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# R functions to run PKanalix

## On the use of a R-functions

PKanalix can be called via R-functions. It is possible to have access to the project exactly in the same way as you would do with the interface.  All the functions are described below.

## Installation and initialization

All the installation guidelines and initialization procedure can be found here.

## Description of the functions concerning the project management

• getData: Get a description of the data used in the current project.
• getStructuralModel: Get the model file for the structural model used in the current project (CA analysis).
• loadProject: Load a project by parsing the mlxtran-formated file whose path has been given as an input.
• newProject: Create a new empty project providing model and data specification.
• saveProject: Save the current project as an Mlxtran-formated file.
• setData: Set project data giving a data file and specifying headers and observations types.
• setStructuralModel: Set the structural model.

## Description of the functions concerning the scenario

• runCAEstimation: Estimate the CA parameters for each individual of the project.
• runEstimation: Run the NCA analysis and the CA analysis if the structural model for the CA calculation is well defined.
• runNCAEstimation: Estimate the NCA parameters for each individual of the project.
• abort: Stop the current task run.
• getLastRunStatus: Return an execution report about the last run with a summary of the error which could have occurred.
• isRunning: Check if a scenario is currently running.

## Description of the functions concerning the results

• getCAIndividualParameters: Get the estimated values for each subject of some of the individual CA parameters of the current project.
• getNCAIndividualParameters: Get the estimated values for each subject of some of the individual NCA parameters of the current project.

## Description of the functions concerning the compartmental and non compartmental analysis 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.

## Example

Below is an example of the functions to call to run an NCA and CA analysis from scratch using one of the demo data sets.

# load library and initialize the API
library(lixoftConnectors)
initializeLixoftConnectors(software="pkanalix")

# create a new project by setting a data set
# replace <userFolder> by the path to your home directory
demoPath = '<userFolder>/lixoft/pkanalix/pkanalix2019R1/demos/2.case_studies/data/'
newProject(data = list(dataFile = paste0(demoPath,'M2000_ivbolus_singledose.csv'),
'catcov','contcov','contcov','contcov'),
observationTypes = 'continuous'))

# set the options for the NCA analysis
indivParams <- getNCAIndividualParameters("AUCINF_pred","Cmax")