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PFIM (version 6.0.3)

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

654

Version

6.0.3

License

GPL (>= 2)

Maintainer

Romain Leroux

Last Published

March 23rd, 2024

Functions in PFIM (6.0.3)

Evaluate a model.

EvaluateFisherMatrix

Evaluate the Fisher matrix ( population, individual and Bayesian )

EvaluateErrorModelDerivatives

Evaluate the error model derivatives.

EvaluateVarianceFIM

Evaluate the variance of the Fisher information matrix.

FedorovWynnAlgorithm_Rcpp

Fedorov-Wynn algorithm in Rcpp.

FedorovWynnAlgorithm-class

Class "FedorovWynnAlgorithm"

Evaluation-class

Class "Evaluation"

EvaluateVarianceModel

Evaluate the variance of a model.

ModelAnalyticBolusSteadyState-class

Class "ModelAnalyticBolusSteadyState"

LibraryOfModels-class

Class "LibraryOfModels"

LogNormal-class

Class "LogNormal"

IndividualFim-class

ModelODEBolus-class

Class "ModelODEBolus"

ModelODEDoseInEquations-class

Class "ModelODEDoseInEquations"

ModelError-class

Class "ModelError" representing a Model error.

LibraryOfPDModels

Library of the PK models

ModelBolus-class

Class "ModelBolus"

ModelAnalyticInfusion-class

Class "ModelAnalyticInfusion"

ModelAnalyticInfusionSteadyState-class

Class "ModelAnalyticInfusionSteadyState"

ModelAnalyticSteadyState-class

Class "ModelAnalyticSteadyState"

LibraryOfPKPDModels-class

Class "LibraryOfPKPDModels"

LibraryOfPKModels

Library of the PK models

ModelODEDoseNotInEquations-class

Class "ModelODEDoseNotInEquations"

PFIMProject-class

Class "PFIMProject"

ModelODEInfusion-class

Class "ModelODEInfusion"

Optimization-class

Class "Optimization"

PGBOAlgorithm-class

Class "PGBOAlgorithm"

PlotEvaluation-class

Class "PlotEvaluation"

PSOAlgorithm-class

Class "PSOAlgorithm"

Class "ModelODE"

ModelAnalyticBolus-class

Class "ModelAnalyticBolus"

ModelAnalytic-class

Class "ModelAnalytic"

ModelInfusion-class

Class "ModelInfusion"

OptimizationAlgorithm-class

Class "OptimizationAlgorithm"

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

checkSamplingTimeConstraintsForContinuousOptimization

Check for the samplingTime constraints for continuous optimization

checkValiditySamplingConstraint

checkValiditySamplingConstraint

PopulationFim-class

Class "PopulationFim"

SamplingTimes-class

Class "SamplingTimes"

MultiplicativeAlgorithm-class

Class "MultiplicativeAlgorithm"

Proportional-class

Class "Proportional"

SimplexAlgorithm-class

Class "SimplexAlgorithm"

MultiplicativeAlgorithm_Rcpp

Function MultiplicativeAlgorithm_Rcpp

ModelParameter-class

Class "ModelParameter"

definePKPDModel

Define a PKPD model.

Add a model to a library of models.

getAdministrationConstraint

getAdministrationConstraint

ModelODEInfusionDoseInEquations-class

Class "ModelODEInfusionDoseInEquations"

Compute the fisher.simplex

getAdministrations

getAdministrations

Add a models to a library of models.

Get the arms of an object.

getAdministrationsConstraints

getAdministrationsConstraints

defineModelType

Define the type of a model.

convertPKModelAnalyticToPKModelODE

Convert an analytic model to a ode model.

defineModelFromLibraryOfModels

Define a model from the library of models.

Define a model.

generateReportEvaluation

Generate the report for the evaluation

SamplingTimeConstraints-class

Class "SamplingTimeConstraints"

generateFimsFromConstraints

Generate the fim from the constraints

defineModelUserDefined

Define a user defined model.

function fun.amoeba

Define a PK model.

Get the determinant of the fim.

getDistribution

Get the distribution.

Get the equations of a model.

getEquationsAfterInfusion

Get the equations after infusion.

getModelEquations

Get the model equations.

getAdministration

getAdministration

getAdjustedGradient

getAdjustedGradient

getCorrelationMatrix

Get the correlation matrix.

generateReportOptimization

Generate report for the optimization.

Get content of a library of models.

Get the D criterion of the fim.

getEvaluationInitialDesignResults

Get the evaluation results of the initial design.

getDataFrameResults

Get the dataframe of the results.

Get the eigenvalues of the fim.

getColumnAndParametersNamesFIM

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

Get the parameter lambda.

Get the designs.

getOutcomesForEvaluation

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

Get the description of a model.

Get the matrix omega of an object.

getColumnAndParametersNamesFIMInLatex

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

getOptimalDesign

Get the optimal design.

generateSamplingsFromSamplingConstraints

Generate samplings from sampling constraints

getNumberOfArms

getNumberOfArms

getLibraryPDModels

Get the library of PD models.

getNumberOfIterations

Get the number of iterations.

getOptimizerParameters

Get the optimization parameters.

getSamplingTime

getSamplingTime

isModelAnalytic

Test if a mode is analytic.

getSamplingTimeConstraint

getSamplingTimeConstraint

Get the equation of a model error.

getEquationsDuringInfusion

Get the equations during infusion.

Get the minimal sampling times.

getElementaryProtocols

Get the elementary protocols.

getEvaluationFIMResults

Get the results of the evaluation.

getLibraryPKModels

Get the library of PK models.

getConditionNumberVarianceEffects

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

Generate the tables for the report.

getFisherMatrix

getConditionNumberFixedEffects

Get the condition number of the matrix of the fixed effects.

getOutcomesGradient

getOutcomesGradient

Test if a mode is bolus.

reportTablesAdministration

reportTablesAdministration

reportTablesDesign

reportTablesDesign

Get the fixed effect.

Get the fixed variance.

Get the parameter delta

Get the derivatives of the model error equation.

Set the equation of a model error.

Set the equations of a model.

setFisherMatrix

getNumberOfParameters

Get the number of parameters.

getModelParametersValues

Get the values of the model parameters.

Get the outcomes of a model.

getNumberOfTimesByWindows

Get the number of sampling times by windows.

Get the shrinkage.

Get the optimization algorithm.

getOptimizationResults

Get the optimization results.

plotOutcomesEvaluation

plotOutcomesEvaluation

Get the parameter sigma inter.

plotFrequencies

Graph of the frequencies for the FW algorithm.

reportTablesFIM

Generate the tables for the report.

getOutcomesEvaluation

getOutcomesEvaluation

Get the sampling of an object.

getFixedEffects

Get the matrix of fixed effects.

setOptimizationResults

Set the optimization results.

setFixedEffects

Set the fixed effects.

getInitialConditions

getInitialConditions

getIterationAndCriteria

Get the iteration with the convergence criteria.

getSamplingsWindows

Get the windows for the sampling times.

Get the parameter sigma slope.

getFixedParameters

Get the fixed parameters.

Get the fixed sampling times.

getOptimalFrequencies

Get the optimal frequencies

Get the model error.

getModelErrorParametersValues

Get the values of the model error parameters.

getOptimalWeights

Get the optimal weights.

Get a PK model.

getSamplingTimes

getSamplingTimes

Get a PD model.

getVarianceEffects

Get the matrix of the variance effects.

getSamplingTimesConstraints

getSamplingTimesConstraints

plotSensitivityIndice

Graphs of the results of the evaluation.

getModelFromLibrary

Get a model from the library of models.

reportTablesModelError

Generate the tables for model errors for the evaluation report.

isModelInfusion

Test if a mode is infusion

getModelParameters

Get the model parameters.

Set the parameters of an object.

Get the infusion duration.

Set the arms of an object.

getNumberOfsamplingsOptimisable

Get the number of sampling times that are optimisable.

setEvaluationFIMResults

Set the evaluation results.

Get the parameters of an object.

getOdeSolverParameters

getOdeSolverParameters

Get a PKPD model.

getProportionsOfSubjects

Get the proportion of subjects.

setEvaluationInitialDesignResults

Set the evaluation results of the initial design.

Get the plot options for graphs responses and SI

Set the mu as fixed or not.

reportTablesSamplingConstraints

reportTablesSamplingConstraints

resizeFisherMatrix

Resize the fisher Matrix from a vector to a matrix.

Test if a mode is ode.

setAdministrations

setAdministrations

Set the parameter sigma inter.

Get the parameter c.

setSamplingConstraintForOptimization

setSamplingConstraintForOptimization

Set the shrinkage.

setIterationAndCriteria

Set the iteration with the convergence criteria.

Set the description of a model.

Set the model error.

setSamplingTimes

setSamplingTimes

setSamplingTime

setSamplingTime

setInitialConditions

setInitialConditions

setOptimalWeights

Set the optimal weights.

Set the designs.

setOptimalDesign

Set the optimal design.

Set the parameter sigma slope.

setOutcomesGradient

setOutcomesGradient

setOutcomesForEvaluation

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

Set the omega as fixed of not.

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

setModelFromLibrary

Set a model from the library of model

isModelSteadyState

Test if a mode is steady state.

isDoseInEquations

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

Graph of the shrinkage.

Optimize a design.

Graph of the weights for the multiplicative algorithm.

Set content of a library of models.

Set the derivatives of the model error equation.

setDistribution

Set the distribution.

Set the outcomes of a model.

setOdeSolverParameters

Set the parameters of the ode solver.

Set the amount of dose

setFimTypeToString

Convert the type of the object fim to a string.

Set the matrix omega of an object.

setOutcomesEvaluation

setOutcomesEvaluation

show,Design-method

Set the parameter c.

parametersForComputingGradient

Define the parameters for computing the gradients of a model.

reportTablesPlot

reportTablesPlot

Graphs of the results of the evaluation.

Graph of the RSE.

reportTablesModelParameters

Generate the tables for model parameters for the evaluation report.

plotOutcomesGradient

plotOutcomesGradient

setEquationsAfterInfusion

Set the equations after infusion.

setEquationsDuringInfusion

Set the equations during infusion.

Set the name of an object.

setNumberOfArms

setNumberOfArms

setSamplingTimesConstraints

setSamplingTimesConstraints

Set the infusion duration.

setVarianceEffects

Set the matrix of the variance effects.

Set the sampling times.

BayesianFim-class

Class "BayesianFim"

Class "Constant"

Combined1-class

Class "Combined1"

AdministrationConstraints-class

Class "AdministrationConstraints"

Distribution-class

Class "Distribution"

Administration-class

Class "Administration"