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## How to use this page |
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You can either read this page from start to end |
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to get an idea of the kinds of queries you can make with ehrQL. |
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Or you can use the navigation bar at the top-right of this page, |
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to see a list of the examples, |
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and then jump to a specific example of interest. |
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The examples are organised firstly by the table which they pull data from - |
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for a more complete guide to the tables, refer to the |
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[Table Schemas](../reference/schemas.md) section of the |
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ehrQL documentation. |
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## Understanding these examples |
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### The populations defined with `define_population()` |
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In each of these examples, |
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we specify that the population is **all patients** |
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via `dataset.define_population(patients.exists_for_patient())`. |
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In practice, |
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you will likely want to adapt an example to filter to a specific population of interest. |
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Refer to the [`define_population()` documentation](../reference/language.md#Dataset.define_population). |
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### Some examples using `codelist_from_csv()` |
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:warning: Some examples refer to CSV codelists using the |
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`codelist_from_csv` function, |
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but are incomplete. |
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To actually use these code example, |
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you will need to correctly complete the function call. |
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The codelists are not provided as a part of these examples. |
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For example, instead of: |
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```python |
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asthma_codelist = codelist_from_csv("XXX", column="YYY") |
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``` |
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you will need a line more like: |
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```python |
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asthma_codelist = codelist_from_csv("your-asthma-codelist.csv", column="code") |
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``` |
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which provides the filename `your-asthma-codelist.csv` |
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and the name of the CSV column with codes. |
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#### Using codelists with category columns |
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Some codelists will have a category column that groups individual codes into categories. For example, [this codelist for ethnicity](https://www.opencodelists.org/codelist/opensafely/ethnicity-snomed-0removed/2e641f61/) has 2 category columns, which represent categories at both 6 and 16 levels. To make use of these categories, you can use `codelist_from_csv()` as follows: |
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```python |
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ethnicity_codelist = codelist_from_csv("ethnicity_codelist_with_categories", column="snomedcode", category_column="Grouping_6") |
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``` |
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If you include an argument for `category_column`, the codelist returned will be a *dictionary* mapping individual codes to their respective categories. Without the `category_column` argument, the codelist returned will be a *list* of codes. |
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You can see an example of [how to access these categories within your dataset definition ](#finding-each-patients-ethnicity) below. |
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## Patients |
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Examples for the [patients table](../reference/schemas/core.md#patients). |
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### Finding patient demographics |
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#### Finding each patient's sex |
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```ehrql |
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from ehrql import create_dataset |
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from ehrql.tables.core import patients |
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dataset = create_dataset() |
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dataset.sex = patients.sex |
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dataset.define_population(patients.exists_for_patient()) |
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``` |
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The possible values are "female", "male", "intersex", and "unknown". |
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#### Finding each patient's date of birth |
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```ehrql |
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from ehrql import create_dataset |
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from ehrql.tables.core import patients |
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dataset = create_dataset() |
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dataset.date_of_birth = patients.date_of_birth |
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dataset.define_population(patients.exists_for_patient()) |
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``` |
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#### Finding each patient's age |
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```ehrql |
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from ehrql import create_dataset |
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from ehrql.tables.core import patients |
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dataset = create_dataset() |
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dataset.age = patients.age_on("2023-01-01") |
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dataset.define_population(patients.exists_for_patient()) |
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``` |
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Alternatively, using a native Python `date`: |
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```ehrql |
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from datetime import date |
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from ehrql import create_dataset |
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from ehrql.tables.core import patients |
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dataset = create_dataset() |
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dataset.age = patients.age_on(date(2023, 1, 1)) |
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dataset.define_population(patients.exists_for_patient()) |
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``` |
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Or using an `index_date` variable: |
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```ehrql |
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from ehrql import create_dataset |
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from ehrql.tables.core import patients |
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index_date = "2023-01-01" |
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dataset = create_dataset() |
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dataset.age = patients.age_on(index_date) |
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dataset.define_population(patients.exists_for_patient()) |
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``` |
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#### Assigning each patient an age band |
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```ehrql |
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from ehrql import create_dataset, case, when |
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from ehrql.tables.core import patients |
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dataset = create_dataset() |
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age = patients.age_on("2023-01-01") |
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dataset.age_band = case( |
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when(age < 20).then("0-19"), |
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when(age < 40).then("20-39"), |
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when(age < 60).then("40-59"), |
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when(age < 80).then("60-79"), |
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when(age >= 80).then("80+"), |
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otherwise="missing", |
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) |
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dataset.define_population(patients.exists_for_patient()) |
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``` |
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#### Finding each patient's date of death in their primary care record |
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```ehrql |
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from ehrql import create_dataset |
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from ehrql.tables.core import patients |
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dataset = create_dataset() |
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dataset.date_of_death = patients.date_of_death |
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dataset.define_population(patients.exists_for_patient()) |
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``` |
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:notepad_spiral: This value comes from the patient's EHR record. You can find more information about the accuracy of this value in the [reference schema](../reference/schemas/core.md#recording-of-death-in-primary-care). |
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## ONS Deaths |
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Examples for the [ons_deaths table](../reference/schemas/core.md#ons_deaths). |
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### Finding patient demographics |
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#### Finding each patient's date, underlying_cause_of_death, and first noted additional medical condition noted on the death certificate from ONS records |
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```ehrql |
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from ehrql import create_dataset |
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from ehrql.tables.core import ons_deaths, patients |
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dataset = create_dataset() |
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dataset.date_of_death = ons_deaths.date |
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dataset.underlying_cause_of_death = ons_deaths.underlying_cause_of_death |
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dataset.cause_of_death = ons_deaths.cause_of_death_01 |
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dataset.define_population(patients.exists_for_patient()) |
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``` |
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:notepad_spiral: There are currently [multiple](https://github.com/opensafely-core/ehrql/blob/d29ff8ab2cebf3522258c408f8225b7a76f7b6f2/ehrql/tables/beta/core.py#L78-L92) cause of death fields. We aim to resolve these to a single feature in the future. |
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#### Finding patients with a particular cause of death |
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The `ons_deaths` table has multiple "cause of death" fields. Using the |
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[`cause_of_death_is_in()`](../reference/schemas/core.md#ons_deaths.cause_of_death_is_in) |
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method we can match a codelist against all of these at once. |
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```ehrql |
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from ehrql import create_dataset, codelist_from_csv |
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from ehrql.tables.core import ons_deaths, patients |
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dataset = create_dataset() |
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cause_of_death_X_codelist = codelist_from_csv("XXX", column="YYY") |
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dataset.died_with_X = ons_deaths.cause_of_death_is_in(cause_of_death_X_codelist) |
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dataset.define_population(patients.exists_for_patient()) |
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``` |
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## Addresses |
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Examples for the [TPP addresses table](../reference/schemas/tpp.md#addresses). |
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### Finding attributes related to each patient's address as of a given date |
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#### Finding each patient's IMD rank |
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```ehrql |
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from ehrql import create_dataset |
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from ehrql.tables.tpp import addresses, patients |
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dataset = create_dataset() |
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dataset.imd = addresses.for_patient_on("2023-01-01").imd_rounded |
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dataset.define_population(patients.exists_for_patient()) |
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``` |
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The original IMD ranking is rounded to the nearest 100. |
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The rounded IMD ranking ranges from 0 to 32,800. |
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See [this code comment](https://github.com/opensafely-core/ehrql/blob/d29ff8ab2cebf3522258c408f8225b7a76f7b6f2/ehrql/tables/beta/tpp.py#L117-L123) about how we choose one address if a patient has multiple registered addresses on the given date. |
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#### Calculating each patient's IMD quintile and/or decile |
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```ehrql |
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from ehrql import create_dataset |
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from ehrql.tables.tpp import addresses, patients |
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dataset = create_dataset() |
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patient_address = addresses.for_patient_on("2023-01-01") |
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dataset.imd_quintile = patient_address.imd_quintile |
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dataset.imd_decile = patient_address.imd_decile |
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dataset.define_population(patients.exists_for_patient()) |
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``` |
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#### Finding each patient's rural/urban classification |
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```ehrql |
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from ehrql import create_dataset |
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from ehrql.tables.tpp import addresses, patients |
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dataset = create_dataset() |
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dataset.rural_urban = addresses.for_patient_on("2023-01-01").rural_urban_classification |
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dataset.define_population(patients.exists_for_patient()) |
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``` |
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The meaning of this value is as follows: |
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* 1 - Urban major conurbation |
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* 2 - Urban minor conurbation |
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* 3 - Urban city and town |
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* 4 - Urban city and town in a sparse setting |
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* 5 - Rural town and fringe |
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* 6 - Rural town and fringe in a sparse setting |
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* 7 - Rural village and dispersed |
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* 8 - Rural village and dispersed in a sparse setting |
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#### Finding each patient's MSOA |
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```ehrql |
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from ehrql import create_dataset |
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from ehrql.tables.tpp import addresses, patients |
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dataset = create_dataset() |
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dataset.msoa_code = addresses.for_patient_on("2023-01-01").msoa_code |
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dataset.define_population(patients.exists_for_patient()) |
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``` |
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#### Finding multiple attributes of each patient's address |
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```ehrql |
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from ehrql import create_dataset |
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from ehrql.tables.tpp import addresses, patients |
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dataset = create_dataset() |
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address = addresses.for_patient_on("2023-01-01") |
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dataset.imd_rounded = address.imd_rounded |
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dataset.rural_urban_classification = address.rural_urban_classification |
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dataset.msoa_code = address.msoa_code |
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dataset.define_population(patients.exists_for_patient()) |
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``` |
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## Practice Registrations |
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Examples for the [practice_registrations table](../reference/schemas/core.md#practice_registrations). |
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### Finding attributes related to each patient's GP practice as of a given date |
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#### Finding each patient's practice's pseudonymised identifier |
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```ehrql |
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from ehrql import create_dataset |
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from ehrql.tables.tpp import practice_registrations, patients |
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dataset = create_dataset() |
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dataset.practice = practice_registrations.for_patient_on("2023-01-01").practice_pseudo_id |
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dataset.define_population(patients.exists_for_patient()) |
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``` |
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#### Finding each patient's practice's STP |
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```ehrql |
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from ehrql import create_dataset |
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from ehrql.tables.tpp import practice_registrations, patients |
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dataset = create_dataset() |
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dataset.stp = practice_registrations.for_patient_on("2023-01-01").practice_stp |
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dataset.define_population(patients.exists_for_patient()) |
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``` |
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#### Finding each patient's practice's region |
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```ehrql |
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from ehrql import create_dataset |
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from ehrql.tables.tpp import practice_registrations, patients |
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dataset = create_dataset() |
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dataset.region = practice_registrations.for_patient_on("2023-01-01").practice_nuts1_region_name |
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dataset.define_population(patients.exists_for_patient()) |
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``` |
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#### Finding multiple attributes of each patient's practice |
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```ehrql |
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from ehrql import create_dataset |
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from ehrql.tables.tpp import practice_registrations, patients |
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dataset = create_dataset() |
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registration = practice_registrations.for_patient_on("2023-01-01") |
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dataset.practice = registration.practice_pseudo_id |
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dataset.stp = registration.practice_stp |
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dataset.region = registration.practice_nuts1_region_name |
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dataset.define_population(patients.exists_for_patient()) |
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``` |
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#### Excluding patients based on study dates |
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The following example ensures that the dataset only includes patients registered at a |
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single practice for the entire duration of the study, plus at least 3 months prior to the |
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study start. |
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```ehrql |
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from ehrql import create_dataset, codelist_from_csv, months |
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from ehrql.tables.tpp import patients, practice_registrations |
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study_start_date = "2022-01-01" |
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study_end_date = "2022-12-31" |
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dataset = create_dataset() |
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# find registrations that exist for the full study period, and at least 3 months |
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# prior |
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registrations = ( |
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practice_registrations.where( |
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practice_registrations.start_date.is_on_or_before(study_start_date - months(3)) |
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) |
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.except_where( |
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practice_registrations.end_date.is_on_or_before(study_end_date) |
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) |
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) |
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dataset.define_population(registrations.exists_for_patient()) |
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``` |
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## Clinical Events |
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Examples for the [clinical_events table](../reference/schemas/core.md#clinical_events). |
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### Finding patient demographics |
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#### Finding each patient's ethnicity |
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Ethnicity can be defined using a codelist. There are a lot of individual codes that can used to indicate a patients' fine-grained ethnicity. To make analysis more manageable, ethnicity is therefore commonly grouped into higher level categories. Above, we described how you can [import codelists that have a category column](#some-examples-using-codelist_from_csv). You can use a codelist with a category column to map clinical event codes for ethnicity to higher level categories as in this example: |
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```ehrql |
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from ehrql import create_dataset |
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from ehrql.tables.core import clinical_events, patients |
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from ehrql import codelist_from_csv |
|
|
379 |
|
|
|
380 |
dataset = create_dataset() |
|
|
381 |
|
|
|
382 |
ethnicity_codelist = codelist_from_csv( |
|
|
383 |
"ethnicity_codelist_with_categories", |
|
|
384 |
column="snomedcode", |
|
|
385 |
category_column="Grouping_6", |
|
|
386 |
) |
|
|
387 |
|
|
|
388 |
dataset.latest_ethnicity_code = ( |
|
|
389 |
clinical_events.where(clinical_events.snomedct_code.is_in(ethnicity_codelist)) |
|
|
390 |
.where(clinical_events.date.is_on_or_before("2023-01-01")) |
|
|
391 |
.sort_by(clinical_events.date) |
|
|
392 |
.last_for_patient() |
|
|
393 |
.snomedct_code |
|
|
394 |
) |
|
|
395 |
dataset.latest_ethnicity_group = dataset.latest_ethnicity_code.to_category( |
|
|
396 |
ethnicity_codelist |
|
|
397 |
) |
|
|
398 |
dataset.define_population(patients.exists_for_patient()) |
|
|
399 |
``` |
|
|
400 |
|
|
|
401 |
### Does each patient have an event matching some criteria? |
|
|
402 |
|
|
|
403 |
#### Does each patient have a clinical event matching a code in a codelist? |
|
|
404 |
|
|
|
405 |
```ehrql |
|
|
406 |
from ehrql import create_dataset, codelist_from_csv |
|
|
407 |
from ehrql.tables.core import clinical_events, patients |
|
|
408 |
|
|
|
409 |
asthma_codelist = codelist_from_csv("XXX", column="YYY") |
|
|
410 |
|
|
|
411 |
dataset = create_dataset() |
|
|
412 |
dataset.has_had_asthma_diagnosis = clinical_events.where( |
|
|
413 |
clinical_events.snomedct_code.is_in(asthma_codelist) |
|
|
414 |
).exists_for_patient() |
|
|
415 |
dataset.define_population(patients.exists_for_patient()) |
|
|
416 |
``` |
|
|
417 |
|
|
|
418 |
#### Does each patient have a clinical event matching a code in a codelist in a time period? |
|
|
419 |
|
|
|
420 |
```ehrql |
|
|
421 |
from ehrql import create_dataset, codelist_from_csv |
|
|
422 |
from ehrql.tables.core import clinical_events, patients |
|
|
423 |
|
|
|
424 |
asthma_codelist = codelist_from_csv("XXX", column="YYY") |
|
|
425 |
|
|
|
426 |
dataset = create_dataset() |
|
|
427 |
dataset.has_recent_asthma_diagnosis = clinical_events.where( |
|
|
428 |
clinical_events.snomedct_code.is_in(asthma_codelist) |
|
|
429 |
).where( |
|
|
430 |
clinical_events.date.is_on_or_between("2022-07-01", "2023-01-01") |
|
|
431 |
).exists_for_patient() |
|
|
432 |
dataset.define_population(patients.exists_for_patient()) |
|
|
433 |
``` |
|
|
434 |
|
|
|
435 |
### What is the first/last event matching some criteria? |
|
|
436 |
|
|
|
437 |
The `first_for_patient()` and `last_for_patient()` methods can only be used on a sorted frame. |
|
|
438 |
Frames can be sorted by calling the `sort_by()` method with the column to sort the frame by. |
|
|
439 |
|
|
|
440 |
#### What is the earliest/latest clinical event matching some criteria? |
|
|
441 |
|
|
|
442 |
```ehrql |
|
|
443 |
from ehrql import create_dataset, codelist_from_csv |
|
|
444 |
from ehrql.tables.core import clinical_events, patients |
|
|
445 |
|
|
|
446 |
asthma_codelist = codelist_from_csv("XXX", column="YYY") |
|
|
447 |
|
|
|
448 |
dataset = create_dataset() |
|
|
449 |
dataset.first_asthma_diagnosis_date = clinical_events.where( |
|
|
450 |
clinical_events.snomedct_code.is_in(asthma_codelist) |
|
|
451 |
).where( |
|
|
452 |
clinical_events.date.is_on_or_after("2022-07-01") |
|
|
453 |
).sort_by( |
|
|
454 |
clinical_events.date |
|
|
455 |
).first_for_patient().date |
|
|
456 |
dataset.define_population(patients.exists_for_patient()) |
|
|
457 |
``` |
|
|
458 |
|
|
|
459 |
```ehrql |
|
|
460 |
from ehrql import create_dataset, codelist_from_csv |
|
|
461 |
from ehrql.tables.core import clinical_events, patients |
|
|
462 |
|
|
|
463 |
asthma_codelist = codelist_from_csv("XXX", column="YYY") |
|
|
464 |
|
|
|
465 |
dataset = create_dataset() |
|
|
466 |
dataset.last_asthma_diagnosis_date = clinical_events.where( |
|
|
467 |
clinical_events.snomedct_code.is_in(asthma_codelist) |
|
|
468 |
).where( |
|
|
469 |
clinical_events.date.is_on_or_after("2022-07-01") |
|
|
470 |
).sort_by( |
|
|
471 |
clinical_events.date |
|
|
472 |
).last_for_patient().date |
|
|
473 |
dataset.define_population(patients.exists_for_patient()) |
|
|
474 |
``` |
|
|
475 |
|
|
|
476 |
#### What is the clinical event, matching some criteria, with the least/greatest value? |
|
|
477 |
|
|
|
478 |
```ehrql |
|
|
479 |
from ehrql import create_dataset, codelist_from_csv |
|
|
480 |
from ehrql.tables.core import clinical_events, patients |
|
|
481 |
|
|
|
482 |
hba1c_codelist = codelist_from_csv("XXX", column="YYY") |
|
|
483 |
|
|
|
484 |
dataset = create_dataset() |
|
|
485 |
|
|
|
486 |
hba1c_events = clinical_events.where( |
|
|
487 |
clinical_events.snomedct_code.is_in(hba1c_codelist) |
|
|
488 |
).where( |
|
|
489 |
clinical_events.date.is_on_or_after("2022-07-01") |
|
|
490 |
) |
|
|
491 |
|
|
|
492 |
earliest_min_hba1c_event = hba1c_events.sort_by( |
|
|
493 |
clinical_events.numeric_value, clinical_events.date |
|
|
494 |
).first_for_patient() |
|
|
495 |
|
|
|
496 |
earliest_max_hba1c_event = hba1c_events.sort_by( |
|
|
497 |
# Note the leading minus sign to sort numeric_value in reverse order |
|
|
498 |
-clinical_events.numeric_value, clinical_events.date |
|
|
499 |
).first_for_patient() |
|
|
500 |
|
|
|
501 |
latest_min_hba1c_event = hba1c_events.sort_by( |
|
|
502 |
# Note the leading minus sign to sort numeric_value in reverse order |
|
|
503 |
-clinical_events.numeric_value, clinical_events.date |
|
|
504 |
).last_for_patient() |
|
|
505 |
|
|
|
506 |
latest_max_hba1c_event = hba1c_events.sort_by( |
|
|
507 |
clinical_events.numeric_value, clinical_events.date |
|
|
508 |
).last_for_patient() |
|
|
509 |
|
|
|
510 |
dataset.date_of_first_min_hba1c_observed = earliest_min_hba1c_event.date |
|
|
511 |
dataset.date_of_first_max_hba1c_observed = earliest_max_hba1c_event.date |
|
|
512 |
dataset.date_of_last_min_hba1c_observed = latest_min_hba1c_event.date |
|
|
513 |
dataset.date_of_last_max_hba1c_observed = latest_max_hba1c_event.date |
|
|
514 |
|
|
|
515 |
dataset.value_of_first_min_hba1c_observed = earliest_min_hba1c_event.numeric_value |
|
|
516 |
dataset.value_of_first_max_hba1c_observed = earliest_max_hba1c_event.numeric_value |
|
|
517 |
dataset.value_of_last_min_hba1c_observed = latest_min_hba1c_event.numeric_value |
|
|
518 |
dataset.value_of_last_max_hba1c_observed = latest_max_hba1c_event.numeric_value |
|
|
519 |
|
|
|
520 |
dataset.define_population(patients.exists_for_patient()) |
|
|
521 |
``` |
|
|
522 |
|
|
|
523 |
### Getting properties of an event matching some criteria |
|
|
524 |
|
|
|
525 |
#### What is the code of the first/last clinical event matching some criteria? |
|
|
526 |
|
|
|
527 |
```ehrql |
|
|
528 |
from ehrql import create_dataset, codelist_from_csv |
|
|
529 |
from ehrql.tables.core import clinical_events, patients |
|
|
530 |
|
|
|
531 |
asthma_codelist = codelist_from_csv("XXX", column="YYY") |
|
|
532 |
|
|
|
533 |
dataset = create_dataset() |
|
|
534 |
dataset.first_asthma_diagnosis_code = clinical_events.where( |
|
|
535 |
clinical_events.snomedct_code.is_in(asthma_codelist) |
|
|
536 |
).where( |
|
|
537 |
clinical_events.date.is_on_or_after("2022-07-01") |
|
|
538 |
).sort_by( |
|
|
539 |
clinical_events.date |
|
|
540 |
).first_for_patient().snomedct_code |
|
|
541 |
dataset.define_population(patients.exists_for_patient()) |
|
|
542 |
``` |
|
|
543 |
|
|
|
544 |
#### What is the date of the first/last clinical event matching some criteria? |
|
|
545 |
|
|
|
546 |
```ehrql |
|
|
547 |
from ehrql import create_dataset, codelist_from_csv |
|
|
548 |
from ehrql.tables.core import clinical_events, patients |
|
|
549 |
|
|
|
550 |
asthma_codelist = codelist_from_csv("XXX", column="YYY") |
|
|
551 |
|
|
|
552 |
dataset = create_dataset() |
|
|
553 |
dataset.first_asthma_diagnosis_date = clinical_events.where( |
|
|
554 |
clinical_events.snomedct_code.is_in(asthma_codelist) |
|
|
555 |
).where( |
|
|
556 |
clinical_events.date.is_on_or_after("2022-07-01") |
|
|
557 |
).sort_by( |
|
|
558 |
clinical_events.date |
|
|
559 |
).first_for_patient().date |
|
|
560 |
dataset.define_population(patients.exists_for_patient()) |
|
|
561 |
``` |
|
|
562 |
|
|
|
563 |
#### What is the code and date of the first/last clinical event matching some criteria? |
|
|
564 |
|
|
|
565 |
```ehrql |
|
|
566 |
from ehrql import create_dataset, codelist_from_csv |
|
|
567 |
from ehrql.tables.core import clinical_events, patients |
|
|
568 |
|
|
|
569 |
asthma_codelist = codelist_from_csv("XXX", column="YYY") |
|
|
570 |
|
|
|
571 |
dataset = create_dataset() |
|
|
572 |
first_asthma_diagnosis = clinical_events.where( |
|
|
573 |
clinical_events.snomedct_code.is_in(asthma_codelist) |
|
|
574 |
).where( |
|
|
575 |
clinical_events.date.is_on_or_after("2022-07-01") |
|
|
576 |
).sort_by( |
|
|
577 |
clinical_events.date |
|
|
578 |
).first_for_patient() |
|
|
579 |
dataset.first_asthma_diagnosis_code = first_asthma_diagnosis.snomedct_code |
|
|
580 |
dataset.first_asthma_diagnosis_date = first_asthma_diagnosis.date |
|
|
581 |
dataset.define_population(patients.exists_for_patient()) |
|
|
582 |
``` |
|
|
583 |
|
|
|
584 |
### Performing arithmetic on numeric values of clinical events |
|
|
585 |
|
|
|
586 |
#### Finding the mean observed value of clinical events matching some criteria |
|
|
587 |
|
|
|
588 |
```ehrql |
|
|
589 |
from ehrql import create_dataset, codelist_from_csv |
|
|
590 |
from ehrql.tables.core import clinical_events, patients |
|
|
591 |
|
|
|
592 |
hba1c_codelist = codelist_from_csv("XXX", column="YYY") |
|
|
593 |
|
|
|
594 |
dataset = create_dataset() |
|
|
595 |
dataset.mean_hba1c = clinical_events.where( |
|
|
596 |
clinical_events.snomedct_code.is_in(hba1c_codelist) |
|
|
597 |
).where( |
|
|
598 |
clinical_events.date.is_on_or_after("2022-07-01") |
|
|
599 |
).numeric_value.mean_for_patient() |
|
|
600 |
dataset.define_population(patients.exists_for_patient()) |
|
|
601 |
``` |
|
|
602 |
|
|
|
603 |
### Finding events within a date range |
|
|
604 |
|
|
|
605 |
#### Finding events within a fixed date range |
|
|
606 |
|
|
|
607 |
```ehrql |
|
|
608 |
from ehrql import create_dataset, codelist_from_csv |
|
|
609 |
from ehrql.tables.core import clinical_events, patients |
|
|
610 |
|
|
|
611 |
asthma_codelist = codelist_from_csv("XXX", column="YYY") |
|
|
612 |
|
|
|
613 |
dataset = create_dataset() |
|
|
614 |
dataset.has_recent_asthma_diagnosis = clinical_events.where( |
|
|
615 |
clinical_events.snomedct_code.is_in(asthma_codelist) |
|
|
616 |
).where( |
|
|
617 |
clinical_events.date.is_on_or_between("2022-07-01", "2023-01-01") |
|
|
618 |
).exists_for_patient() |
|
|
619 |
dataset.define_population(patients.exists_for_patient()) |
|
|
620 |
``` |
|
|
621 |
|
|
|
622 |
#### Finding events within a date range plus a constant |
|
|
623 |
|
|
|
624 |
```ehrql |
|
|
625 |
from ehrql import create_dataset, codelist_from_csv, weeks |
|
|
626 |
from ehrql.tables.core import clinical_events, patients |
|
|
627 |
|
|
|
628 |
asthma_codelist = codelist_from_csv("XXX", column="YYY") |
|
|
629 |
|
|
|
630 |
index_date = "2022-07-01" |
|
|
631 |
|
|
|
632 |
dataset = create_dataset() |
|
|
633 |
dataset.has_recent_asthma_diagnosis = clinical_events.where( |
|
|
634 |
clinical_events.snomedct_code.is_in(asthma_codelist) |
|
|
635 |
).where( |
|
|
636 |
clinical_events.date.is_on_or_between(index_date, index_date + weeks(2)) |
|
|
637 |
).exists_for_patient() |
|
|
638 |
dataset.define_population(patients.exists_for_patient()) |
|
|
639 |
``` |
|
|
640 |
|
|
|
641 |
#### Finding events within a dynamic date range |
|
|
642 |
|
|
|
643 |
```ehrql |
|
|
644 |
from ehrql import create_dataset, codelist_from_csv, months |
|
|
645 |
from ehrql.tables.core import clinical_events, patients |
|
|
646 |
|
|
|
647 |
diabetes_codelist = codelist_from_csv("XXX", column="YYY") |
|
|
648 |
hba1c_codelist = codelist_from_csv("XXX", column="YYY") |
|
|
649 |
|
|
|
650 |
dataset = create_dataset() |
|
|
651 |
first_diabetes_code_date = clinical_events.where( |
|
|
652 |
clinical_events.snomedct_code.is_in(diabetes_codelist) |
|
|
653 |
).sort_by( |
|
|
654 |
clinical_events.date |
|
|
655 |
).first_for_patient().date |
|
|
656 |
|
|
|
657 |
dataset.count_of_hba1c_tests_6mo_post_first_diabetes_code = clinical_events.where( |
|
|
658 |
clinical_events.snomedct_code.is_in(hba1c_codelist) |
|
|
659 |
).where( |
|
|
660 |
clinical_events.date.is_on_or_between(first_diabetes_code_date, first_diabetes_code_date + months(6)) |
|
|
661 |
).count_for_patient() |
|
|
662 |
dataset.define_population(patients.exists_for_patient()) |
|
|
663 |
``` |
|
|
664 |
|
|
|
665 |
#### Excluding events which have happened in the future |
|
|
666 |
|
|
|
667 |
Data quality issues with many sources may result in events apparently happening in future dates (e.g. 9999-01-01), it is useful to filter these from your analysis. |
|
|
668 |
|
|
|
669 |
```ehrql |
|
|
670 |
from datetime import date |
|
|
671 |
from ehrql import create_dataset, codelist_from_csv |
|
|
672 |
from ehrql.tables.core import clinical_events, patients |
|
|
673 |
|
|
|
674 |
asthma_codelist = codelist_from_csv("XXX", column="YYY") |
|
|
675 |
|
|
|
676 |
dataset = create_dataset() |
|
|
677 |
dataset.has_recent_asthma_diagnosis = clinical_events.where( |
|
|
678 |
clinical_events.snomedct_code.is_in(asthma_codelist) |
|
|
679 |
).where( |
|
|
680 |
clinical_events.date > "2022-07-01" |
|
|
681 |
).where( |
|
|
682 |
clinical_events.date < date.today() |
|
|
683 |
).exists_for_patient() |
|
|
684 |
dataset.define_population(patients.exists_for_patient()) |
|
|
685 |
``` |
|
|
686 |
|
|
|
687 |
### Extracting parts of dates and date differences |
|
|
688 |
|
|
|
689 |
#### Finding the year an event occurred |
|
|
690 |
|
|
|
691 |
```ehrql |
|
|
692 |
from datetime import date |
|
|
693 |
from ehrql import create_dataset, codelist_from_csv |
|
|
694 |
from ehrql.tables.core import clinical_events, patients |
|
|
695 |
|
|
|
696 |
asthma_codelist = codelist_from_csv("XXX", column="YYY") |
|
|
697 |
|
|
|
698 |
dataset = create_dataset() |
|
|
699 |
dataset.year_of_first = clinical_events.where( |
|
|
700 |
clinical_events.snomedct_code.is_in(asthma_codelist) |
|
|
701 |
).sort_by( |
|
|
702 |
clinical_events.date |
|
|
703 |
).first_for_patient().date.year |
|
|
704 |
dataset.define_population(patients.exists_for_patient()) |
|
|
705 |
``` |
|
|
706 |
|
|
|
707 |
#### Finding the number of weeks between two events |
|
|
708 |
|
|
|
709 |
```ehrql |
|
|
710 |
from ehrql import create_dataset, codelist_from_csv |
|
|
711 |
from ehrql.tables.core import clinical_events, patients |
|
|
712 |
|
|
|
713 |
asthma_codelist = codelist_from_csv("XXX", column="YYY") |
|
|
714 |
asthma_review_codelist = codelist_from_csv("XXX", column="YYY") |
|
|
715 |
|
|
|
716 |
dataset = create_dataset() |
|
|
717 |
first_asthma_diagnosis_date = clinical_events.where( |
|
|
718 |
clinical_events.snomedct_code.is_in(asthma_codelist) |
|
|
719 |
).sort_by(clinical_events.date).first_for_patient().date |
|
|
720 |
|
|
|
721 |
first_asthma_review_date = clinical_events.where( |
|
|
722 |
clinical_events.snomedct_code.is_in(asthma_review_codelist) |
|
|
723 |
).where( |
|
|
724 |
clinical_events.date.is_on_or_after(first_asthma_diagnosis_date) |
|
|
725 |
).sort_by(clinical_events.date).first_for_patient().date |
|
|
726 |
|
|
|
727 |
dataset.weeks_between_diagnosis_and_review = (first_asthma_review_date - first_asthma_diagnosis_date).weeks |
|
|
728 |
dataset.define_population(patients.exists_for_patient()) |
|
|
729 |
``` |
|
|
730 |
|
|
|
731 |
## Admitted Patient Care Spells (APCS) |
|
|
732 |
|
|
|
733 |
Examples for the [TPP apcs table](../reference/schemas/tpp.md#apcs). |
|
|
734 |
|
|
|
735 |
### Does each patient have an event matching some criteria? |
|
|
736 |
|
|
|
737 |
#### Does each patient have a hospitalisation event matching some criteria? |
|
|
738 |
|
|
|
739 |
```ehrql |
|
|
740 |
from ehrql import create_dataset, codelist_from_csv |
|
|
741 |
from ehrql.tables.tpp import apcs, patients |
|
|
742 |
|
|
|
743 |
cardiac_diagnosis_codes = codelist_from_csv("XXX", column="YYY") |
|
|
744 |
|
|
|
745 |
dataset = create_dataset() |
|
|
746 |
dataset.has_recent_cardiac_admission = apcs.where( |
|
|
747 |
apcs.primary_diagnosis.is_in(cardiac_diagnosis_codes) |
|
|
748 |
).where( |
|
|
749 |
apcs.admission_date.is_on_or_between("2022-07-01", "2023-01-01") |
|
|
750 |
).exists_for_patient() |
|
|
751 |
dataset.define_population(patients.exists_for_patient()) |
|
|
752 |
``` |
|
|
753 |
|
|
|
754 |
## Medications |
|
|
755 |
|
|
|
756 |
Examples for the [medications table](../reference/schemas/core.md#medications). |
|
|
757 |
|
|
|
758 |
### Does each patient have an event matching some criteria? |
|
|
759 |
|
|
|
760 |
#### Does each patient have a medication event matching some criteria? |
|
|
761 |
|
|
|
762 |
```ehrql |
|
|
763 |
from ehrql import create_dataset, codelist_from_csv |
|
|
764 |
from ehrql.tables.core import medications, patients |
|
|
765 |
|
|
|
766 |
statin_medications = codelist_from_csv("XXX", column="YYY") |
|
|
767 |
|
|
|
768 |
dataset = create_dataset() |
|
|
769 |
dataset.has_recent_statin_prescription = medications.where( |
|
|
770 |
medications.dmd_code.is_in(statin_medications) |
|
|
771 |
).where( |
|
|
772 |
medications.date.is_on_or_between("2022-07-01", "2023-01-01") |
|
|
773 |
).exists_for_patient() |
|
|
774 |
dataset.define_population(patients.exists_for_patient()) |
|
|
775 |
``` |
|
|
776 |
|
|
|
777 |
#### How many events does each patient have matching some criteria? |
|
|
778 |
|
|
|
779 |
```ehrql |
|
|
780 |
from ehrql import create_dataset, codelist_from_csv |
|
|
781 |
from ehrql.tables.core import medications, patients |
|
|
782 |
|
|
|
783 |
statin_medications = codelist_from_csv("XXX", column="YYY") |
|
|
784 |
|
|
|
785 |
dataset = create_dataset() |
|
|
786 |
dataset.number_of_statin_prescriptions_in_last_year = medications.where( |
|
|
787 |
medications.dmd_code.is_in(statin_medications) |
|
|
788 |
).where( |
|
|
789 |
medications.date.is_on_or_between("2022-01-01", "2023-01-01") |
|
|
790 |
).count_for_patient() |
|
|
791 |
dataset.define_population(patients.exists_for_patient()) |
|
|
792 |
``` |
|
|
793 |
|
|
|
794 |
#### What is the earliest/latest medication event matching some criteria? |
|
|
795 |
|
|
|
796 |
```ehrql |
|
|
797 |
from ehrql import create_dataset, codelist_from_csv |
|
|
798 |
from ehrql.tables.core import medications, patients |
|
|
799 |
|
|
|
800 |
statin_medications = codelist_from_csv("XXX", column="YYY") |
|
|
801 |
|
|
|
802 |
dataset = create_dataset() |
|
|
803 |
dataset.first_statin_prescription_date = medications.where( |
|
|
804 |
medications.dmd_code.is_in(statin_medications) |
|
|
805 |
).where( |
|
|
806 |
medications.date.is_on_or_after("2022-07-01") |
|
|
807 |
).sort_by( |
|
|
808 |
medications.date |
|
|
809 |
).first_for_patient().date |
|
|
810 |
dataset.define_population(patients.exists_for_patient()) |
|
|
811 |
``` |
|
|
812 |
|
|
|
813 |
```ehrql |
|
|
814 |
from ehrql import create_dataset, codelist_from_csv |
|
|
815 |
from ehrql.tables.core import medications, patients |
|
|
816 |
|
|
|
817 |
statin_medications = codelist_from_csv("XXX", column="YYY") |
|
|
818 |
|
|
|
819 |
dataset = create_dataset() |
|
|
820 |
dataset.last_statin_prescription_date = medications.where( |
|
|
821 |
medications.dmd_code.is_in(statin_medications) |
|
|
822 |
).where( |
|
|
823 |
medications.date.is_on_or_after("2022-07-01") |
|
|
824 |
).sort_by( |
|
|
825 |
medications.date |
|
|
826 |
).last_for_patient().date |
|
|
827 |
dataset.define_population(patients.exists_for_patient()) |
|
|
828 |
``` |
|
|
829 |
|
|
|
830 |
### Extracting parts of dates and date differences |
|
|
831 |
|
|
|
832 |
#### Finding prescriptions made in particular months of the year |
|
|
833 |
|
|
|
834 |
```ehrql |
|
|
835 |
from ehrql import create_dataset, codelist_from_csv |
|
|
836 |
from ehrql.tables.core import medications, patients |
|
|
837 |
|
|
|
838 |
amoxicillin_codelist = codelist_from_csv("XXX", column="YYY") |
|
|
839 |
|
|
|
840 |
winter_months = [10,11,12,1,2,3] |
|
|
841 |
|
|
|
842 |
dataset = create_dataset() |
|
|
843 |
dataset.winter_amoxicillin_count = medications.where( |
|
|
844 |
medications.dmd_code.is_in(amoxicillin_codelist) |
|
|
845 |
).where( |
|
|
846 |
medications.date.month.is_in(winter_months) |
|
|
847 |
).count_for_patient() |
|
|
848 |
dataset.define_population(patients.exists_for_patient()) |
|
|
849 |
``` |
|
|
850 |
|
|
|
851 |
### Finding events occuring close in time to another event |
|
|
852 |
|
|
|
853 |
#### Finding the code of the first medication after the first clinical event matching some criteria |
|
|
854 |
|
|
|
855 |
```ehrql |
|
|
856 |
from ehrql import create_dataset, codelist_from_csv, weeks |
|
|
857 |
from ehrql.tables.core import clinical_events, medications, patients |
|
|
858 |
|
|
|
859 |
asthma_codelist = codelist_from_csv("XXX", column="YYY") |
|
|
860 |
inhaled_corticosteroid_codelist = codelist_from_csv("XXX", column="YYY") |
|
|
861 |
|
|
|
862 |
dataset = create_dataset() |
|
|
863 |
first_asthma_diagnosis_date = clinical_events.where( |
|
|
864 |
clinical_events.snomedct_code.is_in(asthma_codelist) |
|
|
865 |
).where( |
|
|
866 |
clinical_events.date.is_on_or_after("2022-07-01") |
|
|
867 |
).sort_by( |
|
|
868 |
clinical_events.date |
|
|
869 |
).first_for_patient().date |
|
|
870 |
dataset.first_asthma_diagnosis_date = first_asthma_diagnosis_date |
|
|
871 |
dataset.count_ics_prescriptions_2wks_post_diagnosis = medications.where( |
|
|
872 |
medications.dmd_code.is_in(inhaled_corticosteroid_codelist) |
|
|
873 |
).where( |
|
|
874 |
medications.date.is_on_or_between(first_asthma_diagnosis_date,first_asthma_diagnosis_date + weeks(2)) |
|
|
875 |
).count_for_patient() |
|
|
876 |
dataset.define_population(patients.exists_for_patient()) |
|
|
877 |
``` |
|
|
878 |
|
|
|
879 |
### Excluding medications for patients who have transferred between practices |
|
|
880 |
|
|
|
881 |
Note that in these examples, the periods defined are illustrative only. |
|
|
882 |
|
|
|
883 |
#### Excluding patients based on prescription date |
|
|
884 |
|
|
|
885 |
```ehrql |
|
|
886 |
from ehrql import case, create_dataset, codelist_from_csv, when, weeks |
|
|
887 |
from ehrql.tables.tpp import medications, patients, practice_registrations |
|
|
888 |
|
|
|
889 |
def meets_registrations_criteria(medication_date): |
|
|
890 |
# For this medication date, find whether a registration exists where |
|
|
891 |
# the start date and end dates are within a 12 weeks |
|
|
892 |
# prior/after to the prescription |
|
|
893 |
|
|
|
894 |
start_cutoff_date = medication_date - weeks(12) |
|
|
895 |
end_cutoff_date = medication_date + weeks(12) |
|
|
896 |
return ( |
|
|
897 |
practice_registrations.where( |
|
|
898 |
practice_registrations.start_date.is_on_or_before(start_cutoff_date) |
|
|
899 |
) |
|
|
900 |
.except_where( |
|
|
901 |
practice_registrations.end_date.is_on_or_before(end_cutoff_date) |
|
|
902 |
) |
|
|
903 |
.exists_for_patient() |
|
|
904 |
) |
|
|
905 |
|
|
|
906 |
medication_codelist = codelist_from_csv("XXX", column="YYY") |
|
|
907 |
|
|
|
908 |
dataset = create_dataset() |
|
|
909 |
|
|
|
910 |
# First relevant prescription per patient |
|
|
911 |
first_prescription = ( |
|
|
912 |
medications.where( |
|
|
913 |
medications.dmd_code.is_in(medication_codelist) |
|
|
914 |
) |
|
|
915 |
.sort_by(medications.date) |
|
|
916 |
.first_for_patient() |
|
|
917 |
) |
|
|
918 |
|
|
|
919 |
# Include only prescriptions that fall within accepatable registration dates |
|
|
920 |
dataset.prescription_date = case( |
|
|
921 |
when(meets_registrations_criteria(first_prescription.date)) |
|
|
922 |
.then(first_prescription.date) |
|
|
923 |
) |
|
|
924 |
dataset.define_population(patients.exists_for_patient()) |
|
|
925 |
``` |
|
|
926 |
|
|
|
927 |
## Decision support values |
|
|
928 |
|
|
|
929 |
Examples for the [TPP decision support values table](../reference/schemas/tpp.md#decision_support_values). |
|
|
930 |
|
|
|
931 |
### Finding the most recent decision support value |
|
|
932 |
|
|
|
933 |
#### Finding each patient's EFI (electronic frailty index) |
|
|
934 |
|
|
|
935 |
```ehrql |
|
|
936 |
from ehrql import create_dataset |
|
|
937 |
from ehrql.tables.tpp import decision_support_values |
|
|
938 |
|
|
|
939 |
dataset = create_dataset() |
|
|
940 |
latest_efi_record = ( |
|
|
941 |
decision_support_values |
|
|
942 |
.electronic_frailty_index() |
|
|
943 |
.sort_by(decision_support_values.calculation_date) |
|
|
944 |
.last_for_patient() |
|
|
945 |
) |
|
|
946 |
dataset.latest_efi = latest_efi_record.numeric_value |
|
|
947 |
dataset.latest_efi_date = latest_efi_record.calculation_date |
|
|
948 |
dataset.define_population(decision_support_values.exists_for_patient()) |
|
|
949 |
``` |