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PFIM (version 6.0)

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

390

Version

6.0

License

GPL (>= 2)

Maintainer

Romain Leroux

Last Published

November 8th, 2023

Functions in PFIM (6.0)

Design-class

Class "Design"
Distribution-class

Class "Distribution"
EvaluateVarianceModel

Evaluate the variance of a model.
Evaluation-class

Class "Evaluation"
ModelAnalytic-class

Class "ModelAnalytic"
Combined1-class

Class "Combined1"
ModelAnalyticBolus-class

Class "ModelAnalyticBolus"
Constant-class

Class "Constant"
ModelAnalyticBolusSteadyState-class

Class "ModelAnalyticBolusSteadyState"
Fim-class

Class "Fim"
ModelAnalyticInfusion-class

Class "ModelAnalyticInfusion"
ModelODEBolus-class

Class "ModelODEBolus"
EvaluateArm

Evaluate an arm.
ModelODEDoseInEquations-class

Class "ModelODEDoseInEquations"
Administration-class

Class "Administration"
AdministrationConstraints-class

Class "AdministrationConstraints"
IndividualFim-class

Class "Fim"
PSOAlgorithm-class

Class "PSOAlgorithm"
FedorovWynnAlgorithm-class

Class "FedorovWynnAlgorithm"
PlotEvaluation-class

Class "PlotEvaluation"
ModelODEInfusionDoseInEquations-class

Class "ModelODEInfusionDoseInEquations"
Arm-class

Class "Arm"
ModelBolus-class

Class "ModelBolus"
ModelError-class

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

Class "ModelParameter"
FedorovWynnAlgorithm_Rcpp

Fedorov-Wynn algorithm in Rcpp.
BayesianFim-class

Class "BayesianFim"
PopulationFim-class

Class "PopulationFim"
Proportional-class

Class "Proportional"
ModelAnalyticInfusionSteadyState-class

Class "ModelAnalyticInfusionSteadyState"
OptimizationAlgorithm-class

Class "OptimizationAlgorithm"
EvaluateErrorModelDerivatives

Evaluate the error model derivatives.
PFIM-package

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

Class "ModelAnalyticSteadyState"
EvaluateFisherMatrix

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

Evaluate an design
convertPKModelAnalyticToPKModelODE

Convert an analytic model to a ode model.
checkSamplingTimeConstraintsForContinuousOptimization

Check for the samplingTime constraints for continuous optimization
EvaluateModel

Evaluate a model.
LogNormal-class

Class "LogNormal"
Model-class

Class "Model"
MultiplicativeAlgorithm-class

Class "MultiplicativeAlgorithm"
ModelInfusion-class

Class "ModelInfusion"
MultiplicativeAlgorithm_Rcpp

Function MultiplicativeAlgorithm_Rcpp
defineModel

Define a model.
EvaluateVarianceFIM

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

Class "LibraryOfModels"
ModelODE-class

Class "ModelODE"
LibraryOfPKPDModels-class

Class "LibraryOfPKPDModels"
Normal-class

Class "Normal"
Optimization-class

Class "Optimization"
ModelODEDoseNotInEquations-class

Class "ModelODEDoseNotInEquations"
checkValiditySamplingConstraint

Check the validity of he sampling times constraints
ModelODEInfusion-class

Class "ModelODEInfusion"
defineModelUserDefined

Define a user defined model.
SamplingTimes-class

Class "SamplingTimes"
definePKModel

Define a PK model.
SimplexAlgorithm-class

Class "SimplexAlgorithm"
PFIMProject-class

Class "PFIMProject"
PGBOAlgorithm-class

Class "PGBOAlgorithm"
addModel

Add a model to a library of models.
fun.amoeba

function fun.amoeba
addModels

Add a models to a library of models.
generateFimsFromConstraints

Generate the fim from the constraints
defineModelFromLibraryOfModels

Define a model from the library of models.
getConditionNumberFixedEffects

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

Report
getConditionNumberVarianceEffects

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

Define the type of a model.
getDescription

Get the description of a model.
getDesigns

Get the designs.
SamplingTimeConstraints-class

Class "SamplingTimeConstraints"
generateReportEvaluation

Generate the report for the evaluation
getAdjustedGradient

Get the adjusted gradient.
generateReportOptimization

Generate report for the optimization.
getAdministration

Get the administrations by outcome.
definePKPDModel

Define a PKPD model.
generateSamplingsFromSamplingConstraints

Generate samplings from sampling constraints
getAdministrationConstraint

Get the administration constraints by outcome.
fisher.simplex

Compute the fisher.simplex
getAdministrations

Get all the administration for an arm.
generateTables

Generate the tables for the report.
getDataFrameResults

Get the dataframe of the results.
getContent

Get content of a library of models.
getColumnAndParametersNamesFIM

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

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

Get the parameter delta
getCorrelationMatrix

Get the correlation matrix.
getEquations

Get the equations of a model.
getEquationsAfterInfusion

Get the equations after infusion.
getAdministrationsConstraints

Get the administrations constraints.
getDerivatives

Get the derivatives of the model error equation.
getDeterminant

Get the determinant of the fim.
getDcriterion

Get the D criterion of the fim.
getArms

Get the arms of an object.
getDistribution

Get the distribution.
getFixedMu

Get the fixed effect.
getFixedOmega

Get the fixed variance.
getDose

Get the amount of doses.
getElementaryProtocols

Get the elementary protocols.
getEigenValues

Get the eigenvalues of the fim.
getInitialConditions

Get the initial condition for the evaluation of an ode model.
getEvaluationInitialDesignResults

Get the evaluation results of the initial design.
getEquationsDuringInfusion

Get the equations during infusion.
getEquation

Get the equation of a model error.
getEvaluationFIMResults

Get the results of the evaluation.
getFim

Get the fim of an of an object.
getLambda

Get the parameter lambda.
getLibraryPKModels

Get the library of PK models.
getMinSampling

Get the minimal sampling times.
getModel

Get the model.
getModelEquations

Get the model equations.
getFisherMatrix

Get the FIM.
getFixedEffects

Get the matrix of fixed effects.
getIterationAndCriteria

Get the iteration with the convergence criteria.
getLibraryPDModels

Get the library of PD models.
getModelError

Get the model error.
getModelErrorParametersValues

Get the values of the model error parameters.
getNumberOfArms

Get the number of arms in a design.
getNumberOfParameters

Get the number of parameters.
getName

Get the name of an object
getNames

Get the names of an object.
getFixedParameters

Get the fixed parameters.
getNumberOfsamplingsOptimisable

Get the number of sampling times that are optimisable.
getModelFromLibrary

Get a model from the library of models.
getNumberOfTimesByWindows

Get the number of sampling times by windows.
getModelParametersValues

Get the values of the model parameters.
getNumberOfIterations

Get the number of iterations.
getFixedTimes

Get the fixed sampling times.
getMu

Get the fixed effect of an object.
getOutcome

Get the outcome of an object.
getOdeSolverParameters

Get the parameters for the ode solvers of an object.
getParameters

Get the parameters of an object.
getPlotOptions

Get the plot options for graphs responses and SI
getOutcomesGradient

Get the results of the evaluation of the outcome gradients.
getOutcomes

Get the outcomes of a model.
getOutcomesEvaluation

Get the results of the evaluation of the outcomes.
getOutcomesForEvaluation

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

Get the optimal weights.
getPDModel

Get a PD model.
getSigmaInter

Get the parameter sigma inter.
getOptimizationResults

Get the optimization results.
getSamplingTimeConstraint

Get the sampling times constraints by outcome.
getOptimizer

Get the optimization algorithm.
getModelParameters

Get the model parameters.
getOptimizerParameters

Get the optimization parameters.
getPKModel

Get a PK model.
getPKPDModel

Get a PKPD model.
getSamplingTimes

Get the vectors of sampling times for an arm.
getShrinkage

Get the shrinkage.
getSamplingTimesConstraints

Get the sampling times constraints.
getSamplingsWindows

Get the windows for the sampling times.
getOmega

Get the matrix omega of an object.
getSamplings

Get the sampling of an object.
getSigmaSlope

Get the parameter sigma slope.
getOptimalDesign

Get the optimal design.
reportTablesSamplingConstraints

Generate table for the report.
getSize

Get the size of an object.
getTau

Get the frequency tau.
plot

Graphs of the results of the evaluation.
plotSE

Graph the SE.
plotOutcomesEvaluation

Plot the evaluation of the outcomes.
getTimeDose

Get the times vector when doses are given.
setFim

Set the fim of the design.
getProportionsOfSubjects

Get the proportion of subjects.
isDoseInEquations

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

Get the infusion duration.
getRSE

Get the RSE
reportTablesPlot

Generate all the table for the evaluation report
isModelAnalytic

Test if a mode is analytic.
getVarianceEffects

Get the matrix of the variance effects.
getSE

Get the SE.
resizeFisherMatrix

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

Get the sampling times by outcome.
plotShrinkage

Graph of the shrinkage.
isModelBolus

Test if a mode is bolus.
isModelInfusion

Test if a mode is infusion
run

run
getcError

Get the parameter c.
reportTablesFIM

Generate the tables for the report.
setEquations

Set the equations of a model.
reportTablesDesign

Generate table for the report.
optimize

Optimize a design.
setFimTypeToString

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

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

Test if a mode is ode.
isModelSteadyState

Test if a mode is steady state.
setDose

Set the amount of dose
setEquation

Set the equation of a model error.
setEvaluationInitialDesignResults

Set the evaluation results of the initial design.
setIterationAndCriteria

Set the iteration with the convergence criteria.
setArms

Set the arms of an object.
setSamplings

Set the sampling times.
setOutcome

Set the outcome of an object.
setMu

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

Set the omega as fixed of not.
reportTablesModelError

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

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

Set the optimal weights.
setContent

Set content of a library of models.
setEquationsDuringInfusion

Set the equations during infusion.
setEquationsAfterInfusion

Set the equations after infusion.
setSamplingTimes

Set the vectors of sampling times for an arm.
setAdministrations

Set all the administration for an arm.
plotRSE

Graph of the RSE.
setTau

Set the frequency tau.
plotOutcomesGradient

Plot the evaluation of the outcome gradients.
setInitialConditions

Set the initial condition for the evaluation of an ode model.
setArm

Set the arms in a design.
setName

Set the name of an object.
setVarianceEffects

Set the matrix of the variance effects.
setOptimizationResults

Set the optimization results.
setOutcomes

Set the outcomes of a model.
setTinf

Set the infusion duration.
plotWeights

Graph of the weights for the multiplicative algorithm.
setSamplingTimesConstraints

Set the sampling times constraints.
setDesigns

Set the designs.
setcError

Set the parameter c.
setFixedEffects

Set the fixed effects.
setDistribution

Set the distribution.
setShrinkage

Set the shrinkage.
setTimeDose

Set the times vector when doses are given.
reportTablesAdministration

Generate table for the report.
setSigmaSlope

Set the parameter sigma slope.
setFixedMu

Set the mu as fixed or not.
setOmega

Set the matrix omega of an object.
setOutcomesForEvaluation

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

Set the FIM.
setNumberOfArms

Set the number of arms in a design.
setEvaluationFIMResults

Set the evaluation results.
setSigmaInter

Set the parameter sigma inter.
setOdeSolverParameters

Set the parameters of the ode solver.
setModel

Set the model.
setDerivatives

Set the derivatives of the model error equation.
setOutcomesGradient

Set the results of the evaluation of the outcomes.
setDescription

Set the description of a model.
setParameters

Set the parameters of an object.
setSamplingConstraintForOptimization

Set the sampling times constraint for optimization with PSO, PGBO and Simplex
setModelError

Set the model error.
setModelFromLibrary

Set a model from the library of model
setOptimalDesign

Set the optimal design.
setSamplingTime

Set the sampling time of an arm.
setOutcomesEvaluation

Set the results of the evaluation of the outcomes.
setSize

Set the size of an object.