Changelog

Source: NEWS.md

EDCimport 0.5.0

New features

• New function lastnews_table() to find the last date an information has been entered for each patient.

• New functions to describe adverse events:

  • ae_table_grade_max(), ae_table_grade_n(), and ae_table_soc() to generate standardized tables. They all can be turned to flextables using as_flextable().
  • ae_plot_grade_max(), ae_plot_grade_n(), and ae_plot_soc() to generate standardized plots.

• New functions edc_data_warn() and assert_no_rows() to help performing data sanity checks.

  
  ae %>% filter(grade>5) %>% assert_no_rows()
  ae %>% filter(is.na(grade)) %>% edc_data_warn("Grade is missing", issue_n=13)
  #> Warning: Issue #13: Grade is missing (Patient 21, 28, 39, 95, 97, 120, 173, and 182)

• New function fct_yesno(), to easily format Yes/No columns.

• New function save_plotly(), to save a plotly to an HTML file.

• New experimental functions table_format(), get_common_cols() and get_meta_cols() that might become useful to find keys to pivot or summarise data.

Bug fixes & Improvements

• read_trialmaster(split_mixed="TRUE") will work as intended.
• extend_lookup() will not fail anymore when the database has a faulty table.
• assert_no_duplicate() has now a by argument to check for duplicate in groups, for example by visit.
• find_keyword() is more robust and inform on the proportion of missing if possible.
• read_trialmaster() will output a readable error when no password is entered although one is needed.
• check_subjid() can either take a vector or a dataframe as input, and the message is more informative.
• get_lookup() will now retreive the lookup table. Use build_lookup() to build is from a table list.
• get_subjid_cols() and get_crfname_cols() replace the now deprecated get_key_cols().

EDCimport 0.4.1

CRAN release: 2023-12-19

Bug fixes & Improvements

• 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.

EDCimport 0.4.0

CRAN release: 2023-12-11

New features

• New function check_subjid() to check if a vector is not missing some patients (#8).

options(edc_subjid_ref=enrolres$subjid)
check_subjid(treatment$subjid)
check_subjid(ae$subjid)

• New function 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).

Bug fixes & Improvements

• 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).

Minor breaking changes

• 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.

EDCimport 0.3.0 _^2023/05/19

CRAN release: 2023-05-19

New features

• New function edc_swimmerplot() to show a swimmer plot of all dates in the database and easily find outliers.

• New features in 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.

Bug fixes

• 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.

EDCimport 0.2.1 _^2022/11/01

CRAN release: 2022-12-02

• 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 build_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.

EDCimport 0.1.0

• Draft version