teal_modules_clinical_dataset_requirements.json

{
  "teal.modules.clinical_simple": {
    "description": "Simple overview of teal.modules.clinical modules showing module name, description and required datasets. Uses flexible BDS_DATASET notation for modules that work with multiple analysis datasets.",
    "total_modules": 37,
    "dataset_types": {
      "ADSL": "Subject-Level Analysis Dataset - required by almost all modules for demographics/baseline",
      "BDS_DATASET": "Basic Data Structure Dataset - can be ADLB, ADVS, ADQS, ADEG, or any ADaM BDS dataset with appropriate variables (PARAMCD, AVAL, etc.)",
      "BDS_CONTINUOUS": "BDS dataset with continuous AVAL (numeric values) - typically ADLB, ADVS, ADQS",
      "BDS_BINARY": "BDS dataset with binary AVAL (0/1 values) or can be derived from BDS_CONTINUOUS",
      "ADTTE": "Time-to-Event Analysis Dataset - specific structure with CNSR, AVAL (time)",
      "ADRS": "Response Analysis Dataset - specific structure for tumor response",
      "ADAE": "Adverse Events Analysis Dataset - specific structure for safety data",
      "ADLB": "Laboratory Analysis Dataset - specific structure with lab tests and grades",
      "ADVS": "Vital Signs Analysis Dataset",
      "ADQS": "Questionnaire Analysis Dataset",
      "ADCM": "Concomitant Medications Analysis Dataset",
      "ADEX": "Exposure Analysis Dataset",
      "ADMH": "Medical History Analysis Dataset",
      "ADAETTE": "Adverse Events Time-to-Event Analysis Dataset"
    },
    "modules": {
      "tm_g_ci": {
        "description": "Confidence Interval Plot",
        "required_datasets": ["ADSL", "BDS_DATASET"],
        "typical_datasets": ["ADLB", "ADVS", "ADQS"],
        "dataset_requirements": {
          "BDS_DATASET": "Any BDS dataset with numeric variables for plotting"
        }
      },
      "tm_g_barchart_simple": {
        "description": "Simple Bar Chart",
        "required_datasets": ["ADSL", "ADAE"],
        "dataset_requirements": {
          "ADAE": "Adverse events with categorical variables for bar charts"
        }
      },
      "tm_g_forest_rsp": {
        "description": "Forest Plot for Response",
        "required_datasets": ["ADSL", "ADRS"],
        "dataset_requirements": {
          "ADRS": "Response data with binary or categorical outcomes"
        }
      },
      "tm_g_forest_tte": {
        "description": "Forest Plot for Time-to-Event",
        "required_datasets": ["ADSL", "ADTTE"],
        "dataset_requirements": {
          "ADTTE": "Time-to-event data with AVAL (time) and CNSR (censor indicator)"
        }
      },
      "tm_g_ipp": {
        "description": "Individual Patient Plot",
        "required_datasets": ["ADSL", "BDS_DATASET"],
        "typical_datasets": ["ADLB", "ADVS", "ADQS"],
        "dataset_requirements": {
          "BDS_DATASET": "Any BDS dataset with variables to plot over time or by visit"
        }
      },
      "tm_g_km": {
        "description": "Kaplan-Meier Plot",
        "required_datasets": ["ADSL", "ADTTE"],
        "dataset_requirements": {
          "ADTTE": "Time-to-event data with AVAL (time) and CNSR (censor indicator)"
        }
      },
      "tm_g_lineplot": {
        "description": "Line Plot",
        "required_datasets": ["ADSL", "BDS_DATASET"],
        "typical_datasets": ["ADLB", "ADVS", "ADQS"],
        "dataset_requirements": {
          "BDS_DATASET": "Any BDS dataset with numeric variables for line plots over time"
        }
      },
      "tm_g_pp_adverse_events": {
        "description": "Patient Profile: Adverse Events",
        "required_datasets": ["ADSL", "ADAE"],
        "dataset_requirements": {
          "ADAE": "Adverse events data for patient-level display"
        }
      },
      "tm_g_pp_patient_timeline": {
        "description": "Patient Profile: Patient Timeline",
        "required_datasets": ["ADSL", "ADCM", "ADAE"],
        "dataset_requirements": {
          "ADCM": "Concomitant medications with start/end dates",
          "ADAE": "Adverse events with start/end dates"
        }
      },
      "tm_g_pp_therapy": {
        "description": "Patient Profile: Therapy",
        "required_datasets": ["ADSL", "ADCM"],
        "dataset_requirements": {
          "ADCM": "Concomitant medications data"
        }
      },
      "tm_g_pp_vitals": {
        "description": "Patient Profile: Vitals",
        "required_datasets": ["ADSL", "ADVS"],
        "dataset_requirements": {
          "ADVS": "Vital signs data"
        }
      },
      "tm_t_abnormality": {
        "description": "Laboratory Abnormality Table",
        "required_datasets": ["ADSL", "ADLB"],
        "dataset_requirements": {
          "ADLB": "Laboratory data with abnormality grades (ANRIND, BNRIND)"
        }
      },
      "tm_t_abnormality_by_worst_grade": {
        "description": "Laboratory Abnormality by Worst Grade",
        "required_datasets": ["ADSL", "ADLB"],
        "dataset_requirements": {
          "ADLB": "Laboratory data with abnormality grades (ANRIND, BNRIND, worst grade variables)"
        }
      },
      "tm_t_ancova": {
        "description": "ANCOVA Table",
        "required_datasets": ["ADSL", "BDS_CONTINUOUS"],
        "typical_datasets": ["ADLB", "ADVS", "ADQS"],
        "dataset_requirements": {
          "BDS_CONTINUOUS": "BDS dataset with continuous AVAL, PARAMCD, AVISIT, covariates"
        }
      },
      "tm_t_binary_outcome": {
        "description": "Binary Outcome Table",
        "required_datasets": ["ADSL", "ADRS"],
        "typical_datasets": ["ADRS", "BDS_BINARY"],
        "dataset_requirements": {
          "ADRS": "Response data, or any BDS dataset with binary outcomes"
        }
      },
      "tm_t_coxreg": {
        "description": "Cox Regression Table",
        "required_datasets": ["ADSL", "ADTTE"],
        "dataset_requirements": {
          "ADTTE": "Time-to-event data with AVAL (time) and CNSR (censor indicator)"
        }
      },
      "tm_t_events": {
        "description": "Adverse Events Table",
        "required_datasets": ["ADSL", "ADAE"],
        "dataset_requirements": {
          "ADAE": "Adverse events data"
        }
      },
      "tm_t_events_by_grade": {
        "description": "Adverse Events by Grade Table",
        "required_datasets": ["ADSL", "ADAE"],
        "dataset_requirements": {
          "ADAE": "Adverse events data with severity grades"
        }
      },
      "tm_t_events_patyear": {
        "description": "Events per Patient Year",
        "required_datasets": ["ADSL", "ADAETTE"],
        "dataset_requirements": {
          "ADAETTE": "Adverse events time-to-event data"
        }
      },
      "tm_t_events_summary": {
        "description": "Events Summary Table",
        "required_datasets": ["ADSL", "ADAE"],
        "dataset_requirements": {
          "ADAE": "Adverse events data"
        }
      },
      "tm_t_exposure": {
        "description": "Exposure Table",
        "required_datasets": ["ADSL", "ADEX"],
        "dataset_requirements": {
          "ADEX": "Exposure data with dosing information"
        }
      },
      "tm_t_logistic": {
        "description": "Logistic Regression Table",
        "required_datasets": ["ADSL", "ADRS"],
        "typical_datasets": ["ADRS", "BDS_BINARY"],
        "dataset_requirements": {
          "ADRS": "Response data, or any BDS dataset with binary outcomes"
        }
      },
      "tm_t_mult_events": {
        "description": "Multiple Events Table",
        "required_datasets": ["ADSL", "ADAE"],
        "dataset_requirements": {
          "ADAE": "Adverse events data"
        }
      },
      "tm_t_pp_basic_info": {
        "description": "Patient Profile: Basic Info",
        "required_datasets": ["ADSL"],
        "dataset_requirements": {
          "ADSL": "Subject-level demographic data"
        }
      },
      "tm_t_pp_laboratory": {
        "description": "Patient Profile: Laboratory",
        "required_datasets": ["ADSL", "ADLB"],
        "dataset_requirements": {
          "ADLB": "Laboratory data"
        }
      },
      "tm_t_pp_medical_history": {
        "description": "Patient Profile: Medical History",
        "required_datasets": ["ADSL", "ADMH"],
        "dataset_requirements": {
          "ADMH": "Medical history data"
        }
      },
      "tm_t_pp_prior_medication": {
        "description": "Patient Profile: Prior Medication",
        "required_datasets": ["ADSL", "ADCM"],
        "dataset_requirements": {
          "ADCM": "Concomitant medications data"
        }
      },
      "tm_t_shift_by_arm": {
        "description": "Shift Table by Arm",
        "required_datasets": ["ADSL", "ADLB"],
        "dataset_requirements": {
          "ADLB": "Laboratory data with baseline and post-baseline values"
        }
      },
      "tm_t_shift_by_arm_by_worst": {
        "description": "Shift Table by Arm by Worst",
        "required_datasets": ["ADSL", "ADLB"],
        "dataset_requirements": {
          "ADLB": "Laboratory data with baseline, post-baseline, and worst values"
        }
      },
      "tm_t_shift_by_grade": {
        "description": "Shift Table by Grade",
        "required_datasets": ["ADSL", "ADLB"],
        "dataset_requirements": {
          "ADLB": "Laboratory data with abnormality grades at baseline and post-baseline"
        }
      },
      "tm_t_smq": {
        "description": "Standardized MedDRA Query Table",
        "required_datasets": ["ADSL", "ADAE"],
        "dataset_requirements": {
          "ADAE": "Adverse events data with SMQ variables"
        }
      },
      "tm_t_summary": {
        "description": "Summary Table",
        "required_datasets": ["ADSL", "BDS_DATASET"],
        "typical_datasets": ["ADLB", "ADVS", "ADQS"],
        "dataset_requirements": {
          "BDS_DATASET": "Any BDS dataset with variables to summarize"
        }
      },
      "tm_t_summary_by": {
        "description": "Summary Table by Group",
        "required_datasets": ["ADSL", "BDS_DATASET"],
        "typical_datasets": ["ADLB", "ADVS", "ADQS"],
        "dataset_requirements": {
          "BDS_DATASET": "Any BDS dataset with variables to summarize by groups"
        }
      },
      "tm_t_tte": {
        "description": "Time-to-Event Table",
        "required_datasets": ["ADSL", "ADTTE"],
        "dataset_requirements": {
          "ADTTE": "Time-to-event data with AVAL (time) and CNSR (censor indicator)"
        }
      },
      "tm_a_gee": {
        "description": "Generalized Estimating Equations",
        "required_datasets": ["ADSL", "BDS_DATASET"],
        "typical_datasets": ["ADLB", "ADVS", "ADQS"],
        "dataset_requirements": {
          "BDS_DATASET": "BDS dataset with AVAL (binary for logistic, continuous for linear), PARAMCD, AVISIT, USUBJID"
        },
        "notes": "Default regression type is logistic (requires binary AVAL). Can use linear regression for continuous AVAL."
      },
      "tm_a_mmrm": {
        "description": "Mixed Model for Repeated Measures",
        "required_datasets": ["ADSL", "BDS_CONTINUOUS"],
        "typical_datasets": ["ADLB", "ADVS", "ADQS"],
        "dataset_requirements": {
          "BDS_CONTINUOUS": "BDS dataset with continuous AVAL, PARAMCD, AVISIT, USUBJID"
        }
      }
    },
    "summary": {
      "module_categories": {
        "Graphics (tm_g_*)": 11,
        "Tables (tm_t_*)": 24,
        "Analysis (tm_a_*)": 2
      },
      "flexible_modules": {
        "description": "Modules that can work with multiple BDS datasets",
        "count": 8,
        "modules": [
          "tm_g_ci",
          "tm_g_ipp",
          "tm_g_lineplot",
          "tm_t_ancova",
          "tm_t_summary",
          "tm_t_summary_by",
          "tm_a_gee",
          "tm_a_mmrm"
        ]
      },
      "dataset_specific_modules": {
        "description": "Modules requiring specific dataset structures",
        "ADTTE_specific": ["tm_g_forest_tte", "tm_g_km", "tm_t_coxreg", "tm_t_tte"],
        "ADAE_specific": ["tm_g_barchart_simple", "tm_g_pp_adverse_events", "tm_t_events", "tm_t_events_by_grade", "tm_t_events_summary", "tm_t_mult_events", "tm_t_smq"],
        "ADRS_specific": ["tm_g_forest_rsp", "tm_t_binary_outcome", "tm_t_logistic"],
        "ADLB_specific": ["tm_t_abnormality", "tm_t_abnormality_by_worst_grade", "tm_t_shift_by_arm", "tm_t_shift_by_arm_by_worst", "tm_t_shift_by_grade", "tm_t_pp_laboratory"]
      },
      "most_common_datasets": {
        "ADSL": "Used in 37/37 modules (100%)",
        "ADAE": "Used in 9 modules (24%)",
        "ADLB": "Used in 10 modules (27%), but 8 modules can use any BDS dataset",
        "ADTTE": "Used in 4 modules (11%)",
        "ADRS": "Used in 3 modules (8%)"
      }
    }
  }
}