update

kingaa · Feb 14, 2024 · a6f92f7 · a6f92f7
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commit a6f92f7
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Showing 24 changed files with 59 additions and 91 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,5 +1,11 @@
-revdep
 examples
+repo
+revdep
+scripts
+tools
+wiki
+www
+yaml
 tests/Makefile
 tests/(.+?)\.png$
 tests/(.+?)\.pdf$
@@ -8,8 +14,9 @@ inst/doc/Makefile
 inst/doc/(.+?).md
 inst/doc/(.+?).Rmd
 man/roxygen
+Doxyfile
 LICENSE\.md$
-README\.md$
+README\.(.?)$
 CRAN\.md$
 TODO\.md$
 ^\.gitignore$
@@ -32,16 +39,13 @@ TODO\.md$
 \.tests
 Makefile
 rules.mk
-scripts
 lib
-tools
+libs
 library
 check
-www
 ^(.+?)\.pdf
 ^(.+?)\.tar\.gz
 ^(.+?)\.tgz
 ^(.+?)\.zip
-data/primates.csv
 covr.html
 covr.rds
diff --git a/.github/workflows/binary-build.yml b/.github/workflows/binary-build.yml
@@ -19,7 +19,7 @@ jobs:
       fail-fast: false
 
     steps:
-      - uses: actions/checkout@v3.1.0
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -36,7 +36,7 @@ jobs:
           mkdir -p ${{ github.workspace }}/artifacts
           cp ${{ env.release_name }}.tar.gz ${{ github.workspace }}/artifacts
 
-      - uses: actions/upload-artifact@v3.1.1
+      - uses: actions/upload-artifact@v4
         with:
           name: Source tarball
           path: ${{ github.workspace }}/artifacts/${{ env.release_name }}.tar.gz
@@ -54,7 +54,7 @@ jobs:
           - {os: windows-latest, r: 'release', ext: "zip"}
 
     steps:
-      - uses: actions/checkout@v3.1.0
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -74,7 +74,7 @@ jobs:
           mkdir -p ${{ github.workspace }}/artifacts
           cp ../${{ env.release_name }}.${{ matrix.config.ext }} ${{ github.workspace }}/artifacts
 
-      - uses: actions/upload-artifact@v3.1.1
+      - uses: actions/upload-artifact@v4
         with:
           name: ${{ matrix.config.os }}-${{ matrix.config.r }}
           path: ${{ github.workspace }}/artifacts/${{ env.release_name }}.${{ matrix.config.ext }}
diff --git a/.github/workflows/r-cmd-check.yml b/.github/workflows/r-cmd-check.yml
@@ -31,31 +31,9 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
-      _R_CHECK_DEPENDS_ONLY_: false
-      _R_CHECK_ALL_NON_ISO_C_: true
-      _R_CHECK_CODE_ASSIGN_TO_GLOBALENV_: true
-      _R_CHECK_CODE_ATTACH_: true
-      _R_CHECK_CODE_DATA_INTO_GLOBALENV_: true
-      _R_CHECK_CODE_USAGE_VIA_NAMESPACES_: true
-      _R_CHECK_DEPRECATED_DEFUNCT_: true
-      _R_CHECK_EXECUTABLES_EXCLUSIONS_: false
-      _R_CHECK_INSTALL_DEPENDS_: true
-      _R_CHECK_NO_RECOMMENDED_: true
-      _R_CHECK_OVERWRITE_REGISTERED_S3_METHODS_: true
-      _R_CHECK_REPLACING_IMPORTS_: true
-      _R_CHECK_S3_METHODS_NOT_REGISTERED_: true
-      _R_CHECK_SCREEN_DEVICE_: stop
-      _R_CHECK_SRC_MINUS_W_IMPLICIT_: true
-      _R_CHECK_SRC_MINUS_W_UNUSED_: true
-      _R_CHECK_SUGGESTS_ONLY_: true
-      _R_CHECK_TOPLEVEL_FILES_: true
-      _R_CHECK_VC_DIRS_: true
-      _R_CHECK_WALL_FORTRAN_: true
-      _R_CHECK_USE_CODETOOLS_: true
-      _R_CHECK_CODETOOLS_PROFILE_: "suppressLocalUnused=FALSE,suppressPartialMatchArgs=FALSE,suppressParamUnused=TRUE,suppressUndefined=FALSE"
 
     steps:
-      - uses: actions/checkout@v3.1.0
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -69,7 +47,7 @@ jobs:
 
       - uses: r-lib/actions/check-r-package@v2
 
-      - uses: actions/upload-artifact@v3.1.1
+      - uses: actions/upload-artifact@v4
         with:
           name: ${{ matrix.config.os }}-${{ matrix.config.r }}-results
-          path: check
+          path: check/${{ vars.repo_name }}.Rcheck
diff --git a/.github/workflows/test-coverage.yml b/.github/workflows/test-coverage.yml
@@ -18,7 +18,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3.1.0
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:

diff --git a/.gitignore b/.gitignore
@@ -22,6 +22,8 @@
 lib
 library
 check
+repo
+wiki
 www
 tmp
 covr.html

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: ouch
 Type: Package
 Title: Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses
-Version: 2.19-0
-Date: 2023-04-24
+Version: 2.19-1
+Date: 2024-02-14
 Authors@R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="kingaa@umich.edu",comment=c(ORCID="0000-0001-6159-3207")),
 	person(given=c("Marguerite","A."),family="Butler",role=c("ctb")))
 Maintainer: Aaron A. King <kingaa@umich.edu>
@@ -15,7 +15,7 @@ License: GPL-3
 LazyLoad: true
 LazyData: true
 Roxygen: list(roclets = c("collate", "namespace", "rd"), markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 BugReports: https://github.com/kingaa/ouch/issues/
 Encoding: UTF-8
 Collate: 

diff --git a/Makefile b/Makefile
@@ -1,4 +1,4 @@
-REPODIR = ../www
+REPODIR = repo
 INCLUDES=
 HEADERS=
 

diff --git a/R/package.R b/R/package.R
@@ -4,9 +4,8 @@
 #' Multivariate data and complex adaptive hypotheses are supported.
 #' 
 #' @name ouch-package
-#' @aliases ouch
+#' @aliases ouch,package ouch-package
 #' @rdname package
-#' @docType package
 #' @family phylogenetic comparative models
 #' @family methods for ouch trees
 #' @family examples
@@ -40,7 +39,7 @@
 #' @useDynLib ouch, .registration = TRUE
 #' @import methods
 #' @keywords models
-NULL
+"_PACKAGE"
 
 pStop <- function (fn, ...) {
   fn <- as.character(fn)

diff --git a/data/primates.csv b/data/primates.csv
diff --git a/man/package.Rd b/man/package.Rd
diff --git a/tests/ape2ouch.Rout b/tests/ape2ouch.Rout
@@ -1,5 +1,5 @@
 
-R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
+R version 4.3.2 (2023-10-31) -- "Eye Holes"
 Copyright (C) 2023 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 

diff --git a/tests/bapst.Rout.save b/tests/bapst.Rout.save
@@ -1,5 +1,5 @@
 
-R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
+R version 4.3.2 (2023-10-31) -- "Eye Holes"
 Copyright (C) 2023 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
@@ -23,6 +23,6 @@ Type 'q()' to quit R.
 > tr <- with(x,ouchtree(nodes=node,ancestors=ancestor,times=time,labels=species))
 > toc <- Sys.time()
 > print(toc-tic)
-Time difference of 0.005033731 secs
+Time difference of 0.005596876 secs
 > plot(tr)
 > 
diff --git a/tests/bergmann.Rout.save b/tests/bergmann.Rout.save
@@ -1,5 +1,5 @@
 
-R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
+R version 4.3.2 (2023-10-31) -- "Eye Holes"
 Copyright (C) 2023 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 

diff --git a/tests/boot.Rout.save b/tests/boot.Rout.save
@@ -1,5 +1,5 @@
 
-R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
+R version 4.3.2 (2023-10-31) -- "Eye Holes"
 Copyright (C) 2023 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
@@ -52,7 +52,7 @@ btstrp> b5 <- sapply(simdat,function(x)summary(update(h5,data=x))$aic.c)
 btstrp> toc <- Sys.time()
 
 btstrp> print(toc-tic)
-Time difference of 12.61242 secs
+Time difference of 13.27121 secs
 
 btstrp> cat("approximate 95% AIC.c cutoff",signif(quantile(b1-b5,0.95),digits=3),"\n")
 approximate 95% AIC.c cutoff 2.58 

diff --git a/tests/brown.Rout.save b/tests/brown.Rout.save
@@ -1,5 +1,5 @@
 
-R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
+R version 4.3.2 (2023-10-31) -- "Eye Holes"
 Copyright (C) 2023 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 

diff --git a/tests/exacttree.Rout.save b/tests/exacttree.Rout.save
@@ -1,5 +1,5 @@
 
-R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
+R version 4.3.2 (2023-10-31) -- "Eye Holes"
 Copyright (C) 2023 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 

diff --git a/tests/glssoln.Rout.save b/tests/glssoln.Rout.save
@@ -1,5 +1,5 @@
 
-R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
+R version 4.3.2 (2023-10-31) -- "Eye Holes"
 Copyright (C) 2023 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
@@ -27,7 +27,7 @@ $residuals
 [1] NA
 
 Warning message:
-in 'ouch:::glssoln': Choleski decomposition of variance-covariance matrix fails with error: "the leading minor of order 1 is not positive definite". 
+in 'ouch:::glssoln': Choleski decomposition of variance-covariance matrix fails with error: "the leading minor of order 1 is not positive". 
 > try(ouch:::glssoln(matrix(c(1,1,0,1),2,2),c(1,1),matrix(c(1,1,1,1),2,2)))
 $coeff
 [1] NA NA
@@ -36,7 +36,7 @@ $residuals
 [1] NA NA
 
 Warning message:
-in 'ouch:::glssoln': Choleski decomposition of variance-covariance matrix fails with error: "the leading minor of order 2 is not positive definite". 
+in 'ouch:::glssoln': Choleski decomposition of variance-covariance matrix fails with error: "the leading minor of order 2 is not positive". 
 > ouch:::glssoln(matrix(c(1,1,0,1),2,2),c(1,1),matrix(c(2,1,1,2),2,2)) -> x
 > stopifnot(
 +   coeff=all.equal(as.numeric(x$coeff),c(1,0)),

diff --git a/tests/hansen.Rout.save b/tests/hansen.Rout.save
@@ -1,5 +1,5 @@
 
-R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
+R version 4.3.2 (2023-10-31) -- "Eye Holes"
 Copyright (C) 2023 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 

diff --git a/tests/ouchtree.Rout.save b/tests/ouchtree.Rout.save
@@ -1,5 +1,5 @@
 
-R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
+R version 4.3.2 (2023-10-31) -- "Eye Holes"
 Copyright (C) 2023 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 

diff --git a/tests/paint.Rout.save b/tests/paint.Rout.save
@@ -1,5 +1,5 @@
 
-R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
+R version 4.3.2 (2023-10-31) -- "Eye Holes"
 Copyright (C) 2023 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 

diff --git a/tests/plot.Rout.save b/tests/plot.Rout.save
@@ -1,5 +1,5 @@
 
-R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
+R version 4.3.2 (2023-10-31) -- "Eye Holes"
 Copyright (C) 2023 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 

diff --git a/tests/simtree.Rout.save b/tests/simtree.Rout.save
@@ -1,5 +1,5 @@
 
-R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
+R version 4.3.2 (2023-10-31) -- "Eye Holes"
 Copyright (C) 2023 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
@@ -92,7 +92,7 @@ Type 'q()' to quit R.
 > tree <- with(x,ouchtree(node,ancestor,time))
 > toc <- Sys.time()
 > print(toc-tic)
-Time difference of 3.478733 secs
+Time difference of 2.687218 secs
 > 
 > bfit <- brown(data=x[c("A","B")],tree)
 > print(summary(bfit))
@@ -135,7 +135,7 @@ $dof
 > hfit <- hansen(data=x[c("A","B")],tree=tree,regimes=x['reg'],sqrt.alpha=a,sigma=s,fit=F)
 > toc <- Sys.time()
 > print(toc-tic)
-Time difference of 5.732939 secs
+Time difference of 6.222583 secs
 > print(summary(hfit))
 $call
 hansen(data = x[c("A", "B")], tree = tree, regimes = x["reg"], 
@@ -203,7 +203,7 @@ $dof
 > tree <- with(x,ouchtree(node,ancestor,time))
 > toc <- Sys.time()
 > print(toc-tic)
-Time difference of 1.490282 secs
+Time difference of 1.404474 secs
 > 
 > bfit <- brown(data=x[c("A","B")],tree)
 > print(summary(bfit))
@@ -283,7 +283,7 @@ $dof
 > hfit <- hansen(data=x[c("A","B")],tree=tree,regimes=x['reg'],sqrt.alpha=a,sigma=s,fit=F)
 > toc <- Sys.time()
 > print(toc-tic)
-Time difference of 3.648121 secs
+Time difference of 3.714571 secs
 > print(summary(hfit))
 $call
 hansen(data = x[c("A", "B")], tree = tree, regimes = x["reg"],