Add SingleFeature NB LME

biocore · Sep 18, 2023 · a1df859 · a1df859
1 parent 60f5a03
commit a1df859
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Showing 3 changed files with 6 additions and 1 deletion.
diff --git a/.gitignore b/.gitignore
@@ -10,6 +10,7 @@ birdman/templates/negative_binomial
 birdman/templates/multinomial
 birdman/templates/negative_binomial_single
 birdman/templates/negative_binomial_lme
+birdman/templates/negative_binomial_lme_single
 tests/custom_model
 
 *__pycache__/

diff --git a/birdman/default_models.py b/birdman/default_models.py
@@ -410,7 +410,8 @@ def __init__(
             "inv_disp_sd": inv_disp_sd,
             "A": A,
             "subj_ids": samp_subj_map,
-            "u_p": group_var_prior
+            "u_p": group_var_prior,
+            "S": len(self.groups)
         }
         self.add_parameters(param_dict)
 

diff --git a/tests/test_model.py b/tests/test_model.py
@@ -73,6 +73,9 @@ def test_single_feat(self, table_biom, metadata):
 
     def test_lme_single_feat(self, table_biom, metadata):
         md = metadata.copy()
+        np.random.seed(42)
+        md["group"] = np.random.randint(low=0, high=3, size=md.shape[0])
+        md["group"] = "G" + md["group"].astype(str)
         for fid in table_biom.ids(axis="observation"):
             nb = NegativeBinomialLMESingle(
                 table=table_biom,