Merge pull request #127 from OHDSI/devH5

new rules 32,33 and 34 and updates and one new analysis

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: Achilles
 Type: Package
 Title: Creates descriptive statistics summary for an entire OMOP CDM instance.
-Version: 1.0
-Date: 2014-04-03
+Version: 1.3
+Date: 2016-06-10
 Author: Patrick Ryan, Martijn Schuemie
 Maintainer: Patrick Ryan <[email protected]>
 LazyData: true

inst/sql/sql_server/AchillesHeel_v5.sql

@@ -136,23 +136,62 @@ select
 
   where analysis_id in (2000,2001,2002,2003);
 
---iris derived measure from visit data
---insert into @results_database_schema.ACHILLES_results_derived (statistic_value,measure_id)    
---    select sum(count_value) as statistic_value, 
---           'Visit:PersonCnt' as measure_id
--- from @results_database_schema.achilles_results where analysis_id = 200;
--- WRONG (has more patients than total)
 
 
+insert into @results_database_schema.ACHILLES_results_derived (statistic_value,measure_id)    
+    select sum(count_value) as statistic_value, 
+           'Visit:InstanceCnt' as measure_id
+ from @results_database_schema.achilles_results where analysis_id = 201;
+
+ --in dist analysis/measure 203 - a number similar to that is computed above but it is on person level 
+
+
+--age at first observation by decile
+insert into @results_database_schema.ACHILLES_results_derived (stratum_1,statistic_value,measure_id)    
+select cast(floor(cast(stratum_1 as int)/10) as varchar) as stratum_1,
+  sum(count_value) as statistic_value,
+  'AgeAtFirstObsByDecile:PersonCnt' as measure_id
+  from @results_database_schema.achilles_results where analysis_id = 101
+group by floor(cast(stratum_1 as int)/10);
+
+--count whether all deciles from 0 to 8 are there  (has later a rule: if less the threshold, issue notification)
+insert into @results_database_schema.ACHILLES_results_derived (statistic_value,measure_id)    
+select count(*) as statistic_value,
+ 'AgeAtFirstObsByDecile:DecileCnt' as measure_id
+from @results_database_schema.ACHILLES_results_derived
+where measure_id = 'AgeAtFirstObsByDecile:PersonCnt' 
+and cast(stratum_1 as int) <=8;
 
---this is also in dist measure 203
---insert into @results_database_schema.ACHILLES_results_derived (statistic_value,measure_id)    
---    select sum(count_value) as statistic_value, 
---           'Visit:InstanceCnt' as measure_id
--- from @results_database_schema.achilles_results where analysis_id = 201;
 
+--data density measures
+--for drug (exposure and eras)
+insert into @results_database_schema.ACHILLES_results_derived (statistic_value,measure_id)    
+select count(*) as statistic_value, 'DrugExposure:ConceptCnt' as measure_id 
+from @results_database_schema.ACHILLES_results where analysis_id = 701;
+
+insert into @results_database_schema.ACHILLES_results_derived (statistic_value,measure_id)    
+select count(*) as statistic_value, 'DrugEra:ConceptCnt' as measure_id 
+from @results_database_schema.ACHILLES_results where analysis_id = 901;
+
+
+--unmapped data (concept_0) derived measures (focusing on source values)
+
+insert into @results_database_schema.ACHILLES_results_derived (stratum_1,statistic_value,measure_id)    
+select stratum_1,
+count(*) as statistic_value,
+'UnmappedDataByDomain:SourceValueCnt' as measure_id
+from @results_database_schema.achilles_results where analysis_id = 1900 group by stratum_1;
+
+
+--count of specialties in the provider table 
+--(subsequent rule can check if this count is > trehshold) (general population dataset only))
+insert into @results_database_schema.ACHILLES_results_derived (statistic_value,measure_id)    
+select 
+count(*) as statistic_value,
+'Provider:SpeciatlyCnt' as measure_id
+from @results_database_schema.achilles_results where analysis_id = 301;
 
---end of derived general measures
+--end of derived general measures ********************************************************************
 
 
 
@@ -1004,7 +1043,7 @@ and d.statistic_value > 10000  --thresholds will be decided in the ongoing DQ-St
 ;
 
 --rule32 DQ rule
---usis iris: patietnts with at least one visit visit 
+--uses iris: patients with at least one visit visit 
 --does 100-THE IRIS MEASURE to check for percentage of patients with no visits
 
 INSERT INTO @results_database_schema.ACHILLES_HEEL_results (ACHILLES_HEEL_warning,rule_id)
@@ -1016,3 +1055,36 @@ where d.measure_id = 'ach_2003:Percentage'
 and 100-d.statistic_value > 5  --thresholds will be decided in the ongoing DQ-Study2
 ;
 
+--rule33 DQ rule (for general population only)
+--NOTIFICATION: database does not have all age 0-80 represented
+
+
+INSERT INTO @results_database_schema.ACHILLES_HEEL_results (ACHILLES_HEEL_warning,rule_id)
+SELECT 
+ 'NOTIFICATION: [GeneralPopulationOnly] Not all deciles represented at first observation' as ACHILLES_HEEL_warning,
+  33 as rule_id
+FROM @results_database_schema.ACHILLES_results_derived d
+where d.measure_id = 'AgeAtFirstObsByDecile:DecileCnt' 
+and d.statistic_value <9  --we expect deciles 0,1,2,3,4,5,6,7,8 
+;
+
+
+--rule34 DQ rule
+--NOTIFICATION: number of unmapped source values exceeds threshold
+--related to rule 27 that looks at percentage of unmapped rows (rows as focus)
+--this rule is looking at source values (as focus)
+
+
+INSERT INTO @results_database_schema.ACHILLES_HEEL_results (ACHILLES_HEEL_warning,rule_id,record_count)
+SELECT 
+ 'NOTIFICATION: Count of unmapped source values exceeds threshold in: ' +cast(stratum_1 as varchar) as ACHILLES_HEEL_warning,
+  34 as rule_id,
+  cast(statistic_value as int) as record_count
+FROM @results_database_schema.ACHILLES_results_derived d
+where measure_id = 'UnmappedDataByDomain:SourceValueCnt'
+and statistic_value > 1000; --threshold will be decided in DQ study 2
+
+
+
+
+

inst/sql/sql_server/Achilles_v5.sql

@@ -615,6 +615,10 @@ insert into @results_database_schema.ACHILLES_analysis (analysis_id, analysis_na
 insert into @results_database_schema.ACHILLES_analysis (analysis_id, analysis_name)
   values (118, 'Number of observation periods with invalid person_id');
 
+insert into @results_database_schema.ACHILLES_analysis (analysis_id, analysis_name, stratum_1_name)
+  values (119, 'Number of observation period records by period_type_concept_id','period_type_concept_id');
+
+
 
 
 --200- VISIT_OCCURRENCE
@@ -1943,6 +1947,18 @@ where p1.person_id is null
 ;
 --}
 
+--{119 IN (@list_of_analysis_ids)}?{
+-- 119  Number of observation period records by period_type_concept_id
+insert into @results_database_schema.ACHILLES_results (analysis_id, stratum_1,count_value)
+select 119 as analysis_id,
+  op1.period_type_concept_id as stratum_1,
+  COUNT_BIG(*) as count_value
+from
+  @cdm_database_schema.observation_period op1
+group by op1.period_type_concept_id
+;
+--}
+
 
 /********************************************
 
@@ -2278,6 +2294,23 @@ group by YEAR(visit_start_date)*100 + month(visit_start_date)
 ;
 --}
 
+
+--{221 IN (@list_of_analysis_ids)}?{
+-- 221	Number of persons by visit start year 
+insert into @results_database_schema.ACHILLES_results (analysis_id, stratum_1, count_value)
+select 221 as analysis_id,   
+	YEAR(visit_start_date) as stratum_1, 
+	COUNT_BIG(distinct PERSON_ID) as count_value
+from
+@cdm_database_schema.visit_occurrence vo1
+group by YEAR(visit_start_date)
+;
+--}
+
+
+
+
+
 /********************************************
 
 ACHILLES Analyses on PROVIDER table
@@ -7281,6 +7314,31 @@ where m.value_as_number is null
 
 --end of measurment analyses
 
+/********************************************
+
+Reports 
+
+*********************************************/
+
+
+--{1900 IN (@list_of_analysis_ids)}?{
+-- 1900	concept_0 report
+
+INSERT INTO @results_database_schema.ACHILLES_results (analysis_id, stratum_1, stratum_2, count_value)
+select 1900 as analysis_id, table_name as stratum_1, source_value as stratum_2, cnt as count_value
+ from (
+select 'measurement' as table_name,measurement_source_value as source_value, COUNT_BIG(*) as cnt from @cdm_database_schema.measurement where measurement_concept_id = 0 group by measurement_source_value 
+union
+select 'procedure_occurrence' as table_name,procedure_source_value as source_value, COUNT_BIG(*) as cnt from @cdm_database_schema.procedure_occurrence where procedure_concept_id = 0 group by procedure_source_value 
+union
+select 'drug_exposure' as table_name,drug_source_value as source_value, COUNT_BIG(*) as cnt from @cdm_database_schema.drug_exposure where drug_concept_id = 0 group by drug_source_value 
+union
+select 'condition_occurrence' as table_name,condition_source_value as source_value, COUNT_BIG(*) as cnt from @cdm_database_schema.condition_occurrence where condition_concept_id = 0 group by condition_source_value 
+) a
+where cnt >= 1 --use other threshold if needed (e.g., 10)
+order by a.table_name desc, cnt desc
+;
+--}
 
 
 /********************************************
@@ -7347,6 +7405,8 @@ select 2002 as analysis_id,
 
 --{2003 IN (@list_of_analysis_ids)}?{
 -- 2003	Patients with at least one visit
+-- this analysis is in fact redundant, since it is possible to get it via
+-- dist analysis 203 and query select count_value from achilles_results_dist where analysis_id = 203;
 insert into @results_database_schema.ACHILLES_results (analysis_id, count_value)
 select 2003 as analysis_id,  COUNT_BIG(distinct person_id) as count_value
 from @cdm_database_schema.visit_occurrence;