/*-------------------------------------------------------------------------------------*\
| PROGRAM NAME: |
| scdm_data_qa_review-prescribing.sas |
| |
|---------------------------------------------------------------------------------------|
| PURPOSE: |
| The purpose of this program is to perform data quality checks on the |
| Prescribing table. |
|---------------------------------------------------------------------------------------|
| PROGRAM INPUT: |
| see 00.0_scdm_data_qa_review_master_file.sas |
| |
| PROGRAM OUTPUT: |
| see Workplan PDF |
|---------------------------------------------------------------------------------------|
| CONTACT: |
| Sentinel Coordinating Center |
| info@sentinelsystem.org |
\*-------------------------------------------------------------------------------------*/
*-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-;
* PLEASE DO NOT EDIT BELOW WITHOUT CONTACTING THE SENTINEL OPERATIONS CENTER ;
*-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-;
/*-------------------------------------------------------------------------------------*/
/* START Level 2 */
/*-------------------------------------------------------------------------------------*/
%let level=2;
%macro l2_tables (varlist=);
%local l selectlist var ct;
%let selectlist=%sysfunc(tranwrd(&varlist,%str( ),%str(,) ));
%let ct=%sysfunc(countw(&varlist));
%let qa_table= ;
%macro get_qa_table ;
%if &do_partitions and not %eval(&module in &tabid_exc) %then %do ;
data t_view /view=t_view ;
set qadata.&&&module.table.: (keep = &varlist.) ;
run;
%let qa_table = t_view ;
%end ;
%else %do;
%let qa_table = qadata.&&&module.table (keep = &varlist.) ;
%end;
%mend;
%get_qa_table ;
proc sql noprint;
create table dplocal.&module._temp as
select &selectlist.
, count(*) as n
from &qa_table
group by &selectlist.
;
quit;
%remove_labels(dplocal, &module._temp);
%do l=1 %to &ct.;
%let var=%scan(&varlist,&l);
proc sql noprint;
create table msoc.&module._l2_&var. as
select &var.
, sum(n) as count format=comma15.
from dplocal.&module._temp (keep= n &var.)
group by 1
;
quit;
%end;
proc sql noprint;
drop table dplocal.&module._temp;
quit;
%mend l2_tables;
%l2_tables (varlist=RxSource RxRoute RxDoseQuantity RxDoseUnit RxDoseForm);
%l2_tables (varlist=RxFreqQuantity RxFreqUnit RxRefills RxPrnFlag RxDAW);
%macro get_qa_table ;
%if &do_partitions and not %eval(&module in &tabid_exc) %then %do ;
data t_view /view=t_view ;
set qadata.&&&module.table.: (keep= orderdate rx_codetype rx rxsup rxamt providerid) ;
run;
%let qa_table = t_view ;
%end ;
%else %do;
%let qa_table = qadata.&&&module.table (keep= orderdate rx_codetype rx rxsup rxamt providerid) ;
%end;
%mend;
%get_qa_table ;
/* create temp table, used to source creation of remaining level 2 prescribing tables */
proc sql noprint;
create table dplocal.&module._temp as
select put(a.orderdate,yymmd.) as YearMonth
, a.rx_codetype
, a.rx
, a.rxsup
, a.rxamt
, b.specialty
, count(*) as n
from &qa_table as a
left join
qadata.&PVDTABLE. (keep = providerid specialty ) as b
on a.providerid = b.providerid
group by 1,2,3,4,5,6;
quit;
%remove_labels(dplocal, &module._temp);
/* frequency of Rx by Rx_CodeType */
proc sql noprint;
create table msoc.&module._l2_rx_rxtype_spec as
select rx_codetype
, rx
, specialty
, sum(n) as count format=comma15.
from dplocal.&module._temp (keep= n rx rx_codetype specialty)
group by 1,2,3 ;
quit;
/* frequency of OrderDate */
proc sql noprint;
create table msoc.&module._l2_orderdate_ym as
select yearmonth
, sum(n) as count format=comma15.
from dplocal.&module._temp (keep= n yearmonth)
group by 1;
quit;
/*-------------------------------------------------------------------------------------*/
/* START Level 2 Flags */
/*-------------------------------------------------------------------------------------*/
%level2;
/*-------------------------------------------------------------------------------------*/
/* START Level 3 */
/*-------------------------------------------------------------------------------------*/
%let level=3;
/* frequency of RxAmt by RxSup */
proc sql noprint;
create table msoc.&module._l3_rxamt_rxsup as
select rxamt
, rxsup
, sum(n) as count format=comma15.
from dplocal.&module._temp (keep= n rxamt rxsup)
group by 1,2
;
drop table dplocal.&module._temp
;
quit;
%macro get_qa_table ;
%if &do_partitions and not %eval(&module in &tabid_exc) %then %do ;
data t_view /view=t_view ;
set qadata.&&&module.table: (keep=orderdate) ;
run;
%let qa_table = t_view ;
%end ;
%else %do;
%let qa_table = qadata.&&&module.table (keep=orderdate) ;
%end;
%mend;
%get_qa_table ;
proc sql noprint;
create table dplocal.&module._temp_dates as
select orderdate
, count(*) as n
from &qa_table
group by 1
;
quit;
%remove_labels(dplocal, &module._temp_dates);
%date_percentiles (libin=dplocal, dsin=&module._temp_dates
, libout=dplocal, dsout=date_dist_&module., vars=orderdate );
proc sql noprint;
drop table dplocal.&module._temp_dates
;
quit;
/* Temporary PatID and OrderDate for L3 Stats tables */
/* Note: by patid by orderdate, not using EncounterID, as it is allowed to be missing */
%macro get_qa_table ;
%if &do_partitions and not %eval(&module in &tabid_exc) %then %do ;
data t_view /view=t_view ;
set qadata.&&&module.table.: (keep=patid orderdate) ;
run;
%let qa_table = t_view ;
%end ;
%else %do;
%let qa_table = qadata.&&&module.table (keep=patid orderdate) ;
%end;
%mend;
%get_qa_table ;
proc sql noprint;
create table dplocal.&module._temp as
select patid
, orderdate
, put(orderdate,yymmd.) as YearMonth
, count(*) as n
from &qa_table
group by 1,2,3
;
quit;
%remove_labels(dplocal,&module._temp);
/* number of ordered prescriptions per patient per day */
proc sql noprint;
create table dplocal.&module._n_patid_preid as
select *
from dplocal.&module._temp (drop=yearmonth)
;
quit;
*level 3 <statistics on number prescriptions per date visit: overall >;
%l2_procmeans_sum(libin=dplocal,dsin=&module._n_patid_preid,
libout=msoc, dsout=&module._l3_pt_orderdate_stats,
keepvars=, vars=n, classvars=,
names= n=pre sum=rxs
mean=mean std=std min=min p1=p1 p5=p5 p25=p25 median=median
p75=p75 p95=p95 p99=p99 max=max, numobs=max);
proc datasets library=msoc nolist nodetails nowarn;
modify &module._l3_pt_orderdate_stats;
format pre rxs comma15. mean std 10.2 median 10.1;
informat mean std 10.2 median 10.1;
run;quit;
/*< number of prescriptions per patid per year-month > */
proc sql noprint;
drop table dplocal.&module._n_patid_preid
;
create table dplocal.&module._pat_y as
select patid
, substr(yearmonth,1,4) as Year
, sum(n) as n
from dplocal.&module._temp (drop=orderdate)
group by 1,2
;
drop table dplocal.&module._temp
;
quit;
/*< Distribution of number of prescriptions per patid per year > */
proc means nolabels nonobs data=dplocal.&module._pat_y missing StackODSOutput n sum mean std min p1 P5 P25 median P75 P95 p99 max;
var n;
class year;
ods output summary=msoc.&module._l3_rx_pt_y_stats (drop=_: variable rename=(n=n_ptyr sum=n_rx stddev=Std));
run;
proc datasets library=msoc nolist nodetails nowarn;
modify &module._l3_rx_pt_y_stats;
format n_: comma15. mean std 10.2 p: min max median 10.1;
informat mean std 10.2 p: min max median 10.1;
quit;
proc datasets library=dplocal nolist nodetails nowarn;
delete &module._pat_y;
run;quit;
*-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-;
* END scdm-data-qa-review-prescribing.sas ;
*-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-;