From b5b6627ad6e93d08ef7b574c7dbcea6ec0eba2e7 Mon Sep 17 00:00:00 2001 From: TuomasBorman <60338854+TuomasBorman@users.noreply.github.com> Date: Fri, 15 Nov 2024 13:58:05 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20microbio?= =?UTF-8?q?me/mia@2dc34304fbd24595dcebdb045f3dc0bc88bbe587=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- 404.html | 2 +- CONTRIBUTING.html | 2 +- LICENSE-text.html | 2 +- articles/index.html | 2 +- articles/mia.html | 6 +++--- authors.html | 8 ++++---- index.html | 2 +- pkgdown.yml | 2 +- reference/GlobalPatterns.html | 4 ++-- reference/HintikkaXOData.html | 4 ++-- reference/Tengeler2020.html | 4 ++-- reference/Tito2024QMP.html | 4 ++-- reference/addAlpha.html | 4 ++-- reference/addCluster.html | 4 ++-- reference/addDivergence.html | 4 ++-- reference/addLDA-1.png | Bin 17671 -> 17733 bytes reference/addLDA.html | 16 ++++++++-------- reference/addNMF.html | 4 ++-- reference/agglomerate-methods.html | 4 ++-- reference/agglomerateByPrevalence.html | 4 ++-- reference/calculateDMN.html | 22 +++++++++++----------- reference/convertFromDADA2.html | 4 ++-- reference/convertFromPhyloseq.html | 4 ++-- reference/deprecate.html | 4 ++-- reference/dmn_se.html | 4 ++-- reference/enterotype.html | 4 ++-- reference/esophagus.html | 4 ++-- reference/getCrossAssociation.html | 4 ++-- reference/getDissimilarity.html | 4 ++-- reference/getDominant.html | 4 ++-- reference/getMediation.html | 4 ++-- reference/getPERMANOVA.html | 4 ++-- reference/getPrevalence.html | 4 ++-- reference/hierarchy-tree.html | 4 ++-- reference/importBIOM.html | 4 ++-- reference/importHUMAnN.html | 4 ++-- reference/importMetaPhlAn.html | 4 ++-- reference/importMothur.html | 4 ++-- reference/importQIIME2.html | 4 ++-- reference/importTaxpasta.html | 4 ++-- reference/index.html | 2 +- reference/isContaminant.html | 4 ++-- reference/meltSE.html | 4 ++-- reference/mergeSEs.html | 4 ++-- reference/mia-datasets.html | 4 ++-- reference/mia-package.html | 4 ++-- reference/peerj13075.html | 4 ++-- reference/rarefyAssay.html | 4 ++-- reference/runCCA.html | 4 ++-- reference/runDPCoA.html | 4 ++-- reference/runNMDS.html | 4 ++-- reference/splitOn.html | 4 ++-- reference/summaries.html | 4 ++-- reference/taxonomy-methods.html | 4 ++-- reference/transformAssay.html | 4 ++-- 55 files changed, 119 insertions(+), 119 deletions(-) diff --git a/404.html b/404.html index ddc2d6713..ec0f6a61b 100644 --- a/404.html +++ b/404.html @@ -32,7 +32,7 @@ mia - 1.15.5 + 1.15.6 diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html index 1edcdbaa5..9ab61e9b4 100644 --- a/CONTRIBUTING.html +++ b/CONTRIBUTING.html @@ -17,7 +17,7 @@ mia - 1.15.5 + 1.15.6 diff --git a/LICENSE-text.html b/LICENSE-text.html index 783432e58..772c6642f 100644 --- a/LICENSE-text.html +++ b/LICENSE-text.html @@ -17,7 +17,7 @@ mia - 1.15.5 + 1.15.6 diff --git a/articles/index.html b/articles/index.html index ad8b6d06b..0336a7468 100644 --- a/articles/index.html +++ b/articles/index.html @@ -17,7 +17,7 @@ mia - 1.15.5 + 1.15.6 diff --git a/articles/mia.html b/articles/mia.html index 57d931aa2..5529efdac 100644 --- a/articles/mia.html +++ b/articles/mia.html @@ -32,7 +32,7 @@ mia - 1.15.5 + 1.15.6 @@ -69,7 +69,7 @@

mia: Microbiome analysis tools

2024-11-15

- Source: vignettes/mia.Rmd + Source: vignettes/mia.Rmd @@ -600,7 +600,7 @@

Session info## other attached packages: ## [1] phyloseq_1.50.0 scater_1.34.0 ## [3] ggplot2_3.5.1 scuttle_1.16.0 -## [5] mia_1.15.5 TreeSummarizedExperiment_2.14.0 +## [5] mia_1.15.6 TreeSummarizedExperiment_2.14.0 ## [7] Biostrings_2.74.0 XVector_0.46.0 ## [9] SingleCellExperiment_1.28.1 MultiAssayExperiment_1.32.0 ## [11] SummarizedExperiment_1.36.0 Biobase_2.66.0 diff --git a/authors.html b/authors.html index 32538cc8e..6d737a941 100644 --- a/authors.html +++ b/authors.html @@ -17,7 +17,7 @@ mia - 1.15.5 + 1.15.6 @@ -168,20 +168,20 @@

Authors and Citation

Citation

- Source: DESCRIPTION + Source: DESCRIPTION

Borman T, Ernst F, Shetty S, Lahti L (2024). mia: Microbiome analysis. -R package version 1.15.5, https://github.com/microbiome/mia. +R package version 1.15.6, https://github.com/microbiome/mia. 

@Manual{,
   title = {mia: Microbiome analysis},
   author = {Tuomas Borman and Felix G.M. Ernst and Sudarshan A. Shetty and Leo Lahti},
   year = {2024},
-  note = {R package version 1.15.5},
+  note = {R package version 1.15.6},
   url = {https://github.com/microbiome/mia},
 }
diff --git a/index.html b/index.html index 0ce75504b..375ae916e 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ mia - 1.15.5 + 1.15.6 diff --git a/pkgdown.yml b/pkgdown.yml index a3d4d2388..cb173d665 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -3,4 +3,4 @@ pkgdown: 2.1.1 pkgdown_sha: ~ articles: mia: mia.html -last_built: 2024-11-15T09:03Z +last_built: 2024-11-15T13:54Z diff --git a/reference/GlobalPatterns.html b/reference/GlobalPatterns.html index f9c42c26b..8b6b3fe6b 100644 --- a/reference/GlobalPatterns.html +++ b/reference/GlobalPatterns.html @@ -24,7 +24,7 @@ mia - 1.15.5 + 1.15.6 @@ -51,7 +51,7 @@

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.

- Source: R/mia.R + Source: R/mia.R
diff --git a/reference/HintikkaXOData.html b/reference/HintikkaXOData.html index 86dd3fea3..0070ac47b 100644 --- a/reference/HintikkaXOData.html +++ b/reference/HintikkaXOData.html @@ -23,7 +23,7 @@ mia - 1.15.5 + 1.15.6
@@ -50,7 +50,7 @@

Multiomics dataset from 40 rat samples

- Source: R/mia.R + Source: R/mia.R
diff --git a/reference/Tengeler2020.html b/reference/Tengeler2020.html index 448ac8353..f603b834a 100644 --- a/reference/Tengeler2020.html +++ b/reference/Tengeler2020.html @@ -22,7 +22,7 @@ mia - 1.15.5 + 1.15.6
@@ -49,7 +49,7 @@

Gut microbiota profiles of 27 individuals with ADHD and healthy controls

- Source: R/mia.R + Source: R/mia.R
diff --git a/reference/Tito2024QMP.html b/reference/Tito2024QMP.html index 747d03af3..0c3c5322b 100644 --- a/reference/Tito2024QMP.html +++ b/reference/Tito2024QMP.html @@ -23,7 +23,7 @@ mia - 1.15.5 + 1.15.6
@@ -50,7 +50,7 @@

Fecal microbiota samples from 589 patients across different colorectal cancer stages

- Source: R/mia.R + Source: R/mia.R
diff --git a/reference/addAlpha.html b/reference/addAlpha.html index 43ac830f3..d9350fbe2 100644 --- a/reference/addAlpha.html +++ b/reference/addAlpha.html @@ -18,7 +18,7 @@ mia - 1.15.5 + 1.15.6
@@ -45,7 +45,7 @@

Estimate alpha diversity indices

- Source: R/addAlpha.R + Source: R/addAlpha.R
diff --git a/reference/addCluster.html b/reference/addCluster.html index 7207d19ad..c9caf1eee 100644 --- a/reference/addCluster.html +++ b/reference/addCluster.html @@ -18,7 +18,7 @@ mia - 1.15.5 + 1.15.6
@@ -45,7 +45,7 @@

Clustering wrapper

- Source: R/cluster.R + Source: R/cluster.R
diff --git a/reference/addDivergence.html b/reference/addDivergence.html index 360151c0d..08c788826 100644 --- a/reference/addDivergence.html +++ b/reference/addDivergence.html @@ -17,7 +17,7 @@ mia - 1.15.5 + 1.15.6
@@ -44,7 +44,7 @@

Estimate divergence

- Source: R/addDivergence.R + Source: R/addDivergence.R
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@@ -46,7 +46,7 @@

Latent Dirichlet Allocation

- Source: R/addLDA.R + Source: R/addLDA.R
@@ -137,12 +137,12 @@

Examples

loadings <- attr(reducedDim(tse, "LDA"), "loadings") head(loadings) #> 1 2 -#> AD3 3.718290e-07 1.000802e-03 -#> Acidobacteria 3.871195e-05 3.712771e-02 -#> Actinobacteria 4.973285e-02 1.101748e-01 -#> Armatimonadetes 2.374916e-07 5.390137e-04 -#> BRC1 1.904096e-07 7.232567e-05 -#> Bacteroidetes 3.687494e-01 9.531335e-02 +#> AD3 1.993547e-07 9.225935e-04 +#> Acidobacteria 2.091706e-05 3.423440e-02 +#> Actinobacteria 4.044494e-02 1.104198e-01 +#> Armatimonadetes 4.946165e-08 4.969461e-04 +#> BRC1 1.057450e-07 6.672523e-05 +#> Bacteroidetes 4.018659e-01 9.897342e-02 # Estimate models with number of topics from 2 to 10 tse <- addLDA(tse, k = c(2, 3, 4, 5, 6, 7, 8, 9, 10), name = "LDA_10") diff --git a/reference/addNMF.html b/reference/addNMF.html index bb948e3d4..bfce4ea13 100644 --- a/reference/addNMF.html +++ b/reference/addNMF.html @@ -19,7 +19,7 @@ mia - 1.15.5 + 1.15.6
@@ -46,7 +46,7 @@

Non-negative Matrix Factorization

- Source: R/addNMF.R + Source: R/addNMF.R
diff --git a/reference/agglomerate-methods.html b/reference/agglomerate-methods.html index da37cc21d..878e9aa0b 100644 --- a/reference/agglomerate-methods.html +++ b/reference/agglomerate-methods.html @@ -36,7 +36,7 @@ mia - 1.15.5 + 1.15.6
@@ -63,7 +63,7 @@

Agglomerate data using taxonomic information or other grouping

- Source: R/agglomerate.R, R/splitByRanks.R + Source: R/agglomerate.R, R/splitByRanks.R
diff --git a/reference/agglomerateByPrevalence.html b/reference/agglomerateByPrevalence.html index 25cec8a88..c0a74dedf 100644 --- a/reference/agglomerateByPrevalence.html +++ b/reference/agglomerateByPrevalence.html @@ -17,7 +17,7 @@ mia - 1.15.5 + 1.15.6
@@ -44,7 +44,7 @@

Agglomerate data based on population prevalence

- Source: R/getPrevalence.R + Source: R/getPrevalence.R
diff --git a/reference/calculateDMN.html b/reference/calculateDMN.html index c49cbd578..295e7f858 100644 --- a/reference/calculateDMN.html +++ b/reference/calculateDMN.html @@ -19,7 +19,7 @@ mia - 1.15.5 + 1.15.6
@@ -46,7 +46,7 @@

Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data

- Source: R/calculateDMM.R + Source: R/calculateDMM.R
@@ -260,7 +260,7 @@

Examples

#> class: DMN #> k: 3 #> samples x taxa: 278 x 130 -#> Laplace: 38848.01 BIC: 39997.42 AIC: 39286.41 +#> Laplace: 38854.25 BIC: 40001.15 AIC: 39290.14 #> # Get and display which objects fits best @@ -274,21 +274,21 @@

Examples

#> class: DMN #> k: 3 #> samples x taxa: 278 x 130 -#> Laplace: 38848.01 BIC: 39997.42 AIC: 39286.41 +#> Laplace: 38854.25 BIC: 40001.15 AIC: 39290.14 # Get the sample-cluster assignment probability matrix head(metadata(tse)$DMM$prob) #> 1 2 3 -#> TS1.2 9.999997e-01 3.042111e-07 6.230944e-09 -#> TS10.2 9.329702e-01 8.746688e-09 6.702980e-02 -#> TS100.2 4.153240e-08 7.120033e-02 9.287996e-01 -#> TS100 9.912894e-01 8.710015e-03 5.830676e-07 -#> TS101.2 1.202136e-12 3.299003e-07 9.999997e-01 -#> TS103.2 9.999971e-01 7.227951e-10 2.915066e-06 +#> TS1.2 9.999997e-01 2.998576e-07 4.862182e-09 +#> TS10.2 9.516067e-01 8.377897e-09 4.839328e-02 +#> TS100.2 4.436338e-08 8.562199e-02 9.143780e-01 +#> TS100 9.919529e-01 8.046703e-03 4.122699e-07 +#> TS101.2 1.352825e-12 4.161738e-07 9.999996e-01 +#> TS103.2 9.999977e-01 7.468125e-10 2.313118e-06 # Get the weight of each component for the best model bestModel@mixture$Weight -#> [1] 0.5684009 0.2213691 0.2102300 +#> [1] 0.5655860 0.2227191 0.2116949
diff --git a/reference/convertFromDADA2.html b/reference/convertFromDADA2.html index 5d5b0d952..582858097 100644 --- a/reference/convertFromDADA2.html +++ b/reference/convertFromDADA2.html @@ -17,7 +17,7 @@ mia - 1.15.5 + 1.15.6 @@ -44,7 +44,7 @@

Create a TreeSummarizedExperiment object from ‘DADA2’ results

- Source: R/convertFromDADA2.R + Source: R/convertFromDADA2.R
diff --git a/reference/convertFromPhyloseq.html b/reference/convertFromPhyloseq.html index 17bf05d77..b17d57dcc 100644 --- a/reference/convertFromPhyloseq.html +++ b/reference/convertFromPhyloseq.html @@ -18,7 +18,7 @@ mia - 1.15.5 + 1.15.6
@@ -45,7 +45,7 @@

Create a TreeSummarizedExperiment object from a phyloseq object

- Source: R/convertFromPhyloseq.R, R/convertToPhyloseq.R + Source: R/convertFromPhyloseq.R, R/convertToPhyloseq.R
diff --git a/reference/deprecate.html b/reference/deprecate.html index e455c73d7..2b6d28022 100644 --- a/reference/deprecate.html +++ b/reference/deprecate.html @@ -17,7 +17,7 @@ mia - 1.15.5 + 1.15.6
@@ -44,7 +44,7 @@

These functions will be deprecated. Please use other functions instead.

- Source: R/deprecate.R + Source: R/deprecate.R
diff --git a/reference/dmn_se.html b/reference/dmn_se.html index 0e31fed22..2828190f7 100644 --- a/reference/dmn_se.html +++ b/reference/dmn_se.html @@ -19,7 +19,7 @@ mia - 1.15.5 + 1.15.6
@@ -46,7 +46,7 @@

Twins' microbiome data from 278 individuals

- Source: R/mia.R + Source: R/mia.R
diff --git a/reference/enterotype.html b/reference/enterotype.html index 5babf797a..8278a5d42 100644 --- a/reference/enterotype.html +++ b/reference/enterotype.html @@ -24,7 +24,7 @@ mia - 1.15.5 + 1.15.6
@@ -51,7 +51,7 @@

Human gut microbiome dataset from 22 subjects based on shotgun DNA sequencing

- Source: R/mia.R + Source: R/mia.R
diff --git a/reference/esophagus.html b/reference/esophagus.html index e6e279dd9..e4e517b3c 100644 --- a/reference/esophagus.html +++ b/reference/esophagus.html @@ -20,7 +20,7 @@ mia - 1.15.5 + 1.15.6
@@ -47,7 +47,7 @@

Human esophageal community from 3 individuals

- Source: R/mia.R + Source: R/mia.R
diff --git a/reference/getCrossAssociation.html b/reference/getCrossAssociation.html index e6c5403a6..d82dd1130 100644 --- a/reference/getCrossAssociation.html +++ b/reference/getCrossAssociation.html @@ -17,7 +17,7 @@ mia - 1.15.5 + 1.15.6
@@ -44,7 +44,7 @@

Calculate correlations between features of two experiments.

- Source: R/getCrossAssociation.R + Source: R/getCrossAssociation.R
diff --git a/reference/getDissimilarity.html b/reference/getDissimilarity.html index d7e6950ed..46c333e8a 100644 --- a/reference/getDissimilarity.html +++ b/reference/getDissimilarity.html @@ -23,7 +23,7 @@ mia - 1.15.5 + 1.15.6
@@ -50,7 +50,7 @@

Calculate dissimilarities

- Source: R/addDissimilarity.R + Source: R/addDissimilarity.R
diff --git a/reference/getDominant.html b/reference/getDominant.html index 2b62357a3..dcf58ef58 100644 --- a/reference/getDominant.html +++ b/reference/getDominant.html @@ -19,7 +19,7 @@ mia - 1.15.5 + 1.15.6
@@ -46,7 +46,7 @@

Get dominant taxa

- Source: R/getDominant.R + Source: R/getDominant.R
diff --git a/reference/getMediation.html b/reference/getMediation.html index 80a749b5c..7235e2c05 100644 --- a/reference/getMediation.html +++ b/reference/getMediation.html @@ -19,7 +19,7 @@ mia - 1.15.5 + 1.15.6
@@ -46,7 +46,7 @@

Perform mediation analysis

- Source: R/mediate.R + Source: R/mediate.R
diff --git a/reference/getPERMANOVA.html b/reference/getPERMANOVA.html index 857c25d53..9223facd0 100644 --- a/reference/getPERMANOVA.html +++ b/reference/getPERMANOVA.html @@ -20,7 +20,7 @@ mia - 1.15.5 + 1.15.6
@@ -47,7 +47,7 @@

Calculate PERMANOVA (Permutational Multivariate Analysis of Variance)

- Source: R/getPERMANOVA.R + Source: R/getPERMANOVA.R
diff --git a/reference/getPrevalence.html b/reference/getPrevalence.html index b41d74d57..23fe705d0 100644 --- a/reference/getPrevalence.html +++ b/reference/getPrevalence.html @@ -18,7 +18,7 @@ mia - 1.15.5 + 1.15.6
@@ -45,7 +45,7 @@

Calculation prevalence information for features across samples

- Source: R/getPrevalence.R + Source: R/getPrevalence.R
diff --git a/reference/hierarchy-tree.html b/reference/hierarchy-tree.html index 06e9ecdaf..4d7ddc789 100644 --- a/reference/hierarchy-tree.html +++ b/reference/hierarchy-tree.html @@ -19,7 +19,7 @@ mia - 1.15.5 + 1.15.6
@@ -46,7 +46,7 @@

Calculate hierarchy tree

- Source: R/taxonomy.R + Source: R/taxonomy.R
diff --git a/reference/importBIOM.html b/reference/importBIOM.html index c13aeeca7..b80045fef 100644 --- a/reference/importBIOM.html +++ b/reference/importBIOM.html @@ -22,7 +22,7 @@ mia - 1.15.5 + 1.15.6
@@ -49,7 +49,7 @@

Convert a TreeSummarizedExperiment object to/from ‘BIOM’ results

- Source: R/convertFromBIOM.R + Source: R/convertFromBIOM.R
diff --git a/reference/importHUMAnN.html b/reference/importHUMAnN.html index e481f74e6..8e9eee1bf 100644 --- a/reference/importHUMAnN.html +++ b/reference/importHUMAnN.html @@ -17,7 +17,7 @@ mia - 1.15.5 + 1.15.6
@@ -44,7 +44,7 @@

Import HUMAnN results to TreeSummarizedExperiment

- Source: R/importHumann.R + Source: R/importHumann.R
diff --git a/reference/importMetaPhlAn.html b/reference/importMetaPhlAn.html index 74ecf57e0..e24d08653 100644 --- a/reference/importMetaPhlAn.html +++ b/reference/importMetaPhlAn.html @@ -17,7 +17,7 @@ mia - 1.15.5 + 1.15.6
@@ -44,7 +44,7 @@

Import Metaphlan results to TreeSummarizedExperiment

- Source: R/importMetaphlan.R + Source: R/importMetaphlan.R
diff --git a/reference/importMothur.html b/reference/importMothur.html index e0fe3cee8..c9cffe09b 100644 --- a/reference/importMothur.html +++ b/reference/importMothur.html @@ -18,7 +18,7 @@ mia - 1.15.5 + 1.15.6
@@ -45,7 +45,7 @@

Import Mothur results as a TreeSummarizedExperiment

- Source: R/importMothur.R + Source: R/importMothur.R
diff --git a/reference/importQIIME2.html b/reference/importQIIME2.html index 0dc5a0371..884f03e06 100644 --- a/reference/importQIIME2.html +++ b/reference/importQIIME2.html @@ -22,7 +22,7 @@ mia - 1.15.5 + 1.15.6
@@ -49,7 +49,7 @@

Import QIIME2 results to TreeSummarizedExperiment

- Source: R/importQIIME2.R + Source: R/importQIIME2.R
diff --git a/reference/importTaxpasta.html b/reference/importTaxpasta.html index 3d214ca93..15c128b33 100644 --- a/reference/importTaxpasta.html +++ b/reference/importTaxpasta.html @@ -18,7 +18,7 @@ mia - 1.15.5 + 1.15.6
@@ -45,7 +45,7 @@

Import taxpasta-specific BIOM results to TreeSummarizedExperiment

- Source: R/importTaxpasta.R + Source: R/importTaxpasta.R
diff --git a/reference/index.html b/reference/index.html index 724f10c48..31bafd915 100644 --- a/reference/index.html +++ b/reference/index.html @@ -17,7 +17,7 @@ mia - 1.15.5 + 1.15.6
diff --git a/reference/isContaminant.html b/reference/isContaminant.html index c9ebd9cac..e1a53cc7d 100644 --- a/reference/isContaminant.html +++ b/reference/isContaminant.html @@ -20,7 +20,7 @@ mia - 1.15.5 + 1.15.6 @@ -47,7 +47,7 @@

decontam functions

- Source: R/decontam.R + Source: R/decontam.R
diff --git a/reference/meltSE.html b/reference/meltSE.html index dcfb77331..f72ad59c4 100644 --- a/reference/meltSE.html +++ b/reference/meltSE.html @@ -19,7 +19,7 @@ mia - 1.15.5 + 1.15.6
@@ -46,7 +46,7 @@

Converting a SummarizedExperiment object into a long data.frame

- Source: R/meltAssay.R + Source: R/meltAssay.R
diff --git a/reference/mergeSEs.html b/reference/mergeSEs.html index 1e740a68b..084f593a6 100644 --- a/reference/mergeSEs.html +++ b/reference/mergeSEs.html @@ -17,7 +17,7 @@ mia - 1.15.5 + 1.15.6
@@ -44,7 +44,7 @@

Merge SE objects into single SE object.

- Source: R/mergeSEs.R + Source: R/mergeSEs.R
diff --git a/reference/mia-datasets.html b/reference/mia-datasets.html index fd7beec3e..6008fa14f 100644 --- a/reference/mia-datasets.html +++ b/reference/mia-datasets.html @@ -20,7 +20,7 @@ mia - 1.15.5 + 1.15.6
@@ -47,7 +47,7 @@

mia datasets

- Source: R/mia.R + Source: R/mia.R
diff --git a/reference/mia-package.html b/reference/mia-package.html index 4e51c6b40..13749925b 100644 --- a/reference/mia-package.html +++ b/reference/mia-package.html @@ -22,7 +22,7 @@ mia - 1.15.5 + 1.15.6
@@ -49,7 +49,7 @@

mia Package.

- Source: R/mia.R + Source: R/mia.R
diff --git a/reference/peerj13075.html b/reference/peerj13075.html index 77cf583ac..b3e0845e8 100644 --- a/reference/peerj13075.html +++ b/reference/peerj13075.html @@ -22,7 +22,7 @@ mia - 1.15.5 + 1.15.6
@@ -49,7 +49,7 @@

Skin microbial profiles 58 genetically unrelated individuals

- Source: R/mia.R + Source: R/mia.R
diff --git a/reference/rarefyAssay.html b/reference/rarefyAssay.html index a9f134e5e..b4508bf89 100644 --- a/reference/rarefyAssay.html +++ b/reference/rarefyAssay.html @@ -20,7 +20,7 @@ mia - 1.15.5 + 1.15.6
@@ -47,7 +47,7 @@

Subsample Counts

- Source: R/rarefyAssay.R + Source: R/rarefyAssay.R
diff --git a/reference/runCCA.html b/reference/runCCA.html index 614179ac8..bfa02d44f 100644 --- a/reference/runCCA.html +++ b/reference/runCCA.html @@ -18,7 +18,7 @@ mia - 1.15.5 + 1.15.6
@@ -45,7 +45,7 @@

Canonical Correspondence Analysis and Redundancy Analysis

- Source: R/runCCA.R + Source: R/runCCA.R
diff --git a/reference/runDPCoA.html b/reference/runDPCoA.html index f3dee7c1e..53d6b3c8f 100644 --- a/reference/runDPCoA.html +++ b/reference/runDPCoA.html @@ -19,7 +19,7 @@ mia - 1.15.5 + 1.15.6
@@ -46,7 +46,7 @@

Calculation of Double Principal Correspondance analysis

- Source: R/runDPCoA.R + Source: R/runDPCoA.R
diff --git a/reference/runNMDS.html b/reference/runNMDS.html index d7aa08c53..879ef0272 100644 --- a/reference/runNMDS.html +++ b/reference/runNMDS.html @@ -18,7 +18,7 @@ mia - 1.15.5 + 1.15.6
@@ -45,7 +45,7 @@

Perform non-metric MDS on sample-level data

- Source: R/runNMDS.R + Source: R/runNMDS.R
diff --git a/reference/splitOn.html b/reference/splitOn.html index d3d85925b..fb9522aee 100644 --- a/reference/splitOn.html +++ b/reference/splitOn.html @@ -18,7 +18,7 @@ mia - 1.15.5 + 1.15.6
@@ -45,7 +45,7 @@

Split TreeSummarizedExperiment column-wise or row-wise based on grouping variable

- Source: R/splitOn.R + Source: R/splitOn.R
diff --git a/reference/summaries.html b/reference/summaries.html index 498e76962..97eef4a64 100644 --- a/reference/summaries.html +++ b/reference/summaries.html @@ -18,7 +18,7 @@ mia - 1.15.5 + 1.15.6
@@ -45,7 +45,7 @@

Summarizing microbiome data

- Source: R/summaries.R + Source: R/summaries.R
diff --git a/reference/taxonomy-methods.html b/reference/taxonomy-methods.html index 5716a9e30..2e57cdc3b 100644 --- a/reference/taxonomy-methods.html +++ b/reference/taxonomy-methods.html @@ -19,7 +19,7 @@ mia - 1.15.5 + 1.15.6
@@ -46,7 +46,7 @@

Functions for accessing taxonomic data stored in rowData.

- Source: R/taxonomy.R + Source: R/taxonomy.R
diff --git a/reference/transformAssay.html b/reference/transformAssay.html index 0965037bc..de8d63c39 100644 --- a/reference/transformAssay.html +++ b/reference/transformAssay.html @@ -18,7 +18,7 @@ mia - 1.15.5 + 1.15.6
@@ -45,7 +45,7 @@

Transform assay

- Source: R/transformCounts.R + Source: R/transformCounts.R