diff --git a/404.html b/404.html index 3ac756d55..d1d7eb8e7 100644 --- a/404.html +++ b/404.html @@ -32,7 +32,7 @@ mia - 1.15.0 + 1.15.1 diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html index 9fc41f9e4..0d70e8b5a 100644 --- a/CONTRIBUTING.html +++ b/CONTRIBUTING.html @@ -17,7 +17,7 @@ mia - 1.15.0 + 1.15.1 diff --git a/LICENSE-text.html b/LICENSE-text.html index 1b84af13e..348228473 100644 --- a/LICENSE-text.html +++ b/LICENSE-text.html @@ -17,7 +17,7 @@ mia - 1.15.0 + 1.15.1 diff --git a/articles/index.html b/articles/index.html index 0ef44445d..226c32d4f 100644 --- a/articles/index.html +++ b/articles/index.html @@ -17,7 +17,7 @@ mia - 1.15.0 + 1.15.1 diff --git a/articles/mia.html b/articles/mia.html index f192a2968..65041f999 100644 --- a/articles/mia.html +++ b/articles/mia.html @@ -32,7 +32,7 @@ mia - 1.15.0 + 1.15.1 @@ -69,7 +69,7 @@

mia: Microbiome analysis tools

2024-11-01

- 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_1.15.0 TreeSummarizedExperiment_2.14.0 +## [5] mia_1.15.1 TreeSummarizedExperiment_2.14.0 ## [7] Biostrings_2.74.0 XVector_0.46.0 ## [9] SingleCellExperiment_1.28.0 MultiAssayExperiment_1.32.0 ## [11] SummarizedExperiment_1.36.0 Biobase_2.66.0 diff --git a/authors.html b/authors.html index 1bdc3b79c..e3266ae17 100644 --- a/authors.html +++ b/authors.html @@ -17,7 +17,7 @@ mia - 1.15.0 + 1.15.1 @@ -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 1.15.0, https://github.com/microbiome/mia. +R package version 1.15.1, 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 1.15.0},
+  note = {R package version 1.15.1},
   url = {https://github.com/microbiome/mia},
 }
diff --git a/index.html b/index.html index 8a9707f99..92d6e8b82 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ mia - 1.15.0 + 1.15.1 diff --git a/pkgdown.yml b/pkgdown.yml index 710c21aca..561f512ba 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -3,4 +3,4 @@ pkgdown: 2.1.1 pkgdown_sha: ~ articles: mia: mia.html -last_built: 2024-11-01T08:05Z +last_built: 2024-11-01T08:42Z diff --git a/reference/GlobalPatterns.html b/reference/GlobalPatterns.html index aac230dfb..6d4da29b9 100644 --- a/reference/GlobalPatterns.html +++ b/reference/GlobalPatterns.html @@ -24,7 +24,7 @@ mia - 1.15.0 + 1.15.1 @@ -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 68bd89a17..feac69f96 100644 --- a/reference/HintikkaXOData.html +++ b/reference/HintikkaXOData.html @@ -23,7 +23,7 @@ mia - 1.15.0 + 1.15.1
@@ -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 252c271f5..2cd39a3e3 100644 --- a/reference/Tengeler2020.html +++ b/reference/Tengeler2020.html @@ -22,7 +22,7 @@ mia - 1.15.0 + 1.15.1
@@ -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 f73f2eda8..e8cc20ab0 100644 --- a/reference/Tito2024QMP.html +++ b/reference/Tito2024QMP.html @@ -23,7 +23,7 @@ mia - 1.15.0 + 1.15.1
@@ -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 73b89ef26..222a1a371 100644 --- a/reference/addAlpha.html +++ b/reference/addAlpha.html @@ -18,7 +18,7 @@ mia - 1.15.0 + 1.15.1
@@ -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 257e480f3..3056edddb 100644 --- a/reference/addCluster.html +++ b/reference/addCluster.html @@ -18,7 +18,7 @@ mia - 1.15.0 + 1.15.1
@@ -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 7f694bb87..022ccefbe 100644 --- a/reference/addDivergence.html +++ b/reference/addDivergence.html @@ -17,7 +17,7 @@ mia - 1.15.0 + 1.15.1
@@ -44,7 +44,7 @@

Estimate divergence

- Source: R/estimateDivergence.R + Source: R/estimateDivergence.R
diff --git a/reference/addLDA-1.png b/reference/addLDA-1.png index 3333248d3..f52729aff 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 94ffc850e..9852f68d8 100644 --- a/reference/addLDA.html +++ b/reference/addLDA.html @@ -19,7 +19,7 @@ mia - 1.15.0 + 1.15.1
@@ -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 9.898628e-04 3.430832e-07 -#> Acidobacteria 3.672249e-02 3.716299e-05 -#> Actinobacteria 1.097381e-01 4.938502e-02 -#> Armatimonadetes 5.330437e-04 3.438614e-07 -#> BRC1 7.155652e-05 1.581298e-07 -#> Bacteroidetes 9.504594e-02 3.737847e-01 +#> 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 # 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 31655903d..1323042e2 100644 --- a/reference/addNMF.html +++ b/reference/addNMF.html @@ -19,7 +19,7 @@ mia - 1.15.0 + 1.15.1
@@ -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 a6a14bf2e..4405b31b7 100644 --- a/reference/agglomerate-methods.html +++ b/reference/agglomerate-methods.html @@ -24,7 +24,7 @@ mia - 1.15.0 + 1.15.1
@@ -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 0b4e88f85..31a6d10b0 100644 --- a/reference/agglomerateByPrevalence.html +++ b/reference/agglomerateByPrevalence.html @@ -17,7 +17,7 @@ mia - 1.15.0 + 1.15.1
@@ -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 752051b72..8bbebfe9c 100644 --- a/reference/calculateDMN.html +++ b/reference/calculateDMN.html @@ -19,7 +19,7 @@ mia - 1.15.0 + 1.15.1
@@ -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 419b97ec9..5fb66582b 100644 --- a/reference/convertFromDADA2.html +++ b/reference/convertFromDADA2.html @@ -17,7 +17,7 @@ mia - 1.15.0 + 1.15.1
@@ -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 fff540549..8a42bd689 100644 --- a/reference/convertFromPhyloseq.html +++ b/reference/convertFromPhyloseq.html @@ -18,7 +18,7 @@ mia - 1.15.0 + 1.15.1
@@ -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 ce2cfc029..64ad51725 100644 --- a/reference/deprecate.html +++ b/reference/deprecate.html @@ -17,7 +17,7 @@ mia - 1.15.0 + 1.15.1
@@ -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 4500cd793..05f7fc282 100644 --- a/reference/dmn_se.html +++ b/reference/dmn_se.html @@ -19,7 +19,7 @@ mia - 1.15.0 + 1.15.1
@@ -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 a3f3e975e..517543567 100644 --- a/reference/enterotype.html +++ b/reference/enterotype.html @@ -24,7 +24,7 @@ mia - 1.15.0 + 1.15.1
@@ -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 7829ee122..cf4c2d5de 100644 --- a/reference/esophagus.html +++ b/reference/esophagus.html @@ -20,7 +20,7 @@ mia - 1.15.0 + 1.15.1
@@ -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 522691a58..7f2340a36 100644 --- a/reference/getCrossAssociation.html +++ b/reference/getCrossAssociation.html @@ -17,7 +17,7 @@ mia - 1.15.0 + 1.15.1
@@ -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 bdccfdd5d..ae015ee92 100644 --- a/reference/getDissimilarity.html +++ b/reference/getDissimilarity.html @@ -23,7 +23,7 @@ mia - 1.15.0 + 1.15.1
@@ -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 c0c677d54..32ccd180d 100644 --- a/reference/getDominant.html +++ b/reference/getDominant.html @@ -19,7 +19,7 @@ mia - 1.15.0 + 1.15.1
@@ -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 292dde948..85c651c61 100644 --- a/reference/getMediation.html +++ b/reference/getMediation.html @@ -19,7 +19,7 @@ mia - 1.15.0 + 1.15.1
@@ -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 05168f630..90f018d6b 100644 --- a/reference/getPrevalence.html +++ b/reference/getPrevalence.html @@ -18,7 +18,7 @@ mia - 1.15.0 + 1.15.1
@@ -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 069b2d87d..4b361ed0e 100644 --- a/reference/hierarchy-tree.html +++ b/reference/hierarchy-tree.html @@ -19,7 +19,7 @@ mia - 1.15.0 + 1.15.1
@@ -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 11cc8794b..f64dbc9fa 100644 --- a/reference/importBIOM.html +++ b/reference/importBIOM.html @@ -22,7 +22,7 @@ mia - 1.15.0 + 1.15.1
@@ -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 88d73c2aa..7d4a6c07c 100644 --- a/reference/importHUMAnN.html +++ b/reference/importHUMAnN.html @@ -17,7 +17,7 @@ mia - 1.15.0 + 1.15.1
@@ -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 f90dd403e..e6525752d 100644 --- a/reference/importMetaPhlAn.html +++ b/reference/importMetaPhlAn.html @@ -17,7 +17,7 @@ mia - 1.15.0 + 1.15.1
@@ -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 94fd04213..3ace77aaf 100644 --- a/reference/importMothur.html +++ b/reference/importMothur.html @@ -18,7 +18,7 @@ mia - 1.15.0 + 1.15.1
@@ -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 6ebfa9061..ae0c9012d 100644 --- a/reference/importQIIME2.html +++ b/reference/importQIIME2.html @@ -22,7 +22,7 @@ mia - 1.15.0 + 1.15.1
@@ -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 fca1122bd..cfa9692d4 100644 --- a/reference/importTaxpasta.html +++ b/reference/importTaxpasta.html @@ -18,7 +18,7 @@ mia - 1.15.0 + 1.15.1
@@ -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 e1e23d0d3..9b3cdafc7 100644 --- a/reference/index.html +++ b/reference/index.html @@ -17,7 +17,7 @@ mia - 1.15.0 + 1.15.1
diff --git a/reference/isContaminant.html b/reference/isContaminant.html index 907bd2b26..58d4defae 100644 --- a/reference/isContaminant.html +++ b/reference/isContaminant.html @@ -20,7 +20,7 @@ mia - 1.15.0 + 1.15.1 @@ -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 f19e08235..8654fd849 100644 --- a/reference/meltSE.html +++ b/reference/meltSE.html @@ -1,7 +1,7 @@ Converting a SummarizedExperiment object into a long data.frame — meltSE • mia @@ -19,7 +19,7 @@ mia - 1.15.0 + 1.15.1
@@ -46,31 +46,18 @@

Converting a SummarizedExperiment object into a long data.frame

- Source: R/meltAssay.R + Source: R/meltAssay.R

meltSE Converts a -SummarizedExperiment object into a -long data.frame which can be used for tidyverse-tools.

+SummarizedExperiment +object into a long data.frame which can be used for tidyverse-tools.

- 
meltSE(
-  x,
-  assay.type = assay_name,
-  assay_name = "counts",
-  add.row = add_row_data,
-  add_row_data = NULL,
-  add.col = add_col_data,
-  add_col_data = NULL,
-  row.name = feature_name,
-  feature_name = "FeatureID",
-  col.name = sample_name,
-  sample_name = "SampleID",
-  ...
-)
+    
meltSE(x, ...)
 
 # S4 method for class 'SummarizedExperiment'
 meltSE(
@@ -97,6 +84,14 @@ 
Arguments

 
TreeSummarizedExperiment.

 
 
+
...

+
optional arguments:
  • check.names: Logical scalar. Passed to data.frame
+function's check.name argument. Determines if sample names are checked
+that they are syntactically valid variable names and are not duplicated.
+If they are not, sample names are modified. (Default: TRUE)
    • 
+

+
+
 
assay.type

 
Character scalar. Specifies which assay to use for
 calculation. (Default: "counts")

@@ -112,8 +107,7 @@ 
Arguments

 If add.row = NULL no data will be added, if
 add.row = TRUE all data will be added and if
 add.row is a character vector, it will be used to subset
-to given column names in rowData. (Default:
-NULL)

+to given column names in rowData. (Default: NULL)

 
 
 
add_row_data

@@ -121,10 +115,10 @@ 
Arguments

 
 
 
add.col

-
Logical scalar. NULL ,or character vector. Used to
-select information from the colData to add to the molten assay data.
-If add.col = NULL no data will be added, if
-add.col = TRUE all data will be added and if
+
Logical scalar. NULL, or
+character vector. Used to select information from the colData
+to add to the molten assay data. If add.col = NULL no data will
+be added, if add.col = TRUE all data will be added and if
 add.col is a character vector, it will be used to subset
 to given column names in colData. (Default: NULL)

 
@@ -150,21 +144,13 @@ 
Arguments

 
sample_name

 
Deprecated. Use col.name instead.

 
-
-
...

-
optional arguments:
  • check_names: Logical scalar. Passed to data.frame function's check.name
-argument. Determines if sample names are checked that they are syntactically
-valid variable names and are not duplicated. If they are not, sample names
-are modified. (Default: TRUE)
    • 
-

-
 

     

     
Value

     
A tibble with the molten data. The assay values are given in a
 column named like the selected assay assay.type. In addition, a
 column “FeatureID” will contain the rownames, if set, and analogously
-a column “SampleID” with the colnames, if set

+a column “SampleID” with the colnames, if set.

     

     

     
Details

@@ -177,11 +163,12 @@ 
Details

     

     
Examples

     
data(GlobalPatterns)
-molten_tse <- meltSE(GlobalPatterns,
-                        assay.type = "counts",
-                        add.row = TRUE,
-                        add.col = TRUE
-                        )
+molten_tse <- meltSE(
+    GlobalPatterns,
+    assay.type = "counts",
+    add.row = TRUE,
+    add.col = TRUE
+    )
 molten_tse
 #> # A tibble: 499,616 × 17
 #>    FeatureID SampleID counts Kingdom Phylum     Class Order Family Genus Species
diff --git a/reference/mergeSEs.html b/reference/mergeSEs.html
index 0f28980d3..d1e09e904 100644
--- a/reference/mergeSEs.html
+++ b/reference/mergeSEs.html
@@ -17,7 +17,7 @@
       
       
         mia
-        1.15.0
+        1.15.1
       
     

 
@@ -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 aebad58db..b1bc6e15f 100644
--- a/reference/mia-datasets.html
+++ b/reference/mia-datasets.html
@@ -20,7 +20,7 @@
       
       
         mia
-        1.15.0
+        1.15.1
       
     

 
@@ -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 09cf8f9f8..7fb5cb47b 100644
--- a/reference/mia-package.html
+++ b/reference/mia-package.html
@@ -22,7 +22,7 @@
       
       
         mia
-        1.15.0
+        1.15.1
       
     

 
@@ -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 3db1b889c..a6fe28910 100644
--- a/reference/peerj13075.html
+++ b/reference/peerj13075.html
@@ -22,7 +22,7 @@
       
       
         mia
-        1.15.0
+        1.15.1
       
     

 
@@ -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 fcb8691f2..5c3a9031a 100644
--- a/reference/rarefyAssay.html
+++ b/reference/rarefyAssay.html
@@ -20,7 +20,7 @@
       
       
         mia
-        1.15.0
+        1.15.1
       
     

 
@@ -47,7 +47,7 @@
   

     

     
Subsample Counts

-    Source: R/rarefyAssay.R
+    Source: R/rarefyAssay.R
     
     

 
diff --git a/reference/runCCA-2.png b/reference/runCCA-2.png
index 3c8ceddb7..4edd0c762 100644
Binary files a/reference/runCCA-2.png and b/reference/runCCA-2.png differ
diff --git a/reference/runCCA.html b/reference/runCCA.html
index f29485f26..dd298307a 100644
--- a/reference/runCCA.html
+++ b/reference/runCCA.html
@@ -18,7 +18,7 @@
       
       
         mia
-        1.15.0
+        1.15.1
       
     

 
@@ -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 25f30c1eb..74a197d05 100644
--- a/reference/runDPCoA.html
+++ b/reference/runDPCoA.html
@@ -19,7 +19,7 @@
       
       
         mia
-        1.15.0
+        1.15.1
       
     

 
@@ -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 e46496477..72bbdf6cc 100644
--- a/reference/runNMDS.html
+++ b/reference/runNMDS.html
@@ -18,7 +18,7 @@
       
       
         mia
-        1.15.0
+        1.15.1
       
     

 
@@ -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 e491ecfe2..7420faf4b 100644
--- a/reference/splitOn.html
+++ b/reference/splitOn.html
@@ -18,7 +18,7 @@
       
       
         mia
-        1.15.0
+        1.15.1
       
     

 
@@ -45,7 +45,7 @@
   

     

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

-    Source: R/splitOn.R
+    Source: R/splitOn.R
     
     

 
@@ -222,7 +222,7 @@ 
Examples

 #> assays(1): counts
 #> rownames(19216): 549322 522457 ... 200359 271582
 #> rowData names(8): Kingdom Phylum ... Species group
-#> colnames(26): CL3 CC1 ... Even2 Even3
+#> colnames(26): CL3 M11Fcsw ... NP2 TS28
 #> colData names(8): X.SampleID Primer ... Description group
 #> reducedDimNames(0):
 #> mainExpName: NULL
diff --git a/reference/summaries.html b/reference/summaries.html
index 6e1141b87..7c20ebd08 100644
--- a/reference/summaries.html
+++ b/reference/summaries.html
@@ -18,7 +18,7 @@
       
       
         mia
-        1.15.0
+        1.15.1
       
     

 
@@ -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 f55dba631..17e308ede 100644
--- a/reference/taxonomy-methods.html
+++ b/reference/taxonomy-methods.html
@@ -19,7 +19,7 @@
       
       
         mia
-        1.15.0
+        1.15.1
       
     

 
@@ -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 7e838bfff..570a58243 100644
--- a/reference/transformAssay.html
+++ b/reference/transformAssay.html
@@ -18,7 +18,7 @@
       
       
         mia
-        1.15.0
+        1.15.1
       
     

 
@@ -45,7 +45,7 @@
   

     

     
Transform assay

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