# Finding Optimal Microsampling Designs for Non-Compartmental Pharmacokinetic Analysis

## Documentation for package ‘microsamplingDesign’ version 1.0.6

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A C D E F G O P R S T misc

## -- A --

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

## -- C --

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'

## -- D --

doAllSchemeChecks | check whether either a 1 subject or multiple subject microsampling scheme meets imposed constraints

## -- E --

extractByRank | extract a timepoint or Scheme choice by its rank
extractByRank-method | extract a timepoint or Scheme choice by its rank

## -- F --

fastRankSchemes | generic function to calulate a 'ranking'-slot
flattenSetOfSchemes | Transform 3 way array to 2 way array
formatTimePoints | Format time points as a set

## -- G --

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

## -- O --

oneCompartmentOralModel | solution of one compartmental oral administration model only use one set of parameters, times can input can be an numeric array

## -- P --

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

## -- R --

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'

## -- S --

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

## -- T --

tMax | calculate summary statistics from a pkCurve

## -- misc --

%ARC% | All Row Combinations (ARC) function take all combination of rows of 2 matrices and bind them together