Incorporate Bioconductor recommendations (#662)

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: mia
 Type: Package
-Version: 1.15.6
+Version: 1.15.7
 Authors@R:
     c(person(given = "Tuomas", family = "Borman", role = c("aut", "cre"),
              email = "[email protected]",
@@ -106,6 +106,8 @@ Suggests:
     topicdoc,
     topicmodels,
     yaml
+Remotes:
+    github::joey711/phyloseq
 URL: https://github.com/microbiome/mia
 BugReports: https://github.com/microbiome/mia/issues
 Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -4,19 +4,22 @@ export("relabundance<-")
 export(IdTaxaToDataFrame)
 export(ZTransform)
 export(addAlpha)
+export(addCCA)
 export(addCluster)
 export(addContaminantQC)
 export(addDPCoA)
 export(addDissimilarity)
 export(addDivergence)
 export(addDominant)
+export(addHierarchyTree)
 export(addLDA)
 export(addMediation)
 export(addNMDS)
 export(addNMF)
 export(addNotContaminantQC)
 export(addPerSampleDominantFeatures)
 export(addPerSampleDominantTaxa)
+export(addRDA)
 export(addTaxonomyTree)
 export(agglomerateByPrevalence)
 export(agglomerateByRank)
@@ -32,6 +35,7 @@ export(calculateNMDS)
 export(calculateOverlap)
 export(calculateRDA)
 export(calculateUnifrac)
+export(checkTaxonomy)
 export(cluster)
 export(convertFromBIOM)
 export(convertFromDADA2)
@@ -48,6 +52,7 @@ export(estimateFaith)
 export(estimateRichness)
 export(full_join)
 export(getBestDMNFit)
+export(getCCA)
 export(getCrossAssociation)
 export(getDMN)
 export(getDPCoA)
@@ -56,18 +61,20 @@ export(getDivergence)
 export(getDominant)
 export(getExperimentCrossAssociation)
 export(getExperimentCrossCorrelation)
+export(getHierarchyTree)
 export(getLDA)
 export(getMediation)
 export(getNMDS)
 export(getNMF)
 export(getPrevalence)
-export(getPrevalent)
 export(getPrevalentAbundance)
 export(getPrevalentFeatures)
 export(getPrevalentTaxa)
+export(getRDA)
 export(getRare)
 export(getRareFeatures)
 export(getRareTaxa)
+export(getTaxonomyLabels)
 export(getTaxonomyRanks)
 export(getTop)
 export(getTopFeatures)
@@ -97,6 +104,7 @@ export(makeTreeSEFromPhyloseq)
 export(makeTreeSummarizedExperimentFromBiom)
 export(makeTreeSummarizedExperimentFromDADA2)
 export(makeTreeSummarizedExperimentFromPhyloseq)
+export(mapTaxonomy)
 export(meltAssay)
 export(meltSE)
 export(mergeCols)
@@ -137,6 +145,9 @@ export(subsetFeatures)
 export(subsetSamples)
 export(subsetTaxa)
 export(summarizeDominance)
+export(summary)
+export(taxonomyRankEmpty)
+export(taxonomyRanks)
 export(taxonomyTree)
 export(testExperimentCrossAssociation)
 export(testExperimentCrossCorrelation)