Man pages for PFIM
Population Fisher Information Matrix

addAdministrationAdd an administration to an arm.
addAdministrationConstraintAdd constraints on the administration for a...
addArmAdd an arm to a design.
addArmsAdd arms to a design.
addDesignAdd a design to the 'PFIMProject' object.
addDesignConstraintsAdd design constraints on the sampling for a design.
addDesignsAdd a list of designs to the 'PFIMProject' object.
addModelAdd a 'Model' object in the 'LibraryOfModels'.
addResponseAdd a response to a statistical model.
addResponsesAdd responses to a statistical model.
addSamplingAdd sampling time for an arm and for a response.
addSamplingConstraintAdd a constraint on the sampling for a design.
addSamplingConstraintsAdd sampling constraints to an arm.
addSamplingsAdd sampling times for an arm and for a response.
AdjustLogNormalDistributionAdjust the mean of a 'LogNormalDistribution' object.
AdjustNormalDistributionAdjust the Normal Distribution.
Administration-classClass "Administration"
AdministrationConstraint-classClass "AdministrationConstraint"
allowedContinuousSamplingTimesSet the allowed continuous sampling times.
allowedDiscretSamplingTimesSet the allowed discret sampling times.
AllowedDosesDefine the vector of allowed amount of dose.
Arm-classClass "Arm"
BayesianFim-classClass "BayesianFim" representing the population Fisher...
CalculatedResidualVarianceCompute the residual variance thanks to the function g of the...
changeVariablePKModelChange variable in a PK Model.
checkParameterInEquationsCheck the parameters in the model equations.
CombinaisonCreate all the possible combinaison for each Design and each...
Combined1c-classClass "Combined1c"
Combined1-classClass "Combined1"
Combined2c-classClass "Combined2c"
Combined2-classClass "Combined2"
Constant-classClass "Constant"
Constraint-classClass "Constraint"
ContinuousConstraint-classClass "ContinuousConstraint" representing the constraints for...
convertAnalyticToODEConvert an equation of a PD model of a 'ModelEquations'...
defineCorrelationSet the correlation.
defineModelEquationsDefine model equations
defineParameterDefine a parameter of a statistical model.
defineParametersDefine the parameters of a statistical model.
defineStatisticalModelDefine the 'StatisticalModel' object of the PFIMProject...
defineVariableDefine a variable in a statistical model.
defineVariablesDefine variables in a statistical model.
Design-classClass "Design"
DesignConstraint-classClass "DesignConstraint"
DiscreteConstraint-classClass "DiscreteConstraint" representing the constraints for a...
Distribution-classClass "Distribution"
EvaluateEvaluate an 'StatisticalModel' object.
EvaluateBayesianFIMEvaluate design for each arm for a Bayesian FIM.
EvaluateDesignEvaluate the design for each arm.
EvaluateDesignForEachArmEvaluate Design for each arm.
EvaluateErrorModelDerivativesEvaluate the Error Model Derivatives.
EvaluateFIMsAndDesignsEvaluate the FIMs and the Designs.
EvaluateIndividualFIMEvaluate design for each arm for a Individual FIM.
EvaluateModelEvaluate an analytic model.
EvaluateModelInfusionEvaluate an analytic model in infusion.
EvaluateModelODEEvaluate an ODE model.
EvaluateModelODEInfusionEvaluate an ODE model in infusion
EvaluateODEErrorModelDerivativesEvaluate the ODE Error Model Derivatives.
EvaluatePopulationFIMEvaluate a design for each arm for a Population FIM.
EvaluateStatisticalModelEvaluate a statistical model for all the administrations and...
EvaluationModelEvaluation for the model, analytic, ode, infusion
FedorovWynnAlgorithm-classClass "FedorovWynnAlgorithm"
FedorovWynnAlgorithm_RcppFedorov-Wynn algorithm in Rcpp.
FillLibraryOfModelsFunction "FillLibraryOfModels"
Fim-classClass "Fim" representing the Fisher information matrix, a...
FinalizeFIMForOneElementaryDesignFinalizeFIMForOneElementaryDesign
fisher.simplexCompute the fisher.simplex
fixedDosesSet the value for the fixed doses in the administration...
FixTimeValuesSet the value for the fixed times.
fun.amoebafunction fun.amoeba
gEvaluation of the model error.
getAdministrationGet the parameters of the administration for an arm.
getAdministrationByOutcomeGet the parameters of the administration for an arm given the...
getAdministrationConstraintGet the constraints on the administration for a...
getallowedContinuousSamplingTimesGet the allowed Continuous SamplingTimes
getallowedDiscretSamplingTimesGet the allowed discret sampling simes
getAllowedDoseGet the constraints on allowed dose
getAllowedDosesGet the vector of allowed amount of dose.
getAllowedTimeGet the constraints on allowed times.
getAllowedTinfGet the constraints on Tinf.
getAmountDoseGet the amount of doses.
getAmountOfArmsGet the amount of arms in a Design.
getArmsGet the arms of a design.
getArmSizeGet the size of an arm.
getCErrorGet the 'CError' of a 'ModelError' object.
getCondInitGet the initial conditions in a arm for an ODE model
getConditionNumberMatrixGet the Condition Number Matrix of the Fisher Information...
getContentsLibraryOfModelsGet the content of the 'LibraryOfModels' object.
getCorrGet the correlation matrix of the Fisher Information Matrix...
getDcriterionGet the D-criterion for a 'Fim' object.
getDerivateGet the derivate of an equation of a 'ModelEquations' object.
getDerivatesAdjustedByDistributionGet the derivates adjusted by distribution of a...
getDerivativesGet the derivatives of a 'ModelODEquations' object.
getDescriptionGet the description of FIM.
getDesignGet the design of 'PFIMProject' object.
getDeterminantGet the Determinant of a Fisher Information Matrix.
getDiscretGet the set of possible values for a 'DiscreteConstraint'...
getDistributionGet the distribution of a 'ModelParameter' object.
getDoseOptimisabilityGet the boolean 'Optimisability' for optimizable dose.
getDVSigmaGet the DV Sigma of a 'ModelError' object.
getEigenValueGet the eigen values of the Fisher Information Matrix for a...
getElementaryProtocolsGet the matrix of all the combination of the elementary...
getEquationGet the equation of a 'ModelError' object by their names.
getEquationsGet the equations of a 'ModelEquations' object.
getEquationsModelGet the equations of a 'Model' object.
getEquationsModelPKPDGet the equations of the PK and PD models of a...
getEquationsStatisticalModelGet the equations of a statistical model.
getErrorModelParametersGet parameters of the error model of a 'ModelError' object.
getErrorModelStandardErrorsGet the SE and RSE of the parameters.
getEvaluationDesignGet the evaluated concentration and sensitivity indices of a...
getEvaluationResponsesGet the evaluated responses of the model.
getFimGet the Fisher Information Matrix.
getFimOfDesignGet the Fisher Information Matrix of a design.
getFimsGet the Fisher Information Matrices.
getFisherMatricesGet the fim matrices from all designs of a PFIMProject...
getFixedParametersGet the fixed and non fixed model parameters.
getfixedTimesGet the fixed times.
getInfusionEquationsGet the Infusion Equations.
getInitialTimeGet the initial time of a 'SamplingTimes' object.
getMfisherGet the Fisher Information Matrix.
getModelGet a model of the 'LibraryOfModels' object.
getModelErrorGet the model error.
getModelNameGet the name of the 'Model' object.
getModelNameListGet the list of all the models in the 'LibraryOfModels'...
getModelParametersGet the model parameters of a statistical model.
getMuGet 'mu' for a 'ModelParameter' object.
getNameAdministrationGet the name of the outcome of an object 'Administration'.
getNameArmGet the name of the arm.
getNameDesignGet the name of the design.
getNameDesignConstraintGet the name of the 'DesignConstraint' object.
getNameModelParameterGet the name of a 'ModelParameter' object.
getNameModelVariableGet the name of the initial variable for an ODE model.
getNamePFIMProjectGet the name of a PFIMProject project.
getNameResponseGet the name of the response of the model.
getNameSampleTimeGet the name of the response of the 'SamplingTimes' object.
getNumberOfDosesGet the vector 'AllowedDoses' of allowed amount of dose.
getNumberOfParameterGet the number of parameters of a 'ModelError' object.
getNumberOfParametersGet the number of parameters of a 'ModelEquations' object.
getNumberOfSamplingsGet the number of sampling times in a arm.
getnumberOfSamplingTimesGet the number of sampling times.
getNumberSamplesGet the number of sampled in a Design.
getNumberTimeGet the number of times in a 'SamplingTimes' object.
getOmegaGet 'Omega' of a 'ModelParameter' object.
getOptimalDesignGet the optimal design.
getOptimisabilityGet the optimisability of a 'SamplingConstraint' object.
getOptimizationResultGet the results of the optimization process.
getParametersGet the parameters of a 'ModelEquations' object.
getParametersOdeSolverGet parameters for the ode solver
getPDModelGet a PD model from a 'PKPDModel' object.
getPKModelGet a PK model from a 'PKPDModel' object.
getPKPDModelGet a PKPD model of the 'LibraryOfModels' object.
getRangeGet the range of a 'ContinuousConstraint' object.
getResponseIndiceGet the index of the response of a 'ModelEquations' object.
getResponseNameGet the name of the response for the administration...
getResponseNameByIndiceGet the response name given the indice of the response.
getResponsesStatisticalModelGet the responses of a statistical model.
getSampleTimeGet the sample time of the response of the 'SamplingTimes'...
getSamplingConstraintsGet the constraints on the sampling for a 'DesignConstraint'...
getSamplingConstraintsInArmGet the sampling constraints of an arm.
getSamplingsGet the vectors of sampling times for an arm.
getSEGet the Standard Errors for a 'Fim' object..
getShrinkageCalculates the shrinkage of individual parameters from a...
getSigGet the values for Sigma derivatives 'DVSigma' for the...
getSigmaInterGet the'sigma_inter' of a 'ModelError' object.
getSigmaNamesGet the names for the error sigma inter.
getSigmaSlopeGet the 'sigma_slope' of a 'ModelError' object.
getSigmaValuesGet the values of the variances 'sigma_inter' and...
getStatisticalModelGet the 'StatisticalModel' object of the PFIMProject object.
getStatisticalModelStandardErrorsGet the SE of 'IndividualFim' object.
getTauGet the frequency 'tau'.
getTimeDoseGet the times vector when doses are given.
getTinfGet the infusion duration.
getTotalNumberOfIndividualsget the total number of individuals in a 'DesignConstraint'...
getTotalSizeGet the total size of a design.
getWeightFrameGet the frame with weight vector after optimisation.
getWeightsGet the weights for the optimal designs.
IndividualFim-classClass "individualFim" representing the individual Fisher...
IndividualFIMEvaluateVarianceEvaluate the individual FIM variance.
isFixedBoolean to set if a model parameters is fixed or not.
isFixedMuBoolean to set if 'mu' is fixed or not.
isLessThanDelaySet the constraint on minimal time delay in sampling times.
is.multidoseTest if an object 'Administration'for a model is multi-doses...
isNotFixedBoolean to set if a model parameters is not fixed or not.
isNotFixedMuBoolean to set if 'mu' is not fixed or not.
isTimeInBetweenBoundsSet the constraint on the sampling times bounds.
knitrAdministrationParametersSet the table knitrAdministrationParameters.
knitrFIMSet the table knitrFIM.
knitrInitialDesignsSet the table knitrInitialDesigns.
knitrModelEquationsSet the table knitrModelEquations.
knitrModelErrorSet the table knitrModelError.
knitrModelParametersSet the table knitrModelParameters.
knitrOptimalDesignSet the table knitrOptimalDesign.
LibraryOfModels-classClass for the library of models.
LogNormalDistribution-classClass "LogNormalDistribution"
Model-classClass "Model" representing a Model
ModelEquations-classClass "ModelEquations" representing a the equations of a...
ModelError-classClass "ModelError" representing a Model error.
ModelInfusionEquations-classClass "ModelInfusionEquations" representing a model with...
ModelInfusionODEquations-classClass "ModelInfusionODEquations" representing a model with...
ModelODEquations-classClass "ModelODEquations" representing the equations of an ODE...
ModelParameter-classClass "ModelParameter"
ModelVariable-classClass "ModelVariable"
modifyArmModify an arm of a design.
modifySamplingTimesModify the sampling times of an arm.
MultiplicativeAlgorithm-classClass "MultiplicativeAlgorithm"
MultiplicativeAlgorithm_RcppFunction MultiplicativeAlgorithm_Rcpp
NormalDistribution-classClass "NormalDistribution"
numberOfSamplingTimesIsOptimisableSet the number of sampling times that are optimisable.
Optimization-classClass "Optimization"
OptimizeSet the optimization process.
OptimizeDesignOptimize the designs for each arms.
parametersForComputingGradientParameters used for computing the model gradient by...
PDModel-classClass "PDModel" representing a PD model.
PFIM-packageFisher Information matrix for design evaluation/optimization...
PFIMProject-classClass "PFIMProject"
PFIMProjectReportEvaluationGenerate the html report for the evaluation.
PFIMProjectReportOptimizationGenerate the html report for the optimization.
PGBOAlgorithm-classClass "PGBOAlgorithm"
PKModel-classClass "PKModel" representing a PK model.
PKPDModel-classClass "PKPDModel" representing a PKPDModel model.
plotCriteriaPlot the D criteria over time.
plotFrequenciesOptimisationPlot the frequencies for the FedorovWynn algorithm.
plotResponsePlot the concentration over time of a model.
plotRSEPlot the relative standard errors RSE of the model...
plotSEPlot the standard errors SE of the model parameters.
plotSensitivityPlot the sensitivity indices of a model over time.
plotShrinkagePlot the shrinkage data.
plotWeightOptimisationPlot the optimal weights for the Multiplicative algorithm.
PopulationFim-classClass "PopulationFim"
PopulationFIMEvaluateVarianceEvaluate the Variance of a Population FIM
PrepareFIMsPrepare the FIMs for the optimization.
ProportionalC-classClass "ProportionalC"
Proportional-classClass "Proportional"
PSOAlgorithm-classClass "PSOAlgorithm"
remplaceDoseFunction to remplace a dose.
ReportAndPlots-classClass "ReportAndPlots"
reportPFIMProjectGenerate a htmal report html.
resizeFisherMatrixResize the fisher Matrix from a vector to a matrix.
Response-classClass "Response"
SamplingConstraint-classClass "SamplingConstraint"
SamplingTimes-classClass "SamplingTimes"
scaleResponsesEvaluationODEfunction to adjust Responses with variables values.
scaleResponsesEvaluationODEInfusionfunction to adjust Responses with variables values.
setAllowedDose-setSet the constraints on allowed dose.
setAllowedTime-setSet the constraints on allowed times.
setAllowedTinf-setSet the constraints on Tinf.
setAmountDoseSet the amount of dose
setAmountOfArmsSet the amount of arms in a Design.
setAmountOfArmsAimSet amount of arms in a 'DesignConstraint' object for the...
setArmsSet the arms of a design.
setArmSizeSet the size of an arm.
setCError-setSet the CError of a 'ModelError' object.
setConstraintSet the constraint to the PFIMProject projet.
setDeltaSet the 'delta' parameters for the Multiplicative algorithm.
setDesignSet the design of 'PFIMProject' object.
setDiscret-setSet the possible values for a 'DiscreteConstraint' object.
setInitialConditionsSet the initial conditions of an Arm for an ODE model.
setIterationSet the number of iterations for the multiplicative...
setMfisher-setSet a matrix value for the Fisher Information Matrix.
setModelError-setSet the model error.
setMuSet the mu vector.
setNameDesignSet the name of the design.
setNamePFIMProjectSet the name of a PFIMProject projet.
setNumberSamples-setSet the number of Sample in a Design.
setOmegaSet the Omega matrix.
setOptimalDesign-setSet an optimal design.
setParametersForEvaluateModelSet the parameters for the evaluation of the model.
setParametersModelSet the parameters of the 'Model' object.
setParametersOdeSolverSet parameters for the ode solver
setPossibleArmsSet the possible arms in a Design or the case when lots of...
setRange-setSet the range of a 'ContinuousConstraint' object.
setSampleTimeSet the sample time of the response of the 'SamplingTimes'...
setSamplings-setSet the sampling times for an arm.
setShowProcessShow the process for the optimization.
setSigmaInter-setSet the value for 'sigma_inter' of a 'ModelError' object.
setSigmaSlope-setSet the value for 'sigma_slope' of a 'ModelError' object.
setTauSet the infusion lag tau.
setTimeDose-setSet the times vector when doses are given.
setTinfSet the infusion duration.
setTotalNumberOfIndividualsSet the total number of individuals in a 'DesignConstraint'...
setTotalSize-setSet the total size of a Design.
showShow the Fisher Information Matrix for a 'Fim' object and its...
showArmDataShow the data of an arm for a design.
showConstraintsShow all the constraints of the 'PFIMProject' object.
showDesignsShow all the Designs.
showFimsShow the Fisher Information Matrix for all the designs.
showStatisticalModelStandardErrorsShow expected standard error data frame.
SimplexAlgorithm-classClass "SimplexAlgorithm"
StandardDistribution-classClass "StandardDistribution"
StatisticalModel-classClass "StatisticalModel"
summarysummary
summaryArmDataGives a summary of all the parameters of an arm for a design.
PFIM documentation built on June 24, 2022, 9:06 a.m.