10ab79f5a1f4fd38b4360341bfd2a22e *DESCRIPTION
c14cb277b046c97084bb6f7955e7c811 *NAMESPACE
98f4ce43e28b90f51b7c901f96b45090 *R/AllClass.r
87a5407f49b2bd3a437dbbe59bb1b7ea *R/AllGeneric.r
f78d68f67edba5a758990a6c1dabf505 *R/DCLEAR.r
16e595e0cde96b706f91862131367efc *R/RcppExports.R
5dd1cbc57f4e8a0bcc3e7df39c5006be *R/WH.R
88029d46bf642495f9fc2709bd3483bd *R/WH_train.r
0232e47342103e42b408771c38bf0311 *R/WH_train_fit.r
a54a9b6e751e88a8ebfc9321a988fb27 *R/as_phylo.r
871edd0682c97cfddca6083b35c9fe4a *R/dist_replacement.r
93a171c5e6535b9a7e67f00178ba1dc0 *R/dist_weighted_hamming.r
59b398138b7826f9ab9eeddef9d11c15 *R/lineages-data.r
34c77d25439d069ec01519ce8bd35564 *R/process_sequence.r
8d78e1a9812eed83f6258ce34d529664 *R/sim_seq.R
f8c02b1a4e1033acc57e03397a0e853a *R/simulate.r
622feba70e67a26cac7fc93a8db4567f *R/substr_kmer.r
0bb11208f3d3630bfeb629205578820b *R/summarize_kmer.r
1c886cb87ad9605ea0c9a211848599d4 *README.md
297cacdece2b2bbfed12c8f80a67dd88 *build/vignette.rds
fd6fc9184b9dab0652bbcd77a7ef3fcc *data/lineages.RData
3d545540910523c021ccdd0c33da48c7 *inst/doc/PrepC3.R
88299388f899e4ae8acc43902b390e57 *inst/doc/PrepC3.Rmd
a9fd7c1022f1f2ded26b0980aa4f273b *inst/doc/PrepC3.html
7878229f52e53f44ccc07160672fedaf *inst/doc/WHhowto.R
4b1d925c6e09b3cc8bade4b832662839 *inst/doc/WHhowto.Rmd
12e197c12c1cdbac5437022782abcd95 *inst/doc/WHhowto.html
f1d5103f3f579e5e565369757ac82150 *man/DCLEAR.Rd
35be448d5fd998967fcfba64ea897c14 *man/WH.Rd
53bf845a7f8f3bbc6932018b8e48b558 *man/WH_train.Rd
03411c77cfd3883e7849fddbb5e5a6c6 *man/WH_train_fit.Rd
8a15de3e19f5cf7c95b99d81c31b00ea *man/as_phylo-igraph-method.Rd
00077ecc00f68fd5087f46ea63bcfdee *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
e9ffd1ad27a3ec234f442c0d7ed94679 *man/dist_replacement.Rd
a9ecb71c1205a3a1aa3e7da6569b05af *man/dist_weighted_hamming-phyDat-numeric-method.Rd
4cc2b34914abec38bbe67af6eda67e76 *man/dist_weighted_hamming.Rd
c9b0583193a2fbe2111da0a66ec75cd9 *man/get_distance_prior.Rd
83b8bb2451751ed54b48514845c6484a *man/get_node_names.Rd
61f945ebb0c8dfe560a378595ce89ddb *man/get_replacement_probability.Rd
aabd3c377df59ea6fd4d77c6486c28a0 *man/get_transition_probability.Rd
f5bdcc47a418f6d1a1d5523b9b923abd *man/lineages.Rd
a6ad3186218444cf11776bf92dd21e52 *man/process_sequence-phyDat-method.Rd
b11a1b982ae573e1d277ddafba7fabb4 *man/process_sequence.Rd
b4627e7dc578c9873a3c2b24745a50e0 *man/random_tree.Rd
c80373bd1b5d349f2595491127a2f7d9 *man/sample_outcome_prob.Rd
7ac21f36e12b34db3c3b40282983b088 *man/sim_seqdata.Rd
be42fb4a0aef141b8d482da72ec64547 *man/simulate-lineage_tree_config-method.Rd
aafe98ed6d0d2786bda717e0f075c2d2 *man/simulate.Rd
e46c883926dcbd2ee8df26e4d45264f8 *man/substr_kmer-kmer_summary-method.Rd
31d065cd17483e5169823adb68a72c58 *man/substr_kmer.Rd
fcab8c3e537e914f90faa8d10454ff88 *man/summarize_kmer-phyDat-method.Rd
be49ce031c21332224248ff6d6f0c176 *man/summarize_kmer.Rd
f2675aab0b9817e6fca0312ed4451a78 *man/summarize_kmer_core.Rd
a999fbc634fc738646368a30d63fa17c *src/DCLEAR.cpp
2a6f9e9e044a78154d3cfda5936d6f48 *src/Makevars
2a6f9e9e044a78154d3cfda5936d6f48 *src/Makevars.win
46b9d3497c0882ccab06f82ed7a280ca *src/RcppExports.cpp
88299388f899e4ae8acc43902b390e57 *vignettes/PrepC3.Rmd
4b1d925c6e09b3cc8bade4b832662839 *vignettes/WHhowto.Rmd
