Main features • References • Installation • Overview • Databases • Data model • Example workflow • Analysis across trials • Tests • Acknowledgements • Future

ctrdata for aggregating and analysing clinical trials

The package ctrdata provides functions for retrieving (downloading), aggregating and analysing clinical trials using information (structured protocol and result data, as well as documents) from public registers. It can be used with the

EU Clinical Trials Register (“EUCTR”, https://www.clinicaltrialsregister.eu/)
EU Clinical Trials Information System (“CTIS”, https://euclinicaltrials.eu/, see example)
ClinicalTrials.gov (“CTGOV2”, see example)
ISRCTN Registry (https://www.isrctn.com/)

The motivation is to investigate the design and conduct of trials of interest, to describe their trends and availability for patients and to facilitate using their detailed results for research and meta-analyses. ctrdata is a package for the R system, but other systems and tools can use the databases created with this package. This README was reviewed on 2025-03-09 for version 1.21.0.

Main features

Protocol- and results-related trial information is easily downloaded: Users define a query in a register’s web interface, then copy the URL and enter it into ctrdata which retrieves in one go all trials found. A script can automate copying the query URL from all registers. Personal annotations can be made when downloading trials. Also, trial documents and historic versions as available in registers on trials can be downloaded.
Downloaded trial information is transformed and stored in a collection of a document-centric database, for fast and offline access. Information from different registers can be accumulated in a single collection. Uses DuckDB, PostgreSQL, RSQLite or MongoDB, via R package nodbi: see section Databases below. Interactively browse through trial structure and data. Easily re-run any previous query in a collection to retrieve and update trial records.
For analyses, convenience functions in ctrdata implement canonical trial concepts to simplify analyses across registers 🔔, allow find synonyms of an active substance, identify unique (de-duplicated) trial records across all registers, to merge and recode fields as well as to easily access deeply-nested fields. Analysis can be done with R (see vignette) or other systems, using the JSON-structured information in the database.

Remember to respect the registers’ terms and conditions (see ctrOpenSearchPagesInBrowser(copyright = TRUE)). Please cite this package in any publication as follows: “Ralf Herold (2025). ctrdata: Retrieve and Analyze Clinical Trials in Public Registers. R package version 1.21.0, https://cran.r-project.org/package=ctrdata”.

References

Package ctrdata has been used for unpublished works and for these publications:

Alzheimer’s disease Horizon Scanning Report (2024) PDF file, p 10 🔔
Kundu et al. (2024) Analysis of Factors Influencing Enrollment Success in Hematology Malignancy Cancer Clinical Trials (2008-2023). Blood Meeting Abstracts https://doi.org/10.1182/blood-2024-207446 🔔
Lasch et al. (2022) The Impact of COVID‐19 on the Initiation of Clinical Trials in Europe and the United States. Clinical Pharmacology & Therapeutics https://doi.org/10.1002/cpt.2534
Sood et al. (2022) Managing the Evidence Infodemic: Automation Approaches Used for Developing NICE COVID-19 Living Guidelines. medRxiv https://doi.org/10.1101/2022.06.13.22276242
Blogging on Innovation coming to paediatric research
Cancer Research UK (2017) The impact of collaboration: The value of UK medical research to EU science and health
EMA (2017) Results of juvenile animal studies (JAS) and impact on anti-cancer medicine development and use in children PDF file, p 34

Installation

1. Install package `ctrdata` in R

Package ctrdata is on CRAN and on GitHub. Within R, use the following commands to install package ctrdata:

# Install CRAN version:
install.packages("ctrdata")

# Alternatively, install development version:
install.packages("devtools")
devtools::install_github("rfhb/ctrdata", build_vignettes = TRUE)

These commands also install the package’s dependencies (jsonlite, httr, curl, clipr, xml2, nodbi, stringi, tibble, lubridate, jqr, dplyr, zip, readr, digest, countrycode, htmlwidgets, stringdist and V8).

2. Script to automatically copy user’s query from web browser

Optional; works with all registers supported by ctrdata and is recommended for CTIS so that its URL in the web browser reflects the user’s parameters for querying this register.

In the web browser, install the Tampermonkey browser extension, click on “New user script” and then on “Tools”, enter into “Import from URL” this URL: https://raw.githubusercontent.com/rfhb/ctrdata/master/tools/ctrdataURLcopier.js and then click on “Install”.

The browser extension can be disabled and enabled by the user. When enabled, the URLs to all user’s queries in the registers are automatically copied to the clipboard and can be pasted into the queryterm = ... parameter of function ctrLoadQueryIntoDb().

Additionally, this script retrieves results for CTIS when opening search URLs such as https://euclinicaltrials.eu/ctis-public/search#searchCriteria={“status”:[3,4]}.

Overview of functions in `ctrdata`

The functions are listed in the approximate order of use in a user’s workflow (in bold, main functions). See also the package documentation overview.

Function name	Function purpose
`ctrOpenSearchPagesInBrowser()`	Open search pages of registers or execute search in web browser
`ctrFindActiveSubstanceSynonyms()`	Find synonyms and alternative names for an active substance
`ctrGenerateQueries()`	From simple user parameters, generates queries for each register to find trials of interest
`ctrGetQueryUrl()`	Import from clipboard the URL of a search in one of the registers
`ctrLoadQueryIntoDb()`	Retrieve (download) or update, and annotate, information on trials from a register and store in a collection in a database
`ctrShowOneTrial()`	🔔 Show full structure and all data of a trial, interactively select fields of interest for `dbGetFieldsIntoDf()`
`dbQueryHistory()`	Show the history of queries that were downloaded into the collection
`dbFindIdsUniqueTrials()`	Get the identifiers of de-duplicated trials in the collection
`dbFindFields()`	Find names of variables (fields) in the collection
`dbGetFieldsIntoDf()`	Create a data frame (or tibble) from trial records in the database with the specified fields
`dfTrials2Long()`	Transform the data.frame from `dbGetFieldsIntoDf()` into a long name-value data.frame, including deeply nested fields
`dfName2Value()`	From a long name-value data.frame, extract values for variables (fields) of interest (e.g., endpoints)
`dfMergeVariablesRelevel()`	Merge variables into a new variable, optionally map values to a new set of levels

Databases for use with `ctrdata`

Package ctrdata retrieves trial information and stores it in a database collection, which has to be given as a connection object to parameter con for several ctrdata functions. This connection object is created almost identically for the four database backends supported by ctrdata, as shown in the table. For a speed comparison, see the nodbi documentation.

Besides ctrdata functions below, such a connection object can be used with functions of other packages, such as nodbi (see last row in table) or, in case of MongoDB as database backend, mongolite (see vignettes).

Purpose	Function call
Create SQLite database connection	`dbc <- nodbi::src_sqlite(dbname = "name_of_my_database", collection = "name_of_my_collection")`
Create DuckDB database connection	`dbc <- nodbi::src_duckdb(dbdir = "name_of_my_database", collection = "name_of_my_collection")`
Create MongoDB database connection	`dbc <- nodbi::src_mongo(db = "name_of_my_database", collection = "name_of_my_collection")`
Create PostgreSQL database connection	`dbc <- nodbi::src_postgres(dbname = "name_of_my_database"); dbc[["collection"]] <- "name_of_my_collection"`
Use connection with `ctrdata` functions	`ctrdata::{ctrLoadQueryIntoDb, dbQueryHistory, dbFindIdsUniqueTrials, dbFindFields, dbGetFieldsIntoDf}(con = dbc, ...)`
Use connection with `nodbi` functions	e.g., `nodbi::docdb_query(src = dbc, key = dbc$collection, ...)`

Data model of `ctrdata`

Package ctrdata uses the data models that are implicit in data as retrieved from the different registers. No mapping is provided for any register’s data model to a putative target data model. The reasons include that registers’ data models are continually evolving over time, that only few data fields have similar values and meaning between registers, and that the retrieved public data may not correspond to the registers’ internal data model. The structure of data for a specific trial can interactively be inspected and searched using function, see the section below.

Thus, the handling of data from different models of registers is to be done at the time of analysis. This approach allows a high level of flexibility, transparency and reproducibility. To support analyses, ctrdata (from version 1.21.0) provides functions that calculate concepts of clinical trials across registers, which are commonly used in analyses, such as start dates, age groups and statistical tests of results. See help(ctrdata-trial-concepts) and the section Analysis across trials in the example workflow below. For further analyses, see examples of function dfMergeVariablesRelevel() on how to align related fields from different registers for a joint analysis.

In any of the databases, one clinical trial is one document, corresponding to one row in a SQLite, PostgreSQL or DuckDB table, and to one document in a MongoDB collection. These NoSQL backends allow documents to have different structures, which is used here to accommodate the different models of data retrieved from the registers. Package ctrdata stores in every such document:

field _id with the trial identification as provided by the register from which it was retrieved
field ctrname with the name of the register (EUCTR, CTGOV, CTGOV2, ISRCTN, CTIS) from which that trial was retrieved
field record_last_import with the date and time when that document was last updated using ctrLoadQueryIntoDb()
only for CTGOV2: object history with a historic version of the trial and with history_version, which contains the fields version_number (starting from 1) and version_date
all original fields as provided by the register for that trial (see examples below)

For visualising the data structure for a trial, see this vignette section.

Vignettes

Example workflow

The aim is to download protocol-related trial information and tabulate the trials’ status of conduct.

Attach package ctrdata:

library(ctrdata)

See help to get started with ctrdata:

help("ctrdata")

Information on trial registers and how they can be used with ctrdata (last updated 2025-03-09):

help("ctrdata-registers")

Trial concepts across registers provided by ctrdata (new 2025-03-09 🔔):

help("ctrdata-trial-concepts")

Open registers’ advanced search pages in browser:

ctrOpenSearchPagesInBrowser()

# Please review and respect register copyrights:
ctrOpenSearchPagesInBrowser(copyright = TRUE)

Adjust search parameters and execute search in browser
When trials of interest are listed in browser, copy the address from the browser’s address bar to the clipboard (you can automate this, see here)
Search used in this example: https://www.clinicaltrialsregister.eu/ctr-search/search?query=neuroblastoma&phase=phase-two&age=children
Get address from clipboard:

q <- ctrGetQueryUrl()
# * Using clipboard content as register query URL: https://www.clinicaltrialsregister.eu/
# ctr-search/search?query=neuroblastoma&phase=phase-two&age=children
# * Found search query from EUCTR: query=neuroblastoma&phase=phase-two&age=children

q
#                                         query-term query-register
# 1 query=neuroblastoma&phase=phase-two&age=children          EUCTR

🔔 Queries in the trial registers can automatically copied to the clipboard (including for “CTIS”, where the URL otherwise does not show the user’s query) using the solution here.

Retrieve protocol-related information, transform and save to database:

For loading the trial information, first a database collection is specified, using nodbi (see above for how to specify PostgreSQL, RSQlite, DuckDB or MongoDB as backend, see section Databases):

# Connect to (or create) an SQLite database
# stored in a file on the local system:
db <- nodbi::src_sqlite(
  dbname = "some_database_name.sqlite_file",
  collection = "some_collection_name"
)

Then, the trial information is retrieved and loaded into the collection:

# Retrieve trials from public register:
ctrLoadQueryIntoDb(
  queryterm = q,
  euctrresults = TRUE,
  con = db
)
# * Checking trials in EUCTR...
# Retrieved overview, multiple records of 73 trial(s) from 4 page(s) to be downloaded (estimate: 9 MB)
# (1/3) Downloading trials...
# Note: register server cannot compress data, transfer takes longer (estimate: 90 s)
# Download status: 4 done; 0 in progress. Total size: 6.39 Mb (100%)... done!             
# (2/3) Converting to NDJSON (estimate: 1 s)...
# (3/3) Importing records into database...
# = Imported or updated 270 records on 73 trial(s) 
# * Checking results if available from EUCTR for 73 trials: 
# (1/4) Downloading results...
# Download status: 73 done; 0 in progress. Total size: 22.57 Mb (100%)... done!             
# Download status: 41 done; 0 in progress. Total size: 165.04 Kb (100%)... done!             
# Download status: 41 done; 0 in progress. Total size: 165.04 Kb (100%)... done!             
# - extracting results (. = data, F = file[s] and data, x = none):
# F F . . . . . . . F . . . F . . . F . . . . . F . . . . . . . F 
# (2/4) Converting to NDJSON (estimate: 3 s)...
# (3/4) Importing results into database (may take some time)...
# (4/4) Results history: not retrieved (euctrresultshistory = FALSE)
# = Imported or updated results for 32 trials
# No history found in expected format.
# Updated history ("meta-info" in "some_collection_name")
# $n
# [1] 270

Under the hood, EUCTR plain text and XML files from EUCTR, CTGOV, ISRCTN are converted using Javascript via V8 in R into NDJSON, which is imported into the database collection.

Easily generate queries for each register and add records from several registers into the same collection

The same parameters can be used to ask ctrdata to generate search queries that apply to each register, for opening the web interfaces and for loading the trial data into the collection:

# Generate queries for each register
queries <- ctrGenerateQueries(
  condition = "neuroblastoma",
  recruitment = "completed",
  phase = "phase 2",
  population = "P"
)

queries
# EUCTR 
# "https://www.clinicaltrialsregister.eu/ctr-search/search?query=neuroblastoma&phase=phase-two
# &age=children&age=adolescent&age=infant-and-toddler&age=newborn&age=preterm-new-born-infants
# &age=under-18&status=completed" 
# CTGOV2 
# "https://clinicaltrials.gov/search?cond=neuroblastoma&aggFilters=phase:2,ages:child,status:com" 
# ISRCTN 
# "https://www.isrctn.com/search?&filters=condition:neuroblastoma,phase:Phase II,ageRange:Child,trialStatus:completed&q=" 
# CTIS 
# "https://euclinicaltrials.eu/ctis-public/search#searchCriteria={\"medicalCondition\":
# \"neuroblastoma\",\"trialPhaseCode\":[4],\"ageGroupCode\":[2],\"status\":[5,8]}" 

# Open queries in registers' web interfaces
sapply(queries, ctrOpenSearchPagesInBrowser)

# Load all queries into database collection
result <- lapply(queries, ctrLoadQueryIntoDb, con = db)

sapply(result, "[[", "n")
# EUCTR CTGOV2 ISRCTN   CTIS 
#   180    111      0      1

Analyse

Tabulate the status of trials that are part of an agreed paediatric development program (paediatric investigation plan, PIP). ctrdata functions return a data.frame (or a tibble, if package tibble is loaded).

# Get all records that have values in the fields of interest:
result <- dbGetFieldsIntoDf(
  # Field of interest 
  fields = c("a7_trial_is_part_of_a_paediatric_investigation_plan"),
  # Trial concepts calculated across registers
  calculate = c("f.statusRecruitment", "f.isUniqueTrial"),
  con = db
)
# Querying database (35 fields)...
# - Finding duplicates among registers' and sponsor ids...     
# - 114 EUCTR _id were not preferred EU Member State record for 40 trials
# - Keeping 111 / 34 / 0 / 0 / 1 records from CTGOV2 / EUCTR / CTGOV / ISRCTN / CTIS

# Tabulate the clinical trial information of interest
with(
  result[result$.isUniqueTrial, ],
  table(
    .statusRecruitment,
    a7_trial_is_part_of_a_paediatric_investigation_plan
  )
)
#                   a7_trial_is_part_of_a_paediatric_investigation_plan
# .statusRecruitment FALSE TRUE
#        ongoing         3    2
#        completed      13    5
#        ended early     5    4
#        other           9    4

Queries to CTGOV and CTGOV2

The new website and API introduced in July 2023 (https://www.clinicaltrials.gov/) is supported by ctrdata since mid-2023 and identified in ctrdata as CTGOV2.

On 2024-06-25, CTGOV has retired the classic website and API used by ctrdata since 2015. To support users, ctrdata 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. Going forward, users are recommended to change to use CTGOV2 queries.

As regards study data, important differences exist between field names and contents of information retrieved using CTGOV or CTGOV2; see the schema for study protocols in CTGOV, the schema for study results and the Study Data Structure for CTGOV2. For more details, call help("ctrdata-registers"). This is one of the reasons why ctrdata handles the situation as if these were two different registers and will continue to identify the current API as register = "CTGOV2", to support the analysis stage.

Note that loading trials with ctrdata overwrites the previous record with CTGOV2 data, whether the previous record was retrieved using CTGOV or CTGOV2 queries.

Example using a CTGOV query:

# CTGOV search query URL
q <- "https://classic.clinicaltrials.gov/ct2/results?cond=neuroblastoma&rslt=With&recrs=e&age=0&intr=Drug"

# Open old URL (CTGOV) in current website (CTGOV2):
ctrOpenSearchPagesInBrowser(q)
# * Appears specific for CTGOV Classic website
# Since 2024-06-25, the classic CTGOV servers are no longer available. 
# Package ctrdata has translated the classic CTGOV query URL from this call 
# of function ctrLoadQueryIntoDb(queryterm = ...) into a query URL that works 
# with the current CTGOV2. This is printed below and is also part of the return 
# value of this function, ctrLoadQueryIntoDb(...)$url. This URL can be used with 
# ctrdata functions. Note that the fields and data schema of trials differ 
# between CTGOV and CTGOV2. 
#
# Replace this URL:
# 
# https://classic.clinicaltrials.gov/ct2/results?cond=neuroblastoma&rslt=With&recrs=e&age=0&intr=Drug
# 
# with this URL:
# 
# https://clinicaltrials.gov/search?cond=neuroblastoma&intr=Drug&aggFilters=ages:child,results:with,status:com
# 
# * Found search query from CTGOV2: cond=neuroblastoma&intr=Drug&aggFilters=ages:child,results:with,status:com

# Count trials:
ctrLoadQueryIntoDb(
  queryterm = q,
  con = db, 
  only.count = TRUE
)
# $n
# [1] 70

Queries to CTIS

Queries in the CTIS search interface can be automatically copied to the clipboard so that a user can paste them into queryterm, see here. Subsequent to the relaunch of CTIS on 2024-07-18, there are more than 8,700 trials publicly accessible in CTIS. See below for how to download documents from CTIS.

# See how many trials are in CTIS publicly accessible:
ctrLoadQueryIntoDb(
  queryterm = "",
  register = "CTIS",
  only.count = TRUE
)
# $n
# [1] 8783

Inspect and search structure of trial information

For a given trial, function ctrShowOneTrial() enables the user to visualise the hiearchy of fields and contents in the user’s local web browser, to search for field names and field values, and to select and copy selected fields’ names for use with function dbGetFieldsIntoDf().

# This opens a local browser for user interaction. 
# If the trial identifier (_id) is not found in the
# specified collection, it will be retrieved from the register. 
ctrShowOneTrial(
  identifier = "2024-518931-12-00", 
  con = db
)

Analysis across trials

Show cumulative start of trials over time. This uses the calculation of trial concepts as available since ctrdata version 1.21.0 🔔.

# use helper package
library(dplyr)
library(ggplot2)

df <- dbGetFieldsIntoDf(
  fields = "",
  calculate = c("f.statusRecruitment", "f.isUniqueTrial", "f.startDate"),
  con = db)

df %>%
  filter(.isUniqueTrial) %>%
  ggplot() +
  stat_ecdf(aes(
    x = .startDate,
    colour = .statusRecruitment)) + 
  labs(
    title = "Evolution over time of selected trials", 
    subtitle = "Data from EUCTR, CTIS, ISRCTN, CTGOV2",
    x = "Date of start (proposed or realised)", 
    y = "Cumulative proportion of trials",
    colour = "Current status",
    caption = Sys.Date()
  )

ggsave(
  filename = "man/figures/README-ctrdata_across_registers.png",
  width = 5, height = 3, units = "in"
)

Result-related trial information

Analyse some simple result details, here from CTGOV2 (see this vignette for more examples):

# use helper package
library(ggplot2)

result <- dbGetFieldsIntoDf(
  calculate = c(
    "f.numSites", 
    "f.sampleSize", 
    "f.controlType", 
    "f.numTestArmsSubstances"),
  con = db
)

ggplot(data = result) +
  labs(
    title = "Selected trials",
    subtitle = "Patients with a neuroblastoma"
  ) +
  geom_point(
    mapping = aes(
      x = .numSites,
      y = .sampleSize,
      size = .numTestArmsSubstances,
      colour = .controlType
    )
  ) +
  scale_x_log10() +
  scale_y_log10() +
  labs(
    x = "Number of sites",
    y = "Total number of participants",
    colour = "Control", 
    size = "# Treatments",
    caption = Sys.Date()
  )
ggsave(
  filename = "man/figures/README-ctrdata_results_neuroblastoma.png",
  width = 5, height = 3, units = "in"
)

Download documents: retrieve protocols, statistical analysis plans and other documents into the local folder ./files-.../

### EUCTR document files can be downloaded when results are requested
# All files are downloaded and saved (documents.regexp is not used with EUCTR) 
ctrLoadQueryIntoDb(
  queryterm = "query=cancer&age=under-18&phase=phase-one",
  register = "EUCTR",
  euctrresults = TRUE,
  documents.path = "./files-euctr/",
  con = db
)
# * Found search query from EUCTR: query=cancer&age=under-18&phase=phase-one
# * Checking trials in EUCTR...
# [...]
# = documents saved in './files-euctr'
# Updated history ("meta-info" in "some_collection_name")


### CTGOV files are downloaded, here corresponding to the default of 
# documents.regexp = "prot|sample|statist|sap_|p1ar|p2ars|ctalett|lay|^[0-9]+ "
ctrLoadQueryIntoDb(
  queryterm = "cond=Neuroblastoma&type=Intr&recrs=e&phase=1&u_prot=Y&u_sap=Y&u_icf=Y",
  register = "CTGOV",
  documents.path = "./files-ctgov/",
  con = db
)
# * Checking for documents...
# - Getting links to documents
# - Downloading documents into 'documents.path' = ./files-ctgov/
# - Created directory ./files-ctgov
# - Applying 'documents.regexp' to 40 missing documents
# - Creating subfolder for each trial
# - Downloading 40 missing documents 
# Download status: 40 done; 0 in progress. Total size: 110.75 Mb (100%)... done!             
# = Newly saved 40 document(s) for 32 trial(s); 0 of such document(s) for 0 trial(s) 
# already existed in ./files-ctgov


### CTGOV2 files are downloaded, using the default of documents.regexp
ctrLoadQueryIntoDb(
  queryterm = "https://clinicaltrials.gov/search?cond=neuroblastoma&aggFilters=phase:1,results:with",
  documents.path = "./files-ctgov2/",
  con = db
)
# * Checking for documents...
# - Getting links to documents
# - Downloading documents into 'documents.path' = ./files-ctgov2/
# - Created directory ./files-ctgov2
# - Creating subfolder for each trial
# - Applying 'documents.regexp' to 42 missing documents
# - Downloading 42 missing documents
# Download status: 42 done; 0 in progress. Total size: 92.57 Mb (100%)... done!             
# = Newly saved 42 document(s) for 26 trial(s); 0 of such document(s) for 0 
# trial(s) already existed in ./files-ctgov2


### ISRCTN files are downloaded, using the default of documents.regexp
ctrLoadQueryIntoDb(
  queryterm = "https://www.isrctn.com/search?q=alzheimer",
  documents.path = "./files-isrctn/",
  con = db
)
# * Found search query from ISRCTN: q=alzheimer
# [...]
# * Checking for documents...                      
# - Getting links to documents
# - Downloading documents into 'documents.path' = ./files-isrctn/
# - Created directory /Users/ralfherold/Daten/mak/r/emea/ctrdata/files-isrctn
# - Applying 'documents.regexp' to 52 missing documents
# - Creating subfolder for each trial
# - Downloading 32 missing documents 
# Download status: 32 done; 0 in progress. Total size: 14.89 Mb (100%)... done!             
# = Newly saved 26 document(s) for 15 trial(s); 0 of such document(s) for 0 
# trial(s) already existed in ./files-isrctn


### CTIS files are downloaded, using the default of documents.regexp
ctrLoadQueryIntoDb(
  queryterm = paste0(
    'https://euclinicaltrials.eu/ctis-public/search#', 
    'searchCriteria={"containAny":"cancer","status":[8]}'),
  documents.path = "./files-ctis/",
  documents.regexp = "icf",
  con = db
)
# * Found search query from CTIS: searchCriteria={"containAny":"cancer"}
# [...]
# * Checking for documents: . . . . . . . . . . . . . . . . . . . 
# - Downloading documents into 'documents.path' = ./files-ctis/
# - Applying 'documents.regexp' to 1114 missing documents
# - Creating subfolder for each trial
# - Downloading 512 missing documents (excluding 2 files with duplicate names 
# for saving, e.g. /Users/ralfherold/Daten/mak/r/emea/ctrdata/files-ctis/2022-
# 500694-14-00/SbjctInfaICF - L1 SIS and ICF Prescreening ICF clean placeholder
# - 137297.PDF, /Users/ralfherold/Daten/mak/r/emea/ctrdata/files-ctis/2022-
# 500694-14-00/SbjctInfaICF - L1 SIS and ICF Pregnant Partner ICF clean - 
# 137297.PDF) 
# Download status: 510 done; 0 in progress. Total size: 377.27 Kb (100%)... done!             
# Redirecting to CDN...
# Download status: 127 done; 0 in progress. Total size: 47.66 Mb (100%)... done!             
# = Newly saved 510 document(s) for 35 trial(s); 0 of such document(s) for 0 
# trial(s) already existed in ./files-ctis

Tests

tinytest::test_all()
# test_ctrdata_ctrfindactivesubstance.R    4 tests OK 0.8s
# test_ctrdata_duckdb_ctgov2.R..   78 tests OK 47.3s
# test_ctrdata_function_ctrgeneratequeries.R   12 tests OK 4ms
# test_ctrdata_function_dfcalculate.R   26 tests OK 2.0s
# test_ctrdata_other_functions.R   67 tests OK 3.1s
# test_ctrdata_postgres_ctgov2.R   50 tests OK 32.0s
# test_ctrdata_sqlite_ctgov.R...  108 tests OK 30.8s
# test_ctrdata_sqlite_ctgov2.R..   50 tests OK 26.8s
# test_ctrdata_sqlite_ctis.R....   63 tests OK 49.4s
# test_ctrdata_sqlite_euctr.R...  115 tests OK 44.2s
# test_ctrdata_sqlite_isrctn.R..   38 tests OK 12.5s
# test_euctr_error_sample.R.....    8 tests OK 0.2s
# All ok, 619 results (4m 9.2s)

covr::package_coverage(path = ".", type = "tests")
# ctrdata Coverage: 94.06%
# R/ctrShowOneTrial.R: 57.89%
# R/ctrRerunQuery.R: 74.85%
# R/zzz.R: 80.95%
# R/dbGetFieldsIntoDf.R: 86.90%
# R/util_functions.R: 89.52%
# R/ctrLoadQueryIntoDbEuctr.R: 90.08%
# R/ctrGetQueryUrl.R: 90.09%
# R/ctrLoadQueryIntoDbIsrctn.R: 92.45%
# R/ctrLoadQueryIntoDbCtgov2.R: 92.90%
# R/ctrFindActiveSubstanceSynonyms.R: 93.62%
# R/dfMergeVariablesRelevel.R: 94.29%
# R/ctrLoadQueryIntoDb.R: 94.81%
# R/ctrLoadQueryIntoDbCtis.R: 95.26%
# R/dbFindFields.R: 95.88%
# R/vct_primaryEndpointResults.R: 96.27%
# R/ctrOpenSearchPagesInBrowser.R: 97.37%
# R/dbFindIdsUniqueTrials.R: 97.87%
# R/vct_numTestArmsSubstances.R: 97.95%
# R/ctrGenerateQueries.R: 100.00%
# R/dbQueryHistory.R: 100.00%
# R/dfName2Value.R: 100.00%
# R/dfTrials2Long.R: 100.00%
# R/vct_controlType.R: 100.00%
# R/vct_isMedIntervTrial.R: 100.00%
# R/vct_isPlatformTrial.R: 100.00%
# R/vct_isUniqueTrial.R: 100.00%
# R/vct_numSites.R: 100.00%
# R/vct_primaryEndpointDescription.R: 100.00%
# R/vct_resultsDate.R: 100.00%
# R/vct_sampleSize.R: 100.00%
# R/vct_sponsorType.R: 100.00%
# R/vct_startDate.R: 100.00%
# R/vct_statusRecruitment.R: 100.00%
# R/vct_trialObjectives.R: 100.00%
# R/vct_trialPhase.R: 100.00%
# R/vct_trialPopulation.R: 100.00%

Future features

See project outline https://github.com/users/rfhb/projects/1
Authentication, expected to be required by CTGOV2; specifications not yet known (work not yet started).
Explore further registers (exploration is continually ongoing; added value, terms and conditions for programmatic access vary; no clear roadmap is established yet).

Implemented:

Retrieve previous versions of protocol- or results-related information. The challenges include, historic versions can only be retrieved one-by-one, do not include results, or are not in structured format. The functionality available with version 1.17.3 to the extent that is possible at this time, namely for protocol- and results-related information in CTGOV2, only
Canonical definitions, filters, calculations are in the works (since August 2023) for data mangling and analyses across registers, e.g. to define study population, identify interventional trials, calculate study duration; public collaboration on these canonical scripts will speed up harmonising analyses.
Merge results-related fields retrieved from different registers, such as corresponding endpoints (work not yet started). The challenge is the incomplete congruency and different structure of data fields.

Acknowledgements

Data providers and curators of the clinical trial registers. Please review and respect their copyrights and terms and conditions, see ctrOpenSearchPagesInBrowser(copyright = TRUE).
Package ctrdata has been made possible building on the work done for R, clipr. curl, dplyr, duckdb, httr, jqr, jsonlite, lubridate, mongolite, nodbi, RPostgres, RSQLite, rvest, stringi and xml2.

Issues and notes

Information in trial registers may not be fully correct; see for example this publication on CTGOV.
A warning may be issued and a record not imported if the complexity of the XML content is too high for processing. The issue can be resolved by increasing in the operating system the stack size available to R, see: https://github.com/rfhb/ctrdata/issues/22
Please file issues and bugs here. Also check out how to handle some of the closed issues, e.g. on C stack usage too close to the limit and on a SSL certificate problem: unable to get local issuer certificate.

Trial records in databases

SQLite

It is recommended to use nodbi >= 0.10.7.9000 which builds on RSQLite >= 2.3.7.9014 (releases expected in November 2024), because these versions enable file-based imports and thus are much faster:

# install latest development versions:
devtools::install_github("ropensci/nodbi")

# requires compilation, for which under MS Windows
# automatically additional R Tools are installed:
devtools::install_github("r-dbi/RSQLite")