dbFindFields() more robust, specify scalar search
fields to identify recordsCTIS search
from an URL, see
https://rfhb.github.io/ctrdata/#id_2-script-to-automatically-copy-users-query-from-web-browserCTIS provides an advanced
searchCTISCTIS 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