| addSchemes | add user defined scheme to an existing 'SetOfSchemes-class' or extend an existing set of schemes object with additional schemes |
| auc | calculate summary statistics from a pkCurve |
| check_scheme_exactNumberObsPerTimePoint | check the number of observations per time points is equal specified value |
| check_scheme_minObsPerTimePoint | check the mimimum observations per time points is above a specified value |
| check_subject_maxConsecSamples | check the maximum of consecutive samples per subject falls below the specified value |
| cMax | calculate summary statistics from a pkCurve |
| construct2CompModel | construct a 2 compartmental 'PkModel-class' by providing parameters and dosing info |
| constructSetOfSchemes | construct user defined 'SetOfSchemes-class' |
| doAllSchemeChecks | check whether either a 1 subject or multiple subject microsampling scheme meets imposed constraints |
| extractByRank | extract a timepoint or Scheme choice by its rank |
| extractByRank-method | extract a timepoint or Scheme choice by its rank |
| fastRankSchemes | generic function to calulate a 'ranking'-slot |
| flattenSetOfSchemes | Transform 3 way array to 2 way array |
| formatTimePoints | Format time points as a set |
| get2ComptModelCurve | provides solution of two compartmental pharmacodynamic model at specified time points |
| getAllTimeOptions | generate all possible time options from eligible time points and number of samples per time interval ( time zone ) |
| getCoeffVariationError | generic function to extract 'coeffVariationError' slot |
| getCoeffVariationError-method | generic function to extract 'coeffVariationError' slot |
| getCombinationsWithMaxNRepetitions | get all combinations with a maximum number of repetitions |
| getConstraintsExample | get a minimal example of a constraint data frame |
| getCorrelationMatrix | generic function to extract the 'correlationMatrix'-slot |
| getCorrelationMatrix-method | generic function to extract the 'correlationMatrix'-slot |
| getData | generic function to extract the '.Data'-slot |
| getData-method | generic function to extract the '.Data'-slot |
| getDosingInfo | generic function to extract 'dosingInfo'-slot |
| getDosingInfo-method | generic function to extract 'dosingInfo'-slot |
| getExampleData | generate an mimimal example of a Pk data without a model |
| getExampleObjective | example objective function for 'rankObject' |
| getExampleParameters | get example parameters to use in 'pkOdeModel2Compartments' example |
| getExamplePkCurve | example of 1 pk curve to be used to test pkCurveStat_[function] |
| getExamplePkModel | get minimal example of 'PkModel-class' |
| getExamplePkModelRange | get minimal example of 'PkModelRange-class' |
| getExampleSetOfSchemes | get a minimal example of a set of schemes object |
| getExampleSetOfTimePoints | get a minimal example set of time points to test functions with |
| getExampleTimeData | generate example PkData object to be used in example rankTimePoints |
| getExampleTimeZones | working example time zone dataframe to use in examples |
| getIndividualParameters | sample subject specific parameters to input in pharmacodynamic model paramaters are sample from a log-normal distribution |
| getMMCurve | calculate Michealis-Menten relation between x and velocity and rate |
| getModelFunction | generic function to extract 'modelFunction' slot from S4-class object |
| getModelFunction-method | generic function to extract 'modelFunction' slot from S4-class object |
| getNames | generic function extract the names of an S4-object |
| getNames-method | generic function extract the names of an S4-object |
| getNSchemes | generic function to extract 'nSchemes'-slot |
| getNSchemes-method | generic function to extract 'nSchemes'-slot |
| getNSubjects | generic function to extract 'nSubjects'-slot |
| getNSubjects-method | generic function to extract 'nSubjects'-slot |
| getParameters | generic function to extract 'parameter'-slot |
| getParameters-method | generic function to extract 'parameter'-slot |
| getPkData | simulate 'PkData-class' from 'PkModel-class' |
| getPkModel | generic function extract a 'PkModel-class' |
| getPkModel-method | generic function extract a 'PkModel-class' |
| getPkModelArticle | reproduce the example of the article of Helen Barnet et al. |
| getPkModels | Generate all possible 'PkModel-class' from 'PkModelRange-class' combination of ranges |
| getRanking | generic function to extract the 'ranking'-slot |
| getRanking-method | generic function to extract the 'ranking'-slot |
| getSetOfSchemes | Generate a 'SetOfSchemes-class' object of speficified dimensions ( subjects, observations per t) for a given set of time points which meets user specified constraints |
| getTimeChoicePerformance | estimate the distance between population average an average over sample datasets with given time points (zero point included) |
| getTimePoints | generic function to extract 'timePoints'-slot |
| getTimePoints-method | generic function to extract 'timePoints'-slot |
| getTopNRanking | extract the top n rankings as numeric vector |
| oneCompartmentOralModel | solution of one compartmental oral administration model only use one set of parameters, times can input can be an numeric array |
| pkCurveStat | calculate summary statistics from a pkCurve |
| pkCurveStat_auc | calculate summary statistics from a pkCurve |
| pkCurveStat_cMax | calculate summary statistics from a pkCurve |
| pkCurveStat_tMax | calculate summary statistics from a pkCurve |
| PkData | An S4 object containing samples from a Pk model |
| pkData | An S4 object containing samples from a Pk model |
| pkdata | An S4 object containing samples from a Pk model |
| PkData-class | An S4 object containing samples from a Pk model |
| PkModel | S4 class PkModel representing a pharmacokinetic model and its parameters |
| pkModel | S4 class PkModel representing a pharmacokinetic model and its parameters |
| pkmodel | S4 class PkModel representing a pharmacokinetic model and its parameters |
| PkModel-class | S4 class PkModel representing a pharmacokinetic model and its parameters |
| PkModelRange | S4 class PkModel representing a pharmacokinetic model and its parameters and uncertainty of parameter choices by ranges |
| pkModelRange | S4 class PkModel representing a pharmacokinetic model and its parameters and uncertainty of parameter choices by ranges |
| pkmodelrange | S4 class PkModel representing a pharmacokinetic model and its parameters and uncertainty of parameter choices by ranges |
| PkModelRange-class | S4 class PkModel representing a pharmacokinetic model and its parameters and uncertainty of parameter choices by ranges |
| plotAverageRat | plot plasma concentration for average individual (i.e average parameter values) in function of dose at time zero |
| plotMMCurve | plot Michealis-Menten curve for either capacity dependent absorption or clearance |
| plotMMKinetics | plot MM kinetics of both absorption and clearance |
| plotObject | generic function to plot an object |
| plotObject-method | generic function to plot an object |
| rankObject | generic function to calulate a 'ranking'-slot |
| rankObject-method | generic function to calulate a 'ranking'-slot |
| rankObjectWithRange | Rank a 'SetOfSchemes-class' or a 'SetOfTimePoints' object using data generated per scneario defined by 'PkModelRange-class' |
| setCoeffVariationError<- | replace 'coeffVariationError'-slot |
| setCoeffVariationError<--method | replace 'coeffVariationError'-slot |
| setCorrelationMatrix<- | replace 'correlationMatrix'-slot |
| setCorrelationMatrix<--method | replace 'correlationMatrix'-slot |
| setDosingInfo<- | replace 'dosingInfo'-slot |
| setDosingInfo<--method | replace 'dosingInfo'-slot |
| setModelToAverageRat | get a model with all variances to zero |
| SetOfSchemes | S4 class SetOfSchemes representing a set of designs with given time points |
| setOfSchemes | S4 class SetOfSchemes representing a set of designs with given time points |
| SetOfSchemes-class | S4 class SetOfSchemes representing a set of designs with given time points |
| SetOfTimePoints | S4 class SetOfTimePoints representing a set of designs with given time points |
| setOfTimePoints | S4 class SetOfTimePoints representing a set of designs with given time points |
| SetOfTimePoints-class | S4 class SetOfTimePoints representing a set of designs with given time points |
| setParameters<- | replace 'parameters'-slot |
| setParameters<--method | replace 'parameters'-slot |
| setRanking<- | replace 'ranking'-slot |
| setRanking<--method | replace 'ranking'-slot |
| setTimePoints<- | generic function to replace 'timePoints'-slot |
| setTimePoints<--method | generic function to replace 'timePoints'-slot |
| subsetOnTimePoints | generic function to subset the 'timePoints'-slot and generate an object of the same class |
| subsetOnTimePoints-method | generic function to subset the 'timePoints'-slot and generate an object of the same class |
| summary-method | summarize object |
| summary-method | function to summarize an object |
| tMax | calculate summary statistics from a pkCurve |
| %ARC% | All Row Combinations (ARC) function take all combination of rows of 2 matrices and bind them together |