extract.mark.output: Extract results from MARK output file (internal use)

In RMark: R Code for Mark Analysis

Extract results from MARK output file (internal use)

Description

Extracts the lnl, AICc, npar, beta and real estimates and returns a list of these results for inclusion in the mark object. The elements beta and real are dataframes with fields estimate,se,lcl,ucl. This function was written for internal use and is called by run.mark.model. It is documented here for more advanced users that might want to modify the code or adapt for their own use.

Usage

extract.mark.output(out, model, adjust, realvcv = FALSE, vcvfile)

Arguments

out	output from MARK analysis (model$output)
model	mark model object
adjust	if TRUE, adjusts number of parameters (npar) to number of columns in design matrix, modifies AIC and records both
realvcv	if TRUE the vcv matrix of the real parameters is extracted and stored in the model results
vcvfile	name of vcv file output

Value

result: list of extracted output elements

lnl	-2xLog-likelihood
deviance	Difference between saturated model and lnl
npar	Number of model parameters
AICc	Small-sample corrected AIC value using npar and n
npar.unadjusted	Number of model parameters as reported by MARK if npar was adjusted
AICc.unadjusted	Small-sample corrected AIC value using npar.unadjusted and n
n	Effective sample size reported by MARK; used in AICc calculation
beta	Dataframe of beta parameters with fields: estimate, se, lcl, ucl
real	Dataframe of real parameters with fields: estimate, se, lcl, ucl
derived.vcv	variance-covariance matrix for derived parameters if any
covariate.values	dataframe with fields Variable and Value which are the covariate names and value used for real parameter estimates in the MARK output
singular	indices of beta parameters that are non-estimable or at a boundary
real.vcv	variance-covariance matrix for real parameters (simplified) if realvcv=TRUE

Author(s)

Jeff Laake

See Also

run.mark.model

RMark documentation built on Aug. 14, 2022, 1:05 a.m.