Mandatory and optional input by analyze type

Optional input - analyze type 1 (AI-REML)

For AI-REML, parameters to control the maximization process can be specified in a file.
The format is three lines with one parameter per line in the sequence shown in the table below.
The values shown are the default values.

   Value        Name               Description
   ______     ___________  __ ______________________________________________________
    10        EMSTEP        Number of steps before full weight on EM in IMET = 1
   1.0d-7     CONV_NDELTA   Convergence criteria for norm of the update vector
   1.0d-6     CONV_GNORM    Convergence criteria for norm of the gradient vector (AI)

Mandatory and optional input - analyze type 2 (MCMC)

Mandatory lines
3 0           | Igibkode, Itest
1111  2111    | Starting seed for random number generator
2000  3000 1  | Burnin, No of rounds, and interleaving
1  0          | CV matrix number and prior degree of belief (DF), one line for each CV matrix
              | (DF < CV matrix dimension + 2 -> non informative prior)

Optional model dependent lines for Reaction norm models with unknown environmental co-variate
1             | No. of traits times no. of class effects used as co-variate
              | 2 lines per each combinations of no. traits times no. of co-variate
1 2 1         | trait (seq. number), E-effect (pos. in model), number of cov
1 0           | RN-cov, associated cov

Additional optional line for Reaction norm models environmental co-variate
0             | 0 (default): original sampled class effects
              | 1= standardized by standard deviation for sampled class effects

Optional input - analyze type 12 (BLUP PCG iteration on data)

BLUP-PCG can read optional input consisting of up two lines.

The first line controls the iteration process by specification of maximum number of iterations and
convergence criteria.

On the next line, the amount of physical RAM (in MB) available can be specified. This is used to optimize
memory utilization and avoid swapping, by storing as much data in memory as possible.

If no optional input is given, the following default values are used:

     Maximum round:           1000
     Convergence criteria:    1e-9
     RAM (MB):                2000