Description Usage Arguments Details Value Author(s)

Write a covariance matrix to the ADMB covariance file.

1 | ```
write.admb.cov(cov.user, model.path = getwd())
``` |

`cov.user` |
(Numeric matrix) A covariance matrix (in bounded space) to write to file. This matrix will be read in by ADMB and can be used in subsequent calculations. |

`model.path` |
The directory path to the folder containing the model. |

The `admodel.hes`

and `admodel.cov`

files are written
by ADMB during the optimization phase. The Hessian matrix contains the
second derivatives evaluated at the maximum likelihood estimates. The
inverse of the Hessian is the covariance matrix used to determine
standard errors and in the MCMC algorithm. The `admodel.hes`

file
is written even if the matrix is not invertible (not positive definite).

The `write`

functions return nothing, but have the side
effect of changing ADMB files (including creating a backup of the
original). The `get`

functions return a list of the number of
parameters (`num.pars`

), the covariance or Hessian matrix in
unbounded space (`cov`

or `hes`

), the hybrid bounded flag
(`hybrid_bounded_flag`

) which controls which bounding functions are
used, and the `scales`

, which are the second derivatives of the
bounding functions evaluated at the MLE.

Cole Monnahan

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