Create submission package for analysis

Copies scripts or NLME models with related datasets into folder structure as required by FDA for submission. Define files and reviewer's guides are prepared in terms of rmd/docx files.

createSubmissionPack(
  project,
  type,
  analysisname,
  pathroot = ".",
  logfile = "logfile.txt",
  datafiles = NULL,
  dataDescription = NULL,
  modelDescription = NULL,
  FLAGusePDFasis = FALSE,
  FLAGcopyATR = FALSE
)

Arguments

project

Named vector with path(s) to folder(s) containing analysis scripts or NLME project

type

either "NLMEmodel" or "scripts"

analysisname

Name of the analysis folder

pathroot

Path where submission package is created

logfile

File with notes on manual postprocessing information.

datafiles

Named vector with datasets to be copied to datasets. Required for scripts. For NLME models optional as the modeling dataset is attempted to be taken from the path given in the NLME project

dataDescription

Named vector with description of the dataset which is inserted as description in define file (default: 'Analysis dataset' or 'Modeling datset for NLME name')

modelDescription

Model description used on reviewer's guide in 'programs'

FLAGusePDFasis

Flag whether to copy the define file for the dataset as found next to data The user is reponsible to provide an appropriate file.

FLAGcopyATR

Flag whether to copy attributes files to the Resources folder (applies only type="scripts")

Value

None. Datasets and programs are copied to the submission package folder structure and a log file with postprocessing information written.

Details

For NLME models, the NONMEM control and output file will be copied to programs and the modeling dataset to datasets. Per default the modeling dataset given in the control file will be used, however, the user can also provide the path (datafiles). For scripts, all script in the given folder and subfolder are copied. It will be attempted to parse the description of the file from the file header. The structure of the created package is 'm5/datasets/analysisname/analysis/legacy' with subfolders 'programs' and 'datasets'. Define files and the reviewer's guides need to be manually opened and stored as PDF. The user should carefully reviewing the generated docx file to do potential manual adjustment required. The logfile is giving an overview on things that need to be done.

See also