medmodels.treatment_effect.builder#

This module contains the TreatmentEffectBuilder class.

Classes

TreatmentEffectBuilder()

Builder class for the TreatmentEffect object.

class TreatmentEffectBuilder[source]#

Bases: object

Builder class for the TreatmentEffect object.

The TreatmentEffectBuilder class is used to build a TreatmentEffect object with the desired configurations for the treatment effect estimation using a builder pattern.

By default, it configures a static treatment effect estimation. To configure a time-dependent treatment effect estimation, the time_attribute must be set.

build()[source]#

Builds the treatment effect with all the provided configurations.

Return type:: TreatmentEffect
Returns:: tee.TreatmentEffect – treatment effect object

filter_controls(query)[source]#

Filter the control group based on the provided query.

Parameters:

query (NodeQuery) – The query to be applied to the control group.

Return type:

TreatmentEffectBuilder

Returns:

TreatmentEffectBuilder –

The current instance of the TreatmentEffectBuilder: with updated time attribute.

filter_controls_query: Optional[NodeQuery]#

follow_up_period_days: Optional[int]#

follow_up_period_reference: Optional[Literal['first', 'last']]#

grace_period_days: Optional[int]#

grace_period_reference: Optional[Literal['first', 'last']]#

matching_essential_covariates: Optional[MedRecordAttributeInputList]#

matching_hyperparameters: Optional[Dict[str, Any]]#

matching_method: Optional[MatchingMethod]#

matching_model: Optional[Model]#

matching_number_of_neighbors: Optional[int]#

matching_one_hot_covariates: Optional[MedRecordAttributeInputList]#

outcome: Group#

outcome_before_treatment_days: Optional[int]#

patients_group: Optional[Group]#

time_attribute: Optional[MedRecordAttribute]#

treatment: Group#

washout_period_days: Optional[Dict[str, int]]#

washout_period_reference: Optional[Literal['first', 'last']]#

with_follow_up_period(days=None, reference=None)[source]#

Sets the follow-up period for the treatment effect estimation.

Parameters:

days (Optional[int], optional) – The duration of the follow-up period in days. If None, the duration is left as it was. Defaults to 365.
reference (Optional[Literal['first', 'last']], optional) – The reference point for the follow-up period. Must be either ‘first’ or ‘last’. Defaults to None.

Return type:

TreatmentEffectBuilder

Returns:

TreatmentEffectBuilder –

The current instance of the TreatmentEffectBuilder: with updated time attribute.

with_grace_period(days=None, reference=None)[source]#

Sets the grace period for the treatment effect estimation.

The grace period is the period of time after the treatment that is not considered in the estimation.

Parameters:

days (Optional[int], optional) – The duration of the grace period in days. If None, the duration is left as it was. Defaults to 0.
reference (Optional[Literal['first', 'last']], optional) – The reference point for the grace period. Must be either ‘first’ or ‘last’. Defaults to None.

Return type:

TreatmentEffectBuilder

Returns:

TreatmentEffectBuilder –

The current instance of the TreatmentEffectBuilder: with updated time attribute.

with_nearest_neighbors_matching(essential_covariates=None, one_hot_covariates=None, number_of_neighbors=1)[source]#

Adjust the treatment effect estimate using nearest neighbors matching.

Parameters:

essential_covariates (Optional[MedRecordAttributeInputList], optional) – Covariates that are essential for matching. Defaults to [“gender”, “age”].
one_hot_covariates (Optional[MedRecordAttributeInputList], optional) – Covariates that are one-hot encoded for matching. Defaults to [“gender”].
number_of_neighbors (int, optional) – Number of neighbors to consider for the matching. Defaults to 1.

Return type:

TreatmentEffectBuilder

Returns:

TreatmentEffectBuilder –

The current instance of the TreatmentEffectBuilder: with updated matching configurations.

with_outcome(outcome)[source]#

Sets the outcome group for the treatment effect estimation.

Parameters:

outcome (Group) – The group to be used as the outcome.

Return type:

TreatmentEffectBuilder

Returns:

TreatmentEffectBuilder –

The current instance of the TreatmentEffectBuilder: with updated outcome group.

with_outcome_before_treatment_exclusion(days)[source]#

Define whether we allow the outcome to exist before the treatment or not.

The outcome_before_treatment_days parameter is used to set the number of days before the treatment that the outcome should not exist. If not set, the outcome is allowed to exist before the treatment.

Parameters:

days (int) – The number of days before the treatment that the outcome should not exist.

Return type:

TreatmentEffectBuilder

Returns:

TreatmentEffectBuilder –

The current instance of the TreatmentEffectBuilder: with updated time attribute.

with_patients_group(group)[source]#

Sets the group of patients to be used in the treatment effect estimation.

Parameters:

group (Group) – The group of patients.

Return type:

TreatmentEffectBuilder

Returns:

TreatmentEffectBuilder –

The current instance of the TreatmentEffectBuilder: with updated patients group.

with_propensity_matching(essential_covariates=None, one_hot_covariates=None, model='logit', number_of_neighbors=1, hyperparameters=None)[source]#

Adjust the treatment effect estimate using propensity score matching.

Parameters:

essential_covariates (Optional[MedRecordAttributeInputList], optional) – Covariates that are essential for matching. Defaults to [“gender”, “age”].
one_hot_covariates (Optional[MedRecordAttributeInputList], optional) – Covariates that are one-hot encoded for matching. Defaults to [“gender”].
model (Model, optional) – Model to choose for the matching. Defaults to “logit”.
number_of_neighbors (int, optional) – Number of neighbors to consider for the matching. Defaults to 1.
hyperparameters (Optional[Dict[str, Any]], optional) – Hyperparameters for the matching model. Defaults to None.

Return type:

TreatmentEffectBuilder

Returns:

TreatmentEffectBuilder –

The current instance of the TreatmentEffectBuilder: with updated matching configurations.

with_time_attribute(attribute)[source]#

Sets the time attribute to be used in the treatment effect estimation.

It turs the treatment effect estimation from a static to a time-dependent analysis.

Parameters:

attribute (MedRecordAttribute) – The time attribute.

Return type:

TreatmentEffectBuilder

Returns:

TreatmentEffectBuilder –

The current instance of the TreatmentEffectBuilder: with updated time attribute.

with_treatment(treatment)[source]#

Sets the treatment group for the treatment effect estimation.

Parameters:: treatment (Group) – The treatment group.
Return type:: TreatmentEffectBuilder
Returns:: TreatmentEffectBuilder – The current instance of the TreatmentEffectBuilder.

with_washout_period(days=None, reference=None)[source]#

Sets the washout period for the treatment effect estimation.

The washout period is the period of time before the treatment that is not considered in the estimation.

Parameters:

days (Optional[Dict[str, int]], optional) – The duration of the washout period in days. If None, the duration is left as it was. Defaults to None.
reference (Optional[Literal['first', 'last']], optional) – The reference point for the washout period. Must be either ‘first’ or ‘last’. Defaults to None.

Return type:

TreatmentEffectBuilder

Returns:

TreatmentEffectBuilder –

The current instance of the TreatmentEffectBuilder: with updated time attribute.