Initialise exporters to raw, qiime and mothur

DESCRIPTION

@@ -118,6 +118,6 @@ LinkingTo:
 URL: https://microbiome.github.io/mia/, https://github.com/microbiome/mia
 BugReports: https://github.com/microbiome/mia/issues
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.3
 VignetteBuilder: knitr
+Config/roxygen2/version: 8.0.0
 RdMacros: Rdpack

NAMESPACE

@@ -60,6 +60,9 @@ export(estimateDominance)
 export(estimateEvenness)
 export(estimateFaith)
 export(estimateRichness)
+export(exportMothur)
+export(exportQIIME2)
+export(exportRaw)
 export(filterRPCAInput)
 export(full_join)
 export(getAbundanceClass)
@@ -421,6 +424,8 @@ importFrom(ape,is.binary)
 importFrom(ape,is.rooted)
 importFrom(ape,read.tree)
 importFrom(ape,reorder.phylo)
+importFrom(ape,write.FASTA)
+importFrom(ape,write.tree)
 importFrom(bluster,clusterRows)
 importFrom(decontam,isContaminant)
 importFrom(decontam,isNotContaminant)
@@ -464,9 +469,11 @@ importFrom(stats,runif)
 importFrom(stats,sd)
 importFrom(stats,setNames)
 importFrom(stats,terms)
+importFrom(stringr,fixed)
 importFrom(stringr,str_extract)
 importFrom(stringr,str_extract_all)
 importFrom(stringr,str_pad)
+importFrom(stringr,str_remove)
 importFrom(stringr,str_replace_all)
 importFrom(tibble,rownames_to_column)
 importFrom(tibble,tibble)

NEWS

@@ -190,8 +190,8 @@ Changes in version 1.19.x
 Changes in version 1.21.x
 + Fixed explained percentages on PCA axes for jointRPCA and hardened
   rank-deficient SVD handling in joint-RPCA (1.21.1, 2026-05-12)
-* Generalise agglomerateByModule to non-binary numerical modules (1.21.2, 2026-05-31)
-* Modify joint-RPCA to match with Gemelli implementation (1.21.3, 2026-06-16)
++ Generalise agglomerateByModule to non-binary numerical modules (1.21.2, 2026-05-31)
++ Modify joint-RPCA to match with Gemelli implementation (1.21.3, 2026-06-16)
 + Implement Striped Unifrac algorithm (1.21.4, 2026-07-29)
 + Added conversion functions between MAE and TreeSE (1.21.8, 2026-09-22)
 + Added applyByModule (1.21.11, 2026-10-02)

R/AllGenerics.R

@@ -105,6 +105,21 @@ setGeneric("convertToBIOM", signature = c("x"),
 setGeneric("convertToPhyloseq", signature = c("x"), function(x, ...)
     standardGeneric("convertToPhyloseq"))
 
+#' @rdname export-methods
+#' @export
+setGeneric("exportRaw", signature = c("x"), function(x, ...)
+    standardGeneric("exportRaw"))
+
+#' @rdname export-methods
+#' @export
+setGeneric("exportQIIME2", signature = c("x"), function(x, ...)
+    standardGeneric("exportQIIME2"))
+
+#' @rdname export-methods
+#' @export
+setGeneric("exportMothur", signature = c("x"), function(x, ...)
+    standardGeneric("exportMothur"))
+
 #' @rdname isContaminant
 #' @export
 setGeneric("addContaminantQC", signature = c("x"),

R/calculateUnifrac.R

@@ -1,6 +1,6 @@
 #' @importFrom ape drop.tip
 .get_unifrac <- function(
-        x, tree, weighted = FALSE, node.label = nodeLab, nodeLab = NULL, ...){
+        x, tree, new = FALSE, weighted = FALSE, node.label = nodeLab, nodeLab = NULL, ...){
     # Transpose the matrix so that the orientation is the same as in other
     # dissimilatity methods
     x <- t(x)