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PFIM (version 6.0.2)

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

390

Version

6.0.2

License

GPL (>= 2)

Maintainer

Romain Leroux

Last Published

November 24th, 2023

Functions in PFIM (6.0.2)

IndividualFim-class

FedorovWynnAlgorithm_Rcpp

Fedorov-Wynn algorithm in Rcpp.

ModelAnalytic-class

Class "ModelAnalytic"

LibraryOfPDModels

Library of the PK models

LibraryOfModels-class

Class "LibraryOfModels"

ModelAnalyticInfusionSteadyState-class

Class "ModelAnalyticInfusionSteadyState"

ModelAnalyticSteadyState-class

Class "ModelAnalyticSteadyState"

ModelODEBolus-class

Class "ModelODEBolus"

LogNormal-class

Class "LogNormal"

PFIMProject-class

Class "PFIMProject"

PGBOAlgorithm-class

Class "PGBOAlgorithm"

ModelAnalyticBolus-class

Class "ModelAnalyticBolus"

ModelODEInfusion-class

Class "ModelODEInfusion"

PSOAlgorithm-class

Class "PSOAlgorithm"

ModelODEDoseInEquations-class

Class "ModelODEDoseInEquations"

ModelODEDoseNotInEquations-class

Class "ModelODEDoseNotInEquations"

LibraryOfPKModels

Library of the PK models

MultiplicativeAlgorithm-class

Class "MultiplicativeAlgorithm"

ModelODEInfusionDoseInEquations-class

Class "ModelODEInfusionDoseInEquations"

ModelParameter-class

Class "ModelParameter"

EvaluateVarianceFIM

Evaluate the variance of the Fisher information matrix.

MultiplicativeAlgorithm_Rcpp

Function MultiplicativeAlgorithm_Rcpp

definePKPDModel

Define a PKPD model.

generateSamplingsFromSamplingConstraints

Generate samplings from sampling constraints

Generate the tables for the report.

Compute the fisher.simplex

PopulationFim-class

Class "PopulationFim"

Define a PK model.

Proportional-class

Class "Proportional"

defineModelUserDefined

Define a user defined model.

ModelAnalyticBolusSteadyState-class

Class "ModelAnalyticBolusSteadyState"

ModelAnalyticInfusion-class

Class "ModelAnalyticInfusion"

LibraryOfPKPDModels-class

Class "LibraryOfPKPDModels"

convertPKModelAnalyticToPKModelODE

Convert an analytic model to a ode model.

SamplingTimeConstraints-class

Class "SamplingTimeConstraints"

Get content of a library of models.

getCorrelationMatrix

Get the correlation matrix.

PlotEvaluation-class

Class "PlotEvaluation"

defineModelFromLibraryOfModels

Define a model from the library of models.

defineModelType

Define the type of a model.

ModelInfusion-class

Class "ModelInfusion"

getDistribution

Get the distribution.

getEvaluationFIMResults

Get the results of the evaluation.

Get the determinant of the fim.

getEquationsDuringInfusion

Get the equations during infusion.

getNumberOfsamplingsOptimisable

Get the number of sampling times that are optimisable.

getAdministrations

getAdministrations

getAdministrationConstraint

getAdministrationConstraint

getIterationAndCriteria

Get the iteration with the convergence criteria.

getModelFromLibrary

Get a model from the library of models.

getInitialConditions

getInitialConditions

Get the description of a model.

Get the D criterion of the fim.

getModelParameters

Get the model parameters.

getDataFrameResults

Get the dataframe of the results.

OptimizationAlgorithm-class

Class "OptimizationAlgorithm"

Class "ModelODE"

ModelBolus-class

Class "ModelBolus"

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

Add a model to a library of models.

ModelError-class

Class "ModelError" representing a Model error.

Get the parameter delta

getFixedParameters

Get the fixed parameters.

Get the derivatives of the model error equation.

Get the fixed sampling times.

Add a models to a library of models.

getOdeSolverParameters

getOdeSolverParameters

Define a model.

generateReportOptimization

Generate report for the optimization.

getOptimizerParameters

Get the optimization parameters.

Get the sampling of an object.

Get the optimization algorithm.

getSamplingTimesConstraints

getSamplingTimesConstraints

function fun.amoeba

getAdministrationsConstraints

getAdministrationsConstraints

generateReportEvaluation

Generate the report for the evaluation

Get the designs.

Get the equations of a model.

getOutcomesEvaluation

getOutcomesEvaluation

getConditionNumberFixedEffects

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

generateFimsFromConstraints

Generate the fim from the constraints

Optimization-class

Class "Optimization"

getEvaluationInitialDesignResults

Get the evaluation results of the initial design.

getLibraryPKModels

Get the library of PK models.

getConditionNumberVarianceEffects

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

Get the minimal sampling times.

getOutcomesForEvaluation

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

SamplingTimes-class

Class "SamplingTimes"

getOptimizationResults

Get the optimization results.

getOptimalWeights

Get the optimal weights.

Set the description of a model.

parametersForComputingGradient

Define the parameters for computing the gradients of a model.

Optimize a design.

Get the parameter sigma slope.

Get the parameter sigma inter.

getVarianceEffects

Get the matrix of the variance effects.

plotOutcomesGradient

plotOutcomesGradient

Get the parameter c.

reportTablesModelParameters

Generate the tables for model parameters for the evaluation report.

SimplexAlgorithm-class

Class "SimplexAlgorithm"

reportTablesModelError

Generate the tables for model errors for the evaluation report.

Set the derivatives of the model error equation.

Set the shrinkage.

Set the outcomes of a model.

getSamplingTime

getSamplingTime

Get the outcomes of a model.

getEquationsAfterInfusion

Get the equations after infusion.

Get the parameter lambda.

checkValiditySamplingConstraint

checkValiditySamplingConstraint

checkSamplingTimeConstraintsForContinuousOptimization

Check for the samplingTime constraints for continuous optimization

Set the amount of dose

Get the arms of an object.

getAdministration

getAdministration

getColumnAndParametersNamesFIM

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

getAdjustedGradient

getAdjustedGradient

Get the infusion duration.

reportTablesDesign

reportTablesDesign

Set the arms of an object.

reportTablesFIM

Generate the tables for the report.

isModelSteadyState

Test if a mode is steady state.

Test if a mode is ode.

Get the equation of a model error.

getElementaryProtocols

Get the elementary protocols.

Graph of the RSE.

getFisherMatrix

getFixedEffects

Get the matrix of fixed effects.

getColumnAndParametersNamesFIMInLatex

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

Get the eigenvalues of the fim.

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

Set the equation of a model error.

getModelEquations

Get the model equations.

Set the name of an object.

Set the sampling times.

getNumberOfParameters

Get the number of parameters.

getNumberOfTimesByWindows

Get the number of sampling times by windows.

getNumberOfIterations

Get the number of iterations.

getNumberOfArms

getNumberOfArms

Get the fixed effect.

Get the fixed variance.

getOutcomesGradient

getOutcomesGradient

setInitialConditions

setInitialConditions

Set the designs.

Set the omega as fixed of not.

setDistribution

Set the distribution.

Set the parameter sigma inter.

getLibraryPDModels

Get the library of PD models.

Get a PD model.

Graph of the shrinkage.

getSamplingsWindows

Get the windows for the sampling times.

Get the shrinkage.

Get the model error.

getModelErrorParametersValues

Get the values of the model error parameters.

Get the parameters of an object.

Set the parameter sigma slope.

Set the infusion duration.

getModelParametersValues

Get the values of the model parameters.

Graphs of the results of the evaluation.

Graph of the weights for the multiplicative algorithm.

reportTablesAdministration

reportTablesAdministration

plotOutcomesEvaluation

plotOutcomesEvaluation

setModelFromLibrary

Set a model from the library of model

setOutcomesEvaluation

setOutcomesEvaluation

setFisherMatrix

Set the model error.

setFimTypeToString

Convert the type of the object fim to a string.

setNumberOfArms

setNumberOfArms

setOutcomesForEvaluation

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

Get the matrix omega of an object.

getOptimalDesign

Get the optimal design.

Get a PK model.

Get a PKPD model.

Set content of a library of models.

getSamplingTimeConstraint

getSamplingTimeConstraint

getSamplingTimes

getSamplingTimes

Get the plot options for graphs responses and SI

Set the equations of a model.

isDoseInEquations

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

isModelAnalytic

Test if a mode is analytic.

setOdeSolverParameters

Set the parameters of the ode solver.

Set the mu as fixed or not.

setSamplingTimes

setSamplingTimes

setEquationsAfterInfusion

Set the equations after infusion.

setVarianceEffects

Set the matrix of the variance effects.

setSamplingTimesConstraints

setSamplingTimesConstraints

setFixedEffects

Set the fixed effects.

setSamplingConstraintForOptimization

setSamplingConstraintForOptimization

getProportionsOfSubjects

Get the proportion of subjects.

setEquationsDuringInfusion

Set the equations during infusion.

Test if a mode is bolus.

setOptimalDesign

Set the optimal design.

setAdministrations

setAdministrations

reportTablesPlot

reportTablesPlot

reportTablesSamplingConstraints

reportTablesSamplingConstraints

isModelInfusion

Test if a mode is infusion

resizeFisherMatrix

Resize the fisher Matrix from a vector to a matrix.

Set the parameters of an object.

Set the parameter c.

setIterationAndCriteria

Set the iteration with the convergence criteria.

setOptimizationResults

Set the optimization results.

show,Design-method

setEvaluationInitialDesignResults

Set the evaluation results of the initial design.

setOptimalWeights

Set the optimal weights.

setEvaluationFIMResults

Set the evaluation results.

Set the matrix omega of an object.

setOutcomesGradient

setOutcomesGradient

setSamplingTime

setSamplingTime

BayesianFim-class

Class "BayesianFim"

EvaluateErrorModelDerivatives

Evaluate the error model derivatives.

FedorovWynnAlgorithm-class

Class "FedorovWynnAlgorithm"

EvaluateFisherMatrix

Evaluate the Fisher matrix ( population, individual and Bayesian )

AdministrationConstraints-class

Class "AdministrationConstraints"

EvaluateVarianceModel

Evaluate the variance of a model.

Administration-class

Class "Administration"

Evaluation-class

Class "Evaluation"

Combined1-class

Class "Combined1"

Class "Constant"

Distribution-class

Class "Distribution"

Evaluate a model.