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
ATAN2(3) BSD Library Functions Manual ATAN2(3)NAME
atan2 -- arc tangent function of two variables
SYNOPSIS
#include <math.h>
double
atan2(double y, double x);
long double
atan2l(long double y, long double x);
float
atan2f(float y, float x);
DESCRIPTION
The atan2() function computes the principal value of the arc tangent of y/x, using the signs of both arguments to determine the quadrant of
the return value.
SPECIAL VALUES
atan2(+-0, -0) returns +-pi.
atan2(+-0, +0) returns +-0.
atan2(+-0, x) returns +-pi for x < 0.
atan2(+-0, x) returns +-0 for x > 0.
atan2(y, +-0) returns +pi/2 for y > 0.
atan2(y, +-0) returns -pi/2 for y < 0.
atan2(+-y, -infinity) returns +-pi for finite y > 0.
atan2(+-y, +infinity) returns +-0 for finite y > 0.
atan2(+-infinity, x) returns +-pi/2 for finite x.
atan2(+-infinity, -infinity) returns +-3*pi/4.
atan2(+-infinity, +infinity) returns +-pi/4.
NOTES
The atan2() function is used mostly to convert from rectangular (x,y) to polar (r,theta) coordinates that must satisfy x = r*cos theta and y
= r*sin theta. In general, conversions to polar coordinates should be computed thus:
r := hypot(x,y); ... := sqrt(x*x+y*y)
theta := atan2(y,x).
VECTOR OPERATIONS
If you need to apply the atan2() function to SIMD vectors or arrays, using the following functions provided by the Accelerate.framework may
give significantly better performance:
#include <Accelerate/Accelerate.h>
vFloat atan2f(vFloat y, vFloat x);
void vvatan2f(float *z, const float *y, const float *x, const int *n);
void vvatan2(double *z, const double *y, const double *x, const int *n);
SEE ALSO acos(3), asin(3), atan(3), cos(3), cosh(3), sin(3), sinh(3), tan(3), tanh(3), math(3),
STANDARDS
The atan2() function conforms to ISO/IEC 9899:2011.
BSD December 11, 2006 BSD