documentation update

R/ctrShowOneTrial.R

@@ -8,6 +8,7 @@
 #' \code{con} is provided or if the trial is not in database \code{con}.
 #'
 #' This is the widget for CTIS trial 2022-501142-30-00:
+#'
 #' \if{html}{
 #'   \out{<span style="text-align: left">}
 #'   \figure{ctrdata_ctrShowOneTrial.jpg}{options: style="width:500px;max-width:75\%;"}

R/ctrdata-package.R

@@ -42,7 +42,6 @@
 #' \link{dfName2Value} (get values for variable(s) of interest).
 #'
 #' @name ctrdata
-#' @docType package
 #' @author Ralf Herold \email{ralf.herold@@mailbox.org}
 #' @keywords package
 #' @md

R/ctrdata-registers.R

@@ -1,67 +1,68 @@
 #' ctrdata: information on clinical trial registers
 #'
-#' Registers of clinical trials from which protocol- and result-related information
-#' can be retrieved and analysed with package \link{ctrdata}, last updated
-#' 2024-12-15.
+#' Information on registers of clinical trials from which package \link{ctrdata}
+#' can retrieve, aggregate and analyse protocol- and result-related information
+#' as well as documents, last updated 2024-12-27.
 #'
 #' @section 1 - Overview:
 #'
-#' - **EUCTR**: The EU Clinical Trials Register contains more than 44,200 clinical
+#' - **EUCTR**: The EU Clinical Trials Register holds more than 44,200 clinical
 #' trials (at least one investigational medicinal product, IMP; in the European
-#' Union and beyond; no new trials, and results of trials continue to be added)
-#' - **CTIS**: The EU Clinical Trials Information System started in January 2023
-#' for new clinical trials. It includes more than 8,000 publicly accessible trials.
-#' How to automatically get the CTIS search query URL: \ifelse{latex}{\out{\href{https://rfhb.github.io/ctrdata/\#id_2-script-to-automatically-copy-users-query-from-web-browser}{here}}}{\href{https://rfhb.github.io/ctrdata/#id_2-script-to-automatically-copy-users-query-from-web-browser}{here}}
-#' - **CTGOV2**: ClinicalTrials.gov includes more than 518,000 interventional and
+#' Union and beyond; results of trials continue to be added)
+#' - **CTIS**: The EU Clinical Trials Information System was launched in January
+#' 2023 and holds more than 8,150 publicly accessible clinical trials
+#' (to automatically get CTIS search query URLs, see \ifelse{latex}{\out{\href{https://rfhb.github.io/ctrdata/\#id_2-script-to-automatically-copy-users-query-from-web-browser}{here}}}{\href{https://rfhb.github.io/ctrdata/#id_2-script-to-automatically-copy-users-query-from-web-browser}{here}})
+#' - **CTGOV2**: ClinicalTrials.gov holds more than 520,500 interventional and
 #' observational studies
-#' - **ISRCTN**: The ISRCTN Registry includes more than 25,700 interventional and
+#' - **ISRCTN**: The ISRCTN Registry holds more than 25,750 interventional and
 #' observational health studies
 #'
 #' @section 2 - Notable changes:
 #'
-#' CTGOV was retired on 2024-06-25; `ctrdata` subsequently translates CTGOV
-#' queries to CTGOV2 queries. The new website (CTGOV2) can be used with `ctrdata`
-#' since 2023-08-27. CTIS was relaunched on 2024-06-17, changing the data
-#' structure and search syntax, to which `ctrdata` was updated. CTIS can be used
+#' CTGOV "classic" was retired on 2024-06-25; `ctrdata` subsequently translates
+#' CTGOV queries to CTGOV2 queries. The new website ("CTGOV2") can be used with
+#' `ctrdata` since 2023-08-27.
+#' CTIS was relaunched on 2024-06-17, changing the data structure and search
+#' syntax, to which `ctrdata` was updated. CTIS can be used
 #' with `ctrdata` since 2023-03-25. More information on changes:
 #' \href{https://rfhb.github.io/ctrdata/news/index.html}{here}.
 #'
 #' @section 3 - References:
 #'
 #' | **Material** | **EUCTR** | **CTGOV2**| **ISRCTN** | **CTIS** |
 #' | -------------- | :--------------: | :--------------: | :--------------: | :--------------: |
-#' | Home page | \href{https://www.clinicaltrialsregister.eu/}{link} | \href{https://clinicaltrials.gov/}{link} | \href{https://www.isrctn.com/}{link} | \href{https://euclinicaltrials.eu/}{link} |
 #' | About | \href{https://www.clinicaltrialsregister.eu/about.html}{link} | \href{https://clinicaltrials.gov/about-site/about-ctg}{link} | \href{https://www.isrctn.com/page/about}{link} | \href{https://euclinicaltrials.eu/about-this-website/}{link} |
-#' | Terms & conditions, disclaimer | \href{https://www.clinicaltrialsregister.eu/disclaimer.html}{link} | \ifelse{latex}{\out{\href{https://clinicaltrials.gov/about-site/terms-conditions\#usage}{link}}}{\href{https://clinicaltrials.gov/about-site/terms-conditions#usage}{link}} | \ifelse{latex}{\out{\href{https://www.isrctn.com/page/faqs\#using-the-isrctn}{link}}}{\href{https://www.isrctn.com/page/faqs#using-the-isrctn}{link}} | \href{https://euclinicaltrials.eu/guidance-and-q-as/}{link} |
+#' | Terms & conditions, disclaimer | \href{https://www.clinicaltrialsregister.eu/disclaimer.html}{link} | \href{https://clinicaltrials.gov/about-site/terms-conditions}{link} | \ifelse{latex}{\out{\href{https://www.isrctn.com/page/faqs\#using-the-isrctn}{link}}}{\href{https://www.isrctn.com/page/faqs#using-the-isrctn}{link}} | \href{https://euclinicaltrials.eu/guidance-and-q-as/}{link} |
 #' | How to search | \href{https://www.clinicaltrialsregister.eu/doc/How_to_Search_EU_CTR.pdf}{link} | \href{https://clinicaltrials.gov/find-studies/how-to-search}{link} | \href{https://www.isrctn.com/page/search-tips}{link} | \href{https://euclinicaltrials.eu/search-tips-and-guidance/}{link} |
 #' | Search interface | \href{https://www.clinicaltrialsregister.eu/ctr-search/search}{link} | \href{https://clinicaltrials.gov/}{link} | \href{https://www.isrctn.com/}{link} | \href{https://euclinicaltrials.eu/search-for-clinical-trials/}{link} |
 #' | Expert / advanced search | \href{https://www.clinicaltrialsregister.eu/ctr-search/search}{link} | \href{https://clinicaltrials.gov/expert-search}{link} | \href{https://www.isrctn.com/editAdvancedSearch}{link} | \href{https://euclinicaltrials.eu/ctis-public/search}{link} |
-#' | Glossary | \href{https://www.clinicaltrialsregister.eu/doc/EU_Clinical_Trials_Register_Glossary.pdf}{link} | \href{https://clinicaltrials.gov/study-basics/glossary}{link} | \href{https://www.who.int/clinical-trials-registry-platform/network/who-data-set}{link} | |
+#' | Glossary / related information | \href{https://www.clinicaltrialsregister.eu/doc/EU_Clinical_Trials_Register_Glossary.pdf}{link} | \href{https://clinicaltrials.gov/study-basics/glossary}{link} | \href{https://www.who.int/clinical-trials-registry-platform/network/who-data-set}{link} | \href{https://accelerating-clinical-trials.europa.eu/}{link} |
 #' | FAQ, caveats, issues | \href{https://www.clinicaltrialsregister.eu/doc/EU_CTR_FAQ.pdf}{link} | \href{https://clinicaltrials.gov/about-site/selected-publications}{link} | \href{https://www.isrctn.com/page/faqs}{link} | \href{https://euclinicaltrials.eu/website-outages-and-system-releases/}{link} |
-#' | Definitions of fields | \href{https://eudract.ema.europa.eu/result.html}{link} | \href{https://clinicaltrials.gov/data-about-studies/study-data-structure}{link}, \href{https://cdn.clinicaltrials.gov/documents/tutorial/content/index.html}{link} | \href{https://www.isrctn.com/page/definitions}{link} | \href{https://www.ema.europa.eu/en/human-regulatory-overview/research-development/clinical-trials-human-medicines/clinical-trials-information-system-ctis-training-support}{link} |
+#' | Data dictionaries / definitions / structure reference | \href{https://eudract.ema.europa.eu/result.html}{link} | \href{https://clinicaltrials.gov/data-about-studies/study-data-structure}{link}, \href{https://cdn.clinicaltrials.gov/documents/tutorial/content/index.html}{link} | \href{https://www.isrctn.com/page/definitions}{link} | \href{https://www.ema.europa.eu/en/human-regulatory-overview/research-development/clinical-trials-human-medicines/clinical-trials-information-system-ctis-training-support}{link} |
 #' | Example* | \ifelse{latex}{\out{\href{https://www.clinicaltrialsregister.eu/ctr-search/search?query=Infections\&age=newborn\&age=preterm-new-born-infants}{link}}}{\href{https://www.clinicaltrialsregister.eu/ctr-search/search?query=Infections&age=newborn&age=preterm-new-born-infants}{link}} | \ifelse{latex}{\out{\href{https://clinicaltrials.gov/search?ageRange=0M_1M\&cond=Infections\&aggFilters=studyType:int\&distance=50\&intr=Investigational+Agent}{link}}}{\href{https://clinicaltrials.gov/search?ageRange=0M_1M&cond=Infections&aggFilters=studyType:int&distance=50&intr=Investigational+Agent}{link}} | \ifelse{latex}{\out{\href{https://www.isrctn.com/search?q=\&filters=ageRange:Neonate,conditionCategory:Infections+and+Infestations\&searchType=advanced-search}{link}}}{\href{https://www.isrctn.com/search?q=&filters=ageRange:Neonate,conditionCategory:Infections+and+Infestations&searchType=advanced-search}{link}} | \ifelse{latex}{\out{\href{https://euclinicaltrials.eu/ctis-public/search\#searchCriteria={"containAll":"infection","containAny":"neonates","containNot":""}}{link}}}{\href{https://euclinicaltrials.eu/ctis-public/search#searchCriteria={"containAll":"infection","containAny":"neonates"}}{link}} |
 #'
 #' @section 4 - Example and ctrdata motivation:
 #'
-#' *The example is an expert search for interventional trials primarily with neonates, investigating infectious conditions.
-#' It shows that searches in registers may not be sufficient to identify the sought trials:
+#' *The example is an expert search for interventional trials primarily with
+#' neonates, investigating treatments for infectious conditions. It shows that
+#' searches in the web interface of most registers are not sufficient to
+#' identify the trials of interest:
 #'
-#' - The CTGOV2 search retrieves trials conducted exclusively with neonates.
 #' - EUCTR retrieves trials with neonates, but not only those exclusively in neonates.
 #' - ISRCTN retrieves studies with interventions other than medicines.
-#' - CTIS retrieves trials that mention the words neonates and infection. To
-#' show search results, see \ifelse{latex}{\out{\href{https://rfhb.github.io/ctrdata/\#id_2-script-to-automatically-copy-users-query-from-web-browser}{here}}}{\href{https://rfhb.github.io/ctrdata/#id_2-script-to-automatically-copy-users-query-from-web-browser}{here}}
+#' - CTIS retrieves trials that mention the words neonates and infection. (To
+#' show CTIS search results, see \ifelse{latex}{\out{\href{https://rfhb.github.io/ctrdata/\#id_2-script-to-automatically-copy-users-query-from-web-browser}{here}}}{\href{https://rfhb.github.io/ctrdata/#id_2-script-to-automatically-copy-users-query-from-web-browser}{here}})
 #'
-#' To address this, trials can be retrieved with \link{ctrLoadQueryIntoDb}
-#' into a database collection and in a second step can be selected,
-#' based on values of relevant fields of all retrieved trial information,
-#' for example:
+#' To address this issue, trials can be retrieved with \link{ctrLoadQueryIntoDb}
+#' into a database collection and in a second step trials of interest can be
+#' selected based on values of relevant fields, for example:
 #'
-#' - EUCTR field \code{f115_children_211years} for age criteria
+#' - EUCTR field \code{f115_children_211years} and other age group criteria
 #' - ISRCTN field \code{interventions.intervention.interventionType} for type of study
 #' - CTIS fields \code{ageGroup} and \code{authorizedApplication.authorizedPartI.medicalConditions.medicalCondition}
 #'
-#' `ctrdata` helps identifying fields with function \link{dbGetFieldsIntoDf}.
+#' `ctrdata` supports users in identifying fields with functions
+#' \link{dbFindFields} and \link{ctrShowOneTrial}.
 #'
 #' @name ctrdata-registers
 #' @docType data

R/ctrdata.R

@@ -0,0 +1,2 @@
+#' @keywords internal
+"_PACKAGE"

R/dbFindFields.R

@@ -57,7 +57,7 @@
 #'
 #' dbFindFields(namepart = "date", con = dbc)[1:5]
 #'
-#' # view all 3350+ fields from all registers:
+#' # view all 1880+ fields from all registers:
 #'
 #' allFields <- dbFindFields(con = dbc, sample = FALSE)
 #'

README.Rmd

@@ -39,14 +39,14 @@ knitr::opts_chunk$set(
 
 # ctrdata for aggregating and analysing clinical trials
 
-The package `ctrdata` provides functions for retrieving (downloading), aggregating and analysing information on clinical trials from public registers. It can be used for the
+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](#workflow-ctis-example))
 - ClinicalTrials.gov ("CTGOV2", see [example](#workflow-ctgov-example))
 - ISRCTN Registry (https://www.isrctn.com/) 
 
-The motivation is to investigate and understand trends in design and conduct of trials, their availability for patients and to facilitate using their detailed results for research and meta-analyses. `ctrdata` is a package for the [R](https://www.r-project.org/) system, but other systems and tools can be used with the databases created with the package. This README was reviewed on 2024-12-15 for version 1.20.0.9000.
+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](https://www.r-project.org/) system, but other systems and tools can use the databases created with this package. This README was reviewed on 2024-12-27 for version 1.20.0.9000.
 
 ## Main features
 

README.md

@@ -20,8 +20,9 @@ model](#data-model-of-ctrdata) • [Example workflow](#example-workflow) •
 # ctrdata for aggregating and analysing clinical trials
 
 The package `ctrdata` provides functions for retrieving (downloading),
-aggregating and analysing information on clinical trials from public
-registers. It can be used for the
+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/>)
@@ -30,12 +31,12 @@ registers. It can be used for the
 - ClinicalTrials.gov (“CTGOV2”, see [example](#workflow-ctgov-example))
 - ISRCTN Registry (<https://www.isrctn.com/>)
 
-The motivation is to investigate and understand trends in design and
-conduct of trials, their availability for patients and to facilitate
-using their detailed results for research and meta-analyses. `ctrdata`
-is a package for the [R](https://www.r-project.org/) system, but other
-systems and tools can be used with the databases created with the
-package. This README was reviewed on 2024-12-15 for version 1.20.0.9000.
+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](https://www.r-project.org/) system,
+but other systems and tools can use the databases created with this
+package. This README was reviewed on 2024-12-27 for version 1.20.0.9000.
 
 ## Main features
 

docs/pkgdown.yml

@@ -5,7 +5,7 @@ articles:
   ctrdata_install: ctrdata_install.html
   ctrdata_retrieve: ctrdata_retrieve.html
   ctrdata_summarise: ctrdata_summarise.html
-last_built: 2024-12-16T17:35Z
+last_built: 2024-12-29T08:22Z
 urls:
   reference: https://rfhb.github.io/ctrdata/reference
   article: https://rfhb.github.io/ctrdata/articles