{smcl}
{hline}
help for {hi:profhap}  {right: (TSJ-1: st0003)}
{hline}


{title:Calculates profile likelihood confidence intervals for results from {hi:hapipf}}

{p 8 27}
{cmdab:profhap}
[{cmd:if}{it: exp}] 
 , {cmd:or}{cmd:(}{it:string}{cmd:)}
 {cmd::ipf}{cmd:(}{it:string}{cmd:)}
 [
 {cmd:by}{cmd:(}{it:varlist}{cmd:)}
 {cmd:acc}{cmd:(}{it:#}{cmd:)}
 {cmdab:lev:el}{cmd:(}{it:#}{cmd:)}
 {cmd:hapacc}{cmd:(}{it:#}{cmd:)}
 {cmd:savegraph}
] 

{p}

{title:Description}

{p 0 0}
This function calculates the confidence intervals for the odds ratios estimated
by the command {cmd:hapipf}. It uses the profile likelihood by estimating the log-likelihood
of a series of constrained log-linear models.

{p}

{title:Options}

{p 0 4}
{cmd:or(}{it:string}{cmd:)}
first the case control variable is specified then two haplotypes/alleles. The
first haplotype/allele indicates the unexposed group and the other
haplotype/allele is the exposed group e.g. {hi:or(D 1 2)} specifies that the
case control variable is D and that the allele 1 represents the unexposed
group and allele 2 the exposed.

{p 0 4}
{cmd:ipf(}{it:string}{cmd:)} specifies the log-linear model in the constrained
table.  It requires special syntax of the form {hi:l1*l2+l3}. {hi:l1*l2}
allows all the interactions between the first two loci and locus 3 is
independent of them.  This syntax is used in most books on Log-linear
modelling, "-" terms and brackets are not allowed.

{p 0 4}
{cmd:by(}{it:string}{cmd:)} 
specifies a stratifying variable.

{p 0 4}
{cmd:acc(}{it:real}{cmd:)} specifies the accuracy of the estimated upper and
lower bounds of the confidence interval.

{p 0 4}
{cmd:level(}{it:real}{cmd:)} specifies the significance level of the
confidence interval.

{p 0 4}
{cmd:hapacc(}{it:real}{cmd:)} specifies the convergence threshold of both {\tt
hapipf} and {\tt ipf}.

{p 0 4}
{cmd:savegraph} specifies that the profile graph is saved to file
{hi:profile.gph}

{p}

{title:Examples}

{inp:. profhap a1 a2, ipf(l1+D) or(D 1 2)}

{inp:. profhap a1 a2 b1 b2, ipf(S*D+l1*l2*S) or(D 1.1 2.2) by(S) acc(0.0001)}


{title:Author}

{p}
 Adrian Mander, MRC Biostatistics Unit, Forvie Site, Addenbrookes, Cambridge,UK.

Click here to see Adrian Mander's {browse "http://www.mrc-bsu.cam.ac.uk/personal/adrian":WEB site}
Email {browse "mailto:adrian.mander@mrc-bsu.cam.ac.uk":adrian.mander@mrc-bsu.cam.ac.uk}


{title:Also see}

{p 0 19}
On-line: help for {help qhapipf} (if installed), {help hapipf} (if installed), {help ipf} (if installed). 
