extractLL function

Extract Log-Likelihood of Model

This function extracts the log-likelihood from an object of coxme, coxph, lmekin, maxlikeFit, vglm, or various unmarkedFit classes. 1.1

extractLL(mod, ...)

## S3 method for class 'coxme'
extractLL(mod, type = "Integrated", ...)

## S3 method for class 'coxph'
extractLL(mod, ...)

## S3 method for class 'lmekin'
extractLL(mod, ...)

## S3 method for class 'maxlikeFit'
extractLL(mod, ...)

## S3 method for class 'unmarkedFit'
extractLL(mod, ...)

## S3 method for class 'vglm'
extractLL(mod, ...)

Arguments

• mod: an object of coxme, coxph, lmekin, maxlikeFit, vglm, or unmarkedFit class resulting from the fit of distsamp, gdistsamp, gmultmix, multinomPois, gpcount, occu, occuRN, colext, pcount, or pcountOpen.
• ...: additional arguments passed to the function.
• type: a character string indicating whether the integrated partial likelihood ("Integrated") or penalized likelihood ("Penalized") is to be used for a coxme object.

Details

This utility function extracts the information from a coxme, coxph, lmekin, maxlikeFit, vglm, or unmarkedFit object resulting from distsamp, gdistsamp, gmultmix, multinomPois, gpcount, occu, occuRN, colext, pcount, or pcountOpen.

Returns

These functions return the value of the log-likelihood of the model and associated degrees of freedom.

Author(s)

Marc J. Mazerolle

See Also

AICc, aictab, coxme, coxph, lmekin, maxlike, distsamp, gdistsamp, occu, occuRN, colext, pcount, pcountOpen

Examples

##single-season occupancy model example modified from ?occu
## Not run:

require(unmarked)
##single season
data(frogs)
pferUMF <- unmarkedFrameOccu(pfer.bin)
## add some fake covariates for illustration
siteCovs(pferUMF) <- data.frame(sitevar1 = rnorm(numSites(pferUMF)),
                                sitevar2 = rnorm(numSites(pferUMF))) 
     
## observation covariates are in site-major, observation-minor order
obsCovs(pferUMF) <- data.frame(obsvar1 = rnorm(numSites(pferUMF) *
                                 obsNum(pferUMF))) 

##run model set
fm1 <- occu(~ obsvar1 ~ sitevar1, pferUMF)

##extract log-likelihood
extractLL(fm1)
detach(package:unmarked)
## End(Not run)