6c9ceb2 (HEAD -> devel, origin/devel, origin/HEAD) Default alpha diversity indices (#713) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-03-27 12:01:18 +0200;
5914752 addPrevalentAbundance (#716) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-03-25 11:59:02 +0200;
570ac14 Add pseudocount as method (#715) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-03-25 10:43:56 +0200;
3b6ce6b Add Tito2024QMP to mia dataset vignettes (#714) by
Giulio Benedetti <giuliobene2000@gmail.com>2025-03-19 16:20:23 +0200;
172c193 C++ implementation of the Stacked Faith algorithm (#697) by
jepasan <148062058+jepasan@users.noreply.github.com>2025-03-17 21:34:47 +0200;
198360c Fix phyloseq converter (#711) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-03-14 15:24:29 +0200;
f7ec6c3 Calculate binary Jaccard by default (#709) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-03-13 13:09:30 +0200;
671660d Support precalculated dissimilarity matrix in dbRDA (#708) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-03-13 12:16:40 +0200;
025e99c decontam fix (#705) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-03-12 13:08:25 +0200;
401423c Improve decontam functions (#704) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-03-12 11:32:13 +0200;
47f2972 Fix philr (#702) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-03-12 10:07:30 +0200;
1b520d8 Improve splitOn message (#703) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-03-11 15:10:33 +0200;
ee8e37d Fix tree merging (#701) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-03-06 11:41:56 +0200;
5e1bfb6 getReducedDimElement (#693) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-02-28 11:35:18 +0200;
2329374 Fixes for tree merging and agglomeration (#698) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-02-26 11:14:46 +0200;
fc6908b Fix alpha rarefaction (#699) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-02-24 09:11:06 +0200;
41a3525 Install phyloseq from Bioconductor (#674) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-02-16 12:55:00 +0200;
1aa5455 Update docs (#696) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-02-14 18:39:42 +0200;
b93863b Update importMetaphlan() to use default name "metaphlan" (#694) by
Muluh <127390183+Daenarys8@users.noreply.github.com>2025-02-13 10:44:53 +0100;
8c0bdd7 Update getCrossAssociation() examples to hide logs (#695) by
Muluh <127390183+Daenarys8@users.noreply.github.com>2025-02-13 09:37:34 +0100;
d22a205 getCrossAssociation: assay.type default value (#676) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-02-11 11:11:54 +0200;
a2b426a addMDS and getMDS (#689) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-02-11 09:59:22 +0200;
8a04bd8 Fix message in getCrossAssociation (#687) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-02-06 15:13:36 +0200;
676c69d Support rarefaction in unifrac (#686) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-02-04 17:55:49 +0200;
c6e75ad Update docs (#685) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-02-03 15:09:18 +0200;
0651f11 Polish mediation model metadata (#678) by
Giulio Benedetti <giuliobene2000@gmail.com>2025-01-28 16:59:55 +0200;
f80ea32 Rename tree nodes only when update.tree = TRUE (#682) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-01-26 19:12:44 +0200;
075891b Fix splitOn (#681) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-01-25 18:19:03 +0200;
11eba6c Handle duplicates in getDivergence (#680) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-01-23 17:07:35 +0200;
255ac68 Add PhILR transformation (#679) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-01-22 16:53:58 +0200;
45b1d3e Add getAlpha (#669) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-01-19 19:33:35 +0200;
2bfddc2 Apply transformation only to main object by default (#675) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-01-19 13:43:29 +0200;
a8e1e0a Improve getTaxonomyLabels (#672) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-01-18 23:30:34 +0200;
a371208 Utilize vegan::rrarefy (#670) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-01-18 11:32:58 +0200;
2d2f40d Fix qiime2 importer (#671) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-01-17 22:56:34 +0200;
e4b7e97 Add support for dimred to getCrossAssociation (#668) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-01-17 18:56:59 +0200;
6192112 Improvements to manual pages (#665) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-01-17 15:46:48 +0200;
a2bc35d Add addPrevalence function (#667) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-01-17 14:57:24 +0200;
8c658c9 Abundance classification (#664) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-01-17 13:20:09 +0200;
37d5b21 Default: update.tree = TRUE, improve tree merging (#663) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-01-16 17:53:58 +0200;
77b6f33 Incorporate Bioconductor recommendations (#662) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2025-01-16 13:54:50 +0200;
2dc3430 (origin/master) Add PERMANOVA functions (#657) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2024-11-15 15:21:45 +0200;
c4ac515 agglomeration functions and na.rm (#658) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2024-11-15 10:28:56 +0200;
56cce49 Update tree agglomeration (#656) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2024-11-05 10:06:58 +0200;
161b209 Fix getDivergence (#655) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2024-11-04 10:30:50 +0200;
1c53e54 Improve divergence function (#653) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2024-11-01 10:59:23 +0200;
817f324 Improve support for spaces in variable names (#650) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2024-11-01 10:08:58 +0200;
1fe852c bump x.y.z version to odd y following creation of RELEASE_3_20 branch by
J Wokaty <jennifer.wokaty@sph.cuny.edu>2024-10-29 10:57:18 -0400;
07b2e25 (origin/RELEASE_3_20, RELEASE_3_20) bump x.y.z version to even y prior to creation of RELEASE_3_20 branch by
J Wokaty <jennifer.wokaty@sph.cuny.edu>2024-10-29 10:57:18 -0400;
5d64263 Fix getCrossAssociation (#652) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2024-10-22 00:13:42 +0300;
c76bc90 Update RDA/CCA functions (#639) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2024-10-07 10:25:40 +0300;
1923e87 Fix splitOn (#646) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2024-10-02 18:02:36 +0300;
075697f Update README.md (#644) by
Muluh <127390183+Daenarys8@users.noreply.github.com>2024-10-02 11:47:05 +0100;
739e0cd Alphabetize packages (#640) by
Artur Sannikov <40318410+artur-sannikov@users.noreply.github.com>2024-10-02 05:45:48 +0000;
8cace1b deprecate f in favor of group (#638) by
Muluh <127390183+Daenarys8@users.noreply.github.com>2024-10-01 11:39:10 +0100;
f7bcc66 Minor updates BIOM functions (#645) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2024-09-27 10:17:45 +0300;
3a3c78b adding css method (#614) by
Sam Hillman <116303632+SHillman836@users.noreply.github.com>2024-09-23 10:43:35 +0300;
bb33807 Improve addDivergence (#635) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2024-09-22 11:18:45 +0300;
3f3b968 Fix faith (#642) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2024-09-17 15:28:54 +0300;
fdcd5c9 FIx: capture sk__ prefix (#641) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2024-09-17 14:48:43 +0300;
52d2a23 Give informative error when values are missing in addRDA (#626) by
Giulio Benedetti <giuliobene2000@gmail.com>2024-09-10 07:46:38 +0200;
586392f accept other than ranks in addDominant (#623) by
Muluh <127390183+Daenarys8@users.noreply.github.com>2024-09-09 09:45:18 +0100;
89bad8e Add error for missing tree in unifrac (#632) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2024-09-01 14:28:45 +0300;
2d52298 smaller test file for type-less taxpasta biom (#631) by
Danielle Callan <53306535+d-callan@users.noreply.github.com>2024-08-28 04:56:01 -0400;
dcaa110 remove authors from fxns (#629) by
Muluh <127390183+Daenarys8@users.noreply.github.com>2024-08-17 16:15:06 +0100;
0eb0ebc New dissimilarity functions (#609) by
Théotime Pralas <151254073+thpralas@users.noreply.github.com>2024-08-13 19:10:00 +0200;
dcb48dc spell checker (#625) by
Muluh <127390183+Daenarys8@users.noreply.github.com>2024-08-11 15:31:58 +0100;
5282a72 Fix importTaxpasta (#619) by
Danielle Callan <53306535+d-callan@users.noreply.github.com>2024-08-09 14:39:05 -0400;
552a952 NMF ordination with feature loadings computation (#616) by
Théotime Pralas <151254073+thpralas@users.noreply.github.com>2024-08-09 13:25:41 +0200;
c00541b typo in summary example (#620) by
Muluh <127390183+Daenarys8@users.noreply.github.com>2024-08-06 18:02:25 +0100;
f193173 ignore NAs when pseudocount is TRUE (#615) by
Muluh <127390183+Daenarys8@users.noreply.github.com>2024-08-05 09:30:21 +0100;
b75207a <a href="#601">#601</a> and OMA issue <a href="#482">#482</a> (#602) by
ake <40662956+ake123@users.noreply.github.com>2024-07-30 14:57:10 +0300;
056ad48 Package loading message (#608) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2024-07-30 00:10:55 +0300;
50bd2ea LDA ordination with feature loadings computation (#598) by
Théotime Pralas <151254073+thpralas@users.noreply.github.com>2024-07-23 23:49:25 +0300;
96bddb7 unify param def (#603) by
Muluh <127390183+Daenarys8@users.noreply.github.com>2024-07-23 21:05:42 +0100;
8b8f686 Default pseudocount half of the minimum value (#613) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2024-07-21 11:36:17 +0300;
fb2215b Fix addAlpha (#612) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2024-07-19 18:07:23 +0300;
9012592 Fix pseudocount (#611) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2024-07-18 17:24:11 +0300;
5dc0478 Minor fix to convertToBIOM (#607) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2024-07-12 18:33:24 +0300;
dea9d92 convertToBIOM (#606) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2024-07-12 11:53:02 +0300;
61dc9cf QMP example data <a href="#470">#470</a> (#597) by
Shadman Ishraq <150528639+ShadmanIshraq@users.noreply.github.com>2024-07-10 11:10:11 +0300;
11a9b64 Improve mapTaxonomy (#600) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2024-07-10 10:34:55 +0300;
32a8aa7 import functions and ranks (#590) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2024-07-08 11:59:18 +0300;
bea0851 Minor fixes (#599) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2024-07-07 10:12:07 +0300;
f58207f WIP: Import taxpasta (#574) by
Moritz E. Beber <midnighter@posteo.net>2024-07-06 17:54:42 +0200;
a340211 estimateAlpha (#460) by
ChouaibB <86964562+ChouaibB@users.noreply.github.com>2024-07-05 15:19:25 +0300;
b404b40 Deprecate MARGIN param (#587) by
Muluh <127390183+Daenarys8@users.noreply.github.com>2024-07-02 16:27:26 +0100;
6dab0d7 remove as.relative param (#589) by
Muluh <127390183+Daenarys8@users.noreply.github.com>2024-07-02 14:39:14 +0100;
6131f45 Remove tree rooting in calculateUnifrac (#594) by
Muluh <127390183+Daenarys8@users.noreply.github.com>2024-07-02 10:20:48 +0100;
e62a04e Fix tree merging (#588) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2024-07-02 11:48:39 +0300;
3b1e907 fix tree agglomeration in agglomerateByPrevalence (#575) by
Théotime Pralas <151254073+thpralas@users.noreply.github.com>2024-07-02 10:55:55 +0300;
24d2263 Rename converters (#591) by
Théotime Pralas <151254073+thpralas@users.noreply.github.com>2024-07-01 09:37:04 +0300;
c17fa9f Deprecate z transform in transformAssay (#584) by
Muluh <127390183+Daenarys8@users.noreply.github.com>2024-06-18 16:31:57 +0100;
8035003 Update unit test for unifrac (#586) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2024-06-18 17:44:37 +0300;
7b04dad Clarify detection (#580) (#581) by
Artur Sannikov <40318410+artur-sannikov@users.noreply.github.com>2024-06-18 13:37:48 +0000;
5e26bcd Organize parameter names v2 (#582) by
Muluh <127390183+Daenarys8@users.noreply.github.com>2024-06-18 13:45:35 +0100;
315beb0 Minor fix to message (#576) by
Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>2024-06-12 15:25:49 +0300;
1b9ed9f remove only empty rank cols (#572) by
Muluh <127390183+Daenarys8@users.noreply.github.com>2024-06-12 09:33:18 +0100;
