def test_simple_poisson_map(): y, exog_fe, exog_vc, ident = gen_simple_poisson(10, 10, 0.2) exog_vc = sparse.csr_matrix(exog_vc) glmm1 = PoissonBayesMixedGLM(y, exog_fe, exog_vc, ident, vcp_p=0.5) rslt1 = glmm1.fit_map() assert_allclose(glmm1.logposterior_grad(rslt1.params), np.zeros_like(rslt1.params), atol=1e-3) # This should give the same answer as above glmm2 = PoissonBayesMixedGLM(y, exog_fe, exog_vc, ident, vcp_p=0.5) rslt2 = glmm2.fit_map() assert_allclose(rslt1.params, rslt2.params, atol=1e-4) # Test the predict method for linear in False, True: for exog in None, exog_fe: pr1 = rslt1.predict(linear=linear, exog=exog) pr2 = rslt2.predict(linear=linear, exog=exog) pr3 = glmm1.predict(rslt1.params, linear=linear, exog=exog) pr4 = glmm2.predict(rslt2.params, linear=linear, exog=exog) assert_allclose(pr1, pr2, rtol=1e-5) assert_allclose(pr2, pr3, rtol=1e-5) assert_allclose(pr3, pr4, rtol=1e-5) if not linear: assert_equal(pr1.min() >= 0, True) assert_equal(pr2.min() >= 0, True) assert_equal(pr3.min() >= 0, True)
def test_simple_poisson_map(): y, exog_fe, exog_vc, ident = gen_simple_poisson(10, 10, 0.2) exog_vc = sparse.csr_matrix(exog_vc) glmm1 = PoissonBayesMixedGLM(y, exog_fe, exog_vc, ident, vcp_p=0.5) rslt1 = glmm1.fit_map() assert_allclose(glmm1.logposterior_grad(rslt1.params), np.zeros_like(rslt1.params), atol=1e-3) # This should give the same answer as above glmm2 = PoissonBayesMixedGLM(y, exog_fe, exog_vc, ident, vcp_p=0.5) rslt2 = glmm2.fit_map() assert_allclose(rslt1.params, rslt2.params, atol=1e-4)
def test_simple_poisson_vb(): y, exog_fe, exog_vc, ident = gen_simple_poisson(10, 10, 1) exog_vc = sparse.csr_matrix(exog_vc) glmm1 = PoissonBayesMixedGLM(y, exog_fe, exog_vc, ident, vcp_p=0.5) rslt1 = glmm1.fit_map() glmm2 = PoissonBayesMixedGLM(y, exog_fe, exog_vc, ident, vcp_p=0.5) rslt2 = glmm2.fit_vb(rslt1.params) rslt1.summary() rslt2.summary() assert_allclose(rslt1.params[0:5], np.r_[ -0.07233493, -0.06706505, -0.47159649, 1.12575122, -1.02442201], rtol=1e-4, atol=1e-4) assert_allclose(rslt1.cov_params.flat[0:5], np.r_[ 0.00790914, 0.00080666, -0.00050719, 0.00022648, 0.00046235], rtol=1e-4, atol=1e-4) assert_allclose(rslt2.params[0:5], np.r_[ -0.07088814, -0.06373107, -0.22770786, 1.12923746, -1.26161339], rtol=1e-4, atol=1e-4) assert_allclose(rslt2.cov_params[0:5], np.r_[ 0.00747782, 0.0092554, 0.04508904, 0.02934488, 0.20312746], rtol=1e-4, atol=1e-4)
def test_simple_poisson_vb(): y, exog_fe, exog_vc, ident = gen_simple_poisson(10, 10, 1) exog_vc = sparse.csr_matrix(exog_vc) glmm1 = PoissonBayesMixedGLM(y, exog_fe, exog_vc, ident, vcp_p=0.5) rslt1 = glmm1.fit_map() glmm2 = PoissonBayesMixedGLM(y, exog_fe, exog_vc, ident, vcp_p=0.5) rslt2 = glmm2.fit_vb(rslt1.params) rslt1.summary() rslt2.summary() assert_allclose(rslt1.params[0:5], np.r_[ -0.07233493, -0.06706505, -0.47159649, 1.12575122, -1.02442201], rtol=1e-4, atol=1e-4) assert_allclose(rslt1.cov_params.flat[0:5], np.r_[ 0.00790914, 0.00080666, -0.00050719, 0.00022648, 0.00046235], rtol=1e-4, atol=1e-4) assert_allclose(rslt2.params[0:5], np.r_[ -0.07088814, -0.06373107, -0.22770786, 1.12923746, -1.26161339], rtol=1e-4, atol=1e-4) assert_allclose(rslt2.cov_params[0:5], np.r_[ 0.00747782, 0.0092554, 0.04508904, 0.02934488, 0.20312746], rtol=1e-4, atol=1e-4)
def test_simple_poisson_map(): y, exog_fe, exog_vc, ident = gen_simple_poisson(10, 10, 0.2) exog_vc = sparse.csr_matrix(exog_vc) glmm1 = PoissonBayesMixedGLM(y, exog_fe, exog_vc, ident, vcp_p=0.5) rslt1 = glmm1.fit_map() assert_allclose(glmm1.logposterior_grad(rslt1.params), np.zeros_like(rslt1.params), atol=1e-3) # This should give the same answer as above glmm2 = PoissonBayesMixedGLM(y, exog_fe, exog_vc, ident, vcp_p=0.5) rslt2 = glmm2.fit_map() assert_allclose(rslt1.params, rslt2.params, atol=1e-4)
def test_crossed_poisson_map(): y, exog_fe, exog_vc, ident = gen_crossed_poisson(10, 10, 1, 1) exog_vc = sparse.csr_matrix(exog_vc) glmm = PoissonBayesMixedGLM(y, exog_fe, exog_vc, ident, vcp_p=0.5) rslt = glmm.fit_map() assert_allclose(glmm.logposterior_grad(rslt.params), np.zeros_like(rslt.params), atol=1e-4)
def test_crossed_poisson_map(): y, exog_fe, exog_vc, ident = gen_crossed_poisson(10, 10, 1, 1) exog_vc = sparse.csr_matrix(exog_vc) glmm = PoissonBayesMixedGLM(y, exog_fe, exog_vc, ident, vcp_p=0.5) rslt = glmm.fit_map() assert_allclose(glmm.logposterior_grad(rslt.params), np.zeros_like(rslt.params), atol=1e-4)
def test_simple_poisson_map(): y, exog_fe, exog_vc, ident = gen_simple_poisson(10, 10, 0.2) exog_vc = sparse.csr_matrix(exog_vc) glmm1 = PoissonBayesMixedGLM(y, exog_fe, exog_vc, ident, vcp_p=0.5) rslt1 = glmm1.fit_map() assert_allclose( glmm1.logposterior_grad(rslt1.params), np.zeros_like(rslt1.params), atol=1e-3) # This should give the same answer as above glmm2 = PoissonBayesMixedGLM(y, exog_fe, exog_vc, ident, vcp_p=0.5) rslt2 = glmm2.fit_map() assert_allclose(rslt1.params, rslt2.params, atol=1e-4) # Test the predict method for linear in False, True: for exog in None, exog_fe: pr1 = rslt1.predict(linear=linear, exog=exog) pr2 = rslt2.predict(linear=linear, exog=exog) pr3 = glmm1.predict(rslt1.params, linear=linear, exog=exog) pr4 = glmm2.predict(rslt2.params, linear=linear, exog=exog) assert_allclose(pr1, pr2, rtol=1e-5) assert_allclose(pr2, pr3, rtol=1e-5) assert_allclose(pr3, pr4, rtol=1e-5) if not linear: assert_equal(pr1.min() >= 0, True) assert_equal(pr2.min() >= 0, True) assert_equal(pr3.min() >= 0, True) # Check dimensions and PSD status of cov_params for rslt in rslt1, rslt2: cp = rslt.cov_params() p = len(rslt.params) assert_equal(cp.shape, np.r_[p, p]) np.linalg.cholesky(cp)
def test_simple_poisson_map(): y, exog_fe, exog_vc, ident = gen_simple_poisson(10, 10, 0.2) exog_vc = sparse.csr_matrix(exog_vc) glmm1 = PoissonBayesMixedGLM(y, exog_fe, exog_vc, ident, vcp_p=0.5) rslt1 = glmm1.fit_map() assert_allclose( glmm1.logposterior_grad(rslt1.params), np.zeros_like(rslt1.params), atol=1e-3) # This should give the same answer as above glmm2 = PoissonBayesMixedGLM(y, exog_fe, exog_vc, ident, vcp_p=0.5) rslt2 = glmm2.fit_map() assert_allclose(rslt1.params, rslt2.params, atol=1e-4) # Test the predict method for linear in False, True: for exog in None, exog_fe: pr1 = rslt1.predict(linear=linear, exog=exog) pr2 = rslt2.predict(linear=linear, exog=exog) pr3 = glmm1.predict(rslt1.params, linear=linear, exog=exog) pr4 = glmm2.predict(rslt2.params, linear=linear, exog=exog) assert_allclose(pr1, pr2, rtol=1e-5) assert_allclose(pr2, pr3, rtol=1e-5) assert_allclose(pr3, pr4, rtol=1e-5) if not linear: assert_equal(pr1.min() >= 0, True) assert_equal(pr2.min() >= 0, True) assert_equal(pr3.min() >= 0, True) # Check dimensions and PSD status of cov_params for rslt in rslt1, rslt2: cp = rslt.cov_params() p = len(rslt.params) assert_equal(cp.shape, np.r_[p, p]) np.linalg.cholesky(cp)
def test_simple_poisson_vb(): y, exog_fe, exog_vc, ident = gen_simple_poisson(10, 10, 1) exog_vc = sparse.csr_matrix(exog_vc) glmm1 = PoissonBayesMixedGLM(y, exog_fe, exog_vc, ident, vcp_p=0.5) rslt1 = glmm1.fit_map() glmm2 = PoissonBayesMixedGLM(y, exog_fe, exog_vc, ident, vcp_p=0.5) rslt2 = glmm2.fit_vb(rslt1.params) rslt1.summary() rslt2.summary() assert_allclose( rslt1.params[0:5], np.r_[-0.07233493, -0.06706505, -0.47159649, 1.12575122, -1.02442201], rtol=1e-4, atol=1e-4) assert_allclose( rslt1.cov_params().flat[0:5], np.r_[0.00790914, 0.00080666, -0.00050719, 0.00022648, 0.00046235], rtol=1e-4, atol=1e-4) assert_allclose( rslt2.params[0:5], np.r_[-0.07088814, -0.06373107, -0.22770786, 1.12923746, -1.26161339], rtol=1e-4, atol=1e-4) assert_allclose( rslt2.cov_params()[0:5], np.r_[0.00747782, 0.0092554, 0.04508904, 0.02934488, 0.20312746], rtol=1e-4, atol=1e-4) for rslt in rslt1, rslt2: cp = rslt.cov_params() p = len(rslt.params) if rslt is rslt1: assert_equal(cp.shape, np.r_[p, p]) np.linalg.cholesky(cp) else: assert_equal(cp.shape, np.r_[p,]) assert_equal(cp > 0, True*np.ones(p))
def test_simple_poisson_vb(): y, exog_fe, exog_vc, ident = gen_simple_poisson(10, 10, 1) exog_vc = sparse.csr_matrix(exog_vc) glmm1 = PoissonBayesMixedGLM(y, exog_fe, exog_vc, ident, vcp_p=0.5) rslt1 = glmm1.fit_map() glmm2 = PoissonBayesMixedGLM(y, exog_fe, exog_vc, ident, vcp_p=0.5) rslt2 = glmm2.fit_vb(rslt1.params) rslt1.summary() rslt2.summary() assert_allclose(rslt1.params[0:5], np.r_[-0.07233493, -0.06706505, -0.47159649, 1.12575122, -1.02442201], rtol=1e-4, atol=1e-4) assert_allclose(rslt1.cov_params().flat[0:5], np.r_[0.00790914, 0.00080666, -0.00050719, 0.00022648, 0.00046235], rtol=1e-4, atol=1e-4) assert_allclose(rslt2.params[0:5], np.r_[-0.07088814, -0.06373107, -0.22770786, 1.12923746, -1.26161339], rtol=1e-4, atol=1e-4) assert_allclose(rslt2.cov_params()[0:5], np.r_[0.00747782, 0.0092554, 0.04508904, 0.02934488, 0.20312746], rtol=1e-4, atol=1e-4) for rslt in rslt1, rslt2: cp = rslt.cov_params() p = len(rslt.params) if rslt is rslt1: assert_equal(cp.shape, np.r_[p, p]) np.linalg.cholesky(cp) else: assert_equal(cp.shape, np.r_[p, ]) assert_equal(cp > 0, True * np.ones(p))
def test_poisson_formula(): y, exog_fe, exog_vc, ident = gen_crossed_poisson(10, 10, 1, 0.5) for vb in False, True: glmm1 = PoissonBayesMixedGLM( y, exog_fe, exog_vc, ident) if vb: rslt1 = glmm1.fit_vb() else: rslt1 = glmm1.fit_map() # Build categorical variables that match exog_vc df = pd.DataFrame({"y": y, "x1": exog_fe[:, 0]}) z1 = np.zeros(len(y)) for j,k in enumerate(np.flatnonzero(ident == 0)): z1[exog_vc[:, k] == 1] = j df["z1"] = z1 z2 = np.zeros(len(y)) for j,k in enumerate(np.flatnonzero(ident == 1)): z2[exog_vc[:, k] == 1] = j df["z2"] = z2 fml = "y ~ 0 + x1" from collections import OrderedDict vc_fml = OrderedDict({}) vc_fml["z1"] = "0 + C(z1)" vc_fml["z2"] = "0 + C(z2)" glmm2 = PoissonBayesMixedGLM.from_formula(fml, vc_fml, df) if vb: rslt2 = glmm2.fit_vb() else: rslt2 = glmm2.fit_map() assert_allclose(rslt1.params, rslt2.params, rtol=1e-5) for rslt in rslt1, rslt2: cp = rslt.cov_params() p = len(rslt.params) if vb: assert_equal(cp.shape, np.r_[p,]) assert_equal(cp > 0, True*np.ones(p)) else: assert_equal(cp.shape, np.r_[p, p]) np.linalg.cholesky(cp)
def test_crossed_poisson_map(): y, exog_fe, exog_vc, ident = gen_crossed_poisson(10, 10, 1, 1) exog_vc = sparse.csr_matrix(exog_vc) glmm = PoissonBayesMixedGLM(y, exog_fe, exog_vc, ident, vcp_p=0.5) rslt = glmm.fit_map() assert_allclose(glmm.logposterior_grad(rslt.params), np.zeros_like(rslt.params), atol=1e-4) # Check dimensions and PSD status of cov_params cp = rslt.cov_params() p = len(rslt.params) assert_equal(cp.shape, np.r_[p, p]) np.linalg.cholesky(cp)
def test_poisson_formula(): y, exog_fe, exog_vc, ident = gen_crossed_poisson(10, 10, 1, 0.5) for vb in False, True: glmm1 = PoissonBayesMixedGLM( y, exog_fe, exog_vc, ident) if vb: rslt1 = glmm1.fit_vb() else: rslt1 = glmm1.fit_map() # Build categorical variables that match exog_vc df = pd.DataFrame({"y": y, "x1": exog_fe[:, 0]}) z1 = np.zeros(len(y)) for j,k in enumerate(np.flatnonzero(ident == 0)): z1[exog_vc[:, k] == 1] = j df["z1"] = z1 z2 = np.zeros(len(y)) for j,k in enumerate(np.flatnonzero(ident == 1)): z2[exog_vc[:, k] == 1] = j df["z2"] = z2 fml = "y ~ 0 + x1" vc_fml = {} vc_fml["z1"] = "0 + C(z1)" vc_fml["z2"] = "0 + C(z2)" glmm2 = PoissonBayesMixedGLM.from_formula(fml, vc_fml, df) if vb: rslt2 = glmm2.fit_vb() else: rslt2 = glmm2.fit_map() assert_allclose(rslt1.params, rslt2.params, rtol=1e-5) for rslt in rslt1, rslt2: cp = rslt.cov_params() p = len(rslt.params) if vb: assert_equal(cp.shape, np.r_[p,]) assert_equal(cp > 0, True*np.ones(p)) else: assert_equal(cp.shape, np.r_[p, p]) np.linalg.cholesky(cp)
def test_crossed_poisson_map(): y, exog_fe, exog_vc, ident = gen_crossed_poisson(10, 10, 1, 1) exog_vc = sparse.csr_matrix(exog_vc) glmm = PoissonBayesMixedGLM(y, exog_fe, exog_vc, ident, vcp_p=0.5) rslt = glmm.fit_map() assert_allclose( glmm.logposterior_grad(rslt.params), np.zeros_like(rslt.params), atol=1e-4) # Check dimensions and PSD status of cov_params cp = rslt.cov_params() p = len(rslt.params) assert_equal(cp.shape, np.r_[p, p]) np.linalg.cholesky(cp)
def test_crossed_poisson_vb(): y, exog_fe, exog_vc, ident = gen_crossed_poisson(10, 10, 1, 0.5) glmm1 = PoissonBayesMixedGLM(y, exog_fe, exog_vc, ident, vcp_p=0.5, fe_p=0.5) rslt1 = glmm1.fit_map() glmm2 = PoissonBayesMixedGLM(y, exog_fe, exog_vc, ident, vcp_p=0.5, fe_p=0.5) rslt2 = glmm2.fit_vb(mean=rslt1.params) rslt1.summary() rslt2.summary() assert_allclose(rslt1.params[0:5], np.r_[-0.54855281, 0.10458834, -0.68777741, -0.01699925, 0.77200546], rtol=1e-4, atol=1e-4) assert_allclose(rslt2.params[0:5], np.r_[-0.54691502, 0.22297158, -0.52673802, -0.06218684, 0.74385237], rtol=1e-4, atol=1e-4) for rslt in rslt1, rslt2: cp = rslt.cov_params() p = len(rslt.params) if rslt is rslt1: assert_equal(cp.shape, np.r_[p, p]) np.linalg.cholesky(cp) else: assert_equal(cp.shape, np.r_[p, ]) assert_equal(cp > 0, True * np.ones(p))
def test_crossed_poisson_vb(): y, exog_fe, exog_vc, ident = gen_crossed_poisson(10, 10, 1, 0.5) glmm1 = PoissonBayesMixedGLM(y, exog_fe, exog_vc, ident, vcp_p=0.5, fe_p=0.5) rslt1 = glmm1.fit_map() glmm2 = PoissonBayesMixedGLM(y, exog_fe, exog_vc, ident, vcp_p=0.5, fe_p=0.5) rslt2 = glmm2.fit_vb(mean=rslt1.params) rslt1.summary() rslt2.summary() assert_allclose(rslt1.params[0:5], np.r_[ -0.54855281, 0.10458834, -0.68777741, -0.01699925, 0.77200546], rtol=1e-4, atol=1e-4) assert_allclose(rslt2.params[0:5], np.r_[ -0.54691502, 0.22297158, -0.52673802, -0.06218684, 0.74385237], rtol=1e-4, atol=1e-4)
def test_crossed_poisson_vb(): y, exog_fe, exog_vc, ident = gen_crossed_poisson(10, 10, 1, 0.5) glmm1 = PoissonBayesMixedGLM( y, exog_fe, exog_vc, ident, vcp_p=0.5, fe_p=0.5) rslt1 = glmm1.fit_map() glmm2 = PoissonBayesMixedGLM( y, exog_fe, exog_vc, ident, vcp_p=0.5, fe_p=0.5) rslt2 = glmm2.fit_vb(mean=rslt1.params) rslt1.summary() rslt2.summary() assert_allclose( rslt1.params[0:5], np.r_[-0.54855281, 0.10458834, -0.68777741, -0.01699925, 0.77200546], rtol=1e-4, atol=1e-4) assert_allclose( rslt2.params[0:5], np.r_[-0.54691502, 0.22297158, -0.52673802, -0.06218684, 0.74385237], rtol=1e-4, atol=1e-4) for rslt in rslt1, rslt2: cp = rslt.cov_params() p = len(rslt.params) if rslt is rslt1: assert_equal(cp.shape, np.r_[p, p]) np.linalg.cholesky(cp) else: assert_equal(cp.shape, np.r_[p,]) assert_equal(cp > 0, True*np.ones(p))