read_pars: Read in parameters from an AD Model Builder run

In R2admb: 'ADMB' to R Interface Functions

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, covfn = "admodel.cov",
  warn_nonstd_rep = TRUE)

read_psv(fn, names = NULL)

read_rep(fn, names = NULL, warn_nonstd_rep = TRUE)

Arguments

fn	(character) Base name of AD Model Builder
drop_phase	(logical) drop negative-phase (fixed) parameters from results?
covfn	(character) file name for covariance matrix information
warn_nonstd_rep	warn if report file is in nonstandard format?
names	(character) Names of variables

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.

read_rep (called by read_admb to read the .rep file) first checks if the report file is in a standard format: first line starts with a comment character (#); thereafter, each block starts with a single commented line containing the name of the parameter (possibly ending with a colon), followed by a block of all-numeric lines, which are read as a single vector. If the report file is in a standard format, the values are added to the end of the coefficients list. Otherwise, the numeric values from the report file are included in the results as a single, concantenated numeric vector.

Value

List containing the following elements

• coefficientsparameter estimates

• coeflistparameter estimates in list format, with proper shape (vectors, matrices, etc.)

• seestimated standard errors of coefficients

• logliklog-likelihood

• maxgradmaximum gradient of log-likelihood surface

• corcorrelation matrix

• vcovvariance-covariance matrix

• nparnumber of parameters

• heshessian matrix (only if no vcov matrix)

• reportvalues from report file (if non-standard report file)

Warnings

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

• Because ADMB hard-codes the file name for covariance matrix information (admodel.cov), care is necessary when running different models in the same directory; users may want to rename this file by hand and use the covfn argument

See Also

write_pin, write_dat

R2admb documentation built on Nov. 10, 2022, 5:59 p.m.