RMark (version 2.1.1)

extract.mark.output: 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

See Also

run.mark.model