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Last data update: 2014.03.03

R: Create density contours from a Brownian bridge movement model

bbmm.contour

R Documentation

Create density contours from a Brownian bridge movement model

Description

Calculates and (optionally) plots density contours from a utilization distribution.

Usage

bbmm.contour(x, levels, locations = NULL, plot = TRUE)

Arguments

`x`	An object of class bbmm, which is a list with vectors `x`, `y` and `probabilities`.
`levels`	A numeric vector of desired contour levels (e.g., `c(95, 99)`).
`locations`	(optional) data frame or matrix of `x` and `y` coordinates for original location data used to estimate the Brownian bridge and utilization distribution surface.
`plot`	Logical. If `TRUE`, the countour plot is drawn.

Value

An list with four components.

Components of the returned object are as follows:

`contour`	Requested contour level(s).
`z`	values that separate the specified contour level(s).

Author(s)

Ryan Nielson, Hall Sawyer, and Trent McDonald (WEST, Inc., www.west-inc.com)

Maintainer: Ryan Nielson rnielson@west-inc.com

Examples

data(locations)
BBMM <- brownian.bridge(x=locations$x, y=locations$y, 
            time.lag=locations$time.lag[-1], location.error=20, 
            cell.size=50)
contours <- bbmm.contour(BBMM, levels=c(95, 99), locations=locations, plot=TRUE)

# Create a shapefile with contour lines
# Not run: library(maptools)
# Not run: library(raster)
# Not run: out <- data.frame(x=BBMM$x,y=BBMM$y,z=BBMM$probability)
# Make sure the data is properly projected
# Not run: out.raster <- rasterFromXYZ(out,crs=CRS("+proj=utm +zone=12 +datum=WGS84"),digits=2) 
# Not run: raster.contour <- rasterToContour(out.raster,levels=contours$Z) 
# Not run: raster.contour <- spChFIDs(raster.contour,paste(c(95, 99),"% Contour Line",sep="")) 
# Not run: library(rgdal) # can't be loaded before CRS call in line above
# Not run: writeOGR(obj=raster.contour,dsn=".",layer="BBMM",driver="ESRI Shapefile")

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(BBMM)
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/BBMM/bbmm.contour.Rd_%03d_medium.png", width=480, height=480)
> ### Name: bbmm.contour
> ### Title: Create density contours from a Brownian bridge movement model
> ### Aliases: bbmm.contour
> ### Keywords: ~contour ~Ascii
> 
> ### ** Examples
> 
> data(locations)
> BBMM <- brownian.bridge(x=locations$x, y=locations$y, 
+             time.lag=locations$time.lag[-1], location.error=20, 
+             cell.size=50)
> contours <- bbmm.contour(BBMM, levels=c(95, 99), locations=locations, plot=TRUE)
> 
> # Create a shapefile with contour lines
> # Not run: library(maptools)
> # Not run: library(raster)
> # Not run: out <- data.frame(x=BBMM$x,y=BBMM$y,z=BBMM$probability)
> # Make sure the data is properly projected
> # Not run: out.raster <- rasterFromXYZ(out,crs=CRS("+proj=utm +zone=12 +datum=WGS84"),digits=2) 
> # Not run: raster.contour <- rasterToContour(out.raster,levels=contours$Z) 
> # Not run: raster.contour <- spChFIDs(raster.contour,paste(c(95, 99),"% Contour Line",sep="")) 
> # Not run: library(rgdal) # can't be loaded before CRS call in line above
> # Not run: writeOGR(obj=raster.contour,dsn=".",layer="BBMM",driver="ESRI Shapefile")
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>