Finding Optimal Microsampling Designs for Non-Compartmental Pharmacokinetic Analysis

Documentation for package ‘microsamplingDesign’ version 1.0.8

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-- 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