version 1.1-1

CONTENTS

@@ -339,7 +339,7 @@ URL: ../../../library/habitat/html/speed.html
 Entry: squirrel
 Aliases: squirrel
 Keywords: dataset
-Description: Radio-Tracking of Squirrels
+Description: Radio-Tracking Data of Squirrels
 URL: ../../../library/habitat/html/squirrel.html
 
 Entry: storemapattr

DESCRIPTION

@@ -1,10 +1,10 @@
 Package: adehabitat
-Version: 1.1
-Date: 2004/09/15
+Version: 1.1-1
+Date: 2004/10/04
 Title: Analysis of habitat selection by animals
 Author: Cl�ment Calenge, contributions from Mathieu Basille
 Maintainer: Cl�ment Calenge <calenge@biomserv.univ-lyon1.fr>
 Depends: R (>= 1.8.0), ade4
 Description: A collection of tools for the analysis of habitat selection by animals
 License: GPL version 2 or newer
-Packaged: Thu Sep 23 15:04:00 2004; Clement Calenge
+Packaged: Mon Oct  4 09:27:40 2004; Clement Calenge

INDEX

@@ -74,7 +74,7 @@ setmask                 Applies a Mask on Objects of Class 'asc' or
                         'kasc'
 speed                   Computes the Speed Between Successive
                         Relocations of an Animal
-squirrel                Radio-Tracking of Squirrels
+squirrel                Radio-Tracking Data of Squirrels
 storemapattr            Store attributes of maps of class asc and kasc
 subsetmap               Storing a Part of a Map
 vanoise                 Habitat Use by Three Species of Galliformes in

R/adehabitat.r

@@ -111,99 +111,85 @@ colasc<-function(x, ...)
 ##### import.asc allows to import Arcview ascii raster file
 
 
-import.asc<-function(file, type=c("numeric", "factor"), lev=NULL,
-                     levnb = 1, labnb = 3)
-  {
-    type<-match.arg(type)
-    if (substr(file, nchar(file)-3, nchar(file))!=".asc")
-      stop("not a valid .asc file")
-    if ((type!="numeric")&(type!="factor"))
-      stop("argument type should be \"factor\" or \"numeric\"")
-    if ((type=="numeric")&(!is.null(lev)))
-      stop("lev can be specified only when type is \"factor\" ")
-    if ((type=="factor")&(length(lev)==1))
-      if (!file.exists(lev))
-        stop("lev is not a valid file")
-
-
-### File header reading
-    zz<-file(file, "r")
-    nc<-readLines(zz, 1)
-    nl<-readLines(zz, 1)
-    xll<-readLines(zz, 1)
-    yll<-readLines(zz, 1)
-    cs<-readLines(zz, 1)
-    nas<-readLines(zz, 1)
-
-### Gets the information from the file header
-    cs<-strsplit(cs," ")
-    cs<-as.numeric(cs[[1]][length(cs[[1]])])
-    cornx<-TRUE
-    corny<-TRUE
-    xll<-strsplit(xll," ")
-    if ((xll[[1]][1]=="xllcenter")|(xll[[1]][1]=="XLLCENTER"))
-      cornx<-FALSE
-    xll<-as.numeric(xll[[1]][length(xll[[1]])])
-    yll<-strsplit(yll," ")
-    if ((yll[[1]][1]=="yllcenter")|(xll[[1]][1]=="YLLCENTER"))
-      corny<-FALSE
-    yll<-as.numeric(yll[[1]][length(yll[[1]])])
-    nas<-strsplit(nas," ")
-    nas<-as.numeric(nas[[1]][length(nas[[1]])])
-
-### Temporary file
-    tmp<-readLines(zz)
-    close(zz)
-    file.create("toto230876.tmp")
-    zz<-file("toto230876.tmp", "w")
-    writeLines(tmp, zz)
-    close(zz)
-
-### read the matrix and delete the tmp
-    output<-read.table("toto230876.tmp")
-    file.remove("toto230876.tmp")
-    output<-as.matrix(output)
-    output[output==nas]<-NA
-    output<-t(output)
-    output<-output[,ncol(output):1]
-
-    ## calcul de la table des correspondances
-    if (type=="factor") {
-      if (is.null(lev))
-        lev<-levels(factor(output))
-      if (length(lev)>1) {
-        if (length(lev)!=length(levels(factor(output))))
-          stop("uncorrect length of lev")
-      }
-      if (length(lev)==1) {
-        toto<-read.table(lev, header=TRUE, sep=",")
-        toto<-data.frame(lev=toto[,levnb], hihi=rep(1,nrow(toto)),
-                         lab=toto[,labnb])
-        toto<-toto[order(toto[,1]),]
-        if (nrow(toto)!=nlevels(factor(output)))
-          stop("lev is not a valid correspondence table exported from Arcview")
-        lev<-as.character(toto[,3])
-      }
-
-      ## On remplace les valeurs dans output
-      attr(output, "levels")<-lev
+import.asc<- function (file, type = c("numeric", "factor"), lev = NULL,
+                       levnb = 1, labnb = 3) 
+{
+  type <- match.arg(type)
+  if (substr(file, nchar(file) - 3, nchar(file)) != ".asc") 
+    stop("not a valid .asc file")
+  if ((type != "numeric") & (type != "factor")) 
+    stop("argument type should be \"factor\" or \"numeric\"")
+  if ((type == "numeric") & (!is.null(lev))) 
+    stop("lev can be specified only when type is \"factor\" ")
+  if ((type == "factor") & (length(lev) == 1)) 
+    if (!file.exists(lev)) 
+      stop("lev is not a valid file")
+  zz <- file(file, "r")
+  nc <- readLines(zz, 1)
+  nl <- readLines(zz, 1)
+  xll <- readLines(zz, 1)
+  yll <- readLines(zz, 1)
+  cs <- readLines(zz, 1)
+  nas <- readLines(zz, 1)
+  cs <- strsplit(cs, " ")
+  cs <- as.numeric(cs[[1]][length(cs[[1]])])
+  cornx <- TRUE
+  corny <- TRUE
+  xll <- strsplit(xll, " ")
+  if ((xll[[1]][1] == "xllcenter") | (xll[[1]][1] == "XLLCENTER")) 
+    cornx <- FALSE
+  xll <- as.numeric(xll[[1]][length(xll[[1]])])
+  yll <- strsplit(yll, " ")
+  if ((yll[[1]][1] == "yllcenter") | (xll[[1]][1] == "YLLCENTER")) 
+    corny <- FALSE
+  yll <- as.numeric(yll[[1]][length(yll[[1]])])
+  nas <- strsplit(nas, " ")
+  nas <- as.numeric(nas[[1]][length(nas[[1]])])
+  nc <- strsplit(nc, " ")
+  nc <- as.numeric(nc[[1]][length(nc[[1]])])
+  nl <- strsplit(nl, " ")
+  nl <- as.numeric(nl[[1]][length(nl[[1]])])
+  tmp <- readLines(zz)
+  close(zz)
+  file.create("toto230876.tmp")
+  zz <- file("toto230876.tmp", "w")
+  writeLines(tmp, zz)
+  close(zz)
+  output <-scan("toto230876.tmp", quiet=TRUE)
+  file.remove("toto230876.tmp")
+  output[output == nas] <- NA
+  output<-matrix(c(as.matrix(output)), ncol=nl)
+  output <- output[, ncol(output):1]
+  if (type == "factor") {
+    if (is.null(lev)) 
+      lev <- levels(factor(output))
+    if (length(lev) > 1) {
+      if (length(lev) != length(levels(factor(output)))) 
+        stop("uncorrect length of lev")
     }
-
-    ## setting of the attributes
-    attr(output,"xll")<-xll
-    if (cornx)
-      attr(output,"xll")<-xll+cs/2
-    attr(output,"yll")<-yll
-    if (corny)
-      attr(output,"yll")<-yll+cs/2
-    attr(output,"cellsize")<-cs
-
-    ## Case where output is a factor
-    attr(output, "type")<-type
-
-    class(output)<-"asc"
-    return(output)
+    if (length(lev) == 1) {
+            toto <- read.table(lev, header = TRUE, sep = ",")
+            toto <- data.frame(lev = toto[, levnb],
+                               hihi = rep(1, nrow(toto)),
+                               lab = toto[, labnb])
+            toto <- toto[order(toto[, 1]), ]
+            if (nrow(toto) != nlevels(factor(output))) 
+              stop("lev is not a valid correspondence table exported from Arcview")
+            lev <- as.character(toto[, 3])
+          }
+    attr(output, "levels") <- lev
   }
+  attr(output, "xll") <- xll
+  if (cornx) 
+    attr(output, "xll") <- xll + cs/2
+  attr(output, "yll") <- yll
+  if (corny) 
+    attr(output, "yll") <- yll + cs/2
+  attr(output, "cellsize") <- cs
+  attr(output, "type") <- type
+  class(output) <- "asc"
+  return(output)
+}
 
 
 
@@ -1884,7 +1870,7 @@ print.rand.kselect<-function(x, ...)
     cat("Observed value:", x$global[1], "\n")
     cat("P-value :", x$global[2], "\n")
     cat("\n")
-    cat("Test for each individual\n(to be compared with bonferroni alpha level:",
+    cat("Test of the marginality of each individual\n(to be compared with bonferroni alpha level:",
         x$alpha/nrow(x$marg),"):\n\n")
     print(x$marg, ...)
     cat("\nSign of the mean for each animal and each variable: \n")
@@ -2660,7 +2646,7 @@ print.khr<-function(x, ...)
 
     cat("\nEach animal is a component of the list, and for each animal,\n")
     cat("the following elements are available:\n")
-    cat("$UD       The utilisation distribution (object of class \"asc\")\n")
+    cat("$UD       The utilization distribution (object of class \"asc\")\n")
     cat("$locs     The relocations of the animal\n")
     if (th=="LSCV") {
       cat("$h        A list with the following components:\n")
@@ -2807,7 +2793,8 @@ plot.hrsize<-function(x, ...)
   {
     if (!inherits(x, "hrsize"))
       stop("should be of class hrsize")
-    par(mfrow=n2mfrow(ncol(x)))
+    opar<-par(mfrow=n2mfrow(ncol(x)))
+    on.exit(par(opar))
     for (i in 1:ncol(x)) {
       plot(as.numeric(row.names(x)),
            x[,i],
@@ -2892,6 +2879,7 @@ getverticeshr<-function(x, lev=95)
       ud[!is.na(ud)]<-1
       contour[[i]]<-getcontour(ud)
     }
+    names(contour)<-names(x)
     return(contour)
   }
 
@@ -3806,6 +3794,7 @@ speed<-function(x, id=levels(x$id), burst=levels(x$burst),
   {
     if (!inherits(x, "traj"))
       stop("should be an object of class traj")
+    units<-match.arg(units)
 
     ## sélection des dates
     x<-getburst(x, burst=burst, id=id, date=date)
@@ -4256,10 +4245,10 @@ enfa <- function (kasc, pts, scannf = TRUE, nf = 1)
   co <- matrix(nrow = ncol(tab), ncol = nf+1)
   co[,1] <- mar
   co[,2:(nf+1)] <- (Rs12 %*% eigen(H)$vectors)[,1:nf]
-  f3 <- function(i) co[,i]/sqrt(crossprod(co[,i]))
+  f3 <- function(i) co[,i]/sqrt(crossprod(co[,i])/length(co[,i]))
   c1 <- matrix(unlist(lapply(1:(nf+1), f3)), ncol(tab))
   li <- data.frame(tab %*% c1[,1:(nf+1)])
-  f3 <- function(i) li[,i]/sqrt(crossprod(li[,i]))
+  f3 <- function(i) li[,i]/sqrt(crossprod(li[,i])/length(li[,i]))
   l1 <- matrix(unlist(lapply(1:(nf+1), f3)), nrow(tab))
   co <- data.frame(co)
   c1 <- data.frame(c1)

man/as.area.Rd

@@ -7,7 +7,9 @@
   An object of class \code{area} is a data frame with three variables.
   The first variable is a factor defining the polygons.\cr
   The second and third variables are the xy coordinates of the
-  polygon vertices in the order where they are found.
+  polygon vertices in the order where they are found.  This kind
+  of objects are current in the package \code{ade4}, though this package
+  does not define \code{area} as a special class.
 }
 \usage{
 as.area(x)

man/compana.Rd

@@ -76,9 +76,9 @@ compana(used, avail, test = c("randomisation", "parametric"),
   \item{rank}{the rank of the habitat types.  It is equal to the number
     of \code{"+"} for each habitat type in row of \code{rm}.}
   \item{rmv}{the matrix of statistics used to build \code{rm}.
-    if \code{(test == "parametric")}, the matrix contains the
+    if \code{(test = "parametric")}, the matrix contains the
     values of \code{t}, in the t-test comparing the row and the column
-    habitat.  if \code{(test == "randomisation")}, the matrix contains
+    habitat.  if \code{(test = "randomisation")}, the matrix contains
     the mean difference between the used and available log-ratios (see
     Aebischer et al., 1993).}
   \item{profile}{The profile of preferences: resource types are sorted

man/domain.Rd

@@ -16,7 +16,7 @@ domain(kasc, pts, type = c("value", "potential"), thresh = 0.95)
   \item{type}{a character string. The \code{"value"} of the suitability
     may be returned 
     or the \code{"potential"} area of distribution}
-  \item{thresh}{if \code{value == "potential"}, a threshold value should be
+  \item{thresh}{if \code{value = "potential"}, a threshold value should be
     supplied for the suitability (by default 0.95)}
 }
 \details{
@@ -63,7 +63,9 @@ contour(hsm, add = TRUE)
 
 ## Potential distribution
 hsm <- domain(kasc, pts, type = "potential")
-image(hsm)
+image(elevation, main = "Habitat suitability map")
+image(hsm, add = TRUE, col = "orange")
+points(pts, col = "red", pch = 16)
 
 }
 \keyword{spatial}

man/enfa.Rd

@@ -18,7 +18,7 @@ hist.enfa(x, scores = TRUE, type = c("h", "l"),
   \item{pts}{a data frame with two columns, giving the coordinates of
     the species locations}
   \item{scannf}{logical.  Whether the eigenvalues bar plot should be displayed}
-  \item{nf}{if \code{scannf == FALSE}, an integer indicating the number of kept
+  \item{nf}{if \code{scannf = FALSE}, an integer indicating the number of kept
     specialization axes }
   \item{x}{an object of class \code{enfa}}
   \item{scores}{logical.  If \code{TRUE}, the histograms display
@@ -28,10 +28,10 @@ hist.enfa(x, scores = TRUE, type = c("h", "l"),
   \item{type}{what type of plot should be drawn.  Possible types are:\cr
     * \code{"h"} for histograms,\cr
     * \code{"l"} for kernel density estimates (see \code{?density}).\cr
-    By default, \code{type == "h"} is used.  If \code{type = "l"} is used,
+    By default, \code{type = "h"} is used.  If \code{type = "l"} is used,
     the position of the mean of each distribution is indicated by dotted
     lines}
-  \item{adjust}{if \code{type == "l"}, a parameter used to control the
+  \item{adjust}{if \code{type = "l"}, a parameter used to control the
     bandwidth of the density estimates (see \code{?density})}
   \item{colZ}{color for the histograms of the available pixels}
   \item{colS}{color for the histograms of the used pixels}

man/getascattr.Rd

@@ -21,7 +21,7 @@ getkascattr(xkfrom, xkto)
   \item{type}{a character string giving the type of the map
     (\code{"factor"} for maps of categorical 
     variables, and \code{"numeric"} otherwise)}
-  \item{lev}{if \code{type == "factor"},
+  \item{lev}{if \code{type = "factor"},
     a character vector giving the levels of the mapped variable
     (see \code{help(import.asc)})}
   \item{xkfrom}{an object of class \code{kasc}}

man/getcontour.Rd

@@ -4,8 +4,7 @@
 \description{
   \code{getcontour} computes the contour polygon of a raster object
   of class \code{asc}.  When the object is made of several parts, the
-  function returns one polygon per part.  \cr
-  Warning! holes are not taken into account by the function.
+  function returns one polygon per part.
 }
 \usage{
 getcontour(x)
@@ -17,6 +16,9 @@ getcontour(x)
 \value{
   Returns an object of class \code{area}.
 }
+\section{Warning }{
+  Holes in the polygons are not taken into account by the function.
+}
 \author{ Clément Calenge \email{calenge@biomserv.univ-lyon1.fr} }
 \seealso{ \code{\link{import.asc}} for additionnal information on
   objects of class \code{asc}, \code{\link{as.area}} for

man/hist.kasc.Rd

@@ -13,7 +13,7 @@ hist.kasc(x, type = c("h", "l"), adjust = 1, col = "blue", \dots)
   \item{type}{what type of plot should be drawn.  Possible types are:\cr
     * \code{"h"} for histograms,\cr
     * \code{"l"} for kernel density estimates (see \code{?density}).\cr
-    By default, \code{type == "h"} is used.  If \code{type == "l"} is used,
+    By default, \code{type = "h"} is used.  If \code{type = "l"} is used,
     the position of the mean of each distribution is indicated by dotted
     lines}
   \item{adjust}{if \code{type = "l"}, a parameter used to control the

man/histniche.Rd

@@ -19,10 +19,10 @@ histniche(kasc, pts, type = c("h", "l"), adjust = 1,
   \item{type}{what type of plot should be drawn.  Possible types are:\cr
     * \code{"h"} for histograms,\cr
     * \code{"l"} for kernel density estimates (see \code{?density}).\cr
-    By default, \code{type == "h"} is used.  If \code{type == "l"} is used,
+    By default, \code{type = "h"} is used.  If \code{type = "l"} is used,
     the position of the mean of each distribution is indicated by dotted
     lines}
-  \item{adjust}{if \code{type == "l"}, a parameter used to control the
+  \item{adjust}{if \code{type = "l"}, a parameter used to control the
     bandwidth of the density estimate (see \code{?density})}
   \item{colZ}{color for the histograms of the available pixels}
   \item{colS}{color for the histograms of the used pixels}

man/image.sahrlocs.Rd

@@ -68,7 +68,6 @@ image(sahr, ani = "Chou")
 image(sahr, var = "Elevation")
 
 ## Load and displays the relocations of the animals
-data(puechabon)
 locs <-  puechabon$locs[,c(1,4:5)]
 image(sahr, var = "Elevation", dfidxy = locs, pch = 21)
 }