EDCimport (version 0.6.0)

read_all_csv: Read all .csv files in a directory

Description

Read all .csv files in a directory, with labels if specified.

Usage

read_all_csv(
  path,
  ...,
  labels_from = NULL,
  format_file = NULL,
  subdirectories = FALSE,
  read_fun = "guess",
  datetime_extraction = "guess",
  verbose = getOption("edc_read_verbose", 1),
  clean_names_fun = NULL
)

Value

a list containing one dataframe for each .csv file in the folder, the extraction date (datetime_extraction), and a summary of all imported tables (.lookup).

Arguments

path

[character(1)]
path to the directory containing .csv files.

...

unused

labels_from

[character(1)]
path to the file containing the labels. See section "Labels file" below.

format_file

[character(1)]
the path to the file that should be used to apply formats. See section "Format file" below. Use NULL to not apply formats.

subdirectories

[logical(1)]
whether to read subdirectories

read_fun

[function]
if "guess" doesn't work properly, a function to read the files in path, e.g. read.csv, read.csv2,...

datetime_extraction

[POSIXt(1)]
the datetime of the data extraction. Default to the most common date of last modification in path.

verbose

[numeric(1)]
one of c(0, 1, 2). The higher, the more information will be printed.

clean_names_fun

use edc_clean_names() instead.

Labels file

labels_from should contain the information about column labels. It should be a data file (.csv) containing 2 columns: one for the column name and the other for its associated label. Use options(edc_col_name="xxx", edc_col_label="xxx") to specify the names of the columns.

Format file

format_file should contain the information about SAS formats. It can be either:

• a procformat.sas file, containing the whole PROC FORMAT

• or a data file (.csv or .sas7bdat) containing 3 columns:

  • FMTNAME the SAS format name (repeated)

  • START the variable level

  • LABEL the label associated to the level

  You can get this datafile from SAS using PROC FORMAT with option CNTLOUT. Otherwise, you can use options(edc_var_format_name="xxx", edc_var_level="xxx", edc_var_label="xxx") to specify different column names.

See Also

Other EDCimport reading functions: read_all_sas(), read_all_xpt(), read_trialmaster()

Examples

# Create a directory with multiple csv files and a label lookup.
path = paste0(tempdir(), "/read_all_csv")
dir.create(paste0(path, "/subdir"), recursive=TRUE)
write.csv(iris, paste0(path, "/iris.csv"))
write.csv(mtcars, paste0(path, "/mtcars.csv"))
write.csv(mtcars, paste0(path, "/subdir/mtcars.csv"))
write.csv(airquality, paste0(path, "/airquality.csv"))
labs = c(iris, mtcars, airquality) %>% names()
write.csv(data.frame(name=labs, label=toupper(labs)), paste0(path, "/labels.csv"))


db = read_all_csv(path, labels_from="labels.csv", subdirectories=TRUE) %>% 
  set_project_name("My great project")
db
edc_lookup()