knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
library(NMproject)
It 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.
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