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Bg fix #1200

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Merged
alistairewj merged 2 commits into from
Dec 7, 2021
Merged

Bg fix #1200

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693bc1c
fix specimen itemid, fixes #923 and #1161
alistairewj Dec 7, 2021
d5c1939
remove model predicting specimen
alistairewj Dec 7, 2021
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28 changes: 3 additions & 25 deletions mimic-iv/concepts/measurement/bg.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ select
-- specimen_id *may* have different storetimes, so this is taking the latest
, MAX(storetime) AS storetime
, le.specimen_id
, MAX(CASE WHEN itemid = 52028 THEN value ELSE NULL END) AS specimen
, MAX(CASE WHEN itemid = 52033 THEN value ELSE NULL END) AS specimen
, MAX(CASE WHEN itemid = 50801 THEN valuenum ELSE NULL END) AS aado2
, MAX(CASE WHEN itemid = 50802 THEN valuenum ELSE NULL END) AS baseexcess
, MAX(CASE WHEN itemid = 50803 THEN valuenum ELSE NULL END) AS bicarbonate
Expand Down Expand Up @@ -48,7 +48,7 @@ FROM mimic_hosp.labevents le
where le.ITEMID in
-- blood gases
(
52028 -- specimen
52033 -- specimen
, 50801 -- aado2
, 50802 -- base excess
, 50803 -- bicarb
Expand Down Expand Up @@ -127,22 +127,6 @@ where bg.po2 is not null
select bg.*
, ROW_NUMBER() OVER (partition by bg.subject_id, bg.charttime order by s2.charttime DESC) as lastRowFiO2
, s2.fio2_chartevents
-- create our specimen prediction
, 1/(1+exp(-(-0.02544
+ 0.04598 * po2
+ coalesce(-0.15356 * spo2 , -0.15356 * 97.49420 + 0.13429)
+ coalesce( 0.00621 * fio2_chartevents , 0.00621 * 51.49550 + -0.24958)
+ coalesce( 0.10559 * hemoglobin , 0.10559 * 10.32307 + 0.05954)
+ coalesce( 0.13251 * so2 , 0.13251 * 93.66539 + -0.23172)
+ coalesce(-0.01511 * pco2 , -0.01511 * 42.08866 + -0.01630)
+ coalesce( 0.01480 * fio2 , 0.01480 * 63.97836 + -0.31142)
+ coalesce(-0.00200 * aado2 , -0.00200 * 442.21186 + -0.01328)
+ coalesce(-0.03220 * bicarbonate , -0.03220 * 22.96894 + -0.06535)
+ coalesce( 0.05384 * totalco2 , 0.05384 * 24.72632 + -0.01405)
+ coalesce( 0.08202 * lactate , 0.08202 * 3.06436 + 0.06038)
+ coalesce( 0.10956 * ph , 0.10956 * 7.36233 + -0.00617)
+ coalesce( 0.00848 * o2flow , 0.00848 * 7.59362 + -0.35803)
))) as specimen_prob
from stg2 bg
left join stg_fio2 s2
-- same patient
Expand All @@ -156,14 +140,8 @@ select
stg3.subject_id
, stg3.hadm_id
, stg3.charttime
-- raw data indicating sample type
-- drop down text indicating the specimen type
, specimen
-- prediction of specimen for obs missing the actual specimen
, case
when specimen is not null then specimen
when specimen_prob > 0.75 then 'ART.'
else null end as specimen_pred
, specimen_prob

-- oxygen related parameters
, so2
Expand Down