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Description of the R functions associated to the settings

Description of the functions of the API

 getConditionalDistributionSamplingSettings Get the conditional distribution sampling settings. getConditionalModeEstimationSettings Get the conditional mode estimation settings. getConsoleMode . getGeneralSettings Get a summary of the common settings for Monolix algorithms. getLogLikelihoodEstimationSettings Get the loglikelihood estimation settings. getMCMCSettings Get the MCMC algorithm settings of the current project. getPopulationParameterEstimationSettings Get the population parameter estimation settings. getStandardErrorEstimationSettings Get the standard error estimation settings. setConditionalDistributionSamplingSettings Set the value of one or several of the conditional distribution sampling settings. setConditionalModeEstimationSettings Set the value of one or several of the conditional mode estimation settings. setConsoleMode . setGeneralSettings Set the value of one or several of the common settings for Monolix algorithms. setLogLikelihoodEstimationSettings Set the value of the loglikelihood estimation settings. setMCMCSettings Set the value of one or several of the MCMC algorithm specific settings of the current project. setPopulationParameterEstimationSettings Set the value of one or several of the population parameter estimation settings. setStandardErrorEstimationSettings Set the value of one or several of the standard error estimation settings. getPreferences Get a summary of the project preferences. getProjectSettings Get a summary of the project settings. setPreferences Set the value of one or several of the project preferences. setProjectSettings Set the value of one or several of the settings of the project.

[Monolix] Get conditional distribution sampling settings

Description

Get the conditional distribution sampling settings. Associated settings are:

 “ratio” (0< double <1) Width of the confidence interval. “enableMaxIterations” (bool) Enable maximum of iterations. “nbMinIterations” (int >=1) Minimum number of iterations. “nbMaxIterations” (int >=1) Maximum number of iterations. “nbSimulatedParameters” (int >=1) Number of replicates.

Usage

getConditionalDistributionSamplingSettings(...)


Arguments

 ... [optional] (string) Name of the settings whose value should be displayed. If no argument is provided, all the settings are returned.

Value

An array which associates each setting name to its current value.

 setConditionalDistributionSamplingSettings

getConditionalDistributionSamplingSettings()

# retrieve all the conditional distribution sampling settings

getConditionalDistributionSamplingSettings(“ratio”,”nbMinIterations”)

# retrieve only the ratio and nbMinIterations settings values

## End(Not run)

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[Monolix] Get conditional mode estimation settings

Description

Get the conditional mode estimation settings. Associated settings are:

 “nbOptimizationIterationsMode” (int >=1) Maximum number of iterations. “optimizationToleranceMode” (double >0) Optimization tolerance.

Usage

getConditionalModeEstimationSettings(...)


Arguments

 ... [optional] (string) Name of the settings whose value should be displayed. If no argument is provided, all the settings are returned.

Value

An array which associates each setting name to its current value.

 setConditionalModeEstimationSettings

getConditionalModeEstimationSettings()

# retrieve a list of all the conditional mode estimation settings

getConditionalModeEstimationSettings(“nbOptimizationIterationsMode”)

# retrieve only the nbOptimizationIterationsMode setting value

## End(Not run)

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[Monolix] Get console mode

Description

Get console mode, ie current verbosity level:

 “none” no output “basic” at each algorithm end, associated results are displayed “complete” each algorithm iteration and/or status is displayed

Usage

getConsoleMode()


Value

A string corresponding to current console mode

setConsoleMode

[Monolix] Get project general settings

Description

Get a summary of the common settings for Monolix algorithms. Associated settings are:

 “autoChains” (bool) Automatically adjusted the number of chains to have at least a minimum number of subjects. “nbChains” (int >0) Number of chains. Used only if "autoChains" is set to FALSE. “minIndivForChains” (int >0) Minimum number of individuals by chain.

Usage

getGeneralSettings(...)


Arguments

 ... [optional] (string) Name of the settings whose value should be displayed. If no argument is provided, all the settings are returned.

Value

An array which associates each setting name to its current value.

 setGeneralSettings

getGeneralSettings() # retrieve a list of all the general settings

getGeneralSettings(“nbChains”,”autoChains”)

# retrieve only the nbChains and autoChains settings values.

## End(Not run)

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[Monolix] Get LogLikelihood algorithm settings

Description

Get the loglikelihood estimation settings. Associated settings are:

 “nbFixedIterations” (int >0) Monte Carlo size for the loglikelihood evaluation. “samplingMethod” (string) Should the loglikelihood estimation use a given number of freedom degrees (“fixed”) or test a sequence of degrees of freedom numbers before choosing the best one (“optimized”). “nbFreedomDegrees” (int >0) Degree of freedom of the Student t-distribution. Used only if "samplingMethod" is "fixed". “freedomDegreesSampling” (vector0)>) Sequence of freedom degrees to be tested. Used only if "samplingMethod" is "optimized".

Usage

getLogLikelihoodEstimationSettings(...)


Arguments

 ... [optional] (string) Name of the settings whose value should be displayed. If no argument is provided, all the settings are returned.

Value

An array which associates each setting name to its current value.

 setLogLikelihoodEstimationSettings

getLogLikelihoodEstimationSettings() # retrieve a list of all the loglikelihood estimation settings

getLogLikelihoodEstimationSettings(“nbFixedIterations”,”samplingMethod”)

# retrieve only nbFixedIterations and samplingMethod settings values

## End(Not run)

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[Monolix] Get MCMC algorithm settings

Description

Get the MCMC algorithm settings of the current project. Associated settings are:

 “strategy” (vector[3]) Number of calls for each one of the three MCMC kernels. “acceptanceRatio” (double) Target acceptance ratio.

Usage

getMCMCSettings(...)


Arguments

 ... [optional] (string) Names of the settings whose value should be displayed. If no argument is provided, all the settings are returned.

Value

An array which associates each setting name to its current value.

 setMCMCSettings

getMCMCSettings() # retrieve a list of all the MCMC settings

getMCMCSettings(“strategy”) # retrieve only the strategy setting

## End(Not run)

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[Monolix] Get population parameter estimation settings

Description

Get the population parameter estimation settings. Associated settings are:

 “nbBurningIterations” (int >=0) Number of iterations in the burn-in phase. “nbExploratoryIterations” (int >=0) If “exploratoryAutoStop” is set to FALSE, it is the number of iterations in the exploratory phase. Else wise, if “exploratoryAutoStop” is set to TRUE, it is the maximum of iterations in the exploratory phase. “exploratoryAutoStop” (bool) Should the exploratory step automatically stop. “exploratoryInterval” (int >0) Minimum number of interation in the exploratory phase. Used only if "exploratoryAutoStop" is TRUE “exploratoryAlpha” (0<= double <=1) Convergence memory in the exploratory phase. Used only if "exploratoryAutoStop" is TRUE “nbSmoothingIterations” (int >=0) If “smoothingAutoStop” is set to FALSE, it is the number of iterations in the smoothing phase. Else wise, if “smoothingAutoStop” is set to TRUE, it is the maximum of iterations in the smoothing phase. “smoothingAutoStop” (bool) Should the smoothing step automatically stop. “smoothingInterval” (int >0) inimum number of interation in the smoothing phase. Used only if "smoothingAutoStop" is TRUE. “smoothingAlpha” (0.5< double <=1) Convergence memory in the smoothing phase. Used only if "smoothingAutoStop" is TRUE. “smoothingRatio” (0< double <1) Width of the confidence interval. Used only if "smoothingAutoStop" is TRUE. “simulatedAnnealing” (bool) Should annealing be simulated. “tauOmega” (double >0) Proportional rate on variance. Used only if "simulatedAnnealing" is TRUE. “tauErrorModel” (double >0) Proportional rate on error model. Used only if "simulatedAnnealing" is TRUE. “variability” (string) Estimation method for parameters without variability: “firstStage” | “decreasing” | “none”. Used only if arameters without variability are used in the project. “nbOptimizationIterations” (int >=1) Number of optimization iterations. “optimizationTolerance” (double >0) Tolerance for optimization.

Usage

getPopulationParameterEstimationSettings(...)


Arguments

 ... [optional] (string) Name of the settings whose value should be displayed. If no argument is provided, all the settings are returned.

Value

An array which associates each setting name to its current value.

 setPopulationParameterEstimationSettings

getPopulationParameterEstimationSettings()

# retrieve a list of all the population parameter estimation settings

getPopulationParameterEstimationSettings(“nbBurningIterations”,”smoothingInterval”)

# retrieve only the nbBurningIterations and smoothingInterval settings values

## End(Not run)

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[Monolix] Get standard error estimation settings

Description

Get the standard error estimation settings. Associated settings are:

 “minIterations” (int >=1) Minimum number of iterations. “maxIterations” (int >=1) Maximum number of iterations.

Usage

getStandardErrorEstimationSettings(...)


Arguments

 ... [optional] (string) Name of the settings whose value should be displayed. If no argument is provided, all the settings are returned.

Value

An array which associates each setting name to its current value.

 setStandardErrorEstimationSettings

getStandardErrorEstimationSettings()

# retrieve a list of all the standard error estimation settings

getStandardErrorEstimationSettings(“minIterations”,”maxIterations”)

# retrieve only minIterations and maxIterations settings values

## End(Not run)

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[Monolix] Set conditional distribution sampling settings

Description

Set the value of one or several of the conditional distribution sampling settings. Associated settings are:

 “ratio” (0< double <1) Width of the confidence interval. “enableMaxIterations” (bool) Enable maximum of iterations. “nbMinIterations” (int >=1) Minimum number of iterations. “nbMaxIterations” (int >=1) Maximum number of iterations. “nbSimulatedParameters” (int >=1) Number of replicates.

Usage

setConditionalDistributionSamplingSettings(...)


Arguments

 ... A collection of comma-separated pairs {settingName = settingValue}.

 getConditionalDistributionSamplingSettings

setConditionalDistributionSamplingSettings(ratio = 0.05, nbMinIterations = 50)

## End(Not run)

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[Monolix] Set conditional mode estimation settings

Description

Set the value of one or several of the conditional mode estimation settings. Associated settings are:

 “nbOptimizationIterationsMode” (int >=1) Maximum number of iterations. “optimizationToleranceMode” (double >0) Optimization tolerance.

Usage

setConditionalModeEstimationSettings(...)


Arguments

 ... A collection of comma-separated pairs {settingName = settingValue}.

 getConditionalModeEstimationSettings

setConditionalModeEstimationSettings(nbOptimizationIterationsMode = 20,

optimizationToleranceMode = 0.1)

## End(Not run)

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[Monolix] Set console mode

Description

Set console mode to choose verbosity level:

 “none” no output “basic” for each algorithm, display current iteration then associated results at algorithm end “complete” display all iterations then associated results at algorithm end

Usage

setConsoleMode(mode)


Arguments

 mode (string) Accepted values are: "none" [default], "basic", "complete"

getConsoleMode

[Monolix] Set common settings for algorithms

Description

Set the value of one or several of the common settings for Monolix algorithms. Associated settings are:

 “autoChains” (bool) Automatically adjusted the number of chains to have at least a minimum number of subjects. “nbChains” (int >0) Number of chains to be used if “autoChains” is set to FALSE. “minIndivForChains” (int >0) Minimum number of individuals by chain.

Usage

setGeneralSettings(...)


Arguments

 ... A collection of comma-separated pairs {settingName = settingValue}.

 getGeneralSettings

setGeneralSettings(autoChains = FALSE, nbchains = 10)

## End(Not run)

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[Monolix] Set loglikelihood estimation settings

Description

Set the value of the loglikelihood estimation settings. Associated settings are:

 “nbFixedIterations” (int >0) Monte Carlo size for the loglikelihood evaluation. “samplingMethod” (string) Should the loglikelihood estimation use a given number of freedom degrees (“fixed”) or test a sequence of degrees of freedom numbers before choosing the best one (“optimized”). “nbFreedomDegrees” (int >0) Degree of freedom of the Student t-distribution. Used only if "samplingMethod" is "fixed". “freedomDegreesSampling” (vector0)>) Sequence of freedom degrees to be tested. Used only if "samplingMethod" is "optimized".

Usage

setLogLikelihoodEstimationSettings(...)


Arguments

 ... A collection of comma-separated pairs {settingName = settingValue}.

 getLogLikelihoodEstimationSettings

setLogLikelihoodEstimationSettings(nbFixedIterations = 20000)

## End(Not run)

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[Monolix] Set settings associated to the MCMC algorithm

Description

Set the value of one or several of the MCMC algorithm specific settings of the current project. Associated settings are:

 “strategy” (vector[3]) Number of calls for each one of the three MCMC kernels. “acceptanceRatio” (double) Target acceptance ratio.

Usage

setMCMCSettings(...)


Arguments

 ... A collection of comma-separated pairs {settingName = settingValue}.

 getMCMCSettings

setMCMCSettings(strategy = c(2,1,2))

## End(Not run)

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[Monolix] Set population parameter estimation settings

Description

Set the value of one or several of the population parameter estimation settings. Associated settings are:

 “nbBurningIterations” (int >=0) Number of iterations in the burn-in phase. “nbExploratoryIterations” (int >=0) If “exploratoryAutoStop” is set to FALSE, it is the number of iterations in the exploratory phase. Else wise, if “exploratoryAutoStop” is set to TRUE, it is the maximum of iterations in the exploratory phase. “exploratoryAutoStop” (bool) Should the exploratory step automatically stop. “exploratoryInterval” (int >0) Minimum number of interation in the exploratory phase. Used only if "exploratoryAutoStop" is TRUE “exploratoryAlpha” (0<= double <=1) Convergence memory in the exploratory phase. Used only if "exploratoryAutoStop" is TRUE “nbSmoothingIterations” (int >=0) If “smoothingAutoStop” is set to FALSE, it is the number of iterations in the smoothing phase. Else wise, if “smoothingAutoStop” is set to TRUE, it is the maximum of iterations in the smoothing phase. “smoothingAutoStop” (bool) Should the smoothing step automatically stop. “smoothingInterval” (int >0) Minimum number of interation in the smoothing phase. Used only if "smoothingAutoStop" is TRUE. “smoothingAlpha” (0.5< double <=1) Convergence memory in the smoothing phase. Used only if "smoothingAutoStop" is TRUE. “smoothingRatio” (0< double <1) Width of the confidence interval. Used only if "smoothingAutoStop" is TRUE. “simulatedAnnealing” (bool) Should annealing be simulated. “tauOmega” (double >0) Proportional rate on variance. Used only if "simulatedAnnealing" is TRUE. “tauErrorModel” (double >0) Proportional rate on error model. Used only if "simulatedAnnealing" is TRUE. “variability” (string) Estimation method for parameters without variability: “firstStage” | “decreasing” | “none”. Used only if arameters without variability are used in the project. “nbOptimizationIterations” (int >=1) Number of optimization iterations. “optimizationTolerance” (double >0) Tolerance for optimization.

Usage

setPopulationParameterEstimationSettings(...)


Arguments

 ... A collection of comma-separated pairs {settingName = SettingValue}.

 getPopulationParameterEstimationSettings

setPopulationParameterEstimationSettings(exploratoryAutoStop = TRUE, tauOmega = 0.95)

## End(Not run)

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[Monolix] Set standard error estimation settings

Description

Set the value of one or several of the standard error estimation settings. Associated settings are:

 “minIterations” (int >=1) Minimum number of iterations. “maxIterations” (int >=1) Maximum number of iterations.

Usage

setStandardErrorEstimationSettings(...)


Arguments

 ... A collection of comma-separated pairs {settingName = settingValue}.

 getStandardErrorEstimationSettings

setStandardErrorEstimationSettings(minIterations = 20, maxIterations = 250)

## End(Not run)

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[Monolix – PKanalix – Simulx] Get project preferences

Description

Get a summary of the project preferences. Preferences are:

 “relativepath” (bool) Use relative path for save/load operations. “threads” (int >0) Number of threads. “timestamping” (bool) Create an archive containing result files after each run. “delimiter” (string) Character use as delimiter in exported result files. “exportchartsData” (bool) Should graphics data be exported. “exportsimulationfiles” (bool) [Simulx] Should simulation results files be exported. “headeraliases” (list("header" = vector)) For each header, the list of the recognized aliases. “ncaparameters” (vector) [PKanalix] Defaulty computed NCA parameters.

Usage

getPreferences(...)


Arguments

 ... [optional] (string) Name of the preference whose value should be displayed. If no argument is provided, all the preferences are returned.

Value

An array which associates each preference name to its current value.

getPreferences() # retrieve a list of all the general settings

getPreferences(“imageFormat”,”exportCharts”)

# retrieve only the imageFormat and exportCharts settings values

## End(Not run)

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[Monolix – PKanalix – Simulx] Get project settings

Description

Get a summary of the project settings.
Associated settings for Monolix projects are:

 “directory” (string) Path to the folder where simulation results will be saved. It should be a writable directory. “exportResults” (bool) Should results be exported. “seed” (0< int <2147483647) Seed used by random generators. “grid” (int) Number of points for the continuous simulation grid. “nbSimulations” (int) Number of simulations. “dataAndModelNextToProject” (bool) Should data and model files be saved next to project.

Associated settings for PKanalix projects are:

 “directory” (string) Path to the folder where simulation results will be saved. It should be a writable directory. “dataNextToProject” (bool) Should data files be saved next to project.

Associated settings for Simulx projects are:

 “directory” (string) Path to the folder where simulation results will be saved. It should be a writable directory. “seed” (0< int <2147483647) Seed used by random generators. “userfilesnexttoproject” (bool) Should user files be saved next to project.

Usage

getProjectSettings(...)


Arguments

 ... [optional] (string) Name of the settings whose value should be displayed. If no argument is provided, all the settings are returned.

Value

An array which associates each setting name to its current value.

 getProjectSettings

getProjectSettings() # retrieve a list of all the project settings

getProjectSettings(“directory”,”seed”)

# retrieve only the directopry and the seed settings values

## End(Not run)

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[Monolix – PKanalix – Simulx] Set preferences

Description

Set the value of one or several of the project preferences. Prefenreces are:

 “relativepath” (bool) Use relative path for save/load operations. “threads” (int >0) Number of threads. “timestamping” (bool) Create an archive containing result files after each run. “delimiter” (string) Character use as delimiter in exported result files. “exportchartsData” (bool) Should graphics data be exported. “exportsimulationfiles” (bool) [Simulx] Should simulation results files be exported. “headeraliases” (list("header" = vector)) For each header, the list of the recognized aliases. “ncaparameters” (vector) [PKanalix] Defaulty computed NCA parameters.

Usage

setPreferences(...)


Arguments

 ... A collection of comma-separated pairs {preferenceName = settingValue}.

 getPreferences

setPreferences(exportCharts = FALSE, delimiter = “,”)

## End(Not run)

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[Monolix – PKanalix – Simulx] Set project settings

Description

Set the value of one or several of the settings of the project.
Associated settings for Monolix projects are:

 “directory” (string) Path to the folder where simulation results will be saved. It should be a writable directory. “exportResults” (bool) Should results be exported. “seed” (0< int <2147483647) Seed used by random generators. “grid” (int) Number of points for the continuous simulation grid. “nbSimulations” (int) Number of simulations. “dataAndModelNextToProject” (bool) Should data and model files be saved next to project.

Associated settings for PKanalix projects are:

 “directory” (string) Path to the folder where simulation results will be saved. It should be a writable directory. “dataNextToProject” (bool) Should data files be saved next to project.

Associated settings for Simulx projects are:

 “directory” (string) Path to the folder where simulation results will be saved. It should be a writable directory. “seed” (0< int <2147483647) Seed used by random generators. “userfilesnexttoproject” (bool) Should user files be saved next to project.

Usage

setProjectSettings(...)


Arguments

 ... A collection of comma-separated pairs {settingName = settingValue}.

 getProjectSettings