README.md

EDCimport

EDCimport is a package designed to easily import data from EDC software TrialMaster and Macro.

Installation

# Install last version available on CRAN (once published)
install.packages("EDCimport")

# Install development version on Github
devtools::install_github("DanChaltiel/EDCimport")

You will also need 7-zip installed, and preferably added to the PATH.

Windows-only

This package was developed to work on Windows and is unlikely to work on any other OS. Feel free to submit a PR if you manage to get it to work on another OS.

TrialMaster

Load the data

First, you need to request an export of type SAS Xport, with the checkbox "Include Codelists" ticked. This export should generate a zip archive.

Then, simply provide the archive password using options() (if any), and use read_trialmaster() to load the data from the archive:

library(EDCimport)
filename = "path/to/my/archive"
options(trialmaster_pw="foobar")
tm = read_trialmaster(filename)

Use the data

The resulting object tm is a list containing all the datasets, plus the date of extraction (datetime_extraction) and a dataset summary (.lookup).

You can now either use the resulting list, or load it to the global environment. For instance,

#use it directly
mean(tm$dataset1$column5)

#load it to the global env
load_list(tm) #this also removes `tm` to save RAM
mean(dataset1$column5)

Search the data

The dataset lookup table .lookup is a dataframe containing for each dataset all its column names and labels.

Its main use is to work with find_keyword(). For instance, say you do not remember in which dataset and column is located the "date of ECG". find_keyword() will search every column name and label and will give you the answer:

find_keyword("date")

#> # A tibble: 10 x 3
#>    dataset names   labels                      
#>    <chr>   <chr>   <chr>                       
#>  1 pat     PTRNDT  Randomization Date          
#>  2 pat     RGSTDT  Registration Date           
#>  3 site    INVDAT  Deactivation date           
#>  4 site    TRGTDT  Target Enroll Date          
#>  5 trial   TRSPDT  End Date                    
#>  6 trial   TRSTDT  Start Date                  
#>  7 visit   VISIT2  Visit Date                  
#>  8 visit   EEXPVDT Earliest Expected Visit Date
#>  9 vs      ECGDAT  Date of ECG                 
#> 10 vs      VISITDT Visit Date

Note that find_keyword() uses the edc_lookup option, automatically set by read_trialmaster().

MACRO

Work in progress