Construct capthist Object

Description

Form a capthist object from a data frame of capture records and a traps object.

Usage

make.capthist(captures, traps, fmt = "trapID", noccasions = NULL,
    covnames = NULL, bysession = TRUE, sortrows = TRUE, cut = NULL)

Arguments

Details

make.capthist is the recommended way to prepare data for secr.fit. Each row of the input data frame represents a detection on one occasion. The capture data frame may be formed from a text file with read.captures.

Input formats are based on the Density software (Efford 2007). If fmt = 'XY' the required fields are (session, ID, occasion, x, y) in that order. If fmt = 'trapID' the required fields are (session, ID, occasion, trap), where trap is the numeric index of the relevant detector in traps. session and ID may be character-, vector- or factor-valued; other required fields are numeric. Fields are matched by position (column number), not by name. Columns after the required fields are interpreted as individual covariates that may be continuous (e.g., size) or categorical (e.g., age, sex).

If captures has data from multiple sessions then traps may be either a list of traps objects, one per session, or a single traps object that is assumed to apply throughout. Similarly, noccasions may be a vector specifying the number of occasions in each session.

Covariates are assumed constant for each individual; the first non-missing value is used. The length of covnames should equal the number of covariate fields in captures.

bysession takes effect when the same individual is detected in two or more sessions: TRUE results in one capture history per session, FALSE has the effect of generating a single capture history (this is not appropriate for the models currently provided in secr).

Deaths are coded as negative values in the occasion field of captures. Occasions should be numbered 1, 2, ..., noccasions. By default, the number of occasions is the maximum value of 'occasion' in captures.

Value

An object of class capthist (a matrix or array of detection data with attributes for detector positions etc.). For 'single' and 'multi' detectors this is a matrix with one row per animal and one column per occasion (dim(capthist)=c(nc,noccasions)); each element is either zero (no detection) or a detector number (the row number in traps not the row name). For 'proximity' detectors capthist is an array of values {-1, 0, 1} and dim(capthist)=c(nc,noccasions,ntraps). The number of animals nc is determined from the input, as is noccasions if it is not specified. traps, covariates and other data are retained as attributes of capthist.
Deaths during the experiment are represented as negative values in capthist.
If the input has data from multiple sessions then the output is an object of class c('list','capthist') comprising a list of single-session capthist objects.

Note

make.capthist requires that the data for captures and traps already exist as R objects. To read data from external (text) files, first use read.captures and read.traps.

Author(s)

Murray Efford murray.efford@otago.ac.nz

References

Efford, M. G. (2007) Density 4.1: software for spatially explicit capture–recapture. Department of Zoology, University of Otago, Dunedin, New Zealand. http://www.otago.ac.nz/density.

See Also

capthist, traps, read.captures, secr.fit, sim.capthist

Examples

## load demonstration data and peek at XY data
data(rawdata)
captXY[1:5,]  
trapXY[1:5,]  

demotraps <- read.traps(data = trapXY)   
demoCHxy  <- make.capthist (captXY, demotraps, fmt = 'XY')

demoCHxy            ## print method for capthist
plot(demoCHxy)      ## plot method for capthist
summary(demoCHxy)   ## summary method for capthist