In LisaHopcroft/CTutils: Helpful Functions for Clinical Trial Data Analysis at SCTRU (Public Health Scotland)

GLOSSARY.file_list = grep( "^GLOSSARY.*\\.FILE$", ls(), value=TRUE )

if ( all_files_exist( GLOSSARY.file_list ) ) {
  glossary.dictionary  = readRDS( GLOSSARY.DICTIONARY.FILE )
  glossary.key         = readRDS( GLOSSARY.FILE            )
  parameter.vocabulary = readRDS( GLOSSARY.VOCAB.FILE      )
  print_file_loading_info( GLOSSARY.file_list )
} else {

  # Parse the relevant glossary information out of the XML file.
  # glossary.key = parse_MACRO_DSD_file_for_glossary_and_dependencies( paste(TRIAL.SDD_location,
  #                                                                          TRIAL.SDD_document,
  #                                                                          sep="//" ) )
  DSD_info.raw = parse_MACRO_DSD_file_for_glossary_and_dependencies(
    paste( TRIAL.DSD.LOCATION, TRIAL.DSD.DOCUMENT, sep="//" ),
    verbose=TRUE   ,
    silent =FALSE    )

  ###################################################################
  ### TASK: EXPAND CRF PAGES/TEST BATTERIES HERE ####################
  ###################################################################

  # Some test batteries are repeated but only appear once in the DSD
  # XML file.  This bit requires manual intervension to
  # define which tests are repeated at which visit.

  glossary_expansion = tribble(
    ~param_visit     , ~param_testbattery, ~param_visit_name,
    ### EXAMPLE 1: if the "Lab_Inv_FU" CRF page/test battery is repeated
    ### at the Week 3, 5, 7 and 9 appointments, then add the following lines
    ### (using the correct text for param_visit and param_visit_name):
    # "Week_3"         , "Lab_Inv_FU"      , "Week 3",
    # "Week_5"         , "Lab_Inv_FU"      , "Week 5",
    # "Week_7"         , "Lab_Inv_FU"      , "Week 7",
    # "Week_9"         , "Lab_Inv_FU"      , "Week 9",
    ### EXAMPLE 2: if the "Tumour_Ass_FU", "Phys_Exam_Post" and
    ### "Sign_Symp_Post" CRF pages/test batteries are repeated
    ### at the 12wk Post-surgical visit, then add the following lines
    ### (using the correct text for param_visit and param_visit_name):
    # "Post_Surgery_12", "Tumour_Ass_FU"   , "12wk Post Surgery",
    # "Post_Surgery_12", "Phys_Exam_Post"  , "12wk Post Surgery",
    # "Post_Surgery_12", "Sign_Symp_Post"  , "12wk Post Surgery"
    )


  # glossary.dictionary = expand_glossary( glossary.key,
  #                                   glossary_expansion )
  DSD_info.expanded = expand_glossary( DSD_info.raw,
                                       glossary_expansion,
                                       verbose = FALSE,
                                       silent = FALSE )


  glossary.dictionary = DSD_info.expanded %>%
    select( param_desc,
            param_name,
            param_closedvocab,
            param_visit,
            param_visit_name,
            param_testbattery,
            param_testbattery_name,
            column_name )

  saveRDS(glossary.dictionary, file=GLOSSARY.DICTIONARY.FILE )

  glossary.key = as.list(glossary.dictionary %>% pull(param_desc))
  names(glossary.key) = as.character(glossary.dictionary %>% pull(column_name))

  parameter.vocabulary = as.list( glossary.dictionary %>% pull( param_closedvocab ) )
  names( parameter.vocabulary) = as.character(glossary.dictionary %>% pull(column_name))

  saveRDS( glossary.key        , file=GLOSSARY.FILE)
  saveRDS( parameter.vocabulary, file=GLOSSARY.VOCAB.FILE )

}

LisaHopcroft/CTutils documentation built on Oct. 7, 2021, 11:08 p.m.