secr.design.MS {secr} | R Documentation

## Construct Detection Model Design Matrices and Lookups

### Description

Internal function used by `secr.fit`.

### Usage

    secr.design.MS(capthist, models, timecov = NULL, sessioncov = NULL,
        groups = NULL, dframe = NULL, naive = FALSE, bygroup = FALSE, ...)

### Arguments

`capthist` | `capthist` object
`models` | list of formulae for parameters of detection
`timecov` | optional dataframe of values of time (occasion-specific) covariate(s).
`sessioncov` | optional dataframe of values of session-specific covariate(s).
`groups` | optional vector of one or more variables with which to form groups. Each element should be the name of a factor variable in the `covariates` attribute of `capthist`.
`dframe` | optional data frame of design data for detection parameters
`naive` | logical if TRUE then modelled detection probability is for a naive animal (not caught previously); if FALSE then detection probability is contingent on individual's history of detection
`bygroup` | logical if TRUE then the individual dimension of the parameter matrix is automatically collapsed to one row per group; if FALSE then the full dimensionality is retained (one row per individual)
`...` | other arguments passed to the R function `model.matrix`

### Details

This is an internal secr function that you are unlikely ever to use. ... may be used to pass `contrasts.arg` to `model.matrix`.

Each real parameter is notionally different for each unique combination of session, individual, occasion and detector, i.e., for R sessions, n individuals, S occasions and K detectors there are potentially R x n x S x K different values. Actual models always predict a much reduced set of distinct values, and the number of rows in the design matrix is reduced correspondingly; a parameter index array allows these to retrieved for any combination of session, individual, occasion and detector.

### Value

A list with the components

`designMatrices` | list of reduced design matrices, one for each real detection parameter
`parameterTable` | index to row of the reduced design matrix for each real detection parameter; dim(parameterTable) = c(uniquepar, np), where uniquepar is the number of unique combinations of paramater values (uniquepar < RnSK) and np is the number of parameters in the detection model.
`PIA` | Parameter Index Array - index to row of parameterTable for a given session, animal, occasion and detector; dim(PIA) = c(R,n,S,K)

### Author(s)

Murray Efford murray.efford@otago.ac.nz

### See Also

`D.designdata`

### Examples

    data(captdata)
    secr.design.MS (captdata, models = list(g0 = ~b))$designMatrices
    secr.design.MS (captdata, models = list(g0 = ~b))$parameterTable

[Package secr version 1.3.0 Index]