*! Version 2.1 13December2017
************************************************************************************************************
* nopalera : NOPALERA algorithm
* Version 2: October 24, 2015 
*
* Historic:
* Version 1 (2015-07-20): Jean-Benoit Hardouin /*ICC; rsbynpirt module*/
* Version 1.1 (2015-10-24): Jean-Benoit Hardouin /*NOPALERA module, ISOQOL 2015*/
*
* Jean-benoit Hardouin, phD, Assistant Professor
* INSERM UMR 1246-SPHERE
* MethodS in Patients-centered outcomes and HEalth ResEarches
* University of Nantes - Faculty of Pharmaceutical Sciences
* France
* jean-benoit.hardouin@anaqol.org
*
* News about this program: http://www.anaqol.org
*
* Copyright 2015,2017 Jean-Benoit Hardouin
*
* 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 nopalera, rclass 
version 8.0
syntax varlist(numeric min=4) [,  noGraph noBootstrap corr(numlist) NBBootstrap(int 10)]

set more off
tempfile file1 file3
qui save `file1', replace
preserve
local nbitems : word count `varlist'
qui count
local nind=r(N)
tokenize `varlist'
if mod(`nbitems',2)!=0 {
   di in red "You must indicate an even number of items"
   exit
}
else {
   local nbitems=`nbitems'/2
}
if "`corr'"=="" {
  forvalues i=1/`nbitems'{
     local corr "`corr' 0"
  }
}
local listofitems1
local listofitems2
forvalues i=1/`nbitems' {
   local listofitems1 `listofitems1' ``i''
   local listofitems2 `listofitems2' ``=`i'+`nbitems'''
}

di "NOPALERA: an algorithm to detect Response-shift at items level using non parametric IRT"
di "Number of individuals: `nind'"
di "Number of items: `nbitems'"
di "Number of Boostrap replications: `nbbootstrap'" 

/*******************************************************************************
Une boucle pour calculer le score, définir le score maximum par item et global
*******************************************************************************/
tempvar varscore1 varscore2
qui gen `varscore1'=0
qui gen `varscore2'=0
label variable `varscore1' "Total score time 1"
label variable `varscore2' "Total score time 2"
local scoremax=0
local flag=0


local modamax=0
forvalues i=1/`nbitems' {
   local corr`i': word `i' of `corr'
   qui replace ``=`i'+`nbitems'''=``=`i'+`nbitems'''+`corr`i''
   qui replace `varscore1'=`varscore1'+``i''
   qui replace `varscore2'=`varscore2'+``=`i'+`nbitems'''
   qui su ``i''
   local modamax`i'=r(max)
   qui su ``=`i'+`nbitems'''
   local modamax`i'=r(max)
   if r(min)!=0 {
      local flag=1
   }
   local scoremax=`scoremax'+`modamax`i''
      if `modamax`i''!=1 {
      local flagbin=0
   }
   if `modamax`i''>`modamax' {
      local modamax=`modamax`i''
   }
}
qui save `file3', replace

/*******************************************************************************
Quelques tests de conformité
*******************************************************************************/
if `flag'==1 {
   *di as error "The lower answer category of each item must be 0"
   *exit
}

qui su `varscore1'
local maxscore=r(max)
qui su `varscore1'
if `r(max)'>`maxscore' {
   local maxscore=r(max)
}

/* sauvegarde des données */
tempfile rsbynpirtfile rsbynpirtfile1 rsbynpirtfile2
tempvar score
qui save `rsbynpirtfile', replace

/*On récupère les données des ICC au temps 1 puis au temps 2*/
qui traces `listofitems1', nograph icc saveicc
qui drop _all
tempname mat1
qui matrix `mat1'=r(matscore)
qui svmat `mat1', names(t1item)
forvalues i=1/`nbitems' {
   local j: word `i' of `listofitems1'
   qui rename t1item`i' `j'
}
qui rename t1item`=`nbitems'+1' `score'
qui contract `score' `listofitems1'
qui sort `score'
qui save `rsbynpirtfile1', replace

qui use `rsbynpirtfile', clear
qui traces `listofitems2', nograph icc saveicc
qui drop _all
tempname mat2
qui matrix `mat2'=r(matscore)
qui svmat `mat2', names(t2item)

/*puis on fait un seul fichier avec les deux jeux de données*/
forvalues i=1/`nbitems' {
   local j: word `i' of `listofitems2'
   qui rename t2item`i' `j'
}
qui rename t2item`=`nbitems'+1' `score'
qui contract `score' `listofitems2'
qui sort `score'
qui merge 1:1 `score' using `rsbynpirtfile1'

/*représentation simultanée des ICC aux deux temps pour chaque item*/
if "`graph'"=="" {
   forvalues i=1/`nbitems' {
      twoway (line ``i'' `score') (line ``=`i'+`nbitems''' `score'), name(``i'',replace)
   }
}
qui drop if `score'==0|`score'==`scoremax'

/*calcul des deux AUC pour chaque item*/
local tests
forvalues i=1/`nbitems' {
   qui su ``i'' 
   local AUC``i''=r(mean)
   local AUC``i''=(`AUC``i'''*`scoremax')
   qui su ``=`i'+`nbitems''' 
   local AUC`=`i'+`nbitems''=r(mean)
   local AUC`=`i'+`nbitems''=(`AUC`=`i'+`nbitems'''*`scoremax')
   tempname diff``i''
   gen `diff``i'''=abs(``i''-``=`i'+`nbitems''')
   qui su `diff``i'''
   local d``i''=`r(sum)'/(`scoremax'*`modamax`i'')*100
   local var``i''=`r(sd)'*100
   return scalar AUC``i''=`AUC``i'''
   return scalar AUC``=`i'+`nbitems'''=`AUC`=`i'+`nbitems'''
   local tests `tests' b``i''=(r(AUC``=`i'+`nbitems''')-r(AUC``i''))
}

local abc=0


/* 10 bootstrap pour estimer les intervalles de confiance des différences entre les deux AUC*/
if "`bootstrap'"=="" {
    tempfile file2
    qui save `file2', replace
    qui use `file1', clear
    qui bootstrap `tests' , rep(`nbbootstrap') nol noh nodots : nopalera `varlist', nograph nobootstrap 
    tempname mbootstrap
	matrix `mbootstrap'=r(table)
	*matrix list `mbootstrap'
    qui use `file3', clear
    *set trace on
	set tracedepth 1

	/*Création de la matrice p qui va permettre de décaler les ICC*/
	tempname p
	matrix `p'=J(`=(`scoremax'+1)*(`nbitems'+1)',`=`nbitems'*3+1',.)
	forvalues s=0/`scoremax' {
	   matrix `p'[`=`s'+1',1]=`s'
	   forvalues i=1/`nbitems' {
		  matrix `p'[`=`s'+1',`=3*`i'-1']=`s'
	   }
	}
	forvalues i=1/`nbitems' {
	   forvalues s=0/`scoremax' {
		  qui su ``i'' if `varscore1'==`s'
		  matrix `p'[`=`s'+1',`=3*`i'']=r(mean)
	   }
	   forvalues s=0/`scoremax' {
		  qui su ``=`i'+`nbitems''' if `varscore2'==`s'
		  *di "qui su ``=`i'+`nbitems''' if `varscore2'==`s'"
		  if `mbootstrap'[4,`i']>=0.05 {
			 matrix `p'[`=`s'+1',`=3*`i'+1']=r(mean)
			 local prec=1
			 local prec=0.01 /*pas d'arrondi*/
		  }
		  else {
		     if `nind'/`scoremax'>20 {
			    local prec=0.5
			    local prec=1
			    local prec=0.01 /*pas d'arrondi*/
			 }
			 else {
			    local prec=1
			    local prec=0.01 /*pas d'arrondi*/
			 }
			 matrix `p'[`=`i'*(`scoremax'+1)+`s'+1',`=3*`i'-1']=round(`s'+`mbootstrap'[1,`i']/(`modamax`i''),`prec')
			 matrix `p'[`=`i'*(`scoremax'+1)+`s'+1',`=3*`i'+1']=r(mean)
		  }
	   }
	}
	*matrix list `p'
	*matrix list `p'
	di
	di "Research of uniform recalibration at item-level"
	di
	di "{hline 105}"
	di                                                               _col(45) "Bootstrap"                               _col(78) "  Normal-based"
	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"
	di "{hline 105}"
	forvalues i=1/`nbitems' {
	   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')
	}
	di "{hline 105}"
	local abc=1
}
if `abc'==1 {
	drop _all
	qui svmat `p'  
	qui rename `p'1 score
	local testsb
	forvalues i=1/`nbitems' {
	     qui rename `p'`=`i'*3-1' score``i''
	     qui rename `p'`=`i'*3' t1``i''
	     qui rename `p'`=`i'*3+1' t2``i''
		 /*interpolation linéaire et nouvelles ICC corrigées*/
    	 qui ipolate t2``i'' score``i'' , generate(t2adj``i'')
		 forvalues j=0/`=floor(round(`mbootstrap'[1,`i']/(`modamax`i''),`prec'))' {
		      qui replace t2adj``i''=0 if score``i''==`j'&t2adj``i''==.
	     }
		 forvalues j=`=`scoremax'+floor(round(`mbootstrap'[1,`i']/(`modamax`i''),`prec'))'/`scoremax' {
		      qui replace t2adj``i''=1 if score``i''==`j'&t2adj``i''==.
	     }
		 qui gen diff``i''=abs(t2adj``i''-t1``i'')
		 qui su diff``i''
		 local ABC``i''=`r(mean)'*`scoremax'
		 return scalar ABC``i''=`ABC``i'''
		 if "`graph'"=="" { 
		    qui sort score``i''
			qui gen scoreunadj``i''=score``i''-round(`mbootstrap'[1,`i']/(`modamax`i''),`prec')
			*twoway (line t1``i'' score``i'')(line t2``i'' score``i'')(line t2adj``i'' score``i'') ,name(``i''c,replace)
			twoway (line t1``i'' score``i'')(line t2``i'' scoreunadj``i'')(line t2adj``i'' score``i'') ,name(``i''c,replace)
		    *di "twoway (line t1``i'' score``i'')(line t2``i'' score``i'')(line t2adj``i'' score``i'') ,name(``i''c,replace)"
			*su
		 }
		 local testsb `testsb' c``i''=(r(ABC``i''))

    }
	
	/* 10 bootstrap pour estimer les intervalles de confiance des ABC*/
	if "`bootstrap'"=="" {
		tempfile file3
		qui save `file3', replace
		qui use `file1', clear
		qui bootstrap `tests' , rep(`nbbootstrap') nol noh nodots : nopalera `varlist', nograph nobootstrap 
		tempname mbootstrapb
		matrix `mbootstrapb'=r(table)
		*matrix list `mbootstrapb'
		di
		di "Research of non-uniform recalibration at item-level"
		di
		di "{hline 77}"
		di                        _col(29) "Bootstrap"                               _col(62) "  Normal-based"
		di "Items" _col(24) "ABC" _col(29) "Std. Err." _col(47) "z" _col(54) "P>|z|" _col(62) "[95% Conf. Int.]"
		di "{hline 77}"
		forvalues i=1/`nbitems' {
		   local z`i'=`ABC``i'''/`mbootstrapb'[2,`i']
		   local p`i'=2*(1-normal(abs(`z`i'')))
		   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']'
		}
		di "{hline 77}"
		local abc=1
	}	
	
	
}

if "`bootstrap'"=="" {
   return matrix p=`p'
}
qui restore , preserve
end