change vignette links to html, should also address cran note

Author: rfhb

README.Rmd

@@ -46,7 +46,7 @@ Package `ctrdata` provides functions for retrieving (downloading), aggregating a
 - ClinicalTrials.gov ("CTGOV2", https://clinicaltrials.gov/, [example](#workflow-ctgov-example))
 - ISRCTN Registry ("ISRCTN", https://www.isrctn.com/) 
 
-Additional registers are being explored. The package facilitates investigating across registers 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 2026-01-02 for version 1.25.1.9000.
+Additional registers are being explored. The package facilitates investigating across registers 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 2026-01-03 for version 1.25.1.9000.
 
 ## Main features
 

README.md

@@ -40,7 +40,7 @@ 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 2026-01-02 for version 1.25.1.9000.
+package. This README was reviewed on 2026-01-03 for version 1.25.1.9000.
 
 ## Main features
 

docs/articles/ctrdata_summarise.html

@@ -13,13 +13,11 @@ version 1.24.1. <https://cran.r-project.org/package=ctrdata>
 
 Here using MongoDB, which may be faster than SQLite, can handle
 credentials, provides access to remote servers and can directly retrieve
-nested elements from paths. See
-[README.md](https://rfhb.github.io/ctrdata/README.md) and [Retrieve
-clinical trial
-information](https://rfhb.github.io/ctrdata/articles/ctrdata_retrieve.Rmd)
+nested elements from paths. See [Retrieve clinical trial
+information](https://rfhb.github.io/ctrdata/articles/ctrdata_retrieve.md)
 for examples using SQLite. Also PostgreSQL can be used as database, see
 [Install R package
-ctrdata](https://rfhb.github.io/ctrdata/articles/ctrdata_install.Rmd).
+ctrdata](https://rfhb.github.io/ctrdata/articles/ctrdata_install.md).
 
 ``` r
 
@@ -39,7 +37,7 @@ nodbi::docdb_delete(db, db$collection)
 ```
 
 See [Retrieve clinical trial
-information](https://rfhb.github.io/ctrdata/articles/ctrdata_retrieve.Rmd)
+information](https://rfhb.github.io/ctrdata/articles/ctrdata_retrieve.md)
 for more details.
 
 ``` r

docs/articles/ctrdata_summarise.md

@@ -29,7 +29,7 @@ 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 2026-01-02 for version 1.25.1.9000.
+package. This README was reviewed on 2026-01-03 for version 1.25.1.9000.
 
 ## Main features
 

docs/index.html

@@ -29,7 +29,7 @@ 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 2026-01-02 for version 1.25.1.9000.
+package. This README was reviewed on 2026-01-03 for version 1.25.1.9000.
 
 ## Main features
 

docs/index.md

@@ -5,7 +5,7 @@ articles:
   ctrdata_install: ctrdata_install.html
   ctrdata_retrieve: ctrdata_retrieve.html
   ctrdata_summarise: ctrdata_summarise.html
-last_built: 2026-01-02T08:05Z
+last_built: 2026-01-03T12:05Z
 urls:
   reference: https://rfhb.github.io/ctrdata/reference
   article: https://rfhb.github.io/ctrdata/articles

docs/llms.txt

@@ -29,7 +29,7 @@ Remember to respect the registers' terms and conditions (see `ctrOpenSearchPages
 
 ## Preparations
 
-Here using MongoDB, which may be faster than SQLite, can handle credentials, provides access to remote servers and can directly retrieve nested elements from paths. See [README.md](../README.md) and [Retrieve clinical trial information](ctrdata_retrieve.Rmd) for examples using SQLite. Also PostgreSQL can be used as database, see [Install R package ctrdata](ctrdata_install.Rmd).
+Here using MongoDB, which may be faster than SQLite, can handle credentials, provides access to remote servers and can directly retrieve nested elements from paths. See [Retrieve clinical trial information](ctrdata_retrieve.html) for examples using SQLite. Also PostgreSQL can be used as database, see [Install R package ctrdata](ctrdata_install.html).
 
 ```{r connect_mongodb}
 db <- nodbi::src_mongo(
@@ -47,7 +47,7 @@ db
 nodbi::docdb_delete(db, db$collection)
 ```
 
-See [Retrieve clinical trial information](ctrdata_retrieve.Rmd) for more details.
+See [Retrieve clinical trial information](ctrdata_retrieve.html) for more details.
 
 ```{r ctrLoadQueryIntoDb}
 # Load package