version 1.8.4

cran · May 4, 2009 · 96040fe · 96040fe
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diff --git a/.Rbuildindex.8939 b/.Rbuildindex.8939
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,16 +1,16 @@
 Package: adehabitat
-Version: 1.8.3
+Version: 1.8.4
 Date: 2009/05/04
 Title: Analysis of habitat selection by animals
 Author: Clement Calenge, contributions from Mathieu Basille, Stephane
         Dray and Scott Fortmann-Roe
 Maintainer: Clement Calenge <clement.calenge@oncfs.gouv.fr>
-Depends: R (>= 2.7.0), ade4
+Depends: R (>= 2.10.0), ade4
 Suggests: gpclib, sp, spatstat, MASS, tkrplot, shapefiles, CircStats
 Description: A collection of tools for the analysis of habitat
         selection by animals
 License: GPL (>= 2)
 URL: https://www.faunalia.it/animove/trac/
-Packaged: 2009-05-04 13:19:21 UTC; calenge
+Packaged: 2011-03-18 13:46:16 UTC; calenge
 Repository: CRAN
-Date/Publication: 2009-05-04 15:35:43
+Date/Publication: 2011-03-19 06:18:30
diff --git a/INDEX b/INDEX
diff --git a/R/debut.r b/R/debut.r
@@ -1,12 +1,12 @@
 ##### Chargement de base
 
 .First.lib <- function(lib, pkg) {
-    msg <- paste("This package requires ade4 to be installed\n\n", "Type:\n",
-                 "demo(rastermaps) for demonstration of raster map analysis\n",
-                 "demo(homerange) for demonstration of home-range estimation\n",
-                 "demo(managltraj) for demonstration of animals trajectory management\n",
-                 "demo(analysisltraj) for demonstration of animals trajectory analysis\n",
-                 "demo(nichehs) for demonstration of niche/habitat selection analysis\n\n", sep="")
+    msg <- paste("Be careful: it is now recommended to use the new",
+                 "packages adehabitatMA, adehabitatLT, adehabitatHR, and adehabitatHS.\n",
+                 "These 4 packages are intended to become the future of adehabitat.\n",
+                 "The \"classical\" version of adehabitat will still be maintained for some\n",
+                 "time, but no new method will be added to the package.\n",
+                 sep="")
     cat(msg)
     require(ade4)
     require(gpclib)

diff --git a/R/engen2008.r b/R/engen2008.r
diff --git a/R/mcp.r b/R/mcp.r
@@ -10,10 +10,10 @@
         stop("At least 5 relocations are required to fit an home range")
 
     ## First remove the missing values
-    xy<-xy[!is.na(xy[,1]),]
-    xy<-xy[!is.na(xy[,2]),]
     id<-id[!is.na(xy[,1])]
     id<-id[!is.na(xy[,2])]
+    xy<-xy[!is.na(xy[,1]),]
+    xy<-xy[!is.na(xy[,2]),]
     id<-factor(id)
 
     ## Computes the centroid of the relocations for each animal

diff --git a/data/albatross.rda b/data/albatross.rda
diff --git a/data/bauges.rda b/data/bauges.rda
diff --git a/data/bear.rda b/data/bear.rda
diff --git a/data/bighorn.rda b/data/bighorn.rda
diff --git a/data/capreochiz.rda b/data/capreochiz.rda
diff --git a/data/capreotf.rda b/data/capreotf.rda
diff --git a/data/chamois.rda b/data/chamois.rda
diff --git a/data/hseal.rda b/data/hseal.rda
diff --git a/data/ibex.rda b/data/ibex.rda
diff --git a/data/ibexraw.rda b/data/ibexraw.rda
diff --git a/data/lynxjura.rda b/data/lynxjura.rda
diff --git a/data/mouflon.rda b/data/mouflon.rda
diff --git a/data/pheasant.rda b/data/pheasant.rda
diff --git a/data/porpoise.rda b/data/porpoise.rda
diff --git a/data/puech.rda b/data/puech.rda
diff --git a/data/puechabon.rda b/data/puechabon.rda
diff --git a/data/puechcirc.rda b/data/puechcirc.rda
diff --git a/data/puechdesIII.rda b/data/puechdesIII.rda
diff --git a/data/rupicabau.rda b/data/rupicabau.rda
diff --git a/data/squirrel.rda b/data/squirrel.rda
diff --git a/data/squirreloc.rda b/data/squirreloc.rda
diff --git a/data/teal.rda b/data/teal.rda
diff --git a/data/vanoise.rda b/data/vanoise.rda
diff --git a/data/whale.rda b/data/whale.rda
diff --git a/man/Chi.Rd b/man/Chi.Rd
diff --git a/man/Extract.ltraj.Rd b/man/Extract.ltraj.Rd
diff --git a/man/NNCH.Rd b/man/NNCH.Rd
diff --git a/man/NNCH.area.Rd b/man/NNCH.area.Rd
diff --git a/man/NNCH.select.Rd b/man/NNCH.select.Rd
diff --git a/man/adehabitat-package.Rd b/man/adehabitat-package.Rd
diff --git a/man/albatross.Rd b/man/albatross.Rd
diff --git a/man/altr.Rd b/man/altr.Rd
diff --git a/man/angles.Rd b/man/angles.Rd
diff --git a/man/area2asc.Rd b/man/area2asc.Rd
diff --git a/man/area2dxf.Rd b/man/area2dxf.Rd
diff --git a/man/as.area.Rd b/man/as.area.Rd
diff --git a/man/as.kasc.Rd b/man/as.kasc.Rd
diff --git a/man/as.ltraj.Rd b/man/as.ltraj.Rd
diff --git a/man/as.sahrlocs.Rd b/man/as.sahrlocs.Rd
diff --git a/man/as.traj.Rd b/man/as.traj.Rd
diff --git a/man/asc2im.Rd b/man/asc2im.Rd
diff --git a/man/ascgen.Rd b/man/ascgen.Rd
diff --git a/man/bauges.Rd b/man/bauges.Rd
diff --git a/man/bear.Rd b/man/bear.Rd
diff --git a/man/bighorn.Rd b/man/bighorn.Rd
diff --git a/man/biv.test.Rd b/man/biv.test.Rd
diff --git a/man/buffer.Rd b/man/buffer.Rd
diff --git a/man/burst.Rd b/man/burst.Rd
diff --git a/man/c.ltraj.Rd b/man/c.ltraj.Rd
diff --git a/man/capreochiz.Rd b/man/capreochiz.Rd
diff --git a/man/capreotf.Rd b/man/capreotf.Rd
diff --git a/man/chamois.Rd b/man/chamois.Rd
diff --git a/man/clusthr.Rd b/man/clusthr.Rd
diff --git a/man/colasc.Rd b/man/colasc.Rd
diff --git a/man/compana.Rd b/man/compana.Rd
diff --git a/man/convnum.Rd b/man/convnum.Rd
diff --git a/man/count.points.id.Rd b/man/count.points.id.Rd
diff --git a/man/cutltraj.Rd b/man/cutltraj.Rd
diff --git a/man/distfacmap.Rd b/man/distfacmap.Rd
diff --git a/man/domain.Rd b/man/domain.Rd
diff --git a/man/dunnfa.Rd b/man/dunnfa.Rd
diff --git a/man/eisera.Rd b/man/eisera.Rd
diff --git a/man/enfa.Rd b/man/enfa.Rd
diff --git a/man/engen2008II.Rd b/man/engen2008II.Rd
diff --git a/man/explore.kasc.Rd b/man/explore.kasc.Rd
diff --git a/man/findmaxasc.Rd b/man/findmaxasc.Rd
diff --git a/man/fpt.Rd b/man/fpt.Rd
diff --git a/man/gdltraj.Rd b/man/gdltraj.Rd
diff --git a/man/getXYcoords.Rd b/man/getXYcoords.Rd
diff --git a/man/getascattr.Rd b/man/getascattr.Rd
diff --git a/man/getcontour.Rd b/man/getcontour.Rd
diff --git a/man/gnesfa.Rd b/man/gnesfa.Rd
diff --git a/man/hbrown.Rd b/man/hbrown.Rd
diff --git a/man/hist.kasc.Rd b/man/hist.kasc.Rd
diff --git a/man/hist.ltraj.Rd b/man/hist.ltraj.Rd
diff --git a/man/histniche.Rd b/man/histniche.Rd
diff --git a/man/hr.rast.Rd b/man/hr.rast.Rd
diff --git a/man/hseal.Rd b/man/hseal.Rd
diff --git a/man/ibex.Rd b/man/ibex.Rd
diff --git a/man/ibexraw.Rd b/man/ibexraw.Rd
diff --git a/man/image.asc.Rd b/man/image.asc.Rd
diff --git a/man/image.sahrlocs.Rd b/man/image.sahrlocs.Rd
diff --git a/man/import.asc.Rd b/man/import.asc.Rd
diff --git a/man/indmove.Rd b/man/indmove.Rd
diff --git a/man/is.regular.Rd b/man/is.regular.Rd
diff --git a/man/is.sd.Rd b/man/is.sd.Rd
diff --git a/man/join.asc.Rd b/man/join.asc.Rd
diff --git a/man/kasc2df.Rd b/man/kasc2df.Rd
diff --git a/man/kasc2spixdf.Rd b/man/kasc2spixdf.Rd
diff --git a/man/kernelUD.Rd b/man/kernelUD.Rd
diff --git a/man/kernelbb.Rd b/man/kernelbb.Rd
diff --git a/man/kernelkc.Rd b/man/kernelkc.Rd
diff --git a/man/kerneloverlap.Rd b/man/kerneloverlap.Rd
diff --git a/man/kselect.Rd b/man/kselect.Rd
@@ -86,7 +86,7 @@ kselect(dudi, factor, weight, scannf = TRUE, nf = 2, ewa = FALSE)
   (iii) the barplot of the eigenvalues of the analysis (each eigenvalue
   measure the mean marginality explained by the axis; (iv) the
   projection of the non-recentred marginality vectors on the factorial
-  plane (the origin of the arrow indicates the average used habitat
+  plane (the origin of the arrow indicates the average available habitat
   conditions, and the end of the arrow indicates the average used
   conditions); (v) the projection of the resource units available to
   each animal on the first factorial plane and (vi) the coordinates of

diff --git a/man/kver.Rd b/man/kver.Rd
diff --git a/man/labcon.Rd b/man/labcon.Rd
diff --git a/man/lowres.Rd b/man/lowres.Rd
diff --git a/man/lynxjura.Rd b/man/lynxjura.Rd
diff --git a/man/madifa.Rd b/man/madifa.Rd
diff --git a/man/mahasuhab.Rd b/man/mahasuhab.Rd
diff --git a/man/managNAkasc.Rd b/man/managNAkasc.Rd
diff --git a/man/mcp.Rd b/man/mcp.Rd
diff --git a/man/mcp.rast.Rd b/man/mcp.rast.Rd
diff --git a/man/mindistkeep.Rd b/man/mindistkeep.Rd
diff --git a/man/modpartltraj.Rd b/man/modpartltraj.Rd
diff --git a/man/morphology.Rd b/man/morphology.Rd
diff --git a/man/mouflon.Rd b/man/mouflon.Rd
diff --git a/man/niche.test.Rd b/man/niche.test.Rd
diff --git a/man/offsetdate.Rd b/man/offsetdate.Rd
diff --git a/man/perarea.Rd b/man/perarea.Rd
diff --git a/man/pheasant.Rd b/man/pheasant.Rd
diff --git a/man/plot.area.Rd b/man/plot.area.Rd
diff --git a/man/plot.ltraj.Rd b/man/plot.ltraj.Rd
diff --git a/man/plot.sahrlocs.Rd b/man/plot.sahrlocs.Rd
diff --git a/man/plotltr.Rd b/man/plotltr.Rd
diff --git a/man/porpoise.Rd b/man/porpoise.Rd
diff --git a/man/predict.enfa.Rd b/man/predict.enfa.Rd
diff --git a/man/puech.Rd b/man/puech.Rd
diff --git a/man/puechabon.Rd b/man/puechabon.Rd
diff --git a/man/puechcirc.Rd b/man/puechcirc.Rd
diff --git a/man/puechdesIII.Rd b/man/puechdesIII.Rd
diff --git a/man/qqchi.Rd b/man/qqchi.Rd
diff --git a/man/rand.kselect.Rd b/man/rand.kselect.Rd
diff --git a/man/randtest.enfa.Rd b/man/randtest.enfa.Rd
diff --git a/man/redisltraj.Rd b/man/redisltraj.Rd
diff --git a/man/rotxy.Rd b/man/rotxy.Rd
diff --git a/man/rupicabau.Rd b/man/rupicabau.Rd
diff --git a/man/sahrlocs2kselect.Rd b/man/sahrlocs2kselect.Rd
diff --git a/man/sahrlocs2niche.Rd b/man/sahrlocs2niche.Rd
diff --git a/man/scatter.enfa.Rd b/man/scatter.enfa.Rd
diff --git a/man/scatterniche.Rd b/man/scatterniche.Rd
diff --git a/man/schoener.Rd b/man/schoener.Rd
diff --git a/man/set.limits.Rd b/man/set.limits.Rd
diff --git a/man/setNA.Rd b/man/setNA.Rd
diff --git a/man/setmask.Rd b/man/setmask.Rd
diff --git a/man/sett0.Rd b/man/sett0.Rd
diff --git a/man/showNAltraj.Rd b/man/showNAltraj.Rd
diff --git a/man/simm.bb.Rd b/man/simm.bb.Rd
diff --git a/man/simm.brown.Rd b/man/simm.brown.Rd
diff --git a/man/simm.crw.Rd b/man/simm.crw.Rd
diff --git a/man/simm.levy.Rd b/man/simm.levy.Rd
diff --git a/man/simm.mba.Rd b/man/simm.mba.Rd
diff --git a/man/simm.mou.Rd b/man/simm.mou.Rd
diff --git a/man/sliwinltr.Rd b/man/sliwinltr.Rd
diff --git a/man/speed.Rd b/man/speed.Rd
diff --git a/man/squirrel.Rd b/man/squirrel.Rd
diff --git a/man/squirreloc.Rd b/man/squirreloc.Rd
diff --git a/man/storemapattr.Rd b/man/storemapattr.Rd
diff --git a/man/subsample.Rd b/man/subsample.Rd
diff --git a/man/subsetmap.Rd b/man/subsetmap.Rd
diff --git a/man/teal.Rd b/man/teal.Rd
diff --git a/man/trajdyn.Rd b/man/trajdyn.Rd
diff --git a/man/typeII2typeI.Rd b/man/typeII2typeI.Rd
diff --git a/man/vanoise.Rd b/man/vanoise.Rd
diff --git a/man/wawotest.Rd b/man/wawotest.Rd
diff --git a/man/whale.Rd b/man/whale.Rd
diff --git a/man/which.ltraj.Rd b/man/which.ltraj.Rd
diff --git a/man/wi.Rd b/man/wi.Rd
diff --git a/src/tests.c b/src/tests.c
@@ -5281,7 +5281,7 @@ void regroufacasc(double **asce, double **ascs, int *np,
 {
     /* declaration of variables */
     int i, j, k, l, m, dr, fr, dc, fc, nre, nrs;
-    int nce, ncs, nl, *ll, max, vm, na, *vecmax;
+    int nce, ncs, nl, *ll, max, vm, na, *vecmax, *vecmaxind;
 
     /* Memory allocation */
     nre = asce[0][0];
@@ -5321,7 +5321,7 @@ void regroufacasc(double **asce, double **ascs, int *np,
 		/* One computes the maximum number */
 		vm = ll[1];
 		for (k = 2; k <= nl; k++) {
-		    if (ll[k] >= vm) {
+		    if (ll[k] > vm) {
 			vm = ll[k];
 		    }
 		}
@@ -5336,19 +5336,27 @@ void regroufacasc(double **asce, double **ascs, int *np,
 
 		/* one identifies the levels for which the number is max */
 		vecintalloc(&vecmax, max);
+		vecintalloc(&vecmaxind, max);
+		for (l=1; l <=max; l++) {
+		    vecmaxind[l] = l;
+		}
+
 		l = 1;
 		for (k = 1; k<=nl; k++) {
 		    if (ll[k] == vm) {
-			vecmax[1] = k;
+			vecmax[l] = k;
+			l++;
 		    }
 		}
 
 		/* Random sample of the levels in case of equality */
-		if (max > 1) {
-		    getpermutation(vecmax, i*j); /* random row */
+		if (max > 1) {		    
+		    getpermutation(vecmaxind, i*j); /* random row */
 		}
-		ascs[i][j] = (double) vecmax[1];
+		ascs[i][j] = (double) vecmax[vecmaxind[1]];
 		freeintvec(vecmax);
+		freeintvec(vecmaxind);
+
 	    } else {
 		ascs[i][j] = -9999;
 	    }
@@ -6197,6 +6205,8 @@ void udbbnoeud(double *XG, double **XY, double *T, double *sig1,
 	integrno(XG, Xtmp1, Xtmp2, &dt, sig1, sig2, alpha, &tmp);
 	*res = *res + (poids * tmp);
     }
+    freevec(Xtmp1);
+    freevec(Xtmp2);
 }