merge devel

Merge branch 'devel' of https://github.com/microbiome/mia into getCrossAssociation

# Conflicts:
#	man/deprecate.Rd

.github/workflows/rworkflows.yml

@@ -0,0 +1,58 @@
+name: rworkflows
+'on':
+  push:
+    branches:
+    - master
+    - main
+    - devel
+    - RELEASE_**
+  pull_request:
+    branches:
+    - master
+    - main
+    - devel
+    - RELEASE_**
+jobs:
+  rworkflows:
+    permissions:
+      contents: write
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    container: ${{ matrix.config.cont }}
+    strategy:
+      fail-fast: ${{ false }}
+      matrix:
+        config:
+        - os: ubuntu-latest
+          bioc: devel
+          r: auto
+          cont: bioconductor/bioconductor_docker:devel
+          rspm: https://packagemanager.rstudio.com/cran/__linux__/latest/release
+        - os: macOS-latest
+          bioc: devel
+          r: auto
+          cont: ~
+          rspm: ~
+        - os: windows-latest
+          bioc: devel
+          r: auto
+          cont: ~
+          rspm: ~
+    steps:
+    - uses: neurogenomics/rworkflows@master
+      with:
+        run_bioccheck: ${{ false }}
+        run_rcmdcheck: ${{ true }}
+        as_cran: ${{ true }}
+        run_vignettes: ${{ true }}
+        has_testthat: ${{ true }}
+        run_covr: ${{ true }}
+        run_pkgdown: ${{ true }}
+        has_runit: ${{ false }}
+        has_latex: ${{ false }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run_docker: ${{ false }}
+        DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
+        runner_os: ${{ runner.os }}
+        cache_version: cache-v1
+        enable_act: ${{ false }}

NAMESPACE

@@ -3,6 +3,7 @@
 export(IdTaxaToDataFrame)
 export(TAXONOMY_RANKS)
 export(ZTransform)
+export(addCluster)
 export(addContaminantQC)
 export(addNotContaminantQC)
 export(addPerSampleDominantFeatures)
@@ -17,7 +18,6 @@ export(calculateJSD)
 export(calculateNMDS)
 export(calculateOverlap)
 export(calculateUnifrac)
-export(cluster)
 export(countDominantFeatures)
 export(countDominantTaxa)
 export(estimateDivergence)
@@ -38,6 +38,7 @@ export(getPrevalentFeatures)
 export(getPrevalentTaxa)
 export(getRareFeatures)
 export(getRareTaxa)
+export(getTaxonomyRanks)
 export(getTopFeatures)
 export(getTopTaxa)
 export(getUniqueFeatures)
@@ -79,6 +80,7 @@ export(runJSD)
 export(runNMDS)
 export(runOverlap)
 export(runUnifrac)
+export(setTaxonomyRanks)
 export(splitByRanks)
 export(splitOn)
 export(subsampleCounts)
@@ -99,6 +101,7 @@ export(unsplitByRanks)
 export(unsplitOn)
 exportMethods("relabundance<-")
 exportMethods(ZTransform)
+exportMethods(addCluster)
 exportMethods(addContaminantQC)
 exportMethods(addHierarchyTree)
 exportMethods(addNotContaminantQC)
@@ -310,6 +313,7 @@ importFrom(tibble,rownames_to_column)
 importFrom(tibble,tibble)
 importFrom(tidyr,pivot_longer)
 importFrom(tidyr,pivot_wider)
+importFrom(utils,assignInMyNamespace)
 importFrom(utils,combn)
 importFrom(utils,head)
 importFrom(utils,read.delim)

NEWS

@@ -104,3 +104,5 @@ Changes in version 1.11.x
 + cluster: Overwrite old results instead of failing
 + getPrevalence: bugfix, if assay contains NA values, it does not end up to NA anymore.
 + getExperimentCrossCorrelation fix: enable using of sampleMap in MAE.
++ Implemented the setTaxonomyRanks function to specify which ranks are recognized as taxonomy ranks.
++ Rename cluster to addCluster