Skip to contents

Data handling

Source: vignettes/data-handling.Rmd
data-handling.Rmd

Workflow

The workflow of modeling and simulation involves running simulations and comparing simulated data against observed data. Functionalities of esqlabsR require observed data to be present as DataSet objects. Please refer to the article Observed data for information on how to load data from Excel or *.pkml files.

esqlabsR offers a convenience function loadObservedData() that facilitates loading data in standard esqLABS projects. Assuming the standard project folder structure is followed and a valid ProjectConfiguration (see Standard workflow) and Excel files with observed data are present in the projectConfiguration$dataFolder folder, the following code loads the data:

projectConfiguration <- createDefaultProjectConfiguration()
dataSheets <- "Laskin 1982.Group A"
observedData <- loadObservedData(
  projectConfiguration = projectConfiguration,
  sheets = dataSheets
)

print(names(observedData))
#> [1] "Aciclovir_Laskin 1982.Group A_1_Human_PeripheralVenousBlood_Plasma_2.5 mg/kg_iv"

The function loads the data from the file projectConfiguration$dataFile from the folder projectConfiguration$dataFolder and returns a list of DataSet objects. The resulting object will be used later to plot results to compare simulated and observed data.

Troubleshooting

  • The sheets argument of the loadObservedData() function should be a string or a list of strings. If a specified sheet is not found in the file, it will be omitted with a warning; the observedData variable may then be an empty named list.

  • If the data file specified in projectConfiguration$dataFile is missing in the filesystem, the loadObservedData() function will fail with an Invalid File message.

More detailed information on function signatures can be found in: