a5fed8fb17988f37f4ec843238347549 *DESCRIPTION
1222caa1c0752f0cfb727b258c60f2f7 *LICENSE
b52873f9a2a3b7e7293d355a95c1f5f0 *NAMESPACE
772cdf65a9d2ef3e9184e9e4eafacfba *NEWS.md
224b571e2e5182f0a37d07a3dc26da4a *R/ViralEntropR-package.R
abe5c78ed01652573b8bdb4b88790c87 *R/build_distance_matrix.R
663ff002850dcec3cb6abfe626136901 *R/calculate_entropy.R
72134e25d628532b3f2660bb420629c9 *R/calculate_hellinger_matrix.R
8ed5928542749df477ae3991192ed83f *R/cluster_sites_by_entropy.R
bc929c75c5a5fc6a588b5b0e7474fb34 *R/data.R
3b343e34c61e4151408579728de68056 *R/decode_aa_sequence.R
84584f9b49d9d6549403d52aa183c93c *R/detect_changepoints_ecp.R
e3756d41defe27694874512becd43ab4 *R/detect_changepoints_hdcp.R
792d948b81fdde52103af2a892c83d04 *R/encode_aa_sequence.R
02786ff334d56dfc732c5be7841e8906 *R/extract_fasta_countries.R
66aa0a543d45d6ed882b1bf579b85351 *R/extract_fasta_dates.R
3c0943f7f87f8333f077554c0bca4ce0 *R/fasta_to_char_matrix.R
5265473c8007442923ea50d4642db825 *R/filter_ambiguous_sequences.R
8ea265c66342dfa34aa46ad8d85b6d2a *R/get_site_counts.R
3c906206afa9ddc4567bd5e0f46afad9 *R/get_variants.R
ca235a4b2e7acbd194b5286a1a00360c *R/partition_time_windows.R
aaed0f57b713fb1c3978fcb3ac3df47b *R/plot_entropy_trajectories.R
85408eebfc22853288a6424516c9f65b *R/plot_site_class_trajectory.R
29d07645da1706dd2a2abe0174eb54c7 *R/relabel_entropy_classes.R
83a488fae91985d80727c98a4433f7c9 *R/simulate_variant_evolution.R
cc0304479e0de23b174330da875d4bc4 *R/tabulate_site_evolution.R
308ea2cc4c14a33f1347a3ac65d7acc3 *README.md
d54042561b90aafd8a9a202ea63e1e4b *build/partial.rdb
617ebcef0e219d0d1ee6de867d710265 *build/vignette.rds
a5b5c33a5d7e11d4cba1a8bf211b25d6 *data/sarscov2_variants.rda
56d0704e59cef5732a6d53dfead0bfb1 *inst/REFERENCES.bib
d67a2695b3e569a7b521abb37fb9a180 *inst/WORDLIST
75d7f0b2ba9d083d40e01cb0cef0f00b *inst/american-statistical-association.csl
8b669c8197abab737cedc4b6803183c7 *inst/doc/clustering_accuracy.html
b2ba2a9b18ef2649961d5b82b1e86f19 *inst/doc/clustering_accuracy.html.asis
fbeb199379188956cc1c8fafb33f24a0 *inst/doc/detecting_variants_simulation.html
9832864db22b997684d30e323a863108 *inst/doc/detecting_variants_simulation.html.asis
c753a427e2f1377315b1a52c1b80c78f *inst/doc/preprocessing_pipeline.html
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c61a705cebf4bf599eafcb5a3c0bcce3 *inst/extdata/sarscov2_sample.fasta.gz
0b34e4e4b39023c6682343d0796a3724 *man/ViralEntropR-package.Rd
fa9f5787271aeb8310139490637f8725 *man/build_distance_matrix.Rd
ce54064e1c6b6aa8b9017e2adbeaef6e *man/calculate_entropy.Rd
26cd184b96dfc81fef57cb8430006ae3 *man/calculate_hellinger_matrix.Rd
21f8b2c198ea1f3f35e91f155c624fed *man/cluster_sites_by_entropy.Rd
75d664cbb3b364020e8277a0c774bab5 *man/decode_aa_sequence.Rd
d1d05e56c8f52e4f4fc0c7b9ec0abae4 *man/detect_changepoints_ecp.Rd
d7b0fd2fe15de8490b67d2cd49e0cf65 *man/detect_changepoints_hdcp.Rd
12dec9b8bbedd4e77d659484fcf79d02 *man/encode_aa_sequence.Rd
5badc3912b097151ae068f990de6f4f9 *man/extract_fasta_countries.Rd
b600b528ec24e3da6d72a069aa3082b5 *man/extract_fasta_dates.Rd
78fc13247d27d066edc04cb9cabad711 *man/fasta_to_char_matrix.Rd
31f34f8fd9abc94d6103ed42a2b652f0 *man/filter_ambiguous_sequences.Rd
97b6137f4a946c1526c9784268dcd505 *man/get_site_counts.Rd
63e7eccb800a286d99c5ff2264d0268c *man/get_variants.Rd
ed4152469140a4da0491e9688afd10bb *man/partition_time_windows.Rd
efa5e2f8097cdd80abdcb2c472b25ba3 *man/plot_entropy_trajectories.Rd
206cb4fc0241afb40a63329a7b499fb5 *man/plot_site_class_trajectory.Rd
d08c1161673db66727bf77aff17606d0 *man/relabel_entropy_classes.Rd
250738ff520eb2114ab2dc7e30013d08 *man/sarscov2_sample.Rd
53c56b09ab4d0de11b8432d1b0aaf13a *man/sarscov2_variants.Rd
e89208a35adc23867af3a270976b14b2 *man/simulate_variant_evolution.Rd
18f93142aacb88e5f229fed8fa346d6d *man/tabulate_site_evolution.Rd
b2ba2a9b18ef2649961d5b82b1e86f19 *vignettes/clustering_accuracy.html.asis
9832864db22b997684d30e323a863108 *vignettes/detecting_variants_simulation.html.asis
f18d6693a61e136a18b9dc06829932f4 *vignettes/preprocessing_pipeline.html.asis
