*! version 4 : January 30th, 2013 *! Jean-Benoit Hardouin, Myriam Blanchin ************************************************************************************************************ * raschpower: Estimation of the power of the Wald test in order to compare the means of the latent trait in two groups of individuals * * Version 1 : January 25, 2010 (Jean-Benoit Hardouin) * Version 1.1 : January 26, 2010 (Jean-Benoit Hardouin) * Version 1.2 : November 1st, 2010 (Jean-Benoit Hardouin) * version 1.3 : May 2th, 2011 (Jean-Benoit Hardouin) * version 1.4 : July 7th, 2011 (Jean-Benoit Hardouin) : minor corrections * version 1.5 : July 11th, 2011 (Jean-Benoit Hardouin) : minor corrections * version 2 : August 30th, 2011 (Jean-Benoit Hardouin, Myriam Blanchin) : corrections * version 3 : October 18th, 2011 (Jean-Benoit Hardouin, Myriam Blanchin) : Extension to the PCM, -method- option, -nbpatterns- options, changes in the presentation of the results * version 3.1 : October 25th, 2011 (Jean-Benoit Hardouin, Myriam Blanchin) : POPULATION+GH method * version 3.2 : February 6th, 2012 (Jean-Benoit Hardouin, Myriam Blanchin) : minor corrections * version 4 : January 30th, 2012 (Jean-Benoit Hardouin, Myriam Blanchin) : Extension to longitudinal design * * Jean-benoit Hardouin, jean-benoit.hardouin@univ-nantes.fr * Myriam Blanchin, myriam.blanchin@univ-nantes.fr * EA 4275 "Biostatistics, Pharmacoepidemiology and Subjectives Measures in Health" * Faculty of Pharmaceutical Sciences - University of Nantes - France * http://www.sphere-nantes.org * * News about this program : http://www.anaqol.org * FreeIRT Project : http://www.freeirt.org * * Copyright 2010-2013 Jean-Benoit Hardouin, Myriam Blanchin * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation; either version 2 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ************************************************************************************************************/ program define raschpower,rclass syntax [varlist] [, n0(int 100) n1(int 100) Gamma(real .5) Difficulties(string) Var(string) Method(string) NBPatterns(int 2) nodata EXPectedpower(real -1) LONGitudinal freevar HTML(string)] version 11 if "`html'" != "" { di "" } tempfile raschpowerfile capture qui save "`raschpowerfile'",replace tempname db d dlong matvar if "`difficulties'"=="" { matrix `d'=[-1\-0.5\0\0.5\1] } else { matrix `d'=`difficulties' } local nbitems=rowsof(`d') local nbmodat=colsof(`d')+1 if "`longitudinal'"!="" & `nbmodat'>2{ di in red "{p}The {hi:longitudinal} option is not available with polytomous items{p_end}" error 198 exit } if "`longitudinal'"==""{ local nbt=1 local nbtotitems=`nbitems' local nbpatmax=2*`nbmodat'^`nbitems' if "`var'"==""{ local var=1 } else{ capture confirm number `var' if !_rc { local var=`var' } else{ matrix `matvar'=`var' capture confirm matrix `matvar' if !_rc & colsof(`matvar')==1 & rowsof(`matvar')==1{ local var=`matvar'[1,1] } else{ di in red "{p}The {hi:var} option should contain a number or a 1x1 matrix for transversal studies{p_end}" error 198 exit } } } matrix `dlong'=`d' local sumd=0 forvalues numit=1/`nbitems'{ local sumd=`sumd'+`d'[`numit',1] } local sumd=`sumd'/`nbitems' if `=abs(`sumd')'>=`=2*sqrt(`var')'{ if "`html'" == ""{ di "{p}WARNING: It is not recommended to use Raschpower when the gap between the global mean of the latent trait (fixed to 0) and the mean of the item parameters is greater than or equal to 2 standard deviation of the latent trait. {p_end}" } else { di "

WARNING: It is not recommended to use Raschpower when the gap between the global mean of the latent trait (fixed to 0) and the mean of the item parameters is greater than or equal to 2 standard deviation of the latent trait.


" } } } else{ local nbt=2 local nbtotitems=2*`nbitems' local nbpatmax=`nbmodat'^(`nbitems'*2) local n1=0 local mean1=0 local mean2=`mean1'+`gamma' if "`var'"==""{ matrix matvar=(1,0\0,1) } else{ matrix `matvar'=`var' capture confirm matrix `matvar' if !_rc & colsof(`matvar')==2 & rowsof(`matvar')==2 & issymmetric(`matvar'){ matrix matvar=`matvar' } else{ di in red "{p}The {hi:var} option should contain a symmetric 2x2 matrix for longitudinal studies{p_end}" error 198 exit } } matrix `dlong'=J(`nbtotitems',`=`nbmodat'-1',.) matrix `dlong'[1,1]=`d' matrix `dlong'[`=`nbitems'+1',1]=`d' } if substr("`method'",1,3)=="pop" | substr("`method'",1,3)=="POP"{ local method POPULATION+GH } if "`method'"=="MEAN+GH"&`nbpatterns'*(`n1'+`n0')>=`nbpatmax' { di in gr "The MEAN+GH will be inefficient compared to GH since the maximal number of pattern's responses" di in gr "is lesser than the number of pattern retained by the MEAN+GH method." di in gr "The -method- option is replaced by GH." local method GH } else if ("`method'"=="MEAN+GH" | "`method'"=="MEAN") & `nbpatmax'>1000000{ di in red "The number of patterns is too high for the chosen method" exit } else if "`method'"=="" { if `nbpatmax'<2000 { local method GH } else { local method POPULATION+GH } } if "`method'"!="MEAN+GH" & "`method'"!="MEAN" & "`method'"!="GH" & "`method'"!="POPULATION+GH"{ di in red "Invalid method name" exit } if "`html'" == "" { di in gr "Method: " in ye "`method'" if "`longitudinal'"==""{ di in gr "Number of individuals in the first group: " in ye `n0' di in gr "Number of individuals in the second group: " in ye `n1' di in green "Group effect: " in ye `gamma' di in gr "Variance of the latent trait: " in ye `var' } else{ di in gr "Number of individuals at each time: " in ye `n0' di in green "Time effect: " in ye `gamma' di in gr "Variance matrix of the latent trait: " matrix list matvar } di in gr "Number of items: " in ye `nbitems' di in green "Difficulties parameters of the items: " } else { di "Method: " in ye "`method'" "
" if "`longitudinal'"==""{ di "Number of individuals in the first group: " in ye `n0' "
" di "Number of individuals in the second group: " in ye `n1' "
" di "Group effect: " in ye `gamma' "
" di "Variance of the latent trait: " in ye `var' "
" } else{ di "Number of individuals at each time: " in ye `n0' "
" di "Time effect: " in ye `gamma' "
" /*@TODO * di in gr "Variance matrix of the latent trait: " "
" * matrix list matvar */ } di "Number of items: " in ye `nbitems' "
" } tempname dd matrix `dd'=`d' local items forvalues i=1/`nbitems' { local items "`items' item`i'" } local modalities forvalues i=1/`=`nbmodat'-1' { local modalities "`modalities' delta_`i'" } matrix colnames `dd'=`modalities' matrix rownames `dd'=`items' if "`html'" == "" { matrix list `dd',noblank nohalf noheader di in gr "Number of studied response's patterns: " in ye `nbpatmax' } else { //di in gr "Number of studied response's patterns: " in ye `nbpatmax' "
" } matrix `dd'=`d' local gamma=`gamma' local tmp=1 qui matrix `db'=J(`=`nbitems'*(`nbmodat'-1)',1,.) forvalues j=1/`nbitems' { forvalues m=1/`=`nbmodat'-1' { qui matrix `db'[`tmp',1]=`d'[`j',`m'] local ++tmp } } if "`data'"=="" { clear if "`method'"!="POPULATION+GH"{ local temp=`nbmodat'^(`nbtotitems') qui range x 0 `=`temp'-1' `temp' qui g t=x loc i=`nbtotitems' qui count if t>0 loc z=r(N) qui while `z'>0 { qui gen item`=`nbtotitems'-`i'+1'=floor(t/`nbmodat'^`=`i'-1') qui replace t=mod(t,`nbmodat'^`=`i'-1') qui count if t>0 loc z=r(N) loc i=`i'-1 } drop t if "`longitudinal'"==""{ qui expand 2 qui gen group=0 in 1/`temp' qui replace group=1 in `=`temp'+1'/`=2*`temp'' } } else { if "`longitudinal'"==""{ qui simirt, clear pcm(`d') cov(`var') group(`=`n1'/(`n1'+`n0')') deltagroup(`gamma') nbobs(1000000) qui drop lt1 qui contract item* group, freq(freq) qui count local patobs=r(N) if `patobs'>=`=(`n0'+`n1')*`nbpatterns''{ qui gen keep=0 qui gsort +group -freq qui replace keep=1 in 1/`=`nbpatterns'*`n0'' qui gsort -group -freq qui replace keep=1 in 1/`=`nbpatterns'*`n1'' } else{ qui gen keep=1 } } else{ qui simirt, clear pcm(`dlong') covmat(`matvar') mu(`mean1' `mean2') dim(`nbitems' `nbitems') nbobs(1000000) forvalues j=1/`nbitems'{ rename itemA`j' item`j' rename itemB`j' item`=`nbitems'+`j'' } qui drop lt1 lt2 qui contract item*, freq(freq) local patobs=r(N) if `patobs'>=`=`n0'*`nbpatterns''{ qui gen keep=0 qui gsort -freq qui replace keep=1 in 1/`=`nbpatterns'*`n0'' } else{ qui gen keep=1 } } qui keep if keep==1 qui count local retain=r(N) di "Number of kept patterns:`retain'" local method GH } if "`longitudinal'"==""{ qui gen mean1=-`n1'*`gamma'/(`n0'+`n1') if group==0 qui replace mean1=`n0'*`gamma'/(`n0'+`n1') if group==1 } else{ qui gen mean1=`mean1' qui gen mean2=`mean2' } if "`method'"=="GH" { local temp=`nbmodat'^(`nbtotitems') local diff0=0 qui gen proba=. local dixj=10 qui count local tmp=r(N) forvalues i=1/`tmp' { local dix=floor(`tmp'/10) if mod(`i',`dix')==0 { if "`html'" == "" { if "`dixj'"!="10" { di ".." _c } di "`dixj'%" _c } local dixj=`dixj'+10 } forvalues t=1/`nbt'{ local int`t'=1 forvalues j=`=(`t'-1)*`nbitems'+1'/`=`t'*`nbitems'' { qui su item`j' in `i' local rep=r(mean) local diff0=0 local diff1=`dlong'[`j',1] local sum "1+exp(x`t'-`diff1')" forvalues m=2/`=`nbmodat'-1' { local diff`m'=`diff`=`m'-1''+`dlong'[`j',`m'] local sum "`sum'+exp(`m'*x`t'-`diff`m'')" } local int`t' "(`int`t''*exp(`rep'*x`t'-`diff`rep''))/(`sum')" } } if "`longitudinal'"==""{ qui su mean1 in `i' local mean=r(mean) qui gausshermite `int1',mu(`mean') sigma(`=sqrt(`var')') display name(x1) qui replace proba=r(int) in `i' } else{ local int "`int1'*`int2'" matrix mean=(`mean1',`mean2') qui gausshermite `int',mu(mean) var(matvar) display name(x1 x2) qui replace proba=r(int) in `i' } } di } else { qui gen proba=1 forvalues t=1/`nbt'{ forvalues i=`=(`t'-1)*`nbitems'+1'/`=`t'*`nbitems'' { local diff0=0 local diff1=`dlong'[`i',1] qui gen eps0=1 qui gen eps1=exp(mean`t'-`diff1') qui gen d=eps0+eps1 forvalues m=2/`=`nbmodat'-1' { local diff`m'=`diff`=`m'-1''+`dlong'[`i',`m'] qui gen eps`m'=exp(`m'*mean`t'-`diff`m'') qui replace d=d+eps`m' } local listeps forvalues m=0/`=`nbmodat'-1' { qui replace proba=proba*eps`m'/d if item`i'==`m' local listeps `listeps' eps`m' } qui drop `listeps' d } } if "`method'"=="MEAN+GH" { set tracedepth 1 if "`longitudinal'"==""{ qui gen keep=0 qui gsort -group -proba local min=min(`=`nbmodat'^`nbitems'',`=`n1'*`nbpatterns'') qui replace keep=1 in 1/`min' qui gsort +group -proba local min=min(`=`nbmodat'^`nbitems'',`=`n0'*`nbpatterns'') qui replace keep=1 in 1/`min' qui keep if keep==1 qui su proba if group==0 local sumproba0=r(sum)*100 qui su proba if group==1 local sumproba1=r(sum)*100 } else{ qui gen keep=0 qui gsort -proba local min=min(`nbpatmax',`=`n0'*`nbpatterns'') qui replace keep=1 in 1/`min' qui keep if keep==1 } qui drop keep proba local diff0=0 qui gen proba=. qui count local nnew=r(N) di in gr "Number of studied response's patterns for the GH step: " in ye `nnew' if "`longitudinal'"==""{ di in gr "(" in ye %6.2f `sumproba0' in gr "% of the group 0 and " in ye %6.2f `sumproba1' in gr "% of the group 1)" } local dixj=10 forvalues i=1/`nnew' { local dix=floor(`nnew'/10) if mod(`i',`dix')==0 { if "`dixj'"!="10" { di ".." _c } di "`dixj'%" _c local dixj=`dixj'+10 } forvalues t=1/`nbt'{ local int`t'=1 forvalues j=`=(`t'-1)*`nbitems'+1'/`=`t'*`nbitems'' { qui su item`j' in `i' local rep=r(mean) local diff0=0 local diff1=`dlong'[`j',1] local sum "1+exp(x`t'-`diff1')" forvalues m=2/`=`nbmodat'-1' { local diff`m'=`diff`=`m'-1''+`dlong'[`j',`m'] local sum "`sum'+exp(`m'*x`t'-`diff`m'')" } local int`t' "(`int`t''*exp(`rep'*x`t'-`diff`rep''))/(`sum')" } } if "`longitudinal'"==""{ qui su mean1 in `i' local mean=r(mean) qui gausshermite `int1',mu(`mean') sigma(`=sqrt(`var')') display name(x1) qui replace proba=r(int) in `i' } else{ local int "`int1'*`int2'" matrix mean=(`mean1',`mean2') qui gausshermite `int',mu(mean) sigma(matvar) display qui replace proba=r(int) in `i' } } } } qui gen eff=proba qui gen eff2=. if "`longitudinal'"==""{ qui keep item* eff* group proba local p1=1/`n1' local p0=1/`n0' qui replace eff2=floor(eff/`p1') if group==1 qui replace eff2=floor(eff/`p0') if group==0 qui replace eff=eff-eff2*(`p1'*group+`p0'*(1-group)) qui su eff2 if group==1 local aff1=r(sum) qui su eff2 if group==0 local aff0=r(sum) local unaff1=`n1'-`aff1' local unaff0=`n0'-`aff0' qui gen efftmp=eff2 qui gsort + group - eff qui replace eff2=eff2+1 in 1/`unaff0' qui gsort - group - eff qui replace eff2=eff2+1 in 1/`unaff1' qui drop if eff2==0 gsort group item* qui expand eff2 } else{ qui keep item* eff* proba local p0=1/`n0' qui replace eff2=floor(eff/`p0') qui replace eff=eff-eff2*`p0' qui su eff2 local aff0=r(sum) local unaff0=`n0'-`aff0' qui gen efftmp=eff2 qui gsort - eff qui replace eff2=eff2+1 in 1/`unaff0' qui drop if eff2==0 gsort item* qui expand eff2 } qui drop proba eff eff2 } qui alpha item* local alpha=r(alpha) if "`longitudinal'"==""{ qui gen groupc=-`n1'/(`n0'+`n1') if group==0 qui replace groupc=`n0'/(`n0'+`n1') if group==1 if `nbmodat'==2 { qui gen i=_n tempname diff matrix `diff'=`dd'' qui reshape long item, i(i) qui rename item rep qui rename _j item qui gen offset=0 forvalues i=1/`nbitems' { qui replace offset=-`diff'[1,`i'] if item==`i' } constraint 1 _cons=`=ln(`var')' qui xtlogit rep groupc ,nocons i(i) offset(offset) constraint(1) tempname b V } else { matrix `db'=`db'' qui pcm item*, fixed(`db') covariates(groupc) fixedmu fixedvar(`var') } tempname b V matrix `b'=e(b) matrix `V'=e(V) local gammaest=`b'[1,1] local se=`V'[1,1]^.5 } else{ forvalues i=1/`nbitems'{ rename item`i' t1item`i' } forvalues i=`=`nbitems'+1'/`nbtotitems'{ rename item`i' t2item`=`i'-`nbitems'' } qui gen i=_n local list="" forvalues i=1/`nbitems'{ local list="`list' t@item`i'" } qui reshape long `list', i(i) j(temps) qui reshape long titem, i(i temps) j(item) qui drop if titem==. qui gen offset=0 local itemnb=1 forvalues t=1/`nbt'{ forvalues i=1/`nbitems' { qui replace offset=-`dlong'[`itemnb',1] if item==`i' & temps==`t' local ++itemnb } } gen t1=temps==1 gen t2=temps==2 matrix C=cholesky(matvar) constraint define 1 [i1_1]t1=`=C[1,1]' constraint define 2 [i1_2]t2=`=C[2,2]' constraint define 3 [i1_2_1]_cons=`=C[2,1]' eq b1:t1 eq b2:t2 qui gllamm titem t2,i(i) link(logit) nocons fam(bin) nrf(2) eq(b1 b2) constraints(1 2 3) iterate(20) trace offset(offset) tempname b V matrix `b'=e(b) matrix `V'=e(V) local gammaest=`b'[1,1] local se=`V'[1,1]^.5 local n1=`n0' } local poweruni=1-normal(1.96-`gamma'/`se') if "`html'" == "" { di di di in gr "{hline 91}" di _col(60) "Estimation with the " di _col(50) "Cramer-Rao bound" _col(75) "classical formula" di in gr "{hline 91}" } else { di "" di "" di "" di "" } if "`longitudinal'"==""{ if "`gammafixed'"=="" { if "`html'" == "" { di in green "Estimated value of the group effect" _col(59) in ye %7.2f `gammaest' } else { di "" } } if "`html'" == "" { di in green "Estimation of the s.e. of the group effect" _col(59) in ye %7.2f `se' di in green "Estimation of the variance of the group effect" _col(56) in ye %10.4f `=`se'^2' } else { di "" di "" } local power=1-normal(1.96-`gamma'/`se')+normal(-1.96-`gamma'/`se') local clpower=normal(sqrt(`n1'*`gamma'^2/((`n1'/`n0'+1)*`var'))-1.96) local clnsn=(`n1'/`n0'+1)/((`n1'/`n0')*(`gamma'/sqrt(`var'))^2)*(1.96+invnorm(`poweruni'))^2 } else{ if "`gammafixed'"=="" { if "`html'" == "" { di in green "Estimated value of the time effect" _col(59) in ye %7.2f `gammaest' } else { di "" } } if "`html'" == "" { di in green "Estimation of the s.e. of the time effect" _col(59) in ye %7.2f `se' di in green "Estimation of the variance of the time effect" _col(56) in ye %10.4f `=`se'^2' } else { di "" di "" } local clpower=normal(sqrt(`n0'*`gamma'^2)/(2*(`=matvar[1,1]'-`=matvar[2,1]'))-1.96) local clnsn=2*(`=matvar[1,1]'-`=matvar[2,1]')*(1.96+invnorm(`poweruni'))^2/(`gamma'^2) } if "`html'" == "" { di in green "Estimation of the power" _col(60) in ye %6.4f `poweruni' _col(86) in ye %6.4f `clpower' di in green "Number of patients for a power of" %6.2f `=`poweruni'*100' "%" _col(59) in ye `n0' "/" `n1' _col(77) in ye %7.2f `clnsn' "/" %7.2f `=`clnsn'*`n1'/`n0'' } else { di "" di "" } local ratio=(`n0'+`n1')/(`clnsn'*(1+`n1'/`n0')) if "`html'" == "" { di in green "Ratio of the number of patients" in ye %6.2f _col(68)`ratio' } else { di "" } if `expectedpower'!=-1 { qui sampsi `=-`gamma'/2' `=`gamma'/2', sd1(`=sqrt(`var')') sd2(`=sqrt(`var')') alpha(0.05) power(`expectedpower') ratio(`=`n1'/`n0'') local expn_1=r(N_1) local expn_2=r(N_2) local expn2=`expn_1'*`ratio' di in green "Number of patients for a power of" %6.2f `=`expectedpower'*100' "%" _col(51) in ye %7.2f `expn2' "/" %7.2f `=`expn2'*`n1'/`n0'' _col(77) in ye %7.2f `expn_1' "/" %7.2f `expn_2' } if "`html'" == "" { di in gr "{hline 91}" } else { di "
Estimation with the
Cramer-Rao boundclassical formula
Estimated value of the group effect" in ye %7.2f `gammaest' "
Estimation of the s.e. of the group effect" in ye %7.2f `se' "
Estimation of the variance of the group effect" in ye %10.4f `=`se'^2' "
Estimated value of the time effect" in ye %7.2f `gammaest' "
Estimation of the s.e. of the time effect" in ye %7.2f `se' "
Estimation of the variance of the time effect" in ye %10.4f `=`se'^2' "
Estimation of the power" in ye %6.4f `poweruni' "" in ye %6.4f `clpower' "
Number of patients for a power of" %6.2f `=`poweruni'*100' "%" in ye `n0' "/" `n1' "" in ye %7.2f `clnsn' "/" %7.2f `=`clnsn'*`n1'/`n0'' "
Ratio of the number of patients" in ye %6.2f `ratio' "
" } return scalar EstGamma=`gammaest' return scalar CRbound=`=`se'^2' return scalar CRPower=`poweruni' return scalar ClPower=`clpower' return scalar ClSS=`clnsn' return scalar Ratio=`ratio' return scalar CronbachAlpha=`alpha' capture qui use `raschpowerfile',clear end