/*-------------------------------------------------------------------------------------*\
| PROGRAM NAME: |
| scdm_data_qa_review-diagnosis.sas |
| |
|---------------------------------------------------------------------------------------|
| PURPOSE: |
| The purpose of this program is to perform data quality checks on the Diagnosis |
| 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 ;
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/* summarize diagnosis table at highest level to get base counts for other required summarization */
%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=adate enctype dx_codetype dx pdx padmit providerid) ;
run;
%let qa_table = t_view ;
%end ;
%else %do;
%let qa_table = qadata.&&&module.table (keep=adate enctype dx_codetype dx pdx padmit providerid) ;
%end;
%mend ;
%get_qa_table ;;
proc sql noprint;
create table dplocal.&module._temp as
select a.adate
, a.enctype
, a.dx_codetype
, a.dx
, a.pdx
, a.padmit
, 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 1,2,3,4,5,6,7;
quit;
%remove_labels(dplocal, &module._temp);
/* create additional temp diagnosis table for use in 223 check with patid and encounterid vars to merge w/ encounter */
%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 adate encounterid enctype dx_codetype pdx providerid) ;
run;
%let qa_table = t_view ;
%end ;
%else %do;
%let qa_table = qadata.&&&module.table (keep=patid adate encounterid enctype dx_codetype pdx providerid) ;
%end;
%mend ;
%get_qa_table ;;
proc sql noprint;
create table temp_223 as
select a.patid
, a.adate
, a.encounterid
, a.enctype
, a.dx_codetype
, a.pdx
, b.specialty
from &qa_table as a
left join
qadata.&PVDTABLE (keep=providerid specialty) as b
on a.providerid=b.providerid
where a.enctype in ("IP","IS")
order by 1,2,3,4,5,6,7
;
quit;
/*-------------------------------------------------------------------------------------*/
/* START Level 2 Data */
/*-------------------------------------------------------------------------------------*/
/* join temp_223 dataset to encounter table to get ddate values and counts */
%macro get_qa_table ;
%if &do_partitions and not %eval(&module in &tabid_exc) %then %do ;
data t_view /view=t_view ;
set qadata.&ENCTABLE.: (keep=patid adate encounterid enctype ddate where=(enctype in ("IP", "IS"))) ;
run;
%let qa_table = t_view ;
%end ;
%else %do;
%let qa_table = qadata.&ENCTABLE (keep=patid adate encounterid enctype ddate where=(enctype in ("IP", "IS"))) ;
%end;
%mend ;
%get_qa_table ;;
proc sql noprint;
create table ddate_223 as
select b.ddate
, a.encounterid
, a.enctype
, a.dx_codetype
, a.pdx
, a.specialty
, count(*) as n
from temp_223 as a
left join
&qa_table as b
on a.patid=b.patid and a.adate=b.adate and a.encounterid=b.encounterid
group by 1,2,3,4,5,6
;
quit;
/* create temp dataset for checkid 223 - dx_codetype by ddate where EncType=IP/IS */
proc sql noprint;
create table dplocal.&module._dxtype_ddate as
select dx_codetype
, ddate
, sum(n) as count format=comma15.
from ddate_223 (keep=ddate dx_codetype n enctype)
where dx_codetype in ("09","10") and not missing(ddate)
group by dx_codetype, ddate
;
quit;
proc sql noprint;
/* dx, code type, provider specialty */
create table msoc.&module._l2_dx_dxtype_spec as
select dx_codetype
, dx
, specialty
, sum(n) as count format=comma15.
from dplocal.&module._temp (keep=dx dx_codetype specialty n)
group by 1,2,3
;
/* ym, enc, dx, pds - for YearMonth values, use ddate when EncType=IP/IS, use adate when EncType ne IP/IS */
create table msoc.&module._l2_enc_dxtype_pdx_ym as
select YearMonth
, enctype
, dx_codetype
, pdx
, sum(n) as count format=comma15.
from (select put(adate,yymmd.) as YearMonth
, enctype
, dx_codetype
, pdx
, n
from dplocal.&module._temp (keep=adate enctype dx_codetype pdx n)
where enctype not in ("IP","IS")
outer union corr
select put(ddate,yymmd.) as YearMonth
, enctype
, dx_codetype
, pdx
, n
from ddate_223 (keep=ddate enctype dx_codetype pdx n)
where not missing (ddate))
group by 1,2,3,4
;
/* temp dataset for checkid 223 - dx_codetype by adate where EncType ne IP/IS */
create table dplocal.&module._dxtype_adate as
select dx_codetype
, adate
, sum(n) as count format=comma15.
from dplocal.&module._temp (keep=adate dx_codetype n enctype where=(dx_codetype in ("09","10") and enctype not in ("IP","IS")))
group by 1,2
;
quit;
/*-------------------------------------------------------------------------------------*/
/* START Level 2 Flags */
/*-------------------------------------------------------------------------------------*/
%level2;
/*-------------------------------------------------------------------------------------*/
/* START Level 3 Data */
/*-------------------------------------------------------------------------------------*/
%let level=3;
proc sql noprint;
create table dplocal.&module._temp_dates as
select adate
, sum(n) as n
from dplocal.&module._temp (keep=adate n)
group by 1
;
quit;
%date_percentiles (libin=dplocal, dsin=&module._temp_dates, libout=dplocal, dsout=date_dist_&module., vars=adate);
proc sql noprint;
create table dplocal.&module._adate_ym_count as
select put(adate,yymmd.) as YearMonth
, sum(n) as count format=comma15.
from dplocal.&module._temp_dates
group by YearMonth;
drop table dplocal.&module._temp_dates
;
drop table dplocal.&module._dxtype_adate
;
drop table dplocal.&module._dxtype_ddate
;
/* padmit only: list of padmit with # of records */
create table msoc.&module._l3_padmit as
select padmit
, sum(n) as count format=comma15.
from dplocal.&module._temp (keep=padmit n)
group by 1
;
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=patid encounterid) ;
run;
%let qa_table = t_view ;
%end ;
%else %do;
%let qa_table = qadata.&&&module.table (keep=patid encounterid) ;
%end;
%mend ;
%get_qa_table ;;
proc sql noprint;
/* patid*encounterid (number of diagnosis per patient-encounter - not necessarily unique) */
create table dplocal.&module._n_patid_encid as
select patid, encounterid, count(*) as n
from &qa_table
group by 1,2
;
quit;
*level 3 < statistics on number of diagnosis per encounter visit: overall >;
%l2_procmeans_sum(libin=dplocal,dsin=&module._n_patid_encid,
libout=msoc, dsout=&module._l3_dx_per_enc_stats,
keepvars=, vars=n, classvars=,
names= n=enc sum=dxs 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_dx_per_enc_stats;
format enc dxs comma15. mean std 10.2 median 10.1;
informat mean std 10.2 median 10.1;
run;
quit;
proc datasets lib=dplocal nowarn nolist nodetails;
delete &module._n_patid_encid;
quit;
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* END scdm_data_qa_review-diagnosis.sas ;
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