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# Description of the R functions associated to PKanalix settings

 getCASettings Get the settings associated to the compartmental analysis. getDataSettings Get the data settings associated to the non compartmental analysis. getGlobalObsIdToUse Get the global observation id used in both the compartmental and non compartmental analysis. getNCASettings Get the settings associated to the non compartmental analysis. setCASettings Get the settings associated to the compartmental analysis. setDataSettings Set the value of one or several of the data settings associated to the non compartmental analysis. setGlobalObsIdToUse Get the global observation id used in both the compartmental and non compartmental analysis. setNCASettings Set the value of one or several of the settings associated to the non compartmental analysis.

## Get the settings associated to the compartmental analysis

### Description

Get the settings associated to the compartmental analysis. Associated settings are:

 “weightingCA” (string) Type of weighting objective function. “pool” (logical) Fit with individual parameters or with the same parameters for all individuals. “initialValues” (list) list(param = value, …) value = initial value of individual parameter param. “blqMethod” (string) Method by which the BLQ data should be replaced.

### Usage

getCASettings(...)


### 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.

### See Also

 setCASettings

### Click here to see examples

## Not run:

getCASettings() # retrieve a list of all the CA methodology settings

getCASettings(“weightingca”,”blqmethod”) # retrieve a list containing only the value of the settings whose name has been passed in argument

## End(Not run)

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## Get the data settings associated to the non compartmental analysis

### Description

Get the data settings associated to the non compartmental analysis. Associated settings are:

 “urinevolume” (string) regressor name used as urine volume. “datatype” (list) list(“obsId” = string(“plasma” or “urine”). The type of data associated with each obsId: observation ID from data set.

### Usage

getDataSettings(...)


### 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.

### See Also

 setNCASettings

### Click here to see examples

## Not run:

getDataSettings() # retrieve a list of all the NCA methodology settings

getDataSettings(“urinevolume”) # retrieve a list containing only the value of the settings whose name has been passed in argument

## End(Not run)

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## Get the global observation id used in both the compartmental and non compartmental analysis

### Description

Get the global observation id used in both the compartmental and non compartmental analysis.

### Usage

getGlobalObsIdToUse(...)


### Value

the observation id used in computations.

### See Also

 setGlobalObsIdToUse

### Click here to see examples

## Not run:

getGlobalObsIdToUse() #

## End(Not run)

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## Get the settings associated to the non compartmental analysis

### Description

Get the settings associated to the non compartmental analysis. Associated settings are:

 “administrationType” (list) list(key = “admId”, value = string(“intravenous” or “extravascular”)). admId Admninistration ID from data set or 1 if no admId column in the dataset. “integralMethod” (string) Method for AUC and AUMC calculation and interpolation. “linTrapLinInterp” = Linear trapezoidal linear, “linLogTrapLinLogInterp” = Linear log trapezoidal, “upDownTrapUpDownInterp” = Linear up log down, “linTrapLinLogInterp” = Linear trapezoidal linear/log. “partialAucTime” (list) The first element of the list is a bolean describing if this setting is used. The second element of the list is the value of the bounds of the partial AUC calculation interval. “blqMethodBeforeTmax” (string) Method by which the BLQ data before Tmax should be replaced. “blqMethodAfterTmax” (string) Method by which the BLQ data after Tmax should be replaced. “ajdr2AcceptanceCriteria” (list) The first element of the list is a boolean describing if this setting is used. The second element of the list is the value of the adjusted R2 acceptance criteria for the estimation of lambda_Z. “extrapAucAcceptanceCriteria” (list) The first element of the list is a boolean describing if this setting is used. The second element of the list is the value of the AUC extrapolation acceptance criteria for the estimation of lambda_Z. “spanAcceptanceCriteria” (list) The first element of the list is a boolean describing if this setting is used. The second element of the list is the value of the span acceptance criteria for the estimation of lambda_Z. “lambdaRule” (string) Main rule for the lambda_Z estimation. “timeInterval” (vector) Time interval for the lambda_Z estimation when “lambdaRule” = “interval”. “timeValuesPerId” (list) list(“idName” = idTimes,…): idTimes Observation times to use for the calculation of lambda_Z for the id idName. “nbPoints” (integer) Number of points for the lambda_Z estimation when “lambdaRule” = “points”. “maxNbOfPoints” (list) The first element of the list is a boolean describing if this setting is used. The second element of the list is the value maximum number of points to use for the lambda_Z estimation when “lambdaRule” = “R2” or “adjustedR2”. “startTimeNotBefore” (list) The first element of the list is a boolean describing if this setting is used. The second element of the list is the value minimum time value to use for the lambda_Z estimation when “lambdaRule” = “R2” or “adjustedR2”. “weightingNCA” (string) Weighting method used for the regression that estimates lambda_Z.

### Usage

getNCASettings(...)


### 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.

### See Also

 setNCASettings

### Click here to see examples

## Not run:

getNCASettings() # retrieve a list of all the NCA methodology settings

getNCASettings(“lambdaRule”,”integralMethod”) # retrieve a list containing only the value of the settings whose name has been passed in argument

## End(Not run)

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## Set the settings associated to the compartmental analysis

### Description

Get the settings associated to the compartmental analysis. Associated settings names are:

 “weightingCA” (string) Type of weighting objective function. Possible methods are “uniform”, “Yobs”, “Ypred”, “Ypred2” or “Yobs2” (default). “pool” (logical) If TRUE, fit with individual parameters or with the same parameters for all individuals if FALSE. FALSE (default). “initialValues” (list) list(param = value, …) value = initial value of individual parameter param. “blqMethod” (string) Method by which the BLQ data should be replaced. Possible methods are “zero”, “LOQ”, “LOQ2” or “missing” (default).

### Usage

setCASettings(...)


### Arguments

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

### See Also

 getCASettings

### Click here to see examples

## Not run:

setCASettings(weightingCA = “uniform”, blqMethod = “zero”) # set the settings whose name has been passed in argument

setCASettings(initialValues = list(Cl=0.4, V=.5, ka=0.04) # set the paramters CL, V, and ka to .4, .5 and .04 respectively

## End(Not run)

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## Set the value of one or several of the data settings associated to the non compartmental analysis

### Description

Set the value of one or several of the data settings associated to the non compartmental analysis. Associated settings names are:

 “urinevolume” (string) regressor name used as urine volume. “datatype” (list) list(“obsId” = string(“plasma” or “urine”). The type of data associated with each obsId. Default “plasma”.

### Usage

setDataSettings(...)


### Arguments

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

### See Also

 getDataSettings

### Click here to see examples

## Not run:

setDataSettings(“datatype” = list(“Y” =”plasma”)) # set the settings whose name has been passed in argument

## End(Not run)

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## Set the global observation id used in both the compartmental and non compartmental analysis

### Description

Get the global observation id used in both the compartmental and non compartmental analysis.

### Usage

setGlobalObsIdToUse(...)


### Arguments

(“id” string) the observation id from data section to use for computations.

### See Also

 getGlobalObsIdToUse

### Click here to see examples

## Not run:

setGlobalObsIdToUse(“id”) #

## End(Not run)

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## Set the value of one or several of the settings associated to the non compartmental analysis

### Description

Set the value of one or several of the settings associated to the non compartmental analysis. Associated settings are:

 “administrationType” (list) list(key = “admId”, value = string(“intravenous” or “extravascular”)). admId Admninistration ID from data set or 1 if no admId column in the dataset. “integralMethod” (string) Method for AUC and AUMC calculation and interpolation. “linTrapLinInterp” = Linear trapezoidal linear, “linLogTrapLinLogInterp” = Linear log trapezoidal, “upDownTrapUpDownInterp” = Linear up log down, “linTrapLinLogInterp” = Linear trapezoidal linear/log. “partialAucTime” (list) The first element of the list is a bolean describing if this setting is used. The second element of the list is the value of the bounds of the partial AUC calculation interval. By default, the boolean equals FALSE and the bounds are c(-Inf, +Inf). “blqMethodBeforeTmax” (string) Method by which the BLQ data before Tmax should be replaced. Possible methods are “missing”, “LOQ”, “LOQ2” or “zero” (default). “blqMethodAfterTmax” (string) Method by which the BLQ data after Tmax should be replaced. Possible methods are “zero”, “missing”, “LOQ” or “LOQ2” (default). “ajdr2AcceptanceCriteria” (list) The first element of the list is a boolean describing if this setting is used. The second element of the list is the value of the adjusted R2 acceptance criteria for the estimation of lambda_Z. By default, the boolean equals FALSE and the value is 0.98. “extrapAucAcceptanceCriteria” (list) The first element of the list is a boolean describing if this setting is used. The second element of the list is the value of the AUC extrapolation acceptance criteria for the estimation of lambda_Z. By default, the boolean equals FALSE and the value is 20. “spanAcceptanceCriteria” (list) The first element of the list is a boolean describing if this setting is used. The second element of the list is the value of the span acceptance criteria for the estimation of lambda_Z. By default, the boolean equals FALSE and the value is 3. “lambdaRule” (string) Main rule for the lambda_Z estimation. Possible rules are “R2”, “interval”, “points” or “adjustedR2” (default). “timeInterval” (vector) Time interval for the lambda_Z estimation when “lambdaRule” = “interval”. This is a vector of size two, default = c(-inf, inf) “timeValuesPerId” (list) list(“idName” = idTimes,…): idTimes Observation times to use for the calculation of lambda_Z for the id idName. Default = NULL, all the times values are used. “nbPoints” (integer) Number of points for the lambda_Z estimation when “lambdaRule” = “points”. Default = 3. “maxNbOfPoints” (list) The first element of the list is a boolean describing if this setting is used. The second element of the list is the value maximum number of points to use for the lambda_Z estimation when “lambdaRule” = “R2” or “adjustedR2”. By default, the boolean equals FALSE and the value is inf. “startTimeNotBefore” (list) The first element of the list is a boolean describing if this setting is used. The second element of the list is the value minimum time value to use for the lambda_Z estimation when “lambdaRule” = “R2” or “adjustedR2”. By default, the boolean equals FALSE and the value is 0. “weightingNca” (string) Weighting method used for the regression that estimates lambda_Z. Possible methods are “Y”, “Y2” or “uniform” (default).

### Usage

setNCASettings(...)


### Arguments

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

### See Also

 getNCASettings

### Click here to see examples

## Not run:

setNCASettings(integralMethod = “LinLogTrapLinLogInterp”, weightingnca = “uniform”) # set the settings whose name has been passed in argument

setNCASettings(administrationType = list(“1″=”extravascular”)) # set the administration id “1” to extravascular

setNCASettings(startTimeNotBefore = list(TRUE, 15)) # set the estimation of the lambda_z with points with time over 15

setNCASettings(timeValuesPerId = list(‘1’=c(4, 6, 8, 30), ‘4’=c(8, 12, 18, 24, 30))) # set the points to use for the lambda_z to time={4, 6, 8, 30} for id ‘1’ and ime={8, 12, 18, 24, 30} for id ‘4’

setNCASettings(timeValuesPerId = NULL) # set the points to use for the lambda_z to the default rule

## End(Not run)

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