| OVpossum {secr} | R Documentation |
A dataset from long-term capture-recapture trapping of brushtail possums Trichosurus vulpecula in New Zealand.
OVpossumCHA multi-session capthist object of 6 sessions. Sessions are labeled 49–54, corresponding to February 1996, June 1996, September 1996, February 1997, June 1997 and September 1997.
Brushtail possums are 2-4 kg largely arboreal marsupials that have become pests of forests and farmland in New Zealand since their introduction from Australia in the nineteenth century. Their population dynamics in mixed native forest have been studied by capture-recapture in the Orongorongo Valley near Wellington since 1966 (e.g. Crawley 1973, Efford 1998, Efford and Cowan 2004).
From 1996 to 2006, a grid of 167 traps set on the ground at 30-m spacing was operated in an area of about 14 ha for 5 consecutive days three times each year (Efford and Cowan 2004). Each trap could catch only one animal, with rare exceptions when a young ‘backrider’ entered the trap with its mother. All animals were tagged and tattooed for individual identification and released at the site of capture.
A broad shingle riverbed forms a natural boundary on two sides of the study grid. Much of the grid lies on a gently sloping old alluvial fan and recent terraces, but to the southeast the valley side rises steeply and, except where cut by streams, supports beech forest (Nothofagus truncata and Nothofagus solandri solandri) rather than the mixed broadleaf forest of the valley floor.
This dataset relates to six five-day trapping sessions in 1996 and 1997, a time of high and declining density. Possums are long-lived (up to about 15 years) and as adults restrict their movements to a home range of 1-10 ha. Breeding is seasonal, resulting in an influx of newly independent juveniles in the first trapping of each calendar year.
The dataset includes individual covariates not provided by Efford (2012): ‘sex’ (F or M) and ‘Ageclass’ (1 for first year, 2 for older).
A coarse habitat map is provided for the immediate vicinity of the trapping grid as the shapefile ‘OVforest.shp’ in the package ‘extdata’ folder. This distinguishes two forest classes (‘beech’ and ‘non-beech’), and leaves out the shingle riverbed. The distinction between ‘beech’ and ‘non-beech’ is mapped only to a distance of about 120 m from the outermost traps. A text file 'leftbank.txt' in the same folder contains the x- and y- coordinates of the adjoining bank of the Orongorongo River. All coordinates relate to the old New Zealand Map Grid (NZMG), since replaced by the New Zealand Transverse Mercator grid (NZTM2000).
The example code shows how to import the shapefile as a sp
SpatialPolygonsDataFrame object and use it to construct a mask for
secr.fit.
Efford (2012) and unpublished data.
Crawley, M. C. (1973) A live-trapping study of Australian brush-tailed possums, Trichosurus vulpecula (Kerr), in the Orongorongo Valley, Wellington, New Zealand. Australian Journal of Zoology 21, 75–90.
Efford, M. G. (1998) Demographic consequences of sex-biased dispersal in a population of brushtail possums. Journal of Animal Ecology 67, 503–517.
Efford, M. G. (2012) DENSITY 5.0: software for spatially explicit capture-recapture. Department of Mathematics and Statistics, University of Otago, Dunedin, New Zealand. https://www.otago.ac.nz/density/
Efford, M. G. and Cowan, P. E. (2004) Long-term population trend of Trichosurus vulpecula in the Orongorongo Valley, New Zealand. In: The Biology of Australian Possums and Gliders. Edited by R. L. Goldingay and S. M. Jackson. Surrey Beatty & Sons, Chipping Norton. Pp. 471–483.
Ward, G. D. (1978) Habitat use and home range of radio-tagged opossums Trichosurus vulpecula (Kerr) in New Zealand lowland forest. In: The ecology of arboreal folivores. Edited by G. G. Montgomery. Smithsonian Institute Press. Washington, D.C. Pp. 267–287.
## Not run:
library(sf)
summary(OVpossumCH, terse = TRUE)
ovtrap <- traps(OVpossumCH[[1]])
## retrieve and plot the forest map
OVforest <- st_read(system.file("extdata/OVforest.shp", package = "secr"))
OVforest <- as(OVforest, "Spatial")
forestcol <- terrain.colors(6)[c(4,2,2)]
sp::plot(OVforest, col = forestcol)
plot(ovtrap, add = TRUE)
## construct a mask
## we omit forest across the river by selecting only
## forest polygons 1 and 2
ovmask <- make.mask(ovtrap, buffer = 120, type = 'trapbuffer',
poly = OVforest[1:2,], spacing = 7.5, keep.poly = FALSE)
ovmask <- addCovariates(ovmask, OVforest[1:2,])
## display mask
par(mar = c(0,0,0,8))
plot(ovmask, covariate = 'forest', dots = FALSE, col = forestcol)
plot(ovtrap, add = TRUE)
## add the left bank of the Orongorongo River
lines(read.table(system.file("extdata/leftbank.txt", package = "secr")))
## End(Not run)