secr (version 5.0.0)

usage: Detector Usage

Description

Extract or replace usage (effort) information of a traps object (optional).

Usage

# S3 method for traps
usage(object, noccasions = NULL, ...)
usage(object) <- value

Value

usage(object) returns the usage matrix of the traps

object. usage(object) may be NULL. If noccasions is provided and there is no pre-existing matrix then a matrix of all ones will be generated.

Arguments

object

traps object

noccasions

integer number of occasions (optional)

value

numeric matrix of detectors x occasions

...

other arguments (not used)

Details

In secr versions before 2.5.0, usage was defined as a binary value (1 if trap \(k\) used on occasion \(s\), zero otherwise).

In later versions, usage may take nonnegative real values and will be interpreted as effort. This corresponds to the constant T_s used for the duration of sampling by Borchers and Efford (2008). Effort is modelled as a known linear coefficient of detection probability on the hazard scale (secr-varyingeffort.pdf; Efford et al. 2013).

For replacement of usage, various forms are possible for value:

- a matrix in which the number of rows of value exactly matches the number of traps K in object

- a vector of two values, the usage (typically 1) and the number of occasions S (a K x S matrix will be filled with the first value)

- a vector of R+1 values where R is the number of sessions in a multi-session object and elements 2..R+1 correspond to the numbers of occasions S1, S2,... in each session

- the usage only (typically 1) (only works when replacing an existing usage matrix with known number of occasions).

References

Efford, M. G., Borchers D. L. and Mowat, G. (2013) Varying effort in capture--recapture studies. Methods in Ecology and Evolution 4, 629--636.

See Also

traps, usagePlot, read.capthist, addSightings

Examples

demo.traps <- make.grid(nx = 6, ny = 8)
## random usage over 5 occasions
usage(demo.traps) <- matrix (sample(0:1, 48*5, replace = TRUE, 
    p = c(0.5,0.5)), nc = 5)
usage(demo.traps)
summary(demo.traps)

usage(traps(ovenCH)) <- c(1,9,10,10,10,10)
## restore lost names
names(ovenCH) <- 2005:2009