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323 lines
11 KiB
Plaintext
323 lines
11 KiB
Plaintext
7 months ago
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*! Version 2.1 13December2017
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************************************************************************************************************
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* nopalera : NOPALERA algorithm
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* Version 2: October 24, 2015
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*
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* Historic:
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* Version 1 (2015-07-20): Jean-Benoit Hardouin /*ICC; rsbynpirt module*/
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* Version 1.1 (2015-10-24): Jean-Benoit Hardouin /*NOPALERA module, ISOQOL 2015*/
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*
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* Jean-benoit Hardouin, phD, Assistant Professor
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* INSERM UMR 1246-SPHERE
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* MethodS in Patients-centered outcomes and HEalth ResEarches
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* University of Nantes - Faculty of Pharmaceutical Sciences
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* France
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* jean-benoit.hardouin@anaqol.org
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*
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* News about this program: http://www.anaqol.org
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*
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* Copyright 2015,2017 Jean-Benoit Hardouin
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*
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* This program is free software; you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation; either version 2 of the License, or
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* (at your option) any later version.
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*
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License
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* along with this program; if not, write to the Free Software
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* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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*
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************************************************************************************************************
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program define nopalera, rclass
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version 8.0
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syntax varlist(numeric min=4) [, noGraph noBootstrap corr(numlist) NBBootstrap(int 10)]
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set more off
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tempfile file1 file3
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qui save `file1', replace
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preserve
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local nbitems : word count `varlist'
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qui count
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local nind=r(N)
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tokenize `varlist'
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if mod(`nbitems',2)!=0 {
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di in red "You must indicate an even number of items"
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exit
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}
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else {
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local nbitems=`nbitems'/2
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}
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if "`corr'"=="" {
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forvalues i=1/`nbitems'{
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local corr "`corr' 0"
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}
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}
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local listofitems1
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local listofitems2
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forvalues i=1/`nbitems' {
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local listofitems1 `listofitems1' ``i''
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local listofitems2 `listofitems2' ``=`i'+`nbitems'''
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}
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di "NOPALERA: an algorithm to detect Response-shift at items level using non parametric IRT"
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di "Number of individuals: `nind'"
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di "Number of items: `nbitems'"
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di "Number of Boostrap replications: `nbbootstrap'"
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/*******************************************************************************
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Une boucle pour calculer le score, définir le score maximum par item et global
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*******************************************************************************/
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tempvar varscore1 varscore2
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qui gen `varscore1'=0
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qui gen `varscore2'=0
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label variable `varscore1' "Total score time 1"
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label variable `varscore2' "Total score time 2"
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local scoremax=0
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local flag=0
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local modamax=0
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forvalues i=1/`nbitems' {
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local corr`i': word `i' of `corr'
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qui replace ``=`i'+`nbitems'''=``=`i'+`nbitems'''+`corr`i''
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qui replace `varscore1'=`varscore1'+``i''
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qui replace `varscore2'=`varscore2'+``=`i'+`nbitems'''
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qui su ``i''
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local modamax`i'=r(max)
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qui su ``=`i'+`nbitems'''
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local modamax`i'=r(max)
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if r(min)!=0 {
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local flag=1
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}
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local scoremax=`scoremax'+`modamax`i''
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if `modamax`i''!=1 {
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local flagbin=0
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}
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if `modamax`i''>`modamax' {
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local modamax=`modamax`i''
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}
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}
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qui save `file3', replace
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/*******************************************************************************
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Quelques tests de conformité
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*******************************************************************************/
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if `flag'==1 {
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*di as error "The lower answer category of each item must be 0"
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*exit
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}
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qui su `varscore1'
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local maxscore=r(max)
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qui su `varscore1'
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if `r(max)'>`maxscore' {
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local maxscore=r(max)
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}
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/* sauvegarde des données */
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tempfile rsbynpirtfile rsbynpirtfile1 rsbynpirtfile2
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tempvar score
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qui save `rsbynpirtfile', replace
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/*On récupère les données des ICC au temps 1 puis au temps 2*/
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qui traces `listofitems1', nograph icc saveicc
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qui drop _all
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tempname mat1
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qui matrix `mat1'=r(matscore)
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qui svmat `mat1', names(t1item)
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forvalues i=1/`nbitems' {
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local j: word `i' of `listofitems1'
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qui rename t1item`i' `j'
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}
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qui rename t1item`=`nbitems'+1' `score'
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qui contract `score' `listofitems1'
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qui sort `score'
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qui save `rsbynpirtfile1', replace
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qui use `rsbynpirtfile', clear
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qui traces `listofitems2', nograph icc saveicc
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qui drop _all
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tempname mat2
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qui matrix `mat2'=r(matscore)
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qui svmat `mat2', names(t2item)
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/*puis on fait un seul fichier avec les deux jeux de données*/
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forvalues i=1/`nbitems' {
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local j: word `i' of `listofitems2'
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qui rename t2item`i' `j'
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}
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qui rename t2item`=`nbitems'+1' `score'
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qui contract `score' `listofitems2'
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qui sort `score'
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qui merge 1:1 `score' using `rsbynpirtfile1'
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/*représentation simultanée des ICC aux deux temps pour chaque item*/
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if "`graph'"=="" {
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forvalues i=1/`nbitems' {
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twoway (line ``i'' `score') (line ``=`i'+`nbitems''' `score'), name(``i'',replace)
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}
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}
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qui drop if `score'==0|`score'==`scoremax'
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/*calcul des deux AUC pour chaque item*/
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local tests
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forvalues i=1/`nbitems' {
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qui su ``i''
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local AUC``i''=r(mean)
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local AUC``i''=(`AUC``i'''*`scoremax')
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qui su ``=`i'+`nbitems'''
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local AUC`=`i'+`nbitems''=r(mean)
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local AUC`=`i'+`nbitems''=(`AUC`=`i'+`nbitems'''*`scoremax')
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tempname diff``i''
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gen `diff``i'''=abs(``i''-``=`i'+`nbitems''')
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qui su `diff``i'''
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local d``i''=`r(sum)'/(`scoremax'*`modamax`i'')*100
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local var``i''=`r(sd)'*100
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return scalar AUC``i''=`AUC``i'''
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return scalar AUC``=`i'+`nbitems'''=`AUC`=`i'+`nbitems'''
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local tests `tests' b``i''=(r(AUC``=`i'+`nbitems''')-r(AUC``i''))
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}
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local abc=0
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/* 10 bootstrap pour estimer les intervalles de confiance des différences entre les deux AUC*/
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if "`bootstrap'"=="" {
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tempfile file2
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qui save `file2', replace
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qui use `file1', clear
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qui bootstrap `tests' , rep(`nbbootstrap') nol noh nodots : nopalera `varlist', nograph nobootstrap
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tempname mbootstrap
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matrix `mbootstrap'=r(table)
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*matrix list `mbootstrap'
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qui use `file3', clear
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*set trace on
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set tracedepth 1
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/*Création de la matrice p qui va permettre de décaler les ICC*/
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tempname p
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matrix `p'=J(`=(`scoremax'+1)*(`nbitems'+1)',`=`nbitems'*3+1',.)
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forvalues s=0/`scoremax' {
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matrix `p'[`=`s'+1',1]=`s'
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forvalues i=1/`nbitems' {
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matrix `p'[`=`s'+1',`=3*`i'-1']=`s'
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}
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}
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forvalues i=1/`nbitems' {
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forvalues s=0/`scoremax' {
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qui su ``i'' if `varscore1'==`s'
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matrix `p'[`=`s'+1',`=3*`i'']=r(mean)
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}
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forvalues s=0/`scoremax' {
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qui su ``=`i'+`nbitems''' if `varscore2'==`s'
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*di "qui su ``=`i'+`nbitems''' if `varscore2'==`s'"
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if `mbootstrap'[4,`i']>=0.05 {
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matrix `p'[`=`s'+1',`=3*`i'+1']=r(mean)
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local prec=1
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local prec=0.01 /*pas d'arrondi*/
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}
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else {
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if `nind'/`scoremax'>20 {
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local prec=0.5
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local prec=1
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local prec=0.01 /*pas d'arrondi*/
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}
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else {
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local prec=1
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local prec=0.01 /*pas d'arrondi*/
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}
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matrix `p'[`=`i'*(`scoremax'+1)+`s'+1',`=3*`i'-1']=round(`s'+`mbootstrap'[1,`i']/(`modamax`i''),`prec')
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matrix `p'[`=`i'*(`scoremax'+1)+`s'+1',`=3*`i'+1']=r(mean)
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}
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}
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}
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*matrix list `p'
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*matrix list `p'
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di
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di "Research of uniform recalibration at item-level"
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di
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di "{hline 105}"
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di _col(45) "Bootstrap" _col(78) " Normal-based"
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di "Items" _col(18) "AUC t1" _col(28) "AUC t2" _col(38) "VarAUC" _col(45) "Std. Err." _col(63) "z" _col(70) "P>|z|" _col(78) "[95% Conf. Int.]" _col(96) "Correction"
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di "{hline 105}"
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forvalues i=1/`nbitems' {
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di "``i''/``=`i'+`nbitems'''" _col(19) %5.2f `AUC``i''' _col(29) %5.2f `AUC`=`i'+`nbitems''' _col(39) %5.2f `=`AUC``i'''-`AUC`=`i'+`nbitems'''' _col(49) %5.2f `mbootstrap'[2,`i'] _col(59) %5.2f `mbootstrap'[3,`i'] _col(69) %5.4f `mbootstrap'[4,`i'] _col(79) %5.2f `mbootstrap'[5,`i'] _col(89) %5.2f `mbootstrap'[6,`i'] _col(100) %6.2f round(`mbootstrap'[1,`i']/(`modamax`i''),`prec')
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}
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di "{hline 105}"
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local abc=1
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}
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if `abc'==1 {
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drop _all
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qui svmat `p'
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qui rename `p'1 score
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local testsb
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forvalues i=1/`nbitems' {
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qui rename `p'`=`i'*3-1' score``i''
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qui rename `p'`=`i'*3' t1``i''
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qui rename `p'`=`i'*3+1' t2``i''
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/*interpolation linéaire et nouvelles ICC corrigées*/
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qui ipolate t2``i'' score``i'' , generate(t2adj``i'')
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forvalues j=0/`=floor(round(`mbootstrap'[1,`i']/(`modamax`i''),`prec'))' {
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qui replace t2adj``i''=0 if score``i''==`j'&t2adj``i''==.
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}
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forvalues j=`=`scoremax'+floor(round(`mbootstrap'[1,`i']/(`modamax`i''),`prec'))'/`scoremax' {
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qui replace t2adj``i''=1 if score``i''==`j'&t2adj``i''==.
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}
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qui gen diff``i''=abs(t2adj``i''-t1``i'')
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qui su diff``i''
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local ABC``i''=`r(mean)'*`scoremax'
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return scalar ABC``i''=`ABC``i'''
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if "`graph'"=="" {
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qui sort score``i''
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qui gen scoreunadj``i''=score``i''-round(`mbootstrap'[1,`i']/(`modamax`i''),`prec')
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*twoway (line t1``i'' score``i'')(line t2``i'' score``i'')(line t2adj``i'' score``i'') ,name(``i''c,replace)
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twoway (line t1``i'' score``i'')(line t2``i'' scoreunadj``i'')(line t2adj``i'' score``i'') ,name(``i''c,replace)
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*di "twoway (line t1``i'' score``i'')(line t2``i'' score``i'')(line t2adj``i'' score``i'') ,name(``i''c,replace)"
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*su
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}
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local testsb `testsb' c``i''=(r(ABC``i''))
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}
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/* 10 bootstrap pour estimer les intervalles de confiance des ABC*/
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if "`bootstrap'"=="" {
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tempfile file3
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qui save `file3', replace
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qui use `file1', clear
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qui bootstrap `tests' , rep(`nbbootstrap') nol noh nodots : nopalera `varlist', nograph nobootstrap
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tempname mbootstrapb
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matrix `mbootstrapb'=r(table)
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*matrix list `mbootstrapb'
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di
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di "Research of non-uniform recalibration at item-level"
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di
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di "{hline 77}"
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di _col(29) "Bootstrap" _col(62) " Normal-based"
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di "Items" _col(24) "ABC" _col(29) "Std. Err." _col(47) "z" _col(54) "P>|z|" _col(62) "[95% Conf. Int.]"
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di "{hline 77}"
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forvalues i=1/`nbitems' {
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local z`i'=`ABC``i'''/`mbootstrapb'[2,`i']
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local p`i'=2*(1-normal(abs(`z`i'')))
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di "``i''/``=`i'+`nbitems'''" _col(23) %5.2f `ABC``i''' _col(33) %5.2f `mbootstrapb'[2,`i'] _col(43) %5.2f `z`i'' _col(53) %5.4f `p`i'' _col(63) %5.2f `=`ABC``i'''-1.96*`mbootstrapb'[2,`i']' _col(73) %5.2f `=`ABC``i'''+1.96*`mbootstrapb'[2,`i']'
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}
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di "{hline 77}"
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local abc=1
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}
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}
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if "`bootstrap'"=="" {
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return matrix p=`p'
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}
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qui restore , preserve
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end
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