pmixProfileLL: Mixture Model Check

In secr: Spatially Explicit Capture-Recapture

Mixture Model Check

Description

Compute the profile likelihood of a finite mixture model for a user-specified range of values for the mixing parameter. This provides a check on multimodality.

Usage

pmixProfileLL(CH, model = list(g0 ~ h2, sigma ~ h2), CL = TRUE, pmvals = seq(0.01,
 0.99, 0.01), pmi = 5, ...)

Arguments

CH	capthist object
model	model as in secr.fit
CL	logical as in in secr.fit
pmvals	numeric vector of values for mixing parameter ‘pmix’
pmi	integer index of ‘pmix’ in vector of coefficients (beta parameters) for the specified model
...	other arguments passed to secr.fit

Details

See secr-finitemixtures.pdf.

Choosing the wrong value for pmi results in the error message "invalid fixed beta - require NP-vector". The easiest way to find the value of pmi is to inspect the output from a previously fitted mixture model - either count the coefficients or check fit$parindx$pmix (for a model named ‘fit’). It is assumed that ‘pmix’ is the last real parameter in the model, and that pmix is constant.

Value

Numeric vector of profile likelihoods.

Note

This is slow to execute and the results are hard to interpret. Use only if you are confident.

Examples

## Not run: 

pmvals <- seq(0.02,0.99,0.02)
mask <- make.mask(traps(ovenCH[[1]]), nx = 32, buffer = 100)

## only g0 ~ h2, so reduce pmi from 5 to 4
outPL <- pmixProfileLL(ovenCH[[1]], model = list(g0~h2), 
    mask = mask, pmvals, CL = TRUE, trace = FALSE, pmi = 4) 
    
plot(pmvals, outPL, xlim = c(0,1),
xlab = 'Fixed pmix', ylab = 'Profile log-likelihood')


## End(Not run)

secr documentation built on Nov. 4, 2024, 9:06 a.m.