From 0531bb59d970607c29c73f34d9ab5611fcca7c67 Mon Sep 17 00:00:00 2001 From: TuomasBorman <60338854+TuomasBorman@users.noreply.github.com> Date: Fri, 15 Nov 2024 09:04:04 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20microbio?= =?UTF-8?q?me/mia@c4ac5155a621336ea8c23836396a81cb65ba84a2=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- articles/mia.html | 8 +- 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 17693 -> 17819 bytes reference/addLDA.html | 14 +- reference/addNMF.html | 2 +- reference/agglomerate-methods.html | 199 ++++++++++++++----------- reference/agglomerateByPrevalence.html | 6 +- 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 | 18 +-- 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/index.html | 6 +- 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 | 31 ++-- reference/runDPCoA.html | 2 +- reference/runNMDS.html | 2 +- reference/splitOn.html | 2 +- reference/summaries.html | 6 +- reference/taxonomy-methods.html | 6 +- reference/transformAssay.html | 2 +- sitemap.xml | 1 - 50 files changed, 190 insertions(+), 183 deletions(-) diff --git a/articles/mia.html b/articles/mia.html index eeb3bec24..986613c76 100644 --- a/articles/mia.html +++ b/articles/mia.html @@ -69,7 +69,7 @@

mia: Microbiome analysis tools

2024-11-15

- Source: vignettes/mia.Rmd + Source: vignettes/mia.Rmd @@ -271,13 +271,13 @@

Merging and a sample subsetting becomes very easy.

 altExp(tse, "family") <- x2
-

Keep in mind, that if you set na.rm = TRUE, rows with +

Keep in mind, that if you set empty.rm = TRUE, rows with NA or similar value (defined via the empty.fields argument) will be removed. Depending on these settings different number of rows will be returned.

-x1 <- agglomerateByRank(tse, rank = "Species", na.rm = TRUE)
-altExp(tse,"species") <- agglomerateByRank(tse, rank = "Species", na.rm = FALSE)
+x1 <- agglomerateByRank(tse, rank = "Species", empty.rm = TRUE)
+altExp(tse,"species") <- agglomerateByRank(tse, rank = "Species", empty.rm = FALSE)
 dim(x1)
## [1] 944  26
diff --git a/authors.html b/authors.html
index 32538cc8e..a72924294 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 f4702419c..21ec428d6 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,4 +3,4 @@ pkgdown: 2.1.1
 pkgdown_sha: ~
 articles:
   mia: mia.html
-last_built: 2024-11-15T08:49Z
+last_built: 2024-11-15T09:00Z
diff --git a/reference/GlobalPatterns.html b/reference/GlobalPatterns.html
index f9c42c26b..f7df90a23 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 86dd3fea3..1b3118ba6 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 448ac8353..d8ce42ced 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 747d03af3..058f5f3b7 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 43ac830f3..b613e1def 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 7207d19ad..8f725ab5c 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 360151c0d..a16e8fe44 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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z?m8r-79dXpcr8&HK>3I0j>+ibX}41U9GQBJ;Js$k
     

     
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             4.323231e-09 9.168439e-04
-#> Acidobacteria   9.232478e-06 3.402348e-02
-#> Actinobacteria  3.966549e-02 1.103858e-01
-#> Armatimonadetes 8.978761e-09 4.938148e-04
-#> BRC1            7.185957e-08 6.632039e-05
-#> Bacteroidetes   4.033307e-01 1.001247e-01
+#> 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
 
 # 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 bb948e3d4..d722cabe2 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 5c5c9ff61..dd1abc625 100644
--- a/reference/agglomerate-methods.html
+++ b/reference/agglomerate-methods.html
@@ -1,6 +1,18 @@
 
-Agglomerate or merge data using taxonomic information — agglomerate-methods • miaAgglomerate data using taxonomic information or other grouping — agglomerate-methods • mia
   

     

-    
Agglomerate or merge data using taxonomic information

-    Source: R/agglomerate.R, R/splitByRanks.R
+    
Agglomerate data using taxonomic information or other grouping

+    Source: R/agglomerate.R, R/splitByRanks.R
     
     

 
     

     
Agglomeration functions can be used to sum-up data based on specific criteria
 such as taxonomic ranks, variables or prevalence.

+
agglomerateByRank can be used to sum up data based on associations
+with certain taxonomic ranks, as defined in rowData. Only available
+taxonomyRanks can be used.

+
agglomerateByVariable merges data on rows or columns of a
+SummarizedExperiment as defined by a factor alongside the
+chosen dimension. This function allows agglomeration of data based on other
+variables than taxonomy ranks.
+Metadata from the rowData or colData are
+retained as defined by archetype.
+assay are
+agglomerated, i.e. summed up. If the assay contains values other than counts
+or absolute values, this can lead to meaningless values being produced.

 
agglomerateByRanks takes a SummarizedExperiment, splits it along the
 taxonomic ranks, aggregates the data per rank, converts the input to a
 SingleCellExperiment objects and stores the aggregated data as
@@ -69,19 +93,36 @@ 
Agglomerate or merge data using taxonomic information

     

     
agglomerateByRank(x, ...)
 
-agglomerateByVariable(x, ...)
+# S4 method for class 'TreeSummarizedExperiment'
+agglomerateByRank(
+  x,
+  rank = taxonomyRanks(x)[1],
+  update.tree = agglomerateTree,
+  agglomerate.tree = agglomerateTree,
+  agglomerateTree = FALSE,
+  ...
+)
+
+# S4 method for class 'SingleCellExperiment'
+agglomerateByRank(
+  x,
+  rank = taxonomyRanks(x)[1],
+  altexp = NULL,
+  altexp.rm = strip_altexp,
+  strip_altexp = TRUE,
+  ...
+)
 
 # S4 method for class 'SummarizedExperiment'
 agglomerateByRank(
   x,
   rank = taxonomyRanks(x)[1],
-  na.rm = TRUE,
+  empty.rm = TRUE,
   empty.fields = c(NA, "", " ", "\t", "-", "_"),
   ...
 )
 
-# S4 method for class 'SummarizedExperiment'
-agglomerateByVariable(x, by, group = f, f, ...)
+agglomerateByVariable(x, ...)
 
 # S4 method for class 'TreeSummarizedExperiment'
 agglomerateByVariable(
@@ -94,23 +135,8 @@ 
Agglomerate or merge data using taxonomic information

   ...
 )
 
-# S4 method for class 'SingleCellExperiment'
-agglomerateByRank(
-  x,
-  ...,
-  altexp = NULL,
-  altexp.rm = strip_altexp,
-  strip_altexp = TRUE
-)
-
-# S4 method for class 'TreeSummarizedExperiment'
-agglomerateByRank(
-  x,
-  ...,
-  update.tree = agglomerateTree,
-  agglomerate.tree = agglomerateTree,
-  agglomerateTree = FALSE
-)
+# S4 method for class 'SummarizedExperiment'
+agglomerateByVariable(x, by, group = f, f, ...)
 
 agglomerateByRanks(x, ...)
 
@@ -179,13 +205,43 @@ 
Arguments

 
 
 
rank

-
Character scalar. Defines a taxonomic rank. Must be a value of
-taxonomyRanks() function.

+
Character scalar. Defines a taxonomic rank. Must be a
+value of taxonomyRanks() function.

 
 
-
na.rm

-
Logical scalar. Should NA values be omitted when calculating
-prevalence? (Default: TRUE)

+
update.tree

+
Logical scalar. Should
+rowTree() also be merged? (Default: FALSE)

+
+
+
agglomerate.tree

+
Deprecated. Use update.tree instead.

+
+
+
agglomerateTree

+
Deprecated. Use update.tree instead.

+
+
+
altexp

+
Character scalar or integer scalar.
+Specifies an alternative experiment containing the input data.

+
+
+
altexp.rm

+
Logical scalar. Should alternative
+experiments be removed prior to agglomeration? This prevents too many
+nested alternative experiments by default. (Default:
+TRUE)

+
+
+
strip_altexp

+
Deprecated. Use altexp.rm instead.

+
+
+
empty.rm

+
Logical scalar. Defines whether rows including
+empty.fields in specified rank will be excluded.
+(Default: TRUE)

 
 
 
empty.fields

@@ -214,44 +270,20 @@ 
Arguments

 
Deprecated. Use group instead.

 
 
-
update.tree

-
Logical scalar. Should
-rowTree() also be merged? (Default: FALSE)

-
-
 
mergeTree

 
Deprecated. Use update.tree instead.

 
 
-
altexp

-
Character scalar or integer scalar.
-Specifies an alternative experiment containing the input data.

-
-
-
altexp.rm

-
Logical scalar. Should alternative
-experiments be removed prior to agglomeration? This prevents too many
-nested alternative experiments by default. (Default:
-TRUE)

-
-
-
strip_altexp

-
Deprecated. Use altexp.rm instead.

-
-
-
agglomerate.tree

-
Deprecated. Use update.tree instead.

-
-
-
agglomerateTree

-
Deprecated. Use update.tree instead.

-
-
 
ranks

 
Character vector. Defines taxonomic ranks. Must all be values
 of taxonomyRanks() function.

 
 
+
na.rm

+
Logical scalar. Should NA values be omitted?
+(Default: TRUE)

+
+
 
as.list

 
Logical scalar. Should the list of
 SummarizedExperiment objects be returned by the function
@@ -291,25 +323,10 @@ 
Value

     

     

     
Details

-    
agglomerateByRank can be used to sum up data based on associations
-with certain taxonomic ranks, as defined in rowData. Only available
-taxonomyRanks can be used.

-
agglomerateByVariable merges data on rows or columns of a
-SummarizedExperiment as defined by a factor alongside the
-chosen dimension. This function allows agglomeration of data based on other
-variables than taxonomy ranks.
-Metadata from the rowData or colData are
-retained as defined by archetype.
-assay are
-agglomerated, i.e. summed up. If the assay contains values other than counts
-or absolute values, this can lead to meaningless values being produced.

-
Agglomeration sums up the values of assays at the specified taxonomic level.
-With
-certain assays, e.g. those that include binary or negative values, this
-summing
-can produce meaningless values. In those cases, consider performing
-agglomeration
-first, and then applying the transformation afterwards.

+    
Agglomeration sums up the values of assays at the specified taxonomic level.
+With certain assays, e.g. those that include binary or negative values, this
+summing can produce meaningless values. In those cases, consider performing
+agglomeration first, and then applying the transformation afterwards.

 
agglomerateByVariable works similarly to
 sumCountsAcrossFeatures.
 However, additional support for TreeSummarizedExperiment was added and
@@ -398,10 +415,10 @@ 
Examples

 #> Check the assay, and consider doing transformation againmanually with agglomerated data.
 tse <- transformAssay(tse, method = "pa")
 
-# removing empty labels by setting na.rm = TRUE
+# Removing empty labels by setting empty.rm = TRUE
 sum(is.na(rowData(GlobalPatterns)$Family))
 #> [1] 5603
-x3 <- agglomerateByRank(GlobalPatterns, rank="Family", na.rm = TRUE)
+x3 <- agglomerateByRank(GlobalPatterns, rank="Family", empty.rm = TRUE)
 nrow(x3) # different from x2
 #> [1] 341
 
@@ -416,8 +433,8 @@ 
Examples

 #> [1] "Family:125ds10" "Family:211ds20" "Family:5B-12"  
 
 # use 'empty.ranks.rm' to remove columns that include only NAs
-x4 <- agglomerateByRank(GlobalPatterns, rank="Phylum",
-                        empty.ranks.rm = TRUE)
+x4 <- agglomerateByRank(
+    GlobalPatterns, rank="Phylum", empty.ranks.rm = TRUE)
 head(rowData(x4))
 #> DataFrame with 6 rows and 2 columns
 #>                     Kingdom          Phylum
@@ -429,7 +446,7 @@ 
Examples

 #> Actinobacteria     Bacteria  Actinobacteria
 #> Armatimonadetes    Bacteria Armatimonadetes
 
-# If the assay contains NAs, you might want to consider replacing them,
+# If the assay contains NAs, you might want to specify na.rm=TRUE,
 # since summing-up NAs lead to NA
 x5 <- GlobalPatterns
 # Replace first value with NA
@@ -445,9 +462,8 @@ 
Examples

 #>              NP5 TRRsed1 TRRsed2 TRRsed3   TS28    TS29   Even1  Even2   Even3
 #> Archaea    33996     843    8418   14250   1598    1690     150     23      91
 #> Bacteria 1618758   57845  484708  265454 935868 1209381 1215987 971050 1078150
-# Replace NAs with 0. This is justified when we are summing-up counts.
-assay(x5)[ is.na(assay(x5)) ] <- 0
-x6 <- agglomerateByRank(x5, "Kingdom")
+# Use na.rm=TRUE
+x6 <- agglomerateByRank(x5, "Kingdom", na.rm = TRUE)
 head( assay(x6) )
 #>             CL3     CC1    SV1 M31Fcsw M11Fcsw M31Plmr M11Plmr F21Plmr M31Tong
 #> Archaea    1262    1248  28811      33      57      42     112     140     303
@@ -487,11 +503,11 @@ 
Examples

 #> colTree: NULL
 plot(rowTree(esophagus))
 
-# get a factor for merging
+# Get a factor for merging
 f <- factor(regmatches(rownames(esophagus),
-                       regexpr("^[0-9]*_[0-9]*",rownames(esophagus))))
-merged <- agglomerateByVariable(esophagus, by = "rows", f,
-                                update.tree = TRUE)
+    regexpr("^[0-9]*_[0-9]*",rownames(esophagus))))
+merged <- agglomerateByVariable(
+    esophagus, by = "rows", f, update.tree = TRUE)
 plot(rowTree(merged))
 
 #
@@ -512,8 +528,8 @@ 
Examples

 #> rowTree: 1 phylo tree(s) (19216 leaves)
 #> colLinks: NULL
 #> colTree: NULL
-merged <- agglomerateByVariable(GlobalPatterns, by = "cols",
-                                colData(GlobalPatterns)$SampleType)
+merged <- agglomerateByVariable(
+    GlobalPatterns, by = "cols", colData(GlobalPatterns)$SampleType)
 merged
 #> class: TreeSummarizedExperiment 
 #> dim: 19216 9 
@@ -530,6 +546,7 @@ 
Examples

 #> rowTree: 1 phylo tree(s) (19216 leaves)
 #> colLinks: NULL
 #> colTree: NULL
+
 data(GlobalPatterns)
 # print the available taxonomic ranks
 taxonomyRanks(GlobalPatterns)
diff --git a/reference/agglomerateByPrevalence.html b/reference/agglomerateByPrevalence.html
index 4a0ea49cd..65d41c229 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
     
     

 
@@ -90,8 +90,8 @@ 
Arguments

 
 
 
rank

-
Character scalar. Defines a taxonomic rank. Must be a value of
-taxonomyRanks() function.

+
Character scalar. Defines a taxonomic rank. Must be a
+value of taxonomyRanks() function.

 
 
 
other.name

diff --git a/reference/calculateDMN.html b/reference/calculateDMN.html
index d6e972973..880056415 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 5d5b0d952..eecd2fc0b 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 17bf05d77..12fc272a4 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 e455c73d7..8ee92961f 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 0e31fed22..722cd71d5 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 5babf797a..5dd3dc568 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 e6e279dd9..4d3cff9f8 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 e6c5403a6..796be87a3 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 d7e6950ed..0718ddf39 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 2b62357a3..23f4f02e9 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 80a749b5c..ceceffa96 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 651d420a7..5f1517b03 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
     
     

 
@@ -165,9 +165,7 @@ 
Arguments

 
...

 
additional arguments
  • If !is.null(rank) arguments are passed on to
 agglomerateByRank. See
-?agglomerateByRank for more details.
-Note that you can specify whether to remove empty ranks with
-agg.na.rm instead of na.rm. (default: FALSE)
    • 
+?agglomerateByRank for more details.
    
 
  • for getPrevalent, getRare, subsetByPrevalent
 and subsetByRare additional parameters passed to
 getPrevalence
    • 
@@ -177,8 +175,8 @@ 
    Arguments
    
 
 
 
    detection
    
-
    Numeric scalar. Detection threshold for absence/presence.
-If as_relative = FALSE,
+
    Numeric scalar. Detection threshold for
+absence/presence. If as_relative = FALSE,
 it sets the counts threshold for a taxon to be considered present.
 If as_relative = TRUE, it sets the relative abundance threshold
 for a taxon to be considered present. (Default: 0)
    
@@ -199,8 +197,8 @@ 
    Arguments
    
 
 
 
    na.rm
    
-
    Logical scalar. Should NA values be omitted when calculating
-prevalence? (Default: TRUE)
    
+
    Logical scalar. Should NA values be omitted?
+(Default: TRUE)
    
 
 
 
    assay.type
    
@@ -213,8 +211,8 @@ 
    Arguments
    
 
 
 
    rank
    
-
    Character scalar. Defines a taxonomic rank. Must be a value of
-taxonomyRanks() function.
    
+
    Character scalar. Defines a taxonomic rank. Must be a
+value of taxonomyRanks() function.
    
 
 
 
    prevalence
    
diff --git a/reference/hierarchy-tree.html b/reference/hierarchy-tree.html
index 06e9ecdaf..72f07d5d2 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 c13aeeca7..775e7268e 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 e481f74e6..e58ecdcb7 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 74ecf57e0..1397b18ce 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 e0fe3cee8..15070ac94 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 0dc5a0371..0860d043e 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 3d214ca93..ebf3ad940 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/index.html b/reference/index.html
index 1941d749d..79eabc048 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -58,10 +58,6 @@ 
    Association addMediation() getMediation() 
    
         
         
    Perform mediation analysis
    
-      
-          
    getPERMANOVA() addPERMANOVA() 
    
-        
-        
    Calculate PERMANOVA (Permutational Multivariate Analysis of Variance)
    
       
           
    Clustering 
    
           
    
@@ -85,7 +81,7 @@ 
    Agglomeration 
           
    agglomerateByRank() agglomerateByVariable() agglomerateByRanks() splitByRanks() unsplitByRanks() 
    
         
-        
    Agglomerate or merge data using taxonomic information
    
+        
    Agglomerate data using taxonomic information or other grouping
    
       
           
    agglomerateByPrevalence() 
    
         
diff --git a/reference/isContaminant.html b/reference/isContaminant.html
index c9ebd9cac..e8385cc3e 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 dcfb77331..1b59efbdd 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 1e740a68b..c5e2b917b 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 fd7beec3e..9235a70f0 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 4e51c6b40..a199ce1a5 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 77cf583ac..668b86ae0 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 a9f134e5e..42c234244 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 614179ac8..a0d91a35b 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
     
     
    
 
@@ -121,27 +121,25 @@ 
    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. (Default: "euclidean")
      • 
+possible following homogeneity test. (By default:
+method="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 FALSE, only
+
    • full Logical scalar. should all the results from the
+significance calculations be returned. When full=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).
-(Default: "permanova")
      • 
+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")
      
 
    • permutations a numeric value specifying the number of
 permutations for significance testing in vegan::anova.cca.
-(Default: 999)
      • 
+(By default: permutations=999)
      
 
    
 
 
@@ -166,7 +164,7 @@ 
    Arguments
    
 
 
 
    variables
    
-
    Deprecated. Use col.var instead.
    
+
    Deprecated. Use "col.var" instead.
    
 
 
 
    test.signif
    
@@ -194,8 +192,8 @@ 
    Arguments
    
 
 
 
    name
    
-
    Character scalar. A name for the reducedDim()
-where results will be stored. (Default: "CCA")
    
+
    Character scalar. A name for the column of the
+colData where results will be stored. (Default: "CCA")
    
 
 
    
     
    
@@ -215,8 +213,7 @@ 
    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 f3dee7c1e..6479cd768 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 d7aa08c53..f3d44bd40 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 d3d85925b..1c289e66a 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 b33e8fa39..e3c1b99bf 100644
--- a/reference/summaries.html
+++ b/reference/summaries.html
@@ -45,7 +45,7 @@
   
    
     
    
     
    Summarizing microbiome data
    
-    Source: R/summaries.R
+    Source: R/summaries.R
     
     
    
 
@@ -118,8 +118,8 @@ 
    Arguments
    
 
 
 
    na.rm
    
-
    Logical scalar. Should NA values be omitted when calculating
-prevalence? (Default: TRUE)
    
+
    Logical scalar. Should NA values be omitted?
+(Default: TRUE)
    
 
 
 
    ...
    
diff --git a/reference/taxonomy-methods.html b/reference/taxonomy-methods.html
index 7e9ecfa95..896c6a711 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
     
     
    
 
@@ -123,8 +123,8 @@ 
    Arguments
    
 
 
 
    rank
    
-
    Character scalar. Defines a taxonomic rank. Must be a value of
-taxonomyRanks() function.
    
+
    Character scalar. Defines a taxonomic rank. Must be a
+value of taxonomyRanks() function.
    
 
 
 
    empty.fields
    
diff --git a/reference/transformAssay.html b/reference/transformAssay.html
index 0965037bc..33fcedd87 100644
--- a/reference/transformAssay.html
+++ b/reference/transformAssay.html
@@ -45,7 +45,7 @@
   
    
     
    
     
    Transform assay
    
-    Source: R/transformCounts.R
+    Source: R/transformCounts.R
     
     
    
 
diff --git a/sitemap.xml b/sitemap.xml
index f06933779..81dc8d321 100644
--- a/sitemap.xml
+++ b/sitemap.xml
@@ -28,7 +28,6 @@
 /reference/getDissimilarity.html
 /reference/getDominant.html
 /reference/getMediation.html
-/reference/getPERMANOVA.html
 /reference/getPrevalence.html
 /reference/hierarchy-tree.html
 /reference/importBIOM.html