csrlite 0.1.0__py3-none-any.whl

csrlite/disposition/disposition.py

@@ -0,0 +1,301 @@
+# pyre-strict
+"""
+Disposition Table 1.1 Analysis Functions
+
+This module provides a pipeline for Disposition Table 1.1 summary analysis:
+- disposition_ard: Generate Analysis Results Data (ARD)
+- disposition_df: Transform ARD to display format
+- disposition_rtf: Generate formatted RTF output
+- disposition: Complete pipeline wrapper
+- study_plan_to_disposition_summary: Batch generation from StudyPlan
+"""
+
+from pathlib import Path
+
+import polars as pl
+from rtflite import RTFDocument
+
+from ..ae.ae_utils import create_ae_rtf_table
+from ..common.count import count_subject_with_observation
+from ..common.parse import StudyPlanParser
+from ..common.plan import StudyPlan
+from ..common.utils import apply_common_filters
+
+
+def study_plan_to_disposition_summary(
+    study_plan: StudyPlan,
+) -> list[str]:
+    """
+    Generate Disposition Table 1.1 RTF outputs for all analyses defined in StudyPlan.
+    """
+    # Meta data
+    analysis_type = "disposition_summary"
+    output_dir = study_plan.output_dir
+    footnote = ["Percentages are based on the number of enrolled participants."]
+    source = None
+
+    population_df_name = "adsl"
+    observation_df_name = "ds"  # As per plan_ds_xyz123.yaml
+
+    id = ("USUBJID", "Subject ID")
+    total = True
+    missing_group = "error"
+
+    # Create output directory
+    Path(output_dir).mkdir(parents=True, exist_ok=True)
+
+    # Initialize parser
+    parser = StudyPlanParser(study_plan)
+
+    # Get expanded plan DataFrame
+    plan_df = study_plan.get_plan_df()
+
+    # Filter for disposition analyses
+    disp_plans = plan_df.filter(pl.col("analysis") == analysis_type)
+
+    rtf_files = []
+
+    for row in disp_plans.iter_rows(named=True):
+        population = row["population"]
+        observation = row.get("observation")
+        parameter = row["parameter"]
+        group = row.get("group")
+        title_text = row.get(
+            "title", "Disposition of Participants"
+        )  # Allow title override from plan if we supported it in parser, else default
+
+        # Get datasets
+        population_df, observation_df = parser.get_datasets(population_df_name, observation_df_name)
+
+        # Get filters
+        population_filter = parser.get_population_filter(population)
+        obs_filter = parser.get_observation_filter(observation)
+
+        # Get parameters with indent levels
+        param_names, param_filters, param_labels, param_indents = parser.get_parameter_info(
+            parameter
+        )
+
+        # Apply indentation to labels
+        indented_labels = []
+        for label, indent_level in zip(param_labels, param_indents):
+            indent_str = "    " * indent_level  # 4 spaces per indent level
+            indented_labels.append(f"{indent_str}{label}")
+
+        variables_list = list(zip(param_filters, indented_labels))
+
+        # Get group info (optional)
+        if group is not None:
+            group_var_name, group_labels = parser.get_group_info(group)
+            group_var_label = group_labels[0] if group_labels else group_var_name
+            group_tuple = (group_var_name, group_var_label)
+        else:
+            # When no group specified, use a dummy group column for overall counts
+            group_tuple = None
+
+        # Build title
+        title_parts = [title_text]
+        pop_kw = study_plan.keywords.populations.get(population)
+        if pop_kw and pop_kw.label:
+            title_parts.append(pop_kw.label)
+
+        # Build output filename
+        group_suffix = f"_{group}" if group else ""
+        filename = f"{analysis_type}_{population}{group_suffix}.rtf"
+        output_file = str(Path(output_dir) / filename)
+
+        rtf_path = disposition(
+            population=population_df,
+            observation=observation_df,
+            population_filter=population_filter,
+            observation_filter=obs_filter,
+            id=id,
+            group=group_tuple,
+            variables=variables_list,
+            title=title_parts,
+            footnote=footnote,
+            source=source,
+            output_file=output_file,
+            total=total,
+            missing_group=missing_group,
+        )
+        rtf_files.append(rtf_path)
+
+    return rtf_files
+
+
+def disposition(
+    population: pl.DataFrame,
+    observation: pl.DataFrame,
+    population_filter: str | None,
+    observation_filter: str | None,
+    id: tuple[str, str],
+    group: tuple[str, str] | None,
+    variables: list[tuple[str, str]],
+    title: list[str],
+    footnote: list[str] | None,
+    source: list[str] | None,
+    output_file: str,
+    total: bool = True,
+    col_rel_width: list[float] | None = None,
+    missing_group: str = "error",
+) -> str:
+    """
+    Complete Disposition Table 1.1 pipeline wrapper.
+    """
+    # Step 1: Generate ARD
+    ard = disposition_ard(
+        population=population,
+        observation=observation,
+        population_filter=population_filter,
+        observation_filter=observation_filter,
+        id=id,
+        group=group,
+        variables=variables,
+        total=total,
+        missing_group=missing_group,
+    )
+
+    # Step 2: Transform to display format
+    df = disposition_df(ard)
+
+    # Step 3: Generate RTF
+    rtf_doc = disposition_rtf(
+        df=df,
+        title=title,
+        footnote=footnote,
+        source=source,
+        col_rel_width=col_rel_width,
+    )
+    rtf_doc.write_rtf(output_file)
+
+    return output_file
+
+
+def disposition_ard(
+    population: pl.DataFrame,
+    observation: pl.DataFrame,
+    population_filter: str | None,
+    observation_filter: str | None,
+    id: tuple[str, str],
+    group: tuple[str, str] | None,
+    variables: list[tuple[str, str]],
+    total: bool,
+    missing_group: str,
+) -> pl.DataFrame:
+    """
+    Generate ARD for Disposition Table 1.1.
+    """
+    id_var_name, _ = id
+
+    # Handle optional group
+    if group is not None:
+        group_var_name, _ = group
+    else:
+        # Create a dummy group column for overall counts
+        group_var_name = "__all__"
+        population = population.with_columns(pl.lit("All Subjects").alias(group_var_name))
+        observation = observation.with_columns(pl.lit("All Subjects").alias(group_var_name))
+        total = False  # No need for total column when there's only one group
+
+    # Apply common filters
+    population_filtered, observation_to_filter = apply_common_filters(
+        population=population,
+        observation=observation,
+        population_filter=population_filter,
+        observation_filter=observation_filter,
+    )
+
+    # For each parameter, we create an "observation" dataset and use
+    # count_subject_with_observation. This approach works for both ADSL-based
+    # filters (e.g., "Enrolled") and DS-based filters (e.g., "Discontinued")
+
+    results = []
+
+    for var_filter, var_label in variables:
+        # Try to apply the filter to population first, then observation
+        # This handles both ADSL-based and DS-based parameter filters
+        try:
+            target_obs = population_filtered.filter(pl.sql_expr(var_filter))
+        except Exception:
+            target_obs = observation_to_filter.filter(pl.sql_expr(var_filter))
+
+        # Add the parameter label as a variable for counting
+        target_obs = target_obs.with_columns(pl.lit(var_label).alias("__index__"))
+
+        # Use count_subject_with_observation to get n (%) for each group
+        counts = count_subject_with_observation(
+            population=population_filtered,
+            observation=target_obs,
+            id=id_var_name,
+            group=group_var_name,
+            variable="__index__",
+            total=total,
+            missing_group=missing_group,
+        )
+
+        results.append(
+            counts.select(
+                pl.col("__index__"),
+                pl.col(group_var_name).alias("__group__"),
+                pl.col("n_pct_subj_fmt").alias("__value__"),
+            )
+        )
+
+    # Combine all results
+    ard = pl.concat(results)
+
+    # Sort by the order of variables in the list
+    # Create an Enum for __index__
+    var_labels = [label for _, label in variables]
+    ard = ard.with_columns(pl.col("__index__").cast(pl.Enum(var_labels))).sort(
+        "__index__", "__group__"
+    )
+
+    return ard
+
+
+def disposition_df(ard: pl.DataFrame) -> pl.DataFrame:
+    """
+    Transform ARD to display format.
+    """
+    # Pivot
+    df_wide = ard.pivot(index="__index__", on="__group__", values="__value__")
+
+    # Rename index
+    df_wide = df_wide.rename({"__index__": "Disposition Status"})
+
+    return df_wide
+
+
+def disposition_rtf(
+    df: pl.DataFrame,
+    title: list[str],
+    footnote: list[str] | None,
+    source: list[str] | None,
+    col_rel_width: list[float] | None = None,
+) -> RTFDocument:
+    """
+    Generate RTF.
+    """
+    # Reuse generic table creation
+    # Columns: Disposition Status, Group 1, Group 2, ... Total
+
+    n_cols = len(df.columns)
+    col_header_1 = list(df.columns)
+    col_header_2 = [""] + ["n (%)"] * (n_cols - 1)
+
+    if col_rel_width is None:
+        col_widths = [2.5] + [1] * (n_cols - 1)
+    else:
+        col_widths = col_rel_width
+
+    return create_ae_rtf_table(
+        df=df,
+        col_header_1=col_header_1,
+        col_header_2=col_header_2,
+        col_widths=col_widths,
+        title=title,
+        footnote=footnote,
+        source=source,
+    )

csrlite-0.1.0.dist-info/METADATA

@@ -0,0 +1,68 @@
+Metadata-Version: 2.4
+Name: csrlite
+Version: 0.1.0
+Summary: A hierarchical YAML-based framework for generating Tables, Listings, and Figures in clinical trials
+Author-email: Clinical Biostatistics Team <biostat@example.com>
+License: MIT
+Project-URL: Homepage, https://github.com/elong0527/csrlite
+Project-URL: Documentation, https://elong0527.github.io/csrlite
+Project-URL: Repository, https://github.com/elong0527/csrlite.git
+Project-URL: Bug Tracker, https://github.com/elong0527/csrlite/issues
+Keywords: clinical-trials,biostatistics,yaml,tlf,tables,listings,figures
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: pydantic>=2.0.0
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: polars>=0.20.0
+Requires-Dist: rtflite>=2.1.1
+Provides-Extra: rtf
+Requires-Dist: rtflite; extra == "rtf"
+Provides-Extra: plotting
+Requires-Dist: matplotlib>=3.5.0; extra == "plotting"
+Requires-Dist: plotly>=5.0.0; extra == "plotting"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
+Requires-Dist: black>=22.0.0; extra == "dev"
+Requires-Dist: isort>=5.0.0; extra == "dev"
+Requires-Dist: mypy>=1.0.0; extra == "dev"
+Requires-Dist: pytest>=9.0.1; extra == "dev"
+Requires-Dist: jupyter>=1.1.1; extra == "dev"
+Requires-Dist: jupyter-cache>=1.0.1; extra == "dev"
+Requires-Dist: nbformat>=5.10.4; extra == "dev"
+Requires-Dist: ruff>=0.1.0; extra == "dev"
+Requires-Dist: pyre-check>=0.9.18; extra == "dev"
+Provides-Extra: all
+Requires-Dist: rtflite; extra == "all"
+Requires-Dist: matplotlib>=3.5.0; extra == "all"
+Requires-Dist: plotly>=5.0.0; extra == "all"
+
+# csrlite
+
+[![CI](https://github.com/elong0527/csrlite/actions/workflows/ci.yml/badge.svg)](https://github.com/elong0527/csrlite/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/elong0527/csrlite/branch/main/graph/badge.svg)](https://codecov.io/gh/elong0527/csrlite)
+[![PyPI version](https://badge.fury.io/py/csrlite.svg)](https://badge.fury.io/py/csrlite)
+[![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
+
+A hierarchical YAML-based framework for generating Tables, Listings, and Figures in clinical trials.
+
+## Installation
+
+```bash
+pip install csrlite
+```
+
+## Documentation
+
+Visit [https://elong0527.github.io/csrlite](https://elong0527.github.io/csrlite) for full documentation.
+
+## License
+
+MIT License - see [LICENSE](LICENSE) file for details.

csrlite-0.1.0.dist-info/RECORD

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csrlite-0.1.0.dist-info/WHEEL

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+Generator: setuptools (80.9.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
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csrlite-0.1.0.dist-info/top_level.txt

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