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PFIM (version 5.0)

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

257

Version

5.0

License

GPL (>= 2)

Maintainer

Romain Leroux

Last Published

June 24th, 2022

Functions in PFIM (5.0)

AdjustLogNormalDistribution

Adjust the mean of a LogNormalDistribution object.

AdjustNormalDistribution

Adjust the Normal Distribution.

Combined1c-class

Class "Combined1c"

Create all the possible combinaison for each Design and each Arms.

Combined1-class

Class "Combined1"

Combined2-class

Class "Combined2"

Evaluate an StatisticalModel object.

EvaluateBayesianFIM

Evaluate design for each arm for a Bayesian FIM.

Define the vector of allowed amount of dose.

Administration-class

Class "Administration"

BayesianFim-class

Class "BayesianFim" representing the population Fisher information matrix.

AdministrationConstraint-class

Class "AdministrationConstraint"

EvaluateErrorModelDerivatives

Evaluate the Error Model Derivatives.

Combined2c-class

Class "Combined2c"

EvaluateFIMsAndDesigns

Evaluate the FIMs and the Designs.

Class "Constant"

EvaluatePopulationFIM

Evaluate a design for each arm for a Population FIM.

EvaluateIndividualFIM

Evaluate design for each arm for a Individual FIM.

EvaluateStatisticalModel

Evaluate a statistical model for all the administrations and all the sampling times of an arm.

DiscreteConstraint-class

Class "DiscreteConstraint" representing the constraints for a variable

Evaluate an analytic model.

CalculatedResidualVariance

Compute the residual variance thanks to the function g of the model error.

DesignConstraint-class

Class "DesignConstraint"

Distribution-class

Class "Distribution"

EvaluateModelInfusion

Evaluate an analytic model in infusion.

Constraint-class

Class "Constraint"

EvaluationModel

Evaluation for the model, analytic, ode, infusion

ContinuousConstraint-class

Class "ContinuousConstraint" representing the constraints for a variable

Class "Fim" representing the Fisher information matrix, a parent class used by three classes PopulationFim, IndividualFim and BayesianFim.

EvaluateModelODE

Evaluate an ODE model.

FinalizeFIMForOneElementaryDesign

FinalizeFIMForOneElementaryDesign

EvaluateModelODEInfusion

Evaluate an ODE model in infusion

FedorovWynnAlgorithm-class

Class "FedorovWynnAlgorithm"

EvaluateODEErrorModelDerivatives

Evaluate the ODE Error Model Derivatives.

Evaluate the design for each arm.

IndividualFim-class

Class "individualFim" representing the individual Fisher information matrix

EvaluateDesignForEachArm

Evaluate Design for each arm.

LibraryOfModels-class

Class for the library of models.

ModelInfusionEquations-class

Class "ModelInfusionEquations" representing a model with infusion equations

Set the value for the fixed times.

IndividualFIMEvaluateVariance

Evaluate the individual FIM variance.

FedorovWynnAlgorithm_Rcpp

Fedorov-Wynn algorithm in Rcpp.

ModelInfusionODEquations-class

Class "ModelInfusionODEquations" representing a model with infusion equations in ODE model.

LogNormalDistribution-class

Class "LogNormalDistribution"

Class "Model" representing a Model

FillLibraryOfModels

Function "FillLibraryOfModels"

ModelEquations-class

Class "ModelEquations" representing a the equations of a model.

ModelError-class

Class "ModelError" representing a Model error.

Optimization-class

Class "Optimization"

MultiplicativeAlgorithm_Rcpp

Function MultiplicativeAlgorithm_Rcpp

NormalDistribution-class

Class "NormalDistribution"

Set the optimization process.

Optimize the designs for each arms.

Class "PDModel" representing a PD model.

ModelODEquations-class

Class "ModelODEquations" representing the equations of an ODE model

ModelParameter-class

Class "ModelParameter"

PopulationFIMEvaluateVariance

Evaluate the Variance of a Population FIM

ModelVariable-class

Class "ModelVariable"

MultiplicativeAlgorithm-class

Class "MultiplicativeAlgorithm"

PopulationFim-class

Class "PopulationFim"

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

PFIMProjectReportEvaluation

Generate the html report for the evaluation.

PFIMProject-class

Class "PFIMProject"

PFIMProjectReportOptimization

Generate the html report for the optimization.

Class "Response"

PGBOAlgorithm-class

Class "PGBOAlgorithm"

StandardDistribution-class

Class "StandardDistribution"

Get the derivate of an equation of a ModelEquations object.

Add a response to a statistical model.

StatisticalModel-class

Class "StatisticalModel"

Prepare the FIMs for the optimization.

SamplingConstraint-class

Class "SamplingConstraint"

Proportional-class

Class "Proportional"

Class "PKModel" representing a PK model.

SamplingTimes-class

Class "SamplingTimes"

getAdministration

Get the parameters of the administration for an arm.

PKPDModel-class

Class "PKPDModel" representing a PKPDModel model.

allowedContinuousSamplingTimes

Set the allowed continuous sampling times.

PSOAlgorithm-class

Class "PSOAlgorithm"

allowedDiscretSamplingTimes

Set the allowed discret sampling times.

getContentsLibraryOfModels

Get the content of the LibraryOfModels object.

SimplexAlgorithm-class

Class "SimplexAlgorithm"

Add a design to the PFIMProject object.

Add responses to a statistical model.

Add a list of designs to the PFIMProject object.

ProportionalC-class

Class "ProportionalC"

ReportAndPlots-class

Class "ReportAndPlots"

addSamplingConstraint

Add a constraint on the sampling for a design.

addDesignConstraints

Add design constraints on the sampling for a design.

Get the D-criterion for a Fim object.

setAllowedDose<-

Set the constraints on allowed dose.

addAdministration

Add an administration to an arm.

getEvaluationDesign

Get the evaluated concentration and sensitivity indices of a design.

Add a Model object in the LibraryOfModels.

convertAnalyticToODE

Convert an equation of a PD model of a ModelEquations object from analytic to ODE.

Compute the fisher.simplex

Add an arm to a design.

getModelNameList

Get the list of all the models in the LibraryOfModels object.

getEquationsModelPKPD

Get the equations of the PK and PD models of a ModelEquations object.

addAdministrationConstraint

Add constraints on the administration for a DesignConstraint object.

Set the sample time of the response of the SamplingTimes object.

defineCorrelation

Set the correlation.

checkParameterInEquations

Check the parameters in the model equations.

Get the design of PFIMProject object.

Set the value for the fixed doses in the administration constraints.

addSamplingConstraints

Add sampling constraints to an arm.

defineModelEquations

Define model equations

Add sampling time for an arm and for a response.

Get the sigma_slope of a ModelError object.

getAdministrationByOutcome

Get the parameters of the administration for an arm given the response of the model.

function fun.amoeba

defineParameter

Define a parameter of a statistical model.

Add sampling times for an arm and for a response.

getResponseIndice

Get the index of the response of a ModelEquations object.

Get the range of a ContinuousConstraint object.

Define a variable in a statistical model.

defineVariables

Define variables in a statistical model.

Add arms to a design.

getNumberOfParameters

Get the number of parameters of a ModelEquations object.

getDerivatesAdjustedByDistribution

Get the derivates adjusted by distribution of a ModelParameter object.

Get the Determinant of a Fisher Information Matrix.

Get the constraints on Tinf.

Evaluation of the model error.

Get the correlation matrix of the Fisher Information Matrix for a Fim object.

plotSensitivity

Plot the sensitivity indices of a model over time.

Get mu for a ModelParameter object.

getEquationsStatisticalModel

Get the equations of a statistical model.

getDistribution

Get the distribution of a ModelParameter object.

getInfusionEquations

Get the Infusion Equations.

getAmountOfArms

Get the amount of arms in a Design.

changeVariablePKModel

Change variable in a PK Model.

getAllowedDoses

Get the vector of allowed amount of dose.

getAdministrationConstraint

Get the constraints on the administration for a DesignConstraint object.

Get the initial time of a SamplingTimes object.

plotWeightOptimisation

Plot the optimal weights for the Multiplicative algorithm.

defineStatisticalModel

Define the StatisticalModel object of the PFIMProject object.

Get the constraints on allowed dose

Get the infusion duration.

getModelParameters

Get the model parameters of a statistical model.

getConditionNumberMatrix

Get the Condition Number Matrix of the Fisher Information Matrix for a Fim object..

getEvaluationResponses

Get the evaluated responses of the model.

getNameAdministration

Get the name of the outcome of an object Administration.

Set the times vector when doses are given.

Get the Fisher Information Matrix.

getResponseName

Get the name of the response for the administration constraints.

Boolean to set if a model parameters is fixed or not.

Get a PK model from a PKPDModel object.

Get a model of the LibraryOfModels object.

Get the number of times in a SamplingTimes object.

defineParameters

Define the parameters of a statistical model.

Get the amount of doses.

Get the parameters of a ModelEquations object.

knitrModelEquations

Set the table knitrModelEquations.

Calculates the shrinkage of individual parameters from a BayesianFim object.

getResponseNameByIndice

Get the response name given the indice of the response.

Get the DV Sigma of a ModelError object.

Gives a summary of all the parameters of an arm for a design.

Set a matrix value for the Fisher Information Matrix.

Plot the concentration over time of a model.

getNamePFIMProject

Get the name of a PFIMProject project.

getSamplingConstraintsInArm

Get the sampling constraints of an arm.

Get the equation of a ModelError object by their names.

Get the derivatives of a ModelODEquations object.

Get the size of an arm.

getElementaryProtocols

Get the matrix of all the combination of the elementary protocols.

Get thesigma_inter of a ModelError object.

Get the description of FIM.

Set the constraint to the PFIMProject projet.

Set the infusion lag tau.

Get the Fisher Information Matrices.

Get the Fisher Information Matrix.

getOptimizationResult

Get the results of the optimization process.

Get the vectors of sampling times for an arm.

Get the values of the variances sigma_inter and sigma_slope.

getErrorModelParameters

Get parameters of the error model of a ModelError object.

Get the initial conditions in a arm for an ODE model

getFisherMatrices

Get the fim matrices from all designs of a PFIMProject object.

Set the size of an arm.

setAllowedTinf<-

Set the constraints on Tinf.

Get the name of the arm.

Get the Fisher Information Matrix of a design.

modifySamplingTimes

Modify the sampling times of an arm.

Set the number of iterations for the multiplicative algorithm.

Plot the standard errors SE of the model parameters.

Get the equations of a ModelEquations object.

Get a PKPD model of the LibraryOfModels object.

Get the sample time of the response of the SamplingTimes object.

getErrorModelStandardErrors

Get the SE and RSE of the parameters.

setNamePFIMProject

Set the name of a PFIMProject projet.

getOptimalDesign

Get the optimal design.

knitrOptimalDesign

Set the table knitrOptimalDesign.

Get the values for Sigma derivatives DVSigma for the ModelError object.

getNumberOfSamplings

Get the number of sampling times in a arm.

Set the design of PFIMProject object.

Get the constraints on allowed times.

Boolean to set if mu is fixed or not.

Get the CError of a ModelError object.

Get the model error.

Get the arms of a design.

Get the set of possible values for a DiscreteConstraint object.

Modify an arm of a design.

getNumberSamples

Get the number of sampled in a Design.

getDoseOptimisability

Get the boolean Optimisability for optimizable dose.

getEquationsModel

Get the equations of a Model object.

Get the name of the design.

Set the infusion duration.

Get Omega of a ModelParameter object.

Set the total size of a Design.

Function to remplace a dose.

getNameDesignConstraint

Get the name of the DesignConstraint object.

getParametersOdeSolver

Get parameters for the ode solver

getNumberOfParameter

Get the number of parameters of a ModelError object.

knitrAdministrationParameters

Set the table knitrAdministrationParameters.

getNameResponse

Get the name of the response of the model.

getTotalNumberOfIndividuals

get the total number of individuals in a DesignConstraint object.

getNameSampleTime

Get the name of the response of the SamplingTimes object.

Get the frame with weight vector after optimisation.

Get the total size of a design.

Get the weights for the optimal designs.

resizeFisherMatrix

Resize the fisher Matrix from a vector to a matrix.

knitrModelError

Set the table knitrModelError.

getOptimisability

Get the optimisability of a SamplingConstraint object.

setSigmaSlope<-

Set the value for sigma_slope of a ModelError object.

Get the eigen values of the Fisher Information Matrix for a Fim object.

getSamplingConstraints

Get the constraints on the sampling for a DesignConstraint object.

getFixedParameters

Get the fixed and non fixed model parameters.

knitrInitialDesigns

Set the table knitrInitialDesigns.

getNumberOfDoses

Get the vector AllowedDoses of allowed amount of dose.

Get the names for the error sigma inter.

Set the table knitrFIM.

setAmountOfArms

Set the amount of arms in a Design.

Set the possible values for a DiscreteConstraint object.

getallowedContinuousSamplingTimes

Get the allowed Continuous SamplingTimes

setModelError<-

Set the model error.

reportPFIMProject

Generate a htmal report html.

Plot the shrinkage data.

Get the frequency tau.

summary,Design-method

Get the name of the Model object.

setAllowedTime<-

Set the constraints on allowed times.

setPossibleArms

Set the possible arms in a Design or the case when lots of arms are defined and aim to optimise amoung several of them.

Get the times vector when doses are given.

Set the name of the design.

show,Fim-method

Show the Fisher Information Matrix for a Fim object and its information: Determinant, D-criterion, SE, Eigenvalues, Correlation.

Set the delta parameters for the Multiplicative algorithm.

setNumberSamples<-

Set the number of Sample in a Design.

getnumberOfSamplingTimes

Get the number of sampling times.

Test if an object Administrationfor a model is multi-doses or not.

getNameModelParameter

Get the name of a ModelParameter object.

parametersForComputingGradient

Parameters used for computing the model gradient by finite-differences.

Get the fixed times.

setAmountOfArmsAim

Set amount of arms in a DesignConstraint object for the case we aim to obtain a fixed amount of arms as result.

isLessThanDelay

Set the constraint on minimal time delay in sampling times.

Get a PD model from a PKPDModel object.

Boolean to set if a model parameters is not fixed or not.

setTotalNumberOfIndividuals

Set the total number of individuals in a DesignConstraint object.

numberOfSamplingTimesIsOptimisable

Set the number of sampling times that are optimisable.

Set the mu vector.

plotFrequenciesOptimisation

Plot the frequencies for the FedorovWynn algorithm.

knitrModelParameters

Set the table knitrModelParameters.

getNameModelVariable

Get the name of the initial variable for an ODE model.

setOptimalDesign<-

Set an optimal design.

setInitialConditions

Set the initial conditions of an Arm for an ODE model.

Set the range of a ContinuousConstraint object.

Plot the relative standard errors RSE of the model parameters.

getStatisticalModelStandardErrors

Get the SE of IndividualFim object.

getStatisticalModel

Get the StatisticalModel object of the PFIMProject object.

Show the data of an arm for a design.

scaleResponsesEvaluationODE

function to adjust Responses with variables values.

scaleResponsesEvaluationODEInfusion

function to adjust Responses with variables values.

Set the Omega matrix.

Show the process for the optimization.

setSigmaInter<-

Set the value for sigma_inter of a ModelError object.

getResponsesStatisticalModel

Get the responses of a statistical model.

Get the Standard Errors for a Fim object..

Boolean to set if mu is not fixed or not.

getallowedDiscretSamplingTimes

Get the allowed discret sampling simes

Set the CError of a ModelError object.

Show the Fisher Information Matrix for all the designs.

Set the amount of dose

showConstraints

Show all the constraints of the PFIMProject object.

isTimeInBetweenBounds

Set the constraint on the sampling times bounds.

Plot the D criteria over time.

Show all the Designs.

Set the arms of a design.

Set the sampling times for an arm.

setParametersForEvaluateModel

Set the parameters for the evaluation of the model.

setParametersModel

Set the parameters of the Model object.

setParametersOdeSolver

Set parameters for the ode solver

showStatisticalModelStandardErrors

Show expected standard error data frame.