In maia-sh/ctregistries: Data Package and R Functions for Clinical Trial Registries and other MEDLINE Databanks

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ctregistries

In Development

The goal of ctregistries is to facilitate the detection and analysis of clinical trial registration numbers. ctregistries is primarily a data package of regular expressions (regexes) and provides some R functions for implementing the regexes.

Regular expressions were developed for trial registration numbers (TRN) from World Health Organization (WHO) International Clinical Trials Registry Platform (ICTRP) Primary Registries (https://www.who.int/ictrp/network/primary/en/) and MEDLINE Databank Sources (https://www.nlm.nih.gov/bsd/medline_databank_source.html).

Additional, non-trial databanks indexed by MEDLINE (e.g., figshare) are also included, without regexes.

Installation

You can install the development version of ctregistries from GitHub:

# install.packages("devtools")
devtools::install_github("maia-sh/ctregistries")

Dataset

ctregistries provides the registries dataframe with regular expressions for each registry. The registries dataframe is a subset of the larger databanks dataframe which additionally includes non-trial databanks indexed by MEDLINE (e.g., figshare) without regexes. registries is created by filtering databanks for databank_type == "registry.

library(ctregistries)

head(registries) %>% knitr::kable()

databanks$databank

Functions

ctregistries provides some functions implementing the registries dataset to detect trial registration numbers and registries in both vectors and dataframes.

library(ctregistries)

# Check whether there is a TRN
has_trn(c("NCT00312962", "hello", "euctr2020-001808-42", NA))

# Extract the TRNs
which_trn("NCT00312962 and euctr2020-001808-42")
which_trns(c("NCT00312962", "hello", "euctr2020-001808-42", NA))

# Identify the registry
which_registry("NCT00312962 and euctr2020-001808-42")
which_registries(c("NCT00312962", "hello", "euctr2020-001808-42", NA))

# Add the trn and registry to a dataframe
mutate_trn_registry(sample_trn_df, text)

To Do

• [ ] Add checks within functions
• [ ] Check input variable type
• [ ] Check input (column) name conflicts (e.g., databank, trn_regex)
• [ ] Add tests: use_testthat()
• [ ] Consider removing check_registry since just comparing strings...
• [ ] Change license (CCBY or AGPL, unclear since partially data package)
• https://r-pkgs.org/lsicense.html
• https://thinkr-open.github.io/licensing-r/rlicense.html
• https://kbroman.org/pkg_primer/pages/licenses.html
• [ ] Get functions to work with multiple and no trns (character(0) and NA) in one element
• rapply(~ifelse(. == 1,NA,.), how = "replace")
• purrr::modify_if()
• any(lengths(y) > 1) # flatten if max 1 trn per element...but issue with character(0)

maia-sh/ctregistries documentation built on July 20, 2024, 8:08 p.m.