The easiest way to familiarise your with NMproject is to run through the demo scripts line by line. Here’s a short YouTube video on running the demo.
The video shows that the first step is to create an analysis directory to play in. If you don’t know how to do this, read the Analysis directories vignette.
Open your analysis directory RStudio project and run the following to bring in the files:
This will population the Scripts directory with scripts, and deposit the standard theophylline dataset into the SourceData subdirectory.
Default the subdirectories for model development:
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
After running the above commands, the Scripts directory should contain scripts numbered s01.....Rmd, s02....Rmd etc. These are designed to be read, understood and run in order.
You can run these scripts either as notebooks (Run -> Run All) or as knitted documents via the Knit button. The advantage of notebooks is that code can be re-execute in chunks interactively. Knitr produces one document but the session is run non-interactively. For this reason it is best to start off working with interactive notebooks and then once you’re happy with the script, to knit it non-interactively.
To create your own markdown documents from scratch, see here.