make R CMD check happy again

NAMESPACE

@@ -73,7 +73,6 @@ export(Children)
 export(Descendants)
 export(KF.dist)
 export(NJ)
-export(PNJ)
 export(RF.dist)
 export(RI)
 export(SH.test)

R/distTree.R

@@ -131,7 +131,6 @@ upgma_nni <- function(d, method = "average", opt = "min", trace = 0,
 #' This function performs the neighbor-joining tree estimation of Saitou and
 #' Nei (1987). UNJ is the unweighted version from Gascuel (1997).
 #'
-#' @aliases PNJ
 #'
 #' @param x A distance matrix.
 #' @return an object of class \code{"phylo"}.
@@ -215,8 +214,6 @@ UNJ <- function(x){
 }
 
 
-#' @rdname phangorn-internal
-#' @export
 PNJ <- function(data)
 {
   q <- l <- r <- length(data)

R/phyDat.R

@@ -1114,13 +1114,14 @@ unique.phyDat <- function(x, incomparables=FALSE, identical=TRUE, ...){
 
 #' @rdname phyDat
 #' @export
-removeUndeterminedSites <- function(x, use.contrast=TRUE,
-                                    undetermined=c("?", "n", "-"), ...){
+removeUndeterminedSites <- function(x, ...){
+# , use.contrast=TRUE, undetermined=c("?", "n", "-")
     nc <- attr(x, "nc")
     nr <- attr(x, "nr")
     contrast <- attr(x, "contrast")
-    if(use.contrast) ind <- which( (contrast %*% rep(1, nc)) == nc )
-    else ind <- sort(match(undetermined, attr(x, "allLevels")))
+#    if(use.contrast)
+    ind <- which( (contrast %*% rep(1, nc)) == nc )
+#    else ind <- sort(match(undetermined, attr(x, "allLevels")))
     tmp <- x[[1]] %in% ind
     for(i in 2:length(x)) tmp <- tmp & (x[[i]] %in% ind)
     if(any(tmp)) x <- getRows(x, (1:nr)[!tmp]) #getRows(x, -which(tmp))

R/pmlMix.R

@@ -272,7 +272,7 @@ optimMixEdge <- function(object, omega, trace = 1, ...) {
 #' only allowed on the left-hand side.  The convergence of the algorithm is
 #' very slow and is likely that the algorithm can get stuck in local optima.
 #'
-#' @aliases pmlMix pmlPen
+#' @aliases pmlMix
 #' @param formula a formula object (see details).
 #' @param fit an object of class \code{pml}.
 #' @param m number of mixtures.

R/pmlPen.R

@@ -1,7 +1,7 @@
 ##
 ## pmlPen penalized ML
 ##
-#' @rdname pmlMix
+#' @rdname phangorn-internal
 #' @export
 pmlPen <- function(object, lambda, ...) {
   if (inherits(object, "pmlPart")) return(pmlPartPen(object, lambda, ...))