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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,11 +1,12 @@ | ||
| Package: adehabitat | ||
| Version: 1.3 | ||
| Date: 2005/05/10 | ||
| Version: 1.4 | ||
| Date: 2006/02/21 | ||
| Title: Analysis of habitat selection by animals | ||
| Author: Cl�ment Calenge, contributions from Mathieu Basille | ||
| Author: Cl�ment Calenge, contributions from Mathieu Basille and St�phane Dray | ||
| Maintainer: Cl�ment Calenge <calenge@biomserv.univ-lyon1.fr> | ||
| Depends: R (>= 1.8.0), ade4 | ||
| Suggests: gpclib | ||
| Description: A collection of tools for the analysis of habitat selection by animals | ||
| Encoding: latin1 | ||
| License: GPL version 2 or newer | ||
| Packaged: Wed May 11 10:31:46 2005; hornik | ||
| Packaged: Tue Feb 21 14:33:26 2006; Clement Calenge |
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| @@ -0,0 +1,20 @@ | ||
| "NNCH.area" <- | ||
| function(x, percent=c(95,90,80,70,60,50,40,30,20,10)) | ||
| { | ||
| if (!inherits(x, "NNCH")) | ||
| stop("x should be of class \"NNCH\"") | ||
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| res<-matrix(0,nrow=length(percent), ncol=length(x)) | ||
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| for (kk in 1:length(x)) { | ||
| for (i in 1:length(percent)) | ||
| res[i,kk]<-x[[kk]]$area[max(which(x[[kk]]$area$levels<=percent[i])),2] | ||
| } | ||
| res<-as.data.frame(res) | ||
| row.names(res)<-percent | ||
| names(res)<-names(x) | ||
| class(res) <- c("hrsize", "data.frame") | ||
| attr(res, "units") <- attr(x, "units") | ||
| return(res) | ||
| } | ||
|
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| "NNCH" <- | ||
| function(xy, id=NULL, k=10, unin = c("m", "km"), | ||
| unout = c("ha", "km2", "m2")) | ||
| { | ||
| if (ncol(xy)!=2) | ||
| stop("xy should have two columns") | ||
| if (is.null(id)) | ||
| id<-rep(1,nrow(xy)) | ||
| id<-factor(id) | ||
|
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| if (k>=min(table(id))) | ||
| stop("too large number of neighbors") | ||
| if (nrow(xy)!=length(id)) | ||
| stop("id should have the same length as xy") | ||
| if (min(table(id))<5) | ||
| stop("At least 5 relocations are required to fit an home range") | ||
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| id <- id[!is.na(xy[, 1])] | ||
| xy <- xy[!is.na(xy[, 1]), ] | ||
| id <- id[!is.na(xy[, 2])] | ||
| xy <- xy[!is.na(xy[, 2]), ] | ||
| unin <- match.arg(unin) | ||
| unout <- match.arg(unout) | ||
| class(xy[,1])<-"double" | ||
| class(xy[,2])<-"double" | ||
| if (!require(gpclib)) | ||
| stop("package gpclib required") | ||
| res<-list() | ||
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| for (kk in 1:nlevels(id)) { | ||
| xyt<-xy[id==levels(id)[kk],] | ||
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| li<-list() | ||
| li2<-list() | ||
| lin<-list() | ||
| lin2<-list() | ||
| ar<-0 | ||
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| dij<-as.matrix(dist(xyt)) | ||
| idt<-1:nrow(dij) | ||
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| for (i in 1:nrow(xyt)) { | ||
| iid<-idt[order(dij[i,])][1:k] | ||
| xytmp<-xyt[iid,] | ||
| ch<-chull(xytmp[,1], xytmp[,2]) | ||
| li[[i]]<-as(xytmp[ch,], "gpc.poly") | ||
| lin[[i]]<-iid | ||
| } | ||
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| aa<-unlist(lapply(li, area.poly)) | ||
| li<-li[order(aa)] | ||
| lin<-lin[order(aa)] | ||
| idbis<-idt[order(aa)] | ||
| li2[[1]]<-li[[1]] | ||
| lin2[[1]]<-lin[[1]] | ||
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| for (i in 2:length(li)) { | ||
| li2[[i]]<-union(li2[[i-1]], li[[i]]) | ||
| lin2[[i]]<-unique(c(lin2[[i-1]], lin[[i]])) | ||
| } | ||
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| n<-unlist(lapply(lin2, length))/nrow(xyt) | ||
| ar<-unlist(lapply(li2, area.poly)) | ||
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| cons<-1:length(ar) | ||
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| if (unin == "m") { | ||
| if (unout == "ha") | ||
| ar <- ar/10000 | ||
| if (unout == "km2") | ||
| ar <- ar/1e+06 | ||
| } | ||
| if (unin == "km") { | ||
| if (unout == "ha") | ||
| ar <- ar * 100 | ||
| if (unout == "m2") | ||
| ar <- ar * 1e+06 | ||
| } | ||
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| names(li2)<-round(n*100) | ||
| area<-data.frame(levels=round(n*100,2), area=ar) | ||
| dup<-!duplicated(area) | ||
| area=area[dup,] | ||
| row.names(area)<-1:nrow(area) | ||
| res[[levels(id)[kk]]]<-list(area=area, | ||
| polygons=li2[dup], xy=xyt) | ||
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| } | ||
| attr(res, "units") <- unout | ||
| class(res)<-"NNCH" | ||
| return(res) | ||
| } | ||
|
|
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| "NNCH.rast" <- | ||
| function(y, w) | ||
| { | ||
| x <- y | ||
| if (!inherits(x, "NNCHver")) | ||
| stop("x should be of class NNCHver") | ||
| if (inherits(w, "kasc")) | ||
| w <- getkasc(w, names(w)[1]) | ||
| if (!inherits(w, "asc")) | ||
| stop("w should be of class asc or kasc") | ||
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| ## rastérisation des polygones | ||
| hol<-lapply(lapply(x, function(y) attr(y, "pts")), | ||
| function(y) unlist(lapply(y, function(z) z$hole))) | ||
| xt<-lapply(lapply(x, function(y) attr(y, "pts")), | ||
| function(y) lapply(y, function(z) z$x)) | ||
| yt<-lapply(lapply(x, function(y) attr(y, "pts")), | ||
| function(y) lapply(y, function(z) z$y)) | ||
| res <- list() | ||
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| for (i in 1:length(hol)) { | ||
| rr<-lapply(1:length(xt[[i]]), | ||
| function(j) mcp.rast(data.frame(x=xt[[i]][[j]], | ||
| y = yt[[i]][[j]]), w)) | ||
| rr <- lapply(rr, function(o) {o[is.na(o)] <- 0; return(o)}) | ||
| if (hol[[i]][1]) { | ||
| ee <- -rr[[1]] | ||
| } else { | ||
| ee <- rr[[1]] | ||
| } | ||
| if (length(rr) >1){ | ||
| for (j in 2:length(rr)) { | ||
| if (hol[[i]][j]) | ||
| ee <- ee - rr[[j]] | ||
| if (!hol[[i]][j]) | ||
| ee <- ee + rr[[j]] | ||
| } | ||
| } | ||
| ee[ee==0] <- NA | ||
| res[[i]] <- getascattr(w, ee) | ||
| } | ||
| names(res) <- names(x) | ||
| if (length(res)==1) { | ||
| res<-res[[1]] | ||
| } else { | ||
| res <- as.kasc(res) | ||
| } | ||
| return(res) | ||
| } | ||
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