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added exposure/outcome schema parameters, and made input of user-defi…
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…ned cohort construct works across.
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unknown authored and unknown committed Dec 7, 2014
1 parent f8e5a84 commit dfe0a4d
Showing 1 changed file with 56 additions and 61 deletions.
117 changes: 56 additions & 61 deletions inst/sql/sql_server/CohortMethod.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -38,40 +38,42 @@ Parameterized SQL to create cohorts, covariates, and outcomes datasets to be use
*********************************************************************************/

{DEFAULT @cdm_schema = 'CDM4_SIM'} /*CDM4_SIM CDM_TRUVEN_MDCD*/
{DEFAULT @results_schema = 'scratch'}
{DEFAULT @target_drug_concept_id = 755695} /*fluoxetine*/
{DEFAULT @comparator_drug_concept_id = 739138} /*sertraline*/
{DEFAULT @indication_concept_ids = 439926} /*malaise and fatigue*/
{DEFAULT @washout_window = 183}
{DEFAULT @indication_lookback_window = 183}
{DEFAULT @study_start_date = ''}
{DEFAULT @study_end_date = ''}
{DEFAULT @exclusion_concept_ids = 4027133,4032243,4146536,2002282,2213572,2005890,43534760,21601019}
{DEFAULT @outcome_concept_ids = 194133} /*low back pain*/
{DEFAULT @outcome_condition_type_concept_ids = 38000215,38000216,38000217,38000218,38000183,38000232} /*condition type only applies if @outcome_table = CONDITION_OCCURRENCE*/
{DEFAULT @max_outcome_count = 1} /*number of conditions, 1 is first occurrence*/

{DEFAULT @exposure_table = 'DRUG_ERA'} /*the table that contains the exposure information (DRUG_ERA or COHORT)*/
{DEFAULT @outcome_table = 'CONDITION_OCCURRENCE'} /*the table that contains the outcome information (CONDITION_OCCURRENCE or COHORT)*/

{DEFAULT @use_covariate_demographics = TRUE}
{DEFAULT @use_covariate_condition_occurrence = TRUE}
{DEFAULT @use_covariate_condition_era = FALSE}
{DEFAULT @use_covariate_condition_group = FALSE}
{DEFAULT @use_covariate_drug_exposure = FALSE}
{DEFAULT @use_covariate_drug_era = FALSE}
{DEFAULT @use_covariate_drug_group = FALSE}
{DEFAULT @use_covariate_procedure_occurrence = FALSE}
{DEFAULT @use_covariate_procedure_group = FALSE}
{DEFAULT @use_covariate_observation = FALSE}
{DEFAULT @use_covariate_concept_counts = FALSE}
{DEFAULT @use_covariate_risk_scores = FALSE}
{DEFAULT @use_covariate_interaction_year = FALSE}
{DEFAULT @use_covariate_interaction_month = FALSE}

{DEFAULT @excluded_covariate_concept_ids = 4027133,4032243,4146536,2002282,2213572,2005890,43534760,21601019}
{DEFAULT @delete_covariates_small_count = 100}
{DEFAULT @cdm_schema = 'CDM4_SIM'} /*cdm_schema: @cdm_schema*/
{DEFAULT @results_schema = 'scratch'} /*results_schema: @results_schema*/
{DEFAULT @target_drug_concept_id = ''} /*target_drug_concept_id: @target_drug_concept_id*/
{DEFAULT @comparator_drug_concept_id = ''} /*comparator_drug_concept_id: @comparator_drug_concept_id*/
{DEFAULT @indication_concept_ids = ''} /*indication_concept_ids: @indication_concept_ids*/
{DEFAULT @washout_window = 183} /*washout_window: @washout_window*/
{DEFAULT @indication_lookback_window = 183} /*indication_lookback_window: @indication_lookback_window*/
{DEFAULT @study_start_date = ''} /*study_start_date: @study_start_date*/
{DEFAULT @study_end_date = ''} /*study_end_date: @study_end_date*/
{DEFAULT @exclusion_concept_ids = ''} /*exclusion_concept_ids: @exclusion_concept_ids*/
{DEFAULT @outcome_concept_ids = ''} /*outcome_concept_ids: @outcome_concept_ids*/
{DEFAULT @outcome_condition_type_concept_ids = ''} /*outcome_condition_type_concept_ids: @outcome_condition_type_concept_ids*/ /*condition type only applies if @outcome_table = CONDITION_OCCURRENCE*/
{DEFAULT @max_outcome_count = 1} /*max_outcome_count: @max_outcome_count*/ /*number of conditions, 1 is first occurrence*/

{DEFAULT @exposure_schema = 'CDM4_SIM'} /*exposure_schema: @exposure_schema*/
{DEFAULT @exposure_table = 'DRUG_ERA'} /*exposure_table: @exposure_table*/ /*the table that contains the exposure information (DRUG_ERA or COHORT)*/
{DEFAULT @outcome_schema = 'CDM4_SIM'} /*outcome_schema: @outcome_schema*/
{DEFAULT @outcome_table = 'CONDITION_OCCURRENCE'} /*outcome_table: @outcome_table*/ /*the table that contains the outcome information (CONDITION_OCCURRENCE or COHORT)*/

{DEFAULT @use_covariate_demographics = TRUE} /*use_covariate_demographics: @use_covariate_demographics*/
{DEFAULT @use_covariate_condition_occurrence = TRUE} /*use_covariate_condition_occurrence: @use_covariate_condition_occurrence*/
{DEFAULT @use_covariate_condition_era = FALSE} /*use_covariate_condition_era: @use_covariate_condition_era*/
{DEFAULT @use_covariate_condition_group = FALSE} /*use_covariate_condition_group: @use_covariate_condition_group*/
{DEFAULT @use_covariate_drug_exposure = FALSE} /*use_covariate_drug_exposure: @use_covariate_drug_exposure*/
{DEFAULT @use_covariate_drug_era = FALSE} /*use_covariate_drug_era: @use_covariate_drug_era*/
{DEFAULT @use_covariate_drug_group = FALSE} /*use_covariate_drug_group: @use_covariate_drug_group*/
{DEFAULT @use_covariate_procedure_occurrence = FALSE} /*use_covariate_procedure_occurrence: @use_covariate_procedure_occurrence*/
{DEFAULT @use_covariate_procedure_group = FALSE} /*use_covariate_procedure_group: @use_covariate_procedure_group*/
{DEFAULT @use_covariate_observation = FALSE} /*use_covariate_observation: @use_covariate_observation*/
{DEFAULT @use_covariate_concept_counts = FALSE} /*use_covariate_concept_counts: @use_covariate_concept_counts*/
{DEFAULT @use_covariate_risk_scores = FALSE} /*use_covariate_risk_scores: @use_covariate_risk_scores*/
{DEFAULT @use_covariate_interaction_year = FALSE} /*use_covariate_interaction_year: @use_covariate_interaction_year*/
{DEFAULT @use_covariate_interaction_month = FALSE} /*use_covariate_interaction_month: @use_covariate_interaction_month*/

{DEFAULT @excluded_covariate_concept_ids = ''} /*excluded_covariate_concept_ids: @excluded_covariate_concept_ids*/
{DEFAULT @delete_covariates_small_count = 100} /*delete_covariates_small_count: @delete_covariates_small_count*/

USE @results_schema;

Expand Down Expand Up @@ -247,21 +249,21 @@ FROM (
de1.person_id
}

{@exposure_table == 'COHORT'} ? {
{@exposure_table <> 'DRUG_ERA'} ? {
SELECT CASE
WHEN c1.cohort_concept_id = @target_drug_concept_id
WHEN c1.cohort_definition_id = @target_drug_concept_id
THEN 1
WHEN c1.cohort_concept_id = @comparator_drug_concept_id
WHEN c1.cohort_definition_id = @comparator_drug_concept_id
THEN 0
ELSE - 1
END AS cohort_id,
c1.person_id,
c1.subject_id as person_id,
min(c1.cohort_start_date) AS cohort_start_date,
min(@exposure_extension_window, c1.cohort_end_date) AS cohort_end_date
FROM @cdm_schema.dbo.cohort c1
WHERE c1.cohort_id in (@target_drug_concept_id,@comparator_drug_concept_id)
GROUP BY c1.cohort_concept_id,
c1.person_id
min(c1.cohort_end_date) AS cohort_end_date
FROM @exposure_schema.dbo.@exposure_table c1
WHERE c1.cohort_definition_id in (@target_drug_concept_id,@comparator_drug_concept_id)
GROUP BY c1.cohort_definition_id,
c1.subject_id
}

) raw_cohorts
Expand Down Expand Up @@ -3819,32 +3821,25 @@ INSERT INTO #cohort_outcome (row_id, cohort_id, person_id, outcome_id, time_to_e
datediff(dd, cp1.cohort_start_date, co1.condition_start_date),
ca1.ancestor_concept_id
}
{@outcome_table == 'COHORT'} ? {
{@outcome_table <> 'CONDITION_OCCURRENCE'} ? {
SELECT cp1.row_id,
cp1.cohort_id,
cp1.person_id,
co1.cohort_concept_id AS outcome_id,
co1.cohort_definition_id AS outcome_id,
datediff(dd, cp1.cohort_start_date, co1.cohort_start_date) AS time_to_event
FROM #cohort_person cp1
INNER JOIN
@cdm_schema.dbo.cohort co1
ON cp1.person_id = co1.person_id
INNER JOIN (
SELECT descendant_concept_id,
ancestor_concept_id
FROM @cdm_schema.dbo.concept_ancestor
WHERE ancestor_concept_id IN (@outcome_concept_ids)
) ca1
ON co1.condition_concept_id = descendant_concept_id
@outcome_schema.dbo.@outcome_table co1
ON cp1.person_id = co1.subject_id
WHERE
co1.cohort_concept_id in (@outcome_concept_ids)
co1.cohort_definition_id in (@outcome_concept_ids)
AND co1.cohort_start_date > cp1.cohort_start_date
AND co1.cohort_start_Date <= cp1.observation_period_end_date
GROUP BY cp1.row_id,
cp1.cohort_id,
cp1.person_id,
datediff(dd, cp1.cohort_start_date, co1.cohort_start_date),
co1.cohort_concept_id
co1.cohort_definition_id
}
;

Expand Down Expand Up @@ -3872,16 +3867,16 @@ INSERT INTO #cohort_excluded_person (row_id, cohort_id, person_id, outcome_id)
co1.condition_type_concept_id IN (@outcome_condition_type_concept_ids)
AND co1.condition_start_date < cp1.cohort_start_date
}
{@outcome_table == 'COHORT'} ? {
{@outcome_table <> 'CONDITION_OCCURRENCE'} ? {
SELECT DISTINCT cp1.row_id,
cp1.cohort_id,
cp1.person_id,
co1.cohort_concept_id AS outcome_id
co1.cohort_definition_id AS outcome_id
FROM #cohort_person cp1
INNER JOIN @cdm_schema.dbo.cohort co1
ON cp1.person_id = co1.person_id
INNER JOIN @outcome_schema.dbo.@outcome_table co1
ON cp1.person_id = co1.subject_id
WHERE
co1.cohort_concept_id in (@outcome_concept_ids)
co1.cohort_definition_id in (@outcome_concept_ids)
AND co1.cohort_start_date < cp1.cohort_start_date
}

Expand Down

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