subset.capthist {secr} | R Documentation

## Subset or Split capthist Object

### Description

Create a new `capthist` object or list of objects by selecting rows (individuals), columns (occasions) and traps from an existing `capthist` object.

### Usage

    ## S3 method for class 'capthist':
    subset(x, subset = NULL, occasions = NULL, traps = NULL,
        sessions = NULL, cut = NULL, dropnull = TRUE, renumber = FALSE, ...)
    ## S3 method for class 'capthist':
    split(x, f, drop = FALSE, prefix = 'S', ...)

### Arguments

`x` | object of class `capthist`
`subset` | vector of subscripts to select rows (individuals)
`occasions` | vector of subscripts to select columns (occasions)
`traps` | vector of subscripts to select detectors (traps)
`sessions` | vector of subscripts to select sessions
`cut` | new threshold for signal strength
`dropnull` | logical for whether null (all-zero) capture histories should be dropped
`renumber` | logical for whether row.names should be replaced with sequence number in new `capthist`
`f` | factor or object that may be coerced to a factor
`drop` | logical indicating if levels that do not occur should be dropped (if f is a factor)
`prefix` | a character prefix to be used for component names when values of f are numeric
`...` | other arguments (not used currently)

### Details

Subscript vectors may be either logical (length equal to the relevant dimension of `x`) or integer-valued. Subsetting is applied to attributes (e.g. `covariates`, `traps`) as appropriate. The default action is to include all rows, columns and traps if the relevant argument is omitted.

When `traps` is provided, detections at other detectors are set to zero, as if the detector had not been used, and the corresponding rows are removed from `traps`. If the detector type is 'proximity' then selecting traps also reduces the third dimension of the capthist array.

`split` generates a list in which each component is a `capthist` object. Each component corresponds to a level of `f`.

To combine (pool) occasions use `reduce.capthist`. There is no equivalent of `unlist` for lists of `capthist` objects.

### Value

`capthist` object with the requested subset of observations, or a list of such objects (i.e., a multi-session `capthist` object). List input results in list output, except when a single session is selected.

### Author(s)

Murray Efford murray.efford@otago.ac.nz

### See Also

`capthist`, `rbind.capthist`, `reduce.capthist`

### Examples

    tempcapt <- sim.capthist (make.grid(nx=6, ny=6), nocc=6)
    summary(subset(tempcapt, occ=c(1,3,5)))

    ## Consider 'proximity' detections at a random subset of detectors
    ## This would not make sense for 'multi' detectors, as the
    ## excluded detectors influence detection probabilities in
    ## sim.capthist.

    tempcapt2 <- sim.capthist (make.grid(nx = 6, ny = 6,
        detector = 'proximity'), nocc = 6)
    tempcapt3 <- subset(tempcapt2, traps = sample(1:36, 18,
        replace=FALSE))
    summary(tempcapt3)
    plot(tempcapt3)

    split (tempcapt2, f = sample (c('A','B'), nrow(tempcapt2),
        replace = TRUE))

[Package secr version 1.2.11 Index]