3cd6e28c1493f12bf3633cbe1b771bbf *CONTRIBUTING.md
d124dab896de8b69fa6776467d1ba63d *DESCRIPTION
f6ca07bb20e837b3d4f4f4d509549c1b *LICENSE
92d67cc4f306c979b1671a4d5f1458aa *NAMESPACE
e8f1fdc5837cd88dd53904bb66ff146c *NEWS
1b52f3800b204ccee72372ce2e5a1a9c *R/AllGenerics.R
e05aa32da6ecc23922935d11624bc094 *R/RcppExports.R
0c95dbd66360f35b30cc019f916a0cdb *R/addAlpha.R
6d36896c26b1e6ebfefcf6848113f042 *R/addDissimilarity.R
61afd4cc2c21f99768a225cd68137fae *R/addDivergence.R
6d4727b2bafc22b7bd1d3b76a4ce51bc *R/addLDA.R
7113034e400ea1c1921bb2bf389408b5 *R/addNMF.R
0ecaed5ec89a9db6065511f03142167b *R/agglomerate.R
146a243971782a436366c4725fcb7fbd *R/calculateDMM.R
c468bf04b1f21af7505e92e574f26558 *R/calculateJSD.R
d29c57fa6423ffab9d6b9d0acea217a4 *R/calculateOverlap.R
2ab7af91eb3bbb64889ce4a4a72f5066 *R/calculateUnifrac.R
f07ca19161679251b260066e0f1b6513 *R/cluster.R
7faf7e9088ada86cb49b6d3b0ab45b4c *R/convertFromBIOM.R
17d7b7494e1fa9dc9cad871b4226ac47 *R/convertFromDADA2.R
0ef326e69762e48a39b9ddc2ebbec876 *R/convertFromPhyloseq.R
b5499e9dd1a694e66bfd1d9aebaab99e *R/convertToPhyloseq.R
a668e1c08aacfd65b4d18aed1404d189 *R/decontam.R
55cbfba14ccd85c82b588e1ecc93232f *R/deprecate.R
2855f2e4e9fc037df7d64abdd541d634 *R/estimateDiversity.R
c0f9b34fad824c33c7a8d845e9ddac97 *R/estimateDominance.R
7afb8c4d7fa3980f7b011dec7250b36f *R/estimateEvenness.R
f86f18b89193782518f26e1d1c610146 *R/estimateRichness.R
4d471616097aa4c51cdf2f37e82ba0df *R/getAbundant.R
f6142664589876cf04412b1e27eab5fe *R/getCrossAssociation.R
d3aab1a666f2ef0a2d52fae59123b5fb *R/getDominant.R
0a8c47c5f1a329e2c40aacaddc4f7566 *R/getMDS.R
386ddbc9f76f680e07a2157720c8b095 *R/getPERMANOVA.R
5a6c438e5244ee7bab1e82973469ba0b *R/getPrevalence.R
aac6a5d424d5ba915a5f3e3dee606a83 *R/getRPCA.R
a2d5416da36ffb90346b9a16e83692f3 *R/importHumann.R
5ecead6282cdb55a661a09878ea3b605 *R/importMetaphlan.R
3b869eb97f9884a232d87d9113d09ccf *R/importMothur.R
7102c47fcc7a6d1b5cc7a2d766286cf8 *R/importQIIME2.R
5ee427b9cfda3e64da48e30c4f88fead *R/importTaxpasta.R
6dddbc5efc373f719896858ba6564af7 *R/mediate.R
36219016c03feca0745aa60079e1d425 *R/meltAssay.R
5623f56c629539101a14518ce4e01e5f *R/merge.R
2e15409e2b2804abdc305dc03aa50634 *R/mergeSEs.R
8284e2f751be3bfbd8890b0973873d28 *R/mia.R
adfa7f41208766b090b0e52a4ea557b0 *R/rarefyAssay.R
3de74c051781cebd4e030b0272ba49a0 *R/runCCA.R
d5c24d660a4328c04be54aadd9b7e379 *R/runDPCoA.R
ee551a975ff0d0721c5eccf8f0de8d59 *R/runNMDS.R
4ff6faf4a7b3a83085b8ed5aad911f07 *R/splitByRanks.R
04c36df9435d57a6a330c90f3b11374a *R/splitOn.R
9714cdcb2d3eac29cfbf2d05612312e1 *R/subset.R
cd321a47ca18964e932502e73be0216e *R/summaries.R
f5cb82e1623f5f7f1832634ca58f79b3 *R/taxonomy.R
b56aa25a2460abcc60ba9033f95b221c *R/transformCounts.R
297f2930f0558cc3eea7a4479e088da5 *R/utilization_functions.R
ab41c1a61f0b3e8630c07ed659e0a86f *R/utils.R
501f9022fe762526a88bc8f2c0873b15 *README.md
533839446f70bde34a1050627ce80586 *build/partial.rdb
d426405903c0890001fedd49985ee742 *build/vignette.rds
95b86276576b6ae4c3f3c71c41ac343b *data/GlobalPatterns.rda
db158d0e1dc2bd72a8a44ada22545586 *data/HintikkaXOData.rda
e935d563a0fe50ededf1c224bed8b29d *data/Tengeler2020.rda
83f664953ace3ca6030bd978b71c1f3c *data/Tito2024QMP.rda
eade3adca75dfb1675f42b708174c69b *data/datalist
376127cf0f0a69f91e54cf7f14681976 *data/dmn_se.rda
dbc37743cdb569dc628770aaeb394cde *data/enterotype.rda
ca3dcc1b6c98ae76d1952e77bcd4153e *data/esophagus.rda
dd4c8819890688d720145cd3356b3576 *data/ibdmdb.rda
1187c03b38aac27a8b6a168afd63e5f1 *data/peerj13075.rda
ed3b9e6472c2e6bd9d5e4af2c0962589 *inst/doc/mia.R
e29766636a179b2bd7a07be44b77ba76 *inst/doc/mia.Rmd
eb360ec36ebeaeb5317dc50dfa97913c *inst/doc/mia.html
46b2bf8ade75a500895d26e82cba24f2 *inst/extdata/Aggregated_humanization2.biom
43c75ae04ab42d25ebaf53b3e7bd73a0 *inst/extdata/Data_humanization_phylo_aggregation.tre
739495e92a29bb61f59a578744d20081 *inst/extdata/Mapping_file_ADHD_aggregated.csv
aa567d697e17fa316ea9ab9438462fd7 *inst/extdata/complete.biom
bfaeaac89a134cb88b9a4de2ef4aecf0 *inst/extdata/humann_output.tsv
e3d07fea80e0123ec742ffb7ecb7e93e *inst/extdata/less_ranks.biom
fdbeb0136fc2cec6094b0060e2ede667 *inst/extdata/merged_abundance_table.txt
25b664634b88f86ceff74cb62c4e4b15 *inst/extdata/more_ranks.biom
01bdfc234fdc97c9aecdd634cb96520f *inst/extdata/mothur_example.cons.taxonomy
4759d5b9efd5a336c93c80d2dd696fb4 *inst/extdata/mothur_example.design
42fb3faf5ad6cf3294988769b9b500a7 *inst/extdata/mothur_example.shared
f410dedc634daae3f58f9976f88ceea0 *inst/extdata/mothur_example.taxonomy
353157d31c2638de3080956fa2523915 *inst/extdata/refseq.qza
efa61291acdffbc2968cf55abccfff8f *inst/extdata/sample-metadata.tsv
83e7043382aa67b80dec8da3f85f530a *inst/extdata/simple.biom
1c287c7693852ae39009388f023c1688 *inst/extdata/table-rownamesInSeq.qza
2964bd9042d7c9f1dffb28a9982dd6dc *inst/extdata/table.qza
32a4035b442c8efdbca51c057229533f *inst/extdata/taxonomy.qza
84b1a5863273b792b74fa09f4d4545f6 *inst/extdata/taxpasta_no_type.biom
50f485dc4037d18e1469733789847f80 *inst/extdata/tree.qza
fd13560cc68538aa875cc7f298e096e8 *inst/scripts/Tito2024QMP.R
633816c6f32d8d111fca3b9f7d453daa *inst/scripts/biom_test_data.py
bc4d38519a49529c35a4aeda7da92bc4 *inst/scripts/import.R
f9b1d5f5c933be2fdb3f05fe3e043e4c *inst/scripts/prepare_ibdmdb.R
b46254574ca31206eb329703e16d99c1 *man/GlobalPatterns.Rd
d258336d84123722270961e98a5b9789 *man/HintikkaXOData.Rd
47a6900bafa6c9fc1e8113f5ae22b966 *man/Tengeler2020.Rd
258eff3948570321d7aa2d97b91f4186 *man/Tito2024QMP.Rd
c77b135bedc322f4a87104c71341585e *man/addAlpha.Rd
5a1b2cf0b4c72de329977cb6c33d459a *man/addCluster.Rd
560d3ecd446a43f07b917a3a0a4a24df *man/addDivergence.Rd
061efe1902be3671b51ba278b19c60ac *man/addLDA.Rd
337322647997747ed37b8406525cef7d *man/addMDS.Rd
deb15a6c8d548e3dd4cfee676b8ebc95 *man/addNMF.Rd
e23adb06b52a257d8ef48dc21ebcdc3f *man/agglomerate-methods.Rd
9643d950b6cefa0bcbbd23a339754785 *man/agglomerateByPrevalence.Rd
62718b72c0d03071dd7a1ae238e77257 *man/calculateDMN.Rd
3f1e3dffaff605184389faf111b07b42 *man/convertFromDADA2.Rd
64a736795cb2761c2c00d581b96a4618 *man/convertFromPhyloseq.Rd
affd631ba00dcd25a78b5f3d358f1c65 *man/deprecate.Rd
f4849997ce5a3f2799661413aef53dec *man/dmn_se.Rd
ce6abaae2b73ad2b02164df8652e2c36 *man/enterotype.Rd
29776da801fb5a7d3c1846d77101e0ee *man/esophagus.Rd
7fff613317fad8fd30e2dbd9198c7765 *man/figures/mia_logo.png
1659064c2ad99f8c98321babd20650e4 *man/getAbundant.Rd
6e56a7fd42aee83224fecbf0cf0f6752 *man/getCrossAssociation.Rd
e681e8cf59d830b232d84b3ed41d8582 *man/getDissimilarity.Rd
f3868a4f224c2fb0b273c648382ab1d2 *man/getDominant.Rd
aa6cfc5d71a7d948f99bf7638a623c81 *man/getMediation.Rd
aed35fd11838005bc6760e528f6e786a *man/getPERMANOVA.Rd
9d361228acab7b6042a37234ca01e348 *man/getPrevalence.Rd
80b6c350e75bda4e44e20bd9789b8201 *man/getRPCA.Rd
181f5dbfa27362a9bf20f41bf5c2abb9 *man/hierarchy-tree.Rd
4f5abb8b91a6900b9e4862a753e4103b *man/ibdmdb.Rd
c318fd98548ec4c95f85da5063c498ea *man/importBIOM.Rd
52a41f391a5456c056bc928766fbe70e *man/importHUMAnN.Rd
242b89594b88e229d6b5004270bee1d6 *man/importMetaPhlAn.Rd
2b7e566a4e0a75f31751b729f151942d *man/importMothur.Rd
d24737dccd2b8e49be68f74f5f1e02ca *man/importQIIME2.Rd
81dc9caf9f84dc4ac08da337abeb4fb1 *man/importTaxpasta.Rd
f45d3687696105ac0d4f87e72de50865 *man/isContaminant.Rd
e8ca735ee271d560bd64db92ac8fbead *man/meltSE.Rd
e2f40162f9ec0b29751613e26d6cdb6f *man/mergeSEs.Rd
98c9c0e1b160424be30d36dc14f02897 *man/mia-datasets.Rd
24ad641bbcc7c67d5653852967f76abf *man/mia-package.Rd
80811e081f026d7cf4920ade4a444eb2 *man/peerj13075.Rd
20cd7cbb60e6d687cad76d1485273aae *man/rarefyAssay.Rd
c3351cddc8ab7d4e21a911d1c36b817f *man/runCCA.Rd
fd9719983fb1320b207137fdef9ce010 *man/runDPCoA.Rd
3453d05858414af88a06d7eb0d4563a1 *man/runNMDS.Rd
442fe33ec064d9c20d5acee7f99cf68d *man/splitOn.Rd
376fa2098b73d68c7b288a11ed9196c5 *man/summary.Rd
f529f8dc1886cbc01758b59ea6cb3fb3 *man/taxonomy-methods.Rd
51b759024e42017db0040021fc32f404 *man/transformAssay.Rd
958c8372e59e307100e9de204fc3f62e *man/utilization_functions.Rd
08a2eeb999dca7ab8e376402fd916dd6 *src/RcppExports.cpp
c3b31b2e631b693f39db31bb72b59823 *src/assay.cpp
83bb9dee7935928311a076b4a1c6ac0e *src/assay.h
628aa8acc412d6f45d4f9f397aacd8fd *src/faith_R.cpp
aea80e6fa4ef51098c86420e6274cfa1 *src/propmap.cpp
e0d8b319030eebc89521a16698697cf1 *src/propmap.h
2ebfe30d552a38b03d65225b70e6da3c *src/transformCounts.cpp
4786834a148cf1ee97af9fafe7b5b6f0 *src/tree.cpp
adcd505ef72664fcb24246ed1635ad4d *src/tree.h
e59034a98c3e2b4daa7db2c1c6fa2666 *tests/testthat.R
052b76a561ceb86e68adc3bdd25074b3 *tests/testthat/test-0divergence.R
c9fa8e4fbee8feb639d8e100a97398f4 *tests/testthat/test-0diversity.R
9f81a7c19240543e5fc340942de70b19 *tests/testthat/test-0utilites.R
eb3df8252fae1a9a9f964d55e362314f *tests/testthat/test-2merge.R
ca5e150edd8ad3d4c5f84cdd3fa60823 *tests/testthat/test-2mergeSEs.R
19f9656427a1767f2dc73c31aefa3d66 *tests/testthat/test-2taxonomy.R
7d8f618cefa5b54f3bf5ce2785c43b32 *tests/testthat/test-3agglomerate.R
90889b782052f158f82e23814830199c *tests/testthat/test-4IO.R
f7a19b62fda2bdef35b562e04ca9401a *tests/testthat/test-4splitByRanks.R
cca8a1d6f0df0ee55863b26bca6a5a8b *tests/testthat/test-4splitOn.R
8953df240d739e4ef355e983d261285f *tests/testthat/test-5Unifrac.R
0b34188812b1be056f3979609fe99ac9 *tests/testthat/test-5addLDA.R
80cba75ddb63b3968e67203250fc8a1f *tests/testthat/test-5addNMF.R
7713836bbfcfc28d5dfb365dce281ab8 *tests/testthat/test-5calculateOverlap.R
9b7f554f14bbe53d020191c9ba69d9fc *tests/testthat/test-5dominance.R
df1f2f9a3fa1e142f1497976cda539d6 *tests/testthat/test-5dominantTaxa.R
cf8eefa9bb633c05bea7224b02c107fb *tests/testthat/test-5evenness.R
9c8bc2900d2ff79e3589a3dbbd1465e3 *tests/testthat/test-5getCrossAssociation.R
b5fc605b83f463e176d594e87a60dbcd *tests/testthat/test-5getDissimilarity.R
e2bb022519c3c93bf3053707435f9d48 *tests/testthat/test-5prevalence.R
a17e998b885c32a09e51371f70358fab *tests/testthat/test-5richness.R
7ace0e40b76b6bb985db24bbed7dfd29 *tests/testthat/test-5runDPCoA.R
b67bee8e8cb8909da2ea88232f4cadac *tests/testthat/test-5runNMDS.R
ca783bd74103422643054c8f14b7ab0b *tests/testthat/test-5transformCounts.R
e9c00f1fdc6485329811c7f3a4eb6912 *tests/testthat/test-6cca.R
e676283ba2bd9909b75548141ad0c741 *tests/testthat/test-7decontam.R
859d089004fc626ca1b6c8fc0789bbf3 *tests/testthat/test-8subsample.R
55ca8eab153cd453c74e86ea7a231510 *tests/testthat/test-8summaries.R
1a1d76a5b448c6fd6f12c22f63e3058c *tests/testthat/test-9cluster.R
1bc4621445347ac1aa62e3bd75ddfeb4 *tests/testthat/test-addAlpha.R
92a9c0e363d2acd2739c44309ae3f60f *tests/testthat/test-addMDS.R
af810a2de3fa2f3a83e0949e38bfc642 *tests/testthat/test-getAbundant.R
a459c710f61af9d5937048b65b9664a0 *tests/testthat/test-getPERMANOVA.R
897f103db638379c90a868ed1cca250f *tests/testthat/test-importTaxpasta.R
7743e778e22b8cc6f8aa54abdcad3cff *tests/testthat/test-mediate.R
566874575ff7a63fa87cbf8325bcb315 *tests/testthat/test-utilization_functions.R
e29766636a179b2bd7a07be44b77ba76 *vignettes/mia.Rmd
d0a9534a824984a8a5f619a678e31746 *vignettes/references.bib
