From 12fe54cacf3c9b828c988c6010e7778067969a3a Mon Sep 17 00:00:00 2001 From: TuomasBorman Date: Fri, 1 Nov 2024 08:50:30 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20microbio?= =?UTF-8?q?me/mia@bcae5d32fd11f4adf0897216f06db54035571459=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 18700 -> 17734 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 65041f999..f44ed1601 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 e3266ae17..295546c6f 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 561f512ba..480a45409 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -3,4 +3,4 @@ pkgdown: 2.1.1 pkgdown_sha: ~ articles: mia: mia.html -last_built: 2024-11-01T08:42Z +last_built: 2024-11-01T08:46Z diff --git a/reference/GlobalPatterns.html b/reference/GlobalPatterns.html index 6d4da29b9..4c6ba4040 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 feac69f96..5a0c6c148 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 2cd39a3e3..5fa46e248 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 e8cc20ab0..6471eda58 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 222a1a371..4a9c31f9b 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 3056edddb..7aa137239 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 022ccefbe..43a350a37 100644 --- a/reference/addDivergence.html +++ b/reference/addDivergence.html @@ -44,7 +44,7 @@

Estimate divergence

- Source: R/estimateDivergence.R + Source: R/estimateDivergence.R
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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 1.707504e-07 0.0015134679 -#> Acidobacteria 2.721094e-05 0.0561399673 -#> Actinobacteria 3.115369e-02 0.1693586695 -#> Armatimonadetes 1.074556e-05 0.0007989770 -#> BRC1 1.177907e-07 0.0001093794 -#> Bacteroidetes 2.907042e-01 0.0738571964 +#> AD3 7.801147e-24 9.935388e-04 +#> Acidobacteria 6.248135e-03 3.279089e-02 +#> Actinobacteria 1.316852e-01 5.615627e-02 +#> Armatimonadetes 5.397044e-04 1.823694e-04 +#> BRC1 2.475261e-05 5.573033e-05 +#> Bacteroidetes 8.734034e-02 2.812972e-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 1323042e2..c344c53b8 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 4405b31b7..0d0c2bedf 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 31a6d10b0..da8a68995 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 8bbebfe9c..397a00b80 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 5fb66582b..ba695aea7 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 8a42bd689..9ec5b4b01 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 64ad51725..fdb0764d2 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 05f7fc282..064baad35 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 517543567..a8aa698cc 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 cf4c2d5de..4a9e3d586 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 7f2340a36..cf8a8d62a 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 ae015ee92..beec900ee 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 32ccd180d..9205b70f0 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 85c651c61..07d6b4742 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 90f018d6b..0bd19f173 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 4b361ed0e..db8ba2306 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 f64dbc9fa..36fc90486 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 7d4a6c07c..272614120 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 e6525752d..feafc1cd1 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 3ace77aaf..3a36460d2 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 ae0c9012d..b8357b52b 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 cfa9692d4..6db92ed38 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 58d4defae..65838e16e 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 8654fd849..d771f336d 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 d1e09e904..c8f9b7cfb 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 b1bc6e15f..57b4721be 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 7fb5cb47b..5faf44900 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 a6fe28910..7c3946468 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 5c3a9031a..98671a7e5 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 dd298307a..849e31660 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 74a197d05..3422f77bc 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 72bbdf6cc..166bc6b6c 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 7420faf4b..674365124 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 7c20ebd08..1671ba3ee 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 17e308ede..b572af202 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 570a58243..6abd2187c 100644 --- a/reference/transformAssay.html +++ b/reference/transformAssay.html @@ -45,7 +45,7 @@

Transform assay

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