77159995f1130ab551f0c46319b44fee *DESCRIPTION
fa6ba0d01b536dff93dc916a736ef596 *LICENSE
3ca00afc7fd2da4a020d24e013bdf37b *NAMESPACE
72c25bd7f7f0e088d921b90add812148 *NEWS.md
bed38ba84f85f2238c7cc8ad01089112 *R/as_adj_matrix.R
a11419f53c49117b68f1dfdf8e14d70d *R/as_bn.R
8e46c867fa89e36ae099d0a1e5607fd6 *R/as_sevt.R
b306be52208b9e2e1923bdd266e4f5b9 *R/barplot.R
2c66559e6455c2985507aaa6ccfccdad *R/ceg.R
acea87a1e89b7d63bd9abb8db4106bd7 *R/checks.R
7defde57752d4bcb0f0899bcb8ba0f67 *R/ci_matrices.R
bb464abca4842e67263bda60d9a4c1ad *R/cid.R
2b4fd6644e5d7f58f928185d60c78267 *R/compare.R
5776a9c761946fa3bc4a0d5829191952 *R/confint.R
33f96aeec1c290d684b4b566598ff7b0 *R/data-doc.R
a007994cd376956c7f63c8d715b60e64 *R/erase_fit.R
f72061b6872e8fea2474a1a15f1a5d43 *R/expand_prob.R
e315a01aaac858b3bf21f385f0589afc *R/full_indep.R
8eb1c6e76291bad8af3dc74089b1d678 *R/generate_toy_data.R
96327fa4224e97b32fd2ffeaac353bbd *R/get_paths_stages.R
946ae1c7d5b7d836c142a06a7ae5b054 *R/igraph_conversion.R
64068441dbbb87d2b404a4b0e153c9cd *R/inclusions_stages.R
af1128cab589896df43a1c6fa50042e8 *R/join_positions.R
3ffcfda50e68cf0ba800bf811dd66094 *R/join_stages.R
b2e541bd1e7ad3dc7d89499146c6308c *R/join_unobserved.R
591b1b02b56058cd7ab7904436039746 *R/loglikelihood.R
69e1e244e8eed3fd2ffe82fcd6fd70a1 *R/lr_test.R
6d3b32ae87e94f073a4e2df0b1905d03 *R/make_ctables.R
7e0be1c7e915679925ad7081979ccfa5 *R/model_info.R
bbb6e7ac38eb899bd20d4e82de0c973a *R/parentslist.R
6f92a734b115496d4466ec8ccffd84ef *R/plot.R
1ffe35089daa6aeb7e27947505574702 *R/plot_ceg.R
3425879a69b533c961b5abba40aebd7d *R/predict.R
aa186edd34c724878197074ab7eb8d4f *R/print.R
4f4f47c5052f89e9973ecf84f445f387 *R/print_util.R
5d3d8d3419ada2ede8a247cd9713a633 *R/probability.R
326e8195efdd0fb76e67db57b9fbab7a *R/probdist.R
26106b1f50d6d98720340425b97388d4 *R/random_parentslist.R
c02a8dbd5d19f00f098d929f94665f8b *R/random_sevt.R
9315d242b751a13d0a3b9ffe174a2272 *R/sample_from.R
ff267fbd480db52756a30a32f7fd2189 *R/search_best.R
065ba873a6964e0002314253099cf941 *R/search_greedy.R
b467af71360d676d8224c3ccb71c9a87 *R/sevt.R
eb2ecf94f83f823d5d794f1650d650d3 *R/sevt_add.R
9c158d81a4f8f12299f9e088f1d95b4e *R/sevt_fit.R
a6f3647e1524b39c208210a7f3d76423 *R/sevt_simplify.R
0a5f90406b06fd71f501267688b88da0 *R/stage_operations.R
e4ad4ece3c5a1449564ca922af58636f *R/stagedtrees.R
4054e00c27d6510d88ba166b78e66675 *R/stages.R
6b2f88fda304ecf23546962d4e4e5e55 *R/stages_bhc.R
1ca42f67b312312c7828df786e13fa8b *R/stages_bhcr.R
80d250fe9650cd4f84613ea051c2fd2c *R/stages_bj.R
b9a4960c15930181e893c930161215c2 *R/stages_csbhc.R
810527daea20c4f2d42d09cae0b4db4f *R/stages_fbhc.R
eeeecd8779d75b8f2a585683c206eaa7 *R/stages_hc.R
5758c9f20c5bf679d8e25a640a264864 *R/stages_hclust.R
2a42235b19d8945507d47a42274999a9 *R/stages_kmeans.R
2015a693fd460eb6198969e6de908238 *R/stages_simplebhc.R
1d2b450155076aa8363e0c996b51aea3 *R/stndnaming.R
e984d1e8542468d7f2297d293fb0dcae *R/subtrees.R
01a980edae348d4641b24a7268cb76ad *R/summary.R
1e305c0b39bcb87005044b969e173cf1 *R/tree_indexing.R
4eb3912af4f70d74b49a7a6d14a40b57 *R/util_functions.R
4365e4162ce5a17dd6e19885f135d183 *R/write_tikz.R
ea8a9de090d1d6c0ba3b1c941ed668e8 *README.md
a179349640bea6a73af4c66b9821d1e5 *data/Asym.RData
de5217822a1c88c43c751b92d204ff85 *data/PhDArticles.RData
98aae2eab3a5e1c8285fd85db0993167 *data/Pokemon.RData
414afaf487752f61727d0b368c4e4309 *data/covid_patients.rda
72d9494597ddc4d767e9bf6eefb70d59 *data/trajectories.rda
97804cd58cd0ea63b322e9a926721c45 *inst/CITATION
a52244a79a2d76aecbec6c20e3d0796f *man/Asym.Rd
45111205784bc09150087f882af72bbd *man/PhDArticles.Rd
523ff888d88eea55d3ababf91361a53b *man/Pokemon.Rd
7297545fec83c0850932e64895234225 *man/as_adj_matrix.Rd
8a7f56dca5c29253ff504d868a5443da *man/as_bn.Rd
c13b6d1882c6b6db89f8881ffa3e43fb *man/as_parentslist.Rd
18df78d13ec77328d3a3f39eb6b2dbb5 *man/as_sevt.Rd
dd2de45b8813f807ed4f9a34c505d7bc *man/barplot.sevt.Rd
8bdc4967be9235ff8c65665b0c9b5f13 *man/ceg.Rd
12d09cdcb308120b08bfe2a9d2b2d915 *man/check_sevt.Rd
33cdfb1277d22838803b396bc61fffa6 *man/ci_matrices.Rd
e1da38eded441918285c560b571163d1 *man/cid.Rd
aa7cce1105a8659fd673c78e1cbdf560 *man/compare_stages.Rd
5426c43024201562038ff8184964b987 *man/confint.sevt.Rd
bf96279b39d51761fea19fd5fd67b1fb *man/covid_patients.Rd
e2a38d8394de1db15853388198673f64 *man/depsubtree.Rd
81692c15a6757f050d41263e2ecee37b *man/distance_mat_stages.Rd
9626801b3b07ef105100f193829e50e8 *man/edge.Rd
e73b7f7e67d9d82c30657d9f970960e0 *man/erase_fit.Rd
91fa66ed7edd3e55665008f9975ec818 *man/expand_prob.Rd
f47deda8e3eca190836a1819f469ed0c *man/figures/README-unnamed-chunk-17-1.png
a6d5c33ea2428bf6ec364754e4972265 *man/figures/README-unnamed-chunk-18-1.png
71be55f8496baf24b05f50b22f0e0a5e *man/figures/README-unnamed-chunk-19-1.png
72aa769009e5e0937e9e62749a3b85a4 *man/figures/README-unnamed-chunk-20-1.png
26d91c0af87e8057382497f51fc4d1e1 *man/figures/README-unnamed-chunk-21-1.png
bbc1b13d978d6b657f0bfeb2280a58e5 *man/figures/README-unnamed-chunk-22-1.png
881a521d0bb4080a8bf4f768a7cdf835 *man/figures/README-unnamed-chunk-23-1.png
2c40f499eaef3a9416115e49b4ab92ff *man/figures/README-unnamed-chunk-24-1.png
069b4e72e54748c16b2bc0b5891c57ce *man/figures/README-unnamed-chunk-25-1.png
4e39f0ae3b65c9292d5cb70330df5670 *man/figures/README-unnamed-chunk-3-1.png
b146049c4f72c58ef460d354f02c2fdf *man/find_stage.Rd
c2b8eeed710d87e57b3fe3fd73623e2a *man/full_indep.Rd
b45a9cb98300c14de4d099f717a39bf4 *man/generate_linear_dataset.Rd
3ebb022d746ca2c828d603dd0151b0c9 *man/generate_random_dataset.Rd
5b59306f39f944727cfa3cd001e79bb0 *man/generate_xor_dataset.Rd
ebbcd45f5cff9b3074b6bb7be5225d9a *man/get_stage.Rd
8e25031f23572e278a1a83dda2b5b924 *man/igraph-conversion.Rd
57206fa2635e14638c3439269f5056fb *man/inclusions_stages.Rd
c38bbb8f1d3b27535165f5e5b636ac78 *man/join_positions.Rd
1374120071812eec9b8534eb319a0fbd *man/join_stages.Rd
f859603fcfb8f9fbaa9d2eff080c0f2a *man/join_unobserved.Rd
9b138f10faec9e60291d112a42e01986 *man/logLik.sevt.Rd
ef61ff04e123603408da011d6ae7654c *man/lr_test.Rd
1cc6a0d33cf764e9db92f30a10391036 *man/make_ctables.Rd
2c6fe0d79a514a7b7e1fa70f824f0379 *man/new_label.Rd
b4411a5835bb9753c767da76987348a0 *man/node.Rd
df508b947a5b366c123fb93087d46aa9 *man/noisy_xor.Rd
b6aa414661aaeeab273bda25ea2a574a *man/path_probability.Rd
c8e0859f67e8d7e928d197f758cee6ec *man/plot.ceg.Rd
e1e3f0b8ad0914eb42185136dfd53e9b *man/plot.sevt.Rd
0c13c958f54b2448f5621223fc7e724c *man/predict.sevt.Rd
2de9e2eb42bdfeb92b9dc7d1ac2c1100 *man/print.parentslist.Rd
f581addff97d75c3f651f567c0c8091a *man/print.sevt.Rd
c5681c1ac15155a1e0c78cc5a1beb24b *man/prob.Rd
a5a03369ffe9d1bb2eadb0b5c761f669 *man/probdist.Rd
e8769f98acded03fe8784929a22f59c3 *man/random_parentslist.Rd
41ec11869e2907f6e43f9b2167b7ee57 *man/random_sevt.Rd
995a19fbee13deccc0bbecefabbbc7be *man/rename_stage.Rd
ac0e84421a1abafdfea8ee82c1496744 *man/sample_from.Rd
a5a7ec6135a3ee932a33991751c26277 *man/search_best.Rd
d5ce925d9b10eea1cc92bf6e185f9da8 *man/search_greedy.Rd
976c4a74a97c6e8684200de9ff407886 *man/sevt.Rd
63ccd145b2833445289e306f6c8b9977 *man/sevt_add.Rd
f975518289d7c79300bda457cb93e445 *man/sevt_df.Rd
fe4ceeaa60c6001cbe16966efbcd8aef *man/sevt_fit.Rd
17fbcf08ed62c11c9925042e1ce31255 *man/sevt_nvar.Rd
a0822319080edebb5e29ab5461be5cf7 *man/sevt_simplify.Rd
b7e924410dd030481319db947cb5d623 *man/sevt_varnames.Rd
a840f7e7c2a9786240351fb82fd6becf *man/split_stage_random.Rd
5e55c874184503a816e715df4629c5c9 *man/stagedtrees.Rd
8c9b15376cb9d6026ce28e0390524f03 *man/stages.Rd
fef426df79803aebbc69e8bccd8233d4 *man/stages_bhc.Rd
f389165eac9db7be047f2271d5e79378 *man/stages_bhcr.Rd
9ebd6a05b35381c029a9f9aed5a22c11 *man/stages_bj.Rd
2ea2563e1d47327f4f26fd33b3d94484 *man/stages_csbhc.Rd
d6ee96f9012a81dae2d8856d72e93a25 *man/stages_fbhc.Rd
adcd043ba2894f9372a74b5fcace2bc9 *man/stages_hc.Rd
a22c488d2ec5e197d30f364f1173aeea *man/stages_hclust.Rd
0e1e817a16e41d9b5f821ce7bab0fae3 *man/stages_kmeans.Rd
770a09cac1e7caf28878b89e20ee548e *man/stages_simplebhc.Rd
b27224e35fb7a4fedcfaef619f543d3d *man/stndnaming.Rd
8f0ff872771e228575b4b5babc6146c6 *man/subtree.Rd
435a3c87db2fccd6ae22941cfee2214a *man/summary.sevt.Rd
a18f75eb798ce9f9912fde19de54da4e *man/text.sevt.Rd
a4b56f89afb131c7cceb943e35569e5a *man/trajectories.Rd
74dd59fb566c104df76edbbeafe26cd7 *man/tree_idx.Rd
a788e8658c87afd674d69664bb29a669 *man/tree_string.Rd
3476bd3a58b666b355d71fa47d4f1809 *man/uni_idx.Rd
49604b595751a32c9b5e3a22fc6c0699 *man/which_class.Rd
4972660086dd7184201a76bba289e0f1 *man/write_tikz.Rd
7d596733d31964a10ab0ccaf3378d103 *tests/testthat.R
2c4ae0b0b5b48ad6374cd96262c71afa *tests/testthat/Rplots.pdf
1d991e62c81577c280142777fe1e6b5a *tests/testthat/test-as_adj_matrix.R
3934bf3a1578d208ffdde88fefda8557 *tests/testthat/test-as_bn.R
dd04c3ed2c9c12d1058e5f16a3532254 *tests/testthat/test-as_sevt.R
5771743afa77e12cffaa8d1335780474 *tests/testthat/test-barplot.R
793d8d92230105731f770cb2e458a78e *tests/testthat/test-ceg.R
dee66ae059f12a512bb5ec7bb21fd94a *tests/testthat/test-checks.R
95e173c15354ef99b8a773ee77993d21 *tests/testthat/test-cid.R
6c62b388b6c3b05192ad61910e2ed50c *tests/testthat/test-compare.R
64377c3922c7084f647e7b866a72c2a1 *tests/testthat/test-confint.R
eb18cb4f56d4d039e29f4e6ee550ef6e *tests/testthat/test-erase_fit.R
877785519855ce4dbba4e76cb11d87db *tests/testthat/test-full.R
59f17259d710f90f01e129907b02af3f *tests/testthat/test-generate_toy_data.R
860b75b134944c8fb2def053abef3858 *tests/testthat/test-igraph_conversion.R
607c9355918555aa933afe6d0d2daacb *tests/testthat/test-inclusion_stages.R
e1bafd8f505248f2f19f20f5da1e4b29 *tests/testthat/test-indep.R
14c22030a526b3524f15883190b76d5f *tests/testthat/test-join_stages.R
39dc0a24bd6cb7640e0accaf900f9f50 *tests/testthat/test-join_unobserved.R
07ed1e7bd4c6e9755344ec00a6ffef5f *tests/testthat/test-likelihood.R
5c8325f8eb0b10717c381cafe4699f88 *tests/testthat/test-lr_test.R
5cecf06f24943d8ffab7580c183d2210 *tests/testthat/test-model_info.R
d5a931fa2c207b2900fa1d1509a6ca6d *tests/testthat/test-parentslist.R
c7e5e849a913be67ac315786d44fa235 *tests/testthat/test-plot.R
bd744d3662c0ecfd8c21e9426bccffae *tests/testthat/test-plot_ceg.R
6e00fc15fc1729d7f9809c04e2810387 *tests/testthat/test-predict.R
a6b926c950d4327718cbd13a2e7b4f50 *tests/testthat/test-print.R
91577c950f4f903e73a1238ecf1f91b9 *tests/testthat/test-print_util.R
ec3493a65fd83f450f1029646afa45cf *tests/testthat/test-probability.R
023b118f76470d5d3bb3e82aa7080885 *tests/testthat/test-probdist.R
70648d3d1b1536bb0cb540ae844baa0f *tests/testthat/test-random_parentslist.R
4bc1893a36b7a442925b5bde06f408af *tests/testthat/test-random_sevt.R
50c4343ecb1f771b0db713118958e1d2 *tests/testthat/test-sample_from.R
aeb4275bd3bf6bd95efb459c4f7b1a32 *tests/testthat/test-search_best.R
e03b4c2b086c5f1f02131427d2e08454 *tests/testthat/test-search_greedy.R
397ae3481699964690c80a3632f46317 *tests/testthat/test-sevt.R
9d611513787f92d5e61a85607533de89 *tests/testthat/test-sevt_add.R
c2138d457f61763c926ad7480aa31125 *tests/testthat/test-sevt_fit.R
50293469686338d2f63d21c3ef8260f1 *tests/testthat/test-sevt_simplify.R
a103101fabbb5a1b74c9ab3d9d77301d *tests/testthat/test-stage_operations.R
2cb0870a8d03cb6265dede343266e4e3 *tests/testthat/test-stages.R
3f6a776676e9204fcb44bff22df1b77e *tests/testthat/test-stages_bhc.R
73108bf70fd9cf5dda711e4ba939f859 *tests/testthat/test-stages_bhcr.R
964b4cc07b1b0ca4f6bca24b6ff4db5f *tests/testthat/test-stages_bj.R
a53a1a98045afe0f3509527fd203ec7b *tests/testthat/test-stages_csbhc.R
30194ecff21ca91924a9887d19ecedc0 *tests/testthat/test-stages_fbhc.R
eb1365dc8d6fcf26b92c9dad51c2aa4a *tests/testthat/test-stages_hc.R
025d72d2c1aec3bbf396a3a68b01865e *tests/testthat/test-stages_kmeans.R
e5ac0a9cc6ce387253c5ac485e8896f5 *tests/testthat/test-stages_simplebhc.R
cdb8f10bf2f74a075e5d7a5d1c2d529e *tests/testthat/test-stages_stages_hclust.R
a0eab04930eb16b797917c53bbab5e66 *tests/testthat/test-subtrees.R
2b7cad3738735216874e9642e24f28f0 *tests/testthat/test-summary.R
76a1e9fa165fd067923c669c86f5d905 *tests/testthat/test-tree_indexing.R
19b10a86f2e3f6ef14fe51f4f6dbf88f *tests/testthat/test-util_functions.R
b90d6b46ddafb13e76d30d5a1373f656 *tests/testthat/test-write_tikz.R
d41d8cd98f00b204e9800998ecf8427e *tests/testthat/test_simple.R
