read_pars | R Documentation |

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)

`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 |

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.

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)

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

`write_pin`

, `write_dat`

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