096c896b6d7ea722ec6f57c7c8c09808 *DESCRIPTION
48c29e9dbb1d3609499e15bccdfd69a9 *NAMESPACE
d86c3bfef083abf7c9e88711e420ea6f *R/AllClass.r
fee79354fbff311a3f7598acf306c64a *R/AllGeneric.r
e16224be25b3c8876195a601ee13ca68 *R/DCLEAR.r
16e595e0cde96b706f91862131367efc *R/RcppExports.R
5dd1cbc57f4e8a0bcc3e7df39c5006be *R/WH.R
e92aeef4757426dc47b9b30a607d5412 *R/WH_train.r
0232e47342103e42b408771c38bf0311 *R/WH_train_fit.r
aac7e2fb0658c1a75c1780cb735e0d18 *R/as_igraph.r
61231acb4bffcfd6622f6a29cdb5faa3 *R/as_lineage_tree.r
fedeae6851a0238419ce3b66cae534d0 *R/as_phylo.r
d27d1662b4fd374b2a2c7891f8deea63 *R/dist_replacement.r
93a171c5e6535b9a7e67f00178ba1dc0 *R/dist_weighted_hamming.r
952cc6cdbc99d3f344a28bc6e862e0f0 *R/downsample.r
b5dd9f6eb5b2453061382721802979c9 *R/get_leaves.r
28ff17e2c4caf2a3b32e04a65df08e1e *R/globals.r
59b398138b7826f9ab9eeddef9d11c15 *R/lineages-data.r
10b4f5fef2077d9567b0c22d5ce2a435 *R/process_sequence.r
df5e7e6650b93379fb69337c5805a359 *R/prune.r
6474c0c0d9922d634b7266601afd37f1 *R/rbind.r
8d78e1a9812eed83f6258ce34d529664 *R/sim_seq.R
6b4ef5228f9d6c5989c761762962a8cb *R/simulate.r
d105c7ff539aaf5c6d42e8b35f12b787 *R/substr_kmer.r
6cd598b306177ad275eee9e9b0d59fe8 *R/subtract.r
0bc7cdde0afd58a083dbec73948e6e83 *R/subtree.r
bc1353c8210d78ec3744ce837dfb7b9c *R/summarize_kmer.r
9f563dc2880e3b0556ef436de998e5f2 *README.md
6ad9c781317121c260080423348ff502 *build/vignette.rds
fd6fc9184b9dab0652bbcd77a7ef3fcc *data/lineages.RData
3d545540910523c021ccdd0c33da48c7 *inst/doc/PrepC3.R
88299388f899e4ae8acc43902b390e57 *inst/doc/PrepC3.Rmd
ca26cf0829cbb2e2ccedfc35e8a106c6 *inst/doc/PrepC3.html
7878229f52e53f44ccc07160672fedaf *inst/doc/WHhowto.R
f297e2df6c02a326382fa4ee34bc034c *inst/doc/WHhowto.Rmd
9afed67f2e6be1cdef38421bd3ea4183 *inst/doc/WHhowto.html
f1d5103f3f579e5e565369757ac82150 *man/DCLEAR.Rd
35be448d5fd998967fcfba64ea897c14 *man/WH.Rd
a2ac800fedd3dbc5831dd6997cd99d87 *man/WH_train.Rd
03411c77cfd3883e7849fddbb5e5a6c6 *man/WH_train_fit.Rd
a2e165e41509fa68863ef48981516791 *man/add_deletion.Rd
db67150537ed29d0cf321a90fed58384 *man/add_dropout.Rd
8db04ac62fdc61ea101082285728009e *man/as_igraph-data.frame-method.Rd
58d9c84d1ae06525b18c8eb5f71dbe3c *man/as_igraph-phylo-method.Rd
0e770ad9957b2c4b104eb191cece0bac *man/as_igraph.Rd
2305c34fbfe5767eeff20d86e0d0544a *man/as_lineage_tree-phyDat-phylo-lineage_tree_config-method.Rd
ab47efe160c59b778b241a717f93d4f4 *man/as_lineage_tree.Rd
f01ec4d1520cce0b51c3bff7b1604aa5 *man/as_phylo-igraph-method.Rd
861ac4ac845c6cf24b0e5ffd14fdc5e4 *man/as_phylo.Rd
1727425f87c9d7db6f59d2215cd46a17 *man/dist_kmer_replacement_inference.Rd
e4a15468f2ffa8cb1c870c5844b8d859 *man/dist_replacement-phyDat-kmer_summary-integer-method.Rd
a5114332de754444d7b2f9e5d9b71abc *man/dist_replacement-phyDat-missing-integer-method.Rd
1510ee2f72e27a90cfc09e29639d8823 *man/dist_replacement.Rd
a9ecb71c1205a3a1aa3e7da6569b05af *man/dist_weighted_hamming-phyDat-numeric-method.Rd
531744c1492247a4c18cca36411f604a *man/dist_weighted_hamming.Rd
09574bf5b3149243c34ddf46e3e517af *man/downsample-igraph-method.Rd
9ed18cce16e651e2891d777d1381865f *man/downsample-lineage_tree-method.Rd
7d41cebc5a99ea205238d756f84a8300 *man/downsample.Rd
c9b0583193a2fbe2111da0a66ec75cd9 *man/get_distance_prior.Rd
0bde7e30814cb31f5fbbe721d63a91c0 *man/get_leaves-lineage_tree-method.Rd
24f52820b7eed9885329445e2859cdcf *man/get_leaves.Rd
83b8bb2451751ed54b48514845c6484a *man/get_node_names.Rd
61f945ebb0c8dfe560a378595ce89ddb *man/get_replacement_probability.Rd
bd5e43e5869fe2a1bf2a4ca6045024ef *man/get_sequence.Rd
aabd3c377df59ea6fd4d77c6486c28a0 *man/get_transition_probability.Rd
f5bdcc47a418f6d1a1d5523b9b923abd *man/lineages.Rd
95095eea0849c450d3cc1609e83bde69 *man/positional_mutation_prob.Rd
c0a7eece314f8decf313b4b0c5d2b7c4 *man/process_sequence-phyDat-method.Rd
21446935b8a4a865fc04c5e44a4a24b5 *man/process_sequence.Rd
4f2b26c61e9289556ece4674d5735e6d *man/prune-igraph-method.Rd
bd557370fb615663150928582171ab98 *man/prune-lineage_tree-method.Rd
567e06c502bd956a7b5b45a8acd743c7 *man/prune.Rd
b4627e7dc578c9873a3c2b24745a50e0 *man/random_tree.Rd
864276f25f3ea4f18b45fa02ee2e17a8 *man/rbind-phyDat-method.Rd
85160e152dc1be0e102ba62d42fedaf4 *man/sample_mutation_outcome.Rd
928c523452451215bd50c0f951838681 *man/sample_mutation_site.Rd
c80373bd1b5d349f2595491127a2f7d9 *man/sample_outcome_prob.Rd
4c4eface7fb8d02f2e0c3de860421137 *man/score_simulation.Rd
7ac21f36e12b34db3c3b40282983b088 *man/sim_seqdata.Rd
8e22ce519ba4004488de3e5a02ff1231 *man/simulate-lineage_tree_config-missing-method.Rd
834b583dac7777440206c218f5882acf *man/simulate-lineage_tree_config-phyDat-method.Rd
6f709bb4fa07377f383ef0f7f0d40eb5 *man/simulate.Rd
f8a548f3afbaf14d63bd436b5f2fd45c *man/simulate_core.Rd
e46c883926dcbd2ee8df26e4d45264f8 *man/substr_kmer-kmer_summary-method.Rd
461828bcf1295a8af130f88265444743 *man/substr_kmer.Rd
3975e3e6c6b989df6cd4c8f55f56fd10 *man/subtract-lineage_tree-lineage_tree-method.Rd
f045884f440baf0304440fd9b80db8d8 *man/subtract.Rd
235defd784a0ba0beca601cbbc81fc73 *man/subtree-lineage_tree-method.Rd
4c99e8f951f7c7982b8f77608cf040d8 *man/subtree-phylo-method.Rd
02d8c531a43dfa542ca7e264b7787f8d *man/subtree.Rd
fcab8c3e537e914f90faa8d10454ff88 *man/summarize_kmer-phyDat-method.Rd
a350631f522246576e1a6541c98d615e *man/summarize_kmer.Rd
f2675aab0b9817e6fca0312ed4451a78 *man/summarize_kmer_core.Rd
d24ac670f13526ffd6c5247be8918931 *src/DCLEAR.cpp
2a6f9e9e044a78154d3cfda5936d6f48 *src/Makevars
2a6f9e9e044a78154d3cfda5936d6f48 *src/Makevars.win
c3b62f18817e32a43dc1fa629a61a3aa *src/RcppExports.cpp
88299388f899e4ae8acc43902b390e57 *vignettes/PrepC3.Rmd
f297e2df6c02a326382fa4ee34bc034c *vignettes/WHhowto.Rmd
