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microsamplingDesign (version 1.0.8)

Finding Optimal Microsampling Designs for Non-Compartmental Pharmacokinetic Analysis

Description

Find optimal microsampling designs for non-compartmental pharacokinetic analysis using a general simulation methodology: Algorithm III of Barnett, Helen, Helena Geys, Tom Jacobs, and Thomas Jaki. (2017) "Optimal Designs for Non-Compartmental Analysis of Pharmacokinetic Studies. (currently unpublished)" This methodology consist of (1) specifying a pharmacokinetic model including variability among animals; (2) generating possible sampling times; (3) evaluating performance of each time point choice on simulated data; (4) generating possible schemes given a time point choice and additional constraints and finally (5) evaluating scheme performance on simulated data. The default settings differ from the article of Barnett and others, in the default pharmacokinetic model used and the parameterization of variability among animals. Details can be found in the package vignette. A 'shiny' web application is included, which guides users from model parametrization to optimal microsampling scheme.

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Version

Install

install.packages('microsamplingDesign')

Monthly Downloads

105

Version

1.0.8

License

GPL-3

Maintainer

Adriaan Blommaert

Last Published

October 13th, 2021

Functions in microsamplingDesign (1.0.8)

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

construct2CompModel

construct a 2 compartmental PkModel-class by providing parameters and dosing info

getCorrelationMatrix

generic function to extract the correlationMatrix-slot

constructSetOfSchemes

construct user defined SetOfSchemes-class

generic function to extract the .Data-slot

changeDevSettings

Function to overwrite default settings, print to console when changing default settings and add to default settings

doAllSchemeChecks

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

getCombinationsWithMaxNRepetitions

get all combinations with a maximum number of repetitions

getConstraintsExample

get a minimal example of a constraint data frame

generic function extract a PkModel-class

estimatePopCurve

estimate population Pk curve from a scheme and pkData

extract a timepoint or Scheme choice by its rank

check_scheme_minObsPerTimePoint

check the mimimum observations per time points is above a specified value

getExampleSetOfSchemes

get a minimal example of a set of schemes object

calculate summary statistics from a pkCurve

Generate all possible PkModel-class from PkModelRange-class combination of ranges

generic function to extract the ranking-slot

getPkModelArticle

reproduce the example of the article of Helen Barnet et al.

getExamplePkModel

get minimal example of PkModel-class

getSummaryRanks

internal function to rank by a summary function over criterio

generic function to extract nSchemes-slot

getTimeChoicePerformance

estimate the distance between population average an average over sample datasets with given time points (zero point included)

getExamplePkModelRange

get minimal example of PkModelRange-class

getModelFunction

generic function to extract modelFunction slot from S4-class object

check_subject_maxConsecSamples

check the maximum of consecutive samples per subject falls below the specified value

getDevRankingSettings

function default ranking settings

flattenSetOfSchemes

Transform 3 way array to 2 way array

flagSchemesMeetingConstraints

internal function to check scheme constraints ( faster )

rankObjectWithRange

Rank a SetOfSchemes-class or a SetOfTimePoints object using data generated per scneario defined by PkModelRange-class

getExampleSetOfTimePoints

get a minimal example set of time points to test functions with

runMicrosamplingDesignApp

Run the PkPlotApp in a new tab in your browser

get2ComptModelCurve

provides solution of two compartmental pharmacodynamic model at specified time points

getExamplePkCurve

example of 1 pk curve to be used to test pkCurveStat_[function]

getExampleParameters

get example parameters to use in pkOdeModel2Compartments example

generic function to extract dosingInfo-slot

Internal function to generate multivariate data via a cholesky decompostion ( to have replicability accross systems )

calculate Michealis-Menten relation between x and velocity and rate

getIndividualParameters

sample subject specific parameters to input in pharmacodynamic model paramaters are sample from a log-normal distribution

summary,SetOfSchemes-method

summarize object

generic function to extract timePoints-slot

extract the top n rankings as numeric vector

plot MM kinetics of both absorption and clearance

summary,PkModelParent-method

function to summarize an object

getExampleTimeData

generate example PkData object to be used in example rankTimePoints

generic function extract the names of an S4-object

getExampleTimeZones

working example time zone dataframe to use in examples

generic function to extract nSubjects-slot

setDosingInfo<-

replace dosingInfo-slot

generic function to plot an object

setModelToAverageRat

get a model with all variances to zero

pkOdeModel2Compartments

Set of differential equations representing two compartmental pk model with possible Michaelis-Menten kinetics at absorption and clearance used as interal function

formatTimePoints

Format time points as a set

getResultPerScheme

get a result of the criteria per scheme zero concentration at time zero

setParameters<-

replace parameters-slot

rankBasedOnDirectory

internal function apply ranking per directory

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

generic function to calulate a ranking-slot

replace ranking-slot

subsetOnTimePoints

generic function to subset the timePoints-slot and generate an object of the same class

setTimePoints<-

generic function to replace timePoints-slot

getExampleObjective

example objective function for rankObject

generate an mimimal example of a Pk data without a model

generic function to extract parameter-slot

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

simulate PkData-class from PkModel-class

oneCompartmentOralModel

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

plot plasma concentration for average individual (i.e average parameter values) in function of dose at time zero

setCoeffVariationError<-

replace coeffVariationError-slot

plot Michealis-Menten curve for either capacity dependent absorption or clearance

setCorrelationMatrix<-

replace correlationMatrix-slot

SetOfTimePoints-class

S4 class SetOfTimePoints representing a set of designs with given time points

S4 class PkModel representing a pharmacokinetic model and its parameters

checkConstraintsOk

test constraints well specified

check_scheme_exactNumberObsPerTimePoint

check the number of observations per time points is equal specified value

SetOfSchemes-class

S4 class SetOfSchemes representing a set of designs with given time points

PkModelRange-class

S4 class PkModel representing a pharmacokinetic model and its parameters and uncertainty of parameter choices by ranges

add user defined scheme to an existing SetOfSchemes-class or extend an existing set of schemes object with additional schemes

An S4 object containing samples from a Pk model

PkModelParent-class

virtual class, for testing PkModel-class and PkModelRange-class together