# Population Fisher Information Matrix

## Documentation for package ‘PFIM’ version 7.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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

PFIM-package | 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 | 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 | IndividualFim

## -- L --

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

## -- 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 | 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