prepare for release

rfhb · Jun 30, 2024 · 4047556 · 4047556
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -11,7 +11,7 @@ Description: A system for querying, retrieving and analyzing
  protocol- and results-related information on clinical trials from
  four public registers, the 'European Union Clinical Trials Register'
  ('EUCTR', <https://www.clinicaltrialsregister.eu/>), 
- 'ClinicalTrials.gov' (<https://www.clinicaltrials.gov/> and also 
+ 'ClinicalTrials.gov' (<https://clinicaltrials.gov/> and also 
  translating queries the retired classic interface), the 
  'ISRCTN' (<http:https://www.isrctn.com/>) and the
  'European Union Clinical Trials Information System'

diff --git a/README.Rmd b/README.Rmd
@@ -313,7 +313,7 @@ The new website and API introduced in July 2023 (https://www.clinicaltrials.gov/
 
 On 2024-06-25, `CTGOV` has retired the classic website and API used by `ctrdata` since 2015. To support users, `ctrdata` however 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`](https://prsinfo.clinicaltrials.gov/ProtocolRecordSchema.xsd), the [schema for study results](https://cdn.clinicaltrials.gov/documents/xsd/prs/RRSUploadSchema.xsd) and the [Study Data Structure for `CTGOV2`](https://clinicaltrials.gov/data-api/about-api/study-data-structure). 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. 
+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`](https://cdn.clinicaltrials.gov/documents/xsd/prs/ProtocolRecordSchema.xsd), the [schema for study results](https://cdn.clinicaltrials.gov/documents/xsd/prs/RRSUploadSchema.xsd) and the [Study Data Structure for `CTGOV2`](https://clinicaltrials.gov/data-api/about-api/study-data-structure). 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 `CTGOV` queries. 
 
@@ -874,7 +874,7 @@ covr::package_coverage(path = ".", type = "tests")
 
 * Authentication, expected to be required by CTGOV2; specifications not yet known (work not yet started).
 
-* Explore further registers such as [ICTRP](https://trialsearch.who.int/) (authentication needed), [JPRN](https://rctportal.niph.go.jp/), [jRCT](https://jrct.niph.go.jp/), [UMIN-CTR](https://www.umin.ac.jp/ctr/), ChiCTR (exploration is continually ongoing; added value, terms and conditions for programmatic access vary; no clear roadmap is established yet).
+* Explore further registers (exploration is continually ongoing; added value, terms and conditions for programmatic access vary; no clear roadmap is established yet).
 
 * ~~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.~~ (functionality available with version 1.17.2.9000 to the extent that seems reasonably possible at this time, namely for protocol-related information for CTIS and for protocol- and results-related information in CTGOV2)
 

diff --git a/README.md b/README.md
@@ -424,7 +424,7 @@ 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`](https://prsinfo.clinicaltrials.gov/ProtocolRecordSchema.xsd),
+`CTGOV`](https://cdn.clinicaltrials.gov/documents/xsd/prs/ProtocolRecordSchema.xsd),
 the [schema for study
 results](https://cdn.clinicaltrials.gov/documents/xsd/prs/RRSUploadSchema.xsd)
 and the [Study Data Structure for
@@ -1020,13 +1020,9 @@ covr::package_coverage(path = ".", type = "tests")
 - Authentication, expected to be required by CTGOV2; specifications not
  yet known (work not yet started).
 
-- Explore further registers such as
- [ICTRP](https://trialsearch.who.int/) (authentication needed),
- [JPRN](https://rctportal.niph.go.jp/),
- [jRCT](https://jrct.niph.go.jp/),
- [UMIN-CTR](https://www.umin.ac.jp/ctr/), ChiCTR (exploration is
- continually ongoing; added value, terms and conditions for
- programmatic access vary; no clear roadmap is established yet).
+- Explore further registers (exploration is continually ongoing; added
+ value, terms and conditions for programmatic access vary; no clear
+ roadmap is established yet).
 
 - ~~Retrieve previous versions of protocol- or results-related
  information. The challenges include, historic versions can only be

diff --git a/cran-comments.md b/cran-comments.md
@@ -13,7 +13,7 @@
 
 Explanation of NOTES: 
 - links are accessible manually but may respond with an HTML error 403 in test systems
-- https://eudract.ema.europa.eu/ may present an incomplete certificate chain.
+- https://eudract.ema.europa.eu/ may present an incomplete certificate chain
 
 
 ## Submission reason

diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/pkgdown.yml b/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: 2024-06-30T07:44Z
+last_built: 2024-06-30T12:38Z
 urls:
  reference: https://rfhb.github.io/ctrdata/reference
  article: https://rfhb.github.io/ctrdata/articles

diff --git a/docs/search.json b/docs/search.json
diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -6,21 +6,18 @@ CMD
 COVID
 CTGOV
 CTIS
-CTR
-ChiCTR
 ClinicalTrials
-CtgovNested
+Ctgov
+CtisNested
 DuckDB
 EUCTR
 EudraCT
 Github
 Haenszel
 HistogramNBtrials
-ICTRP
 ISRCTN
 Infodemic
 Investigational
-JPRN
 Javascript
 Lasch
 Mapreduce
@@ -29,6 +26,7 @@ MongoDB
 NCT
 NDJSON
 NL
+NestedResults
 Neuroblastoma
 PostgreSQL
 RCurl
@@ -39,9 +37,10 @@ SQLite
 SbjctInfaICF
 Sood
 Tampermonkey
-UMIN
 Var
+activesubstance
 analyzing
+armsInterventionsModule
 backends
 clipr
 codecov
@@ -96,7 +95,6 @@ gov
 httr
 installFindMongoBinaries
 investigational
-jRCT
 jqr
 json
 jsonlite
@@ -115,11 +113,13 @@ mth
 ndjson
 nodbi
 nonproprietary
+otherNames
 paed
 perl
 pipleline
 postgres
 procotol
+protocolSection
 publicEvaluation
 publicevents
 queryterm
@@ -130,7 +130,6 @@ records’
 regex
 regexp
 registers’
-reigster
 relevel
 rmongodb
 rss