0d186b73bd97ee2a0ec79b2c70e7b2f8 *man/get_beast2_example_filename.Rd
b381efcc1e65cc870cc4f5f30139fbec *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
b1d3c0c3887b98d8bc90737b5d0cc75e *man/get_default_beast2_bin_path.Rd
6fb590843c49a2e75f0fa3ba16ed76db *man/get_default_beast2_download_url.Rd
babda52a2a235a8e10c82c5b5ef0c900 *man/get_default_beast2_download_url_linux.Rd
b2ae0842bd95e0f22dfeaf3bd4b7ee55 *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
8a2d89c99fcea1f70f201fb7a5c3fa04 *man/get_default_java_path.Rd
19ccc400b7bcea0b37f3b0484e66e3f4 *man/get_duplicate_param_ids.Rd
fbc32fdb19460a20f4b60291566b5eee *man/get_java_version.Rd
d46a979098b7383eb7563695eed2d0cd *man/get_trees_filenames.Rd
7faa09d7eb67d6554917c8ea55d0bd4e *man/gives_beast2_warning.Rd
bb3bc4861c65493109d13bb26cea4933 *man/has_unique_ids.Rd
9d0deb1573881a22409e2cadd8e485de *man/install_beast2.Rd
3a57a66697d32afaabd8212857047251 *man/is_alignment.Rd
39d978a00e273e65bc31cab1bb797c65 *man/is_beast2_input_file.Rd
fc3a0c88ac90de959e656deb0be24e23 *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
6d103dbbfa3b31e7cdfb9ad0514b5e46 *man/run_beast2.Rd
d3bc4c9c16fac2e117d0c92062d5ba72 *man/run_beast2_from_options.Rd
3296d46966c6b7defd69ce4e07353e79 *man/save_lines.Rd
a6ebcdff48e0e2ece773481ca367e00e *man/save_nexus_as_fasta.Rd
61db9fc05b3a36f3f0a56f23739e72c4 *man/uninstall_beast2.Rd
94e1539756bcca2f027d2151755d391e *man/update_beastier.Rd
825bc91fc940b7cabfa420eb2c256a51 *man/upgrade_beast2.Rd
57002b68e0eb59e211c93d40911ba46e *vignettes/beastier_logo.png
0628d2da61ef30ea7fc8beba876e5e5b *vignettes/demo.Rmd
