Rcapture (version 1.4-4)

# periodhist: Merge capture occasions

## Description

This function produces a reduced matrix of capture histories from a complete one by merging together some capture occasions.

It can also be used to change the format of a capture-recapture data set with complete capture histories: it transforms a data set with one row per captured unit to a data set with one row per capture history followed by its frequency.

## Usage

`periodhist(X, dfreq=FALSE, vt, drop=TRUE)`

## Arguments

X

The matrix of the observed capture histories (see `Rcapture-package` for a description of the accepted formats).

dfreq

A logical. By default FALSE, which means that `X` has one row per unit. If TRUE, it indicates that the matrix `X` contains frequencies in its last column.

vt

A vector containing the numbers of capture occasions for each pooled capture occasions. The length of this vector equals the number of capture occasions in the reduced matrix (noted \(I\)).

drop

A logical, by default TRUE, meaning that in the output matrix the unobserved capture histories (frequency of 0) are omitted. To keep them, `drop` must be set to FALSE.

## Value

A \(2^I-1\) by \(I+1\) matrix of all the pooled capture histories, with their observed frequencies. If `drop=TRUE` (the default), the number of rows of this matrix is in fact \(2^I-1\) minus the number of unobserved capture histories.

## Details

This function is useful when using an open population model to analyze a robust design data set. It can be used to reduce the data set to one observation per primary period. A one represents a unit caught at least once during the period and a zero a unit never caught.

It is also useful for experiments with a large number of capture occasions but a limited number of catches, especially when there is no capture on some occasions. In such cases, one can pool together some capture occasions with the `periodhist` function.

If a data matrix produced by the `periodhist` function is given as an argument to a Rcapture function, the `dfreq` argument must be set to `TRUE`.

## References

Baillargeon, S. and Rivest, L.P. (2007) Rcapture: Loglinear models for capture-recapture in R. Journal of Statistical Software, 19(5), 10.18637/jss.v019.i05.

`openp`

## Examples

Run this code
``````# NOT RUN {
# mvole data set aggregated per primary period
mvole.op <- periodhist(mvole, vt = rep(5, 6))
openp(mvole.op, dfreq = TRUE)
# }
``````

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