Merge pull request #168 from KlausVigo/master

sync Armadillo

.Rbuildignore

@@ -16,3 +16,5 @@
 ^vignettes/MLbyHand_cache$
 ^vignettes/AdvancedFeatures_cache$
 ^vignettes/logo.png
+^codemeta\.json$
+^codecov\.yml$

.github/workflows/recheck.yml

@@ -0,0 +1,18 @@
+on:
+  workflow_dispatch:
+    inputs:
+      which:
+        type: choice
+        description: Which dependents to check
+        options:
+        - strong
+        - most
+
+name: Reverse dependency check
+
+jobs:
+  revdep_check:
+    name: Reverse check ${{ inputs.which }} dependents
+    uses: r-devel/recheck/.github/workflows/recheck.yml@v1
+    with:
+      which: ${{ inputs.which }}

.github/workflows/test-coverage.yaml

@@ -8,43 +8,54 @@ on:
 
 name: test-coverage
 
+permissions: read-all
+
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: phangorn
 Title: Phylogenetic Reconstruction and Analysis
-Version: 2.12.0.900
+Version: 3.0.0.0
 Authors@R: 
     c(person("Klaus", "Schliep", role = c("aut", "cre"),
              email = "[email protected]",
@@ -38,12 +38,14 @@ URL: https://github.com/KlausVigo/phangorn,
     https://klausvigo.github.io/phangorn/
 BugReports: https://github.com/KlausVigo/phangorn/issues
 Depends:
-    ape (>= 5.7),
+    ape (>= 5.8),
     R (>= 4.1.0)
 Imports:
     digest,
     fastmatch,
     generics,
+    ggseqlogo,
+    ggplot2,
     graphics,
     grDevices,
     igraph (>= 1.0),
@@ -62,18 +64,19 @@ Suggests:
     rgl,
     rmarkdown,
     seqinr,
-    seqLogo,
+    testthat (>= 3.0.0),
     tinytest,
+    vdiffr,
     xtable
 LinkingTo:
-    Rcpp, RcppArmadillo
-Remotes: github::emmanuelparadis/ape
+    Rcpp
 VignetteBuilder: 
     knitr,
     utils
 biocViews: Software, Technology, QualityControl
 Encoding: UTF-8
 Repository: CRAN
 Roxygen: list(old_usage = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Language: en-US
+Config/testthat/edition: 3

NAMESPACE

@@ -19,9 +19,13 @@ S3method(as.data.frame,phyDat)
 S3method(as.matrix,splits)
 S3method(as.networx,phylo)
 S3method(as.networx,splits)
+S3method(as.phyDat,AAStringSet)
+S3method(as.phyDat,AAbin)
+S3method(as.phyDat,DNAStringSet)
 S3method(as.phyDat,DNAbin)
 S3method(as.phyDat,MultipleAlignment)
 S3method(as.phyDat,alignment)
+S3method(as.phyDat,ancestral)
 S3method(as.phyDat,character)
 S3method(as.phyDat,data.frame)
 S3method(as.phyDat,factor)
@@ -40,6 +44,8 @@ S3method(cbind,phyDat)
 S3method(cophenetic,networx)
 S3method(cophenetic,splits)
 S3method(glance,phyDat)
+S3method(glance,pml)
+S3method(glance,pmlMix)
 S3method(hash,multiPhylo)
 S3method(hash,phylo)
 S3method(identify,networx)
@@ -55,6 +61,7 @@ S3method(plot,pml)
 S3method(plot,pmlCluster)
 S3method(plot,pmlPart)
 S3method(print,SOWH)
+S3method(print,ancestral)
 S3method(print,codonTest)
 S3method(print,phyDat)
 S3method(print,pml)
@@ -97,12 +104,14 @@ export(addTrivialSplits)
 export(add_boxplot)
 export(add_ci)
 export(add_edge_length)
+export(add_support)
 export(allCircularSplits)
 export(allCompat)
 export(allDescendants)
 export(allSitePattern)
 export(allSplits)
 export(allTrees)
+export(ancestral)
 export(ancestral.pars)
 export(ancestral.pml)
 export(as.Matrix)
@@ -123,6 +132,7 @@ export(coalSpeciesTree)
 export(codon2dna)
 export(codonTest)
 export(compatible)
+export(composition_test)
 export(consensusNet)
 export(coords)
 export(createLabel)
@@ -140,10 +150,13 @@ export(dist.p)
 export(distanceHadamard)
 export(distinct.splits)
 export(diversity)
+export(dna2aa)
 export(dna2codon)
 export(edQt)
 export(fhm)
 export(fitch)
+export(gap_as_ambiguous)
+export(gap_as_state)
 export(genlight2phyDat)
 export(getClans)
 export(getClips)
@@ -154,10 +167,13 @@ export(glance)
 export(h2st)
 export(h4st)
 export(hadamard)
+export(has_gap_state)
 export(hash)
+export(keep_as_tip)
 export(ldfactorial)
 export(lento)
 export(lli)
+export(ltg2amb)
 export(map_duplicates)
 export(mast)
 export(matchSplits)
@@ -184,6 +200,7 @@ export(phyDat2alignment)
 export(plotAnc)
 export(plotBS)
 export(plotRates)
+export(plotSeqLogo)
 export(plot_gamma_plus_inv)
 export(pml)
 export(pml.control)
@@ -203,7 +220,6 @@ export(rNNI)
 export(rSPR)
 export(random.addition)
 export(ratchet.control)
-export(read.aa)
 export(read.nexus.dist)
 export(read.nexus.networx)
 export(read.nexus.partitions)
@@ -218,17 +234,20 @@ export(simSeq)
 export(splitsNetwork)
 export(sprdist)
 export(superTree)
+export(supgma)
 export(threshStateC)
 export(tidy)
 export(transferBootstrap)
 export(treedist)
 export(upgma)
 export(wRF.dist)
 export(wpgma)
+export(write.ancestral)
 export(write.nexus.dist)
 export(write.nexus.networx)
 export(write.nexus.splits)
 export(write.phyDat)
+export(write.pml)
 export(write.splits)
 export(writeDist)
 import(Rcpp)
@@ -243,6 +262,14 @@ importFrom(Matrix,sparseMatrix)
 importFrom(fastmatch,fmatch)
 importFrom(generics,glance)
 importFrom(generics,tidy)
+importFrom(ggplot2,facet_grid)
+importFrom(ggplot2,facet_wrap)
+importFrom(ggplot2,ggplot)
+importFrom(ggplot2,scale_x_continuous)
+importFrom(ggseqlogo,geom_logo)
+importFrom(ggseqlogo,ggseqlogo)
+importFrom(ggseqlogo,make_col_scheme)
+importFrom(ggseqlogo,theme_logo)
 importFrom(grDevices,adjustcolor)
 importFrom(grDevices,col2rgb)
 importFrom(grDevices,hcl.colors)
@@ -274,9 +301,9 @@ importFrom(graphics,title)
 importFrom(igraph,E)
 importFrom(igraph,all_shortest_paths)
 importFrom(igraph,decompose)
-importFrom(igraph,graph)
 importFrom(igraph,graph_from_adjacency_matrix)
 importFrom(igraph,layout_nicely)
+importFrom(igraph,make_graph)
 importFrom(igraph,shortest_paths)
 importFrom(igraph,topo_sort)
 importFrom(igraph,vcount)
@@ -286,8 +313,12 @@ importFrom(stats,AIC)
 importFrom(stats,BIC)
 importFrom(stats,aggregate)
 importFrom(stats,as.dist)
+importFrom(stats,binomial)
+importFrom(stats,chisq.test)
 importFrom(stats,constrOptim)
 importFrom(stats,cophenetic)
+importFrom(stats,cor)
+importFrom(stats,dbinom)
 importFrom(stats,dgamma)
 importFrom(stats,ecdf)
 importFrom(stats,hclust)
@@ -313,6 +344,7 @@ importFrom(stats,update)
 importFrom(stats,xtabs)
 importFrom(utils,combn)
 importFrom(utils,download.file)
+importFrom(utils,head)
 importFrom(utils,installed.packages)
 importFrom(utils,packageDescription)
 importFrom(utils,read.table)

NEWS

@@ -1,4 +1,45 @@
-    CHANGES in PHANGORN VERSION 2.12.0
+    CHANGES in PHANGORN VERSION 3.0.0
+
+NEW FEATURES
+
+    o new function supgma, performing serial sampled UPGMA
+
+      (Drummond, Rodrigo 2000)
+
+    o new function gap_as_state, treating gaps as a state.
+
+    o new function keep_as_tip allows to prune a tree and keep nodes as a tip
+
+      (suggested by Hedvig Skirgård)
+
+    o nnls now can estimate trees with calibrations and tip dated trees
+
+    o the functions Descendants, Ancestors, Siblings, mrca.phy now also accept a
+
+      character vector for the node argument and not only integers.
+
+    o Ancestral state reconstructionwas in parts rewritten. Output is now an
+
+      object of class ancestral. E.g. 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.
+
+    o plotAnc got an argument scheme allowing to use different color schemes,
+
+      especially for amino acid models shared with image.AAbin.
+
+    o plot.networx gets two additional arguments, direction is in plot.phylo and
+
+      angle to rotate the network.
+
+    o new function composition_test comparing indicating possible problems
+
+      with base / state composition.
+
 
 OTHER CHANGES
 
@@ -12,11 +53,17 @@ OTHER CHANGES
 
       which were implicitly using "estimated".
 
-    o some improvements to pmlPart
+    o some improvements to pmlPart.
+
+    o the sankoff algorithm has been rewritten.
+
+BUG FIXES
+
+    o pml_bb roots the tree, if method is either ultrametric or tipdated. Fixes
 
-    o nicer defaults for plot.pml
+      problem when modelTest object was supplied.
 
-    o the sankoff algorithm has been rewritten
+    o nnls.tree now checks if the tree has singletons.
 
 
     CHANGES in PHANGORN VERSION 2.11.0

R/Coalescent.R

@@ -68,8 +68,13 @@ comp2 <- function(x, y) {
 #' @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.
+#' @examples
+#' ## example in Liu et al. (2010)
+#' tr1 <- read.tree(text = "(((B:0.05,C:0.05):0.01,D:0.06):0.04,A:0.1);")
+#' tr2 <- read.tree(text = "(((A:0.07,C:0.07):0.02,D:0.09):0.03,B:0.12);")
+#' TR <- c(tr1, tr2)
+#' sp_tree <- coalSpeciesTree(TR)
 #' @keywords cluster
-#'
 #' @export
 coalSpeciesTree <- function(tree, X = NULL, sTree = NULL) {
   if (is.null(X)) return(speciesTree(tree))
@@ -98,8 +103,7 @@ coalSpeciesTree <- function(tree, X = NULL, sTree = NULL) {
       Labels = attr(X, "levels"), Size = l, class = "dist",
       Diag = FALSE, Upper = FALSE
     )
-
-    sTree <- upgma(dm, "single")
+    sTree <- as.phylo(hclust(dm, method = "single"))
     # dm of pairwise states
   }
   else {