R: Auxiliary Function for the Positive Bernoulli Family Function...

aux.posbernoulli.t {VGAM} | R Documentation

## Auxiliary Function for the Positive Bernoulli Family Function with Time Effects

### Description

Returns behavioural effects indicator variables from a capture history matrix.

### Usage

    aux.posbernoulli.t(y, check.y = FALSE, rename = TRUE, name = "bei")

### Arguments

`y` | Capture history matrix. Rows are animals, columns are sampling occasions, and values should be 0s and 1s only.
`check.y` | Logical, if `TRUE` then some basic checking is performed.
`rename, name` | If `rename = TRUE` then the behavioural effects indicator are named using the value of `name` as the prefix. If `FALSE` then use the same column names as `y`.

### Details

This function can help fit certain capture–recapture models (commonly known as M_{tb} or M_{tbh} (no prefix h means it is an intercept-only model) in the literature). See `posbernoulli.t` for details.

### Value

A list with the following components.

cap.hist1

  A matrix the same dimension as `y`. In any particular row there are 0s up to the first capture. Then there are 1s thereafter.

cap1

  A vector specifying which time occasion the animal was first captured.

y0i

  Number of noncaptures before the first capture.

yr0i

  Number of noncaptures after the first capture.

yr1i

  Number of recaptures after the first capture.

### See Also

`posbernoulli.t`, `deermice`.

### Examples

    # Fit a M_tbh model to the deermice data:
    (pdata <- aux.posbernoulli.t(with(deermice, cbind(y1, y2, y3, y4, y5, y6))))

    deermice <- data.frame(deermice,
                        bei = 0,  # Add this
                        pdata$cap.hist1)  # Incorporate these
    head(deermice)  # Augmented with behavioural effect indicator variables
    tail(deermice)

[Package VGAM version 1.0-3 Index]