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PFIM (version 7.0.1)

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

307

Version

7.0.1

License

GPL (>= 3)

Homepage

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

Maintainer

Romain Leroux

Last Published

November 26th, 2025

Functions in PFIM (7.0.1)

Linear2BolusSingleDose_ClQV1V2

Model Linear2BolusSingleDose_ClQV1V2

LibraryOfPKModels

LibraryOfPKModels

LibraryOfModels

LibraryOfModels

Linear2InfusionSteadyState_kk12k21Vtau

Model Linear2InfusionSteadyState_kk12k21Vtau

Linear2InfusionSteadyState_ClQV1V2tau

Model Linear2InfusionSteadyState_ClQV1V2tau

Linear2FirstOrderSingleDose_kaClQV1V2

Model Linear2FirstOrderSingleDose_kaClQV1V2

Linear2BolusSteadyState_kk12k21Vtau

Model Linear2BolusSteadyState_kk12k21Vtau

FedorovWynnAlgorithm

FedorovWynnAlgorithm

FedorovWynnAlgorithm_Rcpp

Fedorov-Wynn algorithm in Rcpp.

Linear2FirstOrderSteadyState_kaClQV1V2tau

Model Linear2FirstOrderSteadyState_kaClQV1V2tau

Linear2FirstOrderSingleDose_kakk12k21V

Model Linear2FirstOrderSingleDose_kakk12k21V

ModelODEDoseInEquations

ModelODEDoseNotInEquations

ModelAnalyticSteadyState

ModelAnalyticSteadyState

ModelAnalyticInfusion

ModelAnalyticInfusion

ModelAnalyticInfusionSteadyState

ModelAnalyticInfusionSteadyState

LibraryOfPDModels

LibraryOfPDModels

Linear2InfusionSingleDose_ClQV1V2

Model Linear2InfusionSingleDose_ClQV1V2

Linear2FirstOrderSteadyState_kakk12k21Vtau

Model Linear2FirstOrderSteadyState_kakk12k21Vtau

SimplexAlgorithm

SimplexAlgorithm

convertPKModelAnalyticToPKModelODE

convertPKModelAnalyticToPKModelODE: conversion from analytic to ode

ModelODEDoseNotInEquations

ModelODEDoseNotInEquations

ModelODEInfusion

ModelODEInfusion

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

ModelODEInfusionDoseInEquation

ModelODEInfusionDoseInEquation

defineModelType

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

defineModelWrapper

defineModelWrapper: define the model wrapper for the ode solver

constraintsTableForReport

constraintsTableForReport: table of the PGBOAlgorithm constraints for the report.

defineOptimizationAlgorithm

Define optimization algorithm

defineModelAdministration

defineModelAdministration: define the administration

MultiplicativeAlgorithm

MultiplicativeAlgorithm

MultiplicativeAlgorithm_Rcpp

Function MultiplicativeAlgorithm_Rcpp

generateDosesCombination

generateDosesCombination: generate the combination for the doses.

definePKModel: define a PK model from library of model

Compute the fun.amoeba

Generate optimization report

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

SamplingTimeConstraints

SamplingTimeConstraints

getFisherMatrix

getFisherMatrix: display the Fisher matrix components

getFim: get the Fisher matrix.

evaluateFim: evaluation of the Fim

evaluateInitialConditions

evaluateInitialConditions: evaluate the initial conditions.

defineModelEquationsFromLibraryOfModel

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

getCorrelationMatrix

getCorrelationMatrix : get the correlation matrix

getArmData: extract arm data for The Report

checkSamplingTimeConstraintsForMetaheuristic

checkSamplingTimeConstraintsForMetaheuristic

checkValiditySamplingConstraint

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

plotFrequencies

Plot frequencies for the FedorovWynn algorithm

plotEvaluationSI

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

plotWeightsMultiplicativeAlgorithm

plotWeightsMultiplicativeAlgorithm: plot the optimal weight.

Compute the fisher.simplex

finiteDifferenceHessian

finiteDifferenceHessian: compute the Hessian

processArmEvaluationResults

processArmEvaluationResults: process for the evaluation of an arm.

Run optimization

plotSensitivityIndices

Plot sensitivity indices.

plotSEFIM: barplot for the SE

getSE: get the SE

getDcriterion : get the Dcriterion

getDeterminant: get the determinant

getSamplingData

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

evaluateModelGradient

evaluateModelGradient: evaluate the gradient of the model

setEvaluationFim

setEvaluationFim: set the Fim results.

evaluateModel: evaluate the model

evaluateModelVariance

evaluateModelVariance: evaluate the variance of the model

definePKPDModel

definePKPDModel: define a PKPD model from library of model

evaluateArm: evaluation of the model with the arm parameters.

processArmEvaluationSI

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

replaceVariablesLibraryOfModels

replaceVariablesLibraryOfModels: replace variable in the LibraryOfModels

getArmConstraints

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

generateSamplingsFromSamplingConstraints

generateSamplingsFromSamplingConstraints

generateSamplingTimesCombination

generateSamplingTimesCombination: generate the combination for the samplings.

generateReportOptimization

generateReportOptimization: generate the report for the design optimization.

getModelParametersData

getModelParametersData: get model parameters data for report.

getRSE: get the RSE

adjustGradient: adjust the gradient for the log normal distribution.

armAdministration

getArmAdministration: get the administration parameters of an arm.

setSamplingConstraintForOptimization

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

Plot relative standard errors

plotFrequenciesFedorovWynnAlgorithm

plotFrequenciesFedorovWynnAlgorithm

setOptimalArms: set the optimal arms of an optimization algorithm.

Optimization PGBOAlgorithm

evaluateVarianceFIM

evaluateVarianceFIM: evaluate the variance

getShrinkage: get the shrinkage

evaluateDesign: evaluation of a design.

evaluateErrorModelDerivatives

evaluateErrorModelDerivatives; evaluate the derivatives of the model error.

generateFimsFromConstraints

Generate FIMs from constraints

generateReportEvaluation

generateReportEvaluation: generate the report for the model evaluation.

getListLastName

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

getModelErrorData

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

Plot standard errors

plotEvaluationResults

plotEvaluationResults: process for the evaluation of the responses.

plotEvaluation: plots for the evaluation of the model responses.

plotRSEFIM: barplot for the RSE

tablesForReport

tablesForReport: generate the table for the report.

plotShrinkage: plot the shrinkage values.

Plot weights for the multiplicative algorithm

Show optimization results

updateSamplingTimes

updateSamplingTimes: update sampling times for plotting used for plot

showFIM: show the Fim in the R console.

Dcriterion: get the D-criterion of the Fim.

AdministrationConstraints

AdministrationConstraints

Linear2BolusSingleDose_kk12k21V

Model Linear2BolusSingleDose_kk12k21V

Linear2BolusSteadyState_ClQV1V2tau

Model Linear2BolusSteadyState_ClQV1V2tau

Linear2InfusionSingleDose_kk12k21V

Model Linear2InfusionSingleDose_kk12k21V