reduce.capthist {secr} | R Documentation

## Combine Occasions

### Description

Combine columns (occasions) in a `capthist` object to create a new data set, possibly converting between detector types

### Usage

    ## S3 method for class 'capthist':
    reduce(object, columns = NULL, outputdetector =
        detector(traps(object)), select='last', dropunused = TRUE, verify = TRUE,
        sessions = NULL, ...)

### Arguments

`object` | `capthist` object
`columns` | list in which each component is a vector of subscripts for occasions to be pooled
`outputdetector` | character value giving detector type for output
`select` | character value for method to resolve conflicts
`dropunused` | logical, if TRUE any never-used detectors are dropped
`verify` | logical, if TRUE the `verify` function is applied to the output
`sessions` | vector of session indices or names (optional)
`...` | other arguments (not used currently)

### Details

The first component of `columns` defines the columns of `object` for new occasion 1, the second for new occasion 2, etc. If `columns` is NULL then all occasions are output. When the output detector is one of the trap types ('single', 'multi'), reducing capture occasions can result in locational ambiguity for individuals caught on more than one occasion, and for single-catch traps there may also be conflicts between individuals at the same trap. The method for resolving conflicts among 'multi' detectors is determined by `select` which should be one of 'first', 'last' or 'random'. With 'single' detectors `select` is ignored and the method is: first, randomly select* one trap per animal per day; second, randomly select* one animal per trap per day; third, when collapsing multiple days use the first capture, if any, in each trap. With signal detectors, `select` determines how multiple signal measurements are combined; options 'min', 'max' or 'mean' are also allowed.

Usage data in the `traps` attribute are also pooled if present; a trap is considered 'used' on a pooled occasion if it was used on any contributing occasion.

* i.e., in the case of a single capture, use that capture; in the case of multiple 'competing' captures draw one at random.

### Value

An object of class `capthist` with number of columns equal to `length(occasions)`. The detector type is inherited from `object` unless a new type is specified with the argument `outputdetector`.

### Author(s)

Murray Efford murray.efford@otago.ac.nz

### See Also

`capthist`, `subset.capthist`

### Examples

    tempcapt <- sim.capthist (make.grid(nx = 6, ny = 6), nocc = 6)
    class(tempcapt)

    pooled.tempcapt <- reduce(tempcapt, col = list(1,2:3,4:6))
    summary (pooled.tempcapt)

[Package secr version 1.3.0 Index]