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************************************************************************************************************
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* hcaccprox: Hierachical Clusters Analysis/CCPROX
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* Version 1: May 12, 2004
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* Add-on: Partition version 2 (2004-04-10)
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*
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* Use the Detect Stata program (http://freeirt.free.fr)
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*
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* Historic :
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* Version 1 [2004-01-18], Jean-Benoit Hardouin
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*
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* Jean-benoit Hardouin, Regional Health Observatory of Orl<72>ans - France
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* jean-benoit.hardouin@neuf.fr
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*
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* News about this program : http://anaqol.free.fr
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* FreeIRT Project : http://freeirt.free.fr
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*
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* Copyright 2004 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 hcaccprox , rclass
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version 8.0
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syntax varlist(min=2 numeric) [,PROX(string) METHod(string) PARTition(numlist) MEASures DETails DETect(integer 0)]
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local nbpart:word count `partition'
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tokenize `partition'
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forvalues k=1/`nbpart' {
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local part`k'=``k''
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}
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local nbitems : word count `varlist'
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tokenize `varlist'
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tempname proximity whereitems
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matrix define `proximity'=J(`nbitems',`nbitems',0)
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matrix define `whereitems'=J(`=`nbitems'-1',`nbitems',0)
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if `detect'>`nbitems' {
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di _col(3) in green "The number of partitions analyzed by the DETECT criterion must be inferior to the number of possible partitions"
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di _col(3) in green "This number of possible partitions is `=`nbitems'-1', so your detect option is put to this number"
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local detect=`nbitems'-1
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di
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}
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if "`prox'"!="a"&"`prox'"!="ad"&"`prox'"!="cor"&"`prox'"!="ccov"&"`prox'"!="ccor"&"`prox'"!="mh" {
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if "`prox'"=="" {
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local prox="ccov"
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}
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else {
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di in red "You must define an existing measure of proximity (a, ad, cor, ccov, ccor, mh)."
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di in red "Please correct your prox option."
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exit
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}
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}
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if "`method'"!="UPGMA"&"`method'"!="single"&"`method'"!="complete" {
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if "`method'"=="" {
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local method="UPGMA"
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}
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else {
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di in red "Tou must define an existing method to define the proximity between two clusters of items:"
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di in red _col(10) "- UPGMA: Unweighted Pair-Group Method of Average"
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di in red _col(10) "- single: single linkage"
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di in red _col(10) "- complete: complete linkage "
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di in red "Please correct your method option"
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exit
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}
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}
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forvalues i=1/`nbitems' {
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matrix `whereitems'[1,`i']=`i'
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if "`details'"!="" {
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di in green _col(3) "The item " _col(13) in yellow "``i''" in green " correspond to the node " in yellow "`i'"
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}
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}
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tempvar score
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egen `score'=rmean(`varlist')
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qui replace `score'=`score'*`nbitems'
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forvalues k=0/`nbitems' {
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qui count if `score'==`k'
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local nk`k'=r(N)
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}
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qui count
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local N=r(N)
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if "`prox'"=="ccov"|"`prox'"=="mh" {
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local proxmin=0
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}
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/*************************Measure of proximities*********************************/
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forvalues i=1/`nbitems' {
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forvalues j=`=`i'+1'/`nbitems' {
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/***********************************Proximity A**************************/
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if "`prox'"=="a" {
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qui count if ``i''==1&``j''==1
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local tmp11=r(N)
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qui count if ``i''==0&``j''==0
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local tmp00=r(N)
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matrix `proximity'[`i',`j']=sqrt(1-`tmp11'/(`N'-`tmp00'))
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matrix `proximity'[`j',`i']=`proximity'[`i',`j']
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}
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/***********************************Proximity AD*************************/
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if "`prox'"=="ad" {
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qui count if ``i''==1&``j''==1
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local tmp11=r(N)
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qui count if ``i''==0&``j''==0
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local tmp00=r(N)
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matrix `proximity'[`i',`j']=sqrt(1-(`tmp11'+`tmp00')/`N')
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matrix `proximity'[`j',`i']=`proximity'[`i',`j']
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}
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/**********************************Proximity COR*************************/
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if "`prox'"=="cor" {
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qui count if ``i''==1&``j''==1
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local tmp11=r(N)
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qui count if ``i''==0&``j''==0
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local tmp00=r(N)
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qui count if ``i''==1&``j''==0
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local tmp10=r(N)
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qui count if ``i''==0&``j''==1
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local tmp01=r(N)
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matrix `proximity'[`i',`j']=sqrt(2*(1-(`tmp11'*`tmp00'-`tmp10'*`tmp01')/(sqrt((`tmp11'+`tmp10')*(`tmp11'+`tmp01')*(`tmp00'+`tmp10')*(`tmp00'+`tmp01')))))
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matrix `proximity'[`j',`i']=`proximity'[`i',`j']
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}
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/***********************************Proximity CCOV**********************/
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if "`prox'"=="ccov" {
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local dij=0
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forvalues k=1/`=`nbitems'-1' {
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if `nk`k''!=0 {
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qui corr ``i'' ``j'',cov
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local covi`i'j`j'k`k'=r(cov_12)
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local dij=`dij'+`covi`i'j`j'k`k''*`nk`k''
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}
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}
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matrix `proximity'[`i',`j']=-`dij'/`N'
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matrix `proximity'[`j',`i']=`proximity'[`i',`j']
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if `proxmin'<`dij'/`N' {
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local proxmin=`dij'/`N'
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}
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}
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/***********************************Proximity CCOR**********************/
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if "`prox'"=="ccor" {
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local dij=0
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forvalues k=1/`=`nbitems'-1' {
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if `nk`k''!=0 {
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qui corr ``i'' ``j''
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local cori`i'j`j'k`k'=r(rho)
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local dij=`dij'+`cori`i'j`j'k`k''*`nk`k''
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}
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}
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matrix `proximity'[`i',`j']=sqrt(2*(1-`dij'/`N'))
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matrix `proximity'[`j',`i']=`proximity'[`i',`j']
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}
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/***********************************Proximity MH************************/
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if "`prox'"=="mh" {
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local numij=0
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local denom=0
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forvalues k=1/`=`nbitems'-1' {
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if `nk`k''!=0 {
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qui count if ``i''==1&``j''==1
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local A=r(N)
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qui count if ``i''==0&``j''==1
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local B=r(N)
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qui count if ``i''==1&``j''==0
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local C=r(N)
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qui count if ``i''==0&``j''==0
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local D=r(N)
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if `B'!=0&`C'!=0 {
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local numij=`numij'+`A'*`D'/`nk`k''
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local denomij=`denomij'+`B'*`C'/`nk`k''
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}
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}
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}
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matrix `proximity'[`i',`j']=-log(`numij'/`denomij')
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matrix `proximity'[`j',`i']=`proximity'[`i',`j']
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if `proxmin'<log(`numij'/`denomij') {
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local proxmin=-`proximity'[`i',`j']
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}
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}
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}
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}
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if "`prox'"=="ccov"|"`prox'"=="mh" {
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forvalues i=1/`nbitems' {
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forvalues j=`=`i'+1'/`nbitems' {
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matrix `proximity'[`i',`j']=`proximity'[`i',`j']+`proxmin'
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matrix `proximity'[`j',`i']=`proximity'[`i',`j']
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}
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}
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}
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/**********************END OD THE COMPUTING OF THE PROXIMITIES**************************************/
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if "`measures'"!="" {
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di
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matrix rowname `proximity'=`varlist'
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matrix colname `proximity'=`varlist'
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di in green _col(3) "Measures of proximity between the items"
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matrix list `proximity', noheader
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di
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}
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/**********************STEP 0**********************************************************************/
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tempname currentprox nodes conclinesnodes mempart
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matrix `currentprox'=`proximity'
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matrix define `nodes'=J(`=`nbitems'+4',`=2*`nbitems'-1',0)
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matrix define `conclinesnodes'=J(1,`nbitems',0)
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matrix define `mempart'=J(`=`nbitems'+2',`=`nbitems'-1',0)
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forvalues i=1/`nbitems' {
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matrix `nodes'[1,`i']=1
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matrix `nodes'[2,`i']=1
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matrix `nodes'[5,`i']=`i'
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matrix `conclinesnodes'[1,`i']=`i'
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}
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/*********************************CLUSTERING PROCEDURE*************************************/
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forvalues k=1/`=`nbitems'-1' {
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local nbclusters=`nbitems'-`k'+1
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local distmin=`currentprox'[1,2]
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local cl1=1
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local cl2=2
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forvalues i=1/`nbclusters' {
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forvalues j=`=`i'+1'/`nbclusters' {
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if `distmin'>`currentprox'[`i',`j'] {
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local distmin=`currentprox'[`i',`j']
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local cl1=`i'
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local cl2=`j'
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}
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}
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}
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local linescl1=`conclinesnodes'[1,`cl1']
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local nbitemscl1=`nodes'[1,`linescl1']
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matrix `nodes'[2,`linescl1']=0
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local linescl2=`conclinesnodes'[1,`cl2']
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local nbitemscl2=`nodes'[1,`linescl2']
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matrix `nodes'[2,`linescl2']=0
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matrix `nodes'[1,`=`nbitems'+`k'']=`nbitemscl1'+`nbitemscl2'
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matrix `nodes'[2,`=`nbitems'+`k'']=1
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matrix `nodes'[3,`=`nbitems'+`k'']=`linescl1'
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matrix `nodes'[4,`=`nbitems'+`k'']=`linescl2'
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if "`details'"!="" {
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di in green _col(3) "The nodes" _col(13) in yellow "`linescl1'" _col(17) in green "and" _col(21) in yellow "`linescl2'" _col(25) in green "are been aggregated to form the node " in yellow "`=`nbitems'+`k''"
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}
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forvalues i=5/`=`nbitemscl1'+4' {
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local item=`nodes'[`i',`linescl1']
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matrix `nodes'[`i',`=`nbitems'+`k'']=`item'
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matrix `whereitems'[`k',`item']=`=`nbitems'+`k''
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}
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forvalues i=5/`=`nbitemscl2'+4' {
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local item=`nodes'[`i',`linescl2']
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matrix `nodes'[`=`i'+`nbitemscl1'',`=`nbitems'+`k'']=`item'
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matrix `whereitems'[`k',`item']=`=`nbitems'+`k''
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}
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local tmp=1
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forvalues i=1/`=`nbitems'+`k'' {
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if `nodes'[2,`i']==1 {
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matrix `mempart'[`tmp',`k']=`i'
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local tmp=`tmp'+1
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}
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}
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if `detect'>=`=`nbitems'-`k'' {
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local partdetect
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local compteur=1
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local scaledetect
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forvalues i=1/`=`nbitems'-`k'' {
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local scaledetect`i'
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}
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forvalues i=1/`=`nbitems'+`k'' {
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if `nodes'[2,`i']==1{
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local tmp=`nodes'[1,`i']
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|
local partdetect `partdetect' `tmp'
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local tmp2=4+`tmp'
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forvalues j=5/`tmp2' {
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local tmp3=`nodes'[`j',`i']
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|
local scaledetect`compteur' `scaledetect`compteur'' ``tmp3''
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}
|
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|
|
local scaledetect `scaledetect' `scaledetect`compteur''
|
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|
|
local compteur=`compteur'+1
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|
}
|
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|
}
|
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|
|
qui detect `scaledetect' , partition(`partdetect')
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|
|
local detect`=`nbclusters'-1'=r(DETECT)
|
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|
|
local R`=`nbclusters'-1'=r(R)
|
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|
|
local Iss`=`nbclusters'-1'=r(Iss)
|
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|
|
}
|
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|
|
matrix drop `currentprox'
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|
|
matrix define `currentprox'=J(`=`nbclusters'-1',`=`nbclusters'-1',0)
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|
|
matrix drop `conclinesnodes'
|
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|
|
matrix define `conclinesnodes'=J(1,`=`nbclusters'-1',0)
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|
|
local tmp=1
|
|
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|
|
forvalues i=1/`=`nbitems'+`k'' {
|
|
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|
|
if `nodes'[2,`i']==1 {
|
|
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|
|
matrix `conclinesnodes'[1,`tmp']=`i'
|
|
|
|
|
|
local tmp=`tmp'+1
|
|
|
|
|
|
}
|
|
|
|
|
|
}
|
|
|
|
|
|
forvalues i=1/`=`nbclusters'-1' {
|
|
|
|
|
|
forvalues j=`=`i'+1'/`=`nbclusters'-1' {
|
|
|
|
|
|
if "`method'"=="UPGMA" {
|
|
|
|
|
|
local moy=0
|
|
|
|
|
|
local linescl1=`conclinesnodes'[1,`i']
|
|
|
|
|
|
local nbitemscl1=`nodes'[1,`linescl1']
|
|
|
|
|
|
local linescl2=`conclinesnodes'[1,`j']
|
|
|
|
|
|
local nbitemscl2=`nodes'[1,`linescl2']
|
|
|
|
|
|
forvalues l=5/`=`nbitemscl1'+4' {
|
|
|
|
|
|
forvalues m=5/`=`nbitemscl2'+4' {
|
|
|
|
|
|
local item1=`nodes'[`l',`linescl1']
|
|
|
|
|
|
local item2=`nodes'[`m',`linescl2']
|
|
|
|
|
|
local tmp=`proximity'[`item1',`item2']
|
|
|
|
|
|
local moy=`moy'+`tmp'
|
|
|
|
|
|
}
|
|
|
|
|
|
}
|
|
|
|
|
|
matrix `currentprox'[`i',`j']=`moy'/(`nbitemscl1'*`nbitemscl2')
|
|
|
|
|
|
matrix `currentprox'[`j',`i']=`moy'/(`nbitemscl1'*`nbitemscl2')
|
|
|
|
|
|
}
|
|
|
|
|
|
if "`method'"=="single" {
|
|
|
|
|
|
local moy=0
|
|
|
|
|
|
local linescl1=`conclinesnodes'[1,`i']
|
|
|
|
|
|
local nbitemscl1=`nodes'[1,`linescl1']
|
|
|
|
|
|
local linescl2=`conclinesnodes'[1,`j']
|
|
|
|
|
|
local nbitemscl2=`nodes'[1,`linescl2']
|
|
|
|
|
|
forvalues l=5/`=`nbitemscl1'+4' {
|
|
|
|
|
|
forvalues m=5/`=`nbitemscl2'+4' {
|
|
|
|
|
|
local item1=`nodes'[`l',`linescl1']
|
|
|
|
|
|
local item2=`nodes'[`m',`linescl2']
|
|
|
|
|
|
if `l'==5&`m'==5 {
|
|
|
|
|
|
local distmin=`proximity'[`item1',`item2']
|
|
|
|
|
|
}
|
|
|
|
|
|
else {
|
|
|
|
|
|
if `distmin'>`proximity'[`item1',`item2'] {
|
|
|
|
|
|
local distmin=`proximity'[`item1',`item2']
|
|
|
|
|
|
}
|
|
|
|
|
|
}
|
|
|
|
|
|
}
|
|
|
|
|
|
}
|
|
|
|
|
|
matrix `currentprox'[`i',`j']=`distmin'
|
|
|
|
|
|
matrix `currentprox'[`j',`i']=`distmin'
|
|
|
|
|
|
}
|
|
|
|
|
|
if "`method'"=="complete" {
|
|
|
|
|
|
local moy=0
|
|
|
|
|
|
local linescl1=`conclinesnodes'[1,`i']
|
|
|
|
|
|
local nbitemscl1=`nodes'[1,`linescl1']
|
|
|
|
|
|
local linescl2=`conclinesnodes'[1,`j']
|
|
|
|
|
|
local nbitemscl2=`nodes'[1,`linescl2']
|
|
|
|
|
|
local distmax=0
|
|
|
|
|
|
forvalues l=5/`=`nbitemscl1'+4' {
|
|
|
|
|
|
forvalues m=5/`=`nbitemscl2'+4' {
|
|
|
|
|
|
local item1=`nodes'[`l',`linescl1']
|
|
|
|
|
|
local item2=`nodes'[`m',`linescl2']
|
|
|
|
|
|
if `distmax'<`proximity'[`item1',`item2'] {
|
|
|
|
|
|
local distmax=`proximity'[`item1',`item2']
|
|
|
|
|
|
}
|
|
|
|
|
|
}
|
|
|
|
|
|
}
|
|
|
|
|
|
matrix `currentprox'[`i',`j']=`distmax'
|
|
|
|
|
|
matrix `currentprox'[`j',`i']=`distmax'
|
|
|
|
|
|
}
|
|
|
|
|
|
}
|
|
|
|
|
|
}
|
|
|
|
|
|
}
|
|
|
|
|
|
|
|
|
|
|
|
if `detect'!=0 {
|
|
|
|
|
|
tempname indexes
|
|
|
|
|
|
matrix define `indexes'=J(`detect',4,0)
|
|
|
|
|
|
matrix colnames `indexes'=Clusters DETECT Iss R
|
|
|
|
|
|
di ""
|
|
|
|
|
|
di in green _col(7) "Indexes to test the `detect' latest partitions of the items"
|
|
|
|
|
|
di ""
|
|
|
|
|
|
di in green _col(29) "DETECT" _col(43) "Iss" _col(56) "R"
|
|
|
|
|
|
di _col(5) in green "Only one cluster:" _col(27) in yellow %8.5f `detect1' _col(38) %8.5f `Iss1' _col(49) %8.5f `R1'
|
|
|
|
|
|
matrix `indexes'[1,1]=1
|
|
|
|
|
|
matrix `indexes'[1,2]=`detect1'
|
|
|
|
|
|
matrix `indexes'[1,3]=`Iss1'
|
|
|
|
|
|
matrix `indexes'[1,4]=`R1'
|
|
|
|
|
|
forvalues k=2/`detect' {
|
|
|
|
|
|
matrix `indexes'[`k',1]=`k'
|
|
|
|
|
|
matrix `indexes'[`k',2]=`detect`k''
|
|
|
|
|
|
matrix `indexes'[`k',3]=`Iss`k''
|
|
|
|
|
|
matrix `indexes'[`k',4]=`R`k''
|
|
|
|
|
|
di _col(5) in green "`k' clusters:" _col(27) in yellow %8.5f `detect`k'' _col(38) %8.5f `Iss`k'' _col(49) %8.5f `R`k''
|
|
|
|
|
|
}
|
|
|
|
|
|
return matrix indexes=`indexes'
|
|
|
|
|
|
}
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
forvalues k=1/`nbpart' {
|
|
|
|
|
|
di ""
|
|
|
|
|
|
local rowmempart=`nbitems'-`part`k''
|
|
|
|
|
|
di in green _col(8) "Number of clusters : `part`k''"
|
|
|
|
|
|
tempname affect`part`k''
|
|
|
|
|
|
matrix define `affect`part`k'''=J(1,`nbitems',0)
|
|
|
|
|
|
forvalues i=1/`part`k'' {
|
|
|
|
|
|
di
|
|
|
|
|
|
di in green _col(12) "Cluster `i':"
|
|
|
|
|
|
local rownodes=`mempart'[`i',`rowmempart']
|
|
|
|
|
|
local itemsinthecluster=`nodes'[1,`rownodes']
|
|
|
|
|
|
forvalues j=5/`=4+`itemsinthecluster'' {
|
|
|
|
|
|
local tmp=`nodes'[`j',`rownodes']
|
|
|
|
|
|
matrix `affect`part`k'''[1,`tmp']=`i'
|
|
|
|
|
|
di in yellow _col(13)"``tmp''"
|
|
|
|
|
|
}
|
|
|
|
|
|
}
|
|
|
|
|
|
matrix colnames `affect`part`k'''=`varlist'
|
|
|
|
|
|
return matrix affect`part`k''=`affect`part`k'''
|
|
|
|
|
|
}
|
|
|
|
|
|
|
|
|
|
|
|
return matrix mempart `mempart'
|
|
|
|
|
|
return matrix nodes `nodes'
|
|
|
|
|
|
return local nbitems=`nbitems'
|
|
|
|
|
|
return local varlist `varlist'
|
|
|
|
|
|
end
|
|
|
|
|
|
|
|
|
|
|
|
/*********************************************************
|
|
|
|
|
|
*Partition
|
|
|
|
|
|
*Version 2 (May 10, 2004)
|
|
|
|
|
|
*
|
|
|
|
|
|
*Historic
|
|
|
|
|
|
*Version 1 (January 18, 2004)
|
|
|
|
|
|
***********************************************************/
|
|
|
|
|
|
|
|
|
|
|
|
program define partition
|
|
|
|
|
|
version 8.0
|
|
|
|
|
|
syntax anything(name=partition)
|
|
|
|
|
|
|
|
|
|
|
|
local nbitems=r(nbitems)
|
|
|
|
|
|
tempname mempart nodes
|
|
|
|
|
|
matrix `mempart'=r(mempart)
|
|
|
|
|
|
matrix `nodes'=r(nodes)
|
|
|
|
|
|
local varlist "`r(varlist)'"
|
|
|
|
|
|
|
|
|
|
|
|
local nbpart:word count `partition'
|
|
|
|
|
|
tokenize `partition'
|
|
|
|
|
|
|
|
|
|
|
|
forvalues k=1/`nbpart' {
|
|
|
|
|
|
local part`k'=``k''
|
|
|
|
|
|
}
|
|
|
|
|
|
tokenize `varlist'
|
|
|
|
|
|
|
|
|
|
|
|
forvalues k=1/`nbpart' {
|
|
|
|
|
|
di ""
|
|
|
|
|
|
local rowmempart=`nbitems'-`part`k''
|
|
|
|
|
|
di in green _col(8) "Number of clusters : `part`k''"
|
|
|
|
|
|
forvalues i=1/`part`k'' {
|
|
|
|
|
|
di
|
|
|
|
|
|
di in green _col(12) "Cluster `i':"
|
|
|
|
|
|
local rownodes=`mempart'[`i',`rowmempart']
|
|
|
|
|
|
local itemsinthecluster=`nodes'[1,`rownodes']
|
|
|
|
|
|
forvalues j=5/`=4+`itemsinthecluster'' {
|
|
|
|
|
|
local tmp=`nodes'[`j',`rownodes']
|
|
|
|
|
|
di in yellow _col(13)"``tmp''"
|
|
|
|
|
|
}
|
|
|
|
|
|
}
|
|
|
|
|
|
}
|
|
|
|
|
|
end
|
|
|
|
|
|
|
