Spatially Explicit Capture–Recapture for Linear Habitats

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Description

An secr add-on package for linear habitat models.

Details

Package: secr
Type: Package
Version: 1.0.5
Date: 2015-01-11
License: GNU General Public License Version 2 or later

The important functions in secrlinear are:

read.linearmask import and discretize a linear habitat map (route)
networkdistance compute network distances between detectors and points using a linear habitat mask
sim.linearpopn simulate population along linear mask
make.line place detectors along (part of) a linear route

Other useful functions are:

checkmoves check capthist object for extreme movements
showpath interactive examination of network distances
clipmask drop mask points outside buffer distance
rbind.linearmask combine two linear masks
subset.linearmask select part of a linear mask
asgraph convert linear mask to igraph
snapPointsToLinearMask closest point on graph
make.sldf convert coordinates to SpatialLinesDataFrame

Documentation is provided in a vignette ../doc/secrlinear-vignette.pdf and in the pdf version of the help pages ../doc/secrlinear-manual.pdf

The package draws on the packages sp (Pebesma and Bivand 2005) and igraph (Csardi and Nepusz 2006).

In order to fit a linear-habitat model with the secr function secr.fit:

  1. specify a linear mask for the ‘mask’ argument

  2. specify details = list(userdist = networkdistance) so that secr.fit uses network distances rather than Euclidean distances.

An example dataset arvicola is drawn from trapping of water voles Arvicola amphibius in June 1984 along the River Glyme in the U.K. – the relevant linear mask is glymemask.

A more complex linear network (Silverstream) is provided as an ESRI shapefile.

Author(s)

Murray Efford murray.efford@otago.ac.nz

References

Csardi, G. and Nepusz, T. (2006) The igraph software package for complex network research. InterJournal, Complex Systems 1695. http://igraph.org.

Pebesma, E.J. and Bivand, R. S. (2005) Classes and methods for spatial data in R. R News 5(2), http://cran.r-project.org/doc/Rnews/.

See Also

addedges, asgraph, checkmoves, clipmask, deleteedges, linearmask, linearpopn, make.line, make.sldf, networkdistance, plot.linearmask, rbind.linearmask , read.linearmask, showpath, showedges, sim.linearpopn, snapPointsToLinearMask, subset.linearmask

Examples

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## Water voles in June 1984 on the R. Glyme in Oxfordshire, UK
## capture and trap location files are exactly as for a 2-D analysis

olddir <- setwd(system.file("extdata", package = "secrlinear"))
on.exit(setwd(olddir))
arvicola <- read.capthist("Jun84capt.txt", "glymetrap.txt",
             detector = "multi", covname = "sex")

## Import map of linear habitat
## -- from text file of x-y coordinates
glymemask <- read.linearmask(file = "glymemap.txt", spacing = 4)
## -- from a previously constructed SpatialLinesDataFrame
library(maptools)
SLDF <- readShapeSpatial("glymemap")
glymemask <- read.linearmask(data = SLDF, spacing = 4)

## display the mask and capture data
plot (glymemask)
plot(arvicola, add = TRUE, tracks = TRUE)
plot(traps(arvicola), add = TRUE)

## fit model, estimate density
linearfit <- secr.fit(arvicola, mask = glymemask, trace = FALSE,
    details = list(userdist = networkdistance))
predict(linearfit)

## NOTE : the unit of density (D) is animals / km