5.1 Overview

Running WOMBAT can be as simple as specifying its name at command level, i.e.

EXAMPLE:

wombat

A number of options are available, however, to modify the run time behaviour of WOMBAT. These range from simple options to set the verbosity level of screen output or to select a continuation run, to highly specialised options to modify the search strategies for the maximum of the likelihood function. Multiple options can be combined, but some care is required so that options given last do not unintentionally cancel out some of the effects of options given first. Options available are summarised in 5.1, 5.2 and ??.

Run options can be given in three ways :

1. On the command line, e.g. wombat -v -c myparfile.par
2. In a file with the default name RunOptions in the current working directory.
This file must contain a single option per line. If such file exists, it is read before any command line options are parsed. There are no checks for options specified in duplicate. This implies that the last setting for a particular option is the one to be used, and that the options in RunOptions can be overridden by command line options.
3. On the first line of the parameter file, after a code of RUNOP (see 4.3). Any such options are read before options specified on the command line, i.e. the latter may overide them.

Following Linux standard, run options have the form “-a” where a stands for a single, lower-case letter, or the form “––abcdef” where abcdef stands for a multi-letter code.


Table 5.1: ‘Basic’ run options for WOMBAT
Option

Purpose

-c

Specify a continuation run

-v

Specify verbose screen output

-d

Specify very detailed screen output

-t

Specify terse screen output

Default REML algorithms
--good

Tell that you have good starting values

--bad

Tell that you have bad starting values

Non-estimation runs
--setup

Select a run performing the set-up steps only

--best

Select a run printing out estimates for the currently best point only

--blup

Select a prediction (BLUP) run; direct solution

--solvit

Select a prediction (BLUP) run; solve iteratively

--mmeout

Like --solvit, but write MME out to file.

--simul

Select a run simulating data only

--subset

Write out parameter files for analyses of subsets of traits

--itsum

Iterative summation of partial covariance matrices

--invert

Invert a dense symmetric matrix; pivot on largest diagonal

--invrev

Invert a dense symmetric matrix; reverse pivoting on no. of off-diagonal elements

--inveig

Invert a dense symmetric matrix; use eigen decomposition

--invspa

Invert a sparse symmetric matrix

Miscellaneous
--expiry

Print out the expiry date for the program (to screen)

--limits

Print out the hard-coded program limits (to screen)

--times

Print out various intermediate times for a run

--wide

Write ‘wide’ output files