From 26dcce6fb0cf9df0f458b686a35c681d77e6ae25 Mon Sep 17 00:00:00 2001 From: TuomasBorman <60338854+TuomasBorman@users.noreply.github.com> Date: Fri, 1 Nov 2024 09:35:00 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20microbio?= =?UTF-8?q?me/mia@1c53e54aa815f58b8c6485d4bdcf67ce61758eab=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- articles/mia.html | 2 +- authors.html | 2 +- pkgdown.yml | 2 +- reference/GlobalPatterns.html | 2 +- reference/HintikkaXOData.html | 2 +- reference/Tengeler2020.html | 2 +- reference/Tito2024QMP.html | 2 +- reference/addAlpha.html | 2 +- reference/addCluster.html | 2 +- reference/addDivergence.html | 2 +- reference/addLDA-1.png | Bin 17747 -> 17828 bytes reference/addLDA.html | 14 +++++++------- reference/addNMF.html | 2 +- reference/agglomerate-methods.html | 2 +- reference/agglomerateByPrevalence.html | 2 +- reference/calculateDMN.html | 2 +- reference/convertFromDADA2.html | 2 +- reference/convertFromPhyloseq.html | 2 +- reference/deprecate.html | 2 +- reference/dmn_se.html | 2 +- reference/enterotype.html | 2 +- reference/esophagus.html | 2 +- reference/getCrossAssociation.html | 2 +- reference/getDissimilarity.html | 2 +- reference/getDominant.html | 2 +- reference/getMediation.html | 2 +- reference/getPrevalence.html | 2 +- reference/hierarchy-tree.html | 2 +- reference/importBIOM.html | 2 +- reference/importHUMAnN.html | 2 +- reference/importMetaPhlAn.html | 2 +- reference/importMothur.html | 2 +- reference/importQIIME2.html | 2 +- reference/importTaxpasta.html | 2 +- reference/isContaminant.html | 2 +- reference/meltSE.html | 2 +- reference/mergeSEs.html | 2 +- reference/mia-datasets.html | 2 +- reference/mia-package.html | 2 +- reference/peerj13075.html | 2 +- reference/rarefyAssay.html | 2 +- reference/runCCA.html | 2 +- reference/runDPCoA.html | 2 +- reference/runNMDS.html | 2 +- reference/splitOn.html | 2 +- reference/summaries.html | 2 +- reference/taxonomy-methods.html | 2 +- reference/transformAssay.html | 2 +- 48 files changed, 53 insertions(+), 53 deletions(-) diff --git a/articles/mia.html b/articles/mia.html index 898c3439a..e8d9eb243 100644 --- a/articles/mia.html +++ b/articles/mia.html @@ -69,7 +69,7 @@

mia: Microbiome analysis tools

2024-11-01

- Source: vignettes/mia.Rmd + Source: vignettes/mia.Rmd diff --git a/authors.html b/authors.html index a6242435b..c6a79dba2 100644 --- a/authors.html +++ b/authors.html @@ -168,7 +168,7 @@

Authors and Citation

Citation

- Source: DESCRIPTION + Source: DESCRIPTION
diff --git a/pkgdown.yml b/pkgdown.yml index 671d7070e..b802a612e 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -3,4 +3,4 @@ pkgdown: 2.1.1 pkgdown_sha: ~ articles: mia: mia.html -last_built: 2024-11-01T08:55Z +last_built: 2024-11-01T09:31Z diff --git a/reference/GlobalPatterns.html b/reference/GlobalPatterns.html index bdc194889..aea0cca33 100644 --- a/reference/GlobalPatterns.html +++ b/reference/GlobalPatterns.html @@ -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 088607958..b7eaa1efc 100644 --- a/reference/HintikkaXOData.html +++ b/reference/HintikkaXOData.html @@ -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 2a99ecd88..19586efa2 100644 --- a/reference/Tengeler2020.html +++ b/reference/Tengeler2020.html @@ -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 c51d28d45..f3587a0e3 100644 --- a/reference/Tito2024QMP.html +++ b/reference/Tito2024QMP.html @@ -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 3c5ed9a3b..4dbb6a99a 100644 --- a/reference/addAlpha.html +++ b/reference/addAlpha.html @@ -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 fcd22db28..37d6cbaaa 100644 --- a/reference/addCluster.html +++ b/reference/addCluster.html @@ -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 c99a445d1..075313d39 100644 --- a/reference/addDivergence.html +++ b/reference/addDivergence.html @@ -44,7 +44,7 @@

Estimate divergence

- Source: R/addDivergence.R + Source: R/addDivergence.R
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zcw7q9pImKcjOe6O2eHa#S$5Co^gnEscjtosB`&3LI0*!A46ER8pm_{%4q~6s#Aj=v zYESa+D~F-zYK+j3@qT3N2~g`l+jeLe`|r

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 9.862814e-04 3.184189e-07 -#> Acidobacteria 3.659225e-02 3.228963e-05 -#> Actinobacteria 1.094063e-01 4.956013e-02 -#> Armatimonadetes 5.311847e-04 2.231530e-07 -#> BRC1 7.130103e-05 1.517866e-07 -#> Bacteroidetes 9.777507e-02 3.711116e-01 +#> AD3 9.889885e-04 3.405590e-07 +#> Acidobacteria 3.668990e-02 3.733911e-05 +#> Actinobacteria 1.097003e-01 4.936087e-02 +#> Armatimonadetes 5.325594e-04 3.636575e-07 +#> BRC1 7.149505e-05 1.554466e-07 +#> Bacteroidetes 9.522838e-02 3.738843e-01 # 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 3ebefd765..bd6895759 100644 --- a/reference/addNMF.html +++ b/reference/addNMF.html @@ -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 faf23ca67..61d74fc29 100644 --- a/reference/agglomerate-methods.html +++ b/reference/agglomerate-methods.html @@ -51,7 +51,7 @@

Agglomerate or merge data using taxonomic information

- 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 49fd853e8..3859dc8ad 100644 --- a/reference/agglomerateByPrevalence.html +++ b/reference/agglomerateByPrevalence.html @@ -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 7f9bd35be..fcf9a87d5 100644 --- a/reference/calculateDMN.html +++ b/reference/calculateDMN.html @@ -46,7 +46,7 @@

Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data

- Source: R/calculateDMM.R + Source: R/calculateDMM.R
diff --git a/reference/convertFromDADA2.html b/reference/convertFromDADA2.html index 1c023c5d8..d60147194 100644 --- a/reference/convertFromDADA2.html +++ b/reference/convertFromDADA2.html @@ -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 f8fe5b866..06124a202 100644 --- a/reference/convertFromPhyloseq.html +++ b/reference/convertFromPhyloseq.html @@ -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 be24b196b..db6703381 100644 --- a/reference/deprecate.html +++ b/reference/deprecate.html @@ -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 e264d5389..5f9c08f75 100644 --- a/reference/dmn_se.html +++ b/reference/dmn_se.html @@ -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 524f03c40..415bf9d67 100644 --- a/reference/enterotype.html +++ b/reference/enterotype.html @@ -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 f3ee74c6b..6e3298f39 100644 --- a/reference/esophagus.html +++ b/reference/esophagus.html @@ -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 59c2d747c..d8e40c42c 100644 --- a/reference/getCrossAssociation.html +++ b/reference/getCrossAssociation.html @@ -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 1c1be3c44..04ea84641 100644 --- a/reference/getDissimilarity.html +++ b/reference/getDissimilarity.html @@ -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 afb5692c3..a8a1aa150 100644 --- a/reference/getDominant.html +++ b/reference/getDominant.html @@ -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 af149616f..54b98d56c 100644 --- a/reference/getMediation.html +++ b/reference/getMediation.html @@ -46,7 +46,7 @@

Perform mediation analysis

- Source: R/mediate.R + Source: R/mediate.R
diff --git a/reference/getPrevalence.html b/reference/getPrevalence.html index 8d80dbb0d..58dac112d 100644 --- a/reference/getPrevalence.html +++ b/reference/getPrevalence.html @@ -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 e07e0cabf..e08b5ba84 100644 --- a/reference/hierarchy-tree.html +++ b/reference/hierarchy-tree.html @@ -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 1950beab0..362cdf198 100644 --- a/reference/importBIOM.html +++ b/reference/importBIOM.html @@ -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 b2b2373fa..8ce9d0e71 100644 --- a/reference/importHUMAnN.html +++ b/reference/importHUMAnN.html @@ -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 5a0630008..9ff44ff6b 100644 --- a/reference/importMetaPhlAn.html +++ b/reference/importMetaPhlAn.html @@ -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 f8c54aa1d..88f83bca2 100644 --- a/reference/importMothur.html +++ b/reference/importMothur.html @@ -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 2fcd4b975..dbb500e91 100644 --- a/reference/importQIIME2.html +++ b/reference/importQIIME2.html @@ -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 0a4b010e9..0ed96df4f 100644 --- a/reference/importTaxpasta.html +++ b/reference/importTaxpasta.html @@ -45,7 +45,7 @@

Import taxpasta-specific BIOM results to TreeSummarizedExperiment

- Source: R/importTaxpasta.R + Source: R/importTaxpasta.R
diff --git a/reference/isContaminant.html b/reference/isContaminant.html index 5b0db41d3..95b4c704e 100644 --- a/reference/isContaminant.html +++ b/reference/isContaminant.html @@ -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 71959f8c5..d72ebf60a 100644 --- a/reference/meltSE.html +++ b/reference/meltSE.html @@ -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 4e8caa3a6..eb3f5483a 100644 --- a/reference/mergeSEs.html +++ b/reference/mergeSEs.html @@ -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 bfeda5b01..fa509bb6d 100644 --- a/reference/mia-datasets.html +++ b/reference/mia-datasets.html @@ -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 0f473b063..0db47527b 100644 --- a/reference/mia-package.html +++ b/reference/mia-package.html @@ -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 e6cadb354..dbbb2b520 100644 --- a/reference/peerj13075.html +++ b/reference/peerj13075.html @@ -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 8e63b0159..fc957a8c6 100644 --- a/reference/rarefyAssay.html +++ b/reference/rarefyAssay.html @@ -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 64873e7d4..8d02e1fee 100644 --- a/reference/runCCA.html +++ b/reference/runCCA.html @@ -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 2f0959d4a..e83b3e299 100644 --- a/reference/runDPCoA.html +++ b/reference/runDPCoA.html @@ -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 b0cca334b..d07544cef 100644 --- a/reference/runNMDS.html +++ b/reference/runNMDS.html @@ -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 7122309d5..f5ae8cfe6 100644 --- a/reference/splitOn.html +++ b/reference/splitOn.html @@ -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 e1681b68e..79592032b 100644 --- a/reference/summaries.html +++ b/reference/summaries.html @@ -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 8915cfe04..9ff3fca6b 100644 --- a/reference/taxonomy-methods.html +++ b/reference/taxonomy-methods.html @@ -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 06cf87099..cd2bbf16e 100644 --- a/reference/transformAssay.html +++ b/reference/transformAssay.html @@ -45,7 +45,7 @@

Transform assay

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