7  IE Summary

Objectives

This guide demonstrates Inclusion/Exclusion (IE) summary analysis showing Protocol Deviations.

7.1 Setup

import sys
from pathlib import Path
import polars as pl

sys.path.insert(0, 'src')

from rtflite import LibreOfficeConverter
try:
    converter = LibreOfficeConverter()
except Exception:
    converter = None
    print("WARNING: LibreOffice not found. PDF conversion will be skipped.")

from csrlite import load_plan, study_plan_to_ie_summary
from csrlite.ie.ie_summary import ie_ard, ie_df, ie_rtf

7.2 IE Summary Analysis

The IE analysis focuses on: 1. Identifying screening failures from ADSL/ADIE. 2. Breaking down failures by category (Inclusion vs Exclusion). 3. Detailing specific criteria failures.

7.3 StudyPlan-Driven Workflow

study_plan = load_plan("studies/xyz123/yaml/plan_xyz123.yaml")
study_plan.get_plan_df().filter(pl.col("analysis") == "ie_summary")

2026-02-03 15:26:50,917 - csrlite.common.plan - INFO - Successfully loaded dataset 'adsl' from 'studies/xyz123/yaml/../../../data/adsl.parquet'
2026-02-03 15:26:50,920 - csrlite.common.plan - INFO - Successfully loaded dataset 'adae' from 'studies/xyz123/yaml/../../../data/adae.parquet'
2026-02-03 15:26:50,921 - csrlite.common.plan - INFO - Successfully loaded dataset 'adie' from 'studies/xyz123/yaml/../../../data/adie.parquet'
2026-02-03 15:26:50,923 - csrlite.common.plan - INFO - Successfully loaded dataset 'adpd' from 'studies/xyz123/yaml/../../../data/adpd.parquet'

shape: (1, 5)

analysis	population	observation	parameter	group
str	str	str	str	str
"ie_summary"	"all"	null	null	null

output_files = study_plan_to_ie_summary(study_plan)

studies/xyz123/rtf/ie_summary_all_total.rtf

7.3.1 ie_summary_scrfail

7.4 Complete Pipeline

adsl = pl.read_parquet("data/adsl.parquet")
adie = pl.read_parquet("data/adie.parquet")

ard = ie_ard(
    adsl=adsl,
    adie=adie,
    group_col="TRT01A"
)

df = ie_df(ard)

ie_rtf(
    df,
    "studies/xyz123/rtf/ie_summary_manual.rtf",
    title=[
        "Summary of Protocol Deviations",
        "(Inclusion/Exclusion)"
    ]
)

studies/xyz123/rtf/ie_summary_manual.rtf