Introduction | Input and Output | {admiral} Functions and Options | Handling of Missing Values | Floating Point Comparisons | Expressions in Scripts | Quoting and Unquoting: Introducing expr(), exprs(), !! and !!! | expr() and exprs() | Bang-Bang (!!) and Bang-Bang-Bang (!!!) | Summary | Common pitfalls | 1. Mistakenly passing something that isn't an expression to an argument | 2. Forgetting that expressions must be evaluable in the dataset | See also

Introduction | Grading metadata | Structure of metadata set | Handling floating points when comparing numeric values | Creating the Lab Grade | Mapping ADLB to the TERM variable in the {admiral} metadata data set | Deriving Baseline Toxicity Grades | NCI-CTCAEV4 implementation | Terms graded | Updates made to TERM | Assumptions made when grading | NCI-CTCAEV5 implementation | Criteria dependent on the Baseline Value | NCI-CTCAEV6 implementation | DAIDS implementation | Terms with age or sex dependent grading criteria | US (Conventional) unit implementation | Conclusion

{admiral} Manifesto | Usability | Simplicity | Findability | Readability

Introduction | Programming Flow | Read in Data | Derive Period, Subperiod, and Phase Variables (e.g. APxxSDT, APxxEDT, ...) | Derive Treatment Variables (TRT0xP, TRT0xA) | Derive/Impute Numeric Treatment Date/Time and Duration (TRTSDTM, TRTEDTM, TRTDURD) | Derive Disposition Variables | Disposition Dates (e.g. EOSDT) | Disposition Status (e.g. EOSSTT) | Disposition Reason(s) (e.g. DCSREAS, DCSREASP) | Randomization Date (RANDDT) | Derive Birth Date and Analysis Age (BRTHDT, AAGE, AAGEU) | Derive Death Variables | Death Date (DTHDT) | Cause of Death (DTHCAUS) | Duration Relative to Death | Derive the Last Date Known Alive (LSTALVDT) | Derive Groupings and Populations | Grouping (e.g. AGEGR1 or REGION1) | Population Flags (e.g. SAFFL) | Derive Other Variables | Example Script

Introduction | Programming Workflow | Read in Data | Derive/Impute Numeric Date/Time and Analysis Day (ADT, ADTM, ADY, ADTF, ATMF) | Assign PARAMCD, PARAM, PARAMN, PARCAT1 | Derive Results (AVAL, AVALC) | Derive Additional Parameters (e.g. BSA, BMI or MAP for ADVS) | Derive Timing Variables (e.g. APHASE, AVISIT, APERIOD) | Timing Flag Variables (e.g. ONTRTFL) | Assign Reference Range Indicator (ANRIND) | Derive Baseline (BASETYPE, ABLFL, BASE, BNRIND) | Derive Change from Baseline (CHG, PCHG) | Derive Shift (e.g. SHIFT1) | Derive Analysis Ratio (R2BASE) | Derive Analysis Flags (e.g. ANL01FL) | Assign Treatment (TRTA, TRTP) | Derive Categorization Variables (AVALCATy) | Derive Criterion Variables (CRITy, CRITyFL, CRITyFN) | Derive New Rows | Example 1 (Creating a New Record): | Adding a New Record for the Last Value | Adding a New Record for the Minimum Value | Example 2 (Deriving a Summary Record) | Example 3 (Deriving a New PARAMCD) | Assign ASEQ | Add ADSL variables | Example Scripts

Introduction | Programming Workflow | Read in Data | Derive/Impute End and Start Analysis Date/time and Relative Day | Derive Durations | Derive ATC variables | Derive Planned and Actual Treatment | Derive Date/Date-time of Last Dose | Derive Treatment Dose and Unit | Derive Severity, Causality, and Toxicity Grade | Derive Treatment Emergent Flag | Derive Occurrence Flags | Derive Query Variables | Add the ADSL variables | Derive Analysis Sequence Number | Example Scripts

Introduction | Required Packages | Imputation Rules | Imputation on a Vector | Imputation Level | Minimum/Maximum Dates | Imputation Flags | Imputation Functions | Examples | Create an Imputed Datetime and Date Variable and Imputation Flag Variables | Create an Imputed Date Variable and Imputation Flag Variable | Impute Time without Imputing Date | Avoid Imputed Dates Before a Particular Date | Avoid Imputed Dates After a Particular Date | Imputation Without Creating a New Variable | Using More Than One Imputation Rule for a Variable

Introduction | Required Packages | Visit variables (AVISIT, AVISITN, AWLO, AWHI, ...) | Period, Subperiod, and Phase Variables | A Note on Study Specific Code | The Period/Phase Reference Dataset | Example Creation of the Period/Phase Reference Dataset | Creating the Period/Phase Reference Dataset from EX | Creating the Period/Phase Reference Dataset from ADSL | Creating ADSL Period, Subperiod, or Phase Variables | Creating BDS and OCCDS Period, Subperiod, or Phase Variables | Treatment Variables (TRTxxP, TRTxxA, TRTP, TRTA, ...) | Creating ADSL Treatment Variables | Creating BDS and OCCDS Treatment Variables

Introduction | Dataset Subdivision | Criterion Flags | Affected Eye Derivation | Differences between pre and post-dose IOP

Introduction | Dataset Contents | Required Packages | Programming Workflow | Initial set up of ADBCVA | Deriving LogMAR Score Parameters | Further Derivations of Standard BDS Variables | Deriving Analysis Value Categories for Snellen Scores | Deriving Criterion Flags for BCVA Change | Additional Notes | Example Script

Introduction | Dataset Contents | Required Packages | Programming Workflow | Initial set up of ADOE | Assigning PARAM/PARAMCD and AVISIT/AVISITN | Creating IOP pre to post-dose difference derived parameter | Further Derivations of Standard BDS Variables | Example Script

Introduction | Dataset Contents | Required Packages | Programming Workflow | Reading In Data and Setting Up Lookup Tables | Original Items (param_lookup_original) | Transformed Records (param_lookup_transformed) | Composite Records (param_lookup_composite) | Initial Set Up and Mapping the Raw Records | Deriving the Transformed Parameters | Deriving the Composite Parameters | Composite Scores by Category | Overall Composite Scores | Further Derivations of Standard BDS Variables | Example Script

Introduction | What does {admiralophtha} offer? | Starting a Script | Support

Introduction | Programming Workflow | Read in Data | Derive/Impute Numeric Date/Time and Analysis Day (ADT, ADTM, ADY, ADTF, ATMF) | Compute duration for a record | Create 1:1 mapping records | Create Summary Records | Assign PARAMCD, PARAMN, etc. from Reference tables | Derive Categorization Variables (AVALCATy) | Assign ASEQ | Add the ADSL variables | Example Script

Introduction | Programming PK NCA (ADPC/ADNCA) Analysis Data | ADPC Programming Workflow | Read in Data | Expand Dosing Records | Find First Dose | Find Reference Dose Dates Corresponding to PK Records | Combine PC and EX Records and Derive Relative Time Variables | Derive Analysis Variables | Create DTYPE for Imputed records | Create Duplicated Records for Analysis | Combine ADPC data with Duplicated Records | Calculate Change from Baseline and Assign ASEQ | Add Additional Baseline Variables | Add the ADSL variables | Programming Population PK (ADPPK) Analysis Data | ADPPK Programming Workflow | Find First Dose ADPPK | Find Previous Dose | Combine PC and EX Records for ADPPK | Derive Analysis Variables and Dependent Variable DV | Add ASEQ and Remove Temporary Variables | Derive Numeric Covariates | Derive Additional Covariates from VS and LB | Combine Covariates with ADPPK Data | Example Scripts

Introduction | Required Packages | Programming Workflow | Read in Data | Flagging Elevated Values (CRITy, CRITyFL) | Subsetting by LBTESTCD and Joining by Potential Events | How to Create New Parameters and Rows | Conclusion | Example Script

Introduction | Required Packages | Programming Workflow | Read in Data | Derive Parameters (CNSR, ADT, STARTDT) | Pre-Defined Time-to-Event Source Objects | Single Event | Add Additional Information for Events and Censoring (EVNTDESC, SRCVAR, ...) | Handling Subjects Without Assessment | Deriving a Series of Time-to-Event Parameters | Further Scenarios | Derive Analysis Value (AVAL) | Derive Analysis Sequence Number (ASEQ) | Add ADSL Variables

Introduction | Step-by-step Guidance to Create a Package Extension | Lessons Learned

Introduction | Required Packages | Example Data | Original Items | Transformed Items | Scales and Scores | Time to Deterioration/Improvement | Time to Confirmed/Definitive Deterioration/Improvement | Worst/Best Answer | Completion

Introduction | How to use the @caption, @info and @code tags together in a "block" | How to sequence your blocks | Data sections

Introduction | Required Packages | Characterization of Derivations | Overview of Derivations | Source Data | Single Source Dataset | Multiple Source Datasets | Methods | Selection | Options for Selection | Sort Order | New Values | Summary | Computed

Dear Developers | Why have a separate development package? | How to add new tools to {admiraldev}? | When to add a function to {admiraldev}? | Scenario One: {admiral} core | Scenario Two: {admiral} extension

Introduction | Required Packages | Call Derivation | Restrict Derivation | Slice Derivation | Combining Higher Order Functions

Common R CMD Check Issues | Check Fails Only on One Version | Package Dependencies | Global Variables | Undocumented Function Parameter | Outdated Documentation

Introduction | Structure of the Query Dataset | Variables | Required Content | Input | Output | Example | Query Dataset (ds_query) | Adverse Event Dataset (ae) | Output Dataset | Optional Content | Output Variables