ctrdata (version 1.25.1)

ctrGenerateQueries: Generates queries that work across registers

Description

From high-level search terms provided by the user, generate specific queries for each registers with which ctrdata works, see ctrdata-registers. Search terms that are expanded to concepts such as from MeSH and MedDRA by the search implementations in registers include the 'intervention' and 'condition'. Logical operators only work with 'searchPhrase'.

Usage

ctrGenerateQueries(
  searchPhrase = NULL,
  condition = NULL,
  intervention = NULL,
  phase = NULL,
  population = NULL,
  recruitment = NULL,
  startBefore = NULL,
  startAfter = NULL,
  completedBefore = NULL,
  completedAfter = NULL,
  onlyMedIntervTrials = TRUE,
  onlyWithResults = FALSE,
  countries = NULL
)

Value

Named vector of URLs for finding trials in the registers and as input to functions ctrLoadQueryIntoDb and ctrOpenSearchPagesInBrowser

Arguments

searchPhrase

String with optional logical operators ("AND", "OR") that will be searched in selected fields of registers that can handle logical operators (general or title fields), should not include quotation marks

condition

String with condition / disease

intervention

String with intervention

phase

String, e.g. "phase 2" (note that "phase 2+3" is a specific category, not the union set of "phase 2" and "phase 3")

population

String, e.g. "P" (paediatric), "A" (adult), "P+A" (adult and paediatric), "E" (elderly), "P+A+E" participants can be recruited. For ISRCTN, works only for "P", "A" or "E" but not mixed populations.

recruitment

String, one of "ongoing", "completed", "other" ( which includes "ended early" but this cannot be searched; use trial concept f.statusRecruitment to identify this status)

startBefore

String that can be interpreted as date (for EUCTR, when trial was first registered)

startAfter

String that can be interpreted as date (for EUCTR, when trial was first registered)

completedBefore

String that can be interpreted as date (does not work with EUCTR)

completedAfter

String that can be interpreted as date (does not work with EUCTR)

onlyMedIntervTrials

Logical, default TRUE, which indicates if queries should search only for medicine interventional clinical trial

onlyWithResults

Logical

countries

Vector of country names, two- or three-letter ISO 3166 codes

Examples

urls <- ctrGenerateQueries(
  intervention = "antibody",
  phase = "phase 3",
  startAfter = "2000-01-01")

# open queries in register web interface
sapply(urls, ctrOpenSearchPagesInBrowser)

# For CTIS to accept such a search URL and show results, consider installing
# the Tampermonkey browser extension from https://www.tampermonkey.net/,
# click on the extension icon, "Create a new script", "Utility" and then
# "Import from this URL":
# https://raw.githubusercontent.com/rfhb/ctrdata/master/tools/ctrdataURLcopier.js

# find potential research platform and platform trials
urls <- ctrGenerateQueries(
  searchPhrase = paste0(
   "basket OR platform OR umbrella OR master protocol OR ",
   "multiarm OR multistage OR subprotocol OR substudy OR ",
   "multi-arm OR multi-stage OR sub-protocol OR sub-study"),
 phase = "phase 3",
 startAfter = "01/31/2010",
 countries = c("DE", "US", "United Kingdom"))

# open queries in register web interface
sapply(urls, ctrOpenSearchPagesInBrowser)

urls <- ctrGenerateQueries(
  searchPhrase = "antibody AND covid",
  recruitment = "completed",
  )

if (FALSE) {
# count trials found
sapply(urls, ctrLoadQueryIntoDb, only.count = TRUE)

# load queries into database collection
dbc <- nodbi::src_sqlite(collection = "my_collection")
sapply(urls, ctrLoadQueryIntoDb, con = dbc, euctrprotocolsall = FALSE)
}