Add a flag to LKJCorr to return the unpacked correlation matrix

pymc/distributions/multivariate.py

@@ -1505,6 +1505,7 @@
     def _random_corr_matrix(cls, rng, n, eta, flat_size):
         # original implementation in R see:
         # https://github.com/rmcelreath/rethinking/blob/master/R/distributions.r
+
         beta = eta - 1.0 + n / 2.0
         r12 = 2.0 * stats.beta.rvs(a=beta, b=beta, size=flat_size, random_state=rng) - 1.0
         P = np.full((flat_size, n, n), np.eye(n))
@@ -1531,48 +1532,8 @@
         return super().log_jac_det(*args).sum(-1)
 
 
-class LKJCorr(BoundedContinuous):
-    r"""
-    The LKJ (Lewandowski, Kurowicka and Joe) log-likelihood.
-
-    The LKJ distribution is a prior distribution for correlation matrices.
-    If eta = 1 this corresponds to the uniform distribution over correlation
-    matrices. For eta -> oo the LKJ prior approaches the identity matrix.
-
-    ========  ==============================================
-    Support   Upper triangular matrix with values in [-1, 1]
-    ========  ==============================================
-
-    Parameters
-    ----------
-    n : tensor_like of int
-        Dimension of the covariance matrix (n > 1).
-    eta : tensor_like of float
-        The shape parameter (eta > 0) of the LKJ distribution. eta = 1
-        implies a uniform distribution of the correlation matrices;
-        larger values put more weight on matrices with few correlations.
-
-    Notes
-    -----
-    This implementation only returns the values of the upper triangular
-    matrix excluding the diagonal. Here is a schematic for n = 5, showing
-    the indexes of the elements::
-
-        [[- 0 1 2 3]
-         [- - 4 5 6]
-         [- - - 7 8]
-         [- - - - 9]
-         [- - - - -]]
-
-
-    References
-    ----------
-    .. [LKJ2009] Lewandowski, D., Kurowicka, D. and Joe, H. (2009).
-        "Generating random correlation matrices based on vines and
-        extended onion method." Journal of multivariate analysis,
-        100(9), pp.1989-2001.
-    """
-
+# Returns list of upper triangular values
+class _LKJCorr(BoundedContinuous):
     rv_op = lkjcorr
 
     @classmethod
@@ -1631,11 +1592,97 @@
         )
 
 
-@_default_transform.register(LKJCorr)
+@_default_transform.register(_LKJCorr)
 def lkjcorr_default_transform(op, rv):
     return MultivariateIntervalTransform(floatX(-1.0), floatX(1.0))
 
 
+class LKJCorr:
+    r"""
+    The LKJ (Lewandowski, Kurowicka and Joe) log-likelihood.
+
+    The LKJ distribution is a prior distribution for correlation matrices.
+    If eta = 1 this corresponds to the uniform distribution over correlation
+    matrices. For eta -> oo the LKJ prior approaches the identity matrix.
+
+    ========  ==============================================
+    Support   Upper triangular matrix with values in [-1, 1]
+    ========  ==============================================
+
+    Parameters
+    ----------
+    n : tensor_like of int
+        Dimension of the covariance matrix (n > 1).
+    eta : tensor_like of float
+        The shape parameter (eta > 0) of the LKJ distribution. eta = 1
+        implies a uniform distribution of the correlation matrices;
+        larger values put more weight on matrices with few correlations.
+    return_matrix : bool, default=False
+        If True, returns the full correlation matrix.
+        False only returns the values of the upper triangular matrix excluding
+        diagonal in a single vector of length n(n-1)/2 for memory efficiency
+
+    Notes
+    -----
+    This is mainly useful if you want the standard deviations to be fixed, as
+    LKJCholsekyCov is optimized for the case where they come from a distribution.
+
+    Examples
+    --------
+    .. code:: python
+
+        with pm.Model() as model:
+
+            # Define the vector of fixed standard deviations
+            sds = 3*np.ones(10)
+
+            corr = pm.LKJCorr(
+                'corr', eta=4, n=10, return_matrix=True
+            )
+
+            # Define a new MvNormal with the given correlation matrix
+            vals = sds*pm.MvNormal('vals', mu=np.zeros(10), cov=corr, shape=10)
+
+            # Or transform an uncorrelated normal distribution:
+            vals_raw = pm.Normal('vals_raw', shape=10)
+            chol = pt.linalg.cholesky(corr)
+            vals = sds*pt.dot(chol,vals_raw)
+
+            # The matrix is internally still sampled as a upper triangular vector
+            # If you want access to it in matrix form in the trace, add
+            pm.Deterministic('corr_mat', corr)
+
+
+    References
+    ----------
+    .. [LKJ2009] Lewandowski, D., Kurowicka, D. and Joe, H. (2009).
+        "Generating random correlation matrices based on vines and
+        extended onion method." Journal of multivariate analysis,
+        100(9), pp.1989-2001.
+    """
+
+    def __new__(cls, name, n, eta, *, return_matrix=False, **kwargs):
+        c_vec = _LKJCorr(name, eta=eta, n=n, **kwargs)
+        if not return_matrix:
+            return c_vec
+        else:
+            return cls.vec_to_corr_mat(c_vec, n)
+
+    @classmethod
+    def dist(cls, n, eta, *, return_matrix=False, **kwargs):
+        c_vec = _LKJCorr.dist(eta=eta, n=n, **kwargs)
+        if not return_matrix:
+            return c_vec
+        else:
+            return cls.vec_to_corr_mat(c_vec, n)
+
+    @classmethod
+    def vec_to_corr_mat(cls, vec, n):
+        tri = pt.zeros(pt.concatenate([vec.shape[:-1], (n, n)]))
+        tri = pt.subtensor.set_subtensor(tri[(...,) + np.triu_indices(n, 1)], vec)
+        return tri + pt.moveaxis(tri, -2, -1) + pt.diag(pt.ones(n))
+
+
 class MatrixNormalRV(RandomVariable):
     name = "matrixnormal"
     ndim_supp = 2

tests/distributions/test_multivariate.py

@@ -34,6 +34,7 @@
 from pymc.distributions.multivariate import (
     MultivariateIntervalTransform,
     _LKJCholeskyCov,
+    _LKJCorr,
     _OrderedMultinomial,
     posdef,
     quaddist_matrix,
@@ -558,7 +559,7 @@ def test_wishart(self, n):
     @pytest.mark.parametrize("x,eta,n,lp", LKJ_CASES)
     def test_lkjcorr(self, x, eta, n, lp):
         with pm.Model() as model:
-            pm.LKJCorr("lkj", eta=eta, n=n, transform=None)
+            pm.LKJCorr("lkj", eta=eta, n=n, transform=None, return_matrix=False)
 
         point = {"lkj": x}
         decimals = select_by_precision(float64=6, float32=4)
@@ -1330,7 +1331,7 @@ def test_kronecker_normal_moment(self, mu, covs, size, expected):
     )
     def test_lkjcorr_moment(self, n, eta, size, expected):
         with pm.Model() as model:
-            pm.LKJCorr("x", n=n, eta=eta, size=size)
+            pm.LKJCorr("x", n=n, eta=eta, size=size, return_matrix=False)
         assert_moment_is_expected(model, expected)
 
     @pytest.mark.parametrize(
@@ -1469,6 +1470,22 @@ def test_with_cov_rv(
 
         assert prior["mv"].shape == (10, 4, 3)
 
+    def test_with_lkjcorr_matrix(
+        self,
+    ):
+        with pm.Model() as model:
+            corr = pm.LKJCorr("corr", n=3, eta=2, return_matrix=True)
+            pm.Deterministic("corr_mat", corr)
+            mv = pm.MvNormal("mv", 0.0, cov=corr, size=4)
+            prior = pm.sample_prior_predictive(samples=10, return_inferencedata=False)
+
+        assert prior["corr_mat"].shape == (10, 3, 3)  # square
+        assert (prior["corr_mat"][:, [0, 1, 2], [0, 1, 2]] == 1.0).all()  # 1.0 on diagonal
+        assert (prior["corr_mat"] == prior["corr_mat"].transpose(0, 2, 1)).all()  # symmetric
+        assert (
+            prior["corr_mat"].max() <= 1.0 and prior["corr_mat"].min() >= -1.0
+        )  # constrained between -1 and 1
+
     def test_issue_3758(self):
         np.random.seed(42)
         ndim = 50
@@ -2137,7 +2154,7 @@ class TestOrderedMultinomial(BaseTestDistributionRandom):
 
 
 class TestLKJCorr(BaseTestDistributionRandom):
-    pymc_dist = pm.LKJCorr
+    pymc_dist = _LKJCorr
     pymc_dist_params = {"n": 3, "eta": 1.0}
     expected_rv_op_params = {"n": 3, "eta": 1.0}
 
@@ -2165,7 +2182,7 @@ def ref_rand(size, n, eta):
             return (st.beta.rvs(size=(size, shape), a=beta, b=beta) - 0.5) * 2
 
         continuous_random_tester(
-            pm.LKJCorr,
+            _LKJCorr,
             {
                 "n": Domain([2, 10, 50], edges=(None, None)),
                 "eta": Domain([1.0, 10.0, 100.0], edges=(None, None)),
@@ -2190,7 +2207,7 @@ def ref_rand(size, n, eta):
 )
 def test_LKJCorr_default_transform(shape):
     with pm.Model() as m:
-        x = pm.LKJCorr("x", n=2, eta=1, shape=shape)
+        x = pm.LKJCorr("x", n=2, eta=1, shape=shape, return_matrix=False)
     assert isinstance(m.rvs_to_transforms[x], MultivariateIntervalTransform)
     assert m.logp(sum=False)[0].type.shape == shape[:-1]