SmoothForge · danielward27 · Sep 1, 2025 · Aug 27, 2025 · Aug 27, 2025 · Aug 27, 2025
diff --git a/docs/api/basis_functions.md b/docs/api/basis_functions.md
@@ -35,4 +35,3 @@ Basis functions control how smooth terms behave in your GAM models -- different
 ::: pymgcv.basis_functions.AbstractBasis
     options:
       members: __str__
-      merge_init_into_class: false
diff --git a/docs/api/gam.md b/docs/api/gam.md
@@ -10,18 +10,18 @@ GAM model types from ``pymgcv.gam``.
           - "!fit"
           - "!predict"
           - "!partial_effects"
-          - "all_predictors"
 
 ::: pymgcv.gam.GAM
     options:
+        inherited_members:
+          - __init__
         heading_level: 2
-        inherited_members: __init__
 
 ::: pymgcv.gam.BAM
     options:
         heading_level: 2
-        inherited_members: __init__
-
+        inherited_members:
+          - __init__
 
 ::: pymgcv.gam.FitState
     options:

diff --git a/docs/api/plot.md b/docs/api/plot.md
@@ -14,3 +14,4 @@
 ::: pymgcv.plot.plot_categorical
 ::: pymgcv.plot.plot_qq
 ::: pymgcv.plot.plot_residuals_vs_linear_predictor
+::: pymgcv.plot.hexbin_residuals
diff --git a/docs/api/terms.md b/docs/api/terms.md
@@ -35,7 +35,6 @@ assert L("x0") + S("x1") == [L("x0"), S("x1")]
         - "__init__"
 ::: pymgcv.terms.AbstractTerm
     options:
-        merge_init_into_class: false
         members:
           - label
           - mgcv_identifier

diff --git a/docs/examples/electricity_bam.ipynb b/docs/examples/electricity_bam.ipynb
diff --git a/docs/examples/gamlss.ipynb b/docs/examples/gamlss.ipynb
diff --git a/docs/examples/linear_functional.ipynb b/docs/examples/linear_functional.ipynb
diff --git a/docs/examples/ozone.ipynb b/docs/examples/ozone.ipynb
diff --git a/docs/examples/cyclical_components.ipynb → docs/examples/seasonal_co2.ipynb b/docs/examples/cyclical_components.ipynb → docs/examples/seasonal_co2.ipynb
@@ -20,10 +20,10 @@
    "id": "353f16ed",
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2025-08-25T05:53:18.928690Z",
-     "iopub.status.busy": "2025-08-25T05:53:18.928139Z",
-     "iopub.status.idle": "2025-08-25T05:53:28.161960Z",
-     "shell.execute_reply": "2025-08-25T05:53:28.161346Z"
+     "iopub.execute_input": "2025-09-01T12:05:04.942045Z",
+     "iopub.status.busy": "2025-09-01T12:05:04.941364Z",
+     "iopub.status.idle": "2025-09-01T12:05:15.585855Z",
+     "shell.execute_reply": "2025-09-01T12:05:15.585042Z"
     }
    },
    "outputs": [
@@ -50,7 +50,6 @@
     "data = load_rdata_dataframe_from_url(\n",
     "    \"https://github.com/cran/gamair/raw/master/data/co2s.rda\",\n",
     ")\n",
-    "\n",
     "plt.plot(data[\"c.month\"], data[\"co2\"])\n",
     "plt.xlabel(\"Cumulative month\")\n",
     "plt.ylabel(r\"CO2 concentration\")\n",
@@ -76,10 +75,10 @@
    "id": "c4b87eb8",
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2025-08-25T05:53:28.163817Z",
-     "iopub.status.busy": "2025-08-25T05:53:28.163590Z",
-     "iopub.status.idle": "2025-08-25T05:53:28.989669Z",
-     "shell.execute_reply": "2025-08-25T05:53:28.989014Z"
+     "iopub.execute_input": "2025-09-01T12:05:15.588068Z",
+     "iopub.status.busy": "2025-09-01T12:05:15.587773Z",
+     "iopub.status.idle": "2025-09-01T12:05:17.053952Z",
+     "shell.execute_reply": "2025-09-01T12:05:17.052893Z"
     }
    },
    "outputs": [
@@ -96,7 +95,9 @@
    ],
    "source": [
     "simple_gam = GAM({\"co2\": S(\"c.month\", bs=CubicSpline(), k=100)})\n",
-    "simple_gam.fit(data)\n",
+    "simple_gam.fit(\n",
+    "    data[~data.isna().any(axis=1)],\n",
+    ")\n",
     "\n",
     "cyclic_gam = GAM(\n",
     "    {\n",
@@ -105,7 +106,10 @@
     "    },\n",
     ")\n",
     "\n",
-    "cyclic_gam.fit(data, knots={\"month\": np.arange(1, 13)})\n",
+    "cyclic_gam.fit(\n",
+    "    data[~data.isna().any(axis=1)],\n",
+    "    knots={\"month\": np.arange(1, 13)},\n",
+    "    )\n",
     "\n",
     "def plot_prediction(gam: AbstractGAM, data, predict_data, ax):\n",
     "    predictions = gam.predict(data=predict_data, compute_se=True)\n",

diff --git a/docs/examples/smooth_by_categorical.ipynb b/docs/examples/smooth_by_categorical.ipynb
diff --git a/docs/examples/spatial_interactions.ipynb → docs/examples/spatial_fish_eggs.ipynb b/docs/examples/spatial_interactions.ipynb → docs/examples/spatial_fish_eggs.ipynb
diff --git a/docs/examples/supplement_vs_placebo.ipynb b/docs/examples/supplement_vs_placebo.ipynb
diff --git a/docs/index.ipynb b/docs/index.ipynb
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -49,9 +49,12 @@ nav:
       - GAMLSS: examples/gamlss.ipynb
       - Smooth-by-categorical: examples/smooth_by_categorical.ipynb
       - Linear functional: examples/linear_functional.ipynb
-      - Cyclical components: examples/cyclical_components.ipynb
+  - Applied Examples:
       - Ozone: examples/ozone.ipynb
-      - Spatial interactions: examples/spatial_interactions.ipynb
+      - Seasonal CO2: examples/seasonal_co2.ipynb
+      - Spatial fish eggs: examples/spatial_fish_eggs.ipynb
+      - Electricity demand BAM: examples/electricity_bam.ipynb
+      - Supplement vs placebo: examples/supplement_vs_placebo.ipynb
   - API Reference:
       - api/gam.md
       - api/terms.md
@@ -90,5 +93,9 @@ plugins:
             heading_level: 3
             members_order: source
             show_signature_annotations: true
+            extensions:
+              - griffe_inherited_docstrings
+            merge_init_into_class: true
+
 extra_css:
   - stylesheets/extra.css
diff --git a/pymgcv/basis_functions.py b/pymgcv/basis_functions.py
@@ -26,7 +26,7 @@
 
 class _PassToS(TypedDict, total=False):
     xt: ro.ListVector
-    m: int | float | tuple[int | float, ...]
+    m: int | float | ro.IntVector | ro.FloatVector
 
 
 class AbstractBasis(ABC):
@@ -59,13 +59,16 @@ def _pass_to_s(self) -> _PassToS:
         passing of these arguments to `mgcv.s`. Note the string should
         include the leading comma if it is not empty.
 
+
+
         Returns:
             A dictionary, mapping a keyword (e.g. xt or m) to a dictionary of
             variable values.
         """
         ...
 
 
+@dataclass
 class RandomEffect(AbstractBasis):
     """Random effect basis for correlated grouped data.
 
@@ -74,6 +77,17 @@ class RandomEffect(AbstractBasis):
     the corresponding coefficients with a multiple of the identity matrix (i.e. a ridge
     penalty), corresponding to an assumption of i.i.d. normality of the parameters.
 
+    !!! warning
+
+        Numeric variables (int/float), will be treated as a linear term with a single
+        penalized slope parameter. Do not use an integer variable to encode
+        categorical groups!
+
+    !!! example
+
+        For an example, see the
+        [supplement vs placebo example](../../examples/supplement_vs_placebo).
+
     """
 
     def __str__(self) -> str:
@@ -235,7 +249,7 @@ def __str__(self) -> str:
         return "ds"
 
     def _pass_to_s(self) -> _PassToS:
-        return {"m": (self.m, self.s)}
+        return {"m": ro.FloatVector([self.m, self.s])}
 
 
 @dataclass(kw_only=True)
@@ -292,7 +306,7 @@ def __str__(self) -> str:
         return "bs"
 
     def _pass_to_s(self) -> _PassToS:
-        return {"m": [self.degree] + self.penalty_orders}
+        return {"m": ro.IntVector([self.degree] + self.penalty_orders)}
 
 
 @dataclass(kw_only=True)
@@ -326,7 +340,7 @@ def __str__(self) -> str:
 
     def _pass_to_s(self) -> _PassToS:
         # Note (unlike b-splines) seems mgcv uses m[1] for the penalty order, not degree so subtract 1
-        return {"m": (self.degree - 1, self.penalty_order)}
+        return {"m": ro.IntVector([self.degree - 1, self.penalty_order])}
 
 
 @dataclass(kw_only=True)

diff --git a/pymgcv/families.py b/pymgcv/families.py
@@ -6,14 +6,10 @@
 
 import numpy as np
 import rpy2.robjects as ro
-from rpy2.robjects.packages import importr
 
+from pymgcv.rlibs import rbase, rmgcv, rstats
 from pymgcv.rpy_utils import is_null, to_py, to_rpy
 
-rbase = importr("base")
-rstats = importr("stats")
-rmgcv = importr("mgcv")
-
 # For qq_simulate we need sample, and for qq_cdf we need cdf implemented.
 
 

diff --git a/pymgcv/formula_utils.py b/pymgcv/formula_utils.py
@@ -4,13 +4,10 @@
 from typing import Any
 
 from rpy2 import robjects as ro
-from rpy2.robjects.packages import importr
 
+from pymgcv.rlibs import rbase
 from pymgcv.rpy_utils import to_rpy
 
-rbase = importr("base")
-rutils = importr("utils")
-
 
 @dataclass
 class _Var:
@@ -35,5 +32,6 @@ def _to_r_constructor_string(arg: Any) -> str:
     connection = rbase.textConnection("__r_obj_str", "w")
     rbase.dput(arg, file=connection)
     rbase.close(connection)
-    assert len(ro.r["__r_obj_str"]) == 1
-    return ro.r["__r_obj_str"][0]
+    result = ro.r["__r_obj_str"]
+    assert len(result) == 1  # type: ignore
+    return result[0]  # type: ignore