EDCimport is a package designed to easily import data from EDC software TrialMaster. Browse code at https://github.com/DanChaltiel/EDCimport and read the doc at https://danchaltiel.github.io/EDCimport/.
Changes in testing environment so that the package can be installed from CRAN despite firewall policies forbidding password-protected archive downloading.
Fixed a bug where a corrupted XPT file can prevent the whole import to fail.
check_subjid() to check if a vector is not missing some patients (#8).assert_no_duplicate() to abort if a table has duplicates in a subject ID column(#9).tibble(subjid=c(1:10, 1)) %>% assert_no_duplicate() %>% nrow()
#Error in `assert_no_duplicate()`:
#! Duplicate on column "subjid" for value 1.New function manual_correction() to safely hard-code a correction while waiting for the TrialMaster database to be updated.
New function edc_options() to manage EDCimport global parameterization.
New argument edc_swimmerplot(id_lim) to subset the swimmer plot to some patients only.
New option read_trialmaster(use_cache="write") to read from the zip again but still update the cache.
You can now use the syntax read_trialmaster(split_mixed=c("col1", "col2")) to split only the datasets you need to (#10).
Reading with read_trialmaster() from cache will output an error if parameters (split_mixed, clean_names_fun) are different (#4).
split_mixed_datasets() is now fully case-insensitive.
Non-UTF8 characters in labels are now identified and corrected during reading (#5).
read_trialmaster(use_cache="write") is now the default. Reading from cache is not stable yet, so you should opt-in rather than opt-out.
read_trialmaster(extend_lookup=TRUE) is now the default.
Options edc_id, edc_crfname, and edc_verbose have been respectively renamed edc_cols_id, edc_cols_crfname, and edc_read_verbose for more clarity.
New function edc_swimmerplot() to show a swimmer plot of all dates in the database and easily find outliers.
read_trialmaster():
clean_names_fun=some_fun will clean all names of all tables. For instance, clean_names_fun=janitor::clean_names() will turn default SAS uppercase column names into valid R snake-case column names.split_mixed=TRUE will split tables that contain both long and short data regarding patient ID into one long table and one short table. See ?split_mixed_datasets() for details.extend_lookup=TRUE will improve the lookup table with additional information. See ?extend_lookup() for details.key_columns=get_key_cols() is where you can change the default column names for patient ID and CRF name (used in other new features).Standalone functions extend_lookup() and split_mixed_datasets().
New helper unify(), which turns a vector of duplicate values into a vector of length 1.
Reading errors are now handled by read_trialmaster() instead of failing. If one XPT file is corrupted, the resulting object will contain the error message instead of the dataset.
find_keyword() is now robust to non-UTF8 characters in labels.
Option edc_lookup is now set even when reading from cache.
SAS formats containing a = now work as intended.
Import your data from TrialMaster using tm = read_trialmaster("path/to/archive.zip").
Search for a keyword in any column name or label using find_keyword("date", data=tm$.lookup). You can also generate a lookup table for an arbitrary list of dataframe using get_lookup(my_data).
Load the datasets to the global environment using load_list(tm) to avoid typing tm$ everywhere.
Browse available global options using ?EDCimport_options.