ILINK(1) General Commands Manual ILINK(1)NAME
ilink - GEMINI optimization procedure to find a locally optimal value of the theta vector of recombination fractions
SYNOPSIS
ilink [options] ipedfile.dat pedfile.dat
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 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 esti-
mates 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 male-
theta and femaletheta are allowed to differ (sexdif is set to 1), then the number of dimensions doubles to 2 * (number of loci - 1). Esti-
mating 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.
OPTIONS
There might be options but I did not found any information about them. Please foreward any information about them to <tille@debian.org>
SEE ALSO linkmap(1), lodscore(1), mlink(1), unknown(1).
Word-Wide-Web:
http://www.ncbi.nlm.nih.gov/CBBResearch/Schaffer/fastlink.html
AUTHOR :
Alejandro Schaeffer <schaffer@helix.nih.gov> and others
This manual page was written by Andreas Tille <tille@debian.org>, for the Debian GNU/Linux system (but may be used by others).
April 15, 2003 ILINK(1)
Check Out this Related Man Page
s_curl(3rheolef) rheolef-6.1 s_curl(3rheolef)NAME
s_curl -- curl-like operator for the Stokes stream function computation
SYNOPSIS
form(const space M, const space& V, "s_curl");
DESCRIPTION
Assembly the form associated to the s_curl operator on a finite element space V:
/
|
b(xi,u) = | u.s_curl(xi) dx
|
/ Omega
The M and V space may be a either P1 or P2 finite element space. The M space is scalar-valued while the V is vector-valued. See also
form(2) and space(2).
For cartesian coordinate systems, this form coincide with the usual "curl" one (see curl(3)). In the axisymmetric case:
/
| (d xi d xi )
b(xi,u) = | (---- ur - ---- uz) r dr dz
| (d z d r )
/ Omega
The b form is denoted as "s_curl", for Stokes stream function computation (see s_grad_grad(3)) as it is closely related to the "curl" oper-
ator (see curl(3)), but differs by the r and 1/r factors, as:
( d (r xi) d xi )
curl(xi) = ( (1/r) -------- ; - -----)
( d r d z )
while
( d xi d xi )
s_curl(xi) = ( ---- ; - ---- )
( d r d z )
Notice also that the differentiation is performed on the xi variable here: b(xi,u)=(s_curl(xi),u) while the "curl" form brings the differ-
entiation on the u vector-valued variable: (curl(u),xi), i.e. a transpose formulation.
ORIENTATION AND SIGN FIX
The (r,theta,z) coordinate system has positive orientation, thus (z,r,theta) and (z,r) are positive also. But (r,z,theta) and (r,z) are
negative : the sign of s_curl is then inverted to obtain the same result as if (z,r) was used.
EXAMPLE
The following piece of code build the form associated to the P1 approximation:
geo g("square");
space M(g, "P1");
space V(g, "P1", "vector");
form a(M, V, "s_curl");
SEE ALSO form(2), space(2), curl(3), s_grad_grad(3), curl(3)rheolef-6.1 rheolef-6.1 s_curl(3rheolef)