Package: PFIM 6.1

Romain Leroux

PFIM: Population Fisher Information Matrix

Evaluate or optimize designs for nonlinear mixed effects models using the Fisher Information matrix. Methods used in the package refer to Mentré F, Mallet A, Baccar D (1997) <doi:10.1093/biomet/84.2.429>, Retout S, Comets E, Samson A, Mentré F (2007) <doi:10.1002/sim.2910>, Bazzoli C, Retout S, Mentré F (2009) <doi:10.1002/sim.3573>, Le Nagard H, Chao L, Tenaillon O (2011) <doi:10.1186/1471-2148-11-326>, Combes FP, Retout S, Frey N, Mentré F (2013) <doi:10.1007/s11095-013-1079-3> and Seurat J, Tang Y, Mentré F, Nguyen TT (2021) <doi:10.1016/j.cmpb.2021.106126>.

Authors:France Mentré [aut], Romain Leroux [aut, cre], Jérémy Seurat [aut], Lucie Fayette [aut]

PFIM_6.1.tar.gz
PFIM_6.1.tar.gz(r-4.5-noble)PFIM_6.1.tar.gz(r-4.4-noble)
PFIM_6.1.tgz(r-4.4-emscripten)PFIM_6.1.tgz(r-4.3-emscripten)
PFIM.pdf |PFIM.html✨
PFIM/json (API)

# Install 'PFIM' in R:

install.packages('PFIM', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.08 score 9 scripts 241 downloads 258 exports 116 dependencies

Last updated 6 days agofrom:4efaa8cc66. Checks:OK: 2. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Oct 24 2024
R-4.5-linux	OK	Oct 24 2024

Exports:addModel addModels Administration AdministrationConstraints Arm BayesianFim checkSamplingTimeConstraintsForContinuousOptimization checkValiditySamplingConstraint Combined1 computeVMat Constant convertPKModelAnalyticToPKModelODE dataForArmEvaluation defineModel defineModelEquationsFromStringToFunction defineModelFromLibraryOfModels defineModelType defineModelUserDefined definePKModel definePKPDModel Design Distribution EvaluateArm EvaluateDesign EvaluateErrorModelDerivatives EvaluateFisherMatrix EvaluateModel EvaluateModelGradient EvaluateVarianceFIM EvaluateVarianceModel Evaluation FedorovWynnAlgorithm FedorovWynnAlgorithm_Rcpp Fim fisher.simplex fun.amoeba generateFimsFromConstraints generateReportEvaluation generateReportOptimization generateSamplingsFromSamplingConstraints generateTables getAdjustedGradient getAdministration getAdministrationConstraint getAdministrations getAdministrationsConstraints getArms getcError getColumnAndParametersNamesFIM getColumnAndParametersNamesFIMInLatex getConditionNumberFixedEffects getConditionNumberVarianceEffects getContent getCorrelationMatrix getDataForArmEvaluation getDataFrameResults getDcriterion getDelta getDerivatives getDescription getDesigns getDeterminant getDistribution getDose getEigenValues getElementaryProtocols getEquation getEquations getEquationsAfterInfusion getEquationsDuringInfusion getEvaluationFIMResults getEvaluationInitialDesignResults getFim getFisherMatrix getFixedEffects getFixedMu getFixedOmega getFixedParameters getFixedTimes getInitialConditions getIterationAndCriteria getLambda getLibraryPDModels getLibraryPKModels getMinSampling getModel getModelEquations getModelError getModelErrorParametersValues getModelFromLibrary getModelParameters getModelParametersValues getMu getName getNames getNumberOfArms getNumberOfIterations getNumberOfParameters getNumberOfsamplingsOptimisable getNumberOfTimesByWindows getOdeSolverParameters getOmega getOptimalDesign getOptimalFrequencies getOptimalWeights getOptimizationResults getOptimizer getOptimizerParameters getOutcome getOutcomes getOutcomesEvaluation getOutcomesForEvaluation getOutcomesGradient getParameters getPDModel getPKModel getPKPDModel getPlotOptions getProportionsOfSubjects getRSE getSamplings getSamplingsWindows getSamplingTime getSamplingTimeConstraint getSamplingTimes getSamplingTimesConstraints getSE getShrinkage getSigmaInter getSigmaSlope getSize getTau getTimeDose getTinf getVariables getVarianceEffects getWeightThreshold IndividualFim initialize isDoseInEquations isModelAnalytic isModelBolus isModelInfusion isModelODE isModelSteadyState LibraryOfModels LibraryOfPDModels LibraryOfPKModels LibraryOfPKPDModels LogNormal Model ModelAnalytic ModelAnalyticBolus ModelAnalyticBolusSteadyState ModelAnalyticInfusion ModelAnalyticInfusionSteadyState ModelAnalyticSteadyState ModelBolus ModelError ModelInfusion ModelODE ModelODEBolus ModelODEDoseInEquations ModelODEDoseNotInEquations ModelODEInfusion ModelODEInfusionDoseInEquations ModelParameter MultiplicativeAlgorithm MultiplicativeAlgorithm_Rcpp Normal Optimization OptimizationAlgorithm optimize parametersForComputingGradient PFIMProject PGBOAlgorithm plotEvaluation PlotEvaluation plotFrequencies plotOutcomesEvaluation plotOutcomesGradient plotRSE plotSE plotSensitivityIndice plotShrinkage plotWeights PopulationFim Proportional PSOAlgorithm Report reportTablesAdministration reportTablesDesign reportTablesFIM reportTablesModelError reportTablesModelParameters reportTablesPlot reportTablesSamplingConstraints run SamplingTimeConstraints SamplingTimes setAdministrations setArm setArms setcError setContent setDataForArmEvaluation setDataForModelEvaluation setDerivatives setDescription setDesigns setDistribution setDose setEquation setEquations setEquationsAfterInfusion setEquationsDuringInfusion setEvaluationFIMResults setEvaluationInitialDesignResults setFim setFimTypeToString setFisherMatrix setFixedEffects setFixedMu setFixedOmega setInitialConditions setIterationAndCriteria setModel setModelError setModelFromLibrary setMu setName setNumberOfArms setOdeSolverParameters setOmega setOptimalDesign setOptimalWeights setOptimizationResults setOutcome setOutcomes setOutcomesEvaluation setOutcomesForEvaluation setOutcomesGradient setParameters setSamplingConstraintForOptimization setSamplings setSamplingTime setSamplingTimes setSamplingTimesConstraints setShrinkage setSigmaInter setSigmaSlope setSize setTau setTimeDose setTinf setVarianceEffects show SimplexAlgorithm

Dependencies:askpass base64enc brew brio bslib cachem callr cli clipr colorspace commonmark cpp11 crayon credentials curl Deriv desc deSolve devtools diffobj digest downlit ellipsis evaluate fansi farver fastmap fontawesome fs gert ggplot2 gh gitcreds glue gtable highr htmltools htmlwidgets httpuv httr2 ini inline isoband jquerylib jsonlite kableExtra knitr labeling later lattice lifecycle magrittr MASS Matrix memoise mgcv mime miniUI munsell nlme openssl pillar pkgbuild pkgconfig pkgdown pkgload pracma praise prettyunits processx profvis promises ps purrr R6 ragg rappdirs rcmdcheck RColorBrewer Rcpp rematch2 remotes rlang rmarkdown roxygen2 rprojroot rstudioapi rversions sass scales sessioninfo shiny sourcetools stringi stringr svglite sys systemfonts testthat textshaping tibble tinytex urlchecker usethis utf8 vctrs viridisLite waldo whisker withr xfun xml2 xopen xtable yaml zip

Design evaluation and optimization in continuous space

Rendered fromExample02.Rmdusingknitr::rmarkdownon Oct 24 2024.

Last update: 2024-03-24
Started: 2022-06-24

Design evaluation and optimization in discrete space

Rendered fromExample01.Rmdusingknitr::rmarkdownon Oct 24 2024.

Last update: 2024-10-23
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Library of models

Rendered fromLibraryOfModels.Rmdusingknitr::rmarkdownon Oct 24 2024.

Last update: 2022-06-24
Started: 2022-06-24

Citation

Readme and manuals

Help Manual

Help page	Topics
Fisher Information matrix for design evaluation/optimization for nonlinear mixed effects models.	PFIM-package package-PFIM PFIM PFIM,
Add a model to a library of models.	addModel addModel,LibraryOfModels-method
Add a models to a library of models.	addModels addModels,LibraryOfModels-method
Class "Administration"	Administration Administration-class
Class "AdministrationConstraints"	AdministrationConstraints AdministrationConstraints-class
Class "Arm"	Arm Arm-class
Class "BayesianFim"	BayesianFim BayesianFim-class
Check for the samplingTime constraints for continuous optimization	checkSamplingTimeConstraintsForContinuousOptimization checkSamplingTimeConstraintsForContinuousOptimization,SamplingTimeConstraints-method
checkValiditySamplingConstraint	checkValiditySamplingConstraint checkValiditySamplingConstraint,Design-method
Class "Combined1"	Combined1 Combined1-class
function computeVMat	computeVMat
Class "Constant"	Constant Constant-class
Convert an analytic model to a ode model.	convertPKModelAnalyticToPKModelODE convertPKModelAnalyticToPKModelODE,ModelAnalytic-method convertPKModelAnalyticToPKModelODE,ModelAnalyticInfusion-method convertPKModelAnalyticToPKModelODE,ModelAnalyticSteadyState-method
dataForArmEvaluation	dataForArmEvaluation dataForArmEvaluation,Design-method
Define a model.	defineModel defineModel,Model-method
defineModelEquationsFromStringToFunction	defineModelEquationsFromStringToFunction defineModelEquationsFromStringToFunction,ModelAnalytic-method defineModelEquationsFromStringToFunction,ModelAnalyticInfusion-method defineModelEquationsFromStringToFunction,ModelAnalyticInfusionSteadyState-method defineModelEquationsFromStringToFunction,ModelAnalyticSteadyState-method defineModelEquationsFromStringToFunction,ModelODEBolus-method defineModelEquationsFromStringToFunction,ModelODEDoseInEquations-method defineModelEquationsFromStringToFunction,ModelODEDoseNotInEquations-method defineModelEquationsFromStringToFunction,ModelODEInfusionDoseInEquations-method
Define a model from the library of models.	defineModelFromLibraryOfModels defineModelFromLibraryOfModels,Model-method
Define the type of a model.	defineModelType defineModelType,Model-method
Define a user defined model.	defineModelUserDefined defineModelUserDefined,Model-method
Define a PK model.	definePKModel definePKModel,ModelAnalytic-method definePKModel,ModelAnalyticInfusion-method definePKModel,ModelAnalyticSteadyState-method definePKModel,ModelODE-method definePKModel,ModelODEDoseInEquations-method definePKModel,ModelODEInfusionDoseInEquations-method
Define a PKPD model.	definePKPDModel definePKPDModel,ModelAnalytic,ModelAnalytic-method definePKPDModel,ModelAnalytic,ModelODE-method definePKPDModel,ModelAnalyticInfusion,ModelAnalytic-method definePKPDModel,ModelAnalyticInfusion,ModelODE-method definePKPDModel,ModelAnalyticSteadyState,ModelAnalyticSteadyState-method definePKPDModel,ModelAnalyticSteadyState,ModelODE-method definePKPDModel,ModelODEBolus,ModelODE-method definePKPDModel,ModelODEDoseInEquations,ModelODE-method definePKPDModel,ModelODEDoseNotInEquations,ModelODE-method definePKPDModel,ModelODEInfusion,ModelODE-method definePKPDModel,ModelODEInfusionDoseInEquations,ModelODE-method
Class "Design"	Design Design-class
Class "Distribution"	Distribution Distribution-class
EvaluateArm	EvaluateArm EvaluateArm,Arm-method
EvaluateDesign	EvaluateDesign EvaluateDesign,Design-method
Evaluate the error model derivatives.	EvaluateErrorModelDerivatives EvaluateErrorModelDerivatives,ModelError-method
Evaluate the Fisher matrix ( population, individual and Bayesian )	EvaluateFisherMatrix EvaluateFisherMatrix,BayesianFim-method EvaluateFisherMatrix,IndividualFim-method EvaluateFisherMatrix,PopulationFim-method
Evaluate a model.	EvaluateModel EvaluateModel,ModelAnalytic-method EvaluateModel,ModelAnalyticInfusion-method EvaluateModel,ModelAnalyticInfusionSteadyState-method EvaluateModel,ModelAnalyticSteadyState-method EvaluateModel,ModelODEBolus-method EvaluateModel,ModelODEDoseInEquations-method EvaluateModel,ModelODEDoseNotInEquations-method EvaluateModel,ModelODEInfusionDoseInEquations-method
Evaluate model gradient.	EvaluateModelGradient EvaluateModelGradient,ModelAnalytic-method EvaluateModelGradient,ModelAnalyticInfusion-method EvaluateModelGradient,ModelAnalyticInfusionSteadyState-method EvaluateModelGradient,ModelAnalyticSteadyState-method EvaluateModelGradient,ModelODEBolus-method EvaluateModelGradient,ModelODEDoseInEquations-method EvaluateModelGradient,ModelODEDoseNotInEquations-method EvaluateModelGradient,ModelODEInfusionDoseInEquations-method
Evaluate the variance of the Fisher information matrix.	EvaluateVarianceFIM EvaluateVarianceFIM,IndividualFim-method EvaluateVarianceFIM,PopulationFim-method
Evaluate the variance of a model.	EvaluateVarianceModel EvaluateVarianceModel,Model-method
Class "Evaluation"	Evaluation Evaluation-class
Fedorov-Wynn algorithm in Rcpp.	FedorovWynnAlgorithm_Rcpp
Class "FedorovWynnAlgorithm"	FedorovWynnAlgorithm FedorovWynnAlgorithm-class
Class "Fim"	Fim Fim-class
Compute the fisher.simplex	fisher.simplex
function fun.amoeba	fun.amoeba
Generate the fim from the constraints	generateFimsFromConstraints generateFimsFromConstraints,Optimization-method
Generate the report for the evaluation	generateReportEvaluation generateReportEvaluation,BayesianFim-method generateReportEvaluation,IndividualFim-method generateReportEvaluation,PopulationFim-method
Generate report for the optimization.	generateReportOptimization generateReportOptimization,FedorovWynnAlgorithm-method generateReportOptimization,MultiplicativeAlgorithm-method generateReportOptimization,PGBOAlgorithm-method generateReportOptimization,PSOAlgorithm-method generateReportOptimization,SimplexAlgorithm-method
Generate samplings from sampling constraints	generateSamplingsFromSamplingConstraints generateSamplingsFromSamplingConstraints,SamplingTimeConstraints-method
Generate the tables for the report.	generateTables generateTables,Evaluation-method generateTables,Optimization-method
getAdjustedGradient	getAdjustedGradient getAdjustedGradient,LogNormal-method getAdjustedGradient,Normal-method
getAdministration	getAdministration getAdministration,Arm-method
getAdministrationConstraint	getAdministrationConstraint getAdministrationConstraint,Arm-method
getAdministrations	getAdministrations getAdministrations,Arm-method
getAdministrationsConstraints	getAdministrationsConstraints getAdministrationsConstraints,Arm-method
Get the arms of an object.	getArms getArms,Design-method getArms,OptimizationAlgorithm-method
Get the parameter c.	getcError getcError,ModelError-method
Get the names of the names of the parameters associated to each column of the fim.	getColumnAndParametersNamesFIM getColumnAndParametersNamesFIM,BayesianFim-method getColumnAndParametersNamesFIM,IndividualFim-method getColumnAndParametersNamesFIM,PopulationFim-method
Get the names of the names of the parameters associated to each column of the fim in Latex format.	getColumnAndParametersNamesFIMInLatex getColumnAndParametersNamesFIMInLatex,BayesianFim-method getColumnAndParametersNamesFIMInLatex,IndividualFim-method getColumnAndParametersNamesFIMInLatex,PopulationFim-method
Get the condition number of the matrix of the fixed effects.	getConditionNumberFixedEffects getConditionNumberFixedEffects,Fim-method
Get the condition number of the matrix of the variance effects.	getConditionNumberVarianceEffects getConditionNumberVarianceEffects,BayesianFim-method getConditionNumberVarianceEffects,Fim-method
Get content of a library of models.	getContent getContent,LibraryOfModels-method
Get the correlation matrix.	getCorrelationMatrix getCorrelationMatrix,Evaluation-method getCorrelationMatrix,Fim-method getCorrelationMatrix,Optimization-method
getDataForArmEvaluation	getDataForArmEvaluation getDataForArmEvaluation,Arm-method
Get the dataframe of the results.	getDataFrameResults getDataFrameResults,FedorovWynnAlgorithm-method getDataFrameResults,MultiplicativeAlgorithm-method getDataFrameResults,Optimization-method
Get the D criterion of the fim.	getDcriterion getDcriterion,Evaluation-method getDcriterion,Fim-method getDcriterion,Optimization-method
Get the parameter delta	getDelta getDelta,MultiplicativeAlgorithm-method
Get the derivatives of the model error equation.	getDerivatives getDerivatives,ModelError-method
Get the description of a model.	getDescription getDescription,Model-method
Get the designs.	getDesigns getDesigns,PFIMProject-method
Get the determinant of the fim.	getDeterminant getDeterminant,Evaluation-method getDeterminant,Fim-method getDeterminant,Optimization-method
Get the distribution.	getDistribution getDistribution,ModelParameter-method
getDose	getDose getDose,Administration-method getDose,AdministrationConstraints-method
Get the eigenvalues of the fim.	getEigenValues getEigenValues,Fim-method
Get the elementary protocols.	getElementaryProtocols getElementaryProtocols,Optimization-method
Get the equation of a model error.	getEquation getEquation,ModelError-method
Get the equations of a model.	getEquations getEquations,Model-method
Get the equations after infusion.	getEquationsAfterInfusion getEquationsAfterInfusion,Model-method
Get the equations during infusion.	getEquationsDuringInfusion getEquationsDuringInfusion,Model-method
Get the results of the evaluation.	getEvaluationFIMResults getEvaluationFIMResults,Optimization-method
Get the evaluation results of the initial design.	getEvaluationInitialDesignResults getEvaluationInitialDesignResults,Optimization-method
getFim	getFim getFim,Design-method getFim,OptimizationAlgorithm-method getFim,PFIMProject-method
Get the FIM.	getFisherMatrix getFisherMatrix,Evaluation-method getFisherMatrix,Fim-method getFisherMatrix,Optimization-method
Get the matrix of fixed effects.	getFixedEffects getFixedEffects,Fim-method
Get the fixed effect.	getFixedMu getFixedMu,ModelParameter-method
Get the fixed variance.	getFixedOmega getFixedOmega,ModelParameter-method
Get the fixed parameters.	getFixedParameters getFixedParameters,Model-method
Get the fixed sampling times.	getFixedTimes getFixedTimes,SamplingTimeConstraints-method
getInitialConditions	getInitialConditions getInitialConditions,Arm-method getInitialConditions,Model-method
Get the iteration with the convergence criteria.	getIterationAndCriteria getIterationAndCriteria,OptimizationAlgorithm-method
Get the parameter lambda.	getLambda getLambda,MultiplicativeAlgorithm-method
Get the library of PD models.	getLibraryPDModels getLibraryPDModels,LibraryOfModels-method
Get the library of PK models.	getLibraryPKModels getLibraryPKModels,LibraryOfModels-method
Get the minimal sampling times.	getMinSampling getMinSampling,SamplingTimeConstraints-method
Get the model.	getModel getModel,PFIMProject-method
Get the model equations.	getModelEquations getModelEquations,PFIMProject-method
Get the model error.	getModelError getModelError,Model-method getModelError,PFIMProject-method
Get the values of the model error parameters.	getModelErrorParametersValues getModelErrorParametersValues,Model-method
Get a model from the library of models.	getModelFromLibrary getModelFromLibrary,Model-method
Get the model parameters.	getModelParameters getModelParameters,PFIMProject-method
Get the values of the model parameters.	getModelParametersValues getModelParametersValues,Model-method
getMu	getMu getMu,Distribution-method getMu,ModelParameter-method
getName	getName getName,Arm-method getName,Design-method getName,LibraryOfModels-method getName,Model-method getName,ModelParameter-method getName,PFIMProject-method
getNames	getNames getNames,list-method
getNumberOfArms	getNumberOfArms getNumberOfArms,Design-method
Get the number of iterations.	getNumberOfIterations getNumberOfIterations,MultiplicativeAlgorithm-method
Get the number of parameters.	getNumberOfParameters getNumberOfParameters,Model-method
Get the number of sampling times that are optimisable.	getNumberOfsamplingsOptimisable getNumberOfsamplingsOptimisable,SamplingTimeConstraints-method
Get the number of sampling times by windows.	getNumberOfTimesByWindows getNumberOfTimesByWindows,SamplingTimeConstraints-method
getOdeSolverParameters	getOdeSolverParameters getOdeSolverParameters,Model-method getOdeSolverParameters,PFIMProject-method
Get the matrix omega of an object.	getOmega getOmega,Distribution-method getOmega,ModelParameter-method
Get the optimal design.	getOptimalDesign getOptimalDesign,OptimizationAlgorithm-method
Get the optimal frequencies	getOptimalFrequencies getOptimalFrequencies,FedorovWynnAlgorithm-method
Get the optimal weights.	getOptimalWeights getOptimalWeights,MultiplicativeAlgorithm-method
Get the optimization results.	getOptimizationResults getOptimizationResults,Optimization-method
Get the optimization algorithm.	getOptimizer getOptimizer,PFIMProject-method
Get the optimization parameters.	getOptimizerParameters getOptimizerParameters,PFIMProject-method
getOutcome	getOutcome getOutcome,Administration-method getOutcome,AdministrationConstraints-method getOutcome,ModelError-method getOutcome,SamplingTimeConstraints-method getOutcome,SamplingTimes-method
Get the outcomes of a model.	getOutcomes getOutcomes,Model-method getOutcomes,PFIMProject-method
getOutcomesEvaluation	getOutcomesEvaluation getOutcomesEvaluation,Design-method
Get the outcomes of a model used for the evaluation (is scales outcomes).	getOutcomesForEvaluation getOutcomesForEvaluation,Model-method
getOutcomesGradient	getOutcomesGradient getOutcomesGradient,Design-method
Get the parameters of an object.	getParameters getParameters,Distribution-method getParameters,Model-method getParameters,ModelError-method
Get a PD model.	getPDModel getPDModel,LibraryOfPKPDModels-method
Get a PK model.	getPKModel getPKModel,LibraryOfPKPDModels-method
Get a PKPD model.	getPKPDModel getPKPDModel,LibraryOfPKPDModels-method
Get the plot options for graphs responses and SI	getPlotOptions
Get the proportion of subjects.	getProportionsOfSubjects getProportionsOfSubjects,Optimization-method
Get the RSE	getRSE getRSE,BayesianFim-method getRSE,Evaluation-method getRSE,IndividualFim-method getRSE,Optimization-method getRSE,PopulationFim-method
Get the sampling of an object.	getSamplings getSamplings,SamplingTimeConstraints-method getSamplings,SamplingTimes-method
Get the windows for the sampling times.	getSamplingsWindows getSamplingsWindows,SamplingTimeConstraints-method
getSamplingTime	getSamplingTime getSamplingTime,Arm-method
getSamplingTimeConstraint	getSamplingTimeConstraint getSamplingTimeConstraint,Arm-method
getSamplingTimes	getSamplingTimes getSamplingTimes,Arm-method
getSamplingTimesConstraints	getSamplingTimesConstraints getSamplingTimesConstraints,Arm-method
Get the SE.	getSE getSE,Evaluation-method getSE,Fim-method getSE,Optimization-method
Get the shrinkage.	getShrinkage getShrinkage,BayesianFim-method getShrinkage,Evaluation-method getShrinkage,IndividualFim-method getShrinkage,Optimization-method getShrinkage,PopulationFim-method
Get the parameter sigma inter.	getSigmaInter getSigmaInter,ModelError-method
Get the parameter sigma slope.	getSigmaSlope getSigmaSlope,ModelError-method
getSize	getSize getSize,Arm-method getSize,Design-method
getTau	getTau getTau,Administration-method
getTimeDose	getTimeDose getTimeDose,Administration-method
Get the infusion duration.	getTinf getTinf,Administration-method
Return the variable of an ode model	getVariables getVariables,ModelInfusion-method getVariables,ModelODE-method getVariables,ModelODEBolus-method ModelODEBolus ModelODEBolus-class
Get the matrix of the variance effects.	getVarianceEffects getVarianceEffects,Fim-method
Get the parameter weightThreshold	getWeightThreshold getWeightThreshold,MultiplicativeAlgorithm-method
Class "Fim"	IndividualFim IndividualFim-class
initialize	initialize,Administration-method
initialize	initialize,AdministrationConstraints-method
initialize	initialize,Arm-method
initialize	initialize,Combined1-method
initialize	initialize,Constant-method
initialize	initialize,Design-method
initialize	initialize,Distribution-method
initialize	initialize,Evaluation-method
initialize	initialize,FedorovWynnAlgorithm-method
initialize	initialize,Fim-method
initialize	initialize,LibraryOfModels-method
initialize	initialize,LibraryOfPKPDModels-method
initialize	initialize,LogNormal-method
initialize	initialize,Model-method
initialize	initialize,ModelAnalytic-method
initialize	initialize,ModelAnalyticBolus-method
initialize	initialize,ModelAnalyticBolusSteadyState-method
initialize	initialize,ModelAnalyticInfusion-method
initialize	initialize,ModelAnalyticInfusionSteadyState-method
initialize	initialize,ModelAnalyticSteadyState-method
initialize	initialize,ModelBolus-method
initialize	initialize,ModelError-method
initialize	initialize,ModelInfusion-method
initialize	initialize,ModelParameter-method
initialize	initialize,MultiplicativeAlgorithm-method
initialize	initialize,Normal-method
initialize	initialize,Optimization-method
initialize	initialize,OptimizationAlgorithm-method
initialize	initialize,PFIMProject-method
initialize	initialize,PGBOAlgorithm-method
initialize	initialize,Proportional-method
initialize	initialize,PSOAlgorithm-method
initialize	initialize,SamplingTimeConstraints-method
initialize	initialize,SamplingTimes-method
initialize	initialize,SimplexAlgorithm-method
Test if the dose is in the equations of the model.	isDoseInEquations isDoseInEquations,Model-method
Test if a mode is analytic.	isModelAnalytic isModelAnalytic,Model-method
Test if a mode is bolus.	isModelBolus isModelBolus,Model-method
Test if a mode is infusion	isModelInfusion isModelInfusion,Model-method
Test if a mode is ode.	isModelODE isModelODE,Model-method
Test if a mode is steady state.	isModelSteadyState isModelSteadyState,Model-method
Class "LibraryOfModels"	LibraryOfModels LibraryOfModels-class
Library of the PK models	LibraryOfPDModels
Library of the PK models	LibraryOfPKModels
Class "LibraryOfPKPDModels"	LibraryOfPKPDModels LibraryOfPKPDModels-class
Class "LogNormal"	LogNormal LogNormal-class
Class "Model"	Model Model-class
Class "ModelAnalytic"	ModelAnalytic ModelAnalytic-class
Class "ModelAnalyticBolus"	ModelAnalyticBolus ModelAnalyticBolus-class
Class "ModelAnalyticBolusSteadyState"	ModelAnalyticBolusSteadyState ModelAnalyticBolusSteadyState-class
Class "ModelAnalyticInfusion"	ModelAnalyticInfusion ModelAnalyticInfusion-class
Class "ModelAnalyticInfusionSteadyState"	ModelAnalyticInfusionSteadyState ModelAnalyticInfusionSteadyState-class
Class "ModelAnalyticSteadyState"	ModelAnalyticSteadyState ModelAnalyticSteadyState-class
Class "ModelBolus"	ModelBolus ModelBolus-class
Class "ModelError" representing a Model error.	ModelError ModelError-class
Class "ModelInfusion"	ModelInfusion ModelInfusion-class
Class "ModelODE"	ModelODE ModelODE-class
Class "ModelODEDoseInEquations"	ModelODEDoseInEquations ModelODEDoseInEquations-class
Class "ModelODEDoseNotInEquations"	ModelODEDoseNotInEquations ModelODEDoseNotInEquations-class
Class "ModelODEInfusion"	ModelODEInfusion ModelODEInfusion-class
Class "ModelODEInfusionDoseInEquations"	ModelODEInfusionDoseInEquations ModelODEInfusionDoseInEquations-class
Class "ModelParameter"	ModelParameter ModelParameter-class
Function MultiplicativeAlgorithm_Rcpp	MultiplicativeAlgorithm_Rcpp
Class "MultiplicativeAlgorithm"	MultiplicativeAlgorithm MultiplicativeAlgorithm-class
Class "Normal"	Normal Normal-class
Class "Optimization"	Optimization Optimization-class
Class "OptimizationAlgorithm"	OptimizationAlgorithm OptimizationAlgorithm-class
Optimize a design.	optimize optimize,FedorovWynnAlgorithm-method optimize,MultiplicativeAlgorithm-method optimize,PGBOAlgorithm-method optimize,PSOAlgorithm-method optimize,SimplexAlgorithm-method
Define the parameters for computing the gradients of a model.	parametersForComputingGradient parametersForComputingGradient,Model-method
Class "PFIMProject"	PFIMProject PFIMProject-class
Class "PGBOAlgorithm"	PGBOAlgorithm PGBOAlgorithm-class
Graphs of the results of the evaluation.	plotEvaluation plotEvaluation,Evaluation-method
Class "PlotEvaluation"	PlotEvaluation PlotEvaluation-class
Graph of the frequencies for the FW algorithm.	plotFrequencies plotFrequencies,FedorovWynnAlgorithm-method plotFrequencies,Optimization-method
plotOutcomesEvaluation	plotOutcomesEvaluation plotOutcomesEvaluation,Design-method
plotOutcomesGradient	plotOutcomesGradient plotOutcomesGradient,Design-method
Graph of the RSE.	plotRSE plotRSE,PFIMProject-method
Graph the SE.	plotSE plotSE,PFIMProject-method
Graphs of the results of the evaluation.	plotSensitivityIndice plotSensitivityIndice,Evaluation-method
Graph of the shrinkage.	plotShrinkage plotShrinkage,PFIMProject-method
Graph of the weights for the multiplicative algorithm.	plotWeights plotWeights,MultiplicativeAlgorithm-method plotWeights,Optimization-method
Class "PopulationFim"	PopulationFim PopulationFim-class
Class "Proportional"	Proportional Proportional-class
Class "PSOAlgorithm"	PSOAlgorithm PSOAlgorithm-class
Report	Report Report,Evaluation-method Report,Optimization-method
reportTablesAdministration	reportTablesAdministration reportTablesAdministration,Design-method
reportTablesDesign	reportTablesDesign reportTablesDesign,Design-method
Generate the tables for the report.	reportTablesFIM reportTablesFIM,BayesianFim-method reportTablesFIM,IndividualFim-method reportTablesFIM,PopulationFim-method
Generate the tables for model errors for the evaluation report.	reportTablesModelError reportTablesModelError,Model-method
Generate the tables for model parameters for the evaluation report.	reportTablesModelParameters reportTablesModelParameters,Model-method
reportTablesPlot	reportTablesPlot reportTablesPlot,Evaluation-method
reportTablesSamplingConstraints	reportTablesSamplingConstraints reportTablesSamplingConstraints,Design-method
Resize the fisher Matrix from a vector to a matrix.	resizeFisherMatrix resizeFisherMatrix,ANY-method
run	run run,Evaluation-method run,Optimization-method
Class "SamplingTimeConstraints"	SamplingTimeConstraints SamplingTimeConstraints-class
Class "SamplingTimes"	SamplingTimes SamplingTimes-class
setAdministrations	setAdministrations setAdministrations,Arm-method
setArm	setArm setArm,Design-method
Set the arms of an object.	setArms setArms,Design-method setArms,OptimizationAlgorithm-method
Set the parameter c.	setcError setcError,ModelError-method
Set content of a library of models.	setContent setContent,LibraryOfModels-method
setDataForArmEvaluation	setDataForArmEvaluation setDataForArmEvaluation,Arm-method
Generate the table of dose, time dose etc. for model evaluation	setDataForModelEvaluation setDataForModelEvaluation,ModelAnalytic-method setDataForModelEvaluation,ModelAnalyticInfusion-method setDataForModelEvaluation,ModelAnalyticInfusionSteadyState-method setDataForModelEvaluation,ModelAnalyticSteadyState-method setDataForModelEvaluation,ModelODEBolus-method setDataForModelEvaluation,ModelODEDoseInEquations-method setDataForModelEvaluation,ModelODEDoseNotInEquations-method setDataForModelEvaluation,ModelODEInfusionDoseInEquations-method
Set the derivatives of the model error equation.	setDerivatives setDerivatives,ModelError-method
Set the description of a model.	setDescription setDescription,Model-method
Set the designs.	setDesigns setDesigns,Optimization-method
Set the distribution.	setDistribution setDistribution,ModelParameter-method
Set the amount of dose	setDose setDose,Administration-method
Set the equation of a model error.	setEquation setEquation,ModelError-method
Set the equations of a model.	setEquations setEquations,Model-method
Set the equations after infusion.	setEquationsAfterInfusion setEquationsAfterInfusion,Model-method
Set the equations during infusion.	setEquationsDuringInfusion setEquationsDuringInfusion,Model-method
Set the evaluation results.	setEvaluationFIMResults setEvaluationFIMResults,Optimization-method
Set the evaluation results of the initial design.	setEvaluationInitialDesignResults setEvaluationInitialDesignResults,Optimization-method
setFim	setFim setFim,Design-method
Convert the type of the object fim to a string.	setFimTypeToString setFimTypeToString,Fim-method
Set the FIM.	setFisherMatrix setFisherMatrix,Fim-method
Set the fixed effects.	setFixedEffects setFixedEffects,Fim-method
Set the mu as fixed or not.	setFixedMu setFixedMu,ModelParameter-method
Set the omega as fixed of not.	setFixedOmega setFixedOmega,ModelParameter-method
setInitialConditions	setInitialConditions setInitialConditions,Arm-method setInitialConditions,Model-method
Set the iteration with the convergence criteria.	setIterationAndCriteria setIterationAndCriteria,OptimizationAlgorithm-method
Set the model.	setModel setModel,PFIMProject-method
Set the model error.	setModelError setModelError,Model-method
Set a model from the library of model	setModelFromLibrary setModelFromLibrary,Model-method
Set the value of the fixed effect mu of an object.	setMu setMu,Distribution-method setMu,ModelParameter-method
Set the name of an object.	setName setName,Arm-method setName,Design-method setName,Model-method
setNumberOfArms	setNumberOfArms setNumberOfArms,Design-method
Set the parameters of the ode solver.	setOdeSolverParameters setOdeSolverParameters,Model-method
Set the matrix omega of an object.	setOmega setOmega,Distribution-method setOmega,ModelParameter-method
Set the optimal design.	setOptimalDesign setOptimalDesign,OptimizationAlgorithm-method
Set the optimal weights.	setOptimalWeights setOptimalWeights,MultiplicativeAlgorithm-method
Set the optimization results.	setOptimizationResults setOptimizationResults,Optimization-method
setOutcome	setOutcome setOutcome,Administration-method setOutcome,SamplingTimes-method
Set the outcomes of a model.	setOutcomes setOutcomes,Model-method
setOutcomesEvaluation	setOutcomesEvaluation setOutcomesEvaluation,Design-method
Set the outcomes of a model used for the evaluation (is scales outcomes).	setOutcomesForEvaluation setOutcomesForEvaluation,Model-method
setOutcomesGradient	setOutcomesGradient setOutcomesGradient,Design-method
Set the parameters of an object.	setParameters setParameters,Distribution-method setParameters,FedorovWynnAlgorithm-method setParameters,Model-method setParameters,MultiplicativeAlgorithm-method setParameters,PGBOAlgorithm-method setParameters,PSOAlgorithm-method setParameters,SimplexAlgorithm-method
setSamplingConstraintForOptimization	setSamplingConstraintForOptimization setSamplingConstraintForOptimization,Design-method
Set the sampling times.	setSamplings setSamplings,SamplingTimes-method
setSamplingTime	setSamplingTime setSamplingTime,Arm-method
setSamplingTimes	setSamplingTimes setSamplingTimes,Arm-method
setSamplingTimesConstraints	setSamplingTimesConstraints setSamplingTimesConstraints,Arm-method
Set the shrinkage.	setShrinkage setShrinkage,BayesianFim-method setShrinkage,IndividualFim-method setShrinkage,PopulationFim-method
Set the parameter sigma inter.	setSigmaInter setSigmaInter,ModelError-method
Set the parameter sigma slope.	setSigmaSlope setSigmaSlope,ModelError-method
setSize	setSize setSize,Arm-method setSize,Design-method
setTau	setTau setTau,Administration-method
setTimeDose	setTimeDose setTimeDose,Administration-method
Set the infusion duration.	setTinf setTinf,Administration-method
Set the matrix of the variance effects.	setVarianceEffects setVarianceEffects,Fim-method
show	show,Design-method show,Evaluation-method show,FedorovWynnAlgorithm-method show,MultiplicativeAlgorithm-method show,Optimization-method show,PGBOAlgorithm-method show,PSOAlgorithm-method show,SimplexAlgorithm-method
Class "SimplexAlgorithm"	SimplexAlgorithm SimplexAlgorithm-class