Remove multispati.rtest and multispati.randtest

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)
+}
+
+

_pkgdown.yml

@@ -334,8 +334,6 @@ reference:
   - orthobasis.line
   - orthobasis.mat
   - orthobasis.neig
-  - multispati.randtest
-  - multispati.rtest
   - nb2neig
   - neig
   - neig2mat

man/ade4-deprecated.Rd

@@ -15,6 +15,8 @@
   - \code{freq2genet}: replaced by \code{df2genind} and \code{genind2genpop} in the \code{adegenet} package \cr
   - \code{fuzzygenet}: replaced by \code{df2genind} in the \code{adegenet} package \cr
   - \code{multispati}: replaced by \code{multispati} in the \code{adespatial} package \cr
+  - \code{multispati.rtest} \cr
+  - \code{multispati.randtest} \cr
   - \code{optimEH}: replaced by \code{optimEH} in the \code{adiv} package \cr
   - \code{orisaved}: replaced by \code{orisaved} in the \code{adiv} package \cr
   - \code{orthogram}: replaced by \code{orthogram} in the \code{adephylo} package \cr