| housemouse {secr} | R Documentation |
Data of H. N. Coulombe from live trapping of feral house mice (Mus musculus) in a salt marsh, California, USA.
housemouseH. N. Coulombe conducted a live-trapping study on an outbreak of feral house mice in a salt marsh in mid-December 1962 at Ballana Creek, Los Angeles County, California. A square 10 x 10 grid was used with 100 Sherman traps spaced 3 m apart. Trapping was done twice daily, morning and evening, for 5 days.
The dataset was described by Otis et al. (1978) and distributed with their CAPTURE software (now available from https://eesc.usgs.gov/mbr/software/capture.shtml). Otis et al. (1978 p. 62, 68) cite Coulombe's unpublished 1965 master's thesis from the University of California, Los Angeles, California.
The data are provided as a single-session capthist object. There
are two individual covariates: sex (factor levels ‘f’, ‘m’) and age
class (factor levels ‘j’, ‘sa’, ‘a’). The sex of two animals is not
available (NA); it is necessary to drop these records for analyses
using ‘sex’ unless missing values are specifically allowed, as in hcov.
The datasets were originally in the CAPTURE ‘xy complete’ format which for each detection gives the ‘column’ and ‘row’ numbers of the trap (e.g. ‘ 9 5’ for a capture in the trap at position (x=9, y=5) on the grid). Trap identifiers have been recoded as strings with no spaces by inserting zeros (e.g. ‘0905’ in this example).
Sherman traps are designed to capture one animal at a time, but the data include 30 double captures and one occasion when there were 4 individuals in a trap at one time. The true detector type therefore falls between ‘single’ and ‘multi’. Detector type is set to ‘multi’ in the distributed data objects.
Otis et al. (1978) report various analyses including a closure test on the full data, and model selection and density estimation on data from the mornings only.
File ‘examples’ distributed with program CAPTURE.
Otis, D. L., Burnham, K. P., White, G. C. and Anderson, D. R. (1978) Statistical inference from capture data on closed animal populations. Wildlife Monographs 62, 1–135.
plot(housemouse, title = paste("Coulombe (1965), Mus musculus,",
"California salt marsh"), border = 5, rad = 0.5,
gridlines = FALSE)
morning <- subset(housemouse, occ = c(1,3,5,7,9))
summary(morning)
## drop 2 unknown-sex mice
known.sex <- subset(housemouse, !is.na(covariates(housemouse)$sex))
## reveal multiple captures
table(trap(housemouse), occasion(housemouse))
## Not run:
## assess need to distinguish morning and afternoon samples
housemouse.0 <- secr.fit (housemouse, buffer = 20)
housemouse.ampm <- secr.fit (housemouse, model = g0~tcov, buffer = 20,
timecov = c(0,1,0,1,0,1,0,1,0,1))
AIC(housemouse.0, housemouse.ampm)
## End(Not run)