geocif 0.1.29__tar.gz → 0.1.30__tar.gz

{geocif-0.1.29/geocif.egg-info → geocif-0.1.30}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geocif
-Version: 0.1.29
+Version: 0.1.30
 Summary: Models to visualize and forecast crop conditions and yields
 Home-page: https://ritviksahajpal.github.io/yield_forecasting/
 Author: Ritvik Sahajpal

{geocif-0.1.29 → geocif-0.1.30}/geocif/geocif.py

@@ -17,6 +17,7 @@ from tqdm import tqdm
 from geocif import logger as log
 from .cei import definitions as di
 from .ml import correlations
+from .ml import spatial_autocorrelation as sa
 from .ml import feature_engineering as fe
 from .ml import feature_selection as fs
 from .ml import output
@@ -112,6 +113,10 @@ class Geocif:
         self.analogous_year_yield_as_feature = self.parser.getboolean(
             "ML", "analogous_year_yield_as_feature"
         )
+        self.spatial_autocorrelation = self.parser.getboolean(
+            "ML", "spatial_autocorrelation"
+        )
+        self.sa_method = self.parser.get("ML", "sa_method")
         self.last_year_yield_as_feature = self.parser.getboolean(
             "ML", "last_year_yield_as_feature"
         )
@@ -367,10 +372,10 @@ class Geocif:
                 "Starting Stage": np.full(shp, self.stage_info["Starting Stage"]),
                 "Ending Stage": np.full(shp, self.stage_info["Ending Stage"]),
                 "Model": np.full(shp, self.model_name),
-                "Area (ha)": df_region["Area (ha)"].values,
                 "Region_ID": df_region["Region_ID"].values,
                 "Region": df_region["Region"].values,
                 "Harvest Year": df_region["Harvest Year"].values,
+                "Area (ha)": df_region["Area (ha)"].values,
                 f"Observed {self.target}": np.around(y_test, 3).ravel(),
                 f"Predicted {self.target}": np.around(y_pred, 3).ravel(),
             }
@@ -412,6 +417,12 @@ class Geocif:
             except:
                 breakpoint()
 
+        # if self.spatial_autocorrelation:
+        #     # Compute spatial autocorrelation
+        #     df = sa.compute_spatial_autocorrelation(
+        #         self.dg_country
+        #     )
+
         for col in [
             f"Median {self.target}",
             "Analogous Year",
@@ -425,7 +436,7 @@ class Geocif:
         # Create an index based on following columns
         index_columns = [
             "Model",
-            "Cluster Strategy"
+            "Cluster Strategy",
             "Country",
             "Region",
             "Crop",
@@ -718,7 +729,6 @@ class Geocif:
         )
 
         # cat_features should be converted to category type
-
         df[self.cat_features] = df[self.cat_features].astype("category")
 
         """  Heatmap of correlation of various features with yield at each time step"""
@@ -739,32 +749,35 @@ class Geocif:
             how="outer",
         )
 
-        if self.correlation_plots:
-            dict_kwargs = {}
-            dict_kwargs["all_stages"] = self.all_stages
-            dict_kwargs["target_col"] = self.target
-            dict_kwargs["country"] = self.country
-            dict_kwargs["crop"] = self.crop
-            dict_kwargs["dir_output"] = (
-                self.dir_analysis
-                / self.country
-                / self.crop
-                / self.model_name
-                / str(self.forecast_season)
-            )
-            dict_kwargs["forecast_season"] = self.forecast_season
-            dict_kwargs["method"] = self.method
-            dict_kwargs["national_correlation"] = self.national_correlation
-            dict_kwargs["groupby"] = self.correlation_plot_groupby
-            dict_kwargs["dg_country"] = self.dg_country
-            dict_kwargs["combined_dict"] = self.combined_dict
+        dict_kwargs = {}
+        dict_kwargs["all_stages"] = self.all_stages
+        dict_kwargs["target_col"] = self.target
+        dict_kwargs["country"] = self.country
+        dict_kwargs["crop"] = self.crop
+        dict_kwargs["dir_output"] = (
+            self.dir_analysis
+            / self.country
+            / self.crop
+            / self.model_name
+            / str(self.forecast_season)
+        )
+        dict_kwargs["forecast_season"] = self.forecast_season
+        dict_kwargs["method"] = self.method
+        dict_kwargs["national_correlation"] = self.national_correlation
+        dict_kwargs["groupby"] = self.correlation_plot_groupby
+        dict_kwargs["dg_country"] = self.dg_country
+        dict_kwargs["combined_dict"] = self.combined_dict
 
+        if self.correlation_plots:
             self.logger.info(f"Correlation plot for {self.country} {self.crop}")
             (
                 dict_selected_features,
                 dict_best_cei,
             ) = correlations.all_correlated_feature_by_time(df, **dict_kwargs)
 
+        if self.spatial_autocorrelation:
+           sa.compute_spatial_autocorrelation(self.df_results, **dict_kwargs)
+
         """ Separate into train and test datasets based on forecast_season """
         mask = df["Harvest Year"] == self.forecast_season
         self.df_train = df[~mask]

{geocif-0.1.29 → geocif-0.1.30}/geocif/indices_runner.py

@@ -155,7 +155,7 @@ class cei_runner(base.BaseGeo):
                 "ndvi",
                 False,  # redo
             )
-            for year in range(2023, ar.utcnow().year + 1)
+            for year in range(2001, ar.utcnow().year + 1)
             for status, path, filename, admin_zone, category in combinations
         ]
 

{geocif-0.1.29 → geocif-0.1.30}/geocif/ml/correlations.py

@@ -28,7 +28,9 @@ def most_correlated_feature_by_time(df_train, simulation_stages, target_col):
 
     # Only select columns that have been observed till the current stage
     for stage in tqdm(stages, leave=False, desc="Compute most correlated feature"):
-        current_feature_set = [col for col in df_train.columns if col.endswith(f"_{stage[-1]}")]
+        current_feature_set = [
+            col for col in df_train.columns if col.endswith(f"_{stage[-1]}")
+        ]
 
         # Get the most correlated feature for each region
         top_feature_by_region, counter = embedding.get_top_correlated_features(
@@ -41,7 +43,9 @@ def most_correlated_feature_by_time(df_train, simulation_stages, target_col):
         # Loop through top_feature_by_region and find the average score for _feature
         # Calculate the average score for 'DTR_36'
         _feature_scores = [
-            value[1][0] for key, value in top_feature_by_region.items() if _feature in value[0]
+            value[1][0]
+            for key, value in top_feature_by_region.items()
+            if _feature in value[0]
         ]
         average_score = sum(_feature_scores) / len(_feature_scores)
         _feature = utils.remove_last_part(_feature)
@@ -137,7 +141,9 @@ def plot_feature_corr_by_time(df, **kwargs):
     # Add colorbar label
     # cbar_ax.set_xlabel("Correlation Coefficient", labelpad=3, size="small")
     cbar_ax.set_title("Correlation Coefficient", loc="left", size="small")
-    ax_heatmap.set_xticklabels(ax_heatmap.get_xticklabels(), size="x-small", rotation=0, fontsize=5)
+    ax_heatmap.set_xticklabels(
+        ax_heatmap.get_xticklabels(), size="x-small", rotation=0, fontsize=5
+    )
     ax_heatmap.set_yticklabels(ax_heatmap.get_yticklabels(), size="x-small", fontsize=5)
     ax_heatmap.set_xlabel("")
     ax_heatmap.set_ylabel(" ")
@@ -190,7 +196,9 @@ def _all_correlated_feature_by_time(df, **kwargs):
         pbar.set_description(f"Calculating correlations")
         pbar.update()
 
-        stage_name = stages.get_stage_information_dict(f"GD4_{stage}", method)["Stage Name"]
+        stage_name = stages.get_stage_information_dict(f"GD4_{stage}", method)[
+            "Stage Name"
+        ]
         # starting_stage = stage_name.split("-")[0]
         current_feature_set = [col for col in df.columns if stage_name in col]
 
@@ -210,7 +218,9 @@ def _all_correlated_feature_by_time(df, **kwargs):
 
         all_stage_names = []
         for stage in stages_features:
-            _tmp = stages.get_stage_information_dict(f"GD4_{stage}", method)["Stage Name"]
+            _tmp = stages.get_stage_information_dict(f"GD4_{stage}", method)[
+                "Stage Name"
+            ]
             all_stage_names.append(_tmp)
 
         df_results = df_results.reindex(all_stage_names)
@@ -254,7 +264,12 @@ def all_correlated_feature_by_time(df, **kwargs):
                 df_tmp = df_corr[df_corr.columns[(df_corr.mean() > 0.1)]]
                 dict_selected_features[region_id] = df_tmp.columns
 
-                df_tmp2 = df_tmp.median(axis=0).abs().sort_values(ascending=False).reset_index()
+                df_tmp2 = (
+                    df_tmp.median(axis=0)
+                    .abs()
+                    .sort_values(ascending=False)
+                    .reset_index()
+                )
                 df_tmp2.columns = ["Metric", "Value"]
                 # Add another column based on Type of Metric
                 for idx, row in df_tmp2.iterrows():
@@ -278,8 +293,8 @@ def all_correlated_feature_by_time(df, **kwargs):
                 dict_selected_features[region_id] = df_corr.columns
                 dict_best_cei[region_id] = {}
 
-                #dict_selected_features[region_id] = dict_selected_features[0]
-                #dict_best_cei[region_id] = dict_best_cei[0]
+                # dict_selected_features[region_id] = dict_selected_features[0]
+                # dict_best_cei[region_id] = dict_best_cei[0]
                 # Combine all unique values from the existing dictionary elements
                 # combined_metrics = set()
                 # for key in dict_selected_features:
@@ -310,7 +325,9 @@ def feature_correlation_by_time(**kwargs):
 
     # Only select columns that have been observed till the current stage
     for stage in tqdm(stages, leave=False, desc="Compute feature correlation by time"):
-        current_feature_set = [col for col in df_train.columns if col.endswith(f"_{stage[-1]}")]
+        current_feature_set = [
+            col for col in df_train.columns if col.endswith(f"_{stage[-1]}")
+        ]
 
         # Get the most correlated feature for each region
         top_feature_by_region, counter = embedding.compute_feature_correlations(
@@ -324,7 +341,9 @@ def feature_correlation_by_time(**kwargs):
         # Loop through top_feature_by_region and find the average score for _feature
         # Calculate the average score for 'DTR_36'
         _feature_scores = [
-            value[1][0] for key, value in top_feature_by_region.items() if _feature in value[0]
+            value[1][0]
+            for key, value in top_feature_by_region.items()
+            if _feature in value[0]
         ]
         average_score = sum(_feature_scores) / len(_feature_scores)
         _feature = utils.remove_last_part(_feature)

{geocif-0.1.29 → geocif-0.1.30}/geocif/ml/embedding.py

@@ -79,7 +79,9 @@ def get_top_correlated_features(inputs, targets):
         feature_correlations = _compute_correlations(X, y)
 
         # Exclude any nan values
-        feature_correlations = {k: v for k, v in feature_correlations.items() if not np.isnan(v)}
+        feature_correlations = {
+            k: v for k, v in feature_correlations.items() if not np.isnan(v)
+        }
 
         if not feature_correlations:
             continue
@@ -113,7 +115,9 @@ def get_all_features_correlation(inputs, targets, method):
         feature_correlations = _compute_correlations(X, y)
 
         # Exclude any nan values
-        feature_correlations = {k: v for k, v in feature_correlations.items() if not np.isnan(v)}
+        feature_correlations = {
+            k: v for k, v in feature_correlations.items() if not np.isnan(v)
+        }
 
         if not feature_correlations:
             continue

{geocif-0.1.29 → geocif-0.1.30}/geocif/ml/feature_engineering.py

@@ -21,11 +21,15 @@ def compute_last_year_yield(df, target_col="Yield (tn per ha)"):
     # Initialize the new column with NaNs
     df[f"Last Year {target_col}"] = np.nan
 
-    for region, group in tqdm(df.groupby("Region"), desc="Last year yields", leave=False):
+    for region, group in tqdm(
+        df.groupby("Region"), desc="Last year yields", leave=False
+    ):
         unique_years = group["Harvest Year"].unique()
 
         for harvest_year in unique_years:
-            mask = (group["Harvest Year"] == harvest_year - 1) & (group["Region"] == region)
+            mask = (group["Harvest Year"] == harvest_year - 1) & (
+                group["Region"] == region
+            )
             last_year_yield = group.loc[mask, target_col].values
             if last_year_yield:
                 df.loc[
@@ -89,7 +93,9 @@ def compute_median_yield(
             closest_years = compute_closest_years(
                 all_seasons_with_yield, harvest_year, number_median_years
             )
-            mask = (group["Harvest Year"].isin(closest_years)) & (group["Region"] == region)
+            mask = (group["Harvest Year"].isin(closest_years)) & (
+                group["Region"] == region
+            )
             median_yield = group.loc[mask, target_col].median()
             df.loc[
                 (df["Region"] == region) & (df["Harvest Year"] == harvest_year),
@@ -99,7 +105,9 @@ def compute_median_yield(
     return df
 
 
-def compute_lag_yield(df, all_seasons_with_yield, number_lag_years, target_col="Yield (tn per ha)"):
+def compute_lag_yield(
+    df, all_seasons_with_yield, number_lag_years, target_col="Yield (tn per ha)"
+):
     # For the number of years specified in self.number_lag_years, add the yield of that number of years
     # ago to the dataframe
     # For example, if number_lag_years is 3, then the yield of each year upto 3 years ago will be added
@@ -125,7 +133,9 @@ def compute_lag_yield(df, all_seasons_with_yield, number_lag_years, target_col="
                 col = f"t -{idx + 1} {target_col}"
 
                 mask_group_year = group["Harvest Year"] == year
-                mask_region = (df["Region"] == region) & (df["Harvest Year"] == harvest_year)
+                mask_region = (df["Region"] == region) & (
+                    df["Harvest Year"] == harvest_year
+                )
                 yield_value = group.loc[mask_group_year, target_col].values
 
                 if yield_value.size > 0:
@@ -181,11 +191,15 @@ def compute_analogous_yield(
     all_years = df["Harvest Year"].unique()
 
     for harvest_year in tqdm(all_years, desc="Computing analogous yields", leave=False):
-        lag_years = compute_closest_years(all_seasons_with_yield, harvest_year, number_lag_years)
+        lag_years = compute_closest_years(
+            all_seasons_with_yield, harvest_year, number_lag_years
+        )
 
         for region in df["Region"].unique():
             # Filter current year and region dataset
-            df_current = df[(df["Harvest Year"] == harvest_year) & (df["Region"] == region)]
+            df_current = df[
+                (df["Harvest Year"] == harvest_year) & (df["Region"] == region)
+            ]
             # Filter dataset for lag years and the same region
             df_lag = df[(df["Harvest Year"].isin(lag_years)) & (df["Region"] == region)]
 
@@ -242,6 +256,7 @@ def detect_clusters(df, target_col="Yield (tn per ha)"):
 
     # Suppress warnings in this function
     import warnings
+
     warnings.filterwarnings("ignore")
 
     from kneed import KneeLocator
@@ -291,7 +306,9 @@ def detect_clusters(df, target_col="Yield (tn per ha)"):
         inertia.append(kmeans.inertia_)
 
     # Use KneeLocator to find the elbow point automatically
-    knee_locator = KneeLocator(range_of_clusters, inertia, curve="convex", direction="decreasing")
+    knee_locator = KneeLocator(
+        range_of_clusters, inertia, curve="convex", direction="decreasing"
+    )
 
     # # Plot the Elbow Method for visual confirmation
     # plt.figure(figsize=(10, 6))
@@ -306,7 +323,9 @@ def detect_clusters(df, target_col="Yield (tn per ha)"):
     # Use the detected number of clusters
     optimal_clusters = knee_locator.knee
     if optimal_clusters:
-        optimal_clusters = optimal_clusters + 1 if optimal_clusters > 1 else optimal_clusters
+        optimal_clusters = (
+            optimal_clusters + 1 if optimal_clusters > 1 else optimal_clusters
+        )
 
         # Apply K-Means clustering with the detected optimal number of clusters
         kmeans = KMeans(n_clusters=optimal_clusters, random_state=42)
@@ -321,6 +340,43 @@ def detect_clusters(df, target_col="Yield (tn per ha)"):
         )
     else:
         # If no optimal_clusters is found, then assign all regions to a single cluster
-        clusters_assigned = pd.DataFrame({"Region": df_yield_pivot.index, "Region_ID": 1})
+        clusters_assigned = pd.DataFrame(
+            {"Region": df_yield_pivot.index, "Region_ID": 1}
+        )
 
     return clusters_assigned
+
+
+# breakpoint()
+
+# from libpysal.weights import Queen, Rook
+# from pysal.lib import weights
+# from scipy.linalg import eigh
+#
+# breakpoint()
+# df = pd.DataFrame()
+#
+# # Create a spatial weights matrix (e.g., Queen contiguity)
+# w = weights.Queen.from_dataframe(dg)
+#
+# # Transform weights to row-standardized form
+# w.transform = 'r'
+#
+# # Convert the weights matrix to a dense format for eigen decomposition
+# W_dense = w.full()[0]
+#
+# # Compute eigenvalues and eigenvectors
+# eigenvalues, eigenvectors = eigh(W_dense)
+#
+# # Sort eigenvalues and corresponding eigenvectors
+# sorted_indices = np.argsort(eigenvalues)[::-1]
+# eigenvalues = eigenvalues[sorted_indices]
+# eigenvectors = eigenvectors[:, sorted_indices]
+#
+# # Select a subset of eigenvectors (e.g., first 10)
+# selected_eigenvectors = eigenvectors[:, :2]
+#
+# breakpoint()
+# # Add eigenvectors to the GeoDataFrame
+# for i in range(selected_eigenvectors.shape[1]):
+#     df[f'EV_{i + 1}'] = selected_eigenvectors[:, i]

{geocif-0.1.29 → geocif-0.1.30}/geocif/ml/feature_selection.py

@@ -77,16 +77,22 @@ def select_features(X, y, method="RFE", min_features_to_select=3):
 
         # Step 5: Summarize the SHAP values for feature importance
         shap_importances = np.mean(np.abs(shap_values), axis=0)
-        shap_importance_df = pd.DataFrame({
-            'feature': X.columns,
-            'importance': shap_importances
-        }).sort_values(by='importance', ascending=False)
+        shap_importance_df = pd.DataFrame(
+            {"feature": X.columns, "importance": shap_importances}
+        ).sort_values(by="importance", ascending=False)
 
         def evaluate_model_with_n_features(N, X_train, y_train):
-            top_features = shap_importance_df['feature'].head(N).values
+            top_features = shap_importance_df["feature"].head(N).values
             X_train_selected = X_train[top_features]
             selector = CatBoostRegressor(n_estimators=500, random_state=42, verbose=0)
-            scores = cross_val_score(selector, X_train_selected, y_train, cv=5, scoring='neg_mean_squared_error', n_jobs=-1)
+            scores = cross_val_score(
+                selector,
+                X_train_selected,
+                y_train,
+                cv=5,
+                scoring="neg_mean_squared_error",
+                n_jobs=-1,
+            )
 
             return np.mean(scores)
 
@@ -100,7 +106,9 @@ def select_features(X, y, method="RFE", min_features_to_select=3):
         optimal_N = nrange[np.argmax(cv_scores)]
 
         # Use optimal N to select features
-        selected_features = shap_importance_df['feature'].head(optimal_N).values.tolist()
+        selected_features = (
+            shap_importance_df["feature"].head(optimal_N).values.tolist()
+        )
     elif method == "feature_engine":
         from feature_engine.selection import SmartCorrelatedSelection
 
@@ -202,7 +210,9 @@ def select_features(X, y, method="RFE", min_features_to_select=3):
         }
         model = CatBoostRegressor(**hyperparams)
 
-        selector = BorutaShap(model=model, importance_measure="shap", classification=False)
+        selector = BorutaShap(
+            model=model, importance_measure="shap", classification=False
+        )
         selector.fit(
             X=X,
             y=y,
@@ -237,7 +247,9 @@ def select_features(X, y, method="RFE", min_features_to_select=3):
     elif method == "RFE":
         from sklearn.feature_selection import RFE
 
-        selector = RFE(forest, n_features_to_select=min_features_to_select, step=1, verbose=1)
+        selector = RFE(
+            forest, n_features_to_select=min_features_to_select, step=1, verbose=1
+        )
         selector = selector.fit(X, y)
         selected_features_mask = selector.support_
         selected_features = X.columns[selected_features_mask].tolist()

{geocif-0.1.29 → geocif-0.1.30}/geocif/ml/outliers.py

@@ -94,19 +94,23 @@ if __name__ == "__main__":
 
         if not os.path.isfile(BASE_DIR / crop / f"adm_crop_production_z_{crop}.csv"):
             # In rows where admin_2 != "none", replace admin_1 with admin_2
-            df_fewsnet_sub.loc[df_fewsnet_sub["admin_2"] != "none", "admin_1"] = df_fewsnet_sub[
-                "admin_2"
-            ]
+            df_fewsnet_sub.loc[
+                df_fewsnet_sub["admin_2"] != "none", "admin_1"
+            ] = df_fewsnet_sub["admin_2"]
 
             df_output = find_outlier(df_fewsnet_sub)
 
-            df_output.to_csv(BASE_DIR / crop / f"adm_crop_production_z_{crop}.csv", index=False)
+            df_output.to_csv(
+                BASE_DIR / crop / f"adm_crop_production_z_{crop}.csv", index=False
+            )
         else:
-            df_output = pd.read_csv(BASE_DIR / crop / f"adm_crop_production_z_{crop}.csv")
+            df_output = pd.read_csv(
+                BASE_DIR / crop / f"adm_crop_production_z_{crop}.csv"
+            )
 
-        df_fewsnet_sub.loc[df_fewsnet_sub["admin_2"] != "none", "admin_1"] = df_fewsnet_sub[
-            "admin_2"
-        ]
+        df_fewsnet_sub.loc[
+            df_fewsnet_sub["admin_2"] != "none", "admin_1"
+        ] = df_fewsnet_sub["admin_2"]
 
         # Create a column called Z-Score Category based on the value of the z-score
         # The categories are:
@@ -142,7 +146,9 @@ if __name__ == "__main__":
             df_fewsnet_sub["harvest_year"] = df_fewsnet_sub["harvest_year"].astype(int)
 
             df_yield = df_fewsnet_sub[mask & (df_fewsnet_sub["indicator"] == "yield")]
-            df_production = df_fewsnet_sub[mask & (df_fewsnet_sub["indicator"] == "production")]
+            df_production = df_fewsnet_sub[
+                mask & (df_fewsnet_sub["indicator"] == "production")
+            ]
             df_area = df_fewsnet_sub[mask & (df_fewsnet_sub["indicator"] == "area")]
 
             df_yield["harvest_year"] = df_yield["harvest_year"].astype(int)
@@ -158,9 +164,13 @@ if __name__ == "__main__":
             # Add 3 subplots, first for area
             plt.figure(figsize=(10, 10))
             plt.subplot(3, 1, 1)
-            plt.plot(df_yield[mask]["harvest_year"].astype(int), df_yield[mask]["value"])
+            plt.plot(
+                df_yield[mask]["harvest_year"].astype(int), df_yield[mask]["value"]
+            )
             # Add a circle for each year where yield is available
-            plt.scatter(df_yield[mask]["harvest_year"].astype(int), df_yield[mask]["value"])
+            plt.scatter(
+                df_yield[mask]["harvest_year"].astype(int), df_yield[mask]["value"]
+            )
             # Draw a horizontal line at the average df_yield[mask]["value"]
             plt.axhline(df_yield[mask]["value"].mean(), color="red", linestyle="--")
             # Place a tick on x-axis at every year and make labels vertical
@@ -195,13 +205,17 @@ if __name__ == "__main__":
                 df_production[mask]["value"],
             )
             # Place a tick on x-axis at every year
-            plt.xticks(df_production[mask]["harvest_year"].astype(int)[::2], rotation=90)
+            plt.xticks(
+                df_production[mask]["harvest_year"].astype(int)[::2], rotation=90
+            )
             plt.xlabel("Year")
             plt.ylabel("Production")
 
             plt.subplot(3, 1, 3)
             plt.plot(df_area[mask]["harvest_year"].astype(int), df_area[mask]["value"])
-            plt.scatter(df_area[mask]["harvest_year"].astype(int), df_area[mask]["value"])
+            plt.scatter(
+                df_area[mask]["harvest_year"].astype(int), df_area[mask]["value"]
+            )
             # Place a tick on x-axis at every year
             plt.xticks(df_area[mask]["harvest_year"].astype(int)[::2], rotation=90)
             plt.xlabel("Year")
@@ -210,7 +224,9 @@ if __name__ == "__main__":
             try:
                 os.makedirs(BASE_DIR / crop, exist_ok=True)
                 plt.savefig(
-                    BASE_DIR / crop / f"{fnid}_{country}_{admin_1}_{crop}_{season_name}.png"
+                    BASE_DIR
+                    / crop
+                    / f"{fnid}_{country}_{admin_1}_{crop}_{season_name}.png"
                 )
             except:
                 breakpoint()

geocif-0.1.30/geocif/ml/spatial_autocorrelation.py

@@ -0,0 +1,205 @@
+import pandas as pd
+from pysal.lib import weights
+from pysal.explore import esda
+import matplotlib.pyplot as plt
+
+
+def validate_inputs(df_results, required_columns):
+    """
+
+    Args:
+        df_results:
+        required_columns:
+
+    Returns:
+
+    """
+    if not all(column in df_results.columns for column in required_columns):
+        raise ValueError(
+            f"df_results must contain the following columns: {required_columns}"
+        )
+
+
+def preprocess_data(df_results, dg_country):
+    """
+
+    Args:
+        df_results:
+        dg_country:
+
+    Returns:
+
+    """
+    df = df_results.drop_duplicates()
+    df = df.dropna(subset=["Yield (tn per ha)"])
+
+    dg_country = dg_country.drop_duplicates(subset="Country Region")
+    dg_country = dg_country.dropna(subset=["Country Region", "Region_ID", "geometry"])
+
+    df["Country Region"] = (df["Country"] + " " + df["Region"]).str.lower()
+    dg_country["Country Region"] = dg_country["Country Region"].str.lower()
+    dg_country = dg_country[dg_country["Country Region"].isin(df["Country Region"])]
+
+    merged_df = dg_country.merge(df, on="Country Region", how="inner")
+
+    return merged_df, dg_country
+
+
+def create_base_weights(dg_country):
+    """
+
+    Args:
+        dg_country:
+
+    Returns:
+
+    """
+    dg_subset = dg_country[["Country Region", "geometry"]].drop_duplicates()
+
+    try:
+        w_base = weights.Queen.from_dataframe(dg_subset)
+    except Exception as e:
+        raise RuntimeError(f"Failed to create spatial weights: {e}")
+
+    no_neighbors = [
+        index for index, neighbors in w_base.neighbors.items() if len(neighbors) == 0
+    ]
+    if no_neighbors:
+        print(f"Removing {len(no_neighbors)} polygons with 0 neighbors")
+        dg_country = dg_country.drop(index=no_neighbors).reset_index(drop=True)
+        w_base = weights.Queen.from_dataframe(
+            dg_country[["Country Region", "geometry"]]
+        )
+
+    return w_base, dg_country
+
+
+def create_weights_for_year(dg_country, regions_with_data):
+    """
+
+    Args:
+        dg_country:
+        regions_with_data:
+
+    Returns:
+
+    """
+    dg_subset = dg_country[dg_country["Country Region"].isin(regions_with_data)]
+
+    wt = weights.Queen.from_dataframe(dg_subset)
+
+    return wt
+
+
+def compute_morans_i(merged_df, dg_country):
+    """
+
+    Args:
+        merged_df:
+        dg_country:
+
+    Returns:
+
+    """
+    years = merged_df["Harvest Year"].unique()
+    results = {"Harvest Year": [], "Moran's I": [], "p-value": [], "Significant": []}
+
+    for year in years:
+        year_data = merged_df[merged_df["Harvest Year"] == year]
+        regions_with_data = year_data["Country Region"].unique()
+        year_data = year_data[year_data["Country Region"].isin(regions_with_data)]
+
+        y = year_data[["Region", "Yield (tn per ha)"]].drop_duplicates()
+
+        if len(y) > 1:
+            w = create_weights_for_year(dg_country, regions_with_data)
+
+            try:
+                mi = esda.Moran(y["Yield (tn per ha)"].values, w, permutations=999)
+            except:
+                breakpoint()
+            results["Harvest Year"].append(year)
+            results["Moran's I"].append(mi.I)
+            results["p-value"].append(mi.p_sim)
+            results["Significant"].append(mi.p_sim < 0.1)
+        else:
+            results["Harvest Year"].append(year)
+            results["Moran's I"].append(None)
+            results["p-value"].append(None)
+            results["Significant"].append(False)
+
+    return pd.DataFrame(results)
+
+
+def plot_moransi_time_series(results_df, country, crop, dir_output):
+    """
+
+    Args:
+        results_df:
+        country:
+        crop:
+        dir_output:
+
+    Returns:
+
+    """
+    plt.figure(figsize=(10, 6))
+
+    significant = results_df[results_df["Significant"]]
+    plt.scatter(
+        significant["Harvest Year"],
+        significant["Moran's I"],
+        color="red",
+        label="Significant (p < 0.1)",
+    )
+
+    not_significant = results_df[~results_df["Significant"]]
+    plt.plot(
+        not_significant["Harvest Year"],
+        not_significant["Moran's I"],
+        marker="o",
+        linestyle="-",
+        color="blue",
+        label="Non-Significant",
+    )
+
+    plt.ylabel("Moran's I")
+    plt.legend()
+    plt.grid(True)
+    plt.savefig(dir_output / f"{country}_{crop}.png")
+    plt.close()
+
+
+def compute_spatial_autocorrelation(df_results, **kwargs):
+    """
+
+    Args:
+        df_results:
+        **kwargs:
+
+    Returns:
+
+    """
+    country = kwargs.get("country")
+    crop = kwargs.get("crop")
+    dg_country = kwargs.get("dg_country")
+    dir_output = kwargs.get("dir_output")
+
+    required_columns = [
+        "Country",
+        "Crop",
+        "Region",
+        "Harvest Year",
+        "Yield (tn per ha)",
+    ]
+    validate_inputs(df_results, required_columns)
+
+    merged_df, dg_country = preprocess_data(df_results, dg_country)
+    if merged_df.empty:
+        raise ValueError("No valid data available after preprocessing")
+
+    w_base, dg_country = create_base_weights(dg_country)
+
+    results_df = compute_morans_i(merged_df, dg_country)
+
+    plot_moransi_time_series(results_df, country, crop, dir_output)

{geocif-0.1.29 → geocif-0.1.30}/geocif/ml/stages.py

@@ -17,7 +17,9 @@ def add_stage_information(df, method):
     df["Stage"] = df["Stage"].astype(str)
 
     df["Stage_ID"] = df["Stage"]
-    df["Stage Range"] = df["Stage"].apply(lambda x: "_".join([x.split("_")[0], x.split("_")[-1]]))
+    df["Stage Range"] = df["Stage"].apply(
+        lambda x: "_".join([x.split("_")[0], x.split("_")[-1]])
+    )
 
     # Create a column with starting stage and ending stage
     # Stage looks like this: 13_12_11
@@ -34,14 +36,18 @@ def add_stage_information(df, method):
         dict = utils.dict_growth_stages_biweekly
     elif "monthly" in method:
         dict = utils.dict_growth_stages_monthly
-    df["Stage Names"] = df["Starting Stage"].map(dict) + " - " + df["Ending Stage"].map(dict)
+    df["Stage Names"] = (
+        df["Starting Stage"].map(dict) + " - " + df["Ending Stage"].map(dict)
+    )
 
     # Group by Region, Harvest Year
     # For each group, add a column called Percentage Season
     # that is the percentage of the season that has passed based on the number of rows
     # in the group
     grouped = df.groupby(["Region", "Harvest Year"])
-    df["Percentage Season"] = grouped.cumcount() * 100.0 / grouped["CEI"].transform("size")
+    df["Percentage Season"] = (
+        grouped.cumcount() * 100.0 / grouped["CEI"].transform("size")
+    )
 
     return df
 
@@ -186,7 +192,9 @@ def get_stage_information_dict(stage_str, method):
     end_stage = parts[-1]
 
     # Exclude cei from the stage_str string
-    stage_info["Stage_ID"] = "_".join(parts[1:]) if parts[1].isdigit() else "_".join(parts[2:])
+    stage_info["Stage_ID"] = (
+        "_".join(parts[1:]) if parts[1].isdigit() else "_".join(parts[2:])
+    )
 
     stage_info["CEI"] = cei
     stage_info["Stage Range"] = "_".join([start_stage, end_stage])

{geocif-0.1.29 → geocif-0.1.30}/geocif/ml/stats.py

@@ -29,33 +29,54 @@ def get_yld_prd(df, name_crop, cntr, region, calendar_year, region_column="ADM1_
         #    df_tmp = df.loc[mask_adm1]
 
         df_tmp = df.copy()
-        if name_crop == 'rice':
-            if cntr == 'Viet nam':
-                df_tmp = df.loc[df.Season == 'Spring Paddy']
-            elif cntr == 'Thailand':
-                df_tmp = df.loc[df.Season == 'Major Season']
-            elif cntr == 'China':
-                df_tmp = df.loc[df.Season == 'Single-cropping and Middle-season Rice']
-            elif cntr == 'India':
-                df_tmp = df.loc[df.Season == 'Kharif']
-        elif name_crop == 'maize' and \
-                cntr in ['Austria', 'Belgium', 'Bulgaria', 'Croatia', 'Czech  Republic', 'Denmark','Germany', 'Greece', 'Hungary',
-                         'Italy', 'Lithuania', 'Luxembourg', 'Netherlands', 'Poland', 'Portugal', 'Romania', 'Slovakia', 'Slovenia', 'Spain',
-                         'Sweden', 'United Kingdom']:
-            df_tmp = df.loc[df.Season == 'Grain Maize and Corn-cob-mix']
-        elif name_crop == 'maize' and cntr in ['France']:
-            df_tmp = df.loc[df.Season == 'Green Maize']
+        if name_crop == "rice":
+            if cntr == "Viet nam":
+                df_tmp = df.loc[df.Season == "Spring Paddy"]
+            elif cntr == "Thailand":
+                df_tmp = df.loc[df.Season == "Major Season"]
+            elif cntr == "China":
+                df_tmp = df.loc[df.Season == "Single-cropping and Middle-season Rice"]
+            elif cntr == "India":
+                df_tmp = df.loc[df.Season == "Kharif"]
+        elif name_crop == "maize" and cntr in [
+            "Austria",
+            "Belgium",
+            "Bulgaria",
+            "Croatia",
+            "Czech  Republic",
+            "Denmark",
+            "Germany",
+            "Greece",
+            "Hungary",
+            "Italy",
+            "Lithuania",
+            "Luxembourg",
+            "Netherlands",
+            "Poland",
+            "Portugal",
+            "Romania",
+            "Slovakia",
+            "Slovenia",
+            "Spain",
+            "Sweden",
+            "United Kingdom",
+        ]:
+            df_tmp = df.loc[df.Season == "Grain Maize and Corn-cob-mix"]
+        elif name_crop == "maize" and cntr in ["France"]:
+            df_tmp = df.loc[df.Season == "Green Maize"]
 
         if not df_tmp.empty:
-            if cntr != 'Vietnam':
-                mask_tmp_country = (df_tmp['ADM0_NAME'].str.lower() == cntr.replace('_', ' ').lower())
+            if cntr != "Vietnam":
+                mask_tmp_country = (
+                    df_tmp["ADM0_NAME"].str.lower() == cntr.replace("_", " ").lower()
+                )
             else:
-                mask_tmp_country = (df_tmp['ADM0_NAME'].str.lower() == 'viet nam')
+                mask_tmp_country = df_tmp["ADM0_NAME"].str.lower() == "viet nam"
             if region:
-                mask_tmp_adm1 = (df_tmp[region_column].str.lower() == region.lower())
+                mask_tmp_adm1 = df_tmp[region_column].str.lower() == region.lower()
             else:
                 # ADM1_NAME column should be NaN to get country level stats
-                mask_tmp_adm1 = (df_tmp[region_column].isnull())
+                mask_tmp_adm1 = df_tmp[region_column].isnull()
 
             val = df_tmp.loc[mask_tmp_country & mask_tmp_adm1][calendar_year]
 
@@ -145,7 +166,16 @@ def add_GEOGLAM_statistics(dir_stats, df, stats, method, admin_zone):
     return df
 
 
-def add_statistics(dir_stats, df, country, crop, admin_zone, stats, method, target_col="Yield (tn per ha)"):
+def add_statistics(
+    dir_stats,
+    df,
+    country,
+    crop,
+    admin_zone,
+    stats,
+    method,
+    target_col="Yield (tn per ha)",
+):
     """
 
     Args:
@@ -166,7 +196,9 @@ def add_statistics(dir_stats, df, country, crop, admin_zone, stats, method, targ
 
     # HACK
     if country == "Afghanistan":
-        df_fewsnet.loc[:, "product"] = df_fewsnet["season_name"] + " " + df_fewsnet["product"]
+        df_fewsnet.loc[:, "product"] = (
+            df_fewsnet["season_name"] + " " + df_fewsnet["product"]
+        )
     # Check if country and crop exist in the fewsnet database
     mask = (df_fewsnet["country"] == country) & (df_fewsnet["product"] == crop)
 
@@ -183,12 +215,27 @@ def add_statistics(dir_stats, df, country, crop, admin_zone, stats, method, targ
             mask_region = df_fewsnet[admin_zone] == region
             mask_yield = (
                 df_fewsnet["crop_production_system"].isin(
-                    ["none", "Small-scale (PS)", "Commercial (PS)", "All (PS)", "irrigated", "rainfed"]
+                    [
+                        "none",
+                        "Small-scale (PS)",
+                        "Commercial (PS)",
+                        "All (PS)",
+                        "irrigated",
+                        "rainfed",
+                    ]
                 )
                 & (df_fewsnet["harvest_year"] == harvest_year)
                 & (df_fewsnet["product"] == crop)
                 & df_fewsnet["season_name"].isin(
-                    ["Main", "Meher", "Main harvest", "Annual", "Summer", "Spring", "Winter"]
+                    [
+                        "Main",
+                        "Meher",
+                        "Main harvest",
+                        "Annual",
+                        "Summer",
+                        "Spring",
+                        "Winter",
+                    ]
                 )
                 & (df_fewsnet["indicator"].isin(["yield", "area", "production"]))
             )

{geocif-0.1.29 → geocif-0.1.30}/geocif/ml/trainers.py

@@ -84,7 +84,9 @@ def optuna_objective(model, df, feature_names, target_col, cat_features=[]):
     y = df[target_col]
 
     # Divide the data into training and validation sets
-    train_X, val_X, train_y, val_y = train_test_split(X, y, test_size=0.2, random_state=0)
+    train_X, val_X, train_y, val_y = train_test_split(
+        X, y, test_size=0.2, random_state=0
+    )
 
     model.fit(
         train_X,
@@ -134,7 +136,9 @@ def optimized_model(
                 params = {
                     "depth": trial.suggest_int("depth", 1, 7),
                     "learning_rate": trial.suggest_float("learning_rate", 0.01, 0.1),
-                    "iterations": trial.suggest_int("iterations", low=1000, high=5000, step=500),
+                    "iterations": trial.suggest_int(
+                        "iterations", low=1000, high=5000, step=500
+                    ),
                     "subsample": trial.suggest_float("subsample", 1.0, 1.0),
                     "random_strength": trial.suggest_float("random_strength", 0.3, 1.0),
                     "reg_lambda": trial.suggest_float("reg_lambda", 1e-8, 1.0),
@@ -177,7 +181,9 @@ def optimized_model(
         optuna.logging.set_verbosity(optuna.logging.WARNING)  # Disable verbose
         sampler = optuna.samplers.TPESampler(seed=seed)
         study = optuna.create_study(sampler=sampler, direction="minimize")
-        study.optimize(_optuna_objective, n_trials=n_trials, n_jobs=int(mp.cpu_count() * 0.4))
+        study.optimize(
+            _optuna_objective, n_trials=n_trials, n_jobs=int(mp.cpu_count() * 0.4)
+        )
         if study.best_trial is None:
             raise ValueError("Optimization failed to complete any trials.")
         hyperparams = study.best_trial.params

{geocif-0.1.29 → geocif-0.1.30}/geocif/ml/trend.py

@@ -74,7 +74,9 @@ def compute_trend(detrended_data, future_time_points=None):
     model = detrended_data.trend_model[0]
 
     if model_type == "mean":
-        trend_component = model.predict(np.ones(len(future_time_points)), has_constant="add")
+        trend_component = model.predict(
+            np.ones(len(future_time_points)), has_constant="add"
+        )
     elif model_type == "linear":
         X_linear = add_constant(future_time_points, has_constant="add")
         trend_component = model.predict(X_linear)

{geocif-0.1.29 → geocif-0.1.30/geocif.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geocif
-Version: 0.1.29
+Version: 0.1.30
 Summary: Models to visualize and forecast crop conditions and yields
 Home-page: https://ritviksahajpal.github.io/yield_forecasting/
 Author: Ritvik Sahajpal

{geocif-0.1.29 → geocif-0.1.30}/geocif.egg-info/SOURCES.txt

@@ -37,6 +37,7 @@ geocif/ml/feature_selection.py
 geocif/ml/outliers.py
 geocif/ml/outlook.py
 geocif/ml/output.py
+geocif/ml/spatial_autocorrelation.py
 geocif/ml/stages.py
 geocif/ml/stats.py
 geocif/ml/trainers.py

{geocif-0.1.29 → geocif-0.1.30}/setup.py

@@ -50,6 +50,6 @@ setup(
     test_suite="tests",
     tests_require=test_requirements,
     url="https://ritviksahajpal.github.io/yield_forecasting/",
-    version="0.1.29",
+    version="0.1.30",
     zip_safe=False,
 )