Read in every domain in a source data directory.

This function takes a path to a source data directory (typically SDTM or ADaM folder), reads in every data file, and returns a named list of the data objects.

read_src_dir(.path, .file_types, .read_domains = NULL)

Arguments

.path

Full path to the source data directory.

.file_types

Type of files being read in (e.g. 'sas7bat').

.read_domains

Character vector of domains to read in (e.g. c('dm', 'lb') - default is to load all domains).

Examples

path <- system.file("example-sdtm", package = "mrgda")
# Read in all source files
src_list <- read_src_dir(.path = path, .file_types = "xpt")
#> ℹ User specified file type = 'xpt'
#> Reading in ae.xpt (6.88 KB)
#> ✔ /Users/andersone/Library/R/arm64/4.5/library/mrgda/example-sdtm/ae.xpt
#> Reading in ae.xpt (6.88 KB)

#> Reading in dm.xpt (3.76 KB)
#> ✔ /Users/andersone/Library/R/arm64/4.5/library/mrgda/example-sdtm/dm.xpt
#> Reading in dm.xpt (3.76 KB)

#> Reading in eg.xpt (14 KB)
#> ✔ /Users/andersone/Library/R/arm64/4.5/library/mrgda/example-sdtm/eg.xpt
#> Reading in eg.xpt (14 KB)

#> Reading in lb.xpt (24.24 KB)
#> ✔ /Users/andersone/Library/R/arm64/4.5/library/mrgda/example-sdtm/lb.xpt
#> Reading in lb.xpt (24.24 KB)

#> Reading in mh.xpt (5.12 KB)
#> ✔ /Users/andersone/Library/R/arm64/4.5/library/mrgda/example-sdtm/mh.xpt
#> Reading in mh.xpt (5.12 KB)

#> Reading in pe.xpt (12.8 KB)
#> ✔ /Users/andersone/Library/R/arm64/4.5/library/mrgda/example-sdtm/pe.xpt
#> Reading in pe.xpt (12.8 KB)

#> Reading in vs.xpt (14.08 KB)
#> ✔ /Users/andersone/Library/R/arm64/4.5/library/mrgda/example-sdtm/vs.xpt
#> Reading in vs.xpt (14.08 KB)

#> ┌ read_src_dir Summary ────────────────────────┐
#> │                                              │
#> │   Number of domains successfully loaded: 7   │
#> │   Number of domains that failed to load: 0   │
#> │                                              │
#> └──────────────────────────────────────────────┘

# Read in only "dm" and "lb" domains
src_list <- read_src_dir(.path = path, .file_types = "xpt", .read_domains = c("dm", "lb"))
#> ℹ User specified file type = 'xpt'
#> Reading in dm.xpt (3.76 KB)
#> ✔ /Users/andersone/Library/R/arm64/4.5/library/mrgda/example-sdtm/dm.xpt
#> Reading in dm.xpt (3.76 KB)

#> Reading in lb.xpt (24.24 KB)
#> ✔ /Users/andersone/Library/R/arm64/4.5/library/mrgda/example-sdtm/lb.xpt
#> Reading in lb.xpt (24.24 KB)

#> ┌ read_src_dir Summary ────────────────────────┐
#> │                                              │
#> │   Number of domains successfully loaded: 2   │
#> │   Number of domains that failed to load: 0   │
#> │                                              │
#> └──────────────────────────────────────────────┘