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. |
| 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" |
| BayesianFim | Class "BayesianFim" representing the population Fisher information matrix. |
| BayesianFim-class | Class "BayesianFim" representing the population Fisher information matrix. |
| 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. |
| 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" |
| 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 "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 | 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. |
| 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. |
| 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. |
| LibraryOfModels | Class for the library of models. |
| LibraryOfModels-class | Class for the library of models. |
| LogNormalDistribution | Class "LogNormalDistribution" |
| LogNormalDistribution-class | Class "LogNormalDistribution" |
| 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 |
| NormalDistribution | Class "NormalDistribution" |
| NormalDistribution-class | Class "NormalDistribution" |
| numberOfSamplingTimesIsOptimisable | Set the number of sampling times that are optimisable. |
| 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. |
| 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" |
| 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" |
| 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. |
| [-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. |