Use Rbiom unifrac implementation instead of runUnifrac (microbiome#523)

Co-authored-by: Leo Lahti <[email protected]> Co-authored-by: TuomasBorman <[email protected]> Co-authored-by: Tuomas Borman <[email protected]>
Daenarys8 · Jun 10, 2024 · ba42574 · ba42574
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commit ba42574
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: mia
 Type: Package
-Version: 1.13.20
+Version: 1.13.21
 Authors@R:
     c(person(given = "Felix G.M.", family = "Ernst", role = c("aut"),
              email = "[email protected]",
@@ -68,7 +68,8 @@ Imports:
     tidyr,
     bluster,
     MatrixGenerics,
-    mediation
+    mediation,
+    rbiom
 Suggests:
     testthat,
     knitr,

diff --git a/NAMESPACE b/NAMESPACE
@@ -323,11 +323,7 @@ importFrom(ape,cophenetic.phylo)
 importFrom(ape,drop.tip)
 importFrom(ape,has.singles)
 importFrom(ape,is.rooted)
-importFrom(ape,node.depth)
-importFrom(ape,node.depth.edgelength)
-importFrom(ape,prop.part)
 importFrom(ape,read.tree)
-importFrom(ape,reorder.phylo)
 importFrom(ape,root)
 importFrom(bluster,clusterRows)
 importFrom(decontam,isContaminant)
@@ -344,6 +340,7 @@ importFrom(dplyr,rename)
 importFrom(dplyr,select)
 importFrom(dplyr,tally)
 importFrom(mediation,mediate)
+importFrom(rbiom,unifrac)
 importFrom(rlang,":=")
 importFrom(rlang,sym)
 importFrom(scuttle,sumCountsAcrossFeatures)

diff --git a/NEWS b/NEWS
@@ -136,4 +136,5 @@ Changes in version 1.13.x
 + Fix bug in mergeFeaturesByPrevalence
 + new aliases calculateDPCoA to getDPCoA, calculateNMDS to getNMDS, calculateRDA to getRDA, 
 calculateCCA to getCCA
-+ add informative error message in rarefyAssay on assays with strictly-negative values 
++ add informative error message in rarefyAssay on assays with strictly-negative values 
++ Use rbiom package in unifrac implementation