Finding Optimal Microsampling Designs for Non-Compartmental Pharmacokinetic Analysis


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Documentation for package ‘microsamplingDesign’ version 1.0.8

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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