Add dataset SUPPORT2

docs/api/datasets.rst

@@ -42,6 +42,7 @@ Available Datasets
     datasets/pyhealth.datasets.SHHSDataset
     datasets/pyhealth.datasets.SleepEDFDataset
     datasets/pyhealth.datasets.EHRShotDataset
+    datasets/pyhealth.datasets.Support2Dataset
     datasets/pyhealth.datasets.COVID19CXRDataset
     datasets/pyhealth.datasets.TUABDataset
     datasets/pyhealth.datasets.TUEVDataset

docs/api/datasets/pyhealth.datasets.Support2Dataset.rst

@@ -0,0 +1,15 @@
+pyhealth.datasets.Support2Dataset
+==================================
+
+Overview
+--------
+
+The SUPPORT2 (Study to Understand Prognoses and Preferences for Outcomes and Risks of Treatments) dataset contains data on seriously ill hospitalized adults. It includes patient demographics, diagnoses, clinical measurements, and outcomes such as survival and hospital mortality.
+
+The dataset is commonly used for mortality prediction, length of stay prediction, and other clinical outcome prediction tasks.
+
+.. autoclass:: pyhealth.datasets.Support2Dataset
+    :members:
+    :undoc-members:
+    :show-inheritance:
+

pyhealth/datasets/__init__.py

@@ -63,6 +63,7 @@ def __init__(self, *args, **kwargs):
 from .shhs import SHHSDataset
 from .sleepedf import SleepEDFDataset
 from .bmd_hs import BMDHSDataset
+from .support2 import Support2Dataset
 from .splitter import (
     split_by_patient,
     split_by_patient_conformal,

pyhealth/datasets/configs/support2.yaml

@@ -0,0 +1,55 @@
+version: "1.0"
+tables:
+  support2:
+    file_path: "support2.csv"
+    patient_id: "sno"
+    timestamp: null
+    attributes:
+      - "d.time"
+      - "age"
+      - "death"
+      - "sex"
+      - "hospdead"
+      - "slos"
+      - "dzgroup"
+      - "dzclass"
+      - "num.co"
+      - "edu"
+      - "income"
+      - "scoma"
+      - "charges"
+      - "totcst"
+      - "totmcst"
+      - "avtisst"
+      - "race"
+      - "sps"
+      - "aps"
+      - "surv2m"
+      - "surv6m"
+      - "hday"
+      - "diabetes"
+      - "dementia"
+      - "ca"
+      - "prg2m"
+      - "prg6m"
+      - "dnr"
+      - "dnrday"
+      - "meanbp"
+      - "wblc"
+      - "hrt"
+      - "resp"
+      - "temp"
+      - "pafi"
+      - "alb"
+      - "bili"
+      - "crea"
+      - "sod"
+      - "ph"
+      - "glucose"
+      - "bun"
+      - "urine"
+      - "adlp"
+      - "adls"
+      - "sfdm2"
+      - "adlsc"
+

pyhealth/datasets/support2.py

@@ -0,0 +1,49 @@
+import logging
+from pathlib import Path
+from typing import List, Optional
+
+from .base_dataset import BaseDataset
+
+logger = logging.getLogger(__name__)
+
+
+class Support2Dataset(BaseDataset):
+    """
+    A dataset class for handling SUPPORT2 (Study to Understand Prognoses and Preferences 
+    for Outcomes and Risks of Treatments) data.
+
+    The SUPPORT2 dataset contains data on seriously ill hospitalized adults, including
+    patient demographics, diagnoses, clinical measurements, and outcomes.
+
+    The dataset is available in R packages such as "rms" and "Hmisc".
+    For more information, see: Knaus WA, Harrell FE, Lynn J, et al. The SUPPORT
+    prognostic model: Objective estimates of survival for seriously ill hospitalized
+    adults. Ann Intern Med. 1995;122(3):191-203.
+
+    Attributes:
+        root (str): The root directory where the dataset is stored.
+        tables (List[str]): A list of tables to be included in the dataset.
+        dataset_name (Optional[str]): The name of the dataset.
+        config_path (Optional[str]): The path to the configuration file.
+    """
+
+    def __init__(
+        self,
+        root: str,
+        tables: List[str],
+        dataset_name: Optional[str] = None,
+        config_path: Optional[str] = None,
+        **kwargs
+    ) -> None:
+        if config_path is None:
+            logger.info("No config path provided, using default config")
+            config_path = Path(__file__).parent / "configs" / "support2.yaml"
+        super().__init__(
+            root=root,
+            tables=tables,
+            dataset_name=dataset_name or "support2",
+            config_path=config_path,
+            **kwargs
+        )
+        return
+