Population Fisher Information Matrix

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Documentation for package ‘PFIM’ version 5.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

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A B C D E F G I K L M N O P R S misc

PFIM-package

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

-- A --

addAdministration	Add an administration to an arm.
addAdministrationConstraint	Add constraints on the administration for a 'DesignConstraint' object.
addArm	Add an arm to a design.
addArms	Add arms to a design.
addDesign	Add a design to the 'PFIMProject' object.
addDesignConstraints	Add design constraints on the sampling for a design.
addDesigns	Add a list of designs to the 'PFIMProject' object.
addModel	Add a 'Model' object in the 'LibraryOfModels'.
addResponse	Add a response to a statistical model.
addResponses	Add responses to a statistical model.
addSampling	Add sampling time for an arm and for a response.
addSamplingConstraint	Add a constraint on the sampling for a design.
addSamplingConstraints	Add sampling constraints to an arm.
addSamplings	Add sampling times for an arm and for a response.
AdjustLogNormalDistribution	Adjust the mean of a 'LogNormalDistribution' object.
AdjustLogNormalDistribution-method	Adjust the mean of a 'LogNormalDistribution' object.
AdjustNormalDistribution	Adjust the Normal Distribution.
AdjustNormalDistribution-method	Adjust the Normal Distribution.
Administration	Class "Administration"
Administration-class	Class "Administration"
AdministrationConstraint	Class "AdministrationConstraint"
AdministrationConstraint-class	Class "AdministrationConstraint"
allowedContinuousSamplingTimes	Set the allowed continuous sampling times.
allowedDiscretSamplingTimes	Set the allowed discret sampling times.
AllowedDoses	Define the vector of allowed amount of dose.
Arm	Class "Arm"
Arm-class	Class "Arm"

-- B --

BayesianFim	Class "BayesianFim" representing the population Fisher information matrix.
BayesianFim-class	Class "BayesianFim" representing the population Fisher information matrix.

-- C --

CalculatedResidualVariance	Compute the residual variance thanks to the function g of the model error.
changeVariablePKModel	Change variable in a PK Model.
checkParameterInEquations	Check the parameters in the model equations.
Combinaison	Create all the possible combinaison for each Design and each Arms.
Combined1	Class "Combined1"
Combined1-class	Class "Combined1"
Combined1c	Class "Combined1c"
Combined1c-class	Class "Combined1c"
Combined2	Class "Combined2"
Combined2-class	Class "Combined2"
Combined2c	Class "Combined2c"
Combined2c-class	Class "Combined2c"
Constant	Class "Constant"
Constant-class	Class "Constant"
Constraint	Class "Constraint"
Constraint-class	Class "Constraint"
ContinuousConstraint	Class "ContinuousConstraint" representing the constraints for a variable
ContinuousConstraint-class	Class "ContinuousConstraint" representing the constraints for a variable
convertAnalyticToODE	Convert an equation of a PD model of a 'ModelEquations' object from analytic to ODE.

-- D --

defineCorrelation	Set the correlation.
defineModelEquations	Define model equations
defineParameter	Define a parameter of a statistical model.
defineParameters	Define the parameters of a statistical model.
defineStatisticalModel	Define the 'StatisticalModel' object of the PFIMProject object.
defineVariable	Define a variable in a statistical model.
defineVariables	Define variables in a statistical model.
Design	Class "Design"
Design-class	Class "Design"
DesignConstraint	Class "DesignConstraint"
DesignConstraint-class	Class "DesignConstraint"
DiscreteConstraint	Class "DiscreteConstraint" representing the constraints for a variable
DiscreteConstraint-class	Class "DiscreteConstraint" representing the constraints for a variable
Distribution	Class "Distribution"
Distribution-class	Class "Distribution"

-- E --

Evaluate	Evaluate an 'StatisticalModel' object.
EvaluateBayesianFIM	Evaluate design for each arm for a Bayesian FIM.
EvaluateDesign	Evaluate the design for each arm.
EvaluateDesignForEachArm	Evaluate Design for each arm.
EvaluateErrorModelDerivatives	Evaluate the Error Model Derivatives.
EvaluateFIMsAndDesigns	Evaluate the FIMs and the Designs.
EvaluateIndividualFIM	Evaluate design for each arm for a Individual FIM.
EvaluateModel	Evaluate an analytic model.
EvaluateModelInfusion	Evaluate an analytic model in infusion.
EvaluateModelODE	Evaluate an ODE model.
EvaluateModelODEInfusion	Evaluate an ODE model in infusion
EvaluateODEErrorModelDerivatives	Evaluate the ODE Error Model Derivatives.
EvaluatePopulationFIM	Evaluate a design for each arm for a Population FIM.
EvaluateStatisticalModel	Evaluate a statistical model for all the administrations and all the sampling times of an arm.
EvaluationModel	Evaluation for the model, analytic, ode, infusion

-- F --

FedorovWynnAlgorithm	Class "FedorovWynnAlgorithm"
FedorovWynnAlgorithm-class	Class "FedorovWynnAlgorithm"
FedorovWynnAlgorithm_Rcpp	Fedorov-Wynn algorithm in Rcpp.
FillLibraryOfModels	Function "FillLibraryOfModels"
Fim	Class "Fim" representing the Fisher information matrix, a parent class used by three classes PopulationFim, IndividualFim and BayesianFim.
Fim-class	Class "Fim" representing the Fisher information matrix, a parent class used by three classes PopulationFim, IndividualFim and BayesianFim.
FinalizeFIMForOneElementaryDesign	FinalizeFIMForOneElementaryDesign
FinalizeFIMForOneElementaryDesign-method	FinalizeFIMForOneElementaryDesign
fisher.simplex	Compute the fisher.simplex
fixedDoses	Set the value for the fixed doses in the administration constraints.
FixTimeValues	Set the value for the fixed times.
fun.amoeba	function fun.amoeba

-- G --

g	Evaluation of the model error.
getAdministration	Get the parameters of the administration for an arm.
getAdministrationByOutcome	Get the parameters of the administration for an arm given the response of the model.
getAdministrationConstraint	Get the constraints on the administration for a 'DesignConstraint' object.
getallowedContinuousSamplingTimes	Get the allowed Continuous SamplingTimes
getallowedDiscretSamplingTimes	Get the allowed discret sampling simes
getAllowedDose	Get the constraints on allowed dose
getAllowedDoses	Get the vector of allowed amount of dose.
getAllowedTime	Get the constraints on allowed times.
getAllowedTinf	Get the constraints on Tinf.
getAmountDose	Get the amount of doses.
getAmountOfArms	Get the amount of arms in a Design.
getArms	Get the arms of a design.
getArmSize	Get the size of an arm.
getCError	Get the 'CError' of a 'ModelError' object.
getCondInit	Get the initial conditions in a arm for an ODE model
getConditionNumberMatrix	Get the Condition Number Matrix of the Fisher Information Matrix for a 'Fim' object..
getContentsLibraryOfModels	Get the content of the 'LibraryOfModels' object.
getCorr	Get the correlation matrix of the Fisher Information Matrix for a 'Fim' object.
getDcriterion	Get the D-criterion for a 'Fim' object.
getDerivate	Get the derivate of an equation of a 'ModelEquations' object.
getDerivate-method	Get the derivate of an equation of a 'ModelEquations' object.
getDerivatesAdjustedByDistribution	Get the derivates adjusted by distribution of a 'ModelParameter' object.
getDerivatives	Get the derivatives of a 'ModelODEquations' object.
getDescription	Get the description of FIM.
getDescription-method	Get the description of FIM.
getDesign	Get the design of 'PFIMProject' object.
getDeterminant	Get the Determinant of a Fisher Information Matrix.
getDiscret	Get the set of possible values for a 'DiscreteConstraint' object.
getDistribution	Get the distribution of a 'ModelParameter' object.
getDoseOptimisability	Get the boolean 'Optimisability' for optimizable dose.
getDVSigma	Get the DV Sigma of a 'ModelError' object.
getEigenValue	Get the eigen values of the Fisher Information Matrix for a 'Fim' object.
getElementaryProtocols	Get the matrix of all the combination of the elementary protocols.
getEquation	Get the equation of a 'ModelError' object by their names.
getEquation-method	Get the equation of a 'ModelError' object by their names.
getEquations	Get the equations of a 'ModelEquations' object.
getEquations-method	Get the equations of a 'ModelEquations' object.
getEquationsModel	Get the equations of a 'Model' object.
getEquationsModelPKPD	Get the equations of the PK and PD models of a 'ModelEquations' object.
getEquationsStatisticalModel	Get the equations of a statistical model.
getErrorModelParameters	Get parameters of the error model of a 'ModelError' object.
getErrorModelStandardErrors	Get the SE and RSE of the parameters.
getEvaluationDesign	Get the evaluated concentration and sensitivity indices of a design.
getEvaluationResponses	Get the evaluated responses of the model.
getFim	Get the Fisher Information Matrix.
getFimOfDesign	Get the Fisher Information Matrix of a design.
getFims	Get the Fisher Information Matrices.
getFisherMatrices	Get the fim matrices from all designs of a PFIMProject object.
getFixedParameters	Get the fixed and non fixed model parameters.
getfixedTimes	Get the fixed times.
getInfusionEquations	Get the Infusion Equations.
getInitialTime	Get the initial time of a 'SamplingTimes' object.
getMfisher	Get the Fisher Information Matrix.
getModel	Get a model of the 'LibraryOfModels' object.
getModelError	Get the model error.
getModelName	Get the name of the 'Model' object.
getModelNameList	Get the list of all the models in the 'LibraryOfModels' object.
getModelParameters	Get the model parameters of a statistical model.
getMu	Get 'mu' for a 'ModelParameter' object.
getNameAdministration	Get the name of the outcome of an object 'Administration'.
getNameArm	Get the name of the arm.
getNameDesign	Get the name of the design.
getNameDesignConstraint	Get the name of the 'DesignConstraint' object.
getNameModelParameter	Get the name of a 'ModelParameter' object.
getNameModelVariable	Get the name of the initial variable for an ODE model.
getNamePFIMProject	Get the name of a PFIMProject project.
getNameResponse	Get the name of the response of the model.
getNameSampleTime	Get the name of the response of the 'SamplingTimes' object.
getNumberOfDoses	Get the vector 'AllowedDoses' of allowed amount of dose.
getNumberOfParameter	Get the number of parameters of a 'ModelError' object.
getNumberOfParameters	Get the number of parameters of a 'ModelEquations' object.
getNumberOfSamplings	Get the number of sampling times in a arm.
getnumberOfSamplingTimes	Get the number of sampling times.
getNumberSamples	Get the number of sampled in a Design.
getNumberTime	Get the number of times in a 'SamplingTimes' object.
getOmega	Get 'Omega' of a 'ModelParameter' object.
getOptimalDesign	Get the optimal design.
getOptimisability	Get the optimisability of a 'SamplingConstraint' object.
getOptimizationResult	Get the results of the optimization process.
getParameters	Get the parameters of a 'ModelEquations' object.
getParametersOdeSolver	Get parameters for the ode solver
getPDModel	Get a PD model from a 'PKPDModel' object.
getPKModel	Get a PK model from a 'PKPDModel' object.
getPKPDModel	Get a PKPD model of the 'LibraryOfModels' object.
getRange	Get the range of a 'ContinuousConstraint' object.
getResponseIndice	Get the index of the response of a 'ModelEquations' object.
getResponseName	Get the name of the response for the administration constraints.
getResponseName-method	Get the name of the response for the administration constraints.
getResponseNameByIndice	Get the response name given the indice of the response.
getResponsesStatisticalModel	Get the responses of a statistical model.
getSampleTime	Get the sample time of the response of the 'SamplingTimes' object.
getSamplingConstraints	Get the constraints on the sampling for a 'DesignConstraint' object.
getSamplingConstraintsInArm	Get the sampling constraints of an arm.
getSamplings	Get the vectors of sampling times for an arm.
getSE	Get the Standard Errors for a 'Fim' object..
getShrinkage	Calculates the shrinkage of individual parameters from a 'BayesianFim' object.
getSig	Get the values for Sigma derivatives 'DVSigma' for the 'ModelError' object.
getSigmaInter	Get the'sigma_inter' of a 'ModelError' object.
getSigmaNames	Get the names for the error sigma inter.
getSigmaNames-method	Get the names for the error sigma inter.
getSigmaSlope	Get the 'sigma_slope' of a 'ModelError' object.
getSigmaValues	Get the values of the variances 'sigma_inter' and 'sigma_slope'.
getSigmaValues-method	Get the values of the variances 'sigma_inter' and 'sigma_slope'.
getStatisticalModel	Get the 'StatisticalModel' object of the PFIMProject object.
getStatisticalModelStandardErrors	Get the SE of 'IndividualFim' object.
getStatisticalModelStandardErrors-method	Get the SE of 'IndividualFim' object.
getTau	Get the frequency 'tau'.
getTimeDose	Get the times vector when doses are given.
getTinf	Get the infusion duration.
getTotalNumberOfIndividuals	get the total number of individuals in a 'DesignConstraint' object.
getTotalSize	Get the total size of a design.
getWeightFrame	Get the frame with weight vector after optimisation.
getWeights	Get the weights for the optimal designs.

-- I --

IndividualFim	Class "individualFim" representing the individual Fisher information matrix
IndividualFim-class	Class "individualFim" representing the individual Fisher information matrix
IndividualFIMEvaluateVariance	Evaluate the individual FIM variance.
is.multidose	Test if an object 'Administration'for a model is multi-doses or not.
isFixed	Boolean to set if a model parameters is fixed or not.
isFixedMu	Boolean to set if 'mu' is fixed or not.
isLessThanDelay	Set the constraint on minimal time delay in sampling times.
isNotFixed	Boolean to set if a model parameters is not fixed or not.
isNotFixedMu	Boolean to set if 'mu' is not fixed or not.
isTimeInBetweenBounds	Set the constraint on the sampling times bounds.

-- K --

knitrAdministrationParameters	Set the table knitrAdministrationParameters.
knitrFIM	Set the table knitrFIM.
knitrInitialDesigns	Set the table knitrInitialDesigns.
knitrModelEquations	Set the table knitrModelEquations.
knitrModelError	Set the table knitrModelError.
knitrModelParameters	Set the table knitrModelParameters.
knitrOptimalDesign	Set the table knitrOptimalDesign.

-- L --

LibraryOfModels	Class for the library of models.
LibraryOfModels-class	Class for the library of models.
LogNormalDistribution	Class "LogNormalDistribution"
LogNormalDistribution-class	Class "LogNormalDistribution"

-- M --

Model	Class "Model" representing a Model
Model-class	Class "Model" representing a Model
ModelEquations	Class "ModelEquations" representing a the equations of a model.
ModelEquations-class	Class "ModelEquations" representing a the equations of a model.
ModelError	Class "ModelError" representing a Model error.
ModelError-class	Class "ModelError" representing a Model error.
ModelInfusionEquations	Class "ModelInfusionEquations" representing a model with infusion equations
ModelInfusionEquations-class	Class "ModelInfusionEquations" representing a model with infusion equations
ModelInfusionODEquations	Class "ModelInfusionODEquations" representing a model with infusion equations in ODE model.
ModelInfusionODEquations-class	Class "ModelInfusionODEquations" representing a model with infusion equations in ODE model.
ModelODEquations	Class "ModelODEquations" representing the equations of an ODE model
ModelODEquations-class	Class "ModelODEquations" representing the equations of an ODE model
ModelParameter	Class "ModelParameter"
ModelParameter-class	Class "ModelParameter"
ModelVariable	Class "ModelVariable"
ModelVariable-class	Class "ModelVariable"
modifyArm	Modify an arm of a design.
modifySamplingTimes	Modify the sampling times of an arm.
MultiplicativeAlgorithm	Class "MultiplicativeAlgorithm"
MultiplicativeAlgorithm-class	Class "MultiplicativeAlgorithm"
MultiplicativeAlgorithmClass	Class "MultiplicativeAlgorithm"
MultiplicativeAlgorithm_Rcpp	Function MultiplicativeAlgorithm_Rcpp

-- N --

NormalDistribution	Class "NormalDistribution"
NormalDistribution-class	Class "NormalDistribution"
numberOfSamplingTimesIsOptimisable	Set the number of sampling times that are optimisable.

-- O --

Optimization	Class "Optimization"
Optimization-class	Class "Optimization"
Optimize	Set the optimization process.
Optimize-method	Set the optimization process.
OptimizeDesign	Optimize the designs for each arms.

-- P --

package-PFIM	Fisher Information matrix for design evaluation/optimization for nonlinear mixed effects models.
parametersForComputingGradient	Parameters used for computing the model gradient by finite-differences.
PDModel	Class "PDModel" representing a PD model.
PDModel-class	Class "PDModel" representing a PD model.
PFIM,	Fisher Information matrix for design evaluation/optimization for nonlinear mixed effects models.
PFIMLibraryOfModels	Function "FillLibraryOfModels"
PFIMProject	Class "PFIMProject"
PFIMProject-class	Class "PFIMProject"
PFIMProjectReportEvaluation	Generate the html report for the evaluation.
PFIMProjectReportOptimization	Generate the html report for the optimization.
PGBOAlgorithm	Class "PGBOAlgorithm"
PGBOAlgorithm-class	Class "PGBOAlgorithm"
PKModel	Class "PKModel" representing a PK model.
PKModel-class	Class "PKModel" representing a PK model.
PKPDModel	Class "PKPDModel" representing a PKPDModel model.
PKPDModel-class	Class "PKPDModel" representing a PKPDModel model.
PKPDModelModel	Class "PKPDModel" representing a PKPDModel model.
plotCriteria	Plot the D criteria over time.
plotFrequenciesOptimisation	Plot the frequencies for the FedorovWynn algorithm.
plotResponse	Plot the concentration over time of a model.
plotRSE	Plot the relative standard errors RSE of the model parameters.
plotSE	Plot the standard errors SE of the model parameters.
plotSensitivity	Plot the sensitivity indices of a model over time.
plotShrinkage	Plot the shrinkage data.
plotWeightOptimisation	Plot the optimal weights for the Multiplicative algorithm.
PopulationFim	Class "PopulationFim"
PopulationFim-class	Class "PopulationFim"
PopulationFIMEvaluateVariance	Evaluate the Variance of a Population FIM
PrepareFIMs	Prepare the FIMs for the optimization.
PrepareFIMs-method	Prepare the FIMs for the optimization.
Proportional	Class "Proportional"
Proportional-class	Class "Proportional"
ProportionalC	Class "ProportionalC"
ProportionalC-class	Class "ProportionalC"
PSOAlgorithm	Class "PSOAlgorithm"
PSOAlgorithm-class	Class "PSOAlgorithm"

-- R --

remplaceDose	Function to remplace a dose.
ReportAndPlots	Class "ReportAndPlots"
ReportAndPlots-class	Class "ReportAndPlots"
reportPFIMProject	Generate a htmal report html.
resizeFisherMatrix	Resize the fisher Matrix from a vector to a matrix.
Response	Class "Response"
Response-class	Class "Response"

-- S --

SamplingConstraint	Class "SamplingConstraint"
SamplingConstraint-class	Class "SamplingConstraint"
SamplingTimes	Class "SamplingTimes"
SamplingTimes-class	Class "SamplingTimes"
scaleResponsesEvaluationODE	function to adjust Responses with variables values.
scaleResponsesEvaluationODEInfusion	function to adjust Responses with variables values.
setAllowedDose	Set the constraints on allowed dose.
setAllowedDose<-	Set the constraints on allowed dose.
setAllowedTime<-	Set the constraints on allowed times.
setAllowedTinf<-	Set the constraints on Tinf.
setAmountDose	Set the amount of dose
setAmountOfArms	Set the amount of arms in a Design.
setAmountOfArmsAim	Set amount of arms in a 'DesignConstraint' object for the case we aim to obtain a fixed amount of arms as result.
setArms	Set the arms of a design.
setArmSize	Set the size of an arm.
setCError<-	Set the CError of a 'ModelError' object.
setConstraint	Set the constraint to the PFIMProject projet.
setDelta	Set the 'delta' parameters for the Multiplicative algorithm.
setDesign	Set the design of 'PFIMProject' object.
setDiscret<-	Set the possible values for a 'DiscreteConstraint' object.
setInitialConditions	Set the initial conditions of an Arm for an ODE model.
setIteration	Set the number of iterations for the multiplicative algorithm.
setMfisher<-	Set a matrix value for the Fisher Information Matrix.
setModelError<-	Set the model error.
setMu	Set the mu vector.
setNameDesign	Set the name of the design.
setNamePFIMProject	Set the name of a PFIMProject projet.
setNumberSamples<-	Set the number of Sample in a Design.
setOmega	Set the Omega matrix.
setOptimalDesign	Set an optimal design.
setOptimalDesign<-	Set an optimal design.
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
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.
setRange<-	Set the range of a 'ContinuousConstraint' object.
setSampleTime	Set the sample time of the response of the 'SamplingTimes' object.
setSamplings<-	Set the sampling times for an arm.
setShowProcess	Show the process for the optimization.
setShowProcess-method	Show the process for the optimization.
setSigmaInter<-	Set the value for 'sigma_inter' of a 'ModelError' object.
setSigmaSlope<-	Set the value for 'sigma_slope' of a 'ModelError' object.
setTau	Set the infusion lag tau.
setTimeDose<-	Set the times vector when doses are given.
setTinf	Set the infusion duration.
setTotalNumberOfIndividuals	Set the total number of individuals in a 'DesignConstraint' object.
setTotalSize<-	Set the total size of a Design.
show-method	Show the Fisher Information Matrix for a 'Fim' object and its information: Determinant, D-criterion, SE, Eigenvalues, Correlation.
showArmData	Show the data of an arm for a design.
showConstraints	Show all the constraints of the 'PFIMProject' object.
showDesigns	Show all the Designs.
showFims	Show the Fisher Information Matrix for all the designs.
showStatisticalModelStandardErrors	Show expected standard error data frame.
showStatisticalModelStandardErrors-method	Show expected standard error data frame.
SimplexAlgorithm	Class "SimplexAlgorithm"
SimplexAlgorithm-class	Class "SimplexAlgorithm"
StandardDistribution	Class "StandardDistribution"
StandardDistribution-class	Class "StandardDistribution"
StatisticalModel	Class "StatisticalModel"
StatisticalModel-class	Class "StatisticalModel"
summary-method	summary
summaryArmData	Gives a summary of all the parameters of an arm for a design.

-- misc --

[-method	Class "Arm"
[-method	Class "ContinuousConstraint" representing the constraints for a variable
[-method	Class "SamplingTimes"
[<--method	Class "Arm"
[<--method	Class "ContinuousConstraint" representing the constraints for a variable
[<--method	Class "SamplingTimes"
_PACKAGE	Fisher Information matrix for design evaluation/optimization for nonlinear mixed effects models.