Population Fisher Information Matrix

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Documentation for package ‘PFIM’ version 6.0

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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.
addModels 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
checkValiditySamplingConstraint Check the validity of he sampling times constraints
Combined1 Class "Combined1"
Combined1-class Class "Combined1"
Constant Class "Constant"
Constant-class Class "Constant"
convertPKModelAnalyticToPKModelODE Convert an analytic model to a ode model.

-- D --

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.
Design Class "Design"
Design-class Class "Design"
Distribution Class "Distribution"
Distribution-class Class "Distribution"

-- E --

EvaluateArm Evaluate an arm.
EvaluateDesign Evaluate an design
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 "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
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 Get the adjusted gradient.
getAdministration Get the administrations by outcome.
getAdministrationConstraint Get the administration constraints by outcome.
getAdministrations Get all the administration for an arm.
getAdministrationsConstraints Get the administrations constraints.
getArms Get the arms of an object.
getcError Get the parameter c.
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 Get the amount of doses.
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 Get the fim of an of an object.
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 Get the initial condition for the evaluation of an ode model.
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 Get the fixed effect of an object.
getName Get the name of an object
getNames Get the names of an object.
getNumberOfArms Get the number of arms in a design.
getNumberOfIterations Get the number of iterations.
getNumberOfParameters Get the number of parameters.
getNumberOfsamplingsOptimisable Get the number of sampling times that are optimisable.
getNumberOfTimesByWindows Get the number of sampling times by windows.
getOdeSolverParameters Get the parameters for the ode solvers of an object.
getOmega Get the matrix omega of an object.
getOptimalDesign Get the optimal design.
getOptimalWeights Get the optimal weights.
getOptimizationResults Get the optimization results.
getOptimizer Get the optimization algorithm.
getOptimizerParameters Get the optimization parameters.
getOutcome Get the outcome of an object.
getOutcomes Get the outcomes of a model.
getOutcomesEvaluation Get the results of the evaluation of the outcomes.
getOutcomesForEvaluation Get the outcomes of a model used for the evaluation (is scales outcomes).
getOutcomesGradient Get the results of the evaluation of the outcome gradients.
getParameters Get the parameters of an object.
getPDModel Get a PD model.
getPKModel Get a PK model.
getPKPDModel Get a PKPD model.
getPlotOptions Get the plot options for graphs responses and SI
getProportionsOfSubjects Get the proportion of subjects.
getRSE Get the RSE
getSamplings Get the sampling of an object.
getSamplingsWindows Get the windows for the sampling times.
getSamplingTime Get the sampling times by outcome.
getSamplingTimeConstraint Get the sampling times constraints by outcome.
getSamplingTimes Get the vectors of sampling times for an arm.
getSamplingTimesConstraints Get the sampling times constraints.
getSE Get the SE.
getShrinkage Get the shrinkage.
getSigmaInter Get the parameter sigma inter.
getSigmaSlope Get the parameter sigma slope.
getSize Get the size of an object.
getTau Get the frequency 'tau'.
getTimeDose Get the times vector when doses are given.
getTinf Get the infusion duration.
getVarianceEffects 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.
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.

-- L --

LibraryOfModels Class "LibraryOfModels"
LibraryOfModels-class Class "LibraryOfModels"
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.

-- 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.
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"
plot Graphs of the results of the evaluation.
PlotEvaluation Class "PlotEvaluation"
PlotEvaluation-class Class "PlotEvaluation"
plotOutcomesEvaluation Plot the evaluation of the outcomes.
plotOutcomesGradient Plot the evaluation of the outcome gradients.
plotRSE Graph of the RSE.
plotSE Graph the SE.
plotShrinkage Graph of the shrinkage.
plotWeights 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
reportTablesAdministration Generate table for the report.
reportTablesDesign Generate table for the report.
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 Generate all the table for the evaluation report
reportTablesSamplingConstraints Generate table for the report.
resizeFisherMatrix Resize the fisher Matrix from a vector to a matrix.
run run

-- S --

SamplingTimeConstraints Class "SamplingTimeConstraints"
SamplingTimeConstraints-class Class "SamplingTimeConstraints"
SamplingTimes Class "SamplingTimes"
SamplingTimes-class Class "SamplingTimes"
setAdministrations Set all the administration for an arm.
setArm Set the arms in a design.
setArms Set the arms of an object.
setcError Set the parameter c.
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 Set the fim of the design.
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 Set the initial condition for the evaluation of an ode model.
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 Set the number of arms in a design.
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 Set the outcome of an object.
setOutcomes Set the outcomes of a model.
setOutcomesEvaluation Set the results of the evaluation of the outcomes.
setOutcomesForEvaluation Set the outcomes of a model used for the evaluation (is scales outcomes).
setOutcomesGradient Set the results of the evaluation of the outcomes.
setParameters Set the parameters of an object.
setSamplingConstraintForOptimization Set the sampling times constraint for optimization with PSO, PGBO and Simplex
setSamplings Set the sampling times.
setSamplingTime Set the sampling time of an arm.
setSamplingTimes Set the vectors of sampling times for an arm.
setSamplingTimesConstraints Set the sampling times constraints.
setShrinkage Set the shrinkage.
setSigmaInter Set the parameter sigma inter.
setSigmaSlope Set the parameter sigma slope.
setSize Set the size of an object.
setTau Set the frequency 'tau'.
setTimeDose Set the times vector when doses are given.
setTinf Set the infusion duration.
setVarianceEffects Set the matrix of the variance effects.
SimplexAlgorithm Class "SimplexAlgorithm"
SimplexAlgorithm-class Class "SimplexAlgorithm"

-- misc --

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