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PFIM (version 7.0)

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

7.0

License

GPL (>= 3)

Homepage

http://www.pfim.biostat.fr/

Maintainer

Romain Leroux

Last Published

July 2nd, 2025

Functions in PFIM (7.0)

LibraryOfPDModels

LibraryOfPDModels

LibraryOfModels

LibraryOfModels

Linear2InfusionSingleDose_ClQV1V2

Model Linear2InfusionSingleDose_ClQV1V2

Linear2FirstOrderSteadyState_kakk12k21Vtau

Model Linear2FirstOrderSteadyState_kakk12k21Vtau

FedorovWynnAlgorithm

FedorovWynnAlgorithm

Linear2BolusSteadyState_kk12k21Vtau

Model Linear2BolusSteadyState_kk12k21Vtau

ModelAnalyticSteadyState

ModelAnalyticSteadyState

FedorovWynnAlgorithm_Rcpp

Fedorov-Wynn algorithm in Rcpp.

ModelODEDoseInEquations

ModelODEDoseNotInEquations

Linear2FirstOrderSingleDose_kakk12k21V

Model Linear2FirstOrderSingleDose_kakk12k21V

Linear2FirstOrderSteadyState_kaClQV1V2tau

Model Linear2FirstOrderSteadyState_kaClQV1V2tau

Linear2BolusSingleDose_kk12k21V

Model Linear2BolusSingleDose_kk12k21V

Linear2InfusionSingleDose_kk12k21V

Model Linear2InfusionSingleDose_kk12k21V

Linear2BolusSteadyState_ClQV1V2tau

Model Linear2BolusSteadyState_ClQV1V2tau

ModelODEInfusion

ModelODEInfusion

Linear2FirstOrderSingleDose_kaClQV1V2

Model Linear2FirstOrderSingleDose_kaClQV1V2

ModelODEDoseNotInEquations

ModelODEDoseNotInEquations

Linear2InfusionSteadyState_ClQV1V2tau

Model Linear2InfusionSteadyState_ClQV1V2tau

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

ModelODEInfusionDoseInEquation

ModelODEInfusionDoseInEquation

ModelAnalyticInfusionSteadyState

ModelAnalyticInfusionSteadyState

ModelAnalyticInfusion

ModelAnalyticInfusion

definePKPDModel

definePKPDModel: define a PKPD model from library of model

constraintsTableForReport

constraintsTableForReport: table of the PGBOAlgorithm constraints for the report.

evaluateArm: evaluation of the model with the arm parameters.

generateFimsFromConstraints

Generate FIMs from constraints

generateReportEvaluation

generateReportEvaluation: generate the report for the model evaluation.

MultiplicativeAlgorithm

MultiplicativeAlgorithm

defineModelType

defineModelType: define the class of the model to be evaluated.

MultiplicativeAlgorithm_Rcpp

Function MultiplicativeAlgorithm_Rcpp

getListLastName

getListLastName: routine to get the names of last element of a nested list.

adjustGradient: adjust the gradient for the log normal distribution.

plotEvaluation: plots for the evaluation of the model responses.

getModelErrorData

getModelErrorData: get the parameters sigma slope and sigma inter (used for the report).

plotEvaluationResults

plotEvaluationResults: process for the evaluation of the responses.

SimplexAlgorithm

SimplexAlgorithm

defineModelAdministration

defineModelAdministration: define the administration

SamplingTimeConstraints

SamplingTimeConstraints

Generate optimization report

defineModelEquationsFromLibraryOfModel

defineModelEquationsFromLibraryOfModel: define the model equations giving the models in the library of models.

convertPKModelAnalyticToPKModelODE

convertPKModelAnalyticToPKModelODE: conversion from analytic to ode

define the type of Fisher information matrix: population, individual or Bayesian

defineModelWrapper

defineModelWrapper: define the model wrapper for the ode solver

evaluateErrorModelDerivatives

evaluateErrorModelDerivatives; evaluate the derivatives of the model error.

checkSamplingTimeConstraintsForMetaheuristic

checkSamplingTimeConstraintsForMetaheuristic

evaluateDesign: evaluation of a design.

armAdministration

getArmAdministration: get the administration parameters of an arm.

defineOptimizationAlgorithm

Define optimization algorithm

definePKModel: define a PK model from library of model

evaluateModelVariance

evaluateModelVariance: evaluate the variance of the model

evaluateModel: evaluate the model

evaluateModelGradient

evaluateModelGradient: evaluate the gradient of the model

checkValiditySamplingConstraint

checkValiditySamplingConstraint: check if the constraints used for the design optimization are valid.

getFim: get the Fisher matrix.

finiteDifferenceHessian

finiteDifferenceHessian: compute the Hessian

generateDosesCombination

generateDosesCombination: generate the combination for the doses.

getArmData: extract arm data for The Report

Compute the fun.amoeba

getCorrelationMatrix

getCorrelationMatrix : get the correlation matrix

plotFrequenciesFedorovWynnAlgorithm

plotFrequenciesFedorovWynnAlgorithm

Plot relative standard errors

processArmEvaluationSI

processArmEvaluationSI: process for the evaluation of the gradient of the responses.

replaceVariablesLibraryOfModels

replaceVariablesLibraryOfModels: replace variable in the LibraryOfModels

Compute the fisher.simplex

evaluateVarianceFIM

evaluateVarianceFIM: evaluate the variance

getFisherMatrix

getFisherMatrix: display the Fisher matrix components

plotWeightsMultiplicativeAlgorithm

plotWeightsMultiplicativeAlgorithm: plot the optimal weight.

getSE: get the SE

getSamplingData

getSamplingData: extract sampling times and max sampling time used for plot.

processArmEvaluationResults

processArmEvaluationResults: process for the evaluation of an arm.

Show optimization results

showFIM: show the Fim in the R console.

evaluateInitialConditions

evaluateInitialConditions: evaluate the initial conditions.

evaluateFim: evaluation of the Fim

generateReportOptimization

generateReportOptimization: generate the report for the design optimization.

generateSamplingTimesCombination

generateSamplingTimesCombination: generate the combination for the samplings.

plotRSEFIM: barplot for the RSE

Plot standard errors

setOptimalArms: set the optimal arms of an optimization algorithm.

getShrinkage: get the shrinkage

Optimization PGBOAlgorithm

setSamplingConstraintForOptimization

setSamplingConstraintForOptimization: set the sampling time constraints for an arm for the design optimization.

generateSamplingsFromSamplingConstraints

generateSamplingsFromSamplingConstraints

plotSEFIM: barplot for the SE

plotSensitivityIndices

Plot sensitivity indices.

tablesForReport

tablesForReport: generate the table for the report.

updateSamplingTimes

updateSamplingTimes: update sampling times for plotting used for plot

getArmConstraints

getArmConstraints: get the administration and sampling time constraints for the MultiplicativeAlgorithm.

getModelParametersData

getModelParametersData: get model parameters data for report.

getDcriterion : get the Dcriterion

getDeterminant: get the determinant

plotEvaluationSI

plotEvaluationSI: process for the evaluation of the gradient of the responses.

plotFrequencies

Plot frequencies for the FedorovWynn algorithm

Plot weights for the multiplicative algorithm

plotShrinkage: plot the shrinkage values.

getRSE: get the RSE

Run optimization

setEvaluationFim

setEvaluationFim: set the Fim results.

AdministrationConstraints

AdministrationConstraints

Dcriterion: get the D-criterion of the Fim.

Linear2InfusionSteadyState_kk12k21Vtau

Model Linear2InfusionSteadyState_kk12k21Vtau

LibraryOfPKModels

LibraryOfPKModels

Linear2BolusSingleDose_ClQV1V2

Model Linear2BolusSingleDose_ClQV1V2