# The `--initial-value` command:

--initial-value <parameter>=<value>         Initialize parameter value.

This command should usually not be used, and only works in
certain cases. If you want to set a parameter to a constant, you
can specify it as part of the model.  For example,

   bali-phy dna.fasta -I rs07[log_rate=-4]
   
will set `log_rate` to a constant.  This approach always works,
but will not estimate `log_rate` since the value is fixed at -4.0.

In contrast, setting the initial value allows estimation of the
parameter and uses the value as a starting point:

   bali-phy dna.fasta -I rs07 --initial-value rs07:log_rate=-4.0
   
When setting the initial value it is necessary to specify the
decimal point for floating point values.

However, setting initial values only works when the parameter is
directly modifiable.  For example, if you set

   rs07[mean_length=add[1,~exponential[10]]]
   
the parameter `rs07:mean_length` isn't modifiable.  Instead it is
a function of an unnamed modifiable variable created by
`~exponential[10]`.

Usually a value directly sampled from a distribution is modifiable,
but there are exceptions.  For example, sampling from the logNormal
distributions results in `exp[~normal[lmean,lsigma]]`, which is not
modifiable.

Likewise, components of Dirichlet distributions are not modifiable,
so it is not possible to set the initial values of nucleotide
frequencies constructed from Dirichlet priors.

# Examples:

   # This works.
   bali-phy dna.fasta --initial-value rs07:log_rate=-4.0

   # This does not work.
   bali-phy dna.fasta --initial-value rs07:log_rate=-4

   # This does not work.
   bali-phy dna.fasta --initial-value tn93:kappaPur=4.0
