trialmaster-simple.md
In EDCimport: Import Data from EDC Software

Read a TM archive

Code
  filename = test_path("CRF_Dan_Export_SAS_XPORT_2022_08_25_15_16.zip")
  w = read_trialmaster(filename, use_cache = "write", verbose = 9)
Message
  Unzipping 'CRF_Dan_Export_SAS_XPORT_2022_08_25_15_16.zip'
  7-Zip Copyright 1999-2016 Igor Pavlov

  Scanning the drive for archives:
  1 file, 13576 bytes (14 KiB)

  Extracting archive: CRF_Dan_Export_SAS_XPORT_2022_08_25_15_16.zip
  --
  Path = CRF_Dan_Export_SAS_XPORT_2022_08_25_15_16.zip
  Type = zip
  Physical Size = 13576

  Everything is Ok

  Files: 6
  Size: 61533
  Compressed: 13576
  Writing cache file './trialmaster_export_2022-08-25 15h16.rds'
  v Database loaded: 8 tables, 000 Kb
Code
  w$datetime_extraction
Output
  [1] "2022-08-25 15:16:00 CEST"
Code
  w$.lookup
Output
  -- Lookup table - CRF (extraction of 2022-08-25) - EDCimport v0.0.0 ----------------------------------------------------
    dataset  nrow  ncol  n_id rows_per_id crfname                       
    <chr>   <dbl> <dbl> <int>       <dbl> <chr>                         
  1 site        1    33    NA          NA Trial Site Setup & Information
  2 trial       1    23    NA          NA Trial                         
  3 pat         0    35    NA          NA <NA>                          
  4 visit       0    27    NA          NA <NA>                          
  5 vs          0    31    NA          NA <NA>                          
Code
  lu = edc_lookup()
  expect_identical(lu, w$.lookup)
  df_list = w %>% keep(is.data.frame) %>% discard_at(".lookup")
  df_list %>% map(~ {
    .x %>% get_label() %>% unlist() %>% tibble::enframe()
  })
Output
  $pat
  # A tibble: 35 x 2
     name     value                                   
     <chr>    <chr>                                   
   1 TRNAME   Trial Name                              
   2 TRNO     Trial No                                
   3 TRCAP    Trial Caption                           
   4 STNAME   Site Name                               
   5 STNO     Site No                                 
   6 SITEC    Site Caption                            
   7 CRFNAME  Form Name                               
   8 CRFINSNO Form Instance                           
   9 CRFSTAT  Form Status                             
  10 GRPINSNO Group Instance                          
  11 DATAMIN  Minimum Data Timestamp                  
  12 DATAMAX  Maximum Data Timestamp                  
  13 STATMIN  Minimum Status Change Timestamp         
  14 STATMAX  Maximum Status Change Timestamp         
  15 FORMCAP  The Form caption as defined in TrialBuil
  16 FORMDESC The Form description, as defined in Tria
  17 BITMASK  The state bitmask for the form, which ex
  18 REFUSLAB Message from promotor                   
  19 HCHECK   Hard check                              
  20 FNAME    First name initial                      
  21 LNAME    Last name initial                       
  22 PTNO     Patient Number                          
  23 DNAIS    Birthdate                               
  24 SEX      Sex                                     
  25 PATIEN   Patient Caption                         
  26 PTACTV   Active                                  
  27 PTDROP   Dropped                                 
  28 PTENRL   Enrolled                                
  29 RGSTDT   Registration Date                       
  30 PTERDT   Enroll Date                             
  31 PTRNNO   Randomization Number                    
  32 PTRNDT   Randomization Date                      
  33 CHECKDUP Check of duplicate patient              
  34 OVERDUP  Overrule duplicate check (DM only)      
  35 CHECKDU1 Check of duplicate patient

  $site
  # A tibble: 33 x 2
     name     value                                   
     <chr>    <chr>                                   
   1 TRNAME   Trial Name                              
   2 TRNO     Trial No                                
   3 TRCAP    Trial Caption                           
   4 STNAME   Site Name                               
   5 STNO     Site No                                 
   6 SITEC    Site Caption                            
   7 CRFNAME  Form Name                               
   8 CRFINSNO Form Instance                           
   9 CRFSTAT  Form Status                             
  10 GRPINSNO Group Instance                          
  11 DATAMIN  Minimum Data Timestamp                  
  12 DATAMAX  Maximum Data Timestamp                  
  13 STATMIN  Minimum Status Change Timestamp         
  14 STATMAX  Maximum Status Change Timestamp         
  15 FORMCAP  The Form caption as defined in TrialBuil
  16 FORMDESC The Form description, as defined in Tria
  17 BITMASK  The state bitmask for the form, which ex
  18 STADDA   Address 1                               
  19 STADDB   Address 2                               
  20 STCITY   City                                    
  21 STATE    State                                   
  22 STZIP    Postal Code                             
  23 STCTRY   Country                                 
  24 STTMZN   Time Zone                               
  25 STCFN    Contact First Name                      
  26 STCLN    Contact Last Name                       
  27 STCPH    Phone                                   
  28 TGENRL   Target Enroll                           
  29 TRGTDT   Target Enroll Date                      
  30 INCLSITE Authorisation of inclusion site         
  31 INVSYS   Investigator names list                 
  32 DESACINV Investigator inactive                   
  33 INVDAT   Deactivation date

  $trial
  # A tibble: 23 x 2
     name     value                                   
     <chr>    <chr>                                   
   1 TRNAME   Trial Name                              
   2 TRNO     Trial No                                
   3 CRFNAME  Form Name                               
   4 CRFINSNO Form Instance                           
   5 CRFSTAT  Form Status                             
   6 GRPINSNO Group Instance                          
   7 DATAMIN  Minimum Data Timestamp                  
   8 DATAMAX  Maximum Data Timestamp                  
   9 STATMIN  Minimum Status Change Timestamp         
  10 STATMAX  Maximum Status Change Timestamp         
  11 FORMCAP  The Form caption as defined in TrialBuil
  12 FORMDESC The Form description, as defined in Tria
  13 BITMASK  The state bitmask for the form, which ex
  14 TRIALC   Trial Caption                           
  15 TRSPON   Sponsor                                 
  16 TRSTDT   Start Date                              
  17 TRSPDT   End Date                                
  18 TREFN    Email From Name                         
  19 TREFA    Email From Address                      
  20 TREXPP   Export Password                         
  21 TRTMZN   Trial Time Zone                         
  22 TRMSG    Message of the Day                      
  23 INCLTRIA Authorisation of inclusion

  $visit
  # A tibble: 27 x 2
     name     value                                   
     <chr>    <chr>                                   
   1 TRNAME   Trial Name                              
   2 TRNO     Trial No                                
   3 TRCAP    Trial Caption                           
   4 STNAME   Site Name                               
   5 STNO     Site No                                 
   6 SITEC    Site Caption                            
   7 SUBJINIT Patient Initials                        
   8 SUBJID   Patient No                              
   9 VISITN   Visit Name                              
  10 CRFNAME  Form Name                               
  11 CRFINSNO Form Instance                           
  12 CRFSTAT  Form Status                             
  13 GRPINSNO Group Instance                          
  14 DATAMIN  Minimum Data Timestamp                  
  15 DATAMAX  Maximum Data Timestamp                  
  16 STATMIN  Minimum Status Change Timestamp         
  17 STATMAX  Maximum Status Change Timestamp         
  18 FORMCAP  The Form caption as defined in TrialBuil
  19 FORMDESC The Form description, as defined in Tria
  20 BITMASK  The state bitmask for the form, which ex
  21 VISIT1   Visit Number                            
  22 VISIT2   Visit Date                              
  23 EEXPVDT  Earliest Expected Visit Date            
  24 LEXPVDT  Latest Expected Visit Date              
  25 EXPVDT   Expected Visit Date                     
  26 VISIT3   Visit Caption                           
  27 PRV      PRV

  $vs
  # A tibble: 31 x 2
     name     value                                   
     <chr>    <chr>                                   
   1 TRNAME   Trial Name                              
   2 TRNO     Trial No                                
   3 TRCAP    Trial Caption                           
   4 STNAME   Site Name                               
   5 STNO     Site No                                 
   6 SITEC    Site Caption                            
   7 SUBJINIT Patient Initials                        
   8 SUBJID   Patient No                              
   9 VISITN   Visit Name                              
  10 VISITNO  Visit No                                
  11 VISITDT  Visit Date                              
  12 CRFNAME  Form Name                               
  13 CRFINSNO Form Instance                           
  14 CRFSTAT  Form Status                             
  15 GRPINSNO Group Instance                          
  16 DATAMIN  Minimum Data Timestamp                  
  17 DATAMAX  Maximum Data Timestamp                  
  18 STATMIN  Minimum Status Change Timestamp         
  19 STATMAX  Maximum Status Change Timestamp         
  20 FORMCAP  The Form caption as defined in TrialBuil
  21 FORMDESC The Form description, as defined in Tria
  22 BITMASK  The state bitmask for the form, which ex
  23 VSYN     Clinical Examination done ?             
  24 VSDT     Date of clinical assessment             
  25 HEIGHT   Height (cm)                             
  26 WEIGHT   WEIGHT (kg)                             
  27 VSPS     PS (performance status measured using th
  28 VSSYS    Systolic blood pressure (mmHG)          
  29 VSDIAG   Diastolic blood pressure (mmHG)         
  30 ECG      ECG                                     
  31 ECGDAT   Date of ECG

Code
  df_list %>% map(~ {
    .x %>% select(where(is.factor)) %>% map(~ head(levels(.x), 3))
  })
Output
  $pat
  $pat$SEX
  [1] "Male"   "Female"

  $pat$PTACTV
  [1] "NO"  "YES"

  $pat$PTDROP
  [1] "NO"  "YES"

  $pat$PTENRL
  [1] "NO"  "YES"

  $pat$OVERDUP
  [1] "No"  "Yes"


  $site
  $site$STCTRY
  [1] "AFGHANISTAN"   "ALAND ISLANDS" "ALBANIA"

  $site$STTMZN
  [1] "(GMT+00:00) Dublin, Edinburgh, Lisbon, London" "(GMT+00:00) Monrovia, Reykjavik"              
  [3] "(GMT+00:00) Sao Tome"

  $site$INCLSITE
  [1] "No"  "Yes"


  $trial
  $trial$TRTMZN
  [1] "(GMT+00:00) Dublin, Edinburgh, Lisbon, London" "(GMT+00:00) Monrovia, Reykjavik"              
  [3] "(GMT+00:00) Sao Tome"

  $trial$INCLTRIA
  [1] "No"  "Yes"


  $visit
  named list()

  $vs
  $vs$VSYN
  [1] "Not done" "Done"

  $vs$ECG
  [1] "Not done" "Done"