Merge branch 'master' of github.com:sdray/ade4

.github/workflows/R-CMD-check.yaml

@@ -30,7 +30,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -58,7 +58,7 @@ jobs:
 
       - uses: r-lib/actions/check-r-package@v2
         with:
-          args: 'c("--no-manual", "--as-cran", "--run-dontrun")'
+          args: 'c("--no-manual", "--as-cran")'
           error-on: '"error"'
           check-dir: '"check"'
 

.github/workflows/build-bin-macOS-M1.yaml

@@ -0,0 +1,56 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: build-macOS-M1
+
+jobs:
+  build-bin-macOS-M1:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-14,              r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          pak-version: devel
+          extra-packages: any::rcmdcheck, any::XML
+          needs: check
+          # See https://github.com/r-lib/actions/issues/559 for the XML issue
+
+      - name: Build
+        run: |
+          install.packages("pkgbuild")
+          pkgbuild::build(".", binary = TRUE)
+        shell: Rscript {0}
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: binaries-for-mac-M1
+          path: /Users/runner/work/ade4/ade4_*.tgz
+

.github/workflows/build-bin-macOS-x64.yaml

@@ -26,7 +26,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -49,7 +49,7 @@ jobs:
           pkgbuild::build(".", binary = TRUE)
         shell: Rscript {0}
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: binaries-for-mac-x64
           path: /Users/runner/work/ade4/ade4_*.tgz

.github/workflows/build-bin-windows.yaml

@@ -26,7 +26,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -49,7 +49,7 @@ jobs:
           pkgbuild::build(".", binary = TRUE)
         shell: Rscript {0}
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: binaries-for-windows
           path: D:/a/ade4/ade4*.zip

.github/workflows/pkgdown.yaml

@@ -20,7 +20,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/revdepcheck.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 }}

DESCRIPTION

@@ -53,6 +53,6 @@ VignetteBuilder:
     knitr
 Description: Tools for multivariate data analysis. Several methods are provided for the analysis (i.e., ordination) of one-table (e.g., principal component analysis, correspondence analysis), two-table (e.g., coinertia analysis, redundancy analysis), three-table (e.g., RLQ analysis) and K-table (e.g., STATIS, multiple coinertia analysis). The philosophy of the package is described in Dray and Dufour (2007) <doi:10.18637/jss.v022.i04>.
 License: GPL (>= 2)
-URL: http://pbil.univ-lyon1.fr/ADE-4/
-BugReports: https://github.com/sdray/ade4/issues
+URL: https://adeverse.github.io/ade4/, http://pbil.univ-lyon1.fr/ADE-4/
+BugReports: https://github.com/adeverse/ade4/issues
 Encoding: UTF-8

NAMESPACE

@@ -232,7 +232,7 @@ export("originality")
 export("haar2level", "mld", "orthobasis.circ", "orthobasis.haar", "orthobasis.line", "orthobasis.mat", "orthobasis.neig", "is.orthobasis")
 
 ## ******* spatial *******
-export("area2link", "area2poly", "area.plot", "dist.neig", "gridrowcol", "multispati.randtest", "mstree", "multispati.rtest", "nb2neig", "neig", "neig2mat", "neig2nb", "poly2area", "scores.neig")
+export("area2link", "area2poly", "area.plot", "dist.neig", "gridrowcol", "mstree", "nb2neig", "neig", "neig2mat", "neig2nb", "poly2area", "scores.neig")
 
 ## ******* misc *********
 export("bwca.dpcoa")
@@ -276,6 +276,8 @@ export("testertracenubisCpp")
 ## "plot.multispati"
 ## "print.multispati"
 ## "plot.multispati"
+## "multispati.randtest"
+## "multispati.rtest"
 
 ## ******* internal utilities *******
 

R/ade4-deprecated.R

@@ -1199,3 +1199,81 @@
     s.match(x$li, x$ls, xax = xax, yax = yax, sub = "Scores and lag scores", csub = 2, clabel = 0.75) 
 
 }
+
+"multispati.randtest" <- function (dudi, listw, nrepet = 999, ...) {
+
+    .Deprecated(new="multispati.randtest", package="ade4", 
+                msg="The 'multispati.randtest' function is now deprecated in 'ade4' and will soon be available in the 'adespatial' package.")
+
+    if(!inherits(dudi,"dudi")) stop ("object of class 'dudi' expected") 
+    if(!inherits(listw,"listw")) stop ("object of class 'listw' expected") 
+    if(listw$style!="W") stop ("object of class 'listw' with style 'W' expected") 
+
+    "testmultispati"<- function(nrepet, nr, nc, tab, mat, lw, cw) {
+        .C("testmultispati", 
+           as.integer(nrepet),
+           as.integer(nr),
+           as.integer(nc),
+           as.double(as.matrix(tab)),
+           as.double(mat),
+           as.double(lw),
+           as.double(cw),
+           inersim=double(nrepet+1),
+           PACKAGE="ade4")$inersim
+    }
+
+    tab<- dudi$tab
+    nr<-nrow(tab)
+    nc<-ncol(tab)
+    mat<-spdep::listw2mat(listw)
+    lw<- dudi$lw
+    cw<- dudi$cw
+    if (!(identical(all.equal(lw,rep(1/nrow(tab), nrow(tab))),TRUE))) {
+        stop ("Not implemented for non-uniform weights")
+    }
+    inersim<- testmultispati(nrepet, nr, nc, tab, mat, lw, cw)
+    inertot<- sum(dudi$eig)
+    inersim<- inersim/inertot
+    obs <- inersim[1]
+    w <- as.randtest(sim = inersim[-1], obs = obs, call = match.call(), ...)
+    return(w)
+}
+
+"multispati.rtest" <- function (dudi, listw, nrepet = 99, ...) {
+
+    .Deprecated(new="multispati.rtest", package="ade4", 
+                msg="The 'multispati.rtest' function is now deprecated in 'ade4' and will soon be available in the 'adespatial' package.")
+
+    if(!inherits(listw,"listw")) stop ("object of class 'listw' expected") 
+    if(listw$style!="W") stop ("object of class 'listw' with style 'W' expected") 
+    if (!(identical(all.equal(dudi$lw,rep(1/nrow(dudi$tab), nrow(dudi$tab))),TRUE))) {
+        stop ("Not implemented for non-uniform weights")
+    }
+
+    n <- length(listw$weights)
+    fun.lag <- function (x) spdep::lag.listw(listw,x,TRUE)
+    fun <- function (permuter = TRUE) {
+        if (permuter) {
+            permutation <- sample(n)
+            y <- dudi$tab[permutation,]
+            yw <- dudi$lw[permutation]
+        } else {
+            y <-dudi$tab
+            yw <- dudi$lw
+        }
+        y <- as.matrix(y)
+        ymoy <- apply(y, 2, fun.lag)
+        ymoy <- ymoy*yw
+        y <- y*ymoy
+        indexmoran <- sum(apply(y,2,sum)*dudi$cw)
+        return(indexmoran)
+    }
+    inertot <- sum(dudi$eig)
+    obs <- fun (permuter = FALSE)/inertot
+    if (nrepet == 0) return(obs)
+    perm <- unlist(lapply(1:nrepet, fun))/inertot
+    w <- as.randtest(obs = obs, sim = perm, call = match.call(), ...)
+    return(w)
+}
+
+

R/loocv.R

@@ -55,7 +55,7 @@ loocv.between <- function(x, nax = 0, progress = FALSE, parallel = FALSE, ...)
         ## The original analysis can be any dudi, so wee need to start from dudiCall$call:
         jcall1 <- dudiCall$call
         ## Change the df argument to discard row #ind1:
-        jcall1[[2]] <- data.frame(eval.parent(jcall1[[2]]))[-ind1, , drop = FALSE]
+        jcall1[[2]] <- data.frame(eval.parent(jcall1[[2]], n = 2))[-ind1, , drop = FALSE]
         ## Check that the scannf argument is set to FALSE:
         if (any(names(jcall1) == "scannf")) jcall1[[which(names(jcall1) == "scannf")]] <- FALSE
         else {