/*****************************************************************/
* Converting 1999-2004 NHANES demographic and					 *			
* body measures SAS transport files into SAS datasets		     *
*                            									 *
/****************************************************************/;

%macro transport (transfile);
libname xp xport "C:\NHANES\&transfile..xpt";    

proc copy in=xp out=work;
	run;
proc sort data=&transfile;
	by seqn;
run;

%mend transport;

%transport (demo);
%transport (demo_b);
%transport (demo_c);

%transport (bmx);
%transport (bmx_b);
%transport (bmx_c);

data demoall;
	set demo demo_b demo_c;
	run;

data bmxall;
	set bmx bmx_b bmx_c;
	run;

/*******************************************************************/
* Filename statement specifies local location to which              *
* NHANES Feasibility .DAT data set was copied                       *
* libname statements specifies local location of permanent          *
* SAS data set to be created                                        *
/*******************************************************************/;

* Log/List Options *;
options ls=120 ps=42 missing=' ' nocenter validvarname=upcase compress=binary;
* Output SAS Library *;
libname NHANES 'C:\NHANES'; * <-- Place Output Library Path Here *;
* Input File Reference *;
filename intext1 "C:\NHANES\MEDICARE_FEASIBILITY_NHANES_1999_2000.dat";

data nhanes_99_00_elig_Medicare;
 infile intext1 lrecl=142 ;
 attrib 
   SEQN               length=5  format=Z5. label='NCHS Survey Identifier - Sample Sequence Number'        
   CMS_MEDICARE_MATCH length=3  format=1.  label='CMS MEDICARE MATCH STATUS'

    on_denom_2005   length=3  format=1.  label='ON DENOMINATOR FILE INDICATOR (2005)'
    on_carrier_2005 length=3  format=1.  label='ON CARRIER FILE INDICATOR (2005)';

   input  @  1 SEQN                	5. 
	      @ 15 CMS_MEDICARE_MATCH 	1.
		  @ 31 on_DENOM_2005 		1. 
		  @ 65 on_CARRIER_2005 		1. 
		  ;
run;

* Input File Reference *;
filename intext2 "C:\NHANES\MEDICARE_FEASIBILITY_NHANES_2001_2002.dat";

data nhanes_01_02_elig_Medicare;
 infile intext2 lrecl=142 ;
 attrib 
   SEQN               length=5  format=Z5. label='NCHS Survey Identifier - Sample Sequence Number'        
   CMS_MEDICARE_MATCH length=3  format=1.  label='CMS MEDICARE MATCH STATUS'

    on_denom_2005   length=3  format=1.  label='ON DENOMINATOR FILE INDICATOR (2005)'
    on_carrier_2005 length=3  format=1.  label='ON CARRIER FILE INDICATOR (2005)';

   input  @  1 SEQN                	5. 
	      @ 15 CMS_MEDICARE_MATCH 	1.
		  @ 31 on_DENOM_2005 		1. 
		  @ 65 on_CARRIER_2005 		1. 
		  ;
run;

* Input File Reference *;
filename intext3 "C:\NHANES\MEDICARE_FEASIBILITY_NHANES_2003_2004.dat";

data nhanes_03_04_elig_Medicare;
 infile intext3 lrecl=142 ;
 attrib 
   SEQN               length=5  format=Z5. label='NCHS Survey Identifier - Sample Sequence Number'        
   CMS_MEDICARE_MATCH length=3  format=1.  label='CMS MEDICARE MATCH STATUS'

    on_denom_2005   length=3  format=1.  label='ON DENOMINATOR FILE INDICATOR (2005)'
    on_carrier_2005 length=3  format=1.  label='ON CARRIER FILE INDICATOR (2005)';

   input  @  1 SEQN                	5. 
	      @ 15 CMS_MEDICARE_MATCH 	1.
		  @ 31 on_DENOM_2005 		1. 
		  @ 65 on_CARRIER_2005 		1. 
		  ;
run;

*Append feasibility files together;
data feasall;
	set nhanes_99_00_elig_Medicare
		nhanes_01_02_elig_Medicare
		nhanes_03_04_elig_Medicare;
		run;

proc sort data=demoall;
	by seqn;
proc sort data=bmxall;
	by seqn;
proc sort data=feasall;
	by seqn;
	run;

*Merge feasibility file with NHANES demographic and body measures files;
data feasdemo;
	merge demoall (in=a) bmxall (in=b) feasall (in=c);
	by seqn;
	if a;
	run;

*Create temporary formats of variables to be examined;
proc format;
  value racef
  	0='Overall'
	1='non-Hispanic black'
	2='Mexican American'
	3='non-Hispanic white and others';

  value CMSMATCH 
    1 = 'Linked'
    2 = 'Not Linked'
    3 = 'Ineligible';

  value ON_FILE
  	1='Yes'
	0='No';

  value ynfmt
  	1='Yes'
	0='No';

  value OBESE_
  	1='Obese'
	0='Not Obese';

  value sexfmt
  	1='Male'
  	2='Female';
	run;


/********************************************************************/
* 																	 *
* Until specific recommendations are available, preliminary 		 *
* guidance is for you to create adjusted survey weights that account *
* for linkage-ineligibility and non-matches. Please see Course 4, 	 *
* Module 11 (Non-Response and Weighting Issues with the NHANES-CMS 	 *
* Linked Data) for more information. The examples below include		 *
* a weight variable wt_linkage_adj, which represents the adjusted 	 *
* survey weight.													 *
*																	 *
/********************************************************************/;


data ds1;
	set feasdemo;
	*create obesity indicator;
	If BMXBMI>=30 then obese=1;
	Else if 0<BMXBMI<30 then obese=0;

	if ON_CARRIER_2005=1 then carrier05=100;
	else if ON_CARRIER_2005=0 then carrier05=0;

	*define 3 race and Hispanic origin groups;

	if ridreth1=4 then racecat=1; /*non Hispanic black*/
	else if ridreth1=1 then racecat=2; /*Mexican Americans*/
	else racecat=3; /*non Hispanic whites and others*/
run;

proc freq data=ds1 ;
Tables (CMS_MEDICARE_MATCH ON_CARRIER_2005)*OBESE;
Where ridageyr>=65;
format CMS_MEDICARE_MATCH cmsmatch. ON_CARRIER_2005 on_file. OBESE obese_.;
Title "Merged NHANES Feasibility Data Frequency Distribution of obesity by Medicare Match Status";
run;


******degrees of freedom
using the study population defined in course 3 module 10 task 2;

proc sort data=ds1; 
by sdmvstra sdmvpsu;
run;
proc descript data=ds1 design=WR
DEFT2 ATLEVEL1=1 ATLEVEL2=2 ;
nest sdmvstra sdmvpsu;
Weight wt_linkage_adj;
SUBPOPN ridageyr>=65 and cms_medicare_match=1 and obese=1;
Var carrier05;
class racecat;
Tables racecat;
Output   atlev1=numstrat atlev2=numpsu  mean=mean semean=semean 
NSUM=N /  filetype=SAS filename=test1 replace;
Rtitle "Percent with records on the 2005 carrier file, aged 65 and older that were obese by race and Hispanic origin";
run;
Proc sort data=test1; 
   by racecat;
run;
 
DATA test2;  
SET test1;
percent=round(mean,.01);
sepercent=round(semean,.01);
df=atlev2-atlev1;
tlow=tinv(.025,df);
tup=tinv(.975,df); 
rse=round((semean/mean)*100,.01);
rsese=round((1/sqrt(df)),.01);
ll=round((mean+tlow*semean),.01);
ul=round((mean+tup*semean),.01);
run;
proc print data=test2 noobs; 
VAR Racecat nsum Percent Sepercent df tup ll ul; 
title1 'Degrees of Freedom and Wald 95% Confidence Interval';

title2 Percent Linked to 2005 Carrier file by Race and Hispanic Origin?
title2 'Percent Obese that Linked to 2005 Carrier file by Race and Hispanic Origin';
title3 'for those who were age 65+ and obese: NHANES 1999-2004';

format racecat racef.;
run;

************* t-test;
proc sort data=ds1; 
by sdmvstra sdmvpsu; 
run;    
proc descript 
data=ds1 design=wr;
nest sdmvstra sdmvpsu;                                         
Weight wt_linkage_adj;
subpopn ridageyr >= 65 and cms_medicare_match=1 and on_carrier_2005=1; 
class obese/NoFREQ; 
var ridageyr;
print nsum mean semean/style=nchs; 
rformat obese obese_.;
rtitle "Mean age for those who were obese and on the 2005 carrier file for ages 65+: NHANES 1999-2004 linked to Medicare 1999-2007"; 
run;

*ttest;
proc sort data=ds1; 
by sdmvstra sdmvpsu; 
run;      
proc descript 
data=ds1 design=wr;
nest sdmvstra sdmvpsu;                                      
Weight wt_linkage_adj;
subpopn ridageyr >= 65 and cms_medicare_match=1 and on_carrier_2005=1; 
class obese/NoFREQ; 
var ridageyr; 
contrast obese = (1 -1)/name = "obese vs. not";
print nsum t_mean p_mean/style=nchs;
rformat obese obese_.;
rtitle "Significance test for difference between mean age for those who were obese vs. not obese"; 
rtitle2 "NHANES 1999-2004 linked to Medicare"; 
run;

********
Chi-square
********;
proc sort data=ds1; 
by sdmvstra sdmvpsu;
run;
proc crosstab 
data=ds1 design=wr;
nest sdmvstra sdmvpsu;
Weight wt_linkage_id;
subpopn ridageyr >= 65 and cms_medicare_match=1 and on_carrier_2005=1; 
class riagendr obese/NoFreq;
table riagendr*obese; 
 
print nsum rowper serow colper/tests=all; 
 
rformat riagendr sexfmt.; 
rformat obese obese_.;
rtitle "Chi-square test for gender by obesity status and on the 2005 Carrier File: NHANES 1999-2004 linked to Medicare 1999-2007"; 
run;
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