AdjustLogNormalDistribution
                        Adjust the mean of a 'LogNormalDistribution'
                        object.
AdjustNormalDistribution
                        Adjust the Normal Distribution.
Administration-class    Class "Administration"
AdministrationConstraint-class
                        Class "AdministrationConstraint"
AllowedDoses            Define the vector of allowed amount of dose.
Arm-class               Class "Arm"
BayesianFim-class       Class "BayesianFim" representing the population
                        Fisher information matrix.
CalculatedResidualVariance
                        Compute the residual variance thanks to the
                        function g of the model error.
Combinaison             Create all the possible combinaison for each
                        Design and each Arms.
Combined1-class         Class "Combined1"
Combined1c-class        Class "Combined1c"
Combined2-class         Class "Combined2"
Combined2c-class        Class "Combined2c"
Constant-class          Class "Constant"
Constraint-class        Class "Constraint"
ContinuousConstraint-class
                        Class "ContinuousConstraint" representing the
                        constraints for a variable
Design-class            Class "Design"
DesignConstraint-class
                        Class "DesignConstraint"
DiscreteConstraint-class
                        Class "DiscreteConstraint" representing the
                        constraints for a variable
Distribution-class      Class "Distribution"
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
FedorovWynnAlgorithm-class
                        Class "FedorovWynnAlgorithm"
FedorovWynnAlgorithm_Rcpp
                        Fedorov-Wynn algorithm in Rcpp.
FillLibraryOfModels     Function "FillLibraryOfModels"
Fim-class               Class "Fim" representing the Fisher information
                        matrix, a parent class used by three classes
                        PopulationFim, IndividualFim and BayesianFim.
FinalizeFIMForOneElementaryDesign
                        FinalizeFIMForOneElementaryDesign
FixTimeValues           Set the value for the fixed times.
IndividualFIMEvaluateVariance
                        Evaluate the individual FIM variance.
IndividualFim-class     Class "individualFim" representing the
                        individual Fisher information matrix
LibraryOfModels-class   Class for the library of models.
LogNormalDistribution-class
                        Class "LogNormalDistribution"
Model-class             Class "Model" representing a Model
ModelEquations-class    Class "ModelEquations" representing a the
                        equations of a model.
ModelError-class        Class "ModelError" representing a Model error.
ModelInfusionEquations-class
                        Class "ModelInfusionEquations" representing a
                        model with infusion equations
ModelInfusionODEquations-class
                        Class "ModelInfusionODEquations" representing a
                        model with infusion equations in ODE model.
ModelODEquations-class
                        Class "ModelODEquations" representing the
                        equations of an ODE model
ModelParameter-class    Class "ModelParameter"
ModelVariable-class     Class "ModelVariable"
MultiplicativeAlgorithm-class
                        Class "MultiplicativeAlgorithm"
MultiplicativeAlgorithm_Rcpp
                        Function MultiplicativeAlgorithm_Rcpp
NormalDistribution-class
                        Class "NormalDistribution"
Optimization-class      Class "Optimization"
Optimize                Set the optimization process.
OptimizeDesign          Optimize the designs for each arms.
PDModel-class           Class "PDModel" representing a PD model.
PFIM-package            Fisher Information matrix for design
                        evaluation/optimization for nonlinear mixed
                        effects models.
PFIMProject-class       Class "PFIMProject"
PFIMProjectReportEvaluation
                        Generate the html report for the evaluation.
PFIMProjectReportOptimization
                        Generate the html report for the optimization.
PGBOAlgorithm-class     Class "PGBOAlgorithm"
PKModel-class           Class "PKModel" representing a PK model.
PKPDModel-class         Class "PKPDModel" representing a PKPDModel
                        model.
PSOAlgorithm-class      Class "PSOAlgorithm"
PopulationFIMEvaluateVariance
                        Evaluate the Variance of a Population FIM
PopulationFim-class     Class "PopulationFim"
PrepareFIMs             Prepare the FIMs for the optimization.
Proportional-class      Class "Proportional"
ProportionalC-class     Class "ProportionalC"
ReportAndPlots-class    Class "ReportAndPlots"
Response-class          Class "Response"
SamplingConstraint-class
                        Class "SamplingConstraint"
SamplingTimes-class     Class "SamplingTimes"
SimplexAlgorithm-class
                        Class "SimplexAlgorithm"
StandardDistribution-class
                        Class "StandardDistribution"
StatisticalModel-class
                        Class "StatisticalModel"
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.
allowedContinuousSamplingTimes
                        Set the allowed continuous sampling times.
allowedDiscretSamplingTimes
                        Set the allowed discret sampling times.
changeVariablePKModel   Change variable in a PK Model.
checkParameterInEquations
                        Check the parameters in the model equations.
convertAnalyticToODE    Convert an equation of a PD model of a
                        'ModelEquations' object from analytic to ODE.
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.
fisher.simplex          Compute the fisher.simplex
fixedDoses              Set the value for the fixed doses in the
                        administration constraints.
fun.amoeba              function fun.amoeba
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.
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.
getArmSize              Get the size of an arm.
getArms                 Get the arms of a design.
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.
getDVSigma              Get the DV Sigma of a 'ModelError' object.
getDcriterion           Get the D-criterion for a 'Fim' object.
getDerivate             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.
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.
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.
getEquations            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.
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.
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.
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.
getParameters           Get the parameters of a 'ModelEquations'
                        object.
getParametersOdeSolver
                        Get parameters for the ode solver
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.
getResponseNameByIndice
                        Get the response name given the indice of the
                        response.
getResponsesStatisticalModel
                        Get the responses of a statistical model.
getSE                   Get the Standard Errors for a 'Fim' object..
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.
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.
getSigmaSlope           Get the 'sigma_slope' of a 'ModelError' object.
getSigmaValues          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.
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.
getallowedContinuousSamplingTimes
                        Get the allowed Continuous SamplingTimes
getallowedDiscretSamplingTimes
                        Get the allowed discret sampling simes
getfixedTimes           Get the fixed times.
getnumberOfSamplingTimes
                        Get the number of sampling times.
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.
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.
modifyArm               Modify an arm of a design.
modifySamplingTimes     Modify the sampling times of an arm.
numberOfSamplingTimesIsOptimisable
                        Set the number of sampling times that are
                        optimisable.
parametersForComputingGradient
                        Parameters used for computing the model
                        gradient by finite-differences.
plotCriteria            Plot the D criteria over time.
plotFrequenciesOptimisation
                        Plot the frequencies for the FedorovWynn
                        algorithm.
plotRSE                 Plot the relative standard errors RSE of the
                        model parameters.
plotResponse            Plot the concentration over time of a model.
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.
remplaceDose            Function to remplace a dose.
reportPFIMProject       Generate a htmal report html.
resizeFisherMatrix      Resize the fisher Matrix from a vector to a
                        matrix.
scaleResponsesEvaluationODE
                        function to adjust Responses with variables
                        values.
scaleResponsesEvaluationODEInfusion
                        function to adjust Responses with variables
                        values.
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.
setArmSize              Set the size of an arm.
setArms                 Set the arms of a design.
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.
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.
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,Fim-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.
summary,Design-method   summary
summaryArmData          Gives a summary of all the parameters of an arm
                        for a design.
