updates from master

.github/workflows/release-file-system-image.yml

@@ -0,0 +1,17 @@
+# Workflow derived from https://github.com/r-wasm/actions/tree/v1/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  release:
+    # Must republish release to update assets
+    types: [ published ]
+
+name: Build and deploy wasm R package image
+
+jobs:
+  release-file-system-image:
+    uses: r-wasm/actions/.github/workflows/release-file-system-image.yml@v1
+    permissions:
+      # For publishing artifact files to the release
+      contents: write
+      # To download GitHub Packages within action
+      repository-projects: read

.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 }}

NEWS

@@ -1,4 +1,4 @@
-    CHANGES in PHANGORN VERSION 3.0.0
+    CHANGES in PHANGORN VERSION 2.12.0
 
 NEW FEATURES
 
@@ -18,15 +18,21 @@ NEW FEATURES
 
       character vector for the node argument and not only integers.
 
-    o Ancestral state reconstructionwas in parts rewritten. Output is now an
+    o Ancestral state reconstruction was rewritten. anc_pml and anc_pars are now
 
-      object of class ancestral. E.g. ancestral states of constant sites are now
+      prefered over ancestral.pml and ańcestral.pars.
 
-      always this state.
+      Output is now an object of class ancestral, which contains tree and
+
+      reconstructions.
+
+      Joint reconstruction for ML is now available.
+
+      Ancestral states of constant sites are now always this state.
 
     o Improvements to several plot functions to get nicer plots out of the box.
 
-    o Nicer defaults for plot.pml, mainly for rooted trees.
+      Nicer defaults for plot.pml, mainly for rooted trees.
 
     o plotAnc got an argument scheme allowing to use different color schemes,
 
@@ -38,8 +44,7 @@ NEW FEATURES
 
     o new function composition_test comparing indicating possible problems
 
-      with base / state composition.
-
+      with base / state composition as in iqtree.
 
 OTHER CHANGES
 

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.

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.

R/addConfidences.R

@@ -15,7 +15,7 @@
 #' @return The object \code{x} with added bootstrap / MCMC support values.
 #' @author Klaus Schliep \email{klaus.schliep@@gmail.com}
 #' @seealso \code{\link{as.splits}}, \code{\link{as.networx}},
-#' \code{\link{RF.dist}}, \code{\link{plot.phylo}}
+#' \code{\link{RF.dist}}, \code{\link[ape]{plot.phylo}}
 #' @references Schliep, K., Potts, A. J., Morrison, D. A. and Grimm, G. W.
 #' (2017), Intertwining phylogenetic trees and networks.
 #' \emph{Methods Ecol Evol}.\bold{8}, 1212--1220. doi:10.1111/2041-210X.12760