New dissimilarity functions

NAMESPACE

@@ -7,6 +7,7 @@ export(addAlpha)
 export(addCluster)
 export(addContaminantQC)
 export(addDPCoA)
+export(addDissimilarity)
 export(addDivergence)
 export(addDominant)
 export(addLDA)
@@ -50,6 +51,7 @@ export(getBestDMNFit)
 export(getCrossAssociation)
 export(getDMN)
 export(getDPCoA)
+export(getDissimilarity)
 export(getDominant)
 export(getExperimentCrossAssociation)
 export(getExperimentCrossCorrelation)
@@ -149,6 +151,7 @@ exportMethods(addAlpha)
 exportMethods(addCCA)
 exportMethods(addCluster)
 exportMethods(addContaminantQC)
+exportMethods(addDissimilarity)
 exportMethods(addDivergence)
 exportMethods(addDominant)
 exportMethods(addHierarchyTree)
@@ -188,6 +191,7 @@ exportMethods(getCCA)
 exportMethods(getCrossAssociation)
 exportMethods(getDMN)
 exportMethods(getDPCoA)
+exportMethods(getDissimilarity)
 exportMethods(getDominant)
 exportMethods(getExperimentCrossAssociation)
 exportMethods(getExperimentCrossCorrelation)
@@ -236,6 +240,7 @@ exportMethods(rarefyAssay)
 exportMethods(relAbundanceCounts)
 exportMethods(relabundance)
 exportMethods(right_join)
+exportMethods(runJSD)
 exportMethods(runOverlap)
 exportMethods(splitOn)
 exportMethods(subsampleCounts)
@@ -344,9 +349,7 @@ importFrom(ape,collapse.singles)
 importFrom(ape,cophenetic.phylo)
 importFrom(ape,drop.tip)
 importFrom(ape,has.singles)
-importFrom(ape,is.rooted)
 importFrom(ape,read.tree)
-importFrom(ape,root)
 importFrom(bluster,clusterRows)
 importFrom(decontam,isContaminant)
 importFrom(decontam,isNotContaminant)
@@ -399,6 +402,7 @@ importFrom(utils,read.table)
 importFrom(utils,unzip)
 importFrom(vegan,"sppscores<-")
 importFrom(vegan,anova.cca)
+importFrom(vegan,avgdist)
 importFrom(vegan,betadisper)
 importFrom(vegan,monoMDS)
 importFrom(vegan,scores)