secrdemo {secr} | R Documentation

## SECR Models Fitted to Demonstration Data

### Description

Demonstration data from program Density are provided as text files in the ‘extdata’ folder, as raw dataframes (`trapXY`, `captXY`), and as a combined `capthist` object (`captdata`) ready for input to `secr.fit`.

The fitted models are objects of class `secr` formed by

`secrdemo.0 <- secr.fit (captdata)`

`secrdemo.b <- secr.fit (captdata, model = list(g0 = ~b))`

`secrdemo.CL <- secr.fit (captdata, CL = TRUE)`

### Usage

    data(secrdemo)

### Details

The raw data are 235 fictional captures of 76 animals over 5 occasions in 100 single-catch traps 30 metres apart on a square grid with origin at (365,365).

Dataframe `trapXY` contains the data from the Density input file ‘trap.txt’, and `captXY` contains the data from ‘capt.txt’ (Efford 2012).

The fitted models use a halfnormal detection function and the likelihood for multi-catch traps (expect estimates of g0 to be biased because of trap saturation Efford et al. 2009). The first is a null model (i.e. parameters constant) and the second fits a learned trap response.

Object | Description
captXY | data.frame of capture data
trapXY | data.frame of trap locations
captdata | capthist object
secrdemo.0 | fitted secr model -- null
secrdemo.b | fitted secr model -- g0 trap response
secrdemo.CL | fitted secr model -- null, conditional likelihood

### References

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., Borchers D. L. and Byrom, A. E. (2009) Density estimation by spatially explicit capture-recapture: likelihood-based methods. In: D. L. Thomson, E. G. Cooch and M. J. Conroy (eds) Modeling Demographic Processes in Marked Populations. Springer, New York. Pp. 255–269.

### See Also

`capthist`, `read.capthist`

### Examples

    ## Not run:

    ## navigate to folder with raw data files
    olddir <- setwd (system.file("extdata", package="secr"))

    ## construct capthist object from raw data
    captdata  <- read.capthist ("capt.txt", "trap.txt", fmt = "XY", detector = "single")

    ## generate demonstration fits
    secrdemo.0 <- secr.fit (captdata)
    secrdemo.CL <- secr.fit (captdata, CL = TRUE)
    secrdemo.b <- secr.fit (captdata, model = list(g0 ~ b))

    ## restore previous setting
    setwd(olddir)

    ## End(Not run)

    ## display the null model fit, using the print method for secr
    secrdemo.0

    ## compare fit of models
    AIC(secrdemo.0, secrdemo.b)

    ## display estimates for the two models (single session)
    collate(secrdemo.0, secrdemo.b)[1,,,]

[Package secr version 3.2.1 Index]