diff --git a/DESCRIPTION b/DESCRIPTION index 4f0e4108..16f92cb2 100644 --- a/DESCRIPTION +++ b/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), diff --git a/NEWS.md b/NEWS.md index b7238214..bc63eec3 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# admiralophtha (development version) +# admiralophtha 1.4.0 ## Breaking Changes diff --git a/R/data.R b/R/data.R index 540ad2c8..ac3264f1 100644 --- a/R/data.R +++ b/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" diff --git a/README.md b/README.md index 94023892..38e59f86 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,3 @@ - - - # admiralophtha @@ -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 | diff --git a/_pkgdown.yml b/_pkgdown.yml index 2ae2e694..aa6edb18 100644 --- a/_pkgdown.yml +++ b/_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" > search: diff --git a/inst/WORDLIST b/inst/WORDLIST index b5d8844e..61ada4ae 100644 --- a/inst/WORDLIST +++ b/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 diff --git a/inst/templates/ad_advfq.R b/inst/templates/ad_advfq.R index bb1522b4..5d33d969 100644 --- a/inst/templates/ad_advfq.R +++ b/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) diff --git a/man/admiralophtha_advfq.Rd b/man/admiralophtha_advfq.Rd index 6e077674..8b061246 100644 --- a/man/admiralophtha_advfq.Rd +++ b/man/admiralophtha_advfq.Rd @@ -11,7 +11,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) w Derived from the ADSL and QS datasets using \code{{admiral}}, \code{{admiralophtha}} and the \href{https://github.com/pharmaverse/admiralophtha/blob/main/inst/templates/ad_advfq.R}{ADVFQ template}. The full, open-source VFQ questionnaire can be accessed -\href{https://www.nei.nih.gov/learn-about-eye-health/outreach-resources/outreach-materials/visual-function-questionnaire-25}{here}. +\href{https://www.nei.nih.gov/about/education-and-outreach/outreach-materials/visual-function-questionnaire-25}{here}. } \usage{ admiralophtha_advfq diff --git a/vignettes/admiralophtha.Rmd b/vignettes/admiralophtha.Rmd index 18370cd3..0930fcf8 100644 --- a/vignettes/admiralophtha.Rmd +++ b/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/). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/vignettes/advfq.Rmd b/vignettes/advfq.Rmd index b74b77de..cc6eb675 100644 --- a/vignettes/advfq.Rmd +++ b/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.*