R2admb (version 0.7.10)

read_pars: Read in parameters from an AD Model Builder run

Description

Reads coefficients, standard errors, log-likelihoods, maximum gradients, correlation and variance-covariance matrices from AD Model Builder output files

Usage

read_pars(fn, drop_phase = TRUE)

  read_psv(fn, names = NULL)

  read_rep(fn, names = NULL)

Arguments

fn

(character) Base name of AD Model Builder

drop_phase

(logical) drop negative-phase (fixed) parameters from results?

names

(character) Names of variables

Value

• List containing the following elements
  • coefficients
  {parameter estimates}
• coeflist
  parameter estimates in list format, with proper shape (vectors, matrices, etc.)
• se
  estimated standard errors of coefficients
• loglik
  log-likelihood
• maxgrad
  maximum gradient of log-likelihood surface
• cor
  correlation matrix
• vcov
  variance-covariance matrix
• npar
  number of parameters
• hes
  hessian matrix (only if no vcov matrix)

Warning

The coeflist component is untested for data structures more complicated than scalars, vectors or matrices (i.e. higher-dimensional or ragged arrays)

Details

Given the output from an ADMB run on FOO.tpl, read_pars reads the files FOO.par (parameters, log-likelihood, max gradient); FOO.std (standard deviations); FOO.cor (correlations); FOO.rep (report variables); admodel.hes for hessian; and admodel.cov for covariance matrix. read_psv reads the output of MCMC runs

See Also

write_pin, write_dat