Add unity normalization constant to unfixed leaf nodes

tsdate/core.py

@@ -649,9 +649,7 @@ def inside_pass(self, *, normalize=True, cache_inside=False, progress=None):
         )
         # It is possible that a simple node is non-fixed, in which case we want to
         # provide an inside array that reflects the prior distribution
-        nonfixed_samples = np.intersect1d(
-            self.priors.nonfixed_node_ids(), self.ts.samples()
-        )
+        nonfixed_samples = np.intersect1d(inside.nonfixed_node_ids(), self.ts.samples())
         for u in nonfixed_samples:
             # this is in the same probability space as the prior, so we should be
             # OK just to copy the prior values straight in (but we should check they
@@ -663,6 +661,8 @@ def inside_pass(self, *, normalize=True, cache_inside=False, progress=None):
                 (self.ts.num_edges, self.lik.grid_size), self.lik.identity_constant
             )
         norm = np.full(self.ts.num_nodes, np.nan)
+        to_visit = np.zeros(self.ts.num_nodes, dtype=bool)
+        to_visit[inside.nonfixed_node_ids()] = True
         # Iterate through the nodes via groupby on parent node
         for parent, edges in tqdm(
             self.edges_by_parent_asc(),
@@ -707,6 +707,12 @@ def inside_pass(self, *, normalize=True, cache_inside=False, progress=None):
                     g_i[edge.id] = edge_lik
             norm[parent] = np.max(val) if normalize else 1
             inside[parent] = self.lik.reduce(val, norm[parent])
+            to_visit[parent] = False
+
+        # There may be nodes that are not parents but are also not fixed (e.g.
+        # undated sample nodes). These need an identity normalization constant
+        for unfixed_unvisited in np.where(to_visit)[0]:
+            norm[unfixed_unvisited] = 1
 
         if cache_inside:
             self.g_i = self.lik.reduce(g_i, norm[self.ts.tables.edges.child, None])