Population Fisher Information Matrix


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Documentation for package ‘PFIM’ version 6.0.3

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A B C D E F G I L M N O P R S misc

PFIM-package Fisher Information matrix for design evaluation/optimization for nonlinear mixed effects models.

-- A --

addModel Add a model to a library of models.
addModel-method Add a model to a library of models.
addModels Add a models to a library of models.
addModels-method Add a models to a library of models.
Administration Class "Administration"
Administration-class Class "Administration"
AdministrationConstraints Class "AdministrationConstraints"
AdministrationConstraints-class Class "AdministrationConstraints"
Arm Class "Arm"
Arm-class Class "Arm"

-- B --

BayesianFim Class "BayesianFim"
BayesianFim-class Class "BayesianFim"

-- C --

checkSamplingTimeConstraintsForContinuousOptimization Check for the samplingTime constraints for continuous optimization
checkSamplingTimeConstraintsForContinuousOptimization-method Check for the samplingTime constraints for continuous optimization
checkValiditySamplingConstraint checkValiditySamplingConstraint
checkValiditySamplingConstraint-method checkValiditySamplingConstraint
Combined1 Class "Combined1"
Combined1-class Class "Combined1"
Constant Class "Constant"
Constant-class Class "Constant"
convertPKModelAnalyticToPKModelODE Convert an analytic model to a ode model.
convertPKModelAnalyticToPKModelODE-method Convert an analytic model to a ode model.

-- D --

defineModel Define a model.
defineModel-method Define a model.
defineModelFromLibraryOfModels Define a model from the library of models.
defineModelFromLibraryOfModels-method Define a model from the library of models.
defineModelType Define the type of a model.
defineModelType-method Define the type of a model.
defineModelUserDefined Define a user defined model.
defineModelUserDefined-method Define a user defined model.
definePKModel Define a PK model.
definePKModel-method Define a PK model.
definePKPDModel Define a PKPD model.
definePKPDModel-method Define a PKPD model.
Design Class "Design"
Design-class Class "Design"
Distribution Class "Distribution"
Distribution-class Class "Distribution"

-- E --

EvaluateArm EvaluateArm
EvaluateArm-method EvaluateArm
EvaluateDesign EvaluateDesign
EvaluateDesign-method EvaluateDesign
EvaluateErrorModelDerivatives Evaluate the error model derivatives.
EvaluateErrorModelDerivatives-method Evaluate the error model derivatives.
EvaluateFisherMatrix Evaluate the Fisher matrix ( population, individual and Bayesian )
EvaluateFisherMatrix-method Evaluate the Fisher matrix ( population, individual and Bayesian )
EvaluateModel Evaluate a model.
EvaluateModel-method Evaluate a model.
EvaluateVarianceFIM Evaluate the variance of the Fisher information matrix.
EvaluateVarianceFIM-method Evaluate the variance of the Fisher information matrix.
EvaluateVarianceModel Evaluate the variance of a model.
EvaluateVarianceModel-method Evaluate the variance of a model.
Evaluation Class "Evaluation"
Evaluation-class Class "Evaluation"

-- F --

FedorovWynnAlgorithm Class "FedorovWynnAlgorithm"
FedorovWynnAlgorithm-class Class "FedorovWynnAlgorithm"
FedorovWynnAlgorithm_Rcpp Fedorov-Wynn algorithm in Rcpp.
Fim Class "Fim"
Fim-class Class "Fim"
fisher.simplex Compute the fisher.simplex
fun.amoeba function fun.amoeba

-- G --

generateFimsFromConstraints Generate the fim from the constraints
generateFimsFromConstraints-method Generate the fim from the constraints
generateReportEvaluation Generate the report for the evaluation
generateReportEvaluation-method Generate the report for the evaluation
generateReportOptimization Generate report for the optimization.
generateReportOptimization-method Generate report for the optimization.
generateSamplingsFromSamplingConstraints Generate samplings from sampling constraints
generateSamplingsFromSamplingConstraints-method Generate samplings from sampling constraints
generateTables Generate the tables for the report.
generateTables-method Generate the tables for the report.
getAdjustedGradient getAdjustedGradient
getAdjustedGradient-method getAdjustedGradient
getAdministration getAdministration
getAdministration-method getAdministration
getAdministrationConstraint getAdministrationConstraint
getAdministrationConstraint-method getAdministrationConstraint
getAdministrations getAdministrations
getAdministrations-method getAdministrations
getAdministrationsConstraints getAdministrationsConstraints
getAdministrationsConstraints-method getAdministrationsConstraints
getArms Get the arms of an object.
getArms-method Get the arms of an object.
getcError Get the parameter c.
getcError-method Get the parameter c.
getColumnAndParametersNamesFIM Get the names of the names of the parameters associated to each column of the fim.
getColumnAndParametersNamesFIM-method 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.
getColumnAndParametersNamesFIMInLatex-method 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.
getConditionNumberFixedEffects-method Get the condition number of the matrix of the fixed effects.
getConditionNumberVarianceEffects Get the condition number of the matrix of the variance effects.
getConditionNumberVarianceEffects-method Get the condition number of the matrix of the variance effects.
getContent Get content of a library of models.
getContent-method Get content of a library of models.
getCorrelationMatrix Get the correlation matrix.
getCorrelationMatrix-method Get the correlation matrix.
getDataFrameResults Get the dataframe of the results.
getDataFrameResults-method Get the dataframe of the results.
getDcriterion Get the D criterion of the fim.
getDcriterion-method Get the D criterion of the fim.
getDelta Get the parameter delta
getDelta-method Get the parameter delta
getDerivatives Get the derivatives of the model error equation.
getDerivatives-method Get the derivatives of the model error equation.
getDescription Get the description of a model.
getDescription-method Get the description of a model.
getDesigns Get the designs.
getDesigns-method Get the designs.
getDeterminant Get the determinant of the fim.
getDeterminant-method Get the determinant of the fim.
getDistribution Get the distribution.
getDistribution-method Get the distribution.
getDose getDose
getDose-method getDose
getEigenValues Get the eigenvalues of the fim.
getEigenValues-method Get the eigenvalues of the fim.
getElementaryProtocols Get the elementary protocols.
getElementaryProtocols-method Get the elementary protocols.
getEquation Get the equation of a model error.
getEquation-method Get the equation of a model error.
getEquations Get the equations of a model.
getEquations-method Get the equations of a model.
getEquationsAfterInfusion Get the equations after infusion.
getEquationsAfterInfusion-method Get the equations after infusion.
getEquationsDuringInfusion Get the equations during infusion.
getEquationsDuringInfusion-method Get the equations during infusion.
getEvaluationFIMResults Get the results of the evaluation.
getEvaluationFIMResults-method Get the results of the evaluation.
getEvaluationInitialDesignResults Get the evaluation results of the initial design.
getEvaluationInitialDesignResults-method Get the evaluation results of the initial design.
getFim getFim
getFim-method getFim
getFisherMatrix Get the FIM.
getFisherMatrix-method Get the FIM.
getFixedEffects Get the matrix of fixed effects.
getFixedEffects-method Get the matrix of fixed effects.
getFixedMu Get the fixed effect.
getFixedMu-method Get the fixed effect.
getFixedOmega Get the fixed variance.
getFixedOmega-method Get the fixed variance.
getFixedParameters Get the fixed parameters.
getFixedParameters-method Get the fixed parameters.
getFixedTimes Get the fixed sampling times.
getFixedTimes-method Get the fixed sampling times.
getInitialConditions getInitialConditions
getInitialConditions-method getInitialConditions
getIterationAndCriteria Get the iteration with the convergence criteria.
getIterationAndCriteria-method Get the iteration with the convergence criteria.
getLambda Get the parameter lambda.
getLambda-method Get the parameter lambda.
getLibraryPDModels Get the library of PD models.
getLibraryPDModels-method Get the library of PD models.
getLibraryPKModels Get the library of PK models.
getLibraryPKModels-method Get the library of PK models.
getMinSampling Get the minimal sampling times.
getMinSampling-method Get the minimal sampling times.
getModel Get the model.
getModel-method Get the model.
getModelEquations Get the model equations.
getModelEquations-method Get the model equations.
getModelError Get the model error.
getModelError-method Get the model error.
getModelErrorParametersValues Get the values of the model error parameters.
getModelErrorParametersValues-method Get the values of the model error parameters.
getModelFromLibrary Get a model from the library of models.
getModelFromLibrary-method Get a model from the library of models.
getModelParameters Get the model parameters.
getModelParameters-method Get the model parameters.
getModelParametersValues Get the values of the model parameters.
getModelParametersValues-method Get the values of the model parameters.
getMu getMu
getMu-method getMu
getName getName
getName-method getName
getNames getNames
getNames-method getNames
getNumberOfArms getNumberOfArms
getNumberOfArms-method getNumberOfArms
getNumberOfIterations Get the number of iterations.
getNumberOfIterations-method Get the number of iterations.
getNumberOfParameters Get the number of parameters.
getNumberOfParameters-method Get the number of parameters.
getNumberOfsamplingsOptimisable Get the number of sampling times that are optimisable.
getNumberOfsamplingsOptimisable-method Get the number of sampling times that are optimisable.
getNumberOfTimesByWindows Get the number of sampling times by windows.
getNumberOfTimesByWindows-method Get the number of sampling times by windows.
getOdeSolverParameters getOdeSolverParameters
getOdeSolverParameters-method getOdeSolverParameters
getOmega Get the matrix omega of an object.
getOmega-method Get the matrix omega of an object.
getOptimalDesign Get the optimal design.
getOptimalDesign-method Get the optimal design.
getOptimalFrequencies Get the optimal frequencies
getOptimalFrequencies-method Get the optimal frequencies
getOptimalWeights Get the optimal weights.
getOptimalWeights-method Get the optimal weights.
getOptimizationResults Get the optimization results.
getOptimizationResults-method Get the optimization results.
getOptimizer Get the optimization algorithm.
getOptimizer-method Get the optimization algorithm.
getOptimizerParameters Get the optimization parameters.
getOptimizerParameters-method Get the optimization parameters.
getOutcome getOutcome
getOutcome-method getOutcome
getOutcomes Get the outcomes of a model.
getOutcomes-method Get the outcomes of a model.
getOutcomesEvaluation getOutcomesEvaluation
getOutcomesEvaluation-method getOutcomesEvaluation
getOutcomesForEvaluation Get the outcomes of a model used for the evaluation (is scales outcomes).
getOutcomesForEvaluation-method Get the outcomes of a model used for the evaluation (is scales outcomes).
getOutcomesGradient getOutcomesGradient
getOutcomesGradient-method getOutcomesGradient
getParameters Get the parameters of an object.
getParameters-method Get the parameters of an object.
getPDModel Get a PD model.
getPDModel-method Get a PD model.
getPKModel Get a PK model.
getPKModel-method Get a PK model.
getPKPDModel Get a PKPD model.
getPKPDModel-method Get a PKPD model.
getPlotOptions Get the plot options for graphs responses and SI
getProportionsOfSubjects Get the proportion of subjects.
getProportionsOfSubjects-method Get the proportion of subjects.
getRSE Get the RSE
getRSE-method Get the RSE
getSamplings Get the sampling of an object.
getSamplings-method Get the sampling of an object.
getSamplingsWindows Get the windows for the sampling times.
getSamplingsWindows-method Get the windows for the sampling times.
getSamplingTime getSamplingTime
getSamplingTime-method getSamplingTime
getSamplingTimeConstraint getSamplingTimeConstraint
getSamplingTimeConstraint-method getSamplingTimeConstraint
getSamplingTimes getSamplingTimes
getSamplingTimes-method getSamplingTimes
getSamplingTimesConstraints getSamplingTimesConstraints
getSamplingTimesConstraints-method getSamplingTimesConstraints
getSE Get the SE.
getSE-method Get the SE.
getShrinkage Get the shrinkage.
getShrinkage-method Get the shrinkage.
getSigmaInter Get the parameter sigma inter.
getSigmaInter-method Get the parameter sigma inter.
getSigmaSlope Get the parameter sigma slope.
getSigmaSlope-method Get the parameter sigma slope.
getSize getSize
getSize-method getSize
getTau getTau
getTau-method getTau
getTimeDose getTimeDose
getTimeDose-method getTimeDose
getTinf Get the infusion duration.
getTinf-method Get the infusion duration.
getVarianceEffects Get the matrix of the variance effects.
getVarianceEffects-method Get the matrix of the variance effects.

-- I --

IndividualFim Class "Fim"
IndividualFim-class Class "Fim"
isDoseInEquations Test if the dose is in the equations of the model.
isDoseInEquations-method Test if the dose is in the equations of the model.
isModelAnalytic Test if a mode is analytic.
isModelAnalytic-method Test if a mode is analytic.
isModelBolus Test if a mode is bolus.
isModelBolus-method Test if a mode is bolus.
isModelInfusion Test if a mode is infusion
isModelInfusion-method Test if a mode is infusion
isModelODE Test if a mode is ode.
isModelODE-method Test if a mode is ode.
isModelSteadyState Test if a mode is steady state.
isModelSteadyState-method Test if a mode is steady state.

-- L --

LibraryOfModels Class "LibraryOfModels"
LibraryOfModels-class Class "LibraryOfModels"
LibraryOfPDModels Library of the PK models
LibraryOfPKModels Library of the PK models
LibraryOfPKPDModels Class "LibraryOfPKPDModels"
LibraryOfPKPDModels-class Class "LibraryOfPKPDModels"
LogNormal Class "LogNormal"
LogNormal-class Class "LogNormal"

-- M --

Model Class "Model"
Model-class Class "Model"
ModelAnalytic Class "ModelAnalytic"
ModelAnalytic-class Class "ModelAnalytic"
ModelAnalyticBolus Class "ModelAnalyticBolus"
ModelAnalyticBolus-class Class "ModelAnalyticBolus"
ModelAnalyticBolusSteadyState Class "ModelAnalyticBolusSteadyState"
ModelAnalyticBolusSteadyState-class Class "ModelAnalyticBolusSteadyState"
ModelAnalyticInfusion Class "ModelAnalyticInfusion"
ModelAnalyticInfusion-class Class "ModelAnalyticInfusion"
ModelAnalyticInfusionSteadyState Class "ModelAnalyticInfusionSteadyState"
ModelAnalyticInfusionSteadyState-class Class "ModelAnalyticInfusionSteadyState"
ModelAnalyticSteadyState Class "ModelAnalyticSteadyState"
ModelAnalyticSteadyState-class Class "ModelAnalyticSteadyState"
ModelBolus Class "ModelBolus"
ModelBolus-class Class "ModelBolus"
ModelError Class "ModelError" representing a Model error.
ModelError-class Class "ModelError" representing a Model error.
ModelInfusion Class "ModelInfusion"
ModelInfusion-class Class "ModelInfusion"
ModelODE Class "ModelODE"
ModelODE-class Class "ModelODE"
ModelODEBolus Class "ModelODEBolus"
ModelODEBolus-class Class "ModelODEBolus"
ModelODEDoseInEquations Class "ModelODEDoseInEquations"
ModelODEDoseInEquations-class Class "ModelODEDoseInEquations"
ModelODEDoseNotInEquations Class "ModelODEDoseNotInEquations"
ModelODEDoseNotInEquations-class Class "ModelODEDoseNotInEquations"
ModelODEInfusion Class "ModelODEInfusion"
ModelODEInfusion-class Class "ModelODEInfusion"
ModelODEInfusionDoseInEquations Class "ModelODEInfusionDoseInEquations"
ModelODEInfusionDoseInEquations-class Class "ModelODEInfusionDoseInEquations"
ModelParameter Class "ModelParameter"
ModelParameter-class Class "ModelParameter"
MultiplicativeAlgorithm Class "MultiplicativeAlgorithm"
MultiplicativeAlgorithm-class Class "MultiplicativeAlgorithm"
MultiplicativeAlgorithm_Rcpp Function MultiplicativeAlgorithm_Rcpp

-- N --

Normal Class "Normal"
Normal-class Class "Normal"

-- O --

Optimization Class "Optimization"
Optimization-class Class "Optimization"
OptimizationAlgorithm Class "OptimizationAlgorithm"
OptimizationAlgorithm-class Class "OptimizationAlgorithm"
optimize Optimize a design.
optimize-method Optimize a design.

-- P --

package-PFIM Fisher Information matrix for design evaluation/optimization for nonlinear mixed effects models.
parametersForComputingGradient Define the parameters for computing the gradients of a model.
parametersForComputingGradient-method Define the parameters for computing the gradients of a model.
PFIM, Fisher Information matrix for design evaluation/optimization for nonlinear mixed effects models.
PFIMProject Class "PFIMProject"
PFIMProject-class Class "PFIMProject"
PGBOAlgorithm Class "PGBOAlgorithm"
PGBOAlgorithm-class Class "PGBOAlgorithm"
PlotEvaluation Class "PlotEvaluation"
plotEvaluation Graphs of the results of the evaluation.
PlotEvaluation-class Class "PlotEvaluation"
plotEvaluation-method Graphs of the results of the evaluation.
plotFrequencies Graph of the frequencies for the FW algorithm.
plotFrequencies-method Graph of the frequencies for the FW algorithm.
plotOutcomesEvaluation plotOutcomesEvaluation
plotOutcomesEvaluation-method plotOutcomesEvaluation
plotOutcomesGradient plotOutcomesGradient
plotOutcomesGradient-method plotOutcomesGradient
plotRSE Graph of the RSE.
plotRSE-method Graph of the RSE.
plotSE Graph the SE.
plotSE-method Graph the SE.
plotSensitivityIndice Graphs of the results of the evaluation.
plotSensitivityIndice-method Graphs of the results of the evaluation.
plotShrinkage Graph of the shrinkage.
plotShrinkage-method Graph of the shrinkage.
plotWeights Graph of the weights for the multiplicative algorithm.
plotWeights-method Graph of the weights for the multiplicative algorithm.
PopulationFim Class "PopulationFim"
PopulationFim-class Class "PopulationFim"
Proportional Class "Proportional"
Proportional-class Class "Proportional"
PSOAlgorithm Class "PSOAlgorithm"
PSOAlgorithm-class Class "PSOAlgorithm"

-- R --

Report Report
Report-method Report
reportTablesAdministration reportTablesAdministration
reportTablesAdministration-method reportTablesAdministration
reportTablesDesign reportTablesDesign
reportTablesDesign-method reportTablesDesign
reportTablesFIM Generate the tables for the report.
reportTablesFIM-method Generate the tables for the report.
reportTablesModelError Generate the tables for model errors for the evaluation report.
reportTablesModelError-method Generate the tables for model errors for the evaluation report.
reportTablesModelParameters Generate the tables for model parameters for the evaluation report.
reportTablesModelParameters-method Generate the tables for model parameters for the evaluation report.
reportTablesPlot reportTablesPlot
reportTablesPlot-method reportTablesPlot
reportTablesSamplingConstraints reportTablesSamplingConstraints
reportTablesSamplingConstraints-method reportTablesSamplingConstraints
resizeFisherMatrix Resize the fisher Matrix from a vector to a matrix.
resizeFisherMatrix-method Resize the fisher Matrix from a vector to a matrix.
run run
run-method run

-- S --

SamplingTimeConstraints Class "SamplingTimeConstraints"
SamplingTimeConstraints-class Class "SamplingTimeConstraints"
SamplingTimes Class "SamplingTimes"
SamplingTimes-class Class "SamplingTimes"
setAdministrations setAdministrations
setAdministrations-method setAdministrations
setArm setArm
setArm-method setArm
setArms Set the arms of an object.
setArms-method Set the arms of an object.
setcError Set the parameter c.
setcError-method Set the parameter c.
setContent Set content of a library of models.
setContent-method Set content of a library of models.
setDerivatives Set the derivatives of the model error equation.
setDerivatives-method Set the derivatives of the model error equation.
setDescription Set the description of a model.
setDescription-method Set the description of a model.
setDesigns Set the designs.
setDesigns-method Set the designs.
setDistribution Set the distribution.
setDistribution-method Set the distribution.
setDose Set the amount of dose
setDose-method Set the amount of dose
setEquation Set the equation of a model error.
setEquation-method Set the equation of a model error.
setEquations Set the equations of a model.
setEquations-method Set the equations of a model.
setEquationsAfterInfusion Set the equations after infusion.
setEquationsAfterInfusion-method Set the equations after infusion.
setEquationsDuringInfusion Set the equations during infusion.
setEquationsDuringInfusion-method Set the equations during infusion.
setEvaluationFIMResults Set the evaluation results.
setEvaluationFIMResults-method Set the evaluation results.
setEvaluationInitialDesignResults Set the evaluation results of the initial design.
setEvaluationInitialDesignResults-method Set the evaluation results of the initial design.
setFim setFim
setFim-method setFim
setFimTypeToString Convert the type of the object fim to a string.
setFimTypeToString-method Convert the type of the object fim to a string.
setFisherMatrix Set the FIM.
setFisherMatrix-method Set the FIM.
setFixedEffects Set the fixed effects.
setFixedEffects-method Set the fixed effects.
setFixedMu Set the mu as fixed or not.
setFixedMu-method Set the mu as fixed or not.
setFixedOmega Set the omega as fixed of not.
setFixedOmega-method Set the omega as fixed of not.
setInitialConditions setInitialConditions
setInitialConditions-method setInitialConditions
setIterationAndCriteria Set the iteration with the convergence criteria.
setIterationAndCriteria-method Set the iteration with the convergence criteria.
setModel Set the model.
setModel-method Set the model.
setModelError Set the model error.
setModelError-method Set the model error.
setModelFromLibrary Set a model from the library of model
setModelFromLibrary-method Set a model from the library of model
setMu Set the value of the fixed effect mu of an object.
setMu-method Set the value of the fixed effect mu of an object.
setName Set the name of an object.
setName-method Set the name of an object.
setNumberOfArms setNumberOfArms
setNumberOfArms-method setNumberOfArms
setOdeSolverParameters Set the parameters of the ode solver.
setOdeSolverParameters-method Set the parameters of the ode solver.
setOmega Set the matrix omega of an object.
setOmega-method Set the matrix omega of an object.
setOptimalDesign Set the optimal design.
setOptimalDesign-method Set the optimal design.
setOptimalWeights Set the optimal weights.
setOptimalWeights-method Set the optimal weights.
setOptimizationResults Set the optimization results.
setOptimizationResults-method Set the optimization results.
setOutcome setOutcome
setOutcome-method setOutcome
setOutcomes Set the outcomes of a model.
setOutcomes-method Set the outcomes of a model.
setOutcomesEvaluation setOutcomesEvaluation
setOutcomesEvaluation-method setOutcomesEvaluation
setOutcomesForEvaluation Set the outcomes of a model used for the evaluation (is scales outcomes).
setOutcomesForEvaluation-method Set the outcomes of a model used for the evaluation (is scales outcomes).
setOutcomesGradient setOutcomesGradient
setOutcomesGradient-method setOutcomesGradient
setParameters Set the parameters of an object.
setParameters-method Set the parameters of an object.
setSamplingConstraintForOptimization setSamplingConstraintForOptimization
setSamplingConstraintForOptimization-method setSamplingConstraintForOptimization
setSamplings Set the sampling times.
setSamplings-method Set the sampling times.
setSamplingTime setSamplingTime
setSamplingTime-method setSamplingTime
setSamplingTimes setSamplingTimes
setSamplingTimes-method setSamplingTimes
setSamplingTimesConstraints setSamplingTimesConstraints
setSamplingTimesConstraints-method setSamplingTimesConstraints
setShrinkage Set the shrinkage.
setShrinkage-method Set the shrinkage.
setSigmaInter Set the parameter sigma inter.
setSigmaInter-method Set the parameter sigma inter.
setSigmaSlope Set the parameter sigma slope.
setSigmaSlope-method Set the parameter sigma slope.
setSize setSize
setSize-method setSize
setTau setTau
setTau-method setTau
setTimeDose setTimeDose
setTimeDose-method setTimeDose
setTinf Set the infusion duration.
setTinf-method Set the infusion duration.
setVarianceEffects Set the matrix of the variance effects.
setVarianceEffects-method Set the matrix of the variance effects.
show-method show
SimplexAlgorithm Class "SimplexAlgorithm"
SimplexAlgorithm-class Class "SimplexAlgorithm"

-- misc --

_PACKAGE Fisher Information matrix for design evaluation/optimization for nonlinear mixed effects models.