Administration-class    Class "Administration"
AdministrationConstraints-class
                        Class "AdministrationConstraints"
Arm-class               Class "Arm"
BayesianFim-class       Class "BayesianFim"
Combined1-class         Class "Combined1"
Constant-class          Class "Constant"
Design-class            Class "Design"
Distribution-class      Class "Distribution"
EvaluateArm             EvaluateArm
EvaluateDesign          EvaluateDesign
EvaluateErrorModelDerivatives
                        Evaluate the error model derivatives.
EvaluateFisherMatrix    Evaluate the Fisher matrix ( population,
                        individual and Bayesian )
EvaluateModel           Evaluate a model.
EvaluateVarianceFIM     Evaluate the variance of the Fisher information
                        matrix.
EvaluateVarianceModel   Evaluate the variance of a model.
Evaluation-class        Class "Evaluation"
FedorovWynnAlgorithm-class
                        Class "FedorovWynnAlgorithm"
FedorovWynnAlgorithm_Rcpp
                        Fedorov-Wynn algorithm in Rcpp.
Fim-class               Class "Fim"
IndividualFim-class     Class "Fim"
LibraryOfModels-class   Class "LibraryOfModels"
LibraryOfPDModels       Library of the PK models
LibraryOfPKModels       Library of the PK models
LibraryOfPKPDModels-class
                        Class "LibraryOfPKPDModels"
LogNormal-class         Class "LogNormal"
Model-class             Class "Model"
ModelAnalytic-class     Class "ModelAnalytic"
ModelAnalyticBolus-class
                        Class "ModelAnalyticBolus"
ModelAnalyticBolusSteadyState-class
                        Class "ModelAnalyticBolusSteadyState"
ModelAnalyticInfusion-class
                        Class "ModelAnalyticInfusion"
ModelAnalyticInfusionSteadyState-class
                        Class "ModelAnalyticInfusionSteadyState"
ModelAnalyticSteadyState-class
                        Class "ModelAnalyticSteadyState"
ModelBolus-class        Class "ModelBolus"
ModelError-class        Class "ModelError" representing a Model error.
ModelInfusion-class     Class "ModelInfusion"
ModelODE-class          Class "ModelODE"
ModelODEBolus-class     Class "ModelODEBolus"
ModelODEDoseInEquations-class
                        Class "ModelODEDoseInEquations"
ModelODEDoseNotInEquations-class
                        Class "ModelODEDoseNotInEquations"
ModelODEInfusion-class
                        Class "ModelODEInfusion"
ModelODEInfusionDoseInEquations-class
                        Class "ModelODEInfusionDoseInEquations"
ModelParameter-class    Class "ModelParameter"
MultiplicativeAlgorithm-class
                        Class "MultiplicativeAlgorithm"
MultiplicativeAlgorithm_Rcpp
                        Function MultiplicativeAlgorithm_Rcpp
Normal-class            Class "Normal"
Optimization-class      Class "Optimization"
OptimizationAlgorithm-class
                        Class "OptimizationAlgorithm"
PFIM-package            Fisher Information matrix for design
                        evaluation/optimization for nonlinear mixed
                        effects models.
PFIMProject-class       Class "PFIMProject"
PGBOAlgorithm-class     Class "PGBOAlgorithm"
PSOAlgorithm-class      Class "PSOAlgorithm"
PlotEvaluation-class    Class "PlotEvaluation"
PopulationFim-class     Class "PopulationFim"
Proportional-class      Class "Proportional"
Report                  Report
SamplingTimeConstraints-class
                        Class "SamplingTimeConstraints"
SamplingTimes-class     Class "SamplingTimes"
SimplexAlgorithm-class
                        Class "SimplexAlgorithm"
addModel                Add a model to a library of models.
addModels               Add a models to a library of models.
checkSamplingTimeConstraintsForContinuousOptimization
                        Check for the samplingTime constraints for
                        continuous optimization
checkValiditySamplingConstraint
                        checkValiditySamplingConstraint
convertPKModelAnalyticToPKModelODE
                        Convert an analytic model to a ode model.
defineModel             Define a model.
defineModelFromLibraryOfModels
                        Define a model from the library of models.
defineModelType         Define the type of a model.
defineModelUserDefined
                        Define a user defined model.
definePKModel           Define a PK model.
definePKPDModel         Define a PKPD model.
fisher.simplex          Compute the fisher.simplex
fun.amoeba              function fun.amoeba
generateFimsFromConstraints
                        Generate the fim from the constraints
generateReportEvaluation
                        Generate the report for the evaluation
generateReportOptimization
                        Generate report for the optimization.
generateSamplingsFromSamplingConstraints
                        Generate samplings from sampling constraints
generateTables          Generate the tables for the report.
getAdjustedGradient     getAdjustedGradient
getAdministration       getAdministration
getAdministrationConstraint
                        getAdministrationConstraint
getAdministrations      getAdministrations
getAdministrationsConstraints
                        getAdministrationsConstraints
getArms                 Get the arms of an object.
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.
getConditionNumberFixedEffects
                        Get the condition number of the matrix of the
                        fixed effects.
getConditionNumberVarianceEffects
                        Get the condition number of the matrix of the
                        variance effects.
getContent              Get content of a library of models.
getCorrelationMatrix    Get the correlation matrix.
getDataFrameResults     Get the dataframe of the results.
getDcriterion           Get the D criterion of the fim.
getDelta                Get the parameter delta
getDerivatives          Get the derivatives of the model error
                        equation.
getDescription          Get the description of a model.
getDesigns              Get the designs.
getDeterminant          Get the determinant of the fim.
getDistribution         Get the distribution.
getDose                 getDose
getEigenValues          Get the eigenvalues of the fim.
getElementaryProtocols
                        Get the elementary protocols.
getEquation             Get the equation of a model error.
getEquations            Get the equations of a model.
getEquationsAfterInfusion
                        Get the equations after infusion.
getEquationsDuringInfusion
                        Get the equations during infusion.
getEvaluationFIMResults
                        Get the results of the evaluation.
getEvaluationInitialDesignResults
                        Get the evaluation results of the initial
                        design.
getFim                  getFim
getFisherMatrix         Get the FIM.
getFixedEffects         Get the matrix of fixed effects.
getFixedMu              Get the fixed effect.
getFixedOmega           Get the fixed variance.
getFixedParameters      Get the fixed parameters.
getFixedTimes           Get the fixed sampling times.
getInitialConditions    getInitialConditions
getIterationAndCriteria
                        Get the iteration with the convergence
                        criteria.
getLambda               Get the parameter lambda.
getLibraryPDModels      Get the library of PD models.
getLibraryPKModels      Get the library of PK models.
getMinSampling          Get the minimal sampling times.
getModel                Get the model.
getModelEquations       Get the model equations.
getModelError           Get the model error.
getModelErrorParametersValues
                        Get the values of the model error parameters.
getModelFromLibrary     Get a model from the library of models.
getModelParameters      Get the model parameters.
getModelParametersValues
                        Get the values of the model parameters.
getMu                   getMu
getName                 getName
getNames                getNames
getNumberOfArms         getNumberOfArms
getNumberOfIterations   Get the number of iterations.
getNumberOfParameters   Get the number of parameters.
getNumberOfTimesByWindows
                        Get the number of sampling times by windows.
getNumberOfsamplingsOptimisable
                        Get the number of sampling times that are
                        optimisable.
getOdeSolverParameters
                        getOdeSolverParameters
getOmega                Get the matrix omega of an object.
getOptimalDesign        Get the optimal design.
getOptimalFrequencies   Get the optimal frequencies
getOptimalWeights       Get the optimal weights.
getOptimizationResults
                        Get the optimization results.
getOptimizer            Get the optimization algorithm.
getOptimizerParameters
                        Get the optimization parameters.
getOutcome              getOutcome
getOutcomes             Get the outcomes of a model.
getOutcomesEvaluation   getOutcomesEvaluation
getOutcomesForEvaluation
                        Get the outcomes of a model used for the
                        evaluation (is scales outcomes).
getOutcomesGradient     getOutcomesGradient
getPDModel              Get a PD model.
getPKModel              Get a PK model.
getPKPDModel            Get a PKPD model.
getParameters           Get the parameters of an object.
getPlotOptions          Get the plot options for graphs responses and
                        SI
getProportionsOfSubjects
                        Get the proportion of subjects.
getRSE                  Get the RSE
getSE                   Get the SE.
getSamplingTime         getSamplingTime
getSamplingTimeConstraint
                        getSamplingTimeConstraint
getSamplingTimes        getSamplingTimes
getSamplingTimesConstraints
                        getSamplingTimesConstraints
getSamplings            Get the sampling of an object.
getSamplingsWindows     Get the windows for the sampling times.
getShrinkage            Get the shrinkage.
getSigmaInter           Get the parameter sigma inter.
getSigmaSlope           Get the parameter sigma slope.
getSize                 getSize
getTau                  getTau
getTimeDose             getTimeDose
getTinf                 Get the infusion duration.
getVarianceEffects      Get the matrix of the variance effects.
getcError               Get the parameter c.
isDoseInEquations       Test if the dose is in the equations of the
                        model.
isModelAnalytic         Test if a mode is analytic.
isModelBolus            Test if a mode is bolus.
isModelInfusion         Test if a mode is infusion
isModelODE              Test if a mode is ode.
isModelSteadyState      Test if a mode is steady state.
optimize                Optimize a design.
parametersForComputingGradient
                        Define the parameters for computing the
                        gradients of a model.
plotEvaluation          Graphs of the results of the evaluation.
plotFrequencies         Graph of the frequencies for the FW algorithm.
plotOutcomesEvaluation
                        plotOutcomesEvaluation
plotOutcomesGradient    plotOutcomesGradient
plotRSE                 Graph of the RSE.
plotSE                  Graph the SE.
plotSensitivityIndice   Graphs of the results of the evaluation.
plotShrinkage           Graph of the shrinkage.
plotWeights             Graph of the weights for the multiplicative
                        algorithm.
reportTablesAdministration
                        reportTablesAdministration
reportTablesDesign      reportTablesDesign
reportTablesFIM         Generate the tables for the report.
reportTablesModelError
                        Generate the tables for model errors for the
                        evaluation report.
reportTablesModelParameters
                        Generate the tables for model parameters for
                        the evaluation report.
reportTablesPlot        reportTablesPlot
reportTablesSamplingConstraints
                        reportTablesSamplingConstraints
resizeFisherMatrix      Resize the fisher Matrix from a vector to a
                        matrix.
run                     run
setAdministrations      setAdministrations
setArm                  setArm
setArms                 Set the arms of an object.
setContent              Set content of a library of models.
setDerivatives          Set the derivatives of the model error
                        equation.
setDescription          Set the description of a model.
setDesigns              Set the designs.
setDistribution         Set the distribution.
setDose                 Set the amount of dose
setEquation             Set the equation of a model error.
setEquations            Set the equations of a model.
setEquationsAfterInfusion
                        Set the equations after infusion.
setEquationsDuringInfusion
                        Set the equations during infusion.
setEvaluationFIMResults
                        Set the evaluation results.
setEvaluationInitialDesignResults
                        Set the evaluation results of the initial
                        design.
setFim                  setFim
setFimTypeToString      Convert the type of the object fim to a string.
setFisherMatrix         Set the FIM.
setFixedEffects         Set the fixed effects.
setFixedMu              Set the mu as fixed or not.
setFixedOmega           Set the omega as fixed of not.
setInitialConditions    setInitialConditions
setIterationAndCriteria
                        Set the iteration with the convergence
                        criteria.
setModel                Set the model.
setModelError           Set the model error.
setModelFromLibrary     Set a model from the library of model
setMu                   Set the value of the fixed effect mu of an
                        object.
setName                 Set the name of an object.
setNumberOfArms         setNumberOfArms
setOdeSolverParameters
                        Set the parameters of the ode solver.
setOmega                Set the matrix omega of an object.
setOptimalDesign        Set the optimal design.
setOptimalWeights       Set the optimal weights.
setOptimizationResults
                        Set the optimization results.
setOutcome              setOutcome
setOutcomes             Set the outcomes of a model.
setOutcomesEvaluation   setOutcomesEvaluation
setOutcomesForEvaluation
                        Set the outcomes of a model used for the
                        evaluation (is scales outcomes).
setOutcomesGradient     setOutcomesGradient
setParameters           Set the parameters of an object.
setSamplingConstraintForOptimization
                        setSamplingConstraintForOptimization
setSamplingTime         setSamplingTime
setSamplingTimes        setSamplingTimes
setSamplingTimesConstraints
                        setSamplingTimesConstraints
setSamplings            Set the sampling times.
setShrinkage            Set the shrinkage.
setSigmaInter           Set the parameter sigma inter.
setSigmaSlope           Set the parameter sigma slope.
setSize                 setSize
setTau                  setTau
setTimeDose             setTimeDose
setTinf                 Set the infusion duration.
setVarianceEffects      Set the matrix of the variance effects.
setcError               Set the parameter c.
show,Design-method      show
