Reads coefficients, standard errors, log-likelihoods, maximum gradients, correlation and variance-covariance matrices from AD Model Builder output files
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)
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)
(character) Base name of AD Model Builder
(logical) drop negative-phase (fixed) parameters from results?
(character) file name for covariance matrix information
warn if report file is in nonstandard format?
(character) Names of variables
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
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.
write_pin, write_dat