Add GrassiaIIGeometric Distribution

pymc_extras/distributions/__init__.py

@@ -22,6 +22,7 @@
     BetaNegativeBinomial,
     GeneralizedPoisson,
     Skellam,
+    GrassiaIIGeometric,
 )
 from pymc_extras.distributions.histogram_utils import histogram_approximation
 from pymc_extras.distributions.multivariate import R2D2M2CP
@@ -38,5 +39,6 @@
     "R2D2M2CP",
     "Skellam",
     "histogram_approximation",
+    "GrassiaIIGeometric",
     "PartialOrder",
 ]

pymc_extras/distributions/discrete.py

@@ -16,6 +16,7 @@
 import pymc as pm
 
 from pymc.distributions.dist_math import betaln, check_parameters, factln, logpow
+from pymc.distributions.distribution import Discrete
 from pymc.distributions.shape_utils import rv_size_is_none
 from pytensor import tensor as pt
 from pytensor.tensor.random.op import RandomVariable
@@ -399,3 +400,186 @@ def dist(cls, mu1, mu2, **kwargs):
             class_name="Skellam",
             **kwargs,
         )
+
+
+class GrassiaIIGeometricRV(RandomVariable):
+    name = "g2g"
+    signature = "(),(),()->()"
+
+    dtype = "int64"
+    _print_name = ("GrassiaIIGeometric", "\\operatorname{GrassiaIIGeometric}")
+
+    @classmethod
+    def rng_fn(cls, rng, r, alpha, time_covariate_vector, size):
+        # Determine output size
+        if size is None:
+            size = np.broadcast_shapes(r.shape, alpha.shape, time_covariate_vector.shape)
+
+        # Broadcast parameters to output size
+        r = np.broadcast_to(r, size)
+        alpha = np.broadcast_to(alpha, size)
+        time_covariate_vector = np.broadcast_to(time_covariate_vector, size)
+
+        lam = rng.gamma(shape=r, scale=1 / alpha, size=size)
+
+        # Calculate exp(time_covariate_vector) for all samples
+        exp_time_covar = np.exp(
+            time_covariate_vector
+        ).mean()  # must average over time for correct broadcasting
+        lam_covar = lam * exp_time_covar
+
+        samples = np.ceil(rng.exponential(size=size) / lam_covar)
+
+        return samples
+
+
+g2g = GrassiaIIGeometricRV()
+
+
+# TODO: Add covariate expressions to docstrings.
+class GrassiaIIGeometric(Discrete):
+    r"""Grassia(II)-Geometric distribution.
+
+    This distribution is a flexible alternative to the Geometric distribution for the number of trials until a
+    discrete event, and can be extended to support both static and time-varying covariates.
+
+    Hardie and Fader describe this distribution with the following PMF and survival functions in [1]_:
+
+    .. math::
+        \mathbb{P}T=t|r,\alpha,\beta;Z(t)) = (\frac{\alpha}{\alpha+C(t-1)})^{r} - (\frac{\alpha}{\alpha+C(t)})^{r}  \\
+        \begin{align}
+        \mathbb{S}(t|r,\alpha,\beta;Z(t)) = (\frac{\alpha}{\alpha+C(t)})^{r} \\
+        \end{align}
+
+    .. plot::
+        :context: close-figs
+
+        import matplotlib.pyplot as plt
+        import numpy as np
+        import scipy.stats as st
+        import arviz as az
+        plt.style.use('arviz-darkgrid')
+        t = np.arange(1, 11)
+        alpha_vals = [1., 1., 2., 2.]
+        r_vals = [.1, .25, .5, 1.]
+        for alpha, r in zip(alpha_vals, r_vals):
+            pmf = (alpha/(alpha + t - 1))**r - (alpha/(alpha+t))**r
+            plt.plot(t, pmf, '-o', label=r'$\alpha$ = {}, $r$ = {}'.format(alpha, r))
+        plt.xlabel('t', fontsize=12)
+        plt.ylabel('p(t)', fontsize=12)
+        plt.legend(loc=1)
+        plt.show()
+
+    ========  ===============================================
+    Support   :math:`t \in \mathbb{N}_{>0}`
+    ========  ===============================================
+
+    Parameters
+    ----------
+    r : tensor_like of float
+        Shape parameter (r > 0).
+    alpha : tensor_like of float
+        Scale parameter (alpha > 0).
+    time_covariate_vector : tensor_like of float, optional
+        Optional vector containing dot products of time-varying covariates and coefficients.
+
+    References
+    ----------
+    .. [1] Fader, Peter & G. S. Hardie, Bruce (2020).
+       "Incorporating Time-Varying Covariates in a Simple Mixture Model for Discrete-Time Duration Data."
+       https://www.brucehardie.com/notes/037/time-varying_covariates_in_BG.pdf
+    """
+
+    rv_op = g2g
+
+    @classmethod
+    def dist(cls, r, alpha, time_covariate_vector=None, *args, **kwargs):
+        r = pt.as_tensor_variable(r)
+        alpha = pt.as_tensor_variable(alpha)
+        if time_covariate_vector is None:
+            time_covariate_vector = pt.constant(0.0)
+        time_covariate_vector = pt.as_tensor_variable(time_covariate_vector)
+        return super().dist([r, alpha, time_covariate_vector], *args, **kwargs)
+
+    def logp(value, r, alpha, time_covariate_vector):
+        logp = pt.log(
+            pt.pow(alpha / (alpha + C_t(value - 1, time_covariate_vector)), r)
+            - pt.pow(alpha / (alpha + C_t(value, time_covariate_vector)), r)
+        )
+
+        # Handle invalid values
+        logp = pt.switch(
+            pt.or_(
+                value < 1,  # Value must be >= 1
+                pt.isnan(logp),  # Handle NaN cases
+            ),
+            -np.inf,
+            logp,
+        )
+
+        return check_parameters(
+            logp,
+            r > 0,
+            alpha > 0,
+            msg="r > 0, alpha > 0",
+        )
+
+    def logcdf(value, r, alpha, time_covariate_vector):
+        logcdf = r * (
+            pt.log(C_t(value, time_covariate_vector))
+            - pt.log(alpha + C_t(value, time_covariate_vector))
+        )
+
+        return check_parameters(
+            logcdf,
+            r > 0,
+            alpha > 0,
+            msg="r > 0, alpha > 0",
+        )
+
+    def support_point(rv, size, r, alpha, time_covariate_vector):
+        """Calculate a reasonable starting point for sampling.
+
+        For the GrassiaIIGeometric distribution, we use a point estimate based on
+        the expected value of the mixing distribution. Since the mixing distribution
+        is Gamma(r, 1/alpha), its mean is r/alpha. We then transform this through
+        the geometric link function and round to ensure an integer value.
+
+        When time_covariate_vector is provided, it affects the expected value through
+        the exponential link function: exp(time_covariate_vector).
+        """
+
+        base_lambda = r / alpha
+
+        # Approximate expected value of geometric distribution
+        mean = pt.switch(
+            base_lambda < 0.1,
+            1.0 / base_lambda,  # Approximation for small lambda
+            1.0 / (1.0 - pt.exp(-base_lambda)),  # Full expression for larger lambda
+        )
+
+        # Apply time covariates if provided
+        mean = mean * pt.exp(time_covariate_vector)
+
+        # Round up to nearest integer and ensure >= 1
+        mean = pt.maximum(pt.ceil(mean), 1.0)
+
+        # Handle size parameter
+        if not rv_size_is_none(size):
+            mean = pt.full(size, mean)
+
+        return mean
+
+
+def C_t(t: pt.TensorVariable, time_covariate_vector: pt.TensorVariable) -> pt.TensorVariable:
+    """Utility for processing time-varying covariates in GrassiaIIGeometric distribution."""
+    if time_covariate_vector.ndim == 0:
+        return t
+    else:
+        # Ensure t is a valid index
+        t_idx = pt.maximum(0, t - 1)  # Convert to 0-based indexing
+        # If t_idx exceeds length of time_covariate_vector, use last value
+        max_idx = pt.shape(time_covariate_vector)[0] - 1
+        safe_idx = pt.minimum(t_idx, max_idx)
+        covariate_value = time_covariate_vector[safe_idx]
+        return t * pt.exp(covariate_value)

tests/distributions/test_discrete.py

@@ -11,6 +11,7 @@
 #   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 #   See the License for the specific language governing permissions and
 #   limitations under the License.
+
 import numpy as np
 import pymc as pm
 import pytensor
@@ -26,13 +27,15 @@
     Rplus,
     assert_support_point_is_expected,
     check_logp,
+    check_selfconsistency_discrete_logcdf,
     discrete_random_tester,
 )
 from pytensor import config
 
 from pymc_extras.distributions import (
     BetaNegativeBinomial,
     GeneralizedPoisson,
+    GrassiaIIGeometric,
     Skellam,
 )
 
@@ -208,3 +211,161 @@ def test_logp(self):
                 {"mu1": Rplus_small, "mu2": Rplus_small},
                 lambda value, mu1, mu2: scipy.stats.skellam.logpmf(value, mu1, mu2),
             )
+
+
+class TestGrassiaIIGeometric:
+    class TestRandomVariable(BaseTestDistributionRandom):
+        pymc_dist = GrassiaIIGeometric
+        pymc_dist_params = {"r": 0.5, "alpha": 2.0, "time_covariate_vector": 0.0}
+        expected_rv_op_params = {"r": 0.5, "alpha": 2.0, "time_covariate_vector": 0.0}
+        tests_to_run = [
+            "check_pymc_params_match_rv_op",
+            "check_rv_size",
+        ]
+
+        def test_random_basic_properties(self):
+            """Test basic random sampling properties"""
+            # Test with standard parameter values
+            r_vals = [0.5, 1.0, 2.0]
+            alpha_vals = [0.5, 1.0, 2.0]
+            time_cov_vals = [-1.0, 1.0, 2.0]
+
+            for r in r_vals:
+                for alpha in alpha_vals:
+                    for time_cov in time_cov_vals:
+                        dist = self.pymc_dist.dist(
+                            r=r, alpha=alpha, time_covariate_vector=time_cov, size=1000
+                        )
+                        draws = dist.eval()
+
+                        # Check basic properties
+                        assert np.all(draws > 0)
+                        assert np.all(draws.astype(int) == draws)
+                        assert np.mean(draws) > 0
+                        assert np.var(draws) > 0
+
+        def test_random_edge_cases(self):
+            """Test edge cases with more reasonable parameter values"""
+            # Test with small r and large alpha values
+            r_vals = [0.1, 0.5]
+            alpha_vals = [5.0, 10.0]
+            time_cov_vals = [0.0, 1.0]
+
+            for r in r_vals:
+                for alpha in alpha_vals:
+                    for time_cov in time_cov_vals:
+                        dist = self.pymc_dist.dist(
+                            r=r, alpha=alpha, time_covariate_vector=time_cov, size=1000
+                        )
+                        draws = dist.eval()
+
+                        # Check basic properties
+                        assert np.all(draws > 0)
+                        assert np.all(draws.astype(int) == draws)
+                        assert np.mean(draws) > 0
+                        assert np.var(draws) > 0
+
+        def test_random_none_covariates(self):
+            """Test random sampling with None time_covariate_vector"""
+            r_vals = [0.5, 1.0, 2.0]
+            alpha_vals = [0.5, 1.0, 2.0]
+
+            for r in r_vals:
+                for alpha in alpha_vals:
+                    dist = self.pymc_dist.dist(
+                        r=r,
+                        alpha=alpha,
+                        time_covariate_vector=0.0,  # Changed from None to avoid zip issues
+                        size=1000,
+                    )
+                    draws = dist.eval()
+
+                    # Check basic properties
+                    assert np.all(draws > 0)
+                    assert np.all(draws.astype(int) == draws)
+                    assert np.mean(draws) > 0
+                    assert np.var(draws) > 0
+
+        @pytest.mark.parametrize(
+            "r,alpha,time_covariate_vector",
+            [
+                (0.5, 1.0, 0.0),
+                (1.0, 2.0, 1.0),
+                (2.0, 0.5, -1.0),
+                (5.0, 1.0, 0.0),  # Changed from None to avoid zip issues
+            ],
+        )
+        def test_random_moments(self, r, alpha, time_covariate_vector):
+            dist = self.pymc_dist.dist(
+                r=r, alpha=alpha, time_covariate_vector=time_covariate_vector, size=10_000
+            )
+            draws = dist.eval()
+
+            assert np.all(draws > 0)
+            assert np.all(draws.astype(int) == draws)
+            assert np.mean(draws) > 0
+            assert np.var(draws) > 0
+
+    def test_logp_basic(self):
+        # Create PyTensor variables with explicit values to ensure proper initialization
+        r = pt.as_tensor_variable(1.0)
+        alpha = pt.as_tensor_variable(2.0)
+        time_covariate_vector = pt.as_tensor_variable(0.5)
+        value = pt.vector("value", dtype="int64")
+
+        # Create the distribution with the PyTensor variables
+        dist = GrassiaIIGeometric.dist(r, alpha, time_covariate_vector)
+        logp = pm.logp(dist, value)
+        logp_fn = pytensor.function([value], logp)
+
+        # Test basic properties of logp
+        test_value = np.array([1, 2, 3, 4, 5])
+
+        logp_vals = logp_fn(test_value)
+        assert not np.any(np.isnan(logp_vals))
+        assert np.all(np.isfinite(logp_vals))
+
+        # Test invalid values
+        assert logp_fn(np.array([0])) == -np.inf  # Value must be > 0
+
+        with pytest.raises(TypeError):
+            logp_fn(np.array([1.5]))  # Value must be integer
+
+    def test_logcdf(self):
+        # test logcdf matches log sums across parameter values
+        check_selfconsistency_discrete_logcdf(
+            GrassiaIIGeometric, I, {"r": Rplus, "alpha": Rplus, "time_covariate_vector": I}
+        )
+
+    @pytest.mark.parametrize(
+        "r, alpha, time_covariate_vector, size, expected_shape",
+        [
+            (1.0, 1.0, 0.0, None, ()),  # Scalar output with no covariates (0.0 instead of None)
+            ([1.0, 2.0], 1.0, 0.0, None, (2,)),  # Vector output from r
+            (1.0, [1.0, 2.0], 0.0, None, (2,)),  # Vector output from alpha
+            (1.0, 1.0, [1.0, 2.0], None, (2,)),  # Vector output from time covariates
+            (1.0, 1.0, 1.0, (3, 2), (3, 2)),  # Explicit size with scalar time covariates
+        ],
+    )
+    def test_support_point(self, r, alpha, time_covariate_vector, size, expected_shape):
+        """Test that support_point returns reasonable values with correct shapes"""
+        with pm.Model() as model:
+            GrassiaIIGeometric(
+                "x", r=r, alpha=alpha, time_covariate_vector=time_covariate_vector, size=size
+            )
+
+        init_point = model.initial_point()["x"]
+
+        # Check shape
+        assert init_point.shape == expected_shape
+
+        # Check values are positive integers
+        assert np.all(init_point > 0)
+        assert np.all(init_point.astype(int) == init_point)
+
+        # Check values are finite and reasonable
+        assert np.all(np.isfinite(init_point))
+        assert np.all(init_point < 1e6)  # Should not be extremely large
+
+        # TODO: expected values must be provided
+        # assert_support_point_is_expected(model, init_point)