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Description of the R functions associated to the results

Description of the functions of the API

 getCorrelationOfEstimates Get the inverse of the last estimated Fisher matrix computed either by all the Fisher methods used during the last scenario run or by the specific one passed in argument. getEstimatedIndividualParameters Get the last estimated values for each subject of some of the individual parameters present within the current project. getEstimatedLogLikelihood Get the values computed by using a log-likelihood algorithm during the last scenario run, with or without a method-based filter. getEstimatedPopulationParameters Get the last estimated value of some of the population parameters present within the current project (fixed effects + individual variances + correlations + latent probabilities + error model parameters). getEstimatedRandomEffects Get the random effects for each subject of some of the individual parameters present within the current project. getEstimatedStandardErrors Get the last estimated standard errors of population parameters computed either by all the Fisher methods used during the last scenario run or by the specific one passed in argument. getLaunchedTasks Get a list of the tasks which have results to provide. getSAEMiterations Retrieve the successive values of some of the population parameters present within the current project (fixed effects + individual variances + correlations + latent probabilities + error model parameters) during the previous run of the SAEM algorithm. getSimulatedIndividualParameters Get the simulated values for each replicate of each subject of some of the individual parameters present within the current project. getSimulatedRandomEffects Get the simulated values for each replicate of each subject of some of the individual random effects present within the current project. getTests Get the results of performed statistical tests.

[Monolix] Get the inverse of the Fisher Matrix

Description

Get the inverse of the last estimated Fisher matrix computed either by all the Fisher methods used during the last scenario run or by the specific one passed in argument.
WARNING: The Fisher matrix cannot be accessible until the Fisher algorithm has been launched once.
The user can choose to display only the Fisher matrix estimated with a specific method.
Existing Fisher methods :

 Fisher by Linearization “linearization” Fisher by Stochastic Approximation “stochasticApproximation”

WARNING: Only the methods which have been used during the last scenario run can provide results.

Usage

getCorrelationOfEstimates(method = "")


Arguments

 method [optional](string) Fisher method whose results should be displayed. If this field is not specified, the results provided by all the methods used during the last scenario run are displayed.

Value

A list whose each field contains the Fisher matrix computed by one of the available Fisher methods used during the ast scenario run.
A matrix is defined as a structure containing the following fields :

 rownames list of row names columnnames list of column names rownumber number of rows data vector<…> containing matrix raw values (column major)

getCorrelationOfEstimates(“linearization”)

-> list( linearization = list(data = c(1,0,0,0,1,-0.06,0,-0.06,1),

rownumber = 3,

rownames = c(“Cl_pop”,”omega_Cl”,”a”),

columnnames = c(“Cl_pop”,”omega_Cl”,”a”)))

getCorrelationOfEstimates()

-> list(linearization = list(…), stochasticApproximation = list(…) )

## End(Not run)

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[Monolix] Get last estimated individual parameter values

Description

Get the last estimated values for each subject of some of the individual parameters present within the current project.
WARNING: Estimated individual parameters values cannot be accessible until the individual estimation algorithm has been launched once.
NOTE: The user can choose to display only the individual parameter values estimated with a specific method.
Existing individual estimation methods :

 Conditional Mean SAEM “saem” Conditional Mean “conditionalMean” Conditional Mode “conditionalMode”

WARNING: Only the methods which have been used during the last scenario run can provide estimation results.

Usage

getEstimatedIndividualParameters(..., method = "")


Arguments

 ... (string) Name of the individual parameters whose values must be displayed. Call getIndividualParameterModel to get a list of the individual parameters present within the current project. method [optional](string) Individual parameter estimation method whose results should be displayed. If there are latent covariate used in the model, the estimated modality is displayed too If this field is not specified, the results provided by all the methods used during the last scenario run are displayed.

Value

A data frame giving, for each wanted method, the last estimated values of the individual parameters of interest for each subject with the corresponding standard deviation values.

 getEstimatedRandomEffects

indivParams = getEstimatedIndividualParameters()

# retrieve the values of all the available individual parameters for all methods

-> $saem id Cl V ka 1 0.28 7.71 0.29 . … … … N 0.1047.62 1.51 indivParams = getEstimatedIndividualParameters(“Cl”, “V”, method = “conditionalMean”) # retrieve the values of the individual parameters “Cl” and “V” # estimated by the conditional mode method ## End(Not run) Top of the page, PKanalix API, Monolix API, Simulx API. [Monolix] Get Log-Likelihood values Description Get the values computed by using a log-likelihood algorithm during the last scenario run, with or without a method-based filter. WARNING: The log-likelihood values cannot be accessible until the log-likelihood algorithm has been launched once. The user can choose to display only the log-likelihood values computed with a specific method. Existing log-likelihood methods :  Log-likelihood by Linearization “linearization” Log-likelihood by Important Sampling “importanceSampling” WARNING: Only the methods which have been used during the last scenario run can provide results. Usage getEstimatedLogLikelihood(method = "")  Arguments  method [optional](string) Log-likelihood method whose results should be displayed. If this field is not specified, the results provided by all the methods used during the last scenario run are retrieved. Value A list associating the name of each method passed in argument to the corresponding log-likelihood values computed by during the last scenario run. Click here to see examples getEstimatedLogLikelihood() -> list( linearization = [LL = -170.505, AIC = 350.280, BIC = 365.335] , importanceSampling = […] ) getEstimatedLogLikelihood(“linearization”) -> list( linearization = [LL = -170.505, AIC = 350.280, BIC = 365.335] ) ## End(Not run) Top of the page, PKanalix API, Monolix API, Simulx API. [Monolix] Get last estimated population parameter value Description Get the last estimated value of some of the population parameters present within the current project (fixed effects + individual variances + correlations + latent probabilities + error model parameters). WARNING: Estimated population parameters values cannot be accessible until the SAEM algorithm has been launched once. Usage getEstimatedPopulationParameters(...)  Arguments  ... [optional] (array) Names of the population parameters whose value must be displayed. Call getPopulationParameterInformation to get a list of the population parameters present within the current project. If this field is not specified, the function will retrieve the values of all the available population parameters. Value A named vector containing the last estimated value of each one of the population parameters passed in argument. Click here to see examples getEstimatedPopulationParameters(“V_pop”) -> [V_pop = 0.5] getEstimatedPopulationParameters(“V_pop”,”Cl_pop”) -> [V_pop = 0.5, Cl_pop = 0.25] getEstimatedPopulationParameters() -> [V_pop = 0.5, Cl_pop = 0.25, ka_pop = 0.05] ## End(Not run) Top of the page, PKanalix API, Monolix API, Simulx API. [Monolix] Get estimated the random effects Description Get the random effects for each subject of some of the individual parameters present within the current project. WARNING: Estimated random effects cannot be accessible until the individual estimation algorithm has been launched once. The user can choose to display only the random effects estimated with a specific method. NOTE: The random effects are defined in the gaussian referential, e.g. if ka is lognormally distributed around ka_pop, eta_i = log(ka_i)-log(ka_pop) Existing individual estimation methods :  Conditional Mean SAEM “saem” Conditional Mean “conditionalMean” Conditional Mode “conditionalMode” WARNING: Only the methods which have been used during the last scenario run can provide estimation results. Please call  getLaunchedTasks to get a list of the methods whose results are available. Usage getEstimatedRandomEffects(..., method = "")  Arguments  ... (string) Name of the individual parameters whose random effects must be displayed. Call getIndividualParameterModel to get a list of the individual parameters present within the current project. method [optional](string) Individual parameter estimation method whose results should be displayed. If this field is not specified, the results provided by all the methods used during the last scenario run are displayed. Value A data frame giving, for each wanted method, the last estimated eta values of the individual parameters of interest for each subject with the corresponding standard deviation values. See Also  getEstimatedIndividualParameters Click here to see examples etaParams = getEstimatedRandomEffects() # retrieve the values of all the available random effects for all methods # without the associated standard deviations ->$saem

id Cl V ka

1 0.28 7.71 0.29

. … … …

N 0.1047.62 1.51

etaParams = getEstimatedRandomEffects(“Cl”, “V”, method = “conditionalMode”)

# retrieve the values of the individual parameters “Cl” and “V”

# estimated by the conditional mean from SAEM algorithm

## End(Not run)

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[Monolix] Get standard errors of population parameters

Description

Get the last estimated standard errors of population parameters computed either by all the Fisher methods used during the last scenario run or by the specific one passed in argument.
WARNING: The standard errors cannot be accessible until the Fisher algorithm has been launched once.
Existing Fisher methods :

 Fisher by Linearization “linearization” Fisher by Stochastic Approximation “stochasticApproximation”

WARNING: Only the methods which have been used during the last scenario run can provide results.

Usage

getEstimatedStandardErrors(method = "")


Arguments

 method [optional](string) Fisher method whose results should be displayed. If this field is not specified, the results provided by all the methods used during the last scenario run are retrieved

Value

A list associating each retrieved Fisher algorithm method to a data frame containing the standard errors and relative standard errors (

getEstimatedStandardErrors() ->

$linearization parameter se rse ka_pop 0.313449586 20.451556 V_pop 0.020422507 4.483500 omega_V 0.037975960 30.072470 omega_Cl 0.062976601 23.270939$stochasticApproximation

parameter se rse

ka_pop 0.311284296 20.310278

V_pop 0.020424882 4.484022

omega_V 0.161053665 24.000077

omega_Cl 0.035113095 27.805419

## End(Not run)

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Description

Get a list of the tasks which have results to provide. A task is the association of:

• an algorithm (string)
• a vector of methods (string) relative to this algorithm for the standardErrorEstimation and the loglikelihoodEstimation, TRUE or FALSE for the other one.

Usage

getLaunchedTasks()


Value

The list of tasks with results, indexed by algorithm names.

-> $populationParameterEstimation = TRUE$conditionalModeEstimation = TRUE

$standardErrorEstimation = “linearization” ## End(Not run) Top of the page, PKanalix API, Monolix API, Simulx API. [Monolix] Get SAEM algorithm iterations Description Retrieve the successive values of some of the population parameters present within the current project (fixed effects + individual variances + correlations + latent probabilities + error model parameters) during the previous run of the SAEM algorithm. WARNING: Convergence history of population parameters values cannot be accessible until the SAEM algorithm has been launched once. Usage getSAEMiterations(...)  Arguments  ... [optional] (array) Names of the population parameters whose convergence history must be displayed. Call getPopulationParameterInformation to get a list of the population parameters present within the current project. If this field is not specified, the function will retrieve the values of all the available population parameters. Value A list containing a pair composed by the number of exploratory and smoothing iterations and a data frame which associates each wanted population parameter to its successive values over SAEM algorithm iterations. Click here to see examples report = getSAEMiterations() report ->$iterationNumbers

c(50,25)

\$estimates

V Cl

0.25 0

0.3 0.5

. .

0.35 0.25

## End(Not run)

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[Monolix] Get simulated individual parameters

Description

Get the simulated values for each replicate of each subject of some of the individual parameters present within the current project.
WARNING: Simulated individual parameters values cannot be accessible until the individual estimation with conditional mean algorithm has been launched once.

Usage

getSimulatedIndividualParameters(...)


Arguments

 ... (string) Name of the individual parameters whose values must be displayed. Call getIndividualParameterModel to get a list of the individual parameters present within the current project.

Value

A list giving the last simulated values of the individual parameters of interest for each replicate of each subject.

 getSimulatedRandomEffects

simParams = getSimulatedIndividualParameters()

# retrieve the values of all the available individual parameters

simParams

rep id Cl V ka

1 1 0.022 0.37 1.79

1 2 0.033 0.42 -0.92

. . … … …

2 1 0.021 0.33 1.47

. . … … …

## End(Not run)

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[Monolix] Get simulated random effects

Description

Get the simulated values for each replicate of each subject of some of the individual random effects present within the current project.
WARNING: Simulated individual random effects values cannot be accessible until the individual estimation algorithm with conditional mean has been launched once.

Usage

getSimulatedRandomEffects(...)


Arguments

 ... (string) Name of the individual parameters whose values must be displayed. Call getIndividualParameterModel to get a list of the individual parameters present within the current project.

Value

A list giving the last simulated values of the individual random effects of interest for each replicate of each subject.

getIndividualParameterModel

simEtas = getSimulatedRandomEffects()

# retrieve the values of all the available individual random effects

simEtas

rep id Cl V ka

1 1 0.022 0.37 1.79

1 2 0.033 0.42 -0.92

. . … … …

2 1 0.021 0.33 1.47

. . … … …

## End(Not run)

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[Monolix] Get statistical tests results

Description

Get the results of performed statistical tests.
Existing tests: Wald, Individual parameters normality, individual parameters marginal distribution, random effects normality,
random effects correlation, individual parameters vs covariates correlation, random effects vs covariates correlation,
residual normality and residual symmetry.
WARNING: Only the tests performed during the last scenario run can provide results.

Usage

getTests()


Value

A list associating the name of the test to the corresponding results values computed during the last scenario run.