docs and pkgdown update

Author: rfhb

NEWS.md

@@ -2,11 +2,13 @@
 
 ## Improvements
 - When using `querytoupdate` for CTIS, set `ctishistory = TRUE` to create historic versions from previously downloaded trial record, see `vignette("ctrdata_summarise")`
+- `ctrGenerateQueries()` now also covers countries of trial conduct and now defaults to interventional trials with medicines
 - Trial concept `f.trialObjectives()` improved with structured data from CTIS and EUCTR
-- `ctrGenerateQueries()` now also covers countries of trial conduct
 
-## Bug fix 
-- Fix digesting marginal cases in notifications in `f.statusRecruitment()`
+## Bug fix
+- Fixed for `ISRCTN` API term mangling
+- Fixed digesting marginal cases in notifications in `f.statusRecruitment()`
+- Fixed `ctrGenerateQueries` to handle 'or' as needed for certain filters
 
 # ctrdata 1.21.1
 

R/ctrGenerateQueries.R

@@ -29,9 +29,10 @@
 #' with EUCTR)
 #' @param completedAfter String that can be interpreted as date (does not work
 #' with EUCTR)
+#' @param onlyMedIntervTrials Logical, default \code{TRUE}, which indicates if
+#' queries should search only for medicine interventional clinical trial
 #' @param onlyWithResults Logical
-#' @param countries Vector of country names, two- or three-letter
-#' ISO 3166 codes
+#' @param countries Vector of country names, two- or three-letter ISO 3166 codes
 #'
 #' @returns Named vector of URLs for finding trials in the registers and as
 #' input to functions \link{ctrLoadQueryIntoDb} and

R/ctrdata-registers.R

@@ -2,7 +2,7 @@
 #'
 #' Registers of the four clinical trial registers from which package
 #' \link{ctrdata} can retrieve, aggregate and analyse protocol- and
-#' result-related information as well as documents, last updated 2025-04-06.
+#' result-related information as well as documents, last updated 2025-04-13.
 #'
 #' @section 1 - Overview:
 #'
@@ -12,14 +12,14 @@
 #' to be added (can be loaded by `ctrdata`).
 #'
 #' - **CTIS**: The EU Clinical Trials Information System, launched in 2023,
-#' holds more than 8,700 publicly accessible clinical trials, including
+#' holds more than 8,900 publicly accessible clinical trials, including
 #' around 100 with results or a report (only as PDF files).
 #' _No results in a structured electronic format are foreseeably available_,
 #' thus `ctrdata` cannot load any CTIS results.
 #' (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 529,000 interventional and
+#' - **CTGOV2**: ClinicalTrials.gov holds more than 533,000 interventional and
 #' observational studies, including almost 66,000 interventional studies with
 #' results (can be loaded by `ctrdata`).
 #'
@@ -53,7 +53,7 @@
 #' | 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 / 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/policy/faq}{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} |
-#' | Data dictionaries / definitions / structure reference | \href{https://eudract.ema.europa.eu/result.html}{link} | \href{https://cdn.clinicaltrials.gov/documents/xsd/public.xsd}{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} (XLSX files) |
+#' | Data dictionaries / definitions / structure reference | \href{https://eudract.ema.europa.eu/result.html}{link}, \href{https://eudract.ema.europa.eu/docs/technical/EudraCT%20protocol%20related%20data%20dictionary.xls}{link}, \href{https://eudract.ema.europa.eu/docs/technical/V7_V8_Country_List_20210804.xlsx}{link} | \href{https://cdn.clinicaltrials.gov/documents/xsd/public.xsd}{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} (XLSX files) |
 #' | 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}} |
 #'
 #' Some registers are expanding entered search terms using dictionaries

README.Rmd

@@ -46,7 +46,7 @@ The package `ctrdata` provides functions for retrieving (downloading), aggregati
 - ClinicalTrials.gov ("CTGOV2", see [example](#workflow-ctgov-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](https://www.r-project.org/) system, but other systems and tools can use the databases created with this package. This README was reviewed on 2025-04-02 for version 1.21.1.9000.
+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 2025-04-13 for version 1.21.1.9000.
 
 ## Main features
 
@@ -637,46 +637,32 @@ unlink("./files-isrctn/", recursive = TRUE)
 ```
 
 
-## Tests
+## Tests and coverage
 
 See also [https://app.codecov.io/gh/rfhb/ctrdata/tree/master/R](https://app.codecov.io/gh/rfhb/ctrdata/tree/master/R)
 
 ```{r}
 tinytest::test_all()
-# test_ctrdata_duckdb_ctgov2.R..   78 tests OK 48.7s
-# test_ctrdata_function_activesubstance.R    4 tests OK 1.3s
-# test_ctrdata_function_ctrgeneratequeries.R   14 tests OK 5ms
-# test_ctrdata_function_params.R   25 tests OK 1.0s
-# test_ctrdata_function_trial-concepts.R   80 tests OK 4.6s
-# test_ctrdata_function_various.R   67 tests OK 3.4s
-# test_ctrdata_postgres_ctgov2.R   50 tests OK 32.1s
-# test_ctrdata_sqlite_ctgov.R...   46 tests OK 28.9s
-# test_ctrdata_sqlite_ctgov2.R..   50 tests OK 27.0s
-# test_ctrdata_sqlite_ctis.R....   63 tests OK 56.9s
-# test_ctrdata_sqlite_euctr.R...  115 tests OK 46.3s
-# test_ctrdata_sqlite_isrctn.R..   38 tests OK 10.6s
-# test_euctr_error_sample.R.....    8 tests OK 0.2s
-# All ok, 638 results (4m 21.4s)
 
 covr::package_coverage(path = ".", type = "tests")
-# ctrdata Coverage: 94.30%
+# ctrdata Coverage: 94.69%
 # R/ctrShowOneTrial.R: 57.89%
-# R/ctrRerunQuery.R: 74.85%
 # R/zzz.R: 80.95%
 # R/dbGetFieldsIntoDf.R: 86.99%
-# R/util_functions.R: 89.86%
+# R/ctrRerunQuery.R: 89.18%
+# R/util_functions.R: 89.81%
 # R/ctrLoadQueryIntoDbEuctr.R: 90.08%
 # R/ctrFindActiveSubstanceSynonyms.R: 90.38%
 # R/ctrGetQueryUrl.R: 92.04%
-# R/ctrLoadQueryIntoDbIsrctn.R: 92.45%
-# R/ctrLoadQueryIntoDbCtgov2.R: 92.72%
+# R/ctrLoadQueryIntoDbCtgov2.R: 92.68%
+# R/ctrLoadQueryIntoDbIsrctn.R: 92.81%
 # R/dfMergeVariablesRelevel.R: 94.29%
-# R/ctrLoadQueryIntoDbCtis.R: 95.26%
+# R/ctrLoadQueryIntoDbCtis.R: 95.34%
 # R/dbFindFields.R: 95.88%
 # R/f_primaryEndpointResults.R: 96.00%
-# R/ctrLoadQueryIntoDb.R: 96.77%
-# R/ctrOpenSearchPagesInBrowser.R: 97.37%
-# R/ctrGenerateQueries.R: 97.51%
+# R/ctrLoadQueryIntoDb.R: 96.86%
+# R/ctrGenerateQueries.R: 97.31%
+# R/ctrOpenSearchPagesInBrowser.R: 97.40%
 # R/dbFindIdsUniqueTrials.R: 98.78%
 # R/f_numTestArmsSubstances.R: 98.92%
 # R/f_likelyPlatformTrial.R: 99.13%
@@ -710,11 +696,11 @@ covr::package_coverage(path = ".", type = "tests")
 
 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~~
+* ~~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 at this time, is to retrieve any version in CTGOV2, and to create a version when re-running a CTIS query and retrieving new data.~~
 
-* ~~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.~~ 
+* ~~Canonical definitions, filters, calculations are in the works (since August 2023, released in version 1.20.0) 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.~~
+* ~~Merge results-related fields retrieved from different registers, such as corresponding endpoints. The challenge is the incomplete congruency and different structure of data fields. This has largely been implemented as per the previous bullet point.~~
 
 
 ## Acknowledgements

README.md

@@ -37,7 +37,7 @@ 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 2025-04-02 for version 1.21.1.9000.
+package. This README was reviewed on 2025-04-13 for version 1.21.1.9000.
 
 ## Main features
 
@@ -801,46 +801,32 @@ ctrLoadQueryIntoDb(
 # trial(s) already existed in ./files-ctis
 ```
 
-## Tests
+## Tests and coverage
 
 See also <https://app.codecov.io/gh/rfhb/ctrdata/tree/master/R>
 
 ``` r
 tinytest::test_all()
-# test_ctrdata_duckdb_ctgov2.R..   78 tests OK 48.7s
-# test_ctrdata_function_activesubstance.R    4 tests OK 1.3s
-# test_ctrdata_function_ctrgeneratequeries.R   14 tests OK 5ms
-# test_ctrdata_function_params.R   25 tests OK 1.0s
-# test_ctrdata_function_trial-concepts.R   80 tests OK 4.6s
-# test_ctrdata_function_various.R   67 tests OK 3.4s
-# test_ctrdata_postgres_ctgov2.R   50 tests OK 32.1s
-# test_ctrdata_sqlite_ctgov.R...   46 tests OK 28.9s
-# test_ctrdata_sqlite_ctgov2.R..   50 tests OK 27.0s
-# test_ctrdata_sqlite_ctis.R....   63 tests OK 56.9s
-# test_ctrdata_sqlite_euctr.R...  115 tests OK 46.3s
-# test_ctrdata_sqlite_isrctn.R..   38 tests OK 10.6s
-# test_euctr_error_sample.R.....    8 tests OK 0.2s
-# All ok, 638 results (4m 21.4s)
 
 covr::package_coverage(path = ".", type = "tests")
-# ctrdata Coverage: 94.30%
+# ctrdata Coverage: 94.69%
 # R/ctrShowOneTrial.R: 57.89%
-# R/ctrRerunQuery.R: 74.85%
 # R/zzz.R: 80.95%
 # R/dbGetFieldsIntoDf.R: 86.99%
-# R/util_functions.R: 89.86%
+# R/ctrRerunQuery.R: 89.18%
+# R/util_functions.R: 89.81%
 # R/ctrLoadQueryIntoDbEuctr.R: 90.08%
 # R/ctrFindActiveSubstanceSynonyms.R: 90.38%
 # R/ctrGetQueryUrl.R: 92.04%
-# R/ctrLoadQueryIntoDbIsrctn.R: 92.45%
-# R/ctrLoadQueryIntoDbCtgov2.R: 92.72%
+# R/ctrLoadQueryIntoDbCtgov2.R: 92.68%
+# R/ctrLoadQueryIntoDbIsrctn.R: 92.81%
 # R/dfMergeVariablesRelevel.R: 94.29%
-# R/ctrLoadQueryIntoDbCtis.R: 95.26%
+# R/ctrLoadQueryIntoDbCtis.R: 95.34%
 # R/dbFindFields.R: 95.88%
 # R/f_primaryEndpointResults.R: 96.00%
-# R/ctrLoadQueryIntoDb.R: 96.77%
-# R/ctrOpenSearchPagesInBrowser.R: 97.37%
-# R/ctrGenerateQueries.R: 97.51%
+# R/ctrLoadQueryIntoDb.R: 96.86%
+# R/ctrGenerateQueries.R: 97.31%
+# R/ctrOpenSearchPagesInBrowser.R: 97.40%
 # R/dbFindIdsUniqueTrials.R: 98.78%
 # R/f_numTestArmsSubstances.R: 98.92%
 # R/f_likelyPlatformTrial.R: 99.13%
@@ -879,19 +865,20 @@ 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~~
+  format. The functionality available at this time, is to retrieve any
+  version in CTGOV2, and to create a version when re-running a CTIS
+  query and retrieving new data.~~
 
 - ~~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.~~
+  August 2023, released in version 1.20.0) 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.~~
+  such as corresponding endpoints. The challenge is the incomplete
+  congruency and different structure of data fields. This has largely
+  been implemented as per the previous bullet point.~~
 
 ## Acknowledgements
 

cran-comments.md

@@ -1,10 +1,10 @@
 ## Test environments
 
-* local: R Under development (unstable) (2025-03-10 r87922) on aarch64-apple-darwin20 (ok)
+* local: R version 4.5.0 (2025-04-11) on aarch64-apple-darwin20 (ok)
 
-* Win-builder: R Under development (unstable); R version 4.3.3 (2024-02-29 ucrt) (2025-03-12 r87950 ucrt) (ok)
+* Win-builder:  (ok)
 
-* macOS builder: r-release-macosx-arm64|4.4.2|macosx|macOS 13.3.1 (22E261) (ok)
+* macOS builder: r-release-macosx-arm64|4.4.2|macosx|macOS 13.3.1 (22E261)|Mac mini|Apple M1||en_US.UTF-8|macOS 11.3|clang-1403.0.22.14.1|GNU Fortran (GCC) 14.2.0 (ok)
 
 * GitHub actions: windows-2022, r: 'release'; macOS-latest, r: 'release'; macOS-latest, r: 'oldrel'; ubuntu-latest, r: 'devel' (ok)
 
@@ -16,11 +16,7 @@
 
 ## Submission reason
 
-- Fix user-reported bug, unrelated to recent release
-
-- Fix CRAN "NOTE installed size is  5.3Mb"
-
-- Cannot fix CRAN "ERROR Installation failed. Flavor: r-devel-linux-x86_64-debian-gcc" because this is caused by "Error: ERROR: no permission to install to directory ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’"
+- Several fixes of issues discovered in rare use cases
 
 
 ## Reverse dependency checks