Population Fisher Information Matrix

Documentation for package ‘PFIM’ version 7.0.3

Help Pages

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

-- A --

adjustGradient	Adjust the gradient for the log normal distribution.
Administration	Administration Class
AdministrationConstraints	AdministrationConstraints Class
Arm	Arm Class
armAdministration	Get administration parameters of an arm

-- B --

BayesianFim Class

-- C --

checkSamplingTimeConstraintsForMetaheuristic	Validate New Sampling Schedules Against Constraints
checkValiditySamplingConstraint	Validate optimization constraints
Combined	Combined1 Class
Combined1	Combined1 Class
computeVMat	Compute Variance Matrix Component
Constant	Constant Class
constraintsTableForReport	Generate Algorithm Constraints Table for Reporting
convertPKModelAnalyticToPKModelODE	Conversion from analytic PK model to ODE PK model

-- D --

Dcriterion	Dcriterion
defineFim	Define the Fisher Information Matrix object
defineModelAdministration	Define the administration for an analytic model
defineModelEquationsFromLibraryOfModel	defineModelEquationsFromLibraryOfModel
defineModelType	defineModelType
defineModelWrapper	define the model wrapper for the ode solver
defineOptimizationAlgorithm	Define Optimization Algorithm
definePKModel	Define a PK model from library of model
definePKPDModel	Define a PKPD model from library of model
Design	Design Class
Distribution	Distribution Class

-- E --

evaluateArm	Evaluate an arm
evaluateDesign	Evaluation of a clinical design
evaluateErrorModelDerivatives	evaluate the derivatives of the model error.
evaluateFim	Evaluate the Fim.
evaluateInitialConditions	evaluate the initial conditions.
evaluateModel	Evaluate the analytic model
evaluateModelGradient	evaluate the gradient of the model
evaluateModelVariance	Evaluate Model Variance and Sigma Derivatives
evaluateVarianceFIM	Evaluate the Variance Component of the Fisher Information Matrix
Evaluation	Evaluation Class

-- F --

FedorovWynnAlgorithm	FedorovWynnAlgorithm Class
FedorovWynnAlgorithm_Rcpp	FedorovWynnAlgorithm with Rcpp
Fim	Fisher Information Matrix (FIM) Class
finiteDifferenceHessian	Compute the Hessian
fisherSimplex	Compute the fisher.simplex
fun.amoeba	Compute the Amoeba (Nelder-Mead) Simplex Search

-- G --

generateDosesCombination	Generate dose combinations for optimization
generateFimsFromConstraints	Generate Fisher Information Matrices (FIM) from Design Constraints
generateReportEvaluation	Generate a Comprehensive HTML Evaluation Report
generateReportOptimization	Generate the HTML Report for Design Optimization
generateSamplingsFromSamplingConstraints	Generate Numerical Intervals from Sampling Constraints
generateSamplingTimesCombination	Generate sampling time combinations
getArmConstraints	Get arm constraints for optimization algorithms
getArmData	Extract arm data for reporting
getCorrelationMatrix	getCorrelationMatrix
getDcriterion	getDcriterion: Extract the D-optimality criterion
getDeterminant	getDeterminant
getFisherMatrix	getFisherMatrix
getListLastName	getListLastName: Get names of the deepest elements in a nested list
getModelErrorData	get the parameters sigma slope and sigma inter (used for the report).
getModelParametersData	Extract Model Parameter Data for Reporting
getRSE	getRSE
getSamplingData	Extract sampling times and maximum sampling time
getSE	getSE
getShrinkage	getShrinkage

-- I --

Individual Fisher Information Matrix (IndividualFim) Class

-- L --

-- M --

Model	Model Class
ModelAnalytic	ModelAnalytic Class
ModelAnalyticInfusion	ModelAnalyticInfusion Class
ModelAnalyticInfusionSteadyState	ModelAnalyticInfusionSteadyState Class
ModelAnalyticSteadyState	ModelAnalyticSteadyState Class
ModelError	ModelError Class
ModelInfusion	ModelInfusion Class
ModelODE	ModelODE Class
ModelODEBolus	ModelODEBolus Class
ModelODEDoseInEquations	ModelODEDoseInEquations Class
ModelODEDoseNotInEquations	ModelODEDoseNotInEquations Class
ModelODEInfusion	ModelODEInfusion Class
ModelODEInfusionDoseInEquation	ModelODEInfusionDoseInEquation Class
ModelParameter	ModelParameter Class
MultiplicativeAlgorithm	MultiplicativeAlgorithm Class
MultiplicativeAlgorithm_Rcpp	Rcpp Multiplicative Algorithm for Optimal Design

-- N --

Normal Class

-- O --

Optimization	Optimization Class
optimizeDesign	Optimize Study Design

-- 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 Class
PGBOAlgorithm	PGBOAlgorithm Class
plot	plot
plotEvaluation	plotEvaluation
plotEvaluationResults	Plot model responses for an arm
plotEvaluationSI	Plot sensitivity indices for an arm
plotFrequencies	plotFrequencies: visualize optimal frequencies for the Fedorov-Wynn algorithm
plotFrequenciesFedorovWynnAlgorithm	plotFrequenciesFedorovWynnAlgorithm for the FedorovWynnAlgorithm
plotRSE	plotRSE
plotRSEFIM	Plot Relative Standard Errors (RSE%) for Population FIM
plotSE	plotSE
plotSEFIM	Plot Standard Errors from the Population FIM
plotSensitivityIndices	plotSensitivityIndices
plotShrinkage	Bar plot of the Bayesian shrinkage
plotWeights	Visualize the distribution of optimal design weights
plotWeightsMultiplicativeAlgorithm	Visualize Optimal Weight Distribution from Multiplicative Algorithm
PopulationFim	PopulationFim Class
processArmEvaluationResults	Process arm evaluation for response plots
processArmEvaluationSI	Process arm evaluation for sensitivity index plots
Proportional	Proportional Class
PSOAlgorithm	PSOAlgorithm Class

-- R --

replaceVariablesLibraryOfModels	: replace variable in the LibraryOfModels
Report	Report
run	run

-- S --

SamplingTimeConstraints	SamplingTimeConstraints Class
SamplingTimes	SamplingTimes Class
setEvaluationFim	Finalize and Set Population FIM Results
setOptimalArms	Set Optimal Arms for the MultiplicativeAlgorithm and FedorovWynnAlgorithm
setSamplingConstraintForOptimization	Initialize sampling constraints
show	show
showFIM	Display FIM Results in the R Console
SimplexAlgorithm	SimplexAlgorithm Class

-- T --

Generate Statistical Tables for Evaluation Reports

-- U --

Update sampling times for plotting

-- misc --

plot

LibraryOfModels	LibraryOfModels Class
LibraryOfPDModels	LibraryOfPDModels Class
LibraryOfPKModels	LibraryOfPKModels Class
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 Class