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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,12 +1,12 @@ | ||
| Package: adehabitat | ||
| Version: 1.4 | ||
| Date: 2006/02/21 | ||
| Title: Analysis of habitat selection by animals | ||
| 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: Tue Feb 21 14:33:26 2006; Clement Calenge | ||
| Package: adehabitat | ||
| Version: 1.4-1 | ||
| Date: 2006/02/21 | ||
| Title: Analysis of habitat selection by animals | ||
| Author: Cl�ment Calenge, contributions from Mathieu Basille, St�phane Dray and Scott Fortmann-Roe | ||
| 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: Sat Sep 23 15:32:49 2006; calenge |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,99 +1,99 @@ | ||
| angles Compute Turning Angles - Deprecated | ||
| area2dxf Exportation of Areas | ||
| as.area Objects of Class "area" | ||
| as.kasc Working with Several Raster Maps | ||
| as.ltraj Working with Trajectories in 2D Space: the | ||
| Class ltraj | ||
| as.sahrlocs Exploratory Analysis of Habitat Selection | ||
| as.traj Working with Trajectories in 2D Space - | ||
| Deprecated | ||
| asc2im Conversion of Maps of Class 'asc' and 'im' | ||
| (Package spatstat) | ||
| ascgen Creation of Raster Maps | ||
| bighorn Radio-Tracking of Bighorn Sheeps | ||
| biv.test Bivariate Test | ||
| buffer Compute Buffers | ||
| c.ltraj Combine Bursts of Relocations in Objects of | ||
| Class "ltraj" | ||
| chamois Location of Chamois Groups in the Chartreuse | ||
| Mountains | ||
| colasc Creates a Vector of Colors for a Raster Map of | ||
| Type 'factor' | ||
| compana Compositional Analysis of Habitat Use | ||
| convnum Conversion from Factor to Numeric for Raster | ||
| Map | ||
| count.points.id Number of Points in Each Pixel of a Raster Map | ||
| distfacmap Compute distances to the different levels of a | ||
| factor map | ||
| domain Estimation of the Potential Distribution of a | ||
| Species | ||
| eisera Eigenanalysis of Selection Ratios | ||
| enfa Ecological-Niche Factor Analysis | ||
| Extract.ltraj Extract or Replace Parts of an Object of Class | ||
| ltraj | ||
| gdltraj Working with Trajectories: Specify a Time | ||
| Period | ||
| getascattr Copy the Attributes of an Object of Class 'asc' | ||
| or 'kasc' to another Object | ||
| getcontour Computes the Contour Polygon of a Raster Object | ||
| getXYcoords Computes the X and Y Coordinates of the Pixels | ||
| of a Raster Map | ||
| hist.kasc Histograms of Mapped Variables | ||
| histniche Histograms of the Ecological Niche | ||
| hr.rast Rasterisation of Objects of Class 'area' | ||
| image.asc Displays a Color Image of an Object of Class | ||
| 'asc' | ||
| image.sahrlocs Graphical Display of the Habitat Composition of | ||
| the Home Ranges of Animals Monitored Using | ||
| Radio-Tracking | ||
| import.asc Arcview ASCII Raster File Importation And | ||
| Exportation | ||
| join.asc Finds the Value of Mapped Variables at some | ||
| Specified Locations (Spatial Join) | ||
| kasc2df Conversion of Objects of Class kasc | ||
| kasc2spixdf Conversion of maps from/to the package "sp" | ||
| kernelUD Estimation of Kernel Home-Range | ||
| kselect K-Select Analysis: a Method to Analyse the | ||
| Habitat Selection by Animals | ||
| labcon Labelling Connected Features | ||
| lowres Reducing the Resolution of a Map | ||
| lynxjura Monitoring of Lynx | ||
| mahasuhab Habitat Suitability Mapping with Mahalanobis | ||
| Distances. | ||
| managNAkasc "Cleaning" Objects of Class 'kasc' | ||
| mcp Estimation of the Home Range Using the Minimum | ||
| Convex Polygon Estimator | ||
| mcp.rast Converts a Polygon to Raster | ||
| morphology Morphology: Erosion or Dilatation of Features | ||
| on a Raster Map | ||
| niche.test Monte-Carlo Test on Parameters of the | ||
| Ecological Niche | ||
| NNCH Nearest Neighbor Convex hull | ||
| perarea Compute Areas and Perimeters of Objects of | ||
| Class "area" | ||
| pheasant Radio-Tracking of Pheasants | ||
| plot.area Graphical Display of Objects of Class "area" | ||
| plot.ltraj Graphical Display of an Object of Class "ltraj" | ||
| plot.sahrlocs Exploratory Analysis of Habitat Selection | ||
| predict.enfa Habitat Suitability Maps Built from the ENFA | ||
| puechabon Radio-Tracking Data of Wild Boar | ||
| puechcirc Movements of wild boars tracked at Puechabon | ||
| puechdesIII Habitat Selection by the Wild Boar at Puechabon | ||
| rand.kselect Test of the Third-Order Habitat Selection | ||
| randtest.enfa Randomisation Test for the Ecological Niche | ||
| Factor Analysis | ||
| sahrlocs2kselect Preparation of K-Select Analysis | ||
| sahrlocs2niche OMI Analysis of Radio-Tracking Data | ||
| scatter.enfa Scatter Plot of the Results of the ENFA | ||
| schoener Compute Schoener's ratio | ||
| setmask Applies a Mask on Objects of Class 'asc' or | ||
| 'kasc' | ||
| speed Computes the Speed Between Successive | ||
| Relocations of an Animal - Deprecated | ||
| 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 | ||
| the Vanoise National Parc | ||
| wi Computation of Selection Ratios for Habitat | ||
| Selection Studies. | ||
| angles Compute Turning Angles - Deprecated | ||
| area2dxf Exportation of Areas | ||
| as.area Objects of Class "area" | ||
| as.kasc Working with Several Raster Maps | ||
| as.ltraj Working with Trajectories in 2D Space: the | ||
| Class ltraj | ||
| as.sahrlocs Exploratory Analysis of Habitat Selection | ||
| as.traj Working with Trajectories in 2D Space - | ||
| Deprecated | ||
| asc2im Conversion of Maps of Class 'asc' and 'im' | ||
| (Package spatstat) | ||
| ascgen Creation of Raster Maps | ||
| bighorn Radio-Tracking of Bighorn Sheeps | ||
| biv.test Bivariate Test | ||
| buffer Compute Buffers | ||
| c.ltraj Combine Bursts of Relocations in Objects of | ||
| Class "ltraj" | ||
| chamois Location of Chamois Groups in the Chartreuse | ||
| Mountains | ||
| colasc Creates a Vector of Colors for a Raster Map of | ||
| Type 'factor' | ||
| compana Compositional Analysis of Habitat Use | ||
| convnum Conversion from Factor to Numeric for Raster | ||
| Map | ||
| count.points.id Number of Points in Each Pixel of a Raster Map | ||
| distfacmap Compute distances to the different levels of a | ||
| factor map | ||
| domain Estimation of the Potential Distribution of a | ||
| Species | ||
| eisera Eigenanalysis of Selection Ratios | ||
| enfa Ecological-Niche Factor Analysis | ||
| Extract.ltraj Extract or Replace Parts of an Object of Class | ||
| ltraj | ||
| gdltraj Working with Trajectories: Specify a Time | ||
| Period | ||
| getascattr Copy the Attributes of an Object of Class 'asc' | ||
| or 'kasc' to another Object | ||
| getcontour Computes the Contour Polygon of a Raster Object | ||
| getXYcoords Computes the X and Y Coordinates of the Pixels | ||
| of a Raster Map | ||
| hist.kasc Histograms of Mapped Variables | ||
| histniche Histograms of the Ecological Niche | ||
| hr.rast Rasterisation of Objects of Class 'area' | ||
| image.asc Displays a Color Image of an Object of Class | ||
| 'asc' | ||
| image.sahrlocs Graphical Display of the Habitat Composition of | ||
| the Home Ranges of Animals Monitored Using | ||
| Radio-Tracking | ||
| import.asc Arcview ASCII Raster File Importation And | ||
| Exportation | ||
| join.asc Finds the Value of Mapped Variables at some | ||
| Specified Locations (Spatial Join) | ||
| kasc2df Conversion of Objects of Class kasc | ||
| kasc2spixdf Conversion of maps from/to the package "sp" | ||
| kernelUD Estimation of Kernel Home-Range | ||
| kselect K-Select Analysis: a Method to Analyse the | ||
| Habitat Selection by Animals | ||
| labcon Labelling Connected Features | ||
| lowres Reducing the Resolution of a Map | ||
| lynxjura Monitoring of Lynx | ||
| mahasuhab Habitat Suitability Mapping with Mahalanobis | ||
| Distances. | ||
| managNAkasc "Cleaning" Objects of Class 'kasc' | ||
| mcp Estimation of the Home Range Using the Minimum | ||
| Convex Polygon Estimator | ||
| mcp.rast Converts a Polygon to Raster | ||
| morphology Morphology: Erosion or Dilatation of Features | ||
| on a Raster Map | ||
| niche.test Monte-Carlo Test on Parameters of the | ||
| Ecological Niche | ||
| NNCH Nearest Neighbor Convex hull | ||
| perarea Compute Areas and Perimeters of Objects of | ||
| Class "area" | ||
| pheasant Radio-Tracking of Pheasants | ||
| plot.area Graphical Display of Objects of Class "area" | ||
| plot.ltraj Graphical Display of an Object of Class "ltraj" | ||
| plot.sahrlocs Exploratory Analysis of Habitat Selection | ||
| predict.enfa Habitat Suitability Maps Built from the ENFA | ||
| puechabon Radio-Tracking Data of Wild Boar | ||
| puechcirc Movements of wild boars tracked at Puechabon | ||
| puechdesIII Habitat Selection by the Wild Boar at Puechabon | ||
| rand.kselect Test of the Third-Order Habitat Selection | ||
| randtest.enfa Randomisation Test for the Ecological Niche | ||
| Factor Analysis | ||
| sahrlocs2kselect Preparation of K-Select Analysis | ||
| sahrlocs2niche OMI Analysis of Radio-Tracking Data | ||
| scatter.enfa Scatter Plot of the Results of the ENFA | ||
| schoener Compute Schoener's ratio | ||
| setmask Applies a Mask on Objects of Class 'asc' or | ||
| 'kasc' | ||
| speed Computes the Speed Between Successive | ||
| Relocations of an Animal - Deprecated | ||
| 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 | ||
| the Vanoise National Parc | ||
| wi Computation of Selection Ratios for Habitat | ||
| Selection Studies. |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,68 +1,68 @@ | ||
| "angles" <- | ||
| function (x, id = levels(x$id), burst = levels(x$burst), | ||
| date = NULL, slsp = c("remove", "missing")) | ||
| { | ||
| .Deprecated("as.ltraj") | ||
| if (!inherits(x, "traj")) | ||
| stop("x should be of class \"traj\"") | ||
| slsp <- match.arg(slsp) | ||
|
|
||
| prepangles <- function(x) | ||
| { | ||
| if (!inherits(x, "traj")) | ||
| stop("x should be of class \"traj\"") | ||
| li <- split(x, x$burst) | ||
| foo <- function(y) { | ||
| oo <- unlist(lapply(2:nrow(y), | ||
| function(i) (!all(y[i,c("x","y")]==y[i-1,c("x","y")])))) | ||
| oo <- c(TRUE,oo) | ||
| y <- y[oo,] | ||
| } | ||
| res <- do.call("rbind", lapply(li, foo)) | ||
| return(res) | ||
| } | ||
|
|
||
| x <- getburst(x, burst = burst, id = id, date = date) | ||
| if (slsp=="remove") | ||
| x <- prepangles(x) | ||
| li <- split(x, x$burst) | ||
|
|
||
| foo <- function(x) { | ||
| xy<-as.matrix(x[,c("x","y")]) | ||
| ang<-1:(nrow(xy)-2) | ||
| for (i in 2:(nrow(xy)-1)) { | ||
| na <- 0 | ||
| ref1<-xy[i-1,] | ||
| xyb1<-t(t(xy)-ref1) | ||
| ang1<--atan2(xyb1[i,2],xyb1[i,1]) | ||
|
|
||
| ## calcul de la position de x2 et x3 rotaté | ||
| x2<-c(sqrt(sum(xyb1[i,]^2)), 0) | ||
| if (sum(abs(x2)) < 1e-7) | ||
| na<-1 | ||
| x3b<-x3<-xyb1[i+1,] | ||
| x3b[1]= cos(ang1)*x3[1] - sin(ang1)*x3[2] | ||
| x3b[2]= sin(ang1)*x3[1] + cos(ang1)*x3[2] | ||
| x3<-x3b | ||
|
|
||
| ## et recalcul de l'angle | ||
| x3<-x3-x2 | ||
| if (sum(abs(x3)) < 1e-7) | ||
| na<-1 | ||
| ang[i-1]<-atan2(x3[2],x3[1]) | ||
| if (na > 0.5) | ||
| if (slsp == "missing") | ||
| ang[i - 1] <- NA | ||
| } | ||
| so<-data.frame(id=x$id[-c(1,nrow(xy))], | ||
| x=xy[-c(1,nrow(xy)),1], | ||
| y=xy[-c(1,nrow(xy)),2], | ||
| date=x$date[-c(1,nrow(xy))], | ||
| burst=x$burst[-c(1,nrow(xy))], | ||
| angles=ang) | ||
| } | ||
| lo <- do.call("rbind", lapply(li, foo)) | ||
| row.names(lo) <- 1:nrow(lo) | ||
| return(lo) | ||
| } | ||
|
|
||
| "angles" <- | ||
| function (x, id = levels(x$id), burst = levels(x$burst), | ||
| date = NULL, slsp = c("remove", "missing")) | ||
| { | ||
| .Deprecated("as.ltraj") | ||
| if (!inherits(x, "traj")) | ||
| stop("x should be of class \"traj\"") | ||
| slsp <- match.arg(slsp) | ||
|
|
||
| prepangles <- function(x) | ||
| { | ||
| if (!inherits(x, "traj")) | ||
| stop("x should be of class \"traj\"") | ||
| li <- split(x, x$burst) | ||
| foo <- function(y) { | ||
| oo <- unlist(lapply(2:nrow(y), | ||
| function(i) (!all(y[i,c("x","y")]==y[i-1,c("x","y")])))) | ||
| oo <- c(TRUE,oo) | ||
| y <- y[oo,] | ||
| } | ||
| res <- do.call("rbind", lapply(li, foo)) | ||
| return(res) | ||
| } | ||
|
|
||
| x <- getburst(x, burst = burst, id = id, date = date) | ||
| if (slsp=="remove") | ||
| x <- prepangles(x) | ||
| li <- split(x, x$burst) | ||
|
|
||
| foo <- function(x) { | ||
| xy<-as.matrix(x[,c("x","y")]) | ||
| ang<-1:(nrow(xy)-2) | ||
| for (i in 2:(nrow(xy)-1)) { | ||
| na <- 0 | ||
| ref1<-xy[i-1,] | ||
| xyb1<-t(t(xy)-ref1) | ||
| ang1<--atan2(xyb1[i,2],xyb1[i,1]) | ||
|
|
||
| ## calcul de la position de x2 et x3 rotaté | ||
| x2<-c(sqrt(sum(xyb1[i,]^2)), 0) | ||
| if (sum(abs(x2)) < 1e-7) | ||
| na<-1 | ||
| x3b<-x3<-xyb1[i+1,] | ||
| x3b[1]= cos(ang1)*x3[1] - sin(ang1)*x3[2] | ||
| x3b[2]= sin(ang1)*x3[1] + cos(ang1)*x3[2] | ||
| x3<-x3b | ||
|
|
||
| ## et recalcul de l'angle | ||
| x3<-x3-x2 | ||
| if (sum(abs(x3)) < 1e-7) | ||
| na<-1 | ||
| ang[i-1]<-atan2(x3[2],x3[1]) | ||
| if (na > 0.5) | ||
| if (slsp == "missing") | ||
| ang[i - 1] <- NA | ||
| } | ||
| so<-data.frame(id=x$id[-c(1,nrow(xy))], | ||
| x=xy[-c(1,nrow(xy)),1], | ||
| y=xy[-c(1,nrow(xy)),2], | ||
| date=x$date[-c(1,nrow(xy))], | ||
| burst=x$burst[-c(1,nrow(xy))], | ||
| angles=ang) | ||
| } | ||
| lo <- do.call("rbind", lapply(li, foo)) | ||
| row.names(lo) <- 1:nrow(lo) | ||
| return(lo) | ||
| } | ||
|
|
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