Administration          Administration Class
AdministrationConstraints
                        AdministrationConstraints Class
Arm                     Arm Class
BayesianFim             BayesianFim Class
Combined                Combined1 Class
Constant                Constant Class
Dcriterion              Dcriterion
Design                  Design Class
Distribution            Distribution Class
Evaluation              Evaluation Class
FedorovWynnAlgorithm    FedorovWynnAlgorithm Class
FedorovWynnAlgorithm_Rcpp
                        FedorovWynnAlgorithm with Rcpp
Fim                     Fisher Information Matrix (FIM) Class
IndividualFim           Individual Fisher Information Matrix
                        (IndividualFim) Class
LibraryOfModels         LibraryOfModels Class
LibraryOfPDModels       LibraryOfPDModels Class
LibraryOfPKModels       LibraryOfPKModels Class
Linear2BolusSingleDose_ClQV1V2
                        Model Linear2BolusSingleDose_ClQV1V2
Linear2BolusSingleDose_kk12k21V
                        Model Linear2BolusSingleDose_kk12k21V
Linear2BolusSteadyState_ClQV1V2tau
                        Model Linear2BolusSteadyState_ClQV1V2tau
Linear2BolusSteadyState_kk12k21Vtau
                        Model Linear2BolusSteadyState_kk12k21Vtau
Linear2FirstOrderSingleDose_kaClQV1V2
                        Model Linear2FirstOrderSingleDose_kaClQV1V2
Linear2FirstOrderSingleDose_kakk12k21V
                        Model Linear2FirstOrderSingleDose_kakk12k21V
Linear2FirstOrderSteadyState_kaClQV1V2tau
                        Model Linear2FirstOrderSteadyState_kaClQV1V2tau
Linear2FirstOrderSteadyState_kakk12k21Vtau
                        Model
                        Linear2FirstOrderSteadyState_kakk12k21Vtau
Linear2InfusionSingleDose_ClQV1V2
                        Model Linear2InfusionSingleDose_ClQV1V2
Linear2InfusionSingleDose_kk12k21V
                        Model Linear2InfusionSingleDose_kk12k21V
Linear2InfusionSteadyState_ClQV1V2tau
                        Model Linear2InfusionSteadyState_ClQV1V2tau
Linear2InfusionSteadyState_kk12k21Vtau
                        Model Linear2InfusionSteadyState_kk12k21Vtau
LogNormal               LogNormal Class
Model                   Model Class
ModelAnalytic           ModelAnalytic Class
ModelAnalyticInfusion   ModelAnalyticInfusion Class
ModelAnalyticInfusionSteadyState
                        ModelAnalyticInfusionSteadyState Class
ModelAnalyticSteadyState
                        ModelAnalyticSteadyState Class
ModelError              ModelError Class
ModelInfusion           ModelInfusion Class
ModelODE                ModelODE Class
ModelODEBolus           ModelODEBolus Class
ModelODEDoseInEquations
                        ModelODEDoseInEquations Class
ModelODEDoseNotInEquations
                        ModelODEDoseNotInEquations Class
ModelODEInfusion        ModelODEInfusion Class
ModelODEInfusionDoseInEquation
                        ModelODEInfusionDoseInEquation Class
ModelParameter          ModelParameter Class
MultiplicativeAlgorithm
                        MultiplicativeAlgorithm Class
MultiplicativeAlgorithm_Rcpp
                        Rcpp Multiplicative Algorithm for Optimal
                        Design
Normal                  Normal Class
Optimization            Optimization Class
PFIM-package            Fisher Information matrix for design
                        evaluation/optimization for nonlinear mixed
                        effects models.
PFIMProject             PFIMProject Class
PGBOAlgorithm           PGBOAlgorithm Class
PSOAlgorithm            PSOAlgorithm Class
PopulationFim           PopulationFim Class
Proportional            Proportional Class
Report                  Report
SamplingTimeConstraints
                        SamplingTimeConstraints Class
SamplingTimes           SamplingTimes Class
SimplexAlgorithm        SimplexAlgorithm Class
adjustGradient          Adjust the gradient for the log normal
                        distribution.
armAdministration       Get administration parameters of an arm
checkSamplingTimeConstraintsForMetaheuristic
                        Validate New Sampling Schedules Against
                        Constraints
checkValiditySamplingConstraint
                        Validate optimization constraints
computeVMat             Compute Variance Matrix Component
constraintsTableForReport
                        Generate Algorithm Constraints Table for
                        Reporting
convertPKModelAnalyticToPKModelODE
                        Conversion from analytic PK model to ODE PK
                        model
defineFim               Define the Fisher Information Matrix object
defineModelAdministration
                        Define the administration for an analytic model
defineModelEquationsFromLibraryOfModel
                        defineModelEquationsFromLibraryOfModel
defineModelType         defineModelType
defineModelWrapper      define the model wrapper for the ode solver
defineOptimizationAlgorithm
                        Define Optimization Algorithm
definePKModel           Define a PK model from library of model
definePKPDModel         Define a PKPD model from library of model
evaluateArm             Evaluate an arm
evaluateDesign          Evaluation of a clinical design
evaluateErrorModelDerivatives
                        evaluate the derivatives of the model error.
evaluateFim             Evaluate the Fim.
evaluateInitialConditions
                        evaluate the initial conditions.
evaluateModel           Evaluate the analytic model
evaluateModelGradient   evaluate the gradient of the model
evaluateModelVariance   Evaluate Model Variance and Sigma Derivatives
evaluateVarianceFIM     Evaluate the Variance Component of the Fisher
                        Information Matrix
finiteDifferenceHessian
                        Compute the Hessian
fisherSimplex           Compute the fisher.simplex
fun.amoeba              Compute the Amoeba (Nelder-Mead) Simplex Search
generateDosesCombination
                        Generate dose combinations for optimization
generateFimsFromConstraints
                        Generate Fisher Information Matrices (FIM) from
                        Design Constraints
generateReportEvaluation
                        Generate a Comprehensive HTML Evaluation Report
generateReportOptimization
                        Generate the HTML Report for Design
                        Optimization
generateSamplingTimesCombination
                        Generate sampling time combinations
generateSamplingsFromSamplingConstraints
                        Generate Numerical Intervals from Sampling
                        Constraints
getArmConstraints       Get arm constraints for optimization algorithms
getArmData              Extract arm data for reporting
getCorrelationMatrix    getCorrelationMatrix
getDcriterion           getDcriterion: Extract the D-optimality
                        criterion
getDeterminant          getDeterminant
getFisherMatrix         getFisherMatrix
getListLastName         getListLastName: Get names of the deepest
                        elements in a nested list
getModelErrorData       get the parameters sigma slope and sigma inter
                        (used for the report).
getModelParametersData
                        Extract Model Parameter Data for Reporting
getRSE                  getRSE
getSE                   getSE
getSamplingData         Extract sampling times and maximum sampling
                        time
getShrinkage            getShrinkage
optimizeDesign          Optimize Study Design
plot                    plot
plotEvaluation          plotEvaluation
plotEvaluationResults   Plot model responses for an arm
plotEvaluationSI        Plot sensitivity indices for an arm
plotFrequencies         plotFrequencies: visualize optimal frequencies
                        for the Fedorov-Wynn algorithm
plotFrequenciesFedorovWynnAlgorithm
                        plotFrequenciesFedorovWynnAlgorithm for the
                        FedorovWynnAlgorithm
plotRSE                 plotRSE
plotRSEFIM              Plot Relative Standard Errors (RSE%) for
                        Population FIM
plotSE                  plotSE
plotSEFIM               Plot Standard Errors from the Population FIM
plotSensitivityIndices
                        plotSensitivityIndices
plotShrinkage           Bar plot of the Bayesian shrinkage
plotWeights             Visualize the distribution of optimal design
                        weights
plotWeightsMultiplicativeAlgorithm
                        Visualize Optimal Weight Distribution from
                        Multiplicative Algorithm
processArmEvaluationResults
                        Process arm evaluation for response plots
processArmEvaluationSI
                        Process arm evaluation for sensitivity index
                        plots
replaceVariablesLibraryOfModels
                        : replace variable in the LibraryOfModels
run                     run
setEvaluationFim        Finalize and Set Population FIM Results
setOptimalArms          Set Optimal Arms for the
                        MultiplicativeAlgorithm and
                        FedorovWynnAlgorithm
setSamplingConstraintForOptimization
                        Initialize sampling constraints
show                    show
showFIM                 Display FIM Results in the R Console
tablesForReport         Generate Statistical Tables for Evaluation
                        Reports
updateSamplingTimes     Update sampling times for plotting
