diff --git a/articles/mia.html b/articles/mia.html index e7add08ac..13a5edcde 100644 --- a/articles/mia.html +++ b/articles/mia.html @@ -69,7 +69,7 @@

mia: Microbiome analysis tools

2024-11-04

- Source: vignettes/mia.Rmd + Source: vignettes/mia.Rmd diff --git a/authors.html b/authors.html index 8fc950f25..facdb7b55 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 6649dc2f1..bab5c6e3c 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -3,4 +3,4 @@ pkgdown: 2.1.1 pkgdown_sha: ~ articles: mia: mia.html -last_built: 2024-11-04T08:23Z +last_built: 2024-11-04T09:03Z diff --git a/reference/GlobalPatterns.html b/reference/GlobalPatterns.html index b991023a9..08207ca6a 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 45883f1d5..5a49d3128 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 e64281591..5e45caeba 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 5ce59a8e2..e6d933bd1 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 6960b032e..1d0be237b 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 0b463a902..703ff7f00 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 cf6e80c48..8b412344a 100644 --- a/reference/addDivergence.html +++ b/reference/addDivergence.html @@ -44,7 +44,7 @@

Estimate divergence

- Source: R/addDivergence.R + Source: R/addDivergence.R
diff --git a/reference/addLDA-1.png b/reference/addLDA-1.png index 6cc5d5682..9cdbf9ad6 100644 Binary files a/reference/addLDA-1.png and b/reference/addLDA-1.png differ diff --git a/reference/addLDA.html b/reference/addLDA.html index 9fc8fbe90..877676472 100644 --- a/reference/addLDA.html +++ b/reference/addLDA.html @@ -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 9.863168e-04 3.508266e-07 -#> Acidobacteria 3.658830e-02 4.169420e-05 -#> Actinobacteria 1.095437e-01 4.935151e-02 -#> Armatimonadetes 5.310399e-04 4.957831e-07 -#> BRC1 7.129888e-05 1.614464e-07 -#> Bacteroidetes 9.581504e-02 3.741405e-01 +#> AD3 9.149379e-04 2.894248e-07 +#> Acidobacteria 3.394928e-02 2.647347e-05 +#> Actinobacteria 1.108535e-01 3.851231e-02 +#> Armatimonadetes 4.927965e-04 1.468506e-07 +#> BRC1 6.617345e-05 1.100748e-07 +#> Bacteroidetes 9.676829e-02 4.108586e-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 68c0740d4..72e2bf090 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 7e3fb7e16..bc33a109a 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 c75a301a7..a60a33fe0 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 d57fc1a86..60c9e5ffc 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 de5c739aa..97c25a02d 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 dbf6bcfa8..af94b42ab 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 0d1b8e7e4..44d31d897 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 94e4b35de..cb0503b10 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 e0b608a35..015d8dd65 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 bd74aa680..79a0b9b3c 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 115cc66f2..16e0c823a 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 1933d8bf8..ed69a8fdb 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 da23ce9ff..edc4ad694 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 2da90ad9b..a14bfa0cf 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 41fc83317..ef6735bfb 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 4cf71b35c..4aab0b6f6 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 80e1ee042..e2ed06806 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 8139fa70f..fad7fc3da 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 d78cd906c..ef9d02cca 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 abcc61903..2fbec66eb 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 8689eec88..e35345c2d 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 04da8f3ac..eb0be5b51 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 670207825..9d5f1c262 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 776b02592..9fd7f33af 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 b902df5be..ed12d7821 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 31a155d19..37d84865a 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 6e65ee0f6..e7ccfa5ae 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 725f20c19..5931ca9d0 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 0c2494d7f..30916757c 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 53f0ecbdf..061437f0e 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 dd194f4f2..67ab06120 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 58992069a..a5e8f3df9 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 bb5d1c4d2..a28b161bb 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 0a81d12e5..d29054cfa 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 e9c4f4c18..77d99af0b 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 db1f891b3..c5724c9a1 100644 --- a/reference/transformAssay.html +++ b/reference/transformAssay.html @@ -45,7 +45,7 @@

Transform assay

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