Merge pull request #93 from gibsramen/fix-90

Fix #90

birdman/inference.py

@@ -1,3 +1,4 @@
+from functools import partial
 from typing import List, Sequence, Union
 
 import arviz as az
@@ -21,18 +22,25 @@ def fit_to_inference(
     if posterior_predictive is not None and posterior_predictive not in dims:
         raise KeyError("Must include dimensions for posterior predictive!")
 
+    # Required because as of writing, CmdStanVB.stan_variable defaults to
+    # returning the mean rather than the sample
+    if isinstance(fit, CmdStanVB):
+        stan_var_fn = partial(fit.stan_variable, mean=False)
+    else:
+        stan_var_fn = fit.stan_variable
+
     das = dict()
 
     for param in params:
-        data = fit.stan_variable(param)
+        data = stan_var_fn(param)
 
         _dims = dims[param]
         _coords = {k: coords[k] for k in _dims}
 
         das[param] = stan_var_to_da(data, _coords, _dims, chains, draws)
 
     if log_likelihood:
-        data = fit.stan_variable(log_likelihood)
+        data = stan_var_fn(log_likelihood)
 
         _dims = dims[log_likelihood]
         _coords = {k: coords[k] for k in _dims}
@@ -43,7 +51,7 @@ def fit_to_inference(
         ll_ds = None
 
     if posterior_predictive:
-        data = fit.stan_variable(posterior_predictive)
+        data = stan_var_fn(posterior_predictive)
 
         _dims = dims[posterior_predictive]
         _coords = {k: coords[k] for k in _dims}
@@ -84,21 +92,19 @@ def concatenate_inferences(
     """
     group_list = []
     group_list.append([x.posterior for x in inf_list])
-    group_list.append([x.sample_stats for x in inf_list])
     if "log_likelihood" in inf_list[0].groups():
         group_list.append([x.log_likelihood for x in inf_list])
     if "posterior_predictive" in inf_list[0].groups():
         group_list.append([x.posterior_predictive for x in inf_list])
 
     po_ds = xr.concat(group_list[0], concatenation_name)
-    ss_ds = xr.concat(group_list[1], concatenation_name)
-    group_dict = {"posterior": po_ds, "sample_stats": ss_ds}
+    group_dict = {"posterior": po_ds}
 
     if "log_likelihood" in inf_list[0].groups():
-        ll_ds = xr.concat(group_list[2], concatenation_name)
+        ll_ds = xr.concat(group_list[1], concatenation_name)
         group_dict["log_likelihood"] = ll_ds
     if "posterior_predictive" in inf_list[0].groups():
-        pp_ds = xr.concat(group_list[3], concatenation_name)
+        pp_ds = xr.concat(group_list[2], concatenation_name)
         group_dict["posterior_predictive"] = pp_ds
 
     all_group_inferences = []
@@ -114,16 +120,15 @@ def concatenate_inferences(
     return az.concat(*all_group_inferences)
 
 
+# TODO: Fix docstring
 def stan_var_to_da(
     data: np.ndarray,
     coords: dict,
     dims: dict,
     chains: int,
     draws: int
 ):
-    """Convert Stan variable draws to xr.DataArray.
-
-    """
+    """Convert Stan variable draws to xr.DataArray."""
     data = np.stack(np.split(data, chains))
 
     coords["draw"] = np.arange(draws)

tests/test_inference.py

@@ -1,6 +1,9 @@
 import numpy as np
+import pytest
 
 from birdman import inference as mu
+from birdman.default_models import NegativeBinomialSingle
+from birdman import ModelIterator
 
 
 class TestToInference:
@@ -78,3 +81,30 @@ def test_serial_ppll(self, example_model):
             nb_data = example_model.fit.stan_variable(v)
             nb_data = np.array(np.split(nb_data, 4, axis=0))
             np.testing.assert_array_almost_equal(nb_data, inf_data)
+
+
+@pytest.mark.parametrize("method", ["mcmc", "vi"])
+def test_concat(table_biom, metadata, method):
+    tbl = table_biom
+    md = metadata
+
+    model_iterator = ModelIterator(
+        table=tbl,
+        model=NegativeBinomialSingle,
+        formula="host_common_name",
+        metadata=md,
+    )
+
+    infs = []
+    for fname, model in model_iterator:
+        model.compile_model()
+        model.fit_model(method, num_draws=100)
+        infs.append(model.to_inference())
+
+    inf_concat = mu.concatenate_inferences(
+        infs,
+        coords={"feature": tbl.ids("observation")},
+    )
+    exp_feat_ids = tbl.ids("observation")
+    feat_ids = inf_concat.posterior.coords["feature"].to_numpy()
+    assert (exp_feat_ids == feat_ids).all()