# Population Fisher Information Matrix

## Documentation for package ‘PFIM’ version 7.0.3

- 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 misc

PFIM-package | 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 | 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 --

IndividualFim | Individual Fisher Information Matrix (IndividualFim) Class

## -- L --

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

## -- 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 | 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 --

tablesForReport | Generate Statistical Tables for Evaluation Reports

## -- U --

updateSamplingTimes | Update sampling times for plotting

## -- misc --

.WHICH_EVALUATION | plot