ehrQL tutorial: Handling missing values

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Example dataset definition 5a: Handling missing values

Learning objectives

By the end of this tutorial, you should be able to:

• describe how missing values are represented in ehrQL
• check for missing values
• replace missing values

In the tutorial examples so far, all the data rows have been fully populated with values. There have been no missing values.

This is a somewhat idealised situation. In the real world, data is often incomplete with some values missing. Missing data values in ehrQL are represented with a special "null" value.

We will explore how ehrQL's null values work in the below dataset definition and some approaches to dealing with missing values.

Full example

Dataset definition: 5a_multiple3_dataset_definition.py

from ehrql import Dataset
from ehrql.tables.examples.tutorial import hospitalisations, patient_address

dataset = Dataset()

most_recent_hospitalisation = hospitalisations.sort_by(
    hospitalisations.date
).last_for_patient()

lowest_imd_address = patient_address.sort_by(
    patient_address.index_of_multiple_deprivation_rounded
).first_for_patient()

population = most_recent_hospitalisation.exists_for_patient()
dataset.define_population(population)

dataset.most_recent_hospitalisation_code = most_recent_hospitalisation.code
dataset.most_recent_hospitalisation_system = (
    most_recent_hospitalisation.system.if_null_then("UnknownCodeSystem")
)
dataset.lowest_imd = (
    lowest_imd_address.index_of_multiple_deprivation_rounded.if_null_then(-1)
)
dataset.lowest_imd_is_valid = (
    lowest_imd_address.index_of_multiple_deprivation_rounded.is_not_null()
)

In this section, we will build up a dataset using data that has missing values. We will use two different tables:

• hospitalisations
• patient_address

Both of these tables contain missing data:

• the hospitalisations table has a column called system with missing values
• the patient address table has a column called index_of_multiple_deprivation_rounded We came across this column before in a previous tutorial but this time, we have included some missing data.

For brevity, the tables will not be displayed here but can be reviewed in the example-data/multiple3/ folder.

The output of the query above should generate the table below:

Output dataset: outputs/5a_multiple3_dataset_definition.csv

patient_id	most_recent_hospitalisation_code	most_recent_hospitalisation_system	lowest_imd	lowest_imd_is_valid
1	h5	TutorialCodeSystem	-1	F
2	h1	UnknownCodeSystem	29874	T
4	h10	UnknownCodeSystem	1500	T
6	h8	TutorialCodeSystem	-1	F

Line by line explanation

This dataset definition:

• sets the population to be those patients with a hospitalisation entry
• adds the most recent hospitalisation date for a patient to the dataset
• adds details of the index of multiple deprivation

We will handle the missing data as follows:

• Where most_recent_hospitalisation_system in the hospitalisation table is missing, we will replace this with UnknownCodeSystem
• Where imd is missing, we will replace this with a -1

Most recent hospitalisation

As we have seen before, we can sort and select an entry per patient with methods like sort_by(), and first_for_patient().

This time, we are sorting and taking the last hospitalisation for the patient with last_for_patient().

Lowest IMD address

This is similar to what we have done before. In this case we sort rows by index_of_multiple_deprivation_rounded, and take the first row for the patient.

Define population

We are trying to capture patients who have a recent hospitalisation. For this, we check if a patient has row in the most_recent_hospitalisation subset (created above). We can use exists_for_patient() as we did in a previous tutorial.

Find code for hospitalisation

We want to find the code that is associated with the hospitalisation. This is directly accessible as a column in the hospitalisation table.

Replacing nulls: null hospitalisation coding system values

We now need to deal with the missing data in the hospitalisation code. We can specify a replacement value for nulls as we have done in this dataset definition.

This is via the if_null_then() method.

The result is that the dataset contains UnknownCodeSystem in the data in place of the nulls.

Replacing nulls: IMD

We now need to deal with the missing data in the patient address table in the column of index_of_multiple_deprivation_rounded. You might reasonably think that, since we selected the lowest value of index of multiple deprivation, that this lowest value would be a non-null value.

However, ehrQL sorts null values before non-null values. If a patient has null and non-null values, then the first_for_patient() will be a null value.

This results in the "lowest" IMD value in some cases being null.

In the dataset definition, we replace the missing values with a negative value known to be invalid, but of the correct integer type (-1). This is via the if_null_then() method.

Check if lowest IMD is valid

We want to create a variable that checks if an IMD is valid. If so, returns a True, and if not, returns a False. We use is_not_null() to handle the nulls.

Here, we checked that values were not null with the is_not_null() method. We could have also used the is_null() method to check if values are null. In both cases, the result is a Boolean True or False for each row.

Your Turn

Question

1. Can you modify the dataset definition to eliminate the IMD value nulls? (Hint: you may find except_where() useful to filter out unwanted rows.)
2. Even with that modification, we still get a null IMD value in the dataset? Why? (Hint: look at the patient ID values.)
3. Can you further modify the dataset definition to add an extra criterion in define_population() to remove this row entirely? (Hint: you may find the table operators covered earlier useful.)