Package: admiralonco 1.4.1

Important Note | Introduction | Programming Workflow | Read in Data | Pre-processing of Input Records | Select Overall Response Records and Set Parameter Details | Partial Date Imputation and Deriving ADT, ADTF, AVISIT etc | Derive AVALC and AVAL | Flag Worst Assessment at Each Date (ANL01FL) | Flag Assessments up to First PD (ANL02FL) | Derive Progressive Disease Parameter | Derive Response Parameter | Derive Clinical Benefit Parameter | Derive Best Overall Response Parameter | Derive Best Overall Response of CR/PR Parameter | Derive Response Parameters requiring Confirmation | Derive Parameters using Independent Review Facility (IRF)/Blinded Independent Central Review (BICR) responses | Derive Death Parameter | Derive Last Disease Assessment Parameters | Derive Measurable Disease at Baseline Parameter | Assign ASEQ | Add ADSL variables | Example Script

Introduction | Programming Workflow | Read in Data | Pre-processing of Input Records | Select Overall Response Records and Set Parameter Details | Partial Date Imputation and Deriving ADT, ADTF, AVISIT etc | Derive AVALC and AVAL | Flag Worst Assessment at Each Date (ANL01FL) | Flag Assessments up to First PD (ANL02FL) | Select Source Assessments for Parameter derivations | Define Events | Derive Progressive Disease Parameter | Derive Response Parameter | Derive Clinical Benefit Parameter | Derive Best Overall Response Parameter | Derive Best Overall Response of CR/PR Parameter | Derive Response Parameters requiring Confirmation | Derive Non-standard Parameters | Adding a Criterion for Confirmed Clinical Benefit | Considering Non-Standard Response Values | Derive Parameters using Independent Review Facility (IRF)/Blinded Independent Central Review (BICR) responses | Derive Death Parameter | Derive Last Disease Assessment Parameters | Derive Measurable Disease at Baseline Parameter | Assign ASEQ | Add ADSL variables | Example Script

Introduction | Required Packages | Programming Workflow | Read in Data | Merge TR with TU and Derive New Variables | Pre-processing of Input Records | Partial Date Imputation and Deriving ADT, ADTF, AVISIT etc | Unscheduled visits | Derive Parameters for Lesion Diameters (LDIAMn & NLDIAMn) | Derive Parameter for Sum of Diameter and Analysis Flag ANL01FL | Derive Baseline (ABLFL, BASE) | Derive NADIR | Derive Change from Baseline (CHG, PCHG) | Derive Additional Flag Variables | Derive PDFL | 1. Take the date of PD from ADRS | 2. Take the first date when the overall response is PD from RS | 3. Target lesion response of no CR at the current observation visit and but a CR response at the NADIR observation | 4. Calculate from source data | Derive Analysis Flags ANLzzFL | Derive Analysis Sequence Number (ASEQ) | Add ADSL Variables | Example Script

Introduction | Required Packages | Programming Workflow | Read in Data | Derive Parameters (CNSR, ADT, STARTDT) | Pre-Defined Time-to-Event Source Objects | Creating Your Own Time-to-Event Source Objects | Derive Analysis Value (AVAL) | Derive Analysis Sequence Number (ASEQ) | Add ADSL Variables | Example Script

Introduction | CA-125 response categories | Ways the data is collected in the Ovarian Cancer study CRF | Required: | May be Collected: | Assumptions: | styler: off | styler: on | Required Packages | Programming Workflow | Read in Data | Pre-processing of Input Records | Select Overall Response Records per Response Criteria Category | Partial Date Imputation and Deriving ADT, ADTF, AVISIT etc. | Derive AVALC and AVAL | Analysis Flag Derivation | Flag One Assessment at Each Analysis Date (ANL01FL) | Flag Assessments up to First PD or After Receiving Mouse Antibodies (ANL02FL) | CA-125 Response Evaluable Flag | Select Source Assessments for Parameter Derivations | CA-125 Progression | CA-125 Progression Category | CA-125 Best Confirmed Overall Response | Combined Best Unconfirmed Overall Response | Combined Best Confirmed Overall Response | Other Endpoints

Introduction | Creating Oncology ADaM Datasets | Support

Introduction | PCWG3 Guidelines for Prostate Cancer Response | Prostate-specific antigen (PSA) | Bone Response Categories Based on PCWG3 Guidelines: | Progressive Disease Unconfirmed (PDu) | Progressive Disease (PD) | Not Evaluable (NE) | No Evidence of Disease (NED) | Non-Progressive Disease (Non-PD) | Bone Lesion Confirmation Guidance (The 2+2 Flare Rule) | Examples of the 2+2 Rule | Programming Workflow | Required Packages | Read in Data | Pre-processing of Input Records | Partial Date Imputation and Deriving ADT, ADTF, AVISIT, AVISITN etc. | Derive PARAMCD, PARAM, PARAMN | RECIST 1.1 and Bone Response Combined Based on PCWG3 Guidelines | Derive Combined Overall Time Point Response by Investigator (OVRLRESC) Parameter | Table : Combined Overall Time Point Response as per summarized PCWG3 guidelines | Derive Combined Overall Time Point Response by Investigator (OVRLRESC) Records referenced from above table. | Derive AVAL (Numeric tumor response from AVALC values) | Best Overall Response (BOR) and Confirmed Best Overall Response (CBOR) | Define Events for Best Overall Response (BOR) | Derive Best Overall Response (BOR) | Derive Confirmed BOR (CBOR) | PSA Analysis | Derive BASE, CHG, PCHG for PSA (ADPSA) | Define Events for all PSA endpoints | Derive Unconfirmed PSA50 PSA90 (PSAURS) | Derive Confirmed PSA50 PSA90 (PSACRS) | Other Endpoints

Introduction | Programming Workflow | Read in Data | Pre-processing of Input Records | Select Overall Response Records and Set Parameter Details | Partial Date Imputation and Deriving ADT, ADTF, AVISIT etc | Derive AVALC and AVAL | Derive Confirmed Response Parameter | Handling Non-Evaluable Responses | Additional Variables | Definition of derive_confirmed_response Function | Check Number of NE Values Between Responses | Analysis Flag Derivation | Flag One Assessment at Each Analysis Visit (ANL01FL) | Exclude Assessments After New Anti-Cancer Therapy (ANL02FL) | Flag Assessments up to First PD (ANL03FL) | Select Source Assessments for Parameter derivations | Derive Progressive Disease Parameter | Define Events | Derive Response Parameter | Derive Clinical Benefit Parameter | Derive Best Confirmed Overall Response Parameter | Other Endpoints

Introduction | Programming Workflow | Read in Data | Pre-processing of Input Records | Select Overall Response Records and Set Parameter Details | Partial Date Imputation and Deriving ADT, ADTF, AVISIT etc | Derive AVALC and AVAL | Flag Worst Assessment at Each Date (ANL01FL) | Flag Assessments up to First iCPD (ANL02FL) | Select Source Assessments for Parameter derivations | Define Events | Handling Different Input Response Values | Derive Confirmed and Unconfirmed Progressive Disease Parameter | Derive Response Parameter | Derive Clinical Benefit Parameter | Derive Best Overall Response Parameter | Derive Response Parameters requiring Confirmation | Other Endpoints

Introduction | Programming Workflow | Read in Data | Single Source | Multiple Sources - Prerequisite Steps | Prerequisite | Multiple Sources - Derive New Anti-Cancer Start Date and Merge with ADSL | Using the New Anti-Cancer Therapy Date | Derive Date Parameter