ilink is part of the fastlink software package.
ILINK uses the GEMINI optimization procedure to find a locally optimal value of the theta vector of recombination fractions. If you use the default scripts produced by lcp, your initial guess for theta is .1 in every dimension. GEMINI evaluates each theta by its likelihood, seeking to find theta vectors that have a higher pedigree likelihood.
The GEMINI procedure has multiple iterations. Each iteration corresponds to one line of output. Each iteration includes multiple likelihood function evaluations. Each iteration has two phases. In Phase I GEMINI seeks to improve the current best theta. In Phase II, GEMINI estimates the gradient of the likelihood with respect to the current best theta vector. In the first iteration, Phase I only evaluates the likelihood at the initial candidate theta.
When ILINK prints out a line such as: maxcensor can be reduced to -32767, it has completed the first likelihood function evaluation. On long runs, this fact can be used to estimate running time. A reasonable rough estimate for the number of function evaluations is 10*(number of dimensions of theta vector). The number of dimensions of the theta vector is one fewer than the number of loci in most cases. If maletheta and femaletheta are allowed to differ (sexdif is set to 1), then the number of dimensions doubles to 2 * (number of loci - 1). Estimating other parameters (with fitmodel set to true) can also increase the number of dimensions.
To learn more about ilink it might be useful to read the file /usr/share/doc/fastlink/README.ILINK if you have a Debian GNU/Linux system.
This manual page was written by Andreas Tille <firstname.lastname@example.org>, for the Debian GNU/Linux system (but may be used by others).