deermouse {secr} | R Documentation

## Deermouse Live-trapping Datasets

### Description

Data of V. H. Reid from live trapping of deermice (Peromyscus maniculatus) at two sites in Colorado, USA.

### Usage

    deermouse

### Details

Two datasets of V. H. Reid were described by Otis et al. (1978) and distributed with their CAPTURE software (now available from http://www.mbr-pwrc.usgs.gov/software.html). They have been used in several other papers on closed population methods (e.g., Huggins 1991, Stanley and Richards 2005). This description is based on pages 32 and 87–93 of Otis et al. (1978).

Both datasets are from studies in Rio Blanco County, Colorado, in the summer of 1975. Trapping was for 6 consecutive nights. Traps were arranged in a 9 x 11 grid and spaced 50 feet (15.2 m) apart.

The first dataset was described by Otis et al. (1978: 32) as from 'a drainage bottom of sagebrush, gambel oak, and serviceberry with pinyon pine and juniper on the uplands'. By matching with the ‘examples’ file of CAPTURE this was from East Stuart Gulch (ESG).

The second dataset (Otis et al. 1978: 87) was from Wet Swizer Creek or Gulch (WSG) in August 1975. No specific vegetation description is given for this site, but it is stated that Sherman traps were used and trapping was done twice daily.

Two minor inconsistencies should be noted. Although Otis et al. (1978) said they used data from morning trap clearances, the capture histories in ‘examples’ from CAPTURE include a ‘pm’ tag on each record. We assume the error was in the text description, as their numerical results can be reproduced from the data file. Huggins (1991) reproduced the East Stuart Gulch dataset (omitting spatial data that were not relevant to his method), but omitted two capture histories.

The data are provided as two single-session `capthist` objects ‘deermouse.ESG’ and ‘deermouse.WSG’. Each has a dataframe of individual covariates, but the fields differ between the two study areas. The individual covariates of deermouse.ESG are sex (factor levels ‘f’, ‘m’), age class (factor levels ‘y’, ‘sa’, ‘a’) and body weight in grams. The individual covariates of deermouse.WSG are sex (factor levels ‘f’,‘m’) and age class (factor levels ‘j’, ‘y’, ‘sa’, ‘a’) (no data on body weight). The aging criteria used by Reid are not recorded.

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. ‘905’ in this example).

Sherman traps are designed to capture one animal at a time, but the data include double captures (1 at ESG and 8 at WSG – see Examples). The true detector type therefore falls between ‘single’ and ‘multi’. Detector type is set to ‘multi’ in the distributed data objects.

Some fitted `secr` models are included (ESG.0, ESG.b, ESG.t, ESG.h2, WSG.0, WSG.b, WSG.t, WSG.h2, each with the indicated effect on g0). Otis et al. (1978) draw attention to the tendency of Peromyscus to become ‘trap happy’, and we observe that models with a behavioural response (ESG.b, WSG.b) have the lowest AIC among those fitted here.

Object | Description
deermouse.ESG | capthist object, East Stuart Gulch
deermouse.WSG | capthist object, Wet Swizer Gulch
ESG.0 | fitted secr model -- ESG null
ESG.b | fitted secr model -- ESG trap response g0
ESG.h2 | fitted secr model -- ESG finite mixture g0
ESG.t | fitted secr model -- ESG time-varying g0
WSG.0 | fitted secr model -- WSG null
WSG.b | fitted secr model -- WSG trap response g0
WSG.h2 | fitted secr model -- WSG finite mixture g0
WSG.t | fitted secr model -- WSG time-varying g0

### Source

File ‘examples’ distributed with program CAPTURE.

### References

Huggins, R. M. (1991) Some practical aspects of a conditional likelihood approach to capture experiments. Biometrics 47, 725–732.

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.

Stanley, T. R. and Richards, J. D. (2005) A program for testing capture–recapture data for closure. Wildlife Society Bulletin 33, 782–785.

### See Also

`closure.test`

### Examples

    par(mfrow = c(1,2), mar = c(1,1,4,1))
    plot(deermouse.ESG, title = "Peromyscus data from East Stuart Gulch",
        border = 10, gridlines = FALSE, tracks = TRUE)
    plot(deermouse.WSG, title = "Peromyscus data from Wet Swizer Gulch",
        border = 10, gridlines = FALSE, tracks = TRUE)

    closure.test(deermouse.ESG, SB = TRUE)

    ## reveal multiple captures
    table(trap(deermouse.ESG), occasion(deermouse.ESG))
    table(trap(deermouse.WSG), occasion(deermouse.WSG))

[Package secr version 3.2.1 Index]