From ac087c1daa732fbad371d0d1f63c0565988cae27 Mon Sep 17 00:00:00 2001 From: TuomasBorman Date: Fri, 15 Nov 2024 09:05:18 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20microbio?= =?UTF-8?q?me/mia@2f537347a6548478b1536cce535cf5a260dd971f=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 17819 -> 17802 bytes reference/addLDA.html | 16 ++++++------ reference/addNMF.html | 4 +-- reference/agglomerate-methods.html | 4 +-- reference/agglomerateByPrevalence.html | 4 +-- reference/calculateDMN.html | 4 +-- 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 | 2 +- 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 | 6 ++++- 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 | 33 ++++++++++++++----------- 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 +-- sitemap.xml | 1 + 56 files changed, 130 insertions(+), 122 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 986613c76..128bb3943 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 a72924294..d21ba5365 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 21ec428d6..20b69641d 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -3,4 +3,4 @@ pkgdown: 2.1.1 pkgdown_sha: ~ articles: mia: mia.html -last_built: 2024-11-15T09:00Z +last_built: 2024-11-15T09:01Z diff --git a/reference/GlobalPatterns.html b/reference/GlobalPatterns.html index f7df90a23..beee1f17c 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 1b3118ba6..607f7dbe7 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 d8ce42ced..9e55ccf75 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 058f5f3b7..b8bac06d4 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 b613e1def..03406fcee 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 8f725ab5c..bb62c3369 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 a16e8fe44..d5ff64da0 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 1.783136e-10 9.168795e-04 -#> Acidobacteria 4.721000e-06 3.402709e-02 -#> Actinobacteria 3.937343e-02 1.105420e-01 -#> Armatimonadetes 2.410232e-09 4.938363e-04 -#> BRC1 4.534471e-08 6.633675e-05 -#> Bacteroidetes 4.048758e-01 9.930089e-02 +#> AD3 3.489204e-07 1.003025e-03 +#> Acidobacteria 3.666001e-05 3.721095e-02 +#> Actinobacteria 4.971239e-02 1.103219e-01 +#> Armatimonadetes 1.958561e-07 5.402309e-04 +#> BRC1 1.856114e-07 7.248813e-05 +#> Bacteroidetes 3.685356e-01 9.485291e-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 d722cabe2..ef211c5b2 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 dd1abc625..a6be89654 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 65d41c229..62c0466c4 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 880056415..0d882876e 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
diff --git a/reference/convertFromDADA2.html b/reference/convertFromDADA2.html index eecd2fc0b..ac0872314 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 12fc272a4..a6804fe4c 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 8ee92961f..080895795 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 722cd71d5..259caa624 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 5dd3dc568..da1b5ca88 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 4d3cff9f8..f83361e84 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 796be87a3..14d521280 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 0718ddf39..f06304c46 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 23f4f02e9..9f92b96e4 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 ceceffa96..bb2c8d11b 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..56c6aeaeb 100644 --- a/reference/getPERMANOVA.html +++ b/reference/getPERMANOVA.html @@ -20,7 +20,7 @@ mia - 1.15.5 + 1.15.6
diff --git a/reference/getPrevalence.html b/reference/getPrevalence.html index 5f1517b03..067d3d2e4 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 72f07d5d2..603e6ca2d 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 775e7268e..4e90b8291 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 e58ecdcb7..fa5bcb282 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 1397b18ce..907df323b 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 15070ac94..535954f34 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 0860d043e..bd494778c 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 ebf3ad940..40d29b6f5 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 79eabc048..31bafd915 100644 --- a/reference/index.html +++ b/reference/index.html @@ -17,7 +17,7 @@ mia - 1.15.5 + 1.15.6
@@ -58,6 +58,10 @@

Association addMediation() getMediation()

Perform mediation analysis

+ +

getPERMANOVA() addPERMANOVA()

+ +

Calculate PERMANOVA (Permutational Multivariate Analysis of Variance)

Clustering

diff --git a/reference/isContaminant.html b/reference/isContaminant.html index e8385cc3e..e10ea4cab 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 1b59efbdd..f474c4e41 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 c5e2b917b..a84400b54 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 9235a70f0..e250583c6 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 a199ce1a5..3d1eeacb4 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 668b86ae0..3c6401d44 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 42c234244..0402af0f4 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 a0d91a35b..36c1476f3 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
@@ -121,25 +121,27 @@

Arguments

...

additional arguments passed to vegan::cca or vegan::dbrda and other internal functions.

  • method a dissimilarity measure to be applied in dbRDA and -possible following homogeneity test. (By default: -method="euclidean")

    • +possible following homogeneity test. (Default: "euclidean")

  • scale: Logical scalar. Should the expression values be standardized? scale is disabled when using *RDA functions. Please scale before performing RDA. (Default: TRUE)

  • na.action: function. Action to take when missing values for any of the variables in formula are encountered. (Default: na.fail)

    • -

  • full Logical scalar. should all the results from the -significance calculations be returned. When full=FALSE, only +

  • full Logical scalar. Should all the results from the +significance calculations be returned. When FALSE, only summary tables are returned. (Default: FALSE)

  • homogeneity.test: Character scalar. Specifies -the significance test used to analyse vegan::betadisper results. -Options include 'permanova' (vegan::permutest), 'anova' -(stats::anova) and 'tukeyhsd' (stats::TukeyHSD). -(By default: homogeneity.test="permanova")

    • +the significance test used to analyse +vegan::betadisper results. +Options include 'permanova' +(vegan::permutest), 'anova' +(stats::anova) and 'tukeyhsd' +(stats::TukeyHSD). +(Default: "permanova")

  • permutations a numeric value specifying the number of permutations for significance testing in vegan::anova.cca. -(By default: permutations=999)

    • +(Default: 999)

@@ -164,7 +166,7 @@

Arguments

variables
-

Deprecated. Use "col.var" instead.

+

Deprecated. Use col.var instead.

test.signif
@@ -192,8 +194,8 @@

Arguments

name
-

Character scalar. A name for the column of the -colData where results will be stored. (Default: "CCA")

+

Character scalar. A name for the reducedDim() +where results will be stored. (Default: "CCA")

@@ -213,7 +215,8 @@

Details

which turns the CCA analysis into a CA analysis and dbRDA into PCoA/MDS.

Significance tests are done with vegan:anova.cca (PERMANOVA). Group dispersion, i.e., homogeneity within groups is analyzed with -vegan:betadisper (multivariate homogeneity of groups dispersions +vegan::betadisper +(multivariate homogeneity of groups dispersions (variances)) and statistical significance of homogeneity is tested with a test specified by homogeneity.test parameter.

diff --git a/reference/runDPCoA.html b/reference/runDPCoA.html index 6479cd768..d50289110 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 f3d44bd40..16d3a2885 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 1c289e66a..2124ee8b5 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 e3c1b99bf..bd1ad0e4c 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 896c6a711..02d2c1cf2 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 33fcedd87..1e7c63f53 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
diff --git a/sitemap.xml b/sitemap.xml index 81dc8d321..f06933779 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -28,6 +28,7 @@ /reference/getDissimilarity.html /reference/getDominant.html /reference/getMediation.html +/reference/getPERMANOVA.html /reference/getPrevalence.html /reference/hierarchy-tree.html /reference/importBIOM.html