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diagnosis_analysis.sql
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/*
* This file finds shows stats reagrding Ds-connect vs CDM completeness in diagnosis data
*/
SET search_path TO hb_workspace;
drop table if exists dx_summary;
CREATE TABLE if not exists dx_summary (
key_name text NOT NULL,
avg_sdi numeric,
stdev_sdi numeric,
min_sdi numeric,
max_sdi numeric,
n numeric,
percentage_sdi numeric,
manual_squery_n numeric,
timestamp timestamp default current_timestamp
);
insert into dx_summary
select
'sdi_all' as key_name,
avg(overall_sdi) as avg_sdi,
stddev(overall_sdi) as stdev_sdi,
min(overall_sdi) as min_sdi,
max(overall_sdi) as max_sdi,
count(overall_sdi) as cnt
from
sdi;
-------------------------
---find patient that have
---dementia, alzahimre, cognitive decline
---from CDM and DS connect
-------------------------
-- CDM
insert into dx_summary
select
'Cognitive - CDM' as key_name,
avg(overall_sdi) as avg_sdi,
stddev(overall_sdi) as stdev_sdi,
min(overall_sdi) as min_sdi,
max(overall_sdi) as max_sdi,
count(overall_sdi) as cnt,
null as percentage_sdi, --round(count(overall_sdi)::numeric/91*100,2) as percentage_sdi,
6 as manual_squery_cnt
from
sdi
where record_id in (
SELECT DISTINCT
d.patid
FROM
diagnosis_all d
JOIN consented c ON c.record_id = d.patid
JOIN ds_connect dc ON c.record_id = dc.col4
WHERE
c.ehr_access_agree = 1
AND dx LIKE 'F03%'
OR dx LIKE 'F01%'
OR dx LIKE 'F02%'
OR dx LIKE 'G30'
OR dx IN ('331.0', '331.1', '294.2', '294.1', '331.83', 'R41.81', 'G31.84')
--6
);
-- DS-connect
insert into dx_summary
select
'Cognitive - DS' as key_name,
avg(overall_sdi) as avg_sdi,
stddev(overall_sdi) as stdev_sdi,
min(overall_sdi) as min_sdi,
max(overall_sdi) as max_sdi,
count(overall_sdi) as cnt,
null as percentage_sdi, --round(count(overall_sdi)::numeric/91*100,2) as percentage_sdi,
9 as manual_squery_cnt
from
sdi
where record_id in (
SELECT
col4
-- ,col224,
-- col327,
-- col328,
-- col329,
-- col941
FROM
ds_connect dc
JOIN consented c ON c.record_id = dc.col4
WHERE
c.dsconnect_access_agree = 1
AND col224 != 'No'
AND (length(col224) > 10
OR col327 = 'Yes')
--12 (or 9?)
);
/** DS connect columns(col224, col327, col328, col329, col941):
* Has the participant ever been diagnosed with Dementia, Alzheimer's disease, or cognitive decline?
* Has the participant ever been diagnosed with Dementia, Alzheimer's disease, or cognitive decline?_Adult
* What was the age of the participant at the earliest onset of dementia symptoms?
* What was the age of the participant at diagnosis of Dementia, Alzheimer's disease, or cognitive decline?
* If the participant has had a brain imaging study, what was the reason for obtaining the study? (Select all that apply.) - Symptoms of dementia
*/
-- find the patient in CDM or DS-connect patients
insert into dx_summary
select
'Cognitive - CDM or DS' as key_name,
avg(overall_sdi) as avg_sdi,
stddev(overall_sdi) as stdev_sdi,
min(overall_sdi) as min_sdi,
max(overall_sdi) as max_sdi,
count(overall_sdi) as cnt,
null as percentage_sdi, --round(count(overall_sdi)::numeric/91*100,2) as percentage_sdi,
11 as manual_squery_cnt
from
sdi
where record_id in (
SELECT
col4
FROM
ds_connect dc
JOIN consented c ON c.record_id = dc.col4
WHERE
c.dsconnect_access_agree = 1
AND col224 != 'No'
AND (length(col224) > 10
OR col327 = 'Yes')
UNION
SELECT DISTINCT
d.patid
FROM
diagnosis_all d
JOIN consented c ON c.record_id = d.patid
JOIN ds_connect dc ON c.record_id = dc.col4
WHERE
c.ehr_access_agree = 1
AND dx LIKE 'F03%'
OR dx LIKE 'F01%'
OR dx LIKE 'F02%'
OR dx LIKE 'G30'
OR dx IN ('331.0', '331.1', '294.2', '294.1', '331.83', 'R41.81', 'G31.84')
--11
);
-- find the intersection between CDM and DS-connect patients
insert into dx_summary
select
'Cognitive - CDM & DS' as key_name,
avg(overall_sdi) as avg_sdi,
stddev(overall_sdi) as stdev_sdi,
min(overall_sdi) as min_sdi,
max(overall_sdi) as max_sdi,
count(overall_sdi) as cnt,
null as percentage_sdi, --round(count(overall_sdi)::numeric/91*100,2) as percentage_sdi,
4 as manual_squery_cnt
from
sdi
where record_id in (
SELECT
col4
FROM
ds_connect dc
JOIN consented c ON c.record_id = dc.col4
WHERE
c.dsconnect_access_agree = 1
AND col224 != 'No'
AND (length(col224) > 10
OR col327 = 'Yes')
INTERSECT
SELECT DISTINCT
d.patid
FROM
diagnosis_all d
JOIN consented c ON c.record_id = d.patid
JOIN ds_connect dc ON c.record_id = dc.col4
WHERE
c.ehr_access_agree = 1
AND dx LIKE 'F03%'
OR dx LIKE 'F01%'
OR dx LIKE 'F02%'
OR dx LIKE 'G30'
OR dx IN ('331.0', '331.1', '294.2', '294.1', '331.83', 'R41.81', 'G31.84')
--4
);
-------------------------
---find patient that have
---Sleep Apnea
---from CDM and DS connect
-------------------------
-- CDM
insert into dx_summary
select
'Sleep Apnea - CDM' as key_name,
avg(overall_sdi) as avg_sdi,
stddev(overall_sdi) as stdev_sdi,
min(overall_sdi) as min_sdi,
max(overall_sdi) as max_sdi,
count(overall_sdi) as cnt,
null as percentage_sdi, --round(count(overall_sdi)::numeric/91*100,2) as percentage_sdi,
51 as manual_squery_cnt
from sdi
where record_id in (
SELECT DISTINCT
d.patid
FROM
diagnosis_all d
JOIN consented c ON c.record_id = d.patid
JOIN ds_connect dc ON c.record_id = dc.col4
WHERE
c.ehr_access_agree = 1
AND dx = 'G47.33'
OR dx = '327.23'
--51
);
-- DS-connect
insert into dx_summary
select
'Sleep Apnea - DS' as key_name,
avg(overall_sdi) as avg_sdi,
stddev(overall_sdi) as stdev_sdi,
min(overall_sdi) as min_sdi,
max(overall_sdi) as max_sdi,
count(overall_sdi) as cnt,
null as percentage_sdi, --round(count(overall_sdi)::numeric/91*100,2) as percentage_sdi,
57 as manual_squery_cnt
from sdi
where record_id in (
SELECT
col4
-- ,col91,
-- col487
FROM
ds_connect dc
JOIN consented c ON c.record_id = dc.col4
WHERE
c.dsconnect_access_agree = 1
AND col91 = '1'
);
/* DS connect columns (col91, col487):
* Which of the following sleep problems have been diagnosed? (Select all that apply.) - Sleep apnea
* Has a doctor ever diagnosed the participant with sleep apnea based on a sleep study?
*
*/
-- find the UNION(not intersection) between CDM and DS-connect patients
insert into dx_summary
select
'Sleep Apnea - CDM or DS' as key_name,
avg(overall_sdi) as avg_sdi,
stddev(overall_sdi) as stdev_sdi,
min(overall_sdi) as min_sdi,
max(overall_sdi) as max_sdi,
count(overall_sdi) as cnt,
null as percentage_sdi, --round(count(overall_sdi)::numeric/91*100,2) as percentage_sdi,
68 as manual_squery_cnt
from sdi
where record_id in (
SELECT DISTINCT
d.patid
FROM
diagnosis_all d
JOIN consented c ON c.record_id = d.patid
JOIN ds_connect dc ON c.record_id = dc.col4
WHERE
c.ehr_access_agree = 1
AND dx = 'G47.33'
OR dx = '327.23'
UNION
SELECT
col4
FROM
ds_connect dc
JOIN consented c ON c.record_id = dc.col4
WHERE
c.dsconnect_access_agree = 1
AND col91 = '1'
--68
);
-- find the intersection between CDM and DS-connect patients
insert into dx_summary
select
'Sleep Apnea - CDM & DS' as key_name,
avg(overall_sdi) as avg_sdi,
stddev(overall_sdi) as stdev_sdi,
min(overall_sdi) as min_sdi,
max(overall_sdi) as max_sdi,
count(overall_sdi) as cnt,
null as percentage_sdi, --round(count(overall_sdi)::numeric/91*100,2) as percentage_sdi,
40 as manual_squery_cnt
from sdi
where record_id in (
SELECT DISTINCT
d.patid
FROM
diagnosis_all d
JOIN consented c ON c.record_id = d.patid
JOIN ds_connect dc ON c.record_id = dc.col4
WHERE
c.ehr_access_agree = 1
AND dx = 'G47.33'
OR dx = '327.23'
INTERSECT
SELECT
col4
FROM
ds_connect dc
JOIN consented c ON c.record_id = dc.col4
WHERE
c.dsconnect_access_agree = 1
AND col91 = '1'
--40
);
-------------------------
---find patient that have
---Diabetes
---from CDM and DS connect
-------------------------
-- CDM
insert into dx_summary
select
'Diabetes - CDM' as key_name,
avg(overall_sdi) as avg_sdi,
stddev(overall_sdi) as stdev_sdi,
min(overall_sdi) as min_sdi,
max(overall_sdi) as max_sdi,
count(overall_sdi) as cnt,
null as percentage_sdi, --round(count(overall_sdi)::numeric/91*100,2) as percentage_sdi,
10 as manual_squery_cnt
from sdi
where record_id in (
SELECT DISTINCT
d.patid
FROM
diagnosis_all d
JOIN consented c ON c.record_id = d.patid
JOIN ds_connect dc ON c.record_id = dc.col4
WHERE
c.ehr_access_agree = 1
AND (dx LIKE 'E08%'
OR dx LIKE 'E09%'
OR dx LIKE 'E10%'
OR dx LIKE 'E11%'
OR dx LIKE 'E13%')
--10
);
-- DS-connect
insert into dx_summary
select
'Diabetes - DS' as key_name,
avg(overall_sdi) as avg_sdi,
stddev(overall_sdi) as stdev_sdi,
min(overall_sdi) as min_sdi,
max(overall_sdi) as max_sdi,
count(overall_sdi) as cnt,
null as percentage_sdi, --round(count(overall_sdi)::numeric/91*100,2) as percentage_sdi,
6 as manual_squery_cnt
from sdi
where record_id in (
SELECT
col4
-- ,col132,
-- col735
FROM
ds_connect dc
JOIN consented c ON c.record_id = dc.col4
WHERE
c.dsconnect_access_agree = 1
AND col132 = 'Yes'
--6
);
/* DS connect columns (col132, col735):
* Has the participant ever been diagnosed with diabetes?
* Did the participant's mother have any of the following conditions or treatments during her pregnancy with the participant? (Select all that apply.) - Gestational diabetes (diabetes during pregnancy)
*/
-- find the union between CDM and DS-connect patients
insert into dx_summary
select
'Diabetes - CDM or DS' as key_name,
avg(overall_sdi) as avg_sdi,
stddev(overall_sdi) as stdev_sdi,
min(overall_sdi) as min_sdi,
max(overall_sdi) as max_sdi,
count(overall_sdi) as cnt,
null as percentage_sdi, --round(count(overall_sdi)::numeric/91*100,2) as percentage_sdi,
10 as manual_squery_cnt
from sdi
where record_id in (
SELECT DISTINCT
d.patid
FROM
diagnosis_all d
JOIN consented c ON c.record_id = d.patid
JOIN ds_connect dc ON c.record_id = dc.col4
WHERE
c.ehr_access_agree = 1
AND (dx LIKE 'E08%'
OR dx LIKE 'E09%'
OR dx LIKE 'E10%'
OR dx LIKE 'E11%'
OR dx LIKE 'E13%')
union
SELECT DISTINCT
dc.col4
FROM
ds_connect dc
JOIN consented c ON c.record_id = dc.col4
WHERE
c.dsconnect_access_agree = 1
AND col132 = 'Yes'
--10
);
-- find the intersection between CDM and DS-connect patients
insert into dx_summary
select
'Diabetes - CDM and DS' as key_name,
avg(overall_sdi) as avg_sdi,
stddev(overall_sdi) as stdev_sdi,
min(overall_sdi) as min_sdi,
max(overall_sdi) as max_sdi,
count(overall_sdi) as cnt,
null as percentage_sdi, --round(count(overall_sdi)::numeric/91*100,2) as percentage_sdi,
6 as manual_squery_cnt
from sdi
where record_id in (
SELECT DISTINCT
d.patid
FROM
diagnosis_all d
JOIN consented c ON c.record_id = d.patid
JOIN ds_connect dc ON c.record_id = dc.col4
WHERE
c.ehr_access_agree = 1
AND (dx LIKE 'E08%'
OR dx LIKE 'E09%'
OR dx LIKE 'E10%'
OR dx LIKE 'E11%'
OR dx LIKE 'E13%')
INTERSECT
SELECT DISTINCT
dc.col4
FROM
ds_connect dc
JOIN consented c ON c.record_id = dc.col4
WHERE
c.dsconnect_access_agree = 1
AND col132 = 'Yes'
--6
);
-------------------------
---find patient that have
---Depression
---from CDM and DS connect
-------------------------
--CDM
insert into dx_summary
select
'Depression - CDM' as key_name,
avg(overall_sdi) as avg_sdi,
stddev(overall_sdi) as stdev_sdi,
min(overall_sdi) as min_sdi,
max(overall_sdi) as max_sdi,
count(overall_sdi) as cnt,
null as percentage_sdi, --round(count(overall_sdi)::numeric/91*100,2) as percentage_sdi,
15 as manual_squery_cnt
from sdi
where record_id in (
SELECT DISTINCT
d.patid
FROM
diagnosis_all d
JOIN consented c ON c.record_id = d.patid
JOIN ds_connect dc ON c.record_id = dc.col4
WHERE
c.ehr_access_agree = 1
AND (dx LIKE 'F32%'
OR dx LIKE 'F33%'
OR dx LIKE 'F31%'
OR dx LIKE '296.2%'
OR dx LIKE '296.3%'
OR dx LIKE '296%')
);
-- DS-connect
insert into dx_summary
select
'Depression - DS' as key_name,
avg(overall_sdi) as avg_sdi,
stddev(overall_sdi) as stdev_sdi,
min(overall_sdi) as min_sdi,
max(overall_sdi) as max_sdi,
count(overall_sdi) as cnt,
null as percentage_sdi, --round(count(overall_sdi)::numeric/91*100,2) as percentage_sdi,
21 as manual_squery_cnt
from sdi
where record_id in (
select
col4
-- ,col192,
-- col198,
-- col319,
-- col897,
-- col909
FROM
ds_connect dc
JOIN consented c ON c.record_id = dc.col4
WHERE
c.dsconnect_access_agree = 1
AND (col192 = '1'
OR col198 = '1'
OR col897 = 'Currently a problem'
OR col909 = 'Currently a problem')
--21
);
/* DS connect columns (col192, col198, col319, col897, col909):
* Has the participant ever been diagnosed with any of the following behavioral or mental health conditions? (Select all that apply.) - Depression
* Has the participant ever been diagnosed with any of the following behavioral or mental health conditions? (Select all that apply.) - Bipolar/manic depression
* What is the status and age at diagnosis for each of these conditions? (Select all that apply.) - Depression - Status
* For the following behavioral or mental health conditions, select the status and age in years at diagnosis for the participant. (Select all that apply) - Depression - Status
* For the following behavioral or mental health conditions, select the status and age in years at diagnosis for the participant. (Select all that apply) - Bipolar/manic depression - Status
*
*/
-- find the union between CDM and DS-connect patients
insert into dx_summary
select
'Depression - CDM or DS' as key_name,
avg(overall_sdi) as avg_sdi,
stddev(overall_sdi) as stdev_sdi,
min(overall_sdi) as min_sdi,
max(overall_sdi) as max_sdi,
count(overall_sdi) as cnt,
null as percentage_sdi, --round(count(overall_sdi)::numeric/91*100,2) as percentage_sdi,
29 as manual_squery_cnt
from sdi
where record_id in (
SELECT DISTINCT
d.patid
FROM
diagnosis_all d
JOIN consented c ON c.record_id = d.patid
JOIN ds_connect dc ON c.record_id = dc.col4
WHERE
c.ehr_access_agree = 1
AND (dx LIKE 'F32%'
OR dx LIKE 'F33%'
OR dx LIKE 'F31%'
OR dx LIKE '296.2%'
OR dx LIKE '296.3%'
OR dx LIKE '296%')
union
SELECT
dc.col4
FROM
ds_connect dc
JOIN consented c ON c.record_id = dc.col4
WHERE
c.dsconnect_access_agree = 1
AND (col192 = '1'
OR col198 = '1'
OR col897 = 'Currently a problem'
OR col909 = 'Currently a problem')
--29
);
-- find the intersection between CDM and DS-connect patients
insert into dx_summary
select
'Depression - CDM & DS' as key_name,
avg(overall_sdi) as avg_sdi,
stddev(overall_sdi) as stdev_sdi,
min(overall_sdi) as min_sdi,
max(overall_sdi) as max_sdi,
count(overall_sdi) as cnt,
null as percentage_sdi, --round(count(overall_sdi)::numeric/91*100,2) as percentage_sdi,
7 as manual_squery_cnt
from sdi
where record_id in (
SELECT DISTINCT
d.patid
FROM
diagnosis_all d
JOIN consented c ON c.record_id = d.patid
JOIN ds_connect dc ON c.record_id = dc.col4
WHERE
c.ehr_access_agree = 1
AND (dx LIKE 'F32%'
OR dx LIKE 'F33%'
OR dx LIKE 'F31%'
OR dx LIKE '296.2%'
OR dx LIKE '296.3%'
OR dx LIKE '296%')
INTERSECT
SELECT
dc.col4
FROM
ds_connect dc
JOIN consented c ON c.record_id = dc.col4
WHERE
c.dsconnect_access_agree = 1
AND (col192 = '1'
OR col198 = '1'
OR col897 = 'Currently a problem'
OR col909 = 'Currently a problem')
--7
);
-------------------------
---find patient that have
---any given DX
---from CDM and DS connect
-------------------------
drop table if exists all_cdm_dx;
create table if not exists all_cdm_dx as
SELECT
distinct d.patid
FROM
diagnosis_all d
JOIN consented c ON c.record_id = d.patid
JOIN ds_connect dc ON c.record_id = dc.col4
WHERE
c.ehr_access_agree = 1
-- Depression
and (
dx LIKE 'F32%'
or dx LIKE 'F33%'
or dx LIKE 'F31%'
or dx LIKE '296.2%'
or dx LIKE '296.3%'
or dx LIKE '296%'
--Diabetes
or dx LIKE 'E08%'
or dx LIKE 'E09%'
or dx LIKE 'E10%'
or dx LIKE 'E11%'
or dx LIKE 'E13%'
--Sleep Apnea
or dx = 'G47.33'
or dx = '327.23'
-- dementia, alzahimre, cognitive decline
or dx LIKE 'F03%'
or dx LIKE 'F01%'
or dx LIKE 'F02%'
or dx LIKE 'G30'
or dx IN ('331.0', '331.1', '294.2', '294.1', '331.83', 'R41.81', 'G31.84')
)
--57
;
drop table if exists all_ds_dx;
create table if not exists all_ds_dx as
select
col4
FROM
ds_connect dc
JOIN consented c ON c.record_id = dc.col4
WHERE
c.dsconnect_access_agree = 1
-- Depression
AND (
col192 = '1'
OR col198 = '1'
OR col897 = 'Currently a problem'
OR col909 = 'Currently a problem'
--Diabetes
OR col132 = 'Yes'
--Sleep Apnea
OR col91 = '1'
--dementia, alzahimre, cognitive decline
OR (col224 != 'No'
AND (length(col224) > 10
OR col327 = 'Yes'))
)
--67
;
--CDM
insert into dx_summary
select
'None of the above DX - CDM' as key_name,
avg(overall_sdi) as avg_sdi,
stddev(overall_sdi) as stdev_sdi,
min(overall_sdi) as min_sdi,
max(overall_sdi) as max_sdi,
count(overall_sdi) as cnt,
null as percentage_sdi, --round(count(overall_sdi)::numeric/91*100,2) as percentage_sdi,
57 as manual_squery_cnt
from sdi
where record_id in (
SELECT
distinct d.patid
FROM
diagnosis_all d
JOIN consented c ON c.record_id = d.patid
JOIN ds_connect dc ON c.record_id = dc.col4
where patid not in (select * from all_cdm_dx ) --57
);
-- DS-connect
insert into dx_summary
select
'None of the above DX - DS' as key_name,
avg(overall_sdi) as avg_sdi,
stddev(overall_sdi) as stdev_sdi,
min(overall_sdi) as min_sdi,
max(overall_sdi) as max_sdi,
count(overall_sdi) as cnt,
null as percentage_sdi, --round(count(overall_sdi)::numeric/91*100,2) as percentage_sdi,
67 as manual_squery_cnt
from sdi
where record_id in (
select
col4
FROM
ds_connect dc
JOIN consented c ON c.record_id = dc.col4
WHERE col4 not in (select * from all_ds_dx ) --67
);
-- find the union between CDM and DS-connect patients
insert into dx_summary
select
'None of the above DX - CDM or DS' as key_name,
avg(overall_sdi) as avg_sdi,
stddev(overall_sdi) as stdev_sdi,
min(overall_sdi) as min_sdi,
max(overall_sdi) as max_sdi,
count(overall_sdi) as cnt,
null as percentage_sdi, --round(count(overall_sdi)::numeric/91*100,2) as percentage_sdi,
52 as manual_squery_cnt
from sdi
where record_id in (
SELECT
distinct d.patid
FROM
diagnosis_all d
JOIN consented c ON c.record_id = d.patid
JOIN ds_connect dc ON c.record_id = dc.col4
where patid not in (select * from all_cdm_dx)
union
select
distinct col4
FROM
ds_connect dc
JOIN consented c ON c.record_id = dc.col4
WHERE col4 not in (select * from all_ds_dx)
);
-- find the union between CDM and DS-connect patients
insert into dx_summary
select
'None of the above DX - CDM & DS' as key_name,
avg(overall_sdi) as avg_sdi,
stddev(overall_sdi) as stdev_sdi,
min(overall_sdi) as min_sdi,
max(overall_sdi) as max_sdi,
count(overall_sdi) as cnt,
null as percentage_sdi, --round(count(overall_sdi)::numeric/91*100,2) as percentage_sdi,
22 as manual_squery_cnt
from sdi
where record_id in (
SELECT
distinct d.patid
FROM
diagnosis_all d
JOIN consented c ON c.record_id = d.patid
JOIN ds_connect dc ON c.record_id = dc.col4
where patid not in (select * from all_cdm_dx)
intersect
select
distinct col4
FROM
ds_connect dc
JOIN consented c ON c.record_id = dc.col4
WHERE col4 not in (select * from all_ds_dx)
--22
);
commit;