CTISCTIS trial data processingCTIS by disabling HTTP/2 multiplexing in another functionCTGOV2CTGOV has retired on 2024-06-25 the classic website and API used by ctrdata since 2015. To support users, ctrdata now automatically translates and redirects queries to the current website. This helps with automatically updating previously loaded queries (ctrLoadQueryIntoDb(querytoupdate = <n>)), manually migrating queries and reproducible work on clinical trials information. This new functionality in ctrdata translates a user's search query URL from the classic website into a query for the current CTGOV website, for all search parameters. Since the structure and format of data differs between data retrieved from the current API and previously retrieved from the classic API, ctrdata will continue to identify the current API as register = "CTGOV2", to support the analysis stage. In addition, ctrdata documentation continues to include examples of analyses with CTGOV data, as this may have been downloaded earlier.
CTIS has been relaunched on 2024-06-17, and ctrdata has been fully updated to it. At the moment, CTIS provides basic searches and no search query URL. To support users, ctrdata includes an updated script that extracts a user's search parameters from the register search page to the clipboard and into the browser URL bar. In addition, the script triggers a search for trials when opening such a query URL, see https://rfhb.github.io/ctrdata/#id_2-script-to-automatically-copy-users-query-from-web-browser. File names of CTIS documents start now with the document type, e.g. SbjctInfaICF - L1 SIS and ICF NL for publication.pdf, since the prefix (document source) introduced in version 1.18.0 is no more applicable.
CRAN notesctrFindActiveSubstanceSynonyms() to CTGOV2 API; this is now based on terms used in studiesctrdata-collection for data frames with trial information; same content as attribute ctrdata-table, which will be removed by end 2024CTGOV2CTISCTIS now include the document type and use different separators (e.g., "parts2auth - SbjctInfaICF - ..." as abbreviation of "Subject information and informed consent form (for publication)", was previously "parts2auth_...")CTGOV2 (automatically retrieved from CTIS, not available for other registers)CTISDuckDB and CTGOV2dbGetFieldsIntoDf()unlink of intermediate filesCTISCTISCTIS downloads in a given sessionCTIS field types and possibly documents (associated clinical trials)ctId instead of id as CTIS top-level field (a further synonym used in the API is clinicalTrialId)EUCTREUCTRCTIS query did not result in any trialsdbGetFieldsIntoDf() to accelerate and have more predictable, simplified returns, in particular for nested fields; also attempts to recursively expand simply nested data into additional columns in the returned data framedbFindFields() to accelerate; both based on improved nodbi::docdb_query()dbFindFields() now digests a sample of records to quickly find fields, or all records if sample = FALSE but taking increasing time with increasing number of recordsnodbi::scr_postgres(), parameter fields of dbGetFieldsIntoDf() is limited to less than 50 fields; a message flags for any backend potential compatibility issues, suggesting to use parent fields, e.g., a.b instead of c("a.b.c.d", "a.b.c.e")stopifnodata of dbGetFieldsIntoDf() is no more needed and deprecatedoptions(ctrdata.tempdir = "<user_specified_folder>")cygwin was found so that they may chose to delete itdbGetFieldsIntoDf()CTISJSON from CTIS{"id":"PostAssignmentPeriod-46349"}, was: {"@attributes":{"id":"PostAssignmentPeriod-46349"}}@attributes from field names such as dbGetFieldsIntoDf("clinical_results.baseline.analyzed_list.analyzed.count_list.count.@attributes.value", db)NDJSON (e.g., some but not all records have <start_date type="Actual">March 15, 2004</start_date>, and this is converted to {"start_date":"March 15, 2004"})e83_single_site_trial, was (EU trials): e83_the_trial_involves_single_site_in_the_member_state_concernede83_single_site_trial, was (3rd country trials): e83_will_this_trial_be_conducted_ at_a_single_site_globallye863_trial_sites_planned_in, was (EU trials): e863_specify_the_regions_in_which_trial_sites_are_plannede863_trial_sites_planned_in, was (3rd country trials): e863_specify_the_countries_outside_of_the_eea_in_which_trial_sites_are_plannede84_multiple_sites_in_member_state, was (EU trials): e84_the_trial_involves_multiple_sites_in_the_member_state_concernede840_multiple_sites_globally, was (3rd country trials): e84_will_this_trial_be_conducted_at_multiple_sites_globallySee also https://github.com/rfhb/ctrdata/issues/26#issuecomment-1749555081
totalSize responseCygwin, perl, cat, sed, php functionality for transforming text, XML and NDJSON replaced by Javascript using R package V8); addresses personally communicated concerns and faciliates use of package ctrdata in more environments (e.g., https://github.com/rfhb/ctrdata/issues/26); consequently, this might be a breaking change for analysing certain fields, see above which fields are affected.dbFindFields() returns fields for EU and 3rd country trials in EUCTR (addresses https://github.com/rfhb/ctrdata/issues/26)options(ctrdata.tempdir = ...) if setdfListExtractKey(), long deprecateddfMergeTwoVariablesRelevel(), long deprecatedCTIS, including file name sanitisationCTGOV2CTGOVctrdataURLcopier.js to only rewrite searches and views from CTISpartIIInfo object into array, adding a new partIIIinfoKey so that
'{"partIIInfo": "<int>": {...}, "<int>": {...}}' becomes
'{"partIIInfo": [{"partIIIinfoKey": <int>, ...}, {"partIIIinfoKey": <int>, ...}]}')dbFindIdsUniqueTrials() for single-record register contentsdfMergeVariablesRelevel() superseeds dfMergeTwoVariablesRelevel()dbFindFields()dbFindIdsUniqueTrials()ctrLoadQueryIntoDb() for CTIS with nodbi >=0.9.2.9000dbFindIdsUniqueTrials()dbFindFields() for EUCTRcurl::multi_download() which can resume retrievals from registersctrLoadQueryIntoDb() to always return visible resultdfTrials2Long() identifier (EUCTR no more top "1" across fields)dfName2Value()dfName2Value()dbGetFieldsIntoDf() with missing datadbGetFieldsIntoDf() for rare complex fieldswherevalue in dfName2Value() resultctrLoadQueryIntoDb() new parameter euctrresultsfilespath, deprecating euctrresultspdfpathctrLoadQueryIntoDb() now also extracts and saves results files other than PDF filesctrFindActiveSubstanceSynonyms() returns NULL for non-existing active substancedbFindFields() returns a vector of fields which now has as names the register in which a field occursdbGetFieldsIntoDf() for specific nested data structuresdfTrials2Long() for specific fieldsdbFindIdsUniqueTrials() when only single trial in any registermin_age in CTGOVdbGetFieldsIntoDf() and simplify more fieldsdbFindFields() returns names of all leaf and node fieldsinstallCygwinWindowsDoInstall() to properly update an installation (remove --prune-install)installCygwinWindowsDoInstall() and only cache successful binary testingrequired_header.download_datedfTrials2Long(), covering nested itemsdbFindFields()ctrGetQueryUrlFromBrowser(), long deprecated