Package: PFIM 6.1
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:
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.
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:addModeladdModelsAdministrationAdministrationConstraintsArmBayesianFimcheckSamplingTimeConstraintsForContinuousOptimizationcheckValiditySamplingConstraintCombined1computeVMatConstantconvertPKModelAnalyticToPKModelODEdataForArmEvaluationdefineModeldefineModelEquationsFromStringToFunctiondefineModelFromLibraryOfModelsdefineModelTypedefineModelUserDefineddefinePKModeldefinePKPDModelDesignDistributionEvaluateArmEvaluateDesignEvaluateErrorModelDerivativesEvaluateFisherMatrixEvaluateModelEvaluateModelGradientEvaluateVarianceFIMEvaluateVarianceModelEvaluationFedorovWynnAlgorithmFedorovWynnAlgorithm_RcppFimfisher.simplexfun.amoebagenerateFimsFromConstraintsgenerateReportEvaluationgenerateReportOptimizationgenerateSamplingsFromSamplingConstraintsgenerateTablesgetAdjustedGradientgetAdministrationgetAdministrationConstraintgetAdministrationsgetAdministrationsConstraintsgetArmsgetcErrorgetColumnAndParametersNamesFIMgetColumnAndParametersNamesFIMInLatexgetConditionNumberFixedEffectsgetConditionNumberVarianceEffectsgetContentgetCorrelationMatrixgetDataForArmEvaluationgetDataFrameResultsgetDcriteriongetDeltagetDerivativesgetDescriptiongetDesignsgetDeterminantgetDistributiongetDosegetEigenValuesgetElementaryProtocolsgetEquationgetEquationsgetEquationsAfterInfusiongetEquationsDuringInfusiongetEvaluationFIMResultsgetEvaluationInitialDesignResultsgetFimgetFisherMatrixgetFixedEffectsgetFixedMugetFixedOmegagetFixedParametersgetFixedTimesgetInitialConditionsgetIterationAndCriteriagetLambdagetLibraryPDModelsgetLibraryPKModelsgetMinSamplinggetModelgetModelEquationsgetModelErrorgetModelErrorParametersValuesgetModelFromLibrarygetModelParametersgetModelParametersValuesgetMugetNamegetNamesgetNumberOfArmsgetNumberOfIterationsgetNumberOfParametersgetNumberOfsamplingsOptimisablegetNumberOfTimesByWindowsgetOdeSolverParametersgetOmegagetOptimalDesigngetOptimalFrequenciesgetOptimalWeightsgetOptimizationResultsgetOptimizergetOptimizerParametersgetOutcomegetOutcomesgetOutcomesEvaluationgetOutcomesForEvaluationgetOutcomesGradientgetParametersgetPDModelgetPKModelgetPKPDModelgetPlotOptionsgetProportionsOfSubjectsgetRSEgetSamplingsgetSamplingsWindowsgetSamplingTimegetSamplingTimeConstraintgetSamplingTimesgetSamplingTimesConstraintsgetSEgetShrinkagegetSigmaIntergetSigmaSlopegetSizegetTaugetTimeDosegetTinfgetVariablesgetVarianceEffectsgetWeightThresholdIndividualFiminitializeisDoseInEquationsisModelAnalyticisModelBolusisModelInfusionisModelODEisModelSteadyStateLibraryOfModelsLibraryOfPDModelsLibraryOfPKModelsLibraryOfPKPDModelsLogNormalModelModelAnalyticModelAnalyticBolusModelAnalyticBolusSteadyStateModelAnalyticInfusionModelAnalyticInfusionSteadyStateModelAnalyticSteadyStateModelBolusModelErrorModelInfusionModelODEModelODEBolusModelODEDoseInEquationsModelODEDoseNotInEquationsModelODEInfusionModelODEInfusionDoseInEquationsModelParameterMultiplicativeAlgorithmMultiplicativeAlgorithm_RcppNormalOptimizationOptimizationAlgorithmoptimizeparametersForComputingGradientPFIMProjectPGBOAlgorithmplotEvaluationPlotEvaluationplotFrequenciesplotOutcomesEvaluationplotOutcomesGradientplotRSEplotSEplotSensitivityIndiceplotShrinkageplotWeightsPopulationFimProportionalPSOAlgorithmReportreportTablesAdministrationreportTablesDesignreportTablesFIMreportTablesModelErrorreportTablesModelParametersreportTablesPlotreportTablesSamplingConstraintsrunSamplingTimeConstraintsSamplingTimessetAdministrationssetArmsetArmssetcErrorsetContentsetDataForArmEvaluationsetDataForModelEvaluationsetDerivativessetDescriptionsetDesignssetDistributionsetDosesetEquationsetEquationssetEquationsAfterInfusionsetEquationsDuringInfusionsetEvaluationFIMResultssetEvaluationInitialDesignResultssetFimsetFimTypeToStringsetFisherMatrixsetFixedEffectssetFixedMusetFixedOmegasetInitialConditionssetIterationAndCriteriasetModelsetModelErrorsetModelFromLibrarysetMusetNamesetNumberOfArmssetOdeSolverParameterssetOmegasetOptimalDesignsetOptimalWeightssetOptimizationResultssetOutcomesetOutcomessetOutcomesEvaluationsetOutcomesForEvaluationsetOutcomesGradientsetParameterssetSamplingConstraintForOptimizationsetSamplingssetSamplingTimesetSamplingTimessetSamplingTimesConstraintssetShrinkagesetSigmaIntersetSigmaSlopesetSizesetTausetTimeDosesetTinfsetVarianceEffectsshowSimplexAlgorithm
Dependencies:askpassbase64encbrewbriobslibcachemcallrclicliprcolorspacecommonmarkcpp11crayoncredentialscurlDerivdescdeSolvedevtoolsdiffobjdigestdownlitellipsisevaluatefansifarverfastmapfontawesomefsgertggplot2ghgitcredsgluegtablehighrhtmltoolshtmlwidgetshttpuvhttr2iniinlineisobandjquerylibjsonlitekableExtraknitrlabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimeminiUImunsellnlmeopensslpillarpkgbuildpkgconfigpkgdownpkgloadpracmapraiseprettyunitsprocessxprofvispromisespspurrrR6raggrappdirsrcmdcheckRColorBrewerRcpprematch2remotesrlangrmarkdownroxygen2rprojrootrstudioapirversionssassscalessessioninfoshinysourcetoolsstringistringrsvglitesyssystemfontstestthattextshapingtibbletinytexurlcheckerusethisutf8vctrsviridisLitewaldowhiskerwithrxfunxml2xopenxtableyamlzip
Design evaluation and optimization in continuous space
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on Oct 24 2024.Last update: 2024-03-24
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Design evaluation and optimization in discrete space
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Library of models
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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 |