fix notes

R/ancestral.R

@@ -42,7 +42,7 @@
 ## returned.
 #' @author Klaus Schliep \email{klaus.schliep@@gmail.com}
 #' @seealso \code{\link{pml}}, \code{\link{parsimony}}, \code{\link[ape]{ace}},
-#' \code{\link{plotAnc}}, \code{\link{ltg2amb}}, \code{\link{latag2n}},
+#' \code{\link{plotAnc}}, \code{\link{ltg2amb}}, \code{\link[ape]{latag2n}},
 #' \code{\link{gap_as_state}}, \code{\link[ape]{root}},
 #' \code{\link[ape]{makeNodeLabel}}
 #' @references Felsenstein, J. (2004). \emph{Inferring Phylogenies}. Sinauer
@@ -107,6 +107,9 @@ ancestral.pml <- function(object, type = "marginal", ...) {
   tree$node.label <- node_label
   tmp <- length(data)
 
+  joint <- TRUE
+  if(length(w) > 1 || object$inv > 0) joint <- FALSE
+
   eig <- object$eig
 
   bf <- object$bf
@@ -165,12 +168,15 @@ ancestral.pml <- function(object, type = "marginal", ...) {
       result2[[k]][ind] <- data[[1]][ind]
     }
   }
+  result3 <- NULL
+  if(joint) result3 <- joint_pml(object)
   attrib$names <- node_label
   attributes(result2) <- attrib
   attributes(result) <- attrib
   result <- list2df_ancestral(result, result2)
   result2 <- compress.phyDat(result2)
-  erg <- list(tree=tree, data=data, prob=result, state=result2)
+  erg <- list(tree=tree, data=data, prob=result, state=result2,
+              joint_state = result3)
   class(erg) <- "ancestral"
   erg
 }

R/draw_CI.R

@@ -58,8 +58,9 @@ edge_length_matrix <- function(tree, trees, rooted=TRUE){
 ##'               add_edge_length(bs)
 ##' plot(tree_compat)
 ##' add_boxplot(tree_compat, bs, boxwex=.7)
-##' @seealso \code{\link{node.depth.edgelength}}, \code{\link{consensus}},
-##' \code{\link{maxCladeCred}}, \code{\link{add_boxplot}}
+##' @seealso \code{\link[ape::node.depth]{node.depth.edgelength}},
+##' \code{\link[ape]{consensus}}, \code{\link{maxCladeCred}},
+##' \code{\link{add_boxplot}}
 ##' @keywords aplot
 ##' @export
 add_edge_length <- function(tree, trees, fun=\(x)median(na.omit(x)),
@@ -109,7 +110,7 @@ add_edge_length <- function(tree, trees, fun=\(x)median(na.omit(x)),
 ##' add_ci(tree, trees)
 ##' plot(tree, direction="downwards")
 ##' add_boxplot(tree, trees, boxwex=.7)
-##' @seealso \code{\link{plot.phylo}}, \code{\link{plotBS}},
+##' @seealso \code{\link[ape]{plot.phylo}}, \code{\link{plotBS}},
 ##' \code{\link{add_edge_length}}, \code{\link{maxCladeCred}}
 ##' @keywords aplot
 ##' @rdname add_ci

R/phyDat_conversion.R

@@ -30,7 +30,7 @@
 #' @author Klaus Schliep \email{klaus.schliep@@gmail.com}
 #' @seealso [DNAbin()], [as.DNAbin()],
 #' \code{\link{baseFreq}}, \code{\link{glance.phyDat}},
-#' \code{\link{read.dna}}, \code{\link{read.nexus.data}}
+#' \code{\link[ape]{read.dna}}, \code{\link[ape]{read.nexus.data}}
 #' and the chapter 1 in the \code{vignette("phangorn-specials",
 #' package="phangorn")} and the example of \code{\link{pmlMix}} for the use of
 #' \code{allSitePattern}
@@ -158,6 +158,31 @@ as.phyDat.DNAStringSet <- function(x, ...){
 }
 
 
+# @rdname phyDat
+#' @export
+as.StringSet <- function (x, ...){
+  if (inherits(x, "StringSet")) return(x)
+  UseMethod("as.StringSet")
+}
+
+
+
+#' @rdname as.phyDat
+#' @export
+as.StringSet.phyDat <- function(x, ...){
+  if (requireNamespace("Biostrings")){
+    z <- as.character(x)
+    type <- attr(x, "type")
+    seq <- switch(type,
+                  DNA = tolower(apply(z, 1, paste, collapse="")),
+                  AA = toupper(apply(z, 1, paste, collapse="")))
+    if(type=="DNA") return(Biostrings::DNAStringSet(seq))
+    if(type=="AA") return(Biostrings::AAStringSet(seq))
+  }
+  return(NULL)
+}
+
+
 # @rdname phyDat
 #' @export
 as.MultipleAlignment <- function (x, ...){

R/splits.R

@@ -26,7 +26,7 @@
 #' two splits are incompatible.
 #' @note The internal representation is likely to change.
 #' @author Klaus Schliep \email{klaus.schliep@@gmail.com}
-#' @seealso \code{\link{prop.part}}, \code{\link{lento}},
+#' @seealso \code{\link[ape]{prop.part}}, \code{\link{lento}},
 #' \code{\link{as.networx}}, \code{\link{distanceHadamard}},
 #' \code{\link{read.nexus.splits}}
 #' @keywords cluster

R/treeManipulation.R

@@ -430,7 +430,7 @@ addOneTree <- function(tree, subtree, i, node) {
 #' @param edge.length optional numeric vector with edge length
 #' @return an object of class phylo
 #' @author Klaus Schliep \email{klaus.schliep@@gmail.com}
-#' @seealso \code{\link{bind.tree}}
+#' @seealso \code{\link[ape]{bind.tree}}
 #' @keywords cluster
 #' @examples
 #' tree <- rcoal(10)