The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.
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.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.