# ilink - Online in the Cloud

This is the command ilink that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

### PROGRAM:

#### NAME

ilink - GEMINI optimization procedure to find a locally optimal value of the theta vector
of recombination fractions

#### DESCRIPTION

This manual page documents briefly the ilink command. In fact this is a very raw intend
to provide a manpage because the Debian GNU/Linux distribution requires each program to
have a manpage. Any enhancement would be greatly apreciated.

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.