Output path
SQL:[IDI_Community].[dsbl_fasd].[FASD_YYYYMM]
SAS: libname cmid dsn=idi_community_srvprd schema=dsbl_fasd; run ;
How to access a code module in the Data Lab:Read here
Description
The purpose of this code module is to identify individuals in New Zealand in the IDI who have a recorded diagnosis of Fetal Alcohol Spectrum Disorder.
The dataset will list individuals, the earliest event when an individual has a recorded diagnosis of Fetal Alcohol Spectrum Disorder in the IDI, date of the earliest event, the individual’s age and whether they are alive at the time of the IDI refresh. For those individuals who have died, the dataset lists a date of death and age at death.
This module is not intended to be used to give a true prevalence rate of people in New Zealand with Fetal Alcohol Spectrum Disorder due to limitations of the datasets included in the IDI
and as Fetal Alcohol Spectrum Disorder is recognised as being underdiagnosed in the population (O’Leary, 2004; Elliott et al, 2008).The code module allows researchers to have a consistent way of identifying people with Fetal Alcohol Spectrum Disorder and will allow for comparisons of outcomes for people with Fetal Alcohol Spectrum Disorder and people without Fetal Alcohol Spectrum Disorder.
Key Concepts
- Individuals are identified from a diagnosis recorded using a recognised ICD-9-CM-A diagnosis code for Fetal Alcohol Spectrum Disorder or a diagnosis recorded through other means by a professional.
- An individual may have multiple entries in a source dataset or across a number of source datasets.
- This module collates the earliest reference to the individual with an appropriate diagnosis code in each source dataset and then identifies the earliest reference amongst all datasets.
- The module indicates whether the individual was alive at the time of the most recent IDI refresh.
- The module will record events within the time period that data is included in the IDI. However, as a lifelong condition resulting from exposure to alcohol during gestation, an individual will have had Fetal Alcohol Spectrum Disorder since birth.
- The earliest date recorded in the IDI is not a date of diagnosis or onset of a condition.
Business history
Code history and ICD code notes
ICD codes used are based on the ICD clinical code system for the earliest date of data as per Health New Zealand (HNZ) | Te Whatu Ora best practice. This means ICD-9-CM-A codes have been used in line with the start of the health-related datasets in the IDI.
On advice from HNZ clinical coding/classification staff, codes have first been looked up directly in ICD-10-AM 12th Edition (current Edition used), then back mapped to ICD-10-AM 1st Edition and then back mapped to ICD-9-CM-A codes.
Due to the nature of how clinical coding and classifications using ICD codes work, there are some instances where ICD-10-AM 1st Edition codes back map to ICD-9-CM-A codes that may include more than just the intended diagnosis for this code module due to changes and decisions made with ICD code mapping overtime (see Table 1).
Notes for specific datasets
-
For the MORT dataset, ICD codes have only been provided in their submitted system codes (i.e. not backmapped). This means the source dataset includes both ICD-9-CM-A and editions of ICD-10-AM and the code underlying this module has been written to reflect this.
-
For the PRIMHD dataset, codes have been provided in DSM-IV and ICD-10-AM edition codes. This means the source dataset includes both DSM-IV and ICD-10-AM editions and the code underlying this module has been written to reflect this.
-
For the MHINC dataset, codes have been provided in various ICD code editions as well as backmapping to DSM-IV where possible. This means the source dataset includes both DSM-IV and ICD-9-CM-A and the code underlying this module has been written to reflect this.
References
- Beltran-Castillon L and McLeod K (2023) From Data to Dignity: Health and Wellbeing Indicators for New Zealanders with Intellectual Disability. Published: IHC, Kōtātā Insight
- Elliott et al. (2008) Fetal Alcohol Spectrum Disorders (FASD): a systematic review of prevention, diagnosis and management. HSAC Report 1(9).
- O’Leary CM (2004) Fetal alcohol syndrome: diagnosis, epidemiology, and developmental outcomes. J.Paediatrics and Child Health 40(1-2), 2-7.
Community of Interest
| Domain | Agency | Person |
|---|---|---|
| Initial code | Social Investment Agency (SIA) | Craig Wright |
| Module coder | Whaikaha - Ministry of Disabled People | Adelaide Wilson |
| Module coder | Nicholson Consulting | Sarah Underwood |
| Lead SME/Policy | Whaikaha - Ministry of Disabled People | Michelle Gezentsvey, Claire Bretherton |
Key business rules
| Dataset name | Diagnosis definition | Dataset time period |
|---|---|---|
| Accident Compensation Corporation (ACC) Injury Claims Data | Recorded as having an ACC read code on the ACC45 claim form of: | 1974 - |
| ‘PK80.’ (Fetal alcohol syndrome). | ||
| Publicly funded hospital discharges (NMDS) | A publicly funded hospital discharge with a primary or secondary ICD-9-CM-A diagnosis code of: | 1988 - |
| 76071 (Alcohol affecting fetus or newborn via placenta or breast milk). | ||
| Privately funded hospital discharges (NMDS) | A privately funded hospital discharge with a primary or secondary ICD-9-CM-A diagnosis code of: | 2001 - |
| 76071 (Alcohol affecting fetus or newborn via placenta or breast milk). | ||
| Mortality Collection (MORT) | Identified as an underlying or contributing cause of death with a ICD-9-CM-A code of: | 1988 - |
| 76071 (Alcohol affecting fetus or newborn via placenta or breast milk), | ||
| or an ICD-10-AM code of: | ||
| Q860 (Fetal alcohol syndrome (dysmorphic)). | ||
| Disability Support Services database (SOCRATES) | Recorded as having fetal alcohol syndrome in the Referral Diagnosis/Health Condition with the code of: | 1998 - |
| 1106 (Foetal alcohol syndrome (FAS)). | ||
| Programme for the Integration of Mental Health Data (PRIMHD) | There is no code for fetal alcohol syndrome in the DSM-IV classification system in secondary mental health and addiction services. Identified with a ICD-10-AM (12th edition) code of: | 2009 - |
| Q860 (Fetal alcohol syndrome (dysmorphic)). | ||
| Mental Health Information National Collection (MHINC) | There is no code for fetal alcohol syndrome in the DSM-IV classification system in secondary mental health and addiction services. Identified with an ICD-9-CM-A code of: | July 2001 - 2008 |
| 76071 (Alcohol affecting fetus or newborn via placenta or breast milk). | ||
| Oranga Tamariki Gateway Assessments Data | A need type of foetal alcohol spectrum disorder in a Gateway Assessment. | 2013 - |
Table 1: ICD-10-AM 1st Edition codes that back map to ICD-9-CM-A disease codes included in the code module
Backward mapping provides equivalent codes for new codes in the newer edition.
| ICD-9-CM-A code and definition | ICD-10-AM 1st Edition code and definition |
|---|---|
| 76071 Alcohol affecting fetus or newborn via placenta or breast milk | P043 Fetus and newborn affected by maternal use of alcohol |
Data quality and other known issues
-
Not all individuals in New Zealand diagnosed with Fetal Alcohol Spectrum Disorder will be identified in this module. The module requires that the individual has had an ACC claim form, hospital discharge events, received Mental Health or Disability Support Services, an Oranga Tamariki gateway assessment, or had their death recorded, where the diagnosis of Fetal Alcohol Spectrum Disorder has been specified.
-
Datasets included have different lag times for having updated data available in the IDI. This means the completeness of the data at the time of analysis will depend on the lag time of the different datasets.
-
Individuals identified in the SOCRATES disability dataset do not always appear in the referral or needs assessment datasets as well. Where an individual is only identified through the SOCRATES disability dataset there is no associated event date. In this case a proxy date of ‘3999-12-31’ will be seen in the final table.
-
The diagnosis will not be consistent for all age groups as the diagnosis of Fetal Alcohol Spectrum Disorder was only recognised in the 1970s (O’Leary, 2004). Fetal Alcohol Spectrum Disorder is not diagnosed by a laboratory test but by assessment of patterns of abnormalities with diagnosis generally made on young children (O’Leary, 2004). It is likely that people who are less severely affected are less likely to be diagnosed and thus identified in the data.
-
Registerable stillbirths are included in the mortality dataset.
Comparison against other sources
-
Counts of individuals published in the IHC publication ‘From Data to Dignity’ (2023) were for those individuals with fetal alchohol syndrome in the study population defined as the 2018 Administrative Population Census (APC).The counts from this code module for people with Fetal Alcohol Spectrum Disorder are higher than those in the 2023 publication.
-
No data is available to inform the prevalence of Fetal Alcohol Spectrum Disorder in New Zealand. International studies and opinion suggest that 3% to 5% of people may be affected by the effects of alcohol exposure before birth. Based on this prevalence estimate, in New Zealand it is likely that between 1800 to 3000 babies are born each year with Fetal Alcohol Spectrum Disorder (https://health.govt.nz/strategies-initiatives/programmes-and-initiatives/fetal-alcohol-spectrum-disorder).
-
The New Zealand Paediatric Surveillance Unit (NZPSU) collected reports of ■■■■■■■■ of suspected or definite FASD in 2000 (Elliott et al, 2008). This was noted as being below the incidence seen in other countries, possibly due to low levels of diagnosis of FASD by NZ paediatricians at the time (Elliott et al, 2008). This module undercounts people with Fetal Alcohol Spectrum Disorder.
Parameters
The following parameters should be supplied to this module to run it in the database:
- {targetdb}: The SQL database on which the spell datasets are to be created.
- {idicleanversion}: The IDI Clean version that the spell datasets need to be based on.
- {targetschema}: The project schema under the target database into which the spell datasets are to be created.
Dependencies
{idicleanrefresh}.[acc_clean].[claims]
{idicleanrefresh}.[acc_clean].[medical_codes]
{idicleanrefresh}.[moh_clean].[pub_fund_hosp_discharges_diag]
{idicleanrefresh}.[moh_clean].[pub_fund_hosp_discharges_event]
{idicleanrefresh}.[moh_clean].[priv_fund_hosp_discharges_diag]
{idicleanrefresh}.[moh_clean].[priv_fund_hosp_discharges_event]
{idicleanrefresh}.[moh_clean].[mortality_diagnosis]
{idicleanrefresh}.[moh_clean].[mortality_registrations]
{idicleanrefresh}.[moh_clean].[pop_cohort_demographics]
{idicleanrefresh}.security.concordance
{idicleanrefresh}.[data].[personal_detail]
{idicleanrefresh}.[dia_clean].[deaths]
The following IDI_Adhoc are the most recent versions for this current refresh but changes to the code will need to be made as new datasets are uploaded into the IDI.
[IDI_Adhoc].[clean_read_MOH_SOCRATES].[moh_disability_2022]
[IDI_Adhoc].[clean_read_MOH_SOCRATES].[moh_needs_assessment_2022]
[IDI_Adhoc].[clean_read_MOH_SOCRATES].[moh_referral_2022]
[IDI_Adhoc].[clean_read_MOH_PRIMHD].[primhd_diagnoses_202502]
[IDI_Adhoc].[clean_read_MOH_PRIMHD].[moh_primhd_mhinc]
[IDI_Adhoc].[clean_read_CYF].[cyf_gateway_cli_needs]
Outputs
{targetdb}.{targetschema}.fetal_alcohol_spectrum_disorder
| Column name | Description |
|---|---|
| snz_uid | The unique Stats NZ person identifier for the the individual |
| type | A string indicating which condition of disability this table has identified (hard-coded to “FASD”) |
| entity | A string indicating the organisation or provider ID that has provided a service for mental health services, where relevant |
| source_table | A string that states the data source for the earliest record of diagnosis for an individual in the IDI |
| min_date | The earliest record of diagnosis for an individual in the IDI (Note: not a date of diagnosis or onset of a condition) |
| snz_sex_gender_code | Code for an individual’s gender |
| snz_birth_month_nbr | Month of an individual’s birth |
| snz_birth_year_nbr | Year of an individual’s birth |
| snz_birth_date_proxy | Proxy date of an individual’s birth |
| age | Age of an individual at the time of the IDI refresh |
| death_status | A binary indicator indicating whether an individual is recorded dead (value = 1) or alive (value = 0) at the time of refresh |
| snz_deceased_year_nbr | Year of an individual’s death (if relevant) |
| snz_deceased_month_nbr | Month of an individual’s death (if relevant) |
| dod | Date of death (if relevant) |
| age_at_death | Age of an individual at death (if relevant) |
Variable descriptions
Granularity:
One row represents an individual, the earliest identification of their diagnosis in the IDI, birthdate, gender and death (if applicable).
Module Version & Change History
| Date | Version | Comments |
|---|---|---|
| 26 May 2025 | Initial | Version based on specifications from Commissioning document |
| 09 June 2025 | 1.1 | Update to ACC variable with 202506 refresh. acc_med_read_code updated to acc_med_injury_code and acc_cla_read_code to acc_cla_primary_inj_code with acc_cla_primary_inj_type_code added. |
| 31 October 2025 | 1.2 | Update to MoH publicly funded hospital discharge variable with 20510 refresh. Converted moh_evt_evst_date from datetime to date. |
Code
/*Set Parameters*/
/*Ref date should be the 15th of the month of the refresh used*/
:setvar targetdb "targetdb"
:setvar targetschema "targetschema"
:setvar idicleanversion "idicleanversion"
:setvar refdate "refdate"
:setvar idimetadataversion "idimetadataversion"
USE $(targetdb);
GO
/*ACC claims with a code that includes fetal alcohol syndrome*/
DROP TABLE IF EXISTS #acc_fas;
SELECT
c.snz_uid
,'ACC' AS source_table
,c.code
,c.date AS event_date
,CAST(NULL AS VARCHAR(10)) AS entity
INTO #acc_fas
FROM
(
SELECT
[snz_uid]
,[acc_cla_accident_date] AS date
,[acc_cla_primary_inj_code] AS code
FROM [$(idicleanversion)].[acc_clean].[claims]
WHERE ([acc_cla_primary_inj_code] IN ('PK80.') AND [acc_cla_primary_inj_type_code] = 'Read Code')
UNION ALL
SELECT
b.snz_uid
,b.acc_cla_accident_date AS date
,a.[acc_med_injury_code] AS code
FROM [$(idicleanversion)].[acc_clean].[medical_codes] AS a
LEFT JOIN [$(idicleanversion)].[acc_clean].[claims] AS b ON a.[snz_acc_claim_uid] = b.[snz_acc_claim_uid]
WHERE a.[acc_med_injury_code] IN ('PK80.')
) AS c;
/*Publicly-funded hospital discharges where clinical code matches a diagnosis of fetal alcohol syndrome*/
DROP TABLE IF EXISTS #moh_pub_fas;
SELECT
b.snz_uid
,'MOH_PUB' AS source_table
,a.[moh_dia_submitted_system_code] AS code_sys
,a.[moh_dia_diagnosis_type_code]
,a.[moh_dia_event_id_nbr]
,a.[moh_dia_clinical_code]
,b.moh_evt_birth_year_nbr
,CAST (b.[moh_evt_evst_date] AS DATE) AS event_date
,CAST (NULL AS VARCHAR(10)) AS entity
INTO #moh_pub_fas
FROM [$(idicleanversion)].[moh_clean].[pub_fund_hosp_discharges_diag] AS a
LEFT JOIN [$(idicleanversion)].[moh_clean].[pub_fund_hosp_discharges_event] AS b ON a.moh_dia_event_id_nbr = b.moh_evt_event_id_nbr
WHERE (SUBSTRING(a.[moh_dia_clinical_code],1,5) = '76071' AND a.[moh_dia_clinical_sys_code] = '06' AND a.[moh_dia_diagnosis_type_code] IN ('A','B'));
/*Privately-funded hospital discharges where clinical code matches a diagnosis of fetal alcohol syndrome*/
DROP TABLE IF EXISTS #moh_pri_fas;
SELECT
b.snz_uid
,'MOH_PRI' AS source_table
,a.[moh_pri_diag_event_id_nbr]
,a.[moh_pri_diag_clinic_sys_code]
,a.[moh_pri_diag_sub_sys_code]
,a.[moh_pri_diag_diag_type_code]
,a.[moh_pri_diag_clinic_code]
,b.[moh_pri_evt_start_date] AS event_date
,CAST (NULL AS VARCHAR(10)) AS entity
INTO #moh_pri_fas
FROM [$(idicleanversion)].[moh_clean].[priv_fund_hosp_discharges_diag] AS a
LEFT JOIN [$(idicleanversion)].[moh_clean].[priv_fund_hosp_discharges_event] AS b ON a.moh_pri_diag_event_id_nbr = b.moh_pri_evt_event_id_nbr
WHERE (SUBSTRING(a.[moh_pri_diag_clinic_code],1,5) = '76071' AND a.[moh_pri_diag_clinic_sys_code] = '06' AND a.[moh_pri_diag_diag_type_code] IN ('A','B'));
/*Registrations in the mortality dataset where clinical code matches a diagnosis of fetal alcohol syndrome*/
DROP TABLE IF EXISTS #mos_fas;
SELECT
b.[snz_uid]
,b.[snz_moh_uid]
,'MOH_MOS' AS source_table
,DATEFROMPARTS(b.moh_mor_birth_year_nbr,b.moh_mor_birth_month_nbr,15) AS event_date
,a.[moh_mort_diag_clinical_code] AS code
,a.[moh_mort_diag_clinic_type_code]
,a.[moh_mort_diag_clinic_sys_code]
,a.[moh_mort_diag_diag_type_code]
,CAST (NULL AS VARCHAR(10)) AS entity
INTO #mos_fas
FROM [$(idicleanversion)].[moh_clean].[mortality_diagnosis] AS a
LEFT JOIN [$(idicleanversion)].[moh_clean].[mortality_registrations] AS b ON a.snz_dia_death_reg_uid = b.snz_dia_death_reg_uid
WHERE (SUBSTRING(a.[moh_mort_diag_clinical_code],1,5) = '76071' AND a.[moh_mort_diag_clinic_sys_code] ='06')
OR (SUBSTRING(a.[moh_mort_diag_clinical_code],1,4) = 'Q860' AND a.[moh_mort_diag_clinic_sys_code] >= '10');
/* Individuals in the Ministry of Health SOCRATES database with code 1106. Date can either be first contact date or referral date.
Where an individual appears only in the disability table but not the needs assessment or referral table, an event date of 3999-12-31 is added.
This date will be removed in the collation process if the individual appears in other datasets with an earlier event_date or kept if the
diagnosis table is the only record for the individual*/
DROP TABLE IF EXISTS #moh_soc_fas;
SELECT
DISTINCT
b.snz_uid
,'SOC' AS source_table
,CASE WHEN CAST(SUBSTRING(c.[FirstContactDate],1,7) AS date) IS NOT NULL THEN CAST(SUBSTRING(c.[FirstContactDate],1,7) AS date)
WHEN CAST(SUBSTRING(e.[ReferralDate],1,7) AS date) IS NOT NULL THEN CAST(SUBSTRING(e.[ReferralDate],1,7) AS date)
WHEN CAST(SUBSTRING(e.[ReferralDate],1,7) AS date) IS NULL AND CAST(SUBSTRING(c.[FirstContactDate],1,7) AS date) IS NULL THEN '3999-12-31'
END AS event_date
,CAST (a.code as VARCHAR(7)) AS code
,a.[Description]
,CAST (NULL AS VARCHAR(10)) AS entity
INTO #moh_soc_fas
FROM [IDI_Adhoc].[clean_read_MOH_SOCRATES].[moh_disability_2022] AS a
LEFT JOIN [$(idicleanversion)].[moh_clean].[pop_cohort_demographics] AS b ON a.snz_moh_uid = b.snz_moh_uid
LEFT JOIN (SELECT DISTINCT snz_moh_uid,[FirstContactDate] FROM [IDI_Adhoc].[clean_read_MOH_SOCRATES].[moh_needs_assessment_2022] ) AS c ON a.snz_moh_uid = c.snz_moh_uid
LEFT JOIN (SELECT DISTINCT snz_moh_uid,[ReferralDate] FROM [IDI_Adhoc].[clean_read_MOH_SOCRATES].[moh_referral_2022]) AS e ON a.snz_moh_uid = e.snz_moh_uid
WHERE code IN ('1106');
/* fetal alcohol diagnosis in PRIMHD diagnosis data*/
DROP TABLE IF EXISTS #moh_PRIMHD_fas;
SELECT
b.snz_uid
,a.[snz_moh_uid]
,'MOH_PRIMHD' AS source_table
,CAST (a.[organisation_id] AS VARCHAR(10)) AS entity
,a.[classification_code_id]
,a.[diagnosis_type]
,CONVERT(date,a.[classification_start_date],103) AS event_date
,a.[clinical_coding_system_id]
,a.[clinical_code] AS code
INTO #moh_PRIMHD_fas
FROM [IDI_Adhoc].[clean_read_MOH_PRIMHD].[primhd_diagnoses_202502] AS a
LEFT JOIN [$(idicleanversion)].[moh_clean].[pop_cohort_demographics] AS b ON a.snz_moh_uid = b.snz_moh_uid
WHERE (SUBSTRING(a.[clinical_code],1,4) = 'Q860' AND a.[clinical_coding_system_id] >= '10');
/* fetal alcohol syndrome diagnosis in PRIMHD MHINC data*/
DROP TABLE IF EXISTS #moh_mhinc_fas;
SELECT
b.snz_uid
,'MOH_MHINC' AS source_table
,CAST (a.[organisation_id] AS VARCHAR(10)) AS entity
,a.[classification_start] AS event_date
,a.[clinical_coding_system_id]
,a.[clinical_code] AS code
,a.[diagnosis_type]
INTO #moh_mhinc_fas
FROM [IDI_Adhoc].[clean_read_MOH_PRIMHD].[moh_primhd_mhinc] AS a
LEFT JOIN [$(idicleanversion)].[moh_clean].[pop_cohort_demographics] AS b ON a.snz_moh_uid = b.snz_moh_uid
WHERE (SUBSTRING(a.[clinical_code],1,5) = '76071' AND a.[clinical_coding_system_id] = '06');
/* fetal alcohol spectrum disorder as a client need in gateway assesssments*/
DROP TABLE IF EXISTS #cyf_gateway_fas;
SELECT
b.snz_uid
,a.snz_msd_uid
,a.[need_type_code]
,a.[needs_desc]
,a.[need_category_code] AS code
,a.[needs_cat_desc]
,needs_created_date AS event_date
,'CYF' AS source_table
, CAST (NULL AS VARCHAR (10)) AS entity
INTO #cyf_gateway_fas
FROM [IDI_Adhoc].[clean_read_CYF].[cyf_gateway_cli_needs] AS a
LEFT JOIN [$(idicleanversion)].security.concordance AS b ON a.snz_msd_uid = b.snz_msd_uid
WHERE need_type_code='FAE';
/* collate data from all sources into one table*/
DROP TABLE IF EXISTS #fas;
SELECT
a.snz_uid
,MIN(event_date) AS min_date
,source_table
,entity
INTO #fas
FROM (
SELECT snz_uid, event_date, source_table, entity FROM #moh_pub_fas
UNION ALL
SELECT snz_uid, event_date, source_table, entity FROM #moh_pri_fas
UNION ALL
SELECT snz_uid, event_date, source_table, entity FROM #mos_fas
UNION ALL
SELECT snz_uid, event_date, source_table, entity FROM #moh_soc_fas
UNION ALL
SELECT snz_uid, event_date, source_table, entity FROM #moh_PRIMHD_fas
UNION ALL
SELECT snz_uid, event_date, source_table, entity FROM #moh_mhinc_fas
UNION ALL
SELECT snz_uid, event_date, source_table, entity FROM #acc_fas
UNION ALL
SELECT snz_uid, event_date, source_table, entity FROM #cyf_gateway_fas
) AS a
GROUP BY snz_uid
, source_table
, entity;
/* subset of individuals who are deceased and are in death data*/
DROP TABLE IF EXISTS #fas_dd;
SELECT
a.*
,b.snz_birth_month_nbr
,b.snz_birth_year_nbr
,b.snz_sex_gender_code
,b.snz_deceased_year_nbr
,b.snz_deceased_month_nbr
,b.snz_birth_date_proxy
,NULL AS age
,DATEFROMPARTS(b.snz_deceased_year_nbr, b.snz_deceased_month_nbr, 15) AS dod
,'FASD' AS [type]
INTO #fas_dd
FROM #fas as a
INNER JOIN [$(idicleanversion)].[data].[personal_detail] AS b ON a.snz_uid = b.snz_uid
WHERE a.snz_uid IN (SELECT DISTINCT snz_uid FROM [$(idicleanversion)].[dia_clean].[deaths])
AND b.snz_deceased_year_nbr IS NOT NULL;
/* subset of individuals who are deceased but not in death data*/
DROP TABLE IF EXISTS #fas_od;
SELECT
a.*
,b.snz_birth_month_nbr
,b.snz_birth_year_nbr
,b.snz_sex_gender_code
,b.snz_deceased_year_nbr
,b.snz_deceased_month_nbr
,b.snz_birth_date_proxy
,NULL AS age
,DATEFROMPARTS(b.snz_deceased_year_nbr, b.snz_deceased_month_nbr, 15) AS dod
,'FASD' AS [type]
INTO #fas_od
FROM #fas AS a
INNER JOIN [$(idicleanversion)].[data].[personal_detail] AS b ON a.snz_uid = b.snz_uid
WHERE a.snz_uid NOT IN (SELECT DISTINCT snz_uid FROM [$(idicleanversion)].[dia_clean].[deaths])
AND b.snz_deceased_year_nbr IS NOT NULL;
/* subset of individuals who are alive*/
DROP TABLE IF EXISTS #fas_ad;
SELECT
a.*
,b.snz_birth_month_nbr
,b.snz_birth_year_nbr
,b.snz_sex_gender_code
,b.snz_deceased_year_nbr
,b.snz_deceased_month_nbr
,b.snz_birth_date_proxy
,DATEDIFF(YEAR, b.snz_birth_date_proxy, '$(refdate)') AS age
,'3999-12-31' AS dod
,'FASD' AS [type]
INTO #fas_ad
FROM #fas AS a
INNER JOIN [$(idicleanversion)].[data].[personal_detail] AS b ON a.snz_uid = b.snz_uid
WHERE a.snz_uid NOT IN (SELECT DISTINCT snz_uid FROM [$(idicleanversion)].[dia_clean].[deaths])
AND a.snz_uid NOT IN (SELECT DISTINCT snz_uid FROM #fas_dd)
AND a.snz_uid NOT IN (SELECT DISTINCT snz_uid FROM #fas_od);
/* join all tables together*/
DROP TABLE IF EXISTS #fas_final;
WITH fas_union AS (
SELECT
*
FROM #fas_dd
UNION ALL
SELECT * FROM #fas_od
UNION ALL
SELECT * FROM #fas_ad
)
SELECT
*
,DATEDIFF(YEAR, snz_birth_date_proxy, dod) AS age_at_death
,CASE WHEN age IS NOT NULL THEN 0 ELSE 1 END AS death_status
INTO #fas_final
FROM fas_union;
/* select all required variables */
DROP TABLE IF EXISTS #fas_min;
SELECT
snz_uid
,[type]
,entity
,source_table
,min_date
,snz_sex_gender_code
,snz_birth_month_nbr
,snz_birth_year_nbr
,snz_birth_date_proxy
,age
,death_status
,snz_deceased_year_nbr
,snz_deceased_month_nbr
,CASE WHEN dod = '3999-12-31' THEN NULL ELSE dod END AS dod
,CASE WHEN age_at_death > 1000 THEN NULL ELSE age_at_death END AS age_at_death
INTO #fas_min
FROM #fas_final;
/*take earliest recorded date for each snz_uid and create table */
DROP TABLE IF EXISTS #fas_dbl;
SELECT
snz_uid
,[type]
,entity
,source_table
,min_date
,snz_sex_gender_code
,snz_birth_month_nbr
,snz_birth_year_nbr
,snz_birth_date_proxy
,age
,death_status
,snz_deceased_year_nbr
,snz_deceased_month_nbr
,dod
,age_at_death
INTO #fas_dbl
FROM #fas_min a
WHERE min_date = (
SELECT MIN(min_date)
FROM #fas_min b
WHERE b.snz_uid = a.snz_uid)
ORDER BY snz_uid;
/* remove duplicate snz_uid with the same minimum date but different entities or sources. Create table in IDI_Sandpit */
DROP TABLE IF EXISTS [$(targetdb)].[$(targetschema)].[$(projprefix)_fetal_alcohol_syndrome];
WITH cte AS
(SELECT ROW_NUMBER() OVER(PARTITION BY snz_uid
ORDER BY snz_uid DESC) AS rn
FROM #fas_dbl)
DELETE FROM cte WHERE rn > 1;
SELECT
snz_uid
,[type]
,entity
,source_table
,min_date
,snz_sex_gender_code
,snz_birth_month_nbr
,snz_birth_year_nbr
,snz_birth_date_proxy
,age
,death_status
,snz_deceased_year_nbr
,snz_deceased_month_nbr
,dod
,age_at_death
INTO [$(targetdb)].[$(targetschema)].[$(projprefix)_fetal_alcohol_syndrome]
FROM #fas_dbl