Merge cb19c97 into 7d09eed

pymc-devs · Mar 26, 2019 · 819b9ab · 819b9ab
2 parents 7d09eed + cb19c97
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diff --git a/docs/source/notebooks/AR.ipynb b/docs/source/notebooks/AR.ipynb
diff --git a/docs/source/notebooks/BEST.ipynb b/docs/source/notebooks/BEST.ipynb
diff --git a/docs/source/notebooks/Bayes_factor.ipynb b/docs/source/notebooks/Bayes_factor.ipynb
diff --git a/docs/source/notebooks/GLM-hierarchical-advi-minibatch.ipynb b/docs/source/notebooks/GLM-hierarchical-advi-minibatch.ipynb
diff --git a/docs/source/notebooks/GLM-hierarchical-binominal-model.ipynb b/docs/source/notebooks/GLM-hierarchical-binominal-model.ipynb
diff --git a/docs/source/notebooks/GLM-hierarchical.ipynb b/docs/source/notebooks/GLM-hierarchical.ipynb
diff --git a/docs/source/notebooks/GLM-linear.ipynb b/docs/source/notebooks/GLM-linear.ipynb
diff --git a/docs/source/notebooks/GLM-logistic.ipynb b/docs/source/notebooks/GLM-logistic.ipynb
diff --git a/docs/source/notebooks/GLM-model-selection.ipynb b/docs/source/notebooks/GLM-model-selection.ipynb
diff --git a/docs/source/notebooks/GLM-negative-binomial-regression.ipynb b/docs/source/notebooks/GLM-negative-binomial-regression.ipynb
diff --git a/docs/source/notebooks/GLM-poisson-regression.ipynb b/docs/source/notebooks/GLM-poisson-regression.ipynb
diff --git a/docs/source/notebooks/GLM-robust-with-outlier-detection.ipynb b/docs/source/notebooks/GLM-robust-with-outlier-detection.ipynb
diff --git a/docs/source/notebooks/GLM-robust.ipynb b/docs/source/notebooks/GLM-robust.ipynb
diff --git a/docs/source/notebooks/GLM-rolling-regression.ipynb b/docs/source/notebooks/GLM-rolling-regression.ipynb
diff --git a/docs/source/notebooks/GLM.ipynb b/docs/source/notebooks/GLM.ipynb
diff --git a/docs/source/notebooks/GP-Kron.ipynb b/docs/source/notebooks/GP-Kron.ipynb
diff --git a/docs/source/notebooks/GP-Latent.ipynb b/docs/source/notebooks/GP-Latent.ipynb
diff --git a/docs/source/notebooks/GP-Marginal.ipynb b/docs/source/notebooks/GP-Marginal.ipynb
diff --git a/docs/source/notebooks/GP-MaunaLoa.ipynb b/docs/source/notebooks/GP-MaunaLoa.ipynb
diff --git a/docs/source/notebooks/LKJ.ipynb b/docs/source/notebooks/LKJ.ipynb
diff --git a/docs/source/notebooks/PyMC3_tips_and_heuristic.ipynb b/docs/source/notebooks/PyMC3_tips_and_heuristic.ipynb
diff --git a/docs/source/notebooks/api_quickstart.ipynb b/docs/source/notebooks/api_quickstart.ipynb
diff --git a/docs/source/notebooks/bayes_param_survival_pymc3.ipynb b/docs/source/notebooks/bayes_param_survival_pymc3.ipynb
diff --git a/docs/source/notebooks/bayesian_neural_network_advi.ipynb b/docs/source/notebooks/bayesian_neural_network_advi.ipynb
@@ -101,7 +101,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 28,
    "metadata": {},
    "outputs": [
     {
@@ -221,7 +221,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 31,
    "metadata": {},
    "outputs": [
     {
@@ -299,6 +299,15 @@
     "plt.xlabel('iteration');"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 33,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "trace = approx.sample(draws=5000)"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -740,5 +749,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 2
 }
diff --git a/docs/source/notebooks/censored_data.ipynb b/docs/source/notebooks/censored_data.ipynb
diff --git a/docs/source/notebooks/cox_model.ipynb b/docs/source/notebooks/cox_model.ipynb
diff --git a/docs/source/notebooks/empirical-approx-overview.ipynb b/docs/source/notebooks/empirical-approx-overview.ipynb
diff --git a/docs/source/notebooks/getting_started.ipynb b/docs/source/notebooks/getting_started.ipynb
diff --git a/docs/source/notebooks/hierarchical_partial_pooling.ipynb b/docs/source/notebooks/hierarchical_partial_pooling.ipynb
diff --git a/docs/source/notebooks/lasso_block_update.ipynb b/docs/source/notebooks/lasso_block_update.ipynb
diff --git a/docs/source/notebooks/lda-advi-aevb.ipynb b/docs/source/notebooks/lda-advi-aevb.ipynb
diff --git a/docs/source/notebooks/live_sample_plots.ipynb b/docs/source/notebooks/live_sample_plots.ipynb
diff --git a/docs/source/notebooks/marginalized_gaussian_mixture_model.ipynb b/docs/source/notebooks/marginalized_gaussian_mixture_model.ipynb
diff --git a/docs/source/notebooks/multilevel_modeling.ipynb b/docs/source/notebooks/multilevel_modeling.ipynb
diff --git a/docs/source/notebooks/profiling.ipynb b/docs/source/notebooks/profiling.ipynb
diff --git a/docs/source/notebooks/rugby_analytics.ipynb b/docs/source/notebooks/rugby_analytics.ipynb
diff --git a/docs/source/notebooks/sampler-stats.ipynb b/docs/source/notebooks/sampler-stats.ipynb
diff --git a/docs/source/notebooks/sampling_compound_step.ipynb b/docs/source/notebooks/sampling_compound_step.ipynb
@@ -81,17 +81,12 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "Multiprocess sampling (4 chains in 4 jobs)\n",
+      "Multiprocess sampling (2 chains in 2 jobs)\n",
       "CompoundStep\n",
       ">NUTS: [p]\n",
       ">BinaryGibbsMetropolis: [ni]\n",
-      "100%|██████████| 1000/1000 [00:01<00:00, 657.44it/s]\n",
-      "INFO (theano.gof.compilelock): Waiting for existing lock by process '85686' (I am process '85687')\n",
-      "INFO (theano.gof.compilelock): To manually release the lock, delete /Users/yuanhuang/.theano/compiledir_Darwin-17.7.0-x86_64-i386-64bit-i386-3.6.5-64/lock_dir\n",
-      "INFO (theano.gof.compilelock): Waiting for existing lock by process '85686' (I am process '85688')\n",
-      "INFO (theano.gof.compilelock): To manually release the lock, delete /Users/yuanhuang/.theano/compiledir_Darwin-17.7.0-x86_64-i386-64bit-i386-3.6.5-64/lock_dir\n",
-      "INFO (theano.gof.compilelock): Waiting for existing lock by process '85687' (I am process '85688')\n",
-      "INFO (theano.gof.compilelock): To manually release the lock, delete /Users/yuanhuang/.theano/compiledir_Darwin-17.7.0-x86_64-i386-64bit-i386-3.6.5-64/lock_dir\n"
+      "Sampling 2 chains: 100%|██████████| 2000/2000 [00:00<00:00, 2525.10draws/s]\n",
+      "The number of effective samples is smaller than 25% for some parameters.\n"
      ]
     }
    ],
@@ -220,8 +215,8 @@
     {
      "data": {
       "text/plain": [
-       "({'p_logodds__': array(-0.8881149), 'ni': array(0)},\n",
-       " [{'tune': True, 'accept': 0.7725535007903375}])"
+       "({'p_logodds__': array(-0.24076114), 'ni': array(0)},\n",
+       " [{'tune': True, 'accept': 1.1665159025220422}])"
       ]
      },
      "execution_count": 6,
@@ -256,7 +251,7 @@
     {
      "data": {
       "text/plain": [
-       "{'p_logodds__': array(-0.8881149), 'ni': array(1)}"
+       "{'p_logodds__': array(-0.24076114), 'ni': array(0)}"
       ]
      },
      "execution_count": 7,
@@ -291,8 +286,8 @@
     {
      "data": {
       "text/plain": [
-       "[<pymc3.step_methods.metropolis.Metropolis at 0x10bfadba8>,\n",
-       " <pymc3.step_methods.metropolis.BinaryGibbsMetropolis at 0x10d6442b0>]"
+       "[<pymc3.step_methods.metropolis.Metropolis at 0x7f02ff31e898>,\n",
+       " <pymc3.step_methods.metropolis.BinaryGibbsMetropolis at 0x7f02dba28860>]"
       ]
      },
      "execution_count": 8,
@@ -333,8 +328,8 @@
     {
      "data": {
       "text/plain": [
-       "[<pymc3.step_methods.metropolis.BinaryGibbsMetropolis at 0x10d6442b0>,\n",
-       " <pymc3.step_methods.metropolis.Metropolis at 0x10bfadba8>]"
+       "[<pymc3.step_methods.metropolis.BinaryGibbsMetropolis at 0x7f02dba28860>,\n",
+       " <pymc3.step_methods.metropolis.Metropolis at 0x7f02ff31e898>]"
       ]
      },
      "execution_count": 9,
@@ -374,9 +369,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "PyMC3",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "env_pymc3"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -388,7 +383,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.5"
+   "version": "3.6.7"
   },
   "latex_envs": {
    "LaTeX_envs_menu_present": true,

diff --git a/docs/source/notebooks/stochastic_volatility.ipynb b/docs/source/notebooks/stochastic_volatility.ipynb
diff --git a/docs/source/notebooks/variational_api_quickstart.ipynb b/docs/source/notebooks/variational_api_quickstart.ipynb
diff --git a/docs/source/notebooks/weibull_aft.ipynb b/docs/source/notebooks/weibull_aft.ipynb