{smcl}
{* *! version 1.0.0 05Aug2022}{...}
{title:Title}

{p2colset 5 23 24 2}{...}
{p2col:{hi:power pairspec} {hline 2}} Power and sample-size analysis for specificity between two diagnostic tests in a paired-sample   {p_end}
{p2colreset}{...}


{marker syntax}{...}
{title:Syntax}

{phang}
Compute sample size

{p 8 43 2}
{opt power pairspec} {it:spec1} {it:spec2}
[{cmd:,} {opth p:ower(numlist)} {opth a:lpha(numlist)} {opth prev(numlist)} {opt onesid:ed} 
{opt gr:aph}[{cmd:(}{it:{help power_optgraph##graphopts:graphopts}}{cmd:)}] ]

{phang}
Compute power 

{p 8 43 2}
{opt power pairspec} {it:sens1} {it:sens2}
[{cmd:,} {opth n(numlist)} {opth a:lpha(numlist)} {opth prev(numlist)} {opt onesid:ed} 
{opt gr:aph}[{cmd:(}{it:{help power_optgraph##graphopts:graphopts}}{cmd:)}] ]


{phang}
where {it:spec1} is the specificity of the first diagnostic test and
{it:spec2} is the specificity of the second diagnostic test.
{it:spec1} and {it:spec2} may each be specified either as one 
number or as a list of values in parentheses (see {help numlist}).{p_end}



{synoptset 30 tabbed}{...}
{synopthdr}
{synoptline}
{p2coldent:* {opth a:lpha(numlist)}}significance level; default is {cmd:alpha(0.05)} {p_end}
{p2coldent:* {opth p:ower(numlist)}}power; default is {cmd:power(0.80)} {p_end}
{p2coldent:* {opth n(numlist)}}total sample size; required to compute power {p_end}
{p2coldent:* {opth prev(numlist)}}prevalence rate of disease in the population under study; default is {cmd:prev(0.50)}  {p_end}
{synopt :{opt onesid:ed}}one-sided test; default is two sided{p_end}
{synopt :{cmdab:gr:aph}[{cmd:(}{it:{help power_optgraph##graphopts:graphopts}}{cmd:)}]}graph results; see {manhelp power_optgraph PSS-2:power, graph}{p_end}
{synopt :{opt init(#)}}initial value of the estimated power; default is {cmd:init(10)} {p_end}
{synoptline}
{p2colreset}{...}
{p 4 6 2}* Specifying a list of values in at least two starred options, or 
two command arguments, or at least one starred option and one argument
results in computations for all possible combinations of the values; see
{help numlist}.{p_end}


{marker description}{...}
{title:Description}

{pstd}
{opt power pairspec} computes sample size or power for specificity between two diagnostic tests in paired data,
accounting for the prevalence of the disease in the clinical population. Specificity is the ability 
of a test to correctly identify non-diseased patients. 

{pstd}
{opt power pairspec} computes sample size according to Miettinen (1968), then implements the naive prevalence inflation method 
introduced by Obuchowski and Zhou (2002). Li and Fine (2004) found this method (which they refer to as "Method 0") to be a 
useful approximation to exact sample-size calculations based on unconditional power, which are more computationally intensive. 
   


{title:Options}

{phang}
{opth alpha(numlist)} sets the significance level of the test.  The
default is {cmd:alpha(0.05)}.

{phang} 
{opth power(numlist)} specifies the desired power at which sample size is to be computed. 
The default is {cmd:power(0.80)}. If {cmd:power()} is specified in conjunction with {cmd:n()}, 
then the actual power of the test is presented. 

{phang} 
{opth n(numlist)} specifies the total number of subjects in the study to be used for determining power. 

{phang}
{opth prev(numlist)} specifies the conjectured prevalence of the disease in the clinical population. The default is {cmd:prev(0.50)}.

{phang} 
{cmd:onesided} indicates a one-sided test. The default is two sided. 

{phang}
{cmd:graph}, {cmd:graph()}; see {manhelp power_optgraph PSS-2: power, graph}.

{phang}
{opt init(#)} specifies an initial value for estimating power. 
The default value is {cmd:init(10)} which is a rescaled value of power = 0.001 (10/10,000). 
Increasing the initial value may be helpful if the reported power appears unreasonably low (e.g. 0.001).  



{title:Examples}

    {title:Examples: Computing sample size}

{pstd}
    Compute the sample size required to detect a statistical difference in specificity between
	two tests, where the first test is hypothesized to have a specificity of 0.70 and the second
	test is hypothesized to have a specificity of 0.90 using a two-sided test;
    assume a 5% significance level, 80% power, a conjectured disease prevalence of 0.50,
	and 50% of the sample assigned to test 1 (the defaults) {p_end}
{phang2}{cmd:. power pairspec 0.70 0.90} 

{pstd}
    Same as above, using a power of 90% and a prevalence of 0.10 {p_end}
{phang2}{cmd:. power pairspec 0.70 0.90, power(0.90) prev(0.10)}

{pstd}
    Computing sample size for a range of prevalence rates {p_end}
{phang2}{cmd:. power pairspec 0.70 0.90, power(0.90) prev(0.10(.10).90)}

{pstd}
    Applying a range of specificity values for test 1
	and setting alpha levels to 0.05 and 0.01 with a disease prevalence of 0.10. Here we graph the results {p_end}
{phang2}{cmd:. power pairspec (0.60(0.05).80) 0.90, power(0.90) alpha(0.01 0.05) prev(0.10) graph}


    {title:Examples: Computing power}

{pstd}
    For a total sample of 50 subjects, compute the power of a two-sided test to 
    detect a specificity of 0.90 given a null specificity of 0.70; assume a 5%
    significance level and a prevalence of 0.50 (the default){p_end}
{phang2}{cmd:. power pairspec 0.70 0.90, n(50)}

{pstd}
    Same as above, but change the prevalence to 0.20 and use a one-sided test {p_end}
{phang2}{cmd:. power pairspec 0.70 0.90, n(50) prev(0.20) onesided }

{pstd}
    Same as above, but apply a range prevalence rates {p_end}
{phang2}{cmd:. power pairspec 0.70 0.90, n(50) prev(0.20 0.50 0.70) onesided }

{pstd}
	Compute powers for a range of null specificities and total sample sizes, 
	graphing the results{p_end}
{phang2}{cmd:. power pairspec (0.60(.10)0.80) 0.90, n(5(5)80) onesided graph}


{title:Stored results}

{pstd}
{cmd:power pairspec} stores the following in {cmd:r()}:

{synoptset 20 tabbed}{...}
{p2col 5 20 24 2: Scalars}{p_end}
{synopt:{cmd: r(alpha)}}significance level{p_end}
{synopt:{cmd: r(power)}}power{p_end}
{synopt:{cmd: r(beta)}}probability of a type II error{p_end}
{synopt:{cmd: r(sens1)}}sensitivity of test 1{p_end}
{synopt:{cmd: r(sens2)}}sensitivity of test 2{p_end}
{synopt:{cmd: r(delta)}}effect size{p_end}
{synopt:{cmd: r(prev)}}prevalence of disease{p_end}
{synopt:{cmd: r(divider)}}1 if divider is requested in the table, 0 otherwise{p_end}
{synopt:{cmd: r(init)}}initial value of the estimated power {p_end}
{synopt:{cmd: r(N)}}total sample size{p_end}
{synopt:{cmd: r(N0)}}sample size of the non-diseased group{p_end}
{synopt:{cmd: r(N1)}}sample size of the diseased group{p_end}
{synopt:{cmd: r(onesided)}}1 for a one-sided test, 0 otherwise{p_end}

{synoptset 20 tabbed}{...}
{p2col 5 20 24 2: Macros}{p_end}
{synopt:{cmd:r(type)}}{cmd:test}{p_end}
{synopt:{cmd:r(method)}}{cmd:pairspec}{p_end}
{synopt:{cmd:r(columns)}}displayed table columns{p_end}
{synopt:{cmd:r(labels)}}table column labels{p_end}
{synopt:{cmd:r(widths)}}table column widths{p_end}
{synopt:{cmd:r(formats)}}table column formats{p_end}

{synoptset 20 tabbed}{...}
{p2col 5 15 19 2: Matrices}{p_end}
{synopt:{cmd:r(pss_table)}}table of results{p_end}
{p2colreset}{...}


{title:References}

{p 4 8 2} Li, J. and J. Fine. 2004. On sample size for sensitivity and specificity in prospective diagnostic accuracy studies. {it: Statistics in Medicine} 23:2537-2550.{p_end}
{p 4 8 2} Miettinen O.S. 1968. The matched pairs design in the case of all-or-none responses. {it:Biometrics} 24:339–352.{p_end}
{p 4 8 2} Obuchowski, N.A. and X.H. Zhou. 2002. Prospective studies of diagnostic test accuracy when disease prevalence is low. {it:Biostatistics} 3:477-492.{p_end}


{marker citation}{title:Citation of {cmd:power twosens}}

{p 4 8 2}{cmd:power pairspec} is not an official Stata command. It is a free contribution
to the research community, like a paper. Please cite it as such: {p_end}

{p 4 8 2}
Linden, A. 2022. POWER PAIRSPEC: Stata module to compute power and sample size for specificity between two diagnostic tests in a paired-sample



{title:Authors}

{p 4 4 2}
Ariel Linden{break}
President, Linden Consulting Group, LLC{break}
alinden@lindenconsulting.org{break}



{title:Also see}

{p 4 8 2} Online: {helpb estat classification}, {helpb lsens}, {helpb power}, {helpb power onesens} (if installed), 
{helpb power onespec} (if installed), {helpb power twosens} (if installed), {helpb power twospec} (if installed), 
{helpb power pairspec} (if installed){p_end}