BUGS {secr} | R Documentation

## Convert Data To Or From BUGS Format

### Description

Convert data between ‘capthist’ and BUGS input format.

### Usage

    read.DA(DAlist, detector = "polygonX", units = 1, session = 1,
        Y = "Y", xcoord = "U1", ycoord = "U2", xmin = "Xl",
        xmax = "Xu", ymin = "Yl", ymax = "Yu", buffer = "delta",
        verify = TRUE)

    write.DA(capthist, buffer, nzeros = 200, units = 1)

### Arguments

`DAlist` | list containing data in BUGS format
`detector` | character value for detector type: ‘polygon’ or ‘polygonX’
`units` | numeric for scaling output coordinates
`session` | numeric or character label used in output
`Y` | character, name of binary detection history matrix (animals x occasions)
`xcoord` | character, name of matrix of x-coordinates for each detection in `Y`
`ycoord` | character, name of matrix of y-coordinates for each detection in `Y`
`xmin` | character, name of coordinate of state space boundary
`xmax` | character, name of coordinate of state space boundary
`ymin` | character, name of coordinate of state space boundary
`ymax` | character, name of coordinate of state space boundary
`buffer` | see Details
`verify` | logical if TRUE then the resulting capthist object is checked with `verify`
`capthist` | `capthist` object
`nzeros` | level of data augmentation (all-zero detection histories)

### Details

Data for OpenBUGS or WinBUGS called from R using the package R2WinBUGS (Sturtz et al. 2005) take the form of an R list.

These functions are limited at present to binary data from a square quadrat such as used by Royle and Young (2008). Marques et al. (2011) provide an R function `create.data()` for generating simulated datasets of this sort (see `sim.capthist` for equivalent functionality).

When reading BUGS data –

The character values `Y`, `xcoord`, `ycoord`, `xmin` etc. are used to locate the data within `DAlist`, allowing for variation in the input names.

The number of sampling occasions is taken from the number of columns in `Y`. Each value in `Y` should be 0 or 1. Coordinates may be missing

A numeric value for `buffer` is the distance (in the original units) by which the limits Xl, Xu etc. should be shrunk to give the actual plot limits. If `buffer` is character then a component of `DAlist` contains the required numeric value.

Coordinates in the output will be multiplied by the scalar `units`.

Augmentation rows corresponding to ‘all-zero’ detection histories in `Y`, `xcoord`, and `ycoord` are discarded.

When writing BUGS data –

Null (all-zero) detection histories are added to the matrix of detection histories `Y`, and missing (NA) rows are added to the coordinate matrices `xcoord` and `ycoord`.

Coordinates in the output will be divided by the scalar `units`.

### Value

For `read.DA`, an object of class ‘capthist’.

For `write.DA`, a list with the components

Xl | left edge of state space
Xu | right edge of state space
Yl | bottom edge of state space
Yu | top edge of state space
delta | buffer between edge of state space and quadrat
nind | number of animals observed
nzeros | number of added all-zero detection histories
T | number of sampling occasions
Y | binary matrix of detection histories (dim = c(nind+nzeros, T))
U1 | matrix of x-coordinates, dimensioned as Y
U2 | matrix of y-coordinates, dimensioned as Y

U1 and U2 are ‘NA’ where animal was not detected.

### References

Marques, T. A., Thomas, L. and Royle, J. A. (2011) A hierarchical model for spatial capture–recapture data: Comment. Ecology 92, 526–528.

Royle, J. A. and Young, K. V. (2008) A hierarchical model for spatial capture–recapture data. Ecology 89, 2281–2289.

Sturtz, S., Ligges, U. and Gelman, A. (2005) R2WinBUGS: a package for running WinBUGS from R. Journal of Statistical Software 12, 1–16.

### See Also

`hornedlizardCH`, `verify`, `capthist`

### Examples

    write.DA (hornedlizardCH, buffer = 100, units = 100)

    ## In this example, the input uses Xl, Xu etc.
    ## for the limits of the plot itself, so buffer = 0.
    ## Input is in hundreds of metres.
    ## First, obtain the list lzdata
    olddir <- setwd (system.file("extdata", package="secr"))
    source ("lizarddata.R")
    setwd(olddir)
    str(lzdata)
    ## Now convert to capthist
    tempcapt <- read.DA(lzdata, Y = "H", xcoord = "X",
        ycoord = "Y", buffer = 0, units = 100)
    #summary(tempcapt)

    ## Not run:
    plot(tempcapt)
    secr.fit(tempcapt, trace = FALSE)
    ## etc.

    ## End(Not run)

[Package secr version 3.2.1 Index]