# Copyright 2022 - 2025 The PyMC Labs Developers
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
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# limitations under the License.
"""Custom PyMC models for causal inference"""
from typing import Any, Dict, Optional
import arviz as az
import numpy as np
import pandas as pd
import pymc as pm
import pytensor.tensor as pt
import xarray as xr
from arviz import r2_score
from patsy import dmatrix
from pymc_extras.prior import Prior
from causalpy.utils import round_num
[docs]
class PyMCModel(pm.Model):
"""A wrapper class for PyMC models. This provides a scikit-learn like interface with
methods like `fit`, `predict`, and `score`. It also provides other methods which are
useful for causal inference.
Example
-------
>>> import causalpy as cp
>>> import numpy as np
>>> import pymc as pm
>>> from causalpy.pymc_models import PyMCModel
>>> class MyToyModel(PyMCModel):
... def build_model(self, X, y, coords):
... with self:
... self.add_coords(coords)
... X_ = pm.Data(name="X", value=X)
... y_ = pm.Data(name="y", value=y)
... beta = pm.Normal(
... "beta", mu=0, sigma=1, shape=(y.shape[1], X.shape[1])
... )
... sigma = pm.HalfNormal("sigma", sigma=1, shape=y.shape[1])
... mu = pm.Deterministic(
... "mu", pm.math.dot(X_, beta.T), dims=["obs_ind", "treated_units"]
... )
... pm.Normal("y_hat", mu=mu, sigma=sigma, observed=y_)
>>> rng = np.random.default_rng(seed=42)
>>> X = xr.DataArray(
... rng.normal(loc=0, scale=1, size=(20, 2)),
... dims=["obs_ind", "coeffs"],
... coords={"obs_ind": np.arange(20), "coeffs": ["coeff_0", "coeff_1"]},
... )
>>> y = xr.DataArray(
... rng.normal(loc=0, scale=1, size=(20, 1)),
... dims=["obs_ind", "treated_units"],
... coords={"obs_ind": np.arange(20), "treated_units": ["unit_0"]},
... )
>>> model = MyToyModel(
... sample_kwargs={
... "chains": 2,
... "draws": 2000,
... "progressbar": False,
... "random_seed": 42,
... }
... )
>>> model.fit(
... X,
... y,
... coords={
... "coeffs": ["coeff_0", "coeff_1"],
... "obs_ind": np.arange(20),
... "treated_units": ["unit_0"],
... },
... )
Inference data...
>>> model.score(X, y) # doctest: +ELLIPSIS
unit_0_r2 ...
unit_0_r2_std ...
dtype: float64
>>> X_new = rng.normal(loc=0, scale=1, size=(20, 2))
>>> model.predict(X_new)
Inference data...
"""
default_priors = {}
[docs]
def priors_from_data(self, X, y) -> Dict[str, Any]:
"""
Generate priors dynamically based on the input data.
This method allows models to set sensible priors that adapt to the scale
and characteristics of the actual data being analyzed. It's called during
the `fit()` method before model building, allowing data-driven prior
specification that can improve model performance and convergence.
The priors returned by this method are merged with any user-specified
priors (passed via the `priors` parameter in `__init__`), with
user-specified priors taking precedence in case of conflicts.
Parameters
----------
X : xarray.DataArray
Input features/covariates with dimensions ["obs_ind", "coeffs"].
Used to understand the scale and structure of predictors.
y : xarray.DataArray
Target variable with dimensions ["obs_ind", "treated_units"].
Used to understand the scale and structure of the outcome.
Returns
-------
Dict[str, Prior]
Dictionary mapping parameter names to Prior objects. The keys should
match parameter names used in the model's `build_model()` method.
Notes
-----
The base implementation returns an empty dictionary, meaning no
data-driven priors are set by default. Subclasses should override
this method to implement data-adaptive prior specification.
**Priority Order for Priors:**
1. User-specified priors (passed to `__init__`)
2. Data-driven priors (from this method)
3. Default priors (from `default_priors` property)
Examples
--------
A typical implementation might scale priors based on data variance:
>>> def priors_from_data(self, X, y):
... y_std = float(y.std())
... return {
... "sigma": Prior("HalfNormal", sigma=y_std, dims="treated_units"),
... "beta": Prior(
... "Normal",
... mu=0,
... sigma=2 * y_std,
... dims=["treated_units", "coeffs"],
... ),
... }
Or set shape parameters based on data dimensions:
>>> def priors_from_data(self, X, y):
... n_predictors = X.shape[1]
... return {
... "beta": Prior(
... "Dirichlet",
... a=np.ones(n_predictors),
... dims=["treated_units", "coeffs"],
... )
... }
See Also
--------
WeightedSumFitter.priors_from_data : Example implementation that sets
Dirichlet prior shape based on number of control units.
"""
return {}
[docs]
def __init__(
self,
sample_kwargs: Optional[Dict[str, Any]] = None,
priors: dict[str, Any] | None = None,
):
"""
:param sample_kwargs: A dictionary of kwargs that get unpacked and passed to the
:func:`pymc.sample` function. Defaults to an empty dictionary.
"""
super().__init__()
self.idata = None
self.sample_kwargs = sample_kwargs if sample_kwargs is not None else {}
self.priors = {**self.default_priors, **(priors or {})}
[docs]
def build_model(self, X, y, coords) -> None:
"""Build the model, must be implemented by subclass."""
raise NotImplementedError(
"This method must be implemented by a subclass"
) # pragma: no cover
def _data_setter(self, X: xr.DataArray) -> None:
"""
Set data for the model.
This method is used internally to register new data for the model for
prediction.
NOTE: We are actively changing the `X`. Often, this matrix will have a different
number of rows than the original data. So to make the shapes work, we need to
update all data nodes in the model to have the correct shape. The values are not
used, so we set them to 0. In our case, we just have data nodes X and y, but if
in the future we get more complex models with more data nodes, then we'll need
to update all of them - ideally programmatically.
"""
new_no_of_observations = X.shape[0]
# Use integer indices for obs_ind to avoid datetime compatibility issues with PyMC
obs_coords = np.arange(new_no_of_observations)
with self:
# Get the number of treated units from the model coordinates
treated_units_coord = getattr(self, "coords", {}).get(
"treated_units", ["unit_0"]
)
n_treated_units = len(treated_units_coord)
# Always use 2D format for consistency
pm.set_data(
{"X": X, "y": np.zeros((new_no_of_observations, n_treated_units))},
coords={"obs_ind": obs_coords},
)
[docs]
def fit(self, X, y, coords: Optional[Dict[str, Any]] = None) -> None:
"""Draw samples from posterior, prior predictive, and posterior predictive
distributions, placing them in the model's idata attribute.
"""
# Ensure random_seed is used in sample_prior_predictive() and
# sample_posterior_predictive() if provided in sample_kwargs.
random_seed = self.sample_kwargs.get("random_seed", None)
# Merge priors with precedence: user-specified > data-driven > defaults
# Data-driven priors are computed first, then user-specified priors override them
self.priors = {**self.priors_from_data(X, y), **self.priors}
self.build_model(X, y, coords)
with self:
self.idata = pm.sample(**self.sample_kwargs)
self.idata.extend(pm.sample_prior_predictive(random_seed=random_seed))
self.idata.extend(
pm.sample_posterior_predictive(
self.idata, progressbar=False, random_seed=random_seed
)
)
return self.idata
[docs]
def predict(self, X: xr.DataArray):
"""
Predict data given input data `X`
.. caution::
Results in KeyError if model hasn't been fit.
"""
# Ensure random_seed is used in sample_prior_predictive() and
# sample_posterior_predictive() if provided in sample_kwargs.
random_seed = self.sample_kwargs.get("random_seed", None)
self._data_setter(X)
with self:
pp = pm.sample_posterior_predictive(
self.idata,
var_names=["y_hat", "mu"],
progressbar=False,
random_seed=random_seed,
)
# Assign coordinates from input X to ensure xarray operations work correctly
# This is necessary because PyMC uses integer indices internally, but we need
# to preserve the original coordinates (e.g., datetime indices) for proper
# alignment with other xarray operations like calculate_impact()
if isinstance(X, xr.DataArray) and "obs_ind" in X.coords:
pp["posterior_predictive"] = pp["posterior_predictive"].assign_coords(
obs_ind=X.obs_ind
)
return pp
[docs]
def score(self, X: xr.DataArray, y: xr.DataArray) -> pd.Series:
"""Score the Bayesian :math:`R^2` given inputs ``X`` and outputs ``y``.
Note that the score is based on a comparison of the observed data ``y`` and the
model's expected value of the data, `mu`.
.. caution::
The Bayesian :math:`R^2` is not the same as the traditional coefficient of
determination, https://en.wikipedia.org/wiki/Coefficient_of_determination.
"""
mu = self.predict(X)
mu_data = az.extract(mu, group="posterior_predictive", var_names="mu")
scores = {}
# Always iterate over treated_units dimension - no branching needed!
for i, unit in enumerate(mu_data.coords["treated_units"].values):
unit_mu = mu_data.sel(treated_units=unit).T # (sample, obs_ind)
unit_y = y.sel(treated_units=unit).data
unit_score = r2_score(unit_y, unit_mu.data)
scores[f"unit_{i}_r2"] = unit_score["r2"]
scores[f"unit_{i}_r2_std"] = unit_score["r2_std"]
return pd.Series(scores)
[docs]
def calculate_impact(
self, y_true: xr.DataArray, y_pred: az.InferenceData
) -> xr.DataArray:
impact = y_true - y_pred["posterior_predictive"]["y_hat"]
return impact.transpose(..., "obs_ind")
[docs]
def calculate_cumulative_impact(self, impact):
return impact.cumsum(dim="obs_ind")
[docs]
def print_coefficients(self, labels, round_to=None) -> None:
def print_row(
max_label_length: int, name: str, coeff_samples: xr.DataArray, round_to: int
) -> None:
"""Print one row of the coefficient table"""
formatted_name = f" {name: <{max_label_length}}"
formatted_val = f"{round_num(coeff_samples.mean().data, round_to)}, 94% HDI [{round_num(coeff_samples.quantile(0.03).data, round_to)}, {round_num(coeff_samples.quantile(1 - 0.03).data, round_to)}]" # noqa: E501
print(f" {formatted_name} {formatted_val}")
def print_coefficients_for_unit(
unit_coeffs: xr.DataArray,
unit_sigma: xr.DataArray,
labels: list,
round_to: int,
) -> None:
"""Print coefficients for a single unit"""
# Determine the width of the longest label
max_label_length = max(len(name) for name in labels + ["y_hat_sigma"])
for name in labels:
coeff_samples = unit_coeffs.sel(coeffs=name)
print_row(max_label_length, name, coeff_samples, round_to)
# Add coefficient for measurement std
print_row(max_label_length, "y_hat_sigma", unit_sigma, round_to)
print("Model coefficients:")
coeffs = az.extract(self.idata.posterior, var_names="beta")
# Check if sigma or y_hat_sigma variable exists
sigma_var_name = None
if "sigma" in self.idata.posterior:
sigma_var_name = "sigma"
elif "y_hat_sigma" in self.idata.posterior:
sigma_var_name = "y_hat_sigma"
else:
raise ValueError(
"Neither 'sigma' nor 'y_hat_sigma' found in posterior"
) # pragma: no cover
treated_units = coeffs.coords["treated_units"].values
for unit in treated_units:
if len(treated_units) > 1:
print(f"\nTreated unit: {unit}")
unit_coeffs = coeffs.sel(treated_units=unit)
unit_sigma = az.extract(self.idata.posterior, var_names=sigma_var_name).sel(
treated_units=unit
)
print_coefficients_for_unit(unit_coeffs, unit_sigma, labels, round_to or 2)
[docs]
class LinearRegression(PyMCModel):
r"""
Custom PyMC model for linear regression.
Defines the PyMC model
.. math::
\beta &\sim \mathrm{Normal}(0, 50) \\
\sigma &\sim \mathrm{HalfNormal}(1) \\
\mu &= X \cdot \beta \\
y &\sim \mathrm{Normal}(\mu, \sigma) \\
Example
--------
>>> import causalpy as cp
>>> import numpy as np
>>> import xarray as xr
>>> from causalpy.pymc_models import LinearRegression
>>> rd = cp.load_data("rd")
>>> rd["treated"] = rd["treated"].astype(int)
>>> coeffs = ["x", "treated"]
>>> X = xr.DataArray(
... rd[coeffs].values,
... dims=["obs_ind", "coeffs"],
... coords={"obs_ind": rd.index, "coeffs": coeffs},
... )
>>> y = xr.DataArray(
... rd["y"].values[:, None],
... dims=["obs_ind", "treated_units"],
... coords={"obs_ind": rd.index, "treated_units": ["unit_0"]},
... )
>>> lr = LinearRegression(sample_kwargs={"progressbar": False})
>>> coords={"coeffs": coeffs, "obs_ind": np.arange(rd.shape[0]), "treated_units": ["unit_0"]}
>>> lr.fit(X, y, coords=coords)
Inference data...
""" # noqa: W605
default_priors = {
"beta": Prior("Normal", mu=0, sigma=50, dims=["treated_units", "coeffs"]),
"y_hat": Prior(
"Normal",
sigma=Prior("HalfNormal", sigma=1, dims=["treated_units"]),
dims=["obs_ind", "treated_units"],
),
}
[docs]
def build_model(self, X, y, coords):
"""
Defines the PyMC model
"""
with self:
# Ensure treated_units coordinate exists for consistency
if "treated_units" not in coords:
coords = coords.copy()
coords["treated_units"] = ["unit_0"]
self.add_coords(coords)
X = pm.Data("X", X, dims=["obs_ind", "coeffs"])
y = pm.Data("y", y, dims=["obs_ind", "treated_units"])
beta = self.priors["beta"].create_variable("beta")
mu = pm.Deterministic(
"mu", pt.dot(X, beta.T), dims=["obs_ind", "treated_units"]
)
self.priors["y_hat"].create_likelihood_variable("y_hat", mu=mu, observed=y)
[docs]
class WeightedSumFitter(PyMCModel):
r"""
Used for synthetic control experiments.
Defines the PyMC model:
.. math::
\sigma &\sim \mathrm{HalfNormal}(1) \\
\beta &\sim \mathrm{Dirichlet}(1,...,1) \\
\mu &= X \cdot \beta \\
y &\sim \mathrm{Normal}(\mu, \sigma) \\
Example
--------
>>> import causalpy as cp
>>> import numpy as np
>>> import xarray as xr
>>> from causalpy.pymc_models import WeightedSumFitter
>>> sc = cp.load_data("sc")
>>> control_units = ['a', 'b', 'c', 'd', 'e', 'f', 'g']
>>> X = xr.DataArray(
... sc[control_units].values,
... dims=["obs_ind", "coeffs"],
... coords={"obs_ind": sc.index, "coeffs": control_units},
... )
>>> y = xr.DataArray(
... sc['actual'].values.reshape((sc.shape[0], 1)),
... dims=["obs_ind", "treated_units"],
... coords={"obs_ind": sc.index, "treated_units": ["actual"]},
... )
>>> coords = {
... "coeffs": control_units,
... "treated_units": ["actual"],
... "obs_ind": np.arange(sc.shape[0]),
... }
>>> wsf = WeightedSumFitter(sample_kwargs={"progressbar": False})
>>> wsf.fit(X, y, coords=coords)
Inference data...
""" # noqa: W605
default_priors = {
"y_hat": Prior(
"Normal",
sigma=Prior("HalfNormal", sigma=1, dims=["treated_units"]),
dims=["obs_ind", "treated_units"],
),
}
[docs]
def priors_from_data(self, X, y) -> Dict[str, Any]:
"""
Set Dirichlet prior for weights based on number of control units.
For synthetic control models, this method sets the shape parameter of the
Dirichlet prior on the control unit weights (`beta`) to be uniform across
all available control units. This ensures that all control units have
equal prior probability of contributing to the synthetic control.
Parameters
----------
X : xarray.DataArray
Control unit data with shape (n_obs, n_control_units).
y : xarray.DataArray
Treated unit outcome data.
Returns
-------
Dict[str, Prior]
Dictionary containing:
- "beta": Dirichlet prior with shape=(1,...,1) for n_control_units
"""
n_predictors = X.shape[1]
return {
"beta": Prior(
"Dirichlet", a=np.ones(n_predictors), dims=["treated_units", "coeffs"]
),
}
[docs]
def build_model(self, X, y, coords):
"""
Defines the PyMC model
"""
with self:
self.add_coords(coords)
X = pm.Data("X", X, dims=["obs_ind", "coeffs"])
y = pm.Data("y", y, dims=["obs_ind", "treated_units"])
beta = self.priors["beta"].create_variable("beta")
mu = pm.Deterministic(
"mu", pt.dot(X, beta.T), dims=["obs_ind", "treated_units"]
)
self.priors["y_hat"].create_likelihood_variable("y_hat", mu=mu, observed=y)
[docs]
class InstrumentalVariableRegression(PyMCModel):
"""Custom PyMC model for instrumental linear regression
Example
--------
>>> import causalpy as cp
>>> import numpy as np
>>> from causalpy.pymc_models import InstrumentalVariableRegression
>>> N = 10
>>> e1 = np.random.normal(0, 3, N)
>>> e2 = np.random.normal(0, 1, N)
>>> Z = np.random.uniform(0, 1, N)
>>> ## Ensure the endogeneity of the the treatment variable
>>> X = -1 + 4 * Z + e2 + 2 * e1
>>> y = 2 + 3 * X + 3 * e1
>>> t = X.reshape(10, 1)
>>> y = y.reshape(10, 1)
>>> Z = np.asarray([[1, Z[i]] for i in range(0, 10)])
>>> X = np.asarray([[1, X[i]] for i in range(0, 10)])
>>> COORDS = {"instruments": ["Intercept", "Z"], "covariates": ["Intercept", "X"]}
>>> sample_kwargs = {
... "tune": 5,
... "draws": 10,
... "chains": 2,
... "cores": 2,
... "target_accept": 0.95,
... "progressbar": False,
... }
>>> iv_reg = InstrumentalVariableRegression(sample_kwargs=sample_kwargs)
>>> iv_reg.fit(
... X,
... Z,
... y,
... t,
... COORDS,
... {
... "mus": [[-2, 4], [0.5, 3]],
... "sigmas": [1, 1],
... "eta": 2,
... "lkj_sd": 1,
... },
... None,
... )
Inference data...
"""
[docs]
def build_model(self, X, Z, y, t, coords, priors):
"""Specify model with treatment regression and focal regression data and priors
:param X: A pandas dataframe used to predict our outcome y
:param Z: A pandas dataframe used to predict our treatment variable t
:param y: An array of values representing our focal outcome y
:param t: An array of values representing the treatment t of
which we're interested in estimating the causal impact
:param coords: A dictionary with the coordinate names for our
instruments and covariates
:param priors: An optional dictionary of priors for the mus and
sigmas of both regressions
:code:`priors = {"mus": [0, 0], "sigmas": [1, 1],
"eta": 2, "lkj_sd": 2}`
"""
# --- Priors ---
with self:
self.add_coords(coords)
beta_t = pm.Normal(
name="beta_t",
mu=priors["mus"][0],
sigma=priors["sigmas"][0],
dims="instruments",
)
beta_z = pm.Normal(
name="beta_z",
mu=priors["mus"][1],
sigma=priors["sigmas"][1],
dims="covariates",
)
sd_dist = pm.Exponential.dist(priors["lkj_sd"], shape=2)
chol, corr, sigmas = pm.LKJCholeskyCov(
name="chol_cov",
eta=priors["eta"],
n=2,
sd_dist=sd_dist,
)
# compute and store the covariance matrix
pm.Deterministic(name="cov", var=pt.dot(l=chol, r=chol.T))
# --- Parameterization ---
mu_y = pm.Deterministic(name="mu_y", var=pt.dot(X, beta_z))
# focal regression
mu_t = pm.Deterministic(name="mu_t", var=pt.dot(Z, beta_t))
# instrumental regression
mu = pm.Deterministic(name="mu", var=pt.stack(tensors=(mu_y, mu_t), axis=1))
# --- Likelihood ---
pm.MvNormal(
name="likelihood",
mu=mu,
chol=chol,
observed=np.stack(arrays=(y.flatten(), t.flatten()), axis=1),
shape=(X.shape[0], 2),
)
[docs]
def sample_predictive_distribution(self, ppc_sampler="jax"):
"""Function to sample the Multivariate Normal posterior predictive
Likelihood term in the IV class. This can be slow without
using the JAX sampler compilation method. If using the
JAX sampler it will sample only the posterior predictive distribution.
If using the PYMC sampler if will sample both the prior
and posterior predictive distributions."""
random_seed = self.sample_kwargs.get("random_seed", None)
if ppc_sampler == "jax":
with self:
self.idata.extend(
pm.sample_posterior_predictive(
self.idata,
random_seed=random_seed,
compile_kwargs={"mode": "JAX"},
)
)
elif ppc_sampler == "pymc":
with self:
self.idata.extend(pm.sample_prior_predictive(random_seed=random_seed))
self.idata.extend(
pm.sample_posterior_predictive(
self.idata,
random_seed=random_seed,
)
)
[docs]
def fit(self, X, Z, y, t, coords, priors, ppc_sampler=None):
"""Draw samples from posterior distribution and potentially
from the prior and posterior predictive distributions. The
fit call can take values for the
ppc_sampler = ['jax', 'pymc', None]
We default to None, so the user can determine if they wish
to spend time sampling the posterior predictive distribution
independently.
"""
# Ensure random_seed is used in sample_prior_predictive() and
# sample_posterior_predictive() if provided in sample_kwargs.
# Use JAX for ppc sampling of multivariate likelihood
self.build_model(X, Z, y, t, coords, priors)
with self:
self.idata = pm.sample(**self.sample_kwargs)
self.sample_predictive_distribution(ppc_sampler=ppc_sampler)
return self.idata
[docs]
class PropensityScore(PyMCModel):
r"""
Custom PyMC model for inverse propensity score models
.. note:
Generally, the `.fit()` method should be used rather than
calling `.build_model()` directly.
Defines the PyMC model
.. math::
\beta &\sim \mathrm{Normal}(0, 1) \\
\sigma &\sim \mathrm{HalfNormal}(1) \\
\mu &= X \cdot \beta \\
p &= \text{logit}^{-1}(\mu) \\
t &\sim \mathrm{Bernoulli}(p)
Example
--------
>>> import causalpy as cp
>>> import numpy as np
>>> from causalpy.pymc_models import PropensityScore
>>> df = cp.load_data('nhefs')
>>> X = df[["age", "race"]]
>>> t = np.asarray(df["trt"])
>>> ps = PropensityScore(sample_kwargs={"progressbar": False})
>>> ps.fit(X, t, coords={
... 'coeffs': ['age', 'race'],
... 'obs_ind': np.arange(df.shape[0])
... },
... prior={'b': [0, 1]},
... )
Inference...
""" # noqa: W605
default_priors = {
"b": Prior("Normal", mu=0, sigma=1, dims="coeffs"),
}
[docs]
def build_model(self, X, t, coords, prior=None, noncentred=True):
"Defines the PyMC propensity model"
with self:
self.add_coords(coords)
X_data = pm.Data("X", X, dims=["obs_ind", "coeffs"])
t_data = pm.Data("t", t.flatten(), dims="obs_ind")
b = self.priors["b"].create_variable("b")
mu = pt.dot(X_data, b)
p = pm.Deterministic("p", pm.math.invlogit(mu))
pm.Bernoulli("t_pred", p=p, observed=t_data, dims="obs_ind")
[docs]
def fit(self, X, t, coords, prior={"b": [0, 1]}, noncentred=True):
"""Draw samples from posterior, prior predictive, and posterior predictive
distributions. We overwrite the base method because the base method assumes
a variable y and we use t to indicate the treatment variable here.
"""
# Ensure random_seed is used in sample_prior_predictive() and
# sample_posterior_predictive() if provided in sample_kwargs.
random_seed = self.sample_kwargs.get("random_seed", None)
self.build_model(X, t, coords, prior, noncentred)
with self:
self.idata = pm.sample(**self.sample_kwargs)
self.idata.extend(pm.sample_prior_predictive(random_seed=random_seed))
self.idata.extend(
pm.sample_posterior_predictive(
self.idata, progressbar=False, random_seed=random_seed
)
)
return self.idata
[docs]
def fit_outcome_model(
self,
X_outcome,
y,
coords,
priors={
"b_outcome": [0, 1],
"sigma": 1,
"beta_ps": [0, 1],
},
noncentred=True,
normal_outcome=True,
spline_component=False,
winsorize_boundary=0.0,
):
"""
Fit a Bayesian outcome model using covariates and previously estimated propensity scores.
This function implements the second stage of a modular two-step causal inference procedure.
It uses propensity scores extracted from a prior treatment model (via `self.fit()`) to adjust
for confounding when estimating treatment effects on an outcome variable `y`.
Parameters
----------
X_outcome : array-like, shape (n_samples, n_covariates)
Covariate matrix for the outcome model.
y : array-like, shape (n_samples,)
Observed outcome variable.
coords : dict
Coordinate dictionary for named dimensions in the PyMC model. Should include
a key "outcome_coeffs" for `X_outcome`.
priors : dict, optional
Dictionary specifying priors for outcome model parameters:
- "b_outcome": list [mean, std] for regression coefficients.
- "sigma": standard deviation of the outcome noise (default 1).
noncentred : bool, default True
If True, use a non-centred parameterization for the outcome coefficients.
normal_outcome : bool, default True
If True, assume a Normal likelihood for the outcome.
If False, use a Student-t likelihood with unknown degrees of freedom.
spline_component : bool, default False
If True, include a spline basis expansion on the propensity score to allow
flexible (nonlinear) adjustment. Uses B-splines with 30 internal knots.
winsorize_boundary : float, default 0.0
If we wish to winsorize the propensity score this can be set to clip the high
and low values of the propensity at 0 + winsorize_boundary and 1-winsorize_boundary
Returns
-------
idata_outcome : arviz.InferenceData
The posterior and prior predictive samples from the outcome model.
model_outcome : pm.Model
The PyMC model object.
Raises
------
AttributeError
If the `self.idata` attribute is not available, which indicates that
`fit()` (i.e., the treatment model) has not been called yet.
Notes
-----
- This model uses a sampled version of the propensity score (`p`) from the
posterior of the treatment model, randomly selecting one posterior draw
per call. This term is estimated initially in the InversePropensity
class initialisation.
- The term `beta_ps[0] * p` captures both
main effects of the propensity score.
- Including spline adjustment enables modeling nonlinear relationships
between the propensity score and the outcome.
"""
if not hasattr(self, "idata"):
raise AttributeError("""Object is missing required attribute 'idata'
so cannot proceed. Call fit() first""")
propensity_scores = az.extract(self.idata)["p"]
random_seed = self.sample_kwargs.get("random_seed", None)
with pm.Model(coords=coords) as model_outcome:
X_data_outcome = pm.Data("X_outcome", X_outcome)
Y_data_ = pm.Data("Y", y)
if noncentred:
mu_beta, sigma_beta = priors["b_outcome"]
beta_std = pm.Normal("beta_std", 0, 1, dims="outcome_coeffs")
beta = pm.Deterministic(
"beta_", mu_beta + sigma_beta * beta_std, dims="outcome_coeffs"
)
else:
beta = pm.Normal(
"beta_",
priors["b_outcome"][0],
priors["b_outcome"][1],
dims="outcome_coeffs",
)
beta_ps = pm.Normal("beta_ps", priors["beta_ps"][0], priors["beta_ps"][1])
chosen = np.random.choice(range(propensity_scores.shape[1]))
p = propensity_scores[:, chosen].values
p = np.clip(p, winsorize_boundary, 1 - winsorize_boundary)
mu_outcome = pm.math.dot(X_data_outcome, beta) + beta_ps * p
if spline_component:
beta_ps_spline = pm.Normal(
"beta_ps_spline",
priors["beta_ps"][0],
priors["beta_ps"][1],
size=34,
)
B = dmatrix(
"bs(ps, knots=knots, degree=3, include_intercept=True, lower_bound=0, upper_bound=1) - 1",
{"ps": p, "knots": np.linspace(0, 1, 30)},
)
B_f = np.asarray(B, order="F")
splines_summed = pm.Deterministic(
"spline_features", pm.math.dot(B_f, beta_ps_spline.T)
)
mu_outcome = pm.math.dot(X_data_outcome, beta) + splines_summed
sigma = pm.HalfNormal("sigma", priors["sigma"])
if normal_outcome:
_ = pm.Normal("like", mu_outcome, sigma, observed=Y_data_)
else:
nu = pm.Exponential("nu", lam=1 / 10)
_ = pm.StudentT(
"like", nu=nu, mu=mu_outcome, sigma=sigma, observed=Y_data_
)
idata_outcome = pm.sample_prior_predictive(random_seed=random_seed)
idata_outcome.extend(pm.sample(**self.sample_kwargs))
return idata_outcome, model_outcome
