Update ProphetModel to handle external timestamp

CHANGELOG.md

@@ -57,7 +57,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Update `ResampleWithDistributionTransform` to work with integer timestamp ([#165](https://github.com/etna-team/etna/pull/165))
 - 
 - Update change point transforms (`ChangePointsSegmentationTransform`, `ChangePointsTrendTransform`, `ChangePointsLevelTransform`, `TrendTransform`) to handle integer timestamp ([#176](https://github.com/etna-team/etna/pull/176))
-- 
+- Update `ProphetModel` to handle external timestamp ([#203](https://github.com/etna-team/etna/pull/203))
 
 ### Fixed
 - 

etna/models/prophet.py

@@ -8,6 +8,7 @@
 from typing import Sequence
 from typing import Set
 from typing import Union
+from typing import cast
 
 import pandas as pd
 
@@ -50,6 +51,7 @@ def __init__(
         uncertainty_samples: Union[int, bool] = 1000,
         stan_backend: Optional[str] = None,
         additional_seasonality_params: Iterable[Dict[str, Union[str, float, int]]] = (),
+        timestamp_column: Optional[str] = None,
     ):
 
         self.growth = growth
@@ -69,6 +71,7 @@ def __init__(
         self.uncertainty_samples = uncertainty_samples
         self.stan_backend = stan_backend
         self.additional_seasonality_params = additional_seasonality_params
+        self.timestamp_column = timestamp_column
 
         self.model = self._create_model()
 
@@ -131,8 +134,12 @@ def _select_regressors(self, df: pd.DataFrame) -> Optional[pd.DataFrame]:
             )
 
         if self.regressor_columns:
+            columns = deepcopy(self.regressor_columns)
+            if self.timestamp_column in columns:
+                columns.remove(self.timestamp_column)
+
             try:
-                result = df[self.regressor_columns].apply(pd.to_numeric)
+                result = df[columns].apply(pd.to_numeric)
             except ValueError as e:
                 raise ValueError(f"Only convertible to numeric features are allowed! Error: {str(e)}")
         else:
@@ -156,8 +163,11 @@ def fit(self, df: pd.DataFrame, regressors: List[str]) -> "_ProphetAdapter":
 
         prophet_df = self._prepare_prophet_df(df=df)
         for regressor in self.regressor_columns:
-            if regressor not in self.predefined_regressors_names:
-                self.model.add_regressor(regressor)
+            if regressor in self.predefined_regressors_names:
+                continue
+            if regressor == self.timestamp_column:
+                continue
+            self.model.add_regressor(regressor)
         self.model.fit(prophet_df)
         return self
 
@@ -193,20 +203,45 @@ def predict(self, df: pd.DataFrame, prediction_interval: bool, quantiles: Sequen
         y_pred = y_pred.rename(rename_dict, axis=1)
         return y_pred
 
+    def _validate_timestamp(self, df: pd.DataFrame):
+        self.regressor_columns = cast(List[str], self.regressor_columns)
+
+        if self.timestamp_column is None:
+            if not pd.api.types.is_datetime64_dtype(df["timestamp"]):
+                raise ValueError("Invalid timestamp! Only datetime type is supported.")
+
+        else:
+            if self.timestamp_column not in df.columns:
+                raise ValueError("Invalid timestamp_column! It isn't present in a given dataset.")
+
+            if self.timestamp_column not in self.regressor_columns:
+                raise ValueError("Invalid timestamp_column! It should be a regressor.")
+
+            if not pd.api.types.is_datetime64_dtype(df[self.timestamp_column]):
+                raise ValueError("Invalid timestamp_column! Only datetime type is supported.")
+
+            if len(df[self.timestamp_column]) >= 3 and pd.infer_freq(df[self.timestamp_column]) is None:
+                raise ValueError("Invalid timestamp_column! It doesn't contain sequential timestamps.")
+
     def _prepare_prophet_df(self, df: pd.DataFrame) -> pd.DataFrame:
         """Prepare dataframe for fit and predict."""
         if self.regressor_columns is None:
             raise ValueError("List of regressor is not set!")
 
+        self._validate_timestamp(df)
         df = df.reset_index()
 
         prophet_df = pd.DataFrame()
         prophet_df["y"] = df["target"]
-        prophet_df["ds"] = df["timestamp"]
+
+        if self.timestamp_column is None:
+            prophet_df["ds"] = df["timestamp"]
+        else:
+            prophet_df["ds"] = df[self.timestamp_column]
 
         regressors_data = self._select_regressors(df)
         if regressors_data is not None:
-            prophet_df[self.regressor_columns] = regressors_data[self.regressor_columns]
+            prophet_df[regressors_data.columns] = regressors_data
 
         return prophet_df
 
@@ -358,7 +393,7 @@ class ProphetModel(
     daily_seasonality = 'auto', holidays = None, seasonality_mode = 'additive',
     seasonality_prior_scale = 10.0, holidays_prior_scale = 10.0, changepoint_prior_scale = 0.05,
     mcmc_samples = 0, interval_width = 0.8, uncertainty_samples = 1000, stan_backend = None,
-    additional_seasonality_params = (), )
+    additional_seasonality_params = (), timestamp_column = None, )
     >>> forecast = model.forecast(future)
     >>> forecast
     segment    segment_0 segment_1 segment_2 segment_3
@@ -392,6 +427,7 @@ def __init__(
         uncertainty_samples: Union[int, bool] = 1000,
         stan_backend: Optional[str] = None,
         additional_seasonality_params: Iterable[Dict[str, Union[str, float, int]]] = (),
+        timestamp_column: Optional[str] = None,
     ):
         """
         Create instance of Prophet model.
@@ -467,6 +503,9 @@ def __init__(
             parameters that describe additional (not 'daily', 'weekly', 'yearly') seasonality that should be
             added to model; dict with required keys 'name', 'period', 'fourier_order' and optional ones 'prior_scale',
             'mode', 'condition_name' will be used for :py:meth:`prophet.Prophet.add_seasonality` method call.
+        timestamp_column:
+            Name of a column to be used as timestamp. If not given, index is used.
+            Column is expected to be regressor containing datetime values with some fixed frequency.
         """
         self.growth = growth
         self.n_changepoints = n_changepoints
@@ -485,6 +524,7 @@ def __init__(
         self.uncertainty_samples = uncertainty_samples
         self.stan_backend = stan_backend
         self.additional_seasonality_params = additional_seasonality_params
+        self.timestamp_column = timestamp_column
 
         super(ProphetModel, self).__init__(
             base_model=_ProphetAdapter(
@@ -505,6 +545,7 @@ def __init__(
                 uncertainty_samples=self.uncertainty_samples,
                 stan_backend=self.stan_backend,
                 additional_seasonality_params=self.additional_seasonality_params,
+                timestamp_column=self.timestamp_column,
             )
         )
 

tests/test_models/test_inference/conftest.py

@@ -0,0 +1,17 @@
+import pandas as pd
+import pytest
+
+from etna.datasets import TSDataset
+from etna.datasets import generate_ar_df
+
+
+@pytest.fixture
+def ts_with_external_timestamp() -> TSDataset:
+    df = generate_ar_df(periods=100, start_time=10, n_segments=2, freq=None)
+    df_wide = TSDataset.to_dataset(df)
+    df_exog = generate_ar_df(periods=100, start_time=10, n_segments=2, freq=None)
+    df_exog["target"] = pd.date_range(start="2020-01-01", periods=100).tolist() * 2
+    df_exog_wide = TSDataset.to_dataset(df_exog)
+    df_exog_wide.rename(columns={"target": "external_timestamp"}, level="feature", inplace=True)
+    ts = TSDataset(df=df_wide.iloc[:-10], df_exog=df_exog_wide, known_future="all", freq=None)
+    return ts