Fix reverse-dependency datelife [1]

.Rbuildignore

@@ -1,14 +1,9 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
-<<<<<<< HEAD
-=======
-<<<<<<< HEAD
-=======
 ^dev$
->>>>>>> origin/master
 ^deprecated$
 ^cran-comments.md$
 ^README.Rmd$
 ^CRAN-RELEASE$
 ^data-raw$
->>>>>>> 647ba4c9ae1104b649cacc901c527de0207b7775
+^revdep$

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

.gitignore

@@ -2,3 +2,6 @@
 .Rhistory
 .RData
 .Ruserdata
+dev/DEV-centroid-decomposition.R
+dev/matchPattern.R
+dev/Untitled.R

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ips
 Version: 0.0.12
-Date: 2019-11-14
+Date: 2024-04-21
 Title: Interfaces to Phylogenetic Software in R
 Authors@R: c(
     person("Christoph", "Heibl", email = "[email protected]", 
@@ -18,6 +18,7 @@ Description: Functions that wrap popular phylogenetic software for sequence
     alignment, masking of sequence alignments, and estimation of phylogenies and
     ancestral character states.
 License: GPL-3
+Language: en-US
 Encoding: UTF-8
 NeedsCompilation: no
 Repository: CRAN

R/aliscore.R

@@ -25,7 +25,7 @@
 #' Waegele and B. Misof. 2010. Parametric and non-parametric masking of
 #' randomness in sequence alignments can be improved and leads to better
 #' resolved trees. \emph{Frontiers in Zoology} \bold{7}: 10.
-#' @references \bold{Aliscore website}: \url{https://www.zfmk.de/en/research/research-centres-and-groups/aliscore}
+#' @references \bold{Aliscore website}: \url{https://bonn.leibniz-lib.de/en/research/research-centres-and-groups/aliscore}
 #' @seealso \code{\link{mafft}} and \code{\link{prank}} for multiple sequence
 #'   alignment; \code{\link{gblocks}} for another alignment masking algorithm.
 #' @examples

R/beastLog.R

@@ -2,7 +2,7 @@
 ## © C. Heibl 2019 (last update 2020-03-13)
 
 #' @title XML Parameter Nodes
-#' @description A collection of paramaeter nodes used in the standard template of BEAST2.
+#' @description A collection of parameter nodes used in the standard template of BEAST2.
 #' @param l A character string giving the name (i.e. \code{id} or \code{idref} attribute) of the desired parameter.
 #' @param i Integer giving the index to a partition, internally generated by \code{rbeauti}.
 #' @param x A list, internally generated by \code{rbeauti}.

R/gblocks.R

@@ -22,7 +22,7 @@
 #'   conservative}. Defaults to the number of positions in the alignment.
 #' @param b4 An integer, the \bold{minimum length of a block}, any integer equal
 #'   to or bigger than 2 is allowed. \emph{Larger} values will \emph{decrease}
-#'   the number of selected positions, i.e. are {more conservative}. Defaults to
+#'   the number of selected positions, i.e. are \emph{more conservative}. Defaults to
 #'   2.
 #' @param b5 A character string indicating the \bold{treatment of gap
 #'   positions}. Three choices are possible. 1. \code{"n"}: \emph{No} gap
@@ -69,7 +69,7 @@
 #'   after removing divergent and ambiguously aligned blocks from protein
 #'   sequence alignments. \emph{Systematic Biology} \bold{56}, 564-577.
 #' @references  \bold{Gblocks website}: 
-#'   \url{http://molevol.cmima.csic.es/castresana/Gblocks.html}
+#'   \url{https://www.biologiaevolutiva.org/jcastresana/Gblocks.html}
 #' @seealso \code{\link{mafft}} and \code{\link{prank}} for multiple sequence
 #'   alignment; \code{\link{aliscore}} for another alignment masking algorithm.
 #' @examples

R/mafft.R

@@ -73,7 +73,7 @@
 #'   method for rapid multiple sequence alignment based on fast Fourier 
 #'   transform. \emph{Nucleid Acids Research} \bold{30}: 3059--3066.
 #'   
-#'   \url{http://mafft.cbrc.jp/alignment/software/index.html}
+#'   \url{https://mafft.cbrc.jp/alignment/software/index.html}
 #' @note \code{mafft} was last updated and tested to work with MAFFT 7.205. If 
 #'   you have problems getting the function to work with a newer version of 
 #'   MAFFT, please contact the package maintainer.

R/mrbayes.R

@@ -9,7 +9,7 @@
 #'   \code{mrbayes.mixed}.
 #' @param file A character string, giving the name of the MrBayes input file.
 #' @param lset A list as returned by \code{\link{mrbayes.prset}} containing the
-#'   parameter setting for the prior distirbutions.
+#'   parameter setting for the prior distributions.
 #' @param prset A list as returned by \code{\link{mrbayes.prset}} containing the
 #'   parameter setting for the prior distributions.
 #' @param mcmc A list as returned by \code{\link{mrbayes.mcmc}} containing the
@@ -39,7 +39,7 @@
 
 #' Ronquist F. & J. P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. \emph{Biometrics} \bold{19}: 1572-1574.
 
-#' MrBayes website: \url{http://mrbayes.sourceforge.net/}.
+#' MrBayes website: \url{https://mrbayes.sourceforge.net/}.
 #' @examples
 #' data(ips.cox1)
 #' x <- ips.cox1[, 100:140] # tiny alignment

R/phylo2mafft.R

@@ -11,7 +11,7 @@
 #' @return A matrix coding the MAFFT-formatted tree, as a side effect the same 
 #'   matrix is written to \code{file}.
 #' @references The MAFFT website:
-#'   \url{http://mafft.cbrc.jp/alignment/software/index.html}
+#'   \url{https://mafft.cbrc.jp/alignment/software/index.html}
 #' @seealso \code{\link{mafft}} for an interface to MAFFT.
 #' @importFrom ape is.binary multi2di
 #' @importFrom utils write.table

R/raxml.R

@@ -75,7 +75,7 @@
 #' @note RAxML is a C program and the source code is not contained in this
 #'   package. This means that in order to run this function you will need to
 #'   install RAxML yourself. See
-#'   \url{http://sco.h-its.org/exelixis/web/software/raxml/} for the most recent
+#'   \url{https://cme.h-its.org/exelixis/web/software/raxml/} for the most recent
 #'   documentation and source code of RAxML. Depending on where you chose to
 #'   install RAxML, you need to adjust the \code{exec} argument.
 #'

R/rbeauti.R

@@ -42,8 +42,9 @@
 #'   \code{rbeauti} is intended to make the definition of large numbers of taxon
 #'   sets easy. The creation of taxon sets can be done via R scripts and the
 #'   resulting XML files can be further modified with BEAUti.
-#' @references The BEAST 2 website:
-#'   \url{http://beast.bio.ed.ac.uk/BEAST_v1.5.x_XML_Reference} Drummond, A.J. &
+#' @references The XML reference at the BEAST 2 website:
+#'   \url{http://beast.community/xml_reference} 
+#'   Drummond, A.J. &
 #'   A. Rambaut. 2007. BEAST: Bayesian evolutionary analysis by sampling trees.
 #'   \emph{BMC Evolutionary Biology} \bold{7}: 240.
 #' @seealso \code{\link{read.beast}}, \code{\link{read.beast.table}}

inst/CITATION

@@ -1,10 +1,9 @@
-citHeader("To cite phyloch in a publication use:")
+citHeader("To cite ips in a publication use:")
 
-citEntry(entry="Misc",
-	title = "PHYLOCH: R language tree plotting tools and interfaces to diverse phylogenetic software packages. http://www.christophheibl.de/Rpackages.html",
+x <- bibentry(bibtype="Misc",
+	title = "IPS: R language interfaces to diverse phylogenetic software packages. http://www.christophheibl.de/Rpackages.html",
         author = as.person("C. Heibl"),
   	year = "2008 onwards",
 
-        textVersion = "Heibl C. 2008 onwards. PHYLOCH: R language tree plotting tools and interfaces to diverse phylogenetic software packages. http://www.christophheibl.de/Rpackages.html.")
-
-citFooter("As phyloch is evolving quickly, you may want to cite also its version number (found with 'library(help = phyloch)').")
+        textVersion = "Heibl C. 2008 onwards. IPS: R language interfaces to diverse phylogenetic software packages. http://www.christophheibl.de/Rpackages.html.",
+        mheader = "To cite phyloch in a publication use:")

inst/NEWS.Rd

@@ -66,7 +66,7 @@
   \subsection{NEW FEATURES}{
     \itemize{
       \item The function \code{mafft} received the additional argument \code{options}, which can be used to request options such as e.g. --adjustdirection that are not build into the function's interface.
-      \item This version includes a new internal function \code{phylo2mafft}, which does exactly the same thing as the RUBY script newick2mafft.rb on the MAFFT website (\url{http://mafft.cbrc.jp/alignment/software/newick2mafft.rb}): it converts a user-defined guide tree into a format readible by MAFFT.
+      \item This version includes a new internal function \code{phylo2mafft}, which does exactly the same thing as the RUBY script newick2mafft.rb on the MAFFT website (\url{https://mafft.cbrc.jp/alignment/software/newick2mafft.rb}): it converts a user-defined guide tree into a format readible by MAFFT.
       \item The functions \code{delete.empty.cells} and \code{fillEndsWithN} are now using Emanuel Paradis' bit-level coding for DNA sequences, which makes them much faster.
     }
   }

man/ips.16S.Rd

@@ -13,7 +13,7 @@ This DNA alignment contains 376 positions of 42 sequences of 16S ribosomal DNA o
 The sequences were downloaded and assembled from the Nucleotide repository at GenBank on February 8, 2014.  
 }
 \references{
-The nucleotide database on the NCBI website: \url{http://www.ncbi.nlm.nih.gov/nuccore}
+The nucleotide database on the NCBI website: \url{https://www.ncbi.nlm.nih.gov/nuccore}
 }
 \examples{
 data(ips.16S)

man/ips.28S.Rd

@@ -15,7 +15,7 @@ This DNA alignment contains 562 positions of 28 sequences of 28S ribosomal DNA o
 The sequences were downloaded and assembled from the Nucleotide repository at GenBank on February 8, 2014. 
 }
 \references{
-The nucleotide database on the NCBI website: \url{http://www.ncbi.nlm.nih.gov/nuccore}
+The nucleotide database on the NCBI website: \url{https://www.ncbi.nlm.nih.gov/nuccore}
 }
 \examples{
 data(ips.28S)

man/ips.cox1.Rd

@@ -15,7 +15,7 @@ This DNA alignment contains 770 positions of 26 sequences of cox1 of the bark be
 The sequences were downloaded and assembled from the Nucleotide repository at GenBank on February 8, 2014. 
 }
 \references{
-The nucleotide database on the NCBI website: \url{http://www.ncbi.nlm.nih.gov/nuccore}
+The nucleotide database on the NCBI website: \url{https://www.ncbi.nlm.nih.gov/nuccore}
 }
 \examples{
 data(ips.cox1)

man/mrbayes.lset.Rd

@@ -12,7 +12,7 @@ mrbayes.lset(..., partition)
 arguments in \code{tag = value} form, or a list of tagged values. The tags must come from the names of model parameters described in the ‘Model Parameters’ section.
 }
   \item{partition}{
-%%     ~~Describe \code{partition} here~~
+a character string giving the labelling for a partion.
 }
 }
 %\details{}
@@ -61,7 +61,7 @@ J.P. Huelsenbeck & Ronquist F. 2001. MrBayes: Bayesian inference of phylogenetic
 
 Ronquist F. & J.P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. \emph{Biometrics} \bold{19}: 1572-1574.
 
-MrBayes website: \url{http://mrbayes.sourceforge.net/}.
+MrBayes website: \url{https://mrbayes.sourceforge.net/}.
 }
 \author{Christoph Heibl}
 %\note{}

man/mrbayes.mcmc.Rd

@@ -123,7 +123,7 @@ J.P. Huelsenbeck & Ronquist F. 2001. MrBayes: Bayesian inference of phylogenetic
 
 Ronquist F. & J.P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. \emph{Biometrics} \bold{19}: 1572-1574.
 
-MrBayes website: \url{http://mrbayes.sourceforge.net/}.
+MrBayes website: \url{https://mrbayes.sourceforge.net/}.
 }
 \author{Christoph Heibl}
 \note{The parameters \bold{reweight} and \bold{filename} cannot be set via \code{mrbayes.mcmc}.}

man/mrbayes.prset.Rd

@@ -45,7 +45,7 @@ J.P. Huelsenbeck & Ronquist F. 2001. MrBayes: Bayesian inference of phylogenetic
 
 Ronquist F. & J.P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. \emph{Biometrics} \bold{19}: 1572-1574.
 
-MrBayes website: \url{http://mrbayes.sourceforge.net/}.
+MrBayes website: \url{https://mrbayes.sourceforge.net/}.
 }
 \author{Christoph Heibl}
 

man/multistate.Rd

@@ -24,7 +24,7 @@ multistateMCMC(phy, traits, model = "ARD", anc.states = TRUE,
   \item{traits}{a \code{data.frame} with two columns. The first column contains the taxon labels, the second column contains the character states.
 }
   \item{model}{
-%%     ~~Describe \code{model} here~~
+a character string to select a model of rate evolution. One of \code{"ER"} (equal rates), \code{"FB"}, \code{"ROW"}, \code{"SYM"}, or \code{"ARD"} (all rates different).
 }
 
   \item{anc.states}{either \code{logical} or a \code{list}, the latter containing the tip labels of those internal nodes, for which the likelihood of ancestral character states should be estimated.
@@ -50,7 +50,7 @@ multistateMCMC(phy, traits, model = "ARD", anc.states = TRUE,
 }
 
 \references{
-The BayesTraits manual: \url{http://www.evolution.rdg.ac.uk/Files/BayesTraits-V1.0-Manual.pdf}.
+The BayesTraits manual: \url{http://www.evolution.reading.ac.uk/BayesTraitsV4.1.1/Files/BayesTraitsV4.1.1-Manual.pdf}.
 
 Pagel, M., A. Meade, and D. Barker. 2004. Bayesian estimation of ancestral character states on phylogenies. \emph{Syst. Biol.} \bold{53}: 673-684.