Population Fisher Information Matrix

Documentation for package ‘PFIM’ version 7.0

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

-- A --

adjustGradient	adjustGradient: adjust the gradient for the log normal distribution.
Administration	Administration
AdministrationConstraints	AdministrationConstraints
Arm	Arm
armAdministration	getArmAdministration: get the administration parameters of an arm.

-- B --

BayesianFim

-- C --

checkSamplingTimeConstraintsForMetaheuristic	checkSamplingTimeConstraintsForMetaheuristic
checkValiditySamplingConstraint	checkValiditySamplingConstraint: check if the constraints used for the design optimization are valid.
Combined1	Combined1
computeVMat	computeVMat
Constant	Constant
constraintsTableForReport	constraintsTableForReport: table of the PGBOAlgorithm constraints for the report.
convertPKModelAnalyticToPKModelODE	convertPKModelAnalyticToPKModelODE: conversion from analytic to ode

-- D --

Dcriterion	Dcriterion: get the D-criterion of the Fim.
defineFim	define the type of Fisher information matrix: population, individual or Bayesian
defineModelAdministration	defineModelAdministration: define the administration
defineModelEquationsFromLibraryOfModel	defineModelEquationsFromLibraryOfModel: define the model equations giving the models in the library of models.
defineModelType	defineModelType: define the class of the model to be evaluated.
defineModelWrapper	defineModelWrapper: define the model wrapper for the ode solver
defineOptimizationAlgorithm	Define optimization algorithm
definePKModel	definePKModel: define a PK model from library of model
definePKPDModel	definePKPDModel: define a PKPD model from library of model
Design	Design
Distribution	Distribution

-- E --

evaluateArm	evaluateArm: evaluation of the model with the arm parameters.
evaluateDesign	evaluateDesign: evaluation of a design.
evaluateErrorModelDerivatives	evaluateErrorModelDerivatives; evaluate the derivatives of the model error.
evaluateFim	evaluateFim: evaluation of the Fim
evaluateInitialConditions	evaluateInitialConditions: evaluate the initial conditions.
evaluateModel	evaluateModel: evaluate the model
evaluateModelGradient	evaluateModelGradient: evaluate the gradient of the model
evaluateModelVariance	evaluateModelVariance: evaluate the variance of the model
evaluateVarianceFIM	evaluateVarianceFIM: evaluate the variance
Evaluation	Evaluation

-- F --

FedorovWynnAlgorithm	FedorovWynnAlgorithm
FedorovWynnAlgorithm_Rcpp	Fedorov-Wynn algorithm in Rcpp.
Fim	Fim
finiteDifferenceHessian	finiteDifferenceHessian: compute the Hessian
fisherSimplex	Compute the fisher.simplex
fun.amoeba	Compute the fun.amoeba

-- G --

generateDosesCombination	generateDosesCombination: generate the combination for the doses.
generateFimsFromConstraints	Generate FIMs from constraints
generateReportEvaluation	generateReportEvaluation: generate the report for the model evaluation.
generateReportOptimization	generateReportOptimization: generate the report for the design optimization.
generateSamplingsFromSamplingConstraints	generateSamplingsFromSamplingConstraints
generateSamplingTimesCombination	generateSamplingTimesCombination: generate the combination for the samplings.
getArmConstraints	getArmConstraints: get the administration and sampling time constraints for the MultiplicativeAlgorithm.
getArmData	getArmData: extract arm data for The Report
getCorrelationMatrix	getCorrelationMatrix : get the correlation matrix
getDcriterion	getDcriterion : get the Dcriterion
getDeterminant	getDeterminant: get the determinant
getFim	getFim: get the Fisher matrix.
getFisherMatrix	getFisherMatrix: display the Fisher matrix components
getListLastName	getListLastName: routine to get the names of last element of a nested list.
getModelErrorData	getModelErrorData: get the parameters sigma slope and sigma inter (used for the report).
getModelParametersData	getModelParametersData: get model parameters data for report.
getRSE	getRSE: get the RSE
getSamplingData	getSamplingData: extract sampling times and max sampling time used for plot.
getSE	getSE: get the SE
getShrinkage	getShrinkage: get the shrinkage

-- I --

IndividualFim

-- L --

-- M --

Model	Model
ModelAnalytic	ModelAnalytic
ModelAnalyticInfusion	ModelAnalyticInfusion
ModelAnalyticInfusionSteadyState	ModelAnalyticInfusionSteadyState
ModelAnalyticSteadyState	ModelAnalyticSteadyState
ModelError	ModelError
ModelInfusion	ModelInfusion
ModelODE	ModelODE
ModelODEBolus	ModelODEBolus
ModelODEDoseInEquations	ModelODEDoseNotInEquations
ModelODEDoseNotInEquations	ModelODEDoseNotInEquations
ModelODEInfusion	ModelODEInfusion
ModelODEInfusionDoseInEquation	ModelODEInfusionDoseInEquation
ModelParameter	ModelParameter
MultiplicativeAlgorithm	MultiplicativeAlgorithm
MultiplicativeAlgorithm_Rcpp	Function MultiplicativeAlgorithm_Rcpp

-- N --

Normal

-- O --

Optimization	Optimization
optimizeDesign	Optimization PGBOAlgorithm

-- P --

package-PFIM	Fisher Information matrix for design evaluation/optimization for nonlinear mixed effects models.
PFIM	Fisher Information matrix for design evaluation/optimization for nonlinear mixed effects models.
PFIM,	Fisher Information matrix for design evaluation/optimization for nonlinear mixed effects models.
PFIMProject	PFIMProject
PGBOAlgorithm	PGBOAlgorithm
plotEvaluation	plotEvaluation: plots for the evaluation of the model responses.
plotEvaluationResults	plotEvaluationResults: process for the evaluation of the responses.
plotEvaluationSI	plotEvaluationSI: process for the evaluation of the gradient of the responses.
plotFrequencies	Plot frequencies for the FedorovWynn algorithm
plotFrequenciesFedorovWynnAlgorithm	plotFrequenciesFedorovWynnAlgorithm
plotRSE	Plot relative standard errors
plotRSEFIM	plotRSEFIM: barplot for the RSE
plotSE	Plot standard errors
plotSEFIM	plotSEFIM: barplot for the SE
plotSensitivityIndices	Plot sensitivity indices.
plotShrinkage	plotShrinkage: plot the shrinkage values.
plotWeights	Plot weights for the multiplicative algorithm
plotWeightsMultiplicativeAlgorithm	plotWeightsMultiplicativeAlgorithm: plot the optimal weight.
PopulationFim	PopulationFim
processArmEvaluationResults	processArmEvaluationResults: process for the evaluation of an arm.
processArmEvaluationSI	processArmEvaluationSI: process for the evaluation of the gradient of the responses.
Proportional	Proportional
PSOAlgorithm	PSOAlgorithm

-- R --

replaceVariablesLibraryOfModels	replaceVariablesLibraryOfModels: replace variable in the LibraryOfModels
Report	Generate optimization report
run	Run optimization

-- S --

SamplingTimeConstraints	SamplingTimeConstraints
SamplingTimes	SamplingTimes
setEvaluationFim	setEvaluationFim: set the Fim results.
setOptimalArms	setOptimalArms: set the optimal arms of an optimization algorithm.
setSamplingConstraintForOptimization	setSamplingConstraintForOptimization: set the sampling time constraints for an arm for the design optimization.
show	Show optimization results
showFIM	showFIM: show the Fim in the R console.
SimplexAlgorithm	SimplexAlgorithm

-- T --

tablesForReport

tablesForReport: generate the table for the report.

-- U --

updateSamplingTimes

updateSamplingTimes: update sampling times for plotting used for plot

LibraryOfModels	LibraryOfModels
LibraryOfPDModels	LibraryOfPDModels
LibraryOfPKModels	LibraryOfPKModels
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