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EDCimport

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/.

EDCimport 0.5.2

  • Fixed a bug in lastnews_table() when subjid is not numeric
  • Fixed a bug in read_all_sas() causing metadata (e.g. date_extraction) being converted to dataframes

EDCimport 0.5.1

  • Internal fix for CRAN check

EDCimport 0.5.0

New features

Read functions

  • New function read_all_sas() to read a database of .sas7bdat files.

  • New function read_all_csv() to read a database of .csv files.

Sanity checks alerts

  • New functions edc_data_warn() and edc_data_stop(), to alert if data has inconsistencies (#29, #39, #43).

    ae %>% filter(grade<1 | grade>5) %>% edc_data_stop("AE of invalid grade")
ae %>% filter(is.na(grade)) %>% edc_data_warn("Grade is missing", issue_n=13)
#> Warning: Issue #13: Grade is missing (8 patients: #21, #28, #39, #95, #97, ...)

  • New function edc_data_warnings(), to get a dataframe of all warnings thrown by edc_data_warn().

  • New function edc_warn_extraction_date(), to alert if data is too old.

Miscellaneous utils

  • New function select_distinct() to select all columns that has only one level for a given grouping scope (#57).

  • New function edc_population_plot() to visualize which patient is in which analysis population (#56).

  • New function edc_db_to_excel() to export the whole database to an Excel file, easier to browse than RStudio's table viewer (#55). Use edc_browse_excel() to browse the file without knowing its name.

  • New function edc_inform_code() to show how much code your project contains (#49).

  • New function search_for_newer_data() to search a path (e.g. Downloads) for a newer data archive (#46).

  • New function crf_status_plot() to show the current database completion status (#48).

  • New function save_sessioninfo(), to save sessionInfo() into a text file (#42).

  • New function fct_yesno(), to easily format Yes/No columns (#19, #23, #40).

  • New function lastnews_table() to find the last date an information has been entered for each patient (#37). Useful for survival analyses.

  • New function harmonize_subjid(), to have the same structure for subject IDs in all the datasets of the database (#30).

  • New function save_plotly(), to save a plotly to an HTML file (#15).

  • 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

  • get_datasets() will now work even if a dataset is named after a base function (#67).
  • read_trialmaster() will output a readable error when no password is entered although one is needed.
  • read_trialmaster(split_mixed="TRUE") will work as intended.
  • assert_no_duplicate() has now a by argument to check for duplicate in groups, for example by visit (#17).
  • find_keyword() is more robust and inform on the proportion of missing if possible.
  • edc_lookup() will now retrieve the lookup table. Use build_lookup() to build one from a table list.
  • extend_lookup() will not fail anymore when the database has a faulty table.

Deprecations

  • get_key_cols() is replaced by get_subjid_cols() and get_crfname_cols().
  • check_subjid() is replaced by edc_warn_patient_diffs(). It can either take a vector or a dataframe as input, and the message is more informative.

EDCimport 0.4.1

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

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

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

  • 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