[skip vbump] Closes #291 1.4 release

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: admiralophtha
 Title: ADaM in R Asset Library - Ophthalmology
-Version: 1.3.0.9008
+Version: 1.4.0
 Authors@R: c(
     person("Edoardo", "Mancini", , "edoardo.mancini@roche.com", role = c("aut", "cre"),
            comment = c(ORCID = "0009-0006-4899-8641")),
@@ -35,9 +35,9 @@ BugReports: https://github.com/pharmaverse/admiralophtha/issues/
 Depends: 
     R (>= 4.1)
 Imports:
-    admiral (>= 1.1.1),
-    admiraldev (>= 1.1.0),
-    dplyr (>= 1.0.5),
+    admiral (>= 1.4.0),
+    admiraldev (>= 1.4.0),
+    dplyr (>= 1.1.1),
     hms (>= 0.5.3),
     lifecycle (>= 0.1.0),
     lubridate (>= 1.7.4),

NEWS.md

@@ -1,4 +1,4 @@
-# admiralophtha (development version)
+# admiralophtha 1.4.0
 
 ## Breaking Changes
 

R/data.R

@@ -19,7 +19,7 @@
 #' [ADVFQ template](https://github.com/pharmaverse/admiralophtha/blob/main/inst/templates/ad_advfq.R).
 #' The full, open-source VFQ questionnaire can be accessed
 # #nolint start
-#' [here](https://www.nei.nih.gov/learn-about-eye-health/outreach-resources/outreach-materials/visual-function-questionnaire-25).
+#' [here](https://www.nei.nih.gov/about/education-and-outreach/outreach-materials/visual-function-questionnaire-25).
 # #nolint end
 #'
 "admiralophtha_advfq"

README.md

@@ -1,6 +1,3 @@
-<!-- Please do not edit the README.md file as it is auto-generated after PR merges. Only edit the README.Rmd file -->
-<!-- To test this in your feature branch use code: rmarkdown::render("README.Rmd", output_format ="md_document") -->
-
 # admiralophtha <img src="man/figures/logo.png" align="right" width="200" style="margin-left:50px;"/>
 
 <!-- badges: start -->
@@ -69,6 +66,6 @@ developer community:
 | Month / Year     | Package Version               |                          
 | ---------------- | ----------------------------- |
 |                  |                               |                                          
-| January 2025     | `{admiralophtha}` v. 1.2.0    |
+| ~January 2026    | `{admiralophtha}` v. 1.4.0    |
 |                  |                               | 
-| June 2025        | `{admiralophtha}` v. 1.3.0    |
+| ~June 2026       | `{admiralophtha}` v. 1.5.0    |

_pkgdown.yml

@@ -20,6 +20,7 @@ template:
       data-consent-screen-accept-button-text="Allow tracking"
       data-consent-screen-reject-button-text="No, thanks"
       data-modal-example-questions="Tell me a little about the {admiralophtha} package., How can I convert from LogMAR to ETDRS score using {admiralophtha}?"
+      data-modal-search-placeholder="Ask me a question about {admiralophtha} or the {admiral} ecosystem..."
       data-modal-z-index="9999"
       ></script>
 search:

inst/WORDLIST

@@ -27,6 +27,7 @@ SBCVA
 SDTM
 Snellen
 Thampi
+Tidyverse
 VFQ
 adbcva
 adoe
@@ -53,6 +54,7 @@ recoded
 recoding
 scrutinise
 th
+tidyverse
 toolset
 IOP
 pre

inst/templates/ad_advfq.R

@@ -5,7 +5,7 @@
 # Input: adsl, qs
 #
 # The full, open-source VFQ questionnaire can be accessed here:
-# https://www.nei.nih.gov/learn-about-eye-health/outreach-resources/outreach-materials/visual-function-questionnaire-25 #nolint
+# https://www.nei.nih.gov/about/education-and-outreach/outreach-materials/visual-function-questionnaire-25 #nolint
 
 library(admiral)
 library(dplyr, warn.conflicts = FALSE)

vignettes/admiralophtha.Rmd

@@ -22,15 +22,17 @@ guide. This extension package follows the same main idea and conventions, and re
 functions from `{admiral}`, so it is important to thoroughly understand these to be able to
 use `{admiralophtha}`.
 
-# Derivations
+# What does {admiralophtha} offer?
 
-The most important functions in `{admiralophtha}` are the
-[derivations](../reference/index.html). Again these follow the same
-conventions as `{admiral}` but are focused to ophthalmology-specific needs.
+The contents of `{admiralophtha}` can be broadly divided into three categories:
+
+- **Derivations** (i.e. functions): these follow the same conventions as `{admiral}` but are focused on ophthalmology-specific needs. Please see the Reference page for more details.
+- **ADaM Templates**: these showcase ways to apply `{admiral}`, `{admiralophtha}` and Tidyverse functions to create ophthalmology-specific ADaMs. You can see the available templates in `{admiralophtha}` by running: `list_all_templates(package = "admiralophtha")` in the console.
+- **User Guides** (i.e. vignettes): these are documentation pages which walk users through each step of a template, or discuss other ophthalmology-specific topics such as ophthalmology standards. Please see the User Guides section for more details.
 
 # Starting a Script
 
-For the ophthalmology ADaM data structures, an overview of the flow and example function calls
+For the ophthalmology ADaM datasets, an overview of the flow and example function calls
 for the most common steps are provided by the following vignettes:
 
 - [Creating ADBCVA](adbcva.html)
@@ -41,43 +43,3 @@ for the most common steps are provided by the following vignettes:
 
 Support is provided via the [admiral Slack
 channel](https://pharmaverse.slack.com/).
-
-<!-- This article is in the process of being written. Please use the `{admiralonco}` "Get Started"  -->
-<!-- page (commented out at the moment) as a basis. -->
-
-<!-- # Derivations -->
-
-<!-- The most important functions in `{admiralonco}` are the -->
-<!-- [derivations](../reference/index.html#section-derivations). Again these follow the same -->
-<!-- conventions as `{admiral}` but are focused to oncology-specific needs. -->
-
-<!-- # Starting a Script -->
-
-<!-- For the oncology ADaM data structures, an overview of the flow and example function calls -->
-<!-- for the most common steps are provided by the following vignettes: -->
-
-<!-- - [Creating ADRS](adrs.html) -->
-<!-- - [Creating ADTTE](adtte.html) -->
-
-<!-- `{admiralonco}` also provides template R scripts as a starting point. They can be -->
-<!-- created by calling `use_ad_template()` from {admiral}, e.g., -->
-
-<!-- ```{r} -->
-<!-- library(admiral) -->
-<!-- ``` -->
-
-<!-- there used to be some code calling `use_ad_template here (see corresponding admiralonco file) -->
-<!-- but it was removed as commenting it out errored the file for some reason. Upond development,  -->
-<!-- feel free to locate the code again and paste it in in order to modify it. -->
-
-<!-- A list of all available templates can be obtained by `list_all_templates()` -->
-<!-- from {admiral}: -->
-
-<!-- ```{r} -->
-<!-- list_all_templates(package = "admiralonco") -->
-<!-- ``` -->
-
-<!-- # Support -->
-
-<!-- Support is provided via the [admiral Slack -->
-<!-- channel](https://app.slack.com/client/T028PB489D3/C02M8KN8269). -->

vignettes/advfq.Rmd

@@ -20,7 +20,7 @@ knitr::opts_chunk$set(
 This article describes creating an ADVFQ ADaM with Visual Functioning Questionnaire
 data for ophthalmology endpoints. It is to be used in conjunction with the article on [creating a BDS dataset from SDTM](https://pharmaverse.github.io/admiral/articles/bds_finding.html). As such, derivations and processes that are not specific to ADVFQ are mostly absent, and the user is invited to consult the aforementioned article for guidance. 
 
-The full, open-source VFQ questionnaire can be accessed [here](https://www.nei.nih.gov/learn-about-eye-health/outreach-resources/outreach-materials/visual-function-questionnaire-25).
+The full, open-source VFQ questionnaire can be accessed [here](https://www.nei.nih.gov/about/education-and-outreach/outreach-materials/visual-function-questionnaire-25).
 
 **Note**: *All examples assume CDISC SDTM and/or ADaM format as input unless
 otherwise specified. Also, some of the example datasets in this vignette contain more records than are displayed by default, but the number of displayed records can be expanded using the selectors at the bottom.*