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PFIM (version 6.1)

Population Fisher Information Matrix

Description

Evaluate or optimize designs for nonlinear mixed effects models using the Fisher Information matrix. Methods used in the package refer to Mentré F, Mallet A, Baccar D (1997) , Retout S, Comets E, Samson A, Mentré F (2007) , Bazzoli C, Retout S, Mentré F (2009) , Le Nagard H, Chao L, Tenaillon O (2011) , Combes FP, Retout S, Frey N, Mentré F (2013) and Seurat J, Tang Y, Mentré F, Nguyen TT (2021) .

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Version

Install

install.packages('PFIM')

Monthly Downloads

536

Version

6.1

License

GPL (>= 2)

Maintainer

Romain Leroux

Last Published

October 23rd, 2024

Functions in PFIM (6.1)

Fim-class

Class "Fim"
Model-class

Class "Model"
EvaluateVarianceModel

Evaluate the variance of a model.
ModelAnalyticInfusion-class

Class "ModelAnalyticInfusion"
ModelAnalyticInfusionSteadyState-class

Class "ModelAnalyticInfusionSteadyState"
ModelError-class

Class "ModelError" representing a Model error.
ModelAnalytic-class

Class "ModelAnalytic"
ModelInfusion-class

Class "ModelInfusion"
IndividualFim-class

Class "Fim"
Evaluation-class

Class "Evaluation"
LibraryOfModels-class

Class "LibraryOfModels"
ModelODE-class

Class "ModelODE"
FedorovWynnAlgorithm-class

Class "FedorovWynnAlgorithm"
ModelODEInfusionDoseInEquations-class

Class "ModelODEInfusionDoseInEquations"
ModelODEInfusion-class

Class "ModelODEInfusion"
ModelAnalyticBolusSteadyState-class

Class "ModelAnalyticBolusSteadyState"
ModelParameter-class

Class "ModelParameter"
ModelAnalyticBolus-class

Class "ModelAnalyticBolus"
ModelODEDoseNotInEquations-class

Class "ModelODEDoseNotInEquations"
OptimizationAlgorithm-class

Class "OptimizationAlgorithm"
LibraryOfPKPDModels-class

Class "LibraryOfPKPDModels"
PFIM-package

Fisher Information matrix for design evaluation/optimization for nonlinear mixed effects models.
computeVMat

function computeVMat
PopulationFim-class

Class "PopulationFim"
convertPKModelAnalyticToPKModelODE

Convert an analytic model to a ode model.
Proportional-class

Class "Proportional"
ModelAnalyticSteadyState-class

Class "ModelAnalyticSteadyState"
ModelBolus-class

Class "ModelBolus"
PGBOAlgorithm-class

Class "PGBOAlgorithm"
LibraryOfPKModels

Library of the PK models
PFIMProject-class

Class "PFIMProject"
MultiplicativeAlgorithm-class

Class "MultiplicativeAlgorithm"
LibraryOfPDModels

Library of the PK models
addModel

Add a model to a library of models.
LogNormal-class

Class "LogNormal"
fisher.simplex

Compute the fisher.simplex
SamplingTimes-class

Class "SamplingTimes"
fun.amoeba

function fun.amoeba
SimplexAlgorithm-class

Class "SimplexAlgorithm"
Report

Report
Optimization-class

Class "Optimization"
Normal-class

Class "Normal"
ModelODEDoseInEquations-class

Class "ModelODEDoseInEquations"
definePKPDModel

Define a PKPD model.
definePKModel

Define a PK model.
getDose

getDose
getAdministrationConstraint

getAdministrationConstraint
defineModel

Define a model.
getAdministration

getAdministration
dataForArmEvaluation

dataForArmEvaluation
addModels

Add a models to a library of models.
defineModelUserDefined

Define a user defined model.
defineModelType

Define the type of a model.
getArms

Get the arms of an object.
SamplingTimeConstraints-class

Class "SamplingTimeConstraints"
getEigenValues

Get the eigenvalues of the fim.
getAdministrations

getAdministrations
generateReportOptimization

Generate report for the optimization.
getAdministrationsConstraints

getAdministrationsConstraints
generateSamplingsFromSamplingConstraints

Generate samplings from sampling constraints
getIterationAndCriteria

Get the iteration with the convergence criteria.
getInitialConditions

getInitialConditions
getOmega

Get the matrix omega of an object.
getOptimizer

Get the optimization algorithm.
getOptimizationResults

Get the optimization results.
getOptimalDesign

Get the optimal design.
checkValiditySamplingConstraint

checkValiditySamplingConstraint
checkSamplingTimeConstraintsForContinuousOptimization

Check for the samplingTime constraints for continuous optimization
getDesigns

Get the designs.
getDescription

Get the description of a model.
generateTables

Generate the tables for the report.
getDataFrameResults

Get the dataframe of the results.
getAdjustedGradient

getAdjustedGradient
getEvaluationInitialDesignResults

Get the evaluation results of the initial design.
getLibraryPKModels

Get the library of PK models.
getFim

getFim
getColumnAndParametersNamesFIM

Get the names of the names of the parameters associated to each column of the fim.
getPKPDModel

Get a PKPD model.
getConditionNumberVarianceEffects

Get the condition number of the matrix of the variance effects.
getContent

Get content of a library of models.
getLambda

Get the parameter lambda.
getDelta

Get the parameter delta
getDerivatives

Get the derivatives of the model error equation.
getDcriterion

Get the D criterion of the fim.
getEquationsDuringInfusion

Get the equations during infusion.
getDataForArmEvaluation

getDataForArmEvaluation
getCorrelationMatrix

Get the correlation matrix.
getEquations

Get the equations of a model.
getParameters

Get the parameters of an object.
getTau

getTau
getName

getName
getMinSampling

Get the minimal sampling times.
getModel

Get the model.
getLibraryPDModels

Get the library of PD models.
getModelEquations

Get the model equations.
getNames

getNames
getEvaluationFIMResults

Get the results of the evaluation.
getOptimalFrequencies

Get the optimal frequencies
getOptimalWeights

Get the optimal weights.
MultiplicativeAlgorithm_Rcpp

Function MultiplicativeAlgorithm_Rcpp
PSOAlgorithm-class

Class "PSOAlgorithm"
getProportionsOfSubjects

Get the proportion of subjects.
getPlotOptions

Get the plot options for graphs responses and SI
getNumberOfIterations

Get the number of iterations.
getNumberOfArms

getNumberOfArms
getOptimizerParameters

Get the optimization parameters.
getOutcome

getOutcome
getPDModel

Get a PD model.
getFixedMu

Get the fixed effect.
getPKModel

Get a PK model.
getShrinkage

Get the shrinkage.
getFixedOmega

Get the fixed variance.
getEquationsAfterInfusion

Get the equations after infusion.
getModelParametersValues

Get the values of the model parameters.
getMu

getMu
getNumberOfsamplingsOptimisable

Get the number of sampling times that are optimisable.
getSamplingTimes

getSamplingTimes
getModelFromLibrary

Get a model from the library of models.
getFixedParameters

Get the fixed parameters.
getFixedTimes

Get the fixed sampling times.
getOutcomesForEvaluation

Get the outcomes of a model used for the evaluation (is scales outcomes).
getOdeSolverParameters

getOdeSolverParameters
PlotEvaluation-class

Class "PlotEvaluation"
getSamplingTimesConstraints

getSamplingTimesConstraints
generateReportEvaluation

Generate the report for the evaluation
getVarianceEffects

Get the matrix of the variance effects.
defineModelFromLibraryOfModels

Define a model from the library of models.
defineModelEquationsFromStringToFunction

defineModelEquationsFromStringToFunction
generateFimsFromConstraints

Generate the fim from the constraints
getModelParameters

Get the model parameters.
initialize,Evaluation-method

initialize
initialize,FedorovWynnAlgorithm-method

initialize
getTimeDose

getTimeDose
getSigmaInter

Get the parameter sigma inter.
getTinf

Get the infusion duration.
getNumberOfParameters

Get the number of parameters.
getWeightThreshold

Get the parameter weightThreshold
getColumnAndParametersNamesFIMInLatex

Get the names of the names of the parameters associated to each column of the fim in Latex format.
getSE

Get the SE.
getOutcomesGradient

getOutcomesGradient
getRSE

Get the RSE
initialize,AdministrationConstraints-method

initialize
getSigmaSlope

Get the parameter sigma slope.
getSize

getSize
initialize,Model-method

initialize
getVariables

Return the variable of an ode model
initialize,ModelParameter-method

initialize
initialize,MultiplicativeAlgorithm-method

initialize
initialize,ModelAnalyticBolusSteadyState-method

initialize
initialize,ModelAnalyticBolus-method

initialize
initialize,PGBOAlgorithm-method

initialize
getConditionNumberFixedEffects

Get the condition number of the matrix of the fixed effects.
initialize,Arm-method

initialize
initialize,Normal-method

initialize
initialize,ModelAnalytic-method

initialize
getDistribution

Get the distribution.
getDeterminant

Get the determinant of the fim.
initialize,Proportional-method

initialize
initialize,SamplingTimeConstraints-method

initialize
isModelODE

Test if a mode is ode.
initialize,PSOAlgorithm-method

initialize
initialize,Design-method

initialize
getElementaryProtocols

Get the elementary protocols.
plotWeights

Graph of the weights for the multiplicative algorithm.
reportTablesAdministration

reportTablesAdministration
getEquation

Get the equation of a model error.
setDerivatives

Set the derivatives of the model error equation.
setDescription

Set the description of a model.
run

run
resizeFisherMatrix

Resize the fisher Matrix from a vector to a matrix.
setFixedEffects

Set the fixed effects.
setFixedMu

Set the mu as fixed or not.
setMu

Set the value of the fixed effect mu of an object.
isModelAnalytic

Test if a mode is analytic.
initialize,Optimization-method

initialize
isDoseInEquations

Test if the dose is in the equations of the model.
getNumberOfTimesByWindows

Get the number of sampling times by windows.
getSamplings

Get the sampling of an object.
initialize,ModelAnalyticSteadyState-method

initialize
initialize,Distribution-method

initialize
getFisherMatrix

Get the FIM.
getSamplingsWindows

Get the windows for the sampling times.
getFixedEffects

Get the matrix of fixed effects.
getModelError

Get the model error.
getModelErrorParametersValues

Get the values of the model error parameters.
initialize,ModelBolus-method

initialize
optimize

Optimize a design.
parametersForComputingGradient

Define the parameters for computing the gradients of a model.
setArms

Set the arms of an object.
getOutcomesEvaluation

getOutcomesEvaluation
getOutcomes

Get the outcomes of a model.
getSamplingTime

getSamplingTime
getcError

Get the parameter c.
initialize,Administration-method

initialize
plotOutcomesEvaluation

plotOutcomesEvaluation
plotOutcomesGradient

plotOutcomesGradient
setOutcomesGradient

setOutcomesGradient
setName

Set the name of an object.
plotSensitivityIndice

Graphs of the results of the evaluation.
isModelSteadyState

Test if a mode is steady state.
plotShrinkage

Graph of the shrinkage.
initialize,Fim-method

initialize
initialize,LibraryOfModels-method

initialize
setEvaluationInitialDesignResults

Set the evaluation results of the initial design.
setContent

Set content of a library of models.
setFim

setFim
setParameters

Set the parameters of an object.
setSigmaInter

Set the parameter sigma inter.
plotEvaluation

Graphs of the results of the evaluation.
initialize,SamplingTimes-method

initialize
initialize,SimplexAlgorithm-method

initialize
getSamplingTimeConstraint

getSamplingTimeConstraint
initialize,Constant-method

initialize
initialize,Combined1-method

initialize
initialize,ModelInfusion-method

initialize
initialize,ModelError-method

initialize
setSigmaSlope

Set the parameter sigma slope.
setcError

Set the parameter c.
setVarianceEffects

Set the matrix of the variance effects.
initialize,LibraryOfPKPDModels-method

initialize
reportTablesPlot

reportTablesPlot
initialize,ModelAnalyticInfusion-method

initialize
initialize,ModelAnalyticInfusionSteadyState-method

initialize
initialize,OptimizationAlgorithm-method

initialize
initialize,LogNormal-method

initialize
initialize,PFIMProject-method

initialize
isModelInfusion

Test if a mode is infusion
isModelBolus

Test if a mode is bolus.
plotRSE

Graph of the RSE.
plotSE

Graph the SE.
setAdministrations

setAdministrations
reportTablesDesign

reportTablesDesign
setFimTypeToString

Convert the type of the object fim to a string.
setEquationsAfterInfusion

Set the equations after infusion.
setEquations

Set the equations of a model.
reportTablesFIM

Generate the tables for the report.
plotFrequencies

Graph of the frequencies for the FW algorithm.
reportTablesSamplingConstraints

reportTablesSamplingConstraints
setEquation

Set the equation of a model error.
setDose

Set the amount of dose
setNumberOfArms

setNumberOfArms
setOdeSolverParameters

Set the parameters of the ode solver.
setArm

setArm
setFixedOmega

Set the omega as fixed of not.
setDistribution

Set the distribution.
setDesigns

Set the designs.
setFisherMatrix

Set the FIM.
setInitialConditions

setInitialConditions
setOptimalWeights

Set the optimal weights.
setOmega

Set the matrix omega of an object.
setOptimalDesign

Set the optimal design.
setOutcome

setOutcome
setDataForArmEvaluation

setDataForArmEvaluation
setDataForModelEvaluation

Generate the table of dose, time dose etc. for model evaluation
setOptimizationResults

Set the optimization results.
reportTablesModelParameters

Generate the tables for model parameters for the evaluation report.
reportTablesModelError

Generate the tables for model errors for the evaluation report.
setEquationsDuringInfusion

Set the equations during infusion.
setSamplings

Set the sampling times.
setSamplingTimes

setSamplingTimes
setSamplingTimesConstraints

setSamplingTimesConstraints
setIterationAndCriteria

Set the iteration with the convergence criteria.
setModel

Set the model.
setOutcomesForEvaluation

Set the outcomes of a model used for the evaluation (is scales outcomes).
setOutcomesEvaluation

setOutcomesEvaluation
setEvaluationFIMResults

Set the evaluation results.
setSamplingTime

setSamplingTime
setModelError

Set the model error.
setSamplingConstraintForOptimization

setSamplingConstraintForOptimization
setModelFromLibrary

Set a model from the library of model
setOutcomes

Set the outcomes of a model.
setTimeDose

setTimeDose
setTinf

Set the infusion duration.
setShrinkage

Set the shrinkage.
setSize

setSize
setTau

setTau
show,Design-method

show
EvaluateArm

EvaluateArm
Distribution-class

Class "Distribution"
Constant-class

Class "Constant"
Combined1-class

Class "Combined1"
AdministrationConstraints-class

Class "AdministrationConstraints"
Administration-class

Class "Administration"
Design-class

Class "Design"
Arm-class

Class "Arm"
EvaluateDesign

EvaluateDesign
EvaluateVarianceFIM

Evaluate the variance of the Fisher information matrix.
BayesianFim-class

Class "BayesianFim"
EvaluateModel

Evaluate a model.
EvaluateErrorModelDerivatives

Evaluate the error model derivatives.
EvaluateFisherMatrix

Evaluate the Fisher matrix ( population, individual and Bayesian )
FedorovWynnAlgorithm_Rcpp

Fedorov-Wynn algorithm in Rcpp.
EvaluateModelGradient

Evaluate model gradient.