secrlinear (version 1.2.4)

secrlinear-package: Spatially Explicit Capture--Recapture for Linear Habitats

Description

An secr add-on package for linear habitat models.

Author

Murray Efford

Details

Package:	secrlinear
Type:	Package
Version:	1.2.4
Date:	2024-10-22
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.

References

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

Pebesma, E.J. and Bivand, R. S. (2005) Classes and methods for spatial data in R. R News 5(2), https://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

## 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

inputdir <- system.file("extdata", package = "secrlinear")
arvicola <- read.capthist(captfile = paste0(inputdir, "/Jun84capt.txt"), 
    trapfile = paste0(inputdir, "/glymetrap.txt"), detector = "multi", 
    covname = "sex")

## Import map of linear habitat
## -- from text file of x-y coordinates
glymemask <- read.linearmask(file = paste0(inputdir, "/glymemap.txt"), spacing = 4)
## -- from a previously constructed SpatialLinesDataFrame
SLDF <- as(sf::st_read(paste0(inputdir,"/glymemap.shp")), 'Spatial')
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