/******************************************************************/
/* Title:       CREATION OF ELIXHAUSER COMORBIDITY INDEX SCORES   */
/*              COMORBIDITY INDEX, VERSION 1.0                    */
/*                                                                */
/* PROGRAM:     comindex2012-2015.txt                             */
/*                                                                */
/* Description: Creates two comorbidity index scores based on the */
/*              29 comorbidity variables in HCUP databases or     */
/*              calculated using the Elixhauser comorbidity  	  */
/* 				software (03/27/2017)							  */
/******************************************************************/


/***********************************************************/
/*  Define subdirectory for data files and format library. */
/*  Input files:    C:\DATA\                               */
/*  Output files:   C:\DATA\                               */
/***********************************************************/
LIBNAME IN1     'C:\DATA\';            
LIBNAME OUT1    'C:\DATA\';          

/***********************************************************/
/*  Define dataset that has 29 comorbidity (CM) variables. */
/***********************************************************/
%Let    DS_  = Severity_data;
    ***if 29 variables are from HCUP standard severity file;
%Let    nv_  = 29;

/***********************************************************/
/*  Define logic to calculate scores.                      */
/*  The first 29 parameters are CM variables               */
/*  rscore_ for readmit index score                        */
/*  mscore_ for mortality index score                      */
/***********************************************************/

/***********************************************************/
/* 	If the 29 comorbidity variables have different names   */
/* 	in your data, fill in the variable names here (when	   */
/*	calling the macro get_cmscore)						   */
/***********************************************************/

%macro get_cmscore(
aids_    =CM_AIDS, 
alcohol_ =CM_ALCOHOL,       
anemdef_ =CM_ANEMDEF,       
arth_    =CM_ARTH,          
bldloss_ =CM_BLDLOSS,       
chf_     =CM_CHF,           
chrnlung_=CM_CHRNLUNG,      
coag_    =CM_COAG,          
depress_ =CM_DEPRESS,       
dm_      =CM_DM,            
dmcx_    =CM_DMCX,          
drug_    =CM_DRUG,          
htn_c_   =CM_HTN_C,         
hypothy_ =CM_HYPOTHY,       
liver_   =CM_LIVER,         
lymth_   =CM_LYMPH,         
lytes_   =CM_LYTES,         
mets_    =CM_METS,         
neuro_   =CM_NEURO,         
obese_   =CM_OBESE,         
para_    =CM_PARA,          
perivasc_=CM_PERIVASC,      
psych_   =CM_PSYCH,         
pulmcirc_=CM_PULMCIRC,      
renlfail_=CM_RENLFAIL,      
tumor_   =CM_TUMOR,         
ulcer_   =CM_ULCER,         
valve_   =CM_VALVE,         
wghtloss_=CM_WGHTLOSS,      
rscore_=readmit_score, 
mscore_=mortal_score
       );

/***********************************************************/
/*  Readmission Weights for calculating scores             */
/***********************************************************/

rwAIDS      =   19 ;
rwALCOHOL   =    6 ;
rwANEMDEF   =    9 ;
rwARTH      =    4 ;
rwBLDLOSS   =    3 ;
rwCHF       =   13 ;
rwCHRNLUNG  =    8 ;
rwCOAG      =    7 ;
rwDEPRESS   =    4 ;
rwDM        =    6 ;
rwDMCX      =    9 ;
rwDRUG      =   14 ;
rwHTN_C     =   -1 ;
rwHYPOTHY   =    0 ;
rwLIVER     =   10 ;
rwLYMPH     =   16 ;
rwLYTES     =    8 ;
rwMETS      =   21 ;
rwNEURO     =    7 ;
rwOBESE     =   -3 ;
rwPARA      =    6 ;
rwPERIVASC  =    4 ;
rwPSYCH     =   10 ;
rwPULMCIRC  =    5 ;
rwRENLFAIL  =   15 ;
rwTUMOR     =   15 ;
rwULCER     =    0 ;
rwVALVE     =    0 ;
rwWGHTLOSS  =   10 ;

/***********************************************************/
/*  Mortality Weights for calculating scores               */
/***********************************************************/

mwAIDS      =    0 ;
mwALCOHOL   =   -1 ;
mwANEMDEF   =   -2 ;
mwARTH      =    0 ;
mwBLDLOSS   =   -3 ;
mwCHF       =    9 ;
mwCHRNLUNG  =    3 ;
mwCOAG      =   11 ;
mwDEPRESS   =   -5 ;
mwDM        =    0 ;
mwDMCX      =   -3 ;
mwDRUG      =   -7 ;
mwHTN_C     =   -1 ;
mwHYPOTHY   =    0 ;
mwLIVER     =    4 ;
mwLYMPH     =    6 ;
mwLYTES     =   11 ;
mwMETS      =   14 ;
mwNEURO     =    5 ;
mwOBESE     =   -5 ;
mwPARA      =    5 ;
mwPERIVASC  =    3 ;
mwPSYCH     =   -5 ;
mwPULMCIRC  =    6 ;
mwRENLFAIL  =    6 ;
mwTUMOR     =    7 ;
mwULCER     =    0 ;
mwVALVE     =    0 ;
mwWGHTLOSS  =    9 ;

array cmvars(&nv_) 	&aids_    &alcohol_  &anemdef_ &arth_     &bldloss_  &chf_     &chrnlung_ &coag_    &depress_ &dm_      
					&dmcx_    &drug_     &htn_c_   &hypothy_  &liver_    &lymth_   &lytes_    &mets_    &neuro_   &obese_   
					&para_    &perivasc_ &psych_   &pulmcirc_ &renlfail_ &tumor_   &ulcer_    &valve_   &wghtloss_
					;

array rwcms(&nv_) 	rwAIDS    rwALCOHOL  rwANEMDEF rwARTH     rwBLDLOSS   rwCHF    rwCHRNLUNG  rwCOAG    rwDEPRESS rwDM            
					rwDMCX    rwDRUG     rwHTN_C   rwHYPOTHY  rwLIVER     rwLYMPH  rwLYTES     rwMETS    rwNEURO   rwOBESE         
					rwPARA    rwPERIVASC rwPSYCH   rwPULMCIRC rwRENLFAIL  rwTUMOR  rwULCER     rwVALVE   rwWGHTLOSS      
					;

array mwcms(&nv_) 	mwAIDS    mwALCOHOL  mwANEMDEF mwARTH     mwBLDLOSS   mwCHF    mwCHRNLUNG  mwCOAG    mwDEPRESS  mwDM            
					mwDMCX    mwDRUG     mwHTN_C   mwHYPOTHY  mwLIVER     mwLYMPH  mwLYTES     mwMETS    mwNEURO    mwOBESE         
					mwPARA    mwPERIVASC mwPSYCH   mwPULMCIRC mwRENLFAIL  mwTUMOR  mwULCER     mwVALVE   mwWGHTLOSS      
					;

array ocms(&nv_)  	oAIDS     oALCOHOL   oANEMDEF  oARTH      oBLDLOSS    oCHF     oCHRNLUNG   oCOAG     oDEPRESS   oDM            
					oDMCX     oDRUG      oHTN_C    oHYPOTHY   oLIVER      oLYMPH   oLYTES      oMETS     oNEURO     oOBESE         
					oPARA     oPERIVASC  oPSYCH    oPULMCIRC  oRENLFAIL   oTUMOR   oULCER      oVALVE    oWGHTLOSS      
					;  

*****Calculate readmit score;
do i = 1 to &nv_;
  ocms[i]=cmvars[i]*rwcms[i];
end;

&rscore_ = sum(of ocms[*]);

*****Calculate mortality score;
do i = 1 to &nv_;
  ocms[i]=cmvars[i]*mwcms[i];
end;

&mscore_ = sum(of ocms[*]);

***drop all intermediate variables;
drop rw: mw: o: i;

%mend;

DATA OUT1.ANALYSIS;
    SET  IN1.&DS_ ;
    %get_cmscore;
    ***two output score names are readmit_score and mortal_score;

RUN;


/*************************************************/
/* Sample print and contents of comorbidity file */
/*************************************************/  
PROC PRINT DATA=OUT1.ANALYSIS (OBS=60);
  TITLE3 'Print of analysis file variables';
RUN;

PROC CONTENTS DATA=OUT1.ANALYSIS ;
  TITLE3 'Contents of comorbidity analysis file';
RUN;

/****************************************/
/*  Frequency of comorbidity variables  */
/****************************************/ 
PROC FREQ DATA=OUT1.ANALYSIS;
  TABLE  readmit_score mortal_score
       / LIST MISSING;
  TITLE3 'Frequency of comorbidity variables';
RUN;

/***********************************/
/*  Means of comorbidity variables */
/***********************************/  
PROC MEANS DATA=OUT1.ANALYSIS  N NMISS MEAN STD MIN MAX;
  VAR    readmit_score mortal_score
      ;
   TITLE3 'Means of comorbidity variables';
RUN;