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KlausVigo · Aug 27, 2024 · 469b469 · 469b469
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diff --git a/R/Coalescent.R b/R/Coalescent.R
@@ -64,7 +64,7 @@ comp2 <- function(x, y) {
 #' @param sTree A species tree which fixes the topology.
 #' @return The function returns an object of class \code{phylo}.
 #' @author Klaus Schliep \email{klaus.schliep@@gmail.com} Emmanuel Paradies
-#' @seealso \code{\link{speciesTree}}
+#' @seealso \code{\link[ape]{speciesTree}}
 #' @references Liu, L., Yu, L. and Pearl, D. K. (2010) Maximum tree: a
 #' consistent estimator of the species tree. \emph{Journal of Mathematical
 #' Biology}, \bold{60}, 95--106.

diff --git a/R/Densi.R b/R/Densi.R
@@ -97,8 +97,8 @@ add_tiplabels <- function(xy, tip.label, direction, adj, font, srt = 0, cex = 1,
 #' @param \dots further arguments to be passed to plot.
 #' @returns \code{densiTree} returns silently x.
 #' @author Klaus Schliep \email{klaus.schliep@@gmail.com}
-#' @seealso \code{\link{plot.phylo}}, \code{\link{plot.networx}},
-#' \code{\link{jitter}}, \code{\link{rtt}}
+#' @seealso \code{\link[ape]{plot.phylo}}, \code{\link{plot.networx}},
+#' \code{\link{jitter}}, \code{\link[ape]{rtt}}
 #' @references densiTree is inspired from the great
 #' \href{https://www.cs.auckland.ac.nz/~remco/DensiTree/}{DensiTree} program of
 #' Remco Bouckaert.

diff --git a/R/baseFreq.R b/R/baseFreq.R
@@ -17,7 +17,7 @@
 #'
 #' @return  \code{baseFreq} returns a named vector and \code{glance} a one row
 #' \code{data.frame}.
-#' @seealso \code{\link{phyDat}, \link{base.freq}, \link{glance}}
+#' @seealso \code{\link{phyDat}, \link[ape]{base.freq}, \link{glance}}
 #' @author Klaus Schliep
 #' @examples
 #'

diff --git a/R/bootstrap.R b/R/bootstrap.R
@@ -29,8 +29,8 @@
 #' if not supplied the tree with labels supplied in the \code{node.label} slot.
 #' @author Klaus Schliep \email{klaus.schliep@@gmail.com}
 #' @seealso \code{\link{optim.pml}}, \code{\link{pml}},
-#' \code{\link{plot.phylo}}, \code{\link{maxCladeCred}}
-#' \code{\link{nodelabels}},\code{\link{consensusNet}} and
+#' \code{\link[ape]{plot.phylo}}, \code{\link{maxCladeCred}}
+#' \code{\link[ape]{nodelabels}},\code{\link{consensusNet}} and
 #' \code{\link{SOWH.test}} for parametric bootstrap
 #' @references Felsenstein J. (1985) Confidence limits on phylogenies. An
 #' approach using the bootstrap. \emph{Evolution} \bold{39}, 783--791

diff --git a/R/cladePar.R b/R/cladePar.R
@@ -14,7 +14,7 @@
 #' @param \dots Further arguments passed to or from other methods.
 #' @return A list containing the information about the edges and tips.
 #' @author Klaus Schliep \email{klaus.schliep@@gmail.com}
-#' @seealso \code{\link{plot.phylo}}
+#' @seealso \code{\link[ape]{plot.phylo}}
 #' @keywords plot
 #' @examples
 #'

diff --git a/R/codon.R b/R/codon.R
@@ -45,7 +45,7 @@
 #' @return The functions return an object of class \code{phyDat}.
 #' @author Klaus Schliep \email{klaus.schliep@@gmail.com}
 #' @references \url{https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes}
-#' @seealso \code{\link{trans}}, \code{\link{phyDat}} and the chapter 4 in the
+#' @seealso \code{\link[ape]{trans}}, \code{\link{phyDat}} and the chapter 4 in the
 #' \code{vignette("phangorn-specials", package="phangorn")}
 #' @keywords cluster
 #' @examples

diff --git a/R/gap_as_state.R b/R/gap_as_state.R
@@ -10,7 +10,7 @@
 #' @param ambiguous a character which codes for the ambiguous state
 #' @return The functions return an object of class \code{phyDat}.
 #' @author Klaus Schliep \email{klaus.schliep@@gmail.com}
-#' @seealso \code{\link{phyDat}}, \code{\link{ltg2amb}}, \code{\link{latag2n}},
+#' @seealso \code{\link{phyDat}}, \code{\link[ape]{ltg2amb}}, \code{\link{latag2n}},
 #' \code{\link{ancestral.pml}}, \code{\link{gap_as_state}}
 #' @keywords cluster
 #' @examples

diff --git a/R/image_phyDat.R b/R/image_phyDat.R
@@ -7,7 +7,7 @@
 #' @param x	 an object containing sequences, an object of class \code{phyDat}.
 #' @param ... further arguments passed to or from other methods.
 #' @returns Nothing. The function is called for plotting.
-#' @seealso \code{\link{image.DNAbin}}, \code{\link{image.AAbin}}
+#' @seealso \code{\link[ape]{image.DNAbin}}, \code{\link[ape]{image.AAbin}}
 #' @examples
 #' data("chloroplast")
 #' image(chloroplast[, 1:50], scheme="Clustal", show.aa = TRUE)

diff --git a/R/ltg2amb.R b/R/ltg2amb.R
@@ -7,7 +7,7 @@
 #' @param amb character of the ambiguous state t replace the gaps.
 #' @param gap gap parameter to replace.
 #' @returns returns an object of class \code{phyDat}.
-#' @seealso \code{\link{latag2n}}, \code{\link{ancestral.pml}},
+#' @seealso \code{\link[ape]{latag2n}}, \code{\link{ancestral.pml}},
 #' \code{\link{gap_as_state}}
 #' @examples
 #' x <- phyDat(matrix(c("-", "A", "G", "-", "T", "C"), 2, 3))

diff --git a/R/maxCladeCred.R b/R/maxCladeCred.R
@@ -24,10 +24,10 @@
 #' @return a tree (an object of class \code{phylo}) with the highest clade
 #' credibility or a numeric vector of clade credibilities for each tree.
 #' @author Klaus Schliep \email{klaus.schliep@@gmail.com}
-#' @seealso \code{\link{consensus}}, \code{\link{consensusNet}},
-#' \code{\link{prop.part}}, \code{\link{bootstrap.pml}}, \code{\link{plotBS}},
-#' \code{\link{transferBootstrap}}, \code{\link{add_edge_length}},
-#' \code{\link{add_boxplot}}
+#' @seealso \code{\link[ape]{consensus}}, \code{\link{consensusNet}},
+#' \code{\link[ape]{prop.part}}, \code{\link{bootstrap.pml}},
+#' \code{\link{plotBS}}, \code{\link{transferBootstrap}},
+#' \code{\link{add_edge_length}}, \code{\link{add_boxplot}}
 #' @keywords cluster
 #' @importFrom fastmatch fmatch
 #' @examples

diff --git a/R/phyDat_conversion.R b/R/phyDat_conversion.R
@@ -28,7 +28,7 @@
 #' @param ... further arguments passed to or from other methods.
 #' @return The functions return an object of class \code{phyDat}.
 #' @author Klaus Schliep \email{klaus.schliep@@gmail.com}
-#' @seealso [DNAbin()], [as.DNAbin()],
+#' @seealso \code{\link[ape]{DNAbin}}, \code{\link[ape]{as.DNAbin}},
 #' \code{\link{baseFreq}}, \code{\link{glance.phyDat}},
 #' \code{\link[ape]{read.dna}}, \code{\link[ape]{read.nexus.data}}
 #' and the chapter 1 in the \code{vignette("phangorn-specials",

diff --git a/R/phylo.R b/R/phylo.R
@@ -1247,7 +1247,8 @@ pml.fit <- function(tree, data, bf = rep(1 / length(levels), length(levels)),
 #' @author Klaus Schliep \email{klaus.schliep@@gmail.com}
 #' @seealso \code{\link{pml_bb}}, \code{\link{bootstrap.pml}},
 #' \code{\link{modelTest}}, \code{\link{pmlPart}}, \code{\link{pmlMix}},
-#' \code{\link{plot.phylo}}, \code{\link{SH.test}}, \code{\link{ancestral.pml}}
+#' \code{\link[ape]{plot.phylo}}, \code{\link{SH.test}},
+#' \code{\link{ancestral.pml}}
 #' @references Felsenstein, J. (1981) Evolutionary trees from DNA sequences: a
 #' maximum likelihood approach. \emph{Journal of Molecular Evolution},
 #' \bold{17}, 368--376.

diff --git a/R/plotBS.R b/R/plotBS.R
@@ -75,10 +75,10 @@ support <- function(tree, trees, method="FBP", tol=2e-8, scale=TRUE){
 #' \code{trees} is optional and if not supplied the labels supplied
 #' in the \code{node.label} slot will be used.
 #' @author Klaus Schliep \email{klaus.schliep@@gmail.com}
-#' @seealso  \code{\link{plot.phylo}}, \code{\link{add_ci}},
-#' \code{\link{nodelabels}},
-#' \code{\link{prop.clades}}, \code{\link{maxCladeCred}},
-#' \code{\link{transferBootstrap}}, \code{\link{consensus}},
+#' @seealso  \code{\link[ape]{plot.phylo}}, \code{\link{add_ci}},
+#' \code{\link[ape]{nodelabels}},
+#' \code{\link[ape]{prop.clades}}, \code{\link{maxCladeCred}},
+#' \code{\link{transferBootstrap}}, \code{\link[ape]{consensus}},
 #' \code{\link{consensusNet}}
 #' @references Felsenstein J. (1985) Confidence limits on phylogenies. An
 #' approach using the bootstrap. \emph{Evolution} \bold{39}, 783--791

diff --git a/R/plot_pml.R b/R/plot_pml.R
@@ -14,8 +14,8 @@
 #' @return \code{plot.pml} returns invisibly a list with arguments dexcribing the plot.
 #' For further details see the \code{plot.phylo}.
 #' @author Klaus Schliep \email{klaus.schliep@@gmail.com}
-#' @seealso \code{\link{plot.phylo}}, \code{\link{axisPhylo}},
-#' \code{\link{add.scale.bar}}
+#' @seealso \code{\link[ape]{plot.phylo}}, \code{\link[ape]{axisPhylo}},
+#' \code{\link[ape]{add.scale.bar}}
 #' @keywords plot
 #' @examples
 #' fdir <- system.file("extdata/trees", package = "phangorn")

diff --git a/R/pml_bb.R b/R/pml_bb.R
@@ -36,8 +36,8 @@
 #' @param \dots Further arguments passed to or from other methods.
 #' @return \code{pml_bb} returns an object of class pml.
 #' @author Klaus Schliep \email{klaus.schliep@@gmail.com}
-#' @seealso \code{\link{optim.pml}}, \code{\link{modelTest}}, \code{\link{rtt}},
-#' \code{\link{pml.control}}
+#' @seealso \code{\link{optim.pml}}, \code{\link{modelTest}},
+#' \code{\link[ape]{rtt}}, \code{\link{pml.control}}
 #' @keywords cluster
 #' @examples
 #'

diff --git a/R/read.nexus.partitions.R b/R/read.nexus.partitions.R
@@ -48,7 +48,7 @@ read.nexus.charset <- function(file){
 #' @return a list where each element is a 'phyDat' object or an object of class
 #' 'multiphyDat'.
 #' @author Klaus Schliep \email{klaus.schliep@@gmail.com}
-#' @seealso \code{\link{read.nexus.data}}, \code{\link{read.phyDat}}
+#' @seealso \code{\link[ape]{read.nexus.data}}, \code{\link{read.phyDat}}
 #' @keywords cluster
 #' @examples
 #' tree <- rtree(10)

diff --git a/R/read.nexus.splits.R b/R/read.nexus.splits.R
@@ -30,7 +30,7 @@
 #' assumes that different co-variables are tab delimited and the bipartition
 #' are separated with white-space. Comments in square brackets are ignored.
 #' @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.splits}}, \code{\link{as.networx}}
 #' @keywords cluster
 #' @examples

diff --git a/R/transferBootstrap.R b/R/transferBootstrap.R
@@ -13,7 +13,7 @@
 #' the node labels.
 #' @author Klaus Schliep \email{klaus.schliep@@gmail.com}
 #' @seealso  \code{\link{plotBS}}, \code{\link{maxCladeCred}},
-#' \code{\link{drawSupportOnEdges}}
+#' \code{\link[ape]{drawSupportOnEdges}}
 #' @references Lemoine, F., Entfellner, J. B. D., Wilkinson, E., Correia, D.,
 #' Felipe, M. D., De Oliveira, T., & Gascuel, O. (2018). Renewing Felsenstein’s
 #' phylogenetic bootstrap in the era of big data. \emph{Nature},

diff --git a/R/upgma.R b/R/upgma.R
@@ -20,8 +20,8 @@
 #' @return A phylogenetic tree of class \code{phylo}.
 #' @author Klaus Schliep \email{klaus.schliep@@gmail.com}
 #' @seealso \code{\link{hclust}}, \code{\link{dist.hamming}}, \code{\link{NJ}},
-#' \code{\link{as.phylo}}, \code{\link{fastme}}, \code{\link{nnls.tree}},
-#' \code{\link{rtt}}
+#' \code{\link[ape]{as.phylo}}, \code{\link[ape]{fastme}},
+#' \code{\link{nnls.tree}}, \code{\link[ape]{rtt}}
 #' @references Sneath, P. H., & Sokal, R. R. (1973). \emph{Numerical taxonomy.
 #' The principles and practice of numerical classification.}
 #'

diff --git a/man/as.phyDat.Rd b/man/as.phyDat.Rd
diff --git a/man/baseFreq.Rd b/man/baseFreq.Rd
diff --git a/man/bootstrap.pml.Rd b/man/bootstrap.pml.Rd
diff --git a/man/cladePar.Rd b/man/cladePar.Rd
diff --git a/man/coalSpeciesTree.Rd b/man/coalSpeciesTree.Rd
diff --git a/man/densiTree.Rd b/man/densiTree.Rd
diff --git a/man/dna2codon.Rd b/man/dna2codon.Rd
diff --git a/man/gap_as_state.Rd b/man/gap_as_state.Rd
diff --git a/man/image.phyDat.Rd b/man/image.phyDat.Rd
diff --git a/man/ltg2amb.Rd b/man/ltg2amb.Rd
diff --git a/man/maxCladeCred.Rd b/man/maxCladeCred.Rd
diff --git a/man/plot.pml.Rd b/man/plot.pml.Rd
diff --git a/man/plotBS.Rd b/man/plotBS.Rd
diff --git a/man/pml.Rd b/man/pml.Rd
diff --git a/man/pml_bb.Rd b/man/pml_bb.Rd
diff --git a/man/read.nexus.partitions.Rd b/man/read.nexus.partitions.Rd
diff --git a/man/read.nexus.splits.Rd b/man/read.nexus.splits.Rd
diff --git a/man/transferBootstrap.Rd b/man/transferBootstrap.Rd
diff --git a/man/upgma.Rd b/man/upgma.Rd