vignettes/articles/a02_analysis_directories.Rmd
a02_analysis_directories.RmdIt is recommended to work in structured. Create a new analysis project via the RStudio menu items: FILE -> New Project -> New Directory -> New NMproject. The underlying function being used to create this analysis project is nm_create_analysis_project(). See documentation for detailed information including how to modify the structure to suit your preferences.
Follow through the instructions, you’ll be asked for a location, a name and whether you want to use renv to manage project library directories. See renv documentation for more information.
Once created you’ll see a clean analysis directory with empty subfolders.
Default the subdirectories for model development (these can be modified - see nm_create_analysis_project() documentation):
SourceData : intended for unmodified source datasets entering the analysis project
DerivedData : intended for cleaned and processed NONMEM ready datasets
Scripts : intended for all R scripts
Models : intended for all NONMEM modelling
Results : intended as default location for run diagnostics, plots and tables
There is nothing mandating the use of R markdown in NMproject. You can use scripts. However R markdown documents produce nice shareable model development logs which provide a readable description of what steps were performed and in what order.
It is advisable to always start from a template. Templates can be accessed in File -> New File -> R markdown... -> From Template. Two to get started with are NMproject generic which we’ll use as a generic template for data processing and cleaning and model development for our model development notebook.