update notebooks [skip ci]

hammerlab · Jan 10, 2019 · 41f6502 · 41f6502
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diff --git a/example-notebooks/Test new_gamma_survival_model with simulated data.ipynb b/example-notebooks/Test new_gamma_survival_model with simulated data.ipynb
@@ -53,7 +53,13 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "INFO:stancache.stancache:sim_data_exp_correlated: cache_filename set to sim_data_exp_correlated.cached.N_100.censor_time_20.rate_coefs_54462717316.rate_form_1 + sex.pkl\n",
+      "INFO:stancache.stancache:sim_data_exp_correlated: cache_filename set to sim_data_exp_correlated.cached.N_100.censor_time_20.rate_coefs_54462717316.rate_form_1 + sex.pkl\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
       "INFO:stancache.stancache:sim_data_exp_correlated: Loading result from cache\n"
      ]
     }
@@ -226,7 +232,7 @@
     {
      "data": {
       "text/plain": [
-       "<matplotlib.legend.Legend at 0x7f69382fa2e8>"
+       "<matplotlib.legend.Legend at 0x7f430cb73828>"
       ]
      },
      "execution_count": 4,
@@ -347,31 +353,42 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/home/jacki/projects/survivalstan/survivalstan/formulas.py:96: UserWarning: Pandas doesn't allow columns to be created via a new attribute name - see https://pandas.pydata.org/pandas-docs/stable/indexing.html#attribute-access\n",
-      "  self.stan_data = stan_data\n",
-      "/home/jacki/projects/survivalstan/survivalstan/formulas.py:97: UserWarning: Pandas doesn't allow columns to be created via a new attribute name - see https://pandas.pydata.org/pandas-docs/stable/indexing.html#attribute-access\n",
-      "  self.meta_data = meta_data\n",
-      "/home/jacki/projects/survivalstan/survivalstan/formulas.py:96: UserWarning: Pandas doesn't allow columns to be created via a new attribute name - see https://pandas.pydata.org/pandas-docs/stable/indexing.html#attribute-access\n",
-      "  self.stan_data = stan_data\n",
-      "/home/jacki/projects/survivalstan/survivalstan/formulas.py:97: UserWarning: Pandas doesn't allow columns to be created via a new attribute name - see https://pandas.pydata.org/pandas-docs/stable/indexing.html#attribute-access\n",
-      "  self.meta_data = meta_data\n",
-      "/home/jacki/projects/survivalstan/survivalstan/survivalstan.py:368: FutureWarning: Method .as_matrix will be removed in a future version. Use .values instead.\n",
-      "  'x': self.x_df.as_matrix(),\n",
-      "INFO:stancache.stancache:Step 1: Get compiled model code, possibly from cache\n",
-      "INFO:stancache.stancache:StanModel: cache_filename set to anon_model.cython_0_29_2.model_code_14429915565770599621.pystan_2_18_1_0.stanmodel.pkl\n",
-      "INFO:stancache.stancache:StanModel: Starting execution\n",
-      "INFO:pystan:COMPILING THE C++ CODE FOR MODEL anon_model_f418131a20ef101bf99f9c02185578f1 NOW.\n",
-      "INFO:stancache.stancache:StanModel: Execution completed (0:01:43.433295 elapsed)\n",
-      "INFO:stancache.stancache:StanModel: Saving results to cache\n",
-      "INFO:stancache.stancache:Step 2: Get posterior draws from model, possibly from cache\n",
-      "INFO:stancache.stancache:sampling: cache_filename set to anon_model.cython_0_29_2.model_code_14429915565770599621.pystan_2_18_1_0.stanfit.chains_4.data_36753546383.iter_5000.seed_9001.pkl\n",
-      "INFO:stancache.stancache:sampling: Starting execution\n",
-      "INFO:stancache.stancache:sampling: Execution completed (0:01:33.270480 elapsed)\n",
-      "INFO:stancache.stancache:sampling: Saving results to cache\n",
-      "/srv/conda/lib/python3.6/site-packages/stancache/stancache.py:285: UserWarning: Pickling fit objects is an experimental feature!\n",
-      "The relevant StanModel instance must be pickled along with this fit object.\n",
-      "When unpickling the StanModel must be unpickled first.\n",
-      "  pickle.dump(res, open(cache_filepath, 'wb'), pickle.HIGHEST_PROTOCOL)\n"
+      "INFO:stancache.stancache:Step 1: Get compiled model code, possibly from cache\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "INFO:stancache.stancache:StanModel: cache_filename set to anon_model.cython_0_29_2.model_code_14429915565770599621.pystan_2_18_1_0.stanmodel.pkl\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "INFO:stancache.stancache:StanModel: Loading result from cache\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "INFO:stancache.stancache:Step 2: Get posterior draws from model, possibly from cache\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "INFO:stancache.stancache:sampling: cache_filename set to anon_model.cython_0_29_2.model_code_14429915565770599621.pystan_2_18_1_0.stanfit.chains_4.data_36753546383.iter_5000.seed_9001.pkl\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "INFO:stancache.stancache:sampling: Loading result from cache\n"
      ]
     }
    ],
@@ -486,31 +503,42 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/home/jacki/projects/survivalstan/survivalstan/formulas.py:96: UserWarning: Pandas doesn't allow columns to be created via a new attribute name - see https://pandas.pydata.org/pandas-docs/stable/indexing.html#attribute-access\n",
-      "  self.stan_data = stan_data\n",
-      "/home/jacki/projects/survivalstan/survivalstan/formulas.py:97: UserWarning: Pandas doesn't allow columns to be created via a new attribute name - see https://pandas.pydata.org/pandas-docs/stable/indexing.html#attribute-access\n",
-      "  self.meta_data = meta_data\n",
-      "/home/jacki/projects/survivalstan/survivalstan/formulas.py:96: UserWarning: Pandas doesn't allow columns to be created via a new attribute name - see https://pandas.pydata.org/pandas-docs/stable/indexing.html#attribute-access\n",
-      "  self.stan_data = stan_data\n",
-      "/home/jacki/projects/survivalstan/survivalstan/formulas.py:97: UserWarning: Pandas doesn't allow columns to be created via a new attribute name - see https://pandas.pydata.org/pandas-docs/stable/indexing.html#attribute-access\n",
-      "  self.meta_data = meta_data\n",
-      "/home/jacki/projects/survivalstan/survivalstan/survivalstan.py:368: FutureWarning: Method .as_matrix will be removed in a future version. Use .values instead.\n",
-      "  'x': self.x_df.as_matrix(),\n",
-      "INFO:stancache.stancache:Step 1: Get compiled model code, possibly from cache\n",
-      "INFO:stancache.stancache:StanModel: cache_filename set to anon_model.cython_0_29_2.model_code_9177012762674257483.pystan_2_18_1_0.stanmodel.pkl\n",
-      "INFO:stancache.stancache:StanModel: Starting execution\n",
-      "INFO:pystan:COMPILING THE C++ CODE FOR MODEL anon_model_8758b4bc02931efdf69b3e349afdba01 NOW.\n",
-      "INFO:stancache.stancache:StanModel: Execution completed (0:01:29.291961 elapsed)\n",
-      "INFO:stancache.stancache:StanModel: Saving results to cache\n",
-      "INFO:stancache.stancache:Step 2: Get posterior draws from model, possibly from cache\n",
-      "INFO:stancache.stancache:sampling: cache_filename set to anon_model.cython_0_29_2.model_code_9177012762674257483.pystan_2_18_1_0.stanfit.chains_4.data_36753546383.iter_5000.seed_9001.pkl\n",
-      "INFO:stancache.stancache:sampling: Starting execution\n",
-      "INFO:stancache.stancache:sampling: Execution completed (0:01:20.742172 elapsed)\n",
-      "INFO:stancache.stancache:sampling: Saving results to cache\n",
-      "/srv/conda/lib/python3.6/site-packages/stancache/stancache.py:285: UserWarning: Pickling fit objects is an experimental feature!\n",
-      "The relevant StanModel instance must be pickled along with this fit object.\n",
-      "When unpickling the StanModel must be unpickled first.\n",
-      "  pickle.dump(res, open(cache_filepath, 'wb'), pickle.HIGHEST_PROTOCOL)\n"
+      "INFO:stancache.stancache:Step 1: Get compiled model code, possibly from cache\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "INFO:stancache.stancache:StanModel: cache_filename set to anon_model.cython_0_29_2.model_code_9177012762674257483.pystan_2_18_1_0.stanmodel.pkl\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "INFO:stancache.stancache:StanModel: Loading result from cache\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "INFO:stancache.stancache:Step 2: Get posterior draws from model, possibly from cache\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "INFO:stancache.stancache:sampling: cache_filename set to anon_model.cython_0_29_2.model_code_9177012762674257483.pystan_2_18_1_0.stanfit.chains_4.data_36753546383.iter_5000.seed_9001.pkl\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "INFO:stancache.stancache:sampling: Loading result from cache\n"
      ]
     }
    ],
@@ -532,7 +560,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 11,
    "metadata": {
     "collapsed": true,
     "jupyter": {
@@ -627,29 +655,42 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/home/jacki/projects/survivalstan/survivalstan/formulas.py:96: UserWarning: Pandas doesn't allow columns to be created via a new attribute name - see https://pandas.pydata.org/pandas-docs/stable/indexing.html#attribute-access\n",
-      "  self.stan_data = stan_data\n",
-      "/home/jacki/projects/survivalstan/survivalstan/formulas.py:97: UserWarning: Pandas doesn't allow columns to be created via a new attribute name - see https://pandas.pydata.org/pandas-docs/stable/indexing.html#attribute-access\n",
-      "  self.meta_data = meta_data\n",
-      "/home/jacki/projects/survivalstan/survivalstan/formulas.py:96: UserWarning: Pandas doesn't allow columns to be created via a new attribute name - see https://pandas.pydata.org/pandas-docs/stable/indexing.html#attribute-access\n",
-      "  self.stan_data = stan_data\n",
-      "/home/jacki/projects/survivalstan/survivalstan/formulas.py:97: UserWarning: Pandas doesn't allow columns to be created via a new attribute name - see https://pandas.pydata.org/pandas-docs/stable/indexing.html#attribute-access\n",
-      "  self.meta_data = meta_data\n",
-      "INFO:stancache.stancache:Step 1: Get compiled model code, possibly from cache\n",
-      "INFO:stancache.stancache:StanModel: cache_filename set to anon_model.cython_0_29_2.model_code_1293841621968646714.pystan_2_18_1_0.stanmodel.pkl\n",
-      "INFO:stancache.stancache:StanModel: Starting execution\n",
-      "INFO:pystan:COMPILING THE C++ CODE FOR MODEL anon_model_050903aecc782294461f27307e7596e0 NOW.\n",
-      "INFO:stancache.stancache:StanModel: Execution completed (0:01:42.204878 elapsed)\n",
-      "INFO:stancache.stancache:StanModel: Saving results to cache\n",
-      "INFO:stancache.stancache:Step 2: Get posterior draws from model, possibly from cache\n",
-      "INFO:stancache.stancache:sampling: cache_filename set to anon_model.cython_0_29_2.model_code_1293841621968646714.pystan_2_18_1_0.stanfit.chains_4.data_36753546383.iter_5000.seed_9001.pkl\n",
-      "INFO:stancache.stancache:sampling: Starting execution\n",
-      "INFO:stancache.stancache:sampling: Execution completed (0:00:42.036498 elapsed)\n",
-      "INFO:stancache.stancache:sampling: Saving results to cache\n",
-      "/srv/conda/lib/python3.6/site-packages/stancache/stancache.py:285: UserWarning: Pickling fit objects is an experimental feature!\n",
-      "The relevant StanModel instance must be pickled along with this fit object.\n",
-      "When unpickling the StanModel must be unpickled first.\n",
-      "  pickle.dump(res, open(cache_filepath, 'wb'), pickle.HIGHEST_PROTOCOL)\n"
+      "INFO:stancache.stancache:Step 1: Get compiled model code, possibly from cache\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "INFO:stancache.stancache:StanModel: cache_filename set to anon_model.cython_0_29_2.model_code_1293841621968646714.pystan_2_18_1_0.stanmodel.pkl\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "INFO:stancache.stancache:StanModel: Loading result from cache\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "INFO:stancache.stancache:Step 2: Get posterior draws from model, possibly from cache\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "INFO:stancache.stancache:sampling: cache_filename set to anon_model.cython_0_29_2.model_code_1293841621968646714.pystan_2_18_1_0.stanfit.chains_4.data_36753546383.iter_5000.seed_9001.pkl\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "INFO:stancache.stancache:sampling: Loading result from cache\n"
      ]
     }
    ],
@@ -791,29 +832,42 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/home/jacki/projects/survivalstan/survivalstan/formulas.py:96: UserWarning: Pandas doesn't allow columns to be created via a new attribute name - see https://pandas.pydata.org/pandas-docs/stable/indexing.html#attribute-access\n",
-      "  self.stan_data = stan_data\n",
-      "/home/jacki/projects/survivalstan/survivalstan/formulas.py:97: UserWarning: Pandas doesn't allow columns to be created via a new attribute name - see https://pandas.pydata.org/pandas-docs/stable/indexing.html#attribute-access\n",
-      "  self.meta_data = meta_data\n",
-      "/home/jacki/projects/survivalstan/survivalstan/formulas.py:96: UserWarning: Pandas doesn't allow columns to be created via a new attribute name - see https://pandas.pydata.org/pandas-docs/stable/indexing.html#attribute-access\n",
-      "  self.stan_data = stan_data\n",
-      "/home/jacki/projects/survivalstan/survivalstan/formulas.py:97: UserWarning: Pandas doesn't allow columns to be created via a new attribute name - see https://pandas.pydata.org/pandas-docs/stable/indexing.html#attribute-access\n",
-      "  self.meta_data = meta_data\n",
-      "INFO:stancache.stancache:Step 1: Get compiled model code, possibly from cache\n",
-      "INFO:stancache.stancache:StanModel: cache_filename set to anon_model.cython_0_29_2.model_code_16881928540873162731.pystan_2_18_1_0.stanmodel.pkl\n",
-      "INFO:stancache.stancache:StanModel: Starting execution\n",
-      "INFO:pystan:COMPILING THE C++ CODE FOR MODEL anon_model_b18a6495e568fcff90662e16a3d2aa85 NOW.\n",
-      "INFO:stancache.stancache:StanModel: Execution completed (0:01:34.346981 elapsed)\n",
-      "INFO:stancache.stancache:StanModel: Saving results to cache\n",
-      "INFO:stancache.stancache:Step 2: Get posterior draws from model, possibly from cache\n",
-      "INFO:stancache.stancache:sampling: cache_filename set to anon_model.cython_0_29_2.model_code_16881928540873162731.pystan_2_18_1_0.stanfit.chains_4.data_36753546383.iter_5000.seed_9001.pkl\n",
-      "INFO:stancache.stancache:sampling: Starting execution\n",
-      "INFO:stancache.stancache:sampling: Execution completed (0:00:16.703755 elapsed)\n",
-      "INFO:stancache.stancache:sampling: Saving results to cache\n",
-      "/srv/conda/lib/python3.6/site-packages/stancache/stancache.py:285: UserWarning: Pickling fit objects is an experimental feature!\n",
-      "The relevant StanModel instance must be pickled along with this fit object.\n",
-      "When unpickling the StanModel must be unpickled first.\n",
-      "  pickle.dump(res, open(cache_filepath, 'wb'), pickle.HIGHEST_PROTOCOL)\n"
+      "INFO:stancache.stancache:Step 1: Get compiled model code, possibly from cache\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "INFO:stancache.stancache:StanModel: cache_filename set to anon_model.cython_0_29_2.model_code_16881928540873162731.pystan_2_18_1_0.stanmodel.pkl\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "INFO:stancache.stancache:StanModel: Loading result from cache\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "INFO:stancache.stancache:Step 2: Get posterior draws from model, possibly from cache\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "INFO:stancache.stancache:sampling: cache_filename set to anon_model.cython_0_29_2.model_code_16881928540873162731.pystan_2_18_1_0.stanfit.chains_4.data_36753546383.iter_5000.seed_9001.pkl\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "INFO:stancache.stancache:sampling: Loading result from cache\n"
      ]
     }
    ],

diff --git a/example-notebooks/Test pem_survival_model_randomwalk with simulated data.ipynb b/example-notebooks/Test pem_survival_model_randomwalk with simulated data.ipynb
@@ -356,7 +356,7 @@
     {
      "data": {
       "text/plain": [
-       "<matplotlib.legend.Legend at 0x7f31fc7b59b0>"
+       "<matplotlib.legend.Legend at 0x7f91143b96a0>"
       ]
      },
      "execution_count": 5,
@@ -557,22 +557,6 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/home/jacki/projects/survivalstan/survivalstan/formulas.py:96: UserWarning: Pandas doesn't allow columns to be created via a new attribute name - see https://pandas.pydata.org/pandas-docs/stable/indexing.html#attribute-access\n",
-      "  self.stan_data = stan_data\n",
-      "/home/jacki/projects/survivalstan/survivalstan/formulas.py:97: UserWarning: Pandas doesn't allow columns to be created via a new attribute name - see https://pandas.pydata.org/pandas-docs/stable/indexing.html#attribute-access\n",
-      "  self.meta_data = meta_data\n",
-      "/home/jacki/projects/survivalstan/survivalstan/formulas.py:96: UserWarning: Pandas doesn't allow columns to be created via a new attribute name - see https://pandas.pydata.org/pandas-docs/stable/indexing.html#attribute-access\n",
-      "  self.stan_data = stan_data\n",
-      "/home/jacki/projects/survivalstan/survivalstan/formulas.py:97: UserWarning: Pandas doesn't allow columns to be created via a new attribute name - see https://pandas.pydata.org/pandas-docs/stable/indexing.html#attribute-access\n",
-      "  self.meta_data = meta_data\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/home/jacki/projects/survivalstan/survivalstan/survivalstan.py:368: FutureWarning: Method .as_matrix will be removed in a future version. Use .values instead.\n",
-      "  'x': self.x_df.as_matrix(),\n",
       "INFO:stancache.stancache:Step 1: Get compiled model code, possibly from cache\n"
      ]
     },
@@ -824,7 +808,7 @@
     {
      "data": {
       "text/plain": [
-       "<matplotlib.legend.Legend at 0x7f3122c5fa58>"
+       "<matplotlib.legend.Legend at 0x7f9024bef470>"
       ]
      },
      "execution_count": 14,