Merge pull request #220 from pharmaverse/219_10_release

Closes #219 1.0 release

.github/ISSUE_TEMPLATE/05_onboard.yml

@@ -18,7 +18,7 @@ body:
         - label: Given a tour of Github from a Core member
         - label: Understand how to Create Issues and do a Pull Request
         - label: Understand the Programming Strategy
-        - label: Read and understand [Developer Guides Articles](https://pharmaverse.github.io/admiral/cran-release/index.html)
+        - label: Read and understand [Developer Guides Articles](https://pharmaverse.github.io/admiral/index.html)
         - label: Invited to all relevant meetings - Stand Ups, Retrospective, Sprint Planning, Question/Comments, Backlog, Community Meeting
         - label: Given access to Box and relevant documents
         - label: Given write access to Github Repository

.github/pull_request_template.md

@@ -1,6 +1,6 @@
-Thank you for your Pull Request! We have developed this task checklist from the [Development Process Guide](https://pharmaverse.github.io/admiraldev/articles/development_process.html) to help with the final steps of the process. Completing the below tasks helps to ensure our reviewers can maximize their time on your code as well as making sure the admiral codebase remains robust and consistent.
+Thank you for your Pull Request! We have developed this task checklist from the [Development Process Guide](https://pharmaverse.github.io/admiral/CONTRIBUTING.html) to help with the final steps of the process. Completing the below tasks helps to ensure our reviewers can maximize their time on your code as well as making sure the admiral codebase remains robust and consistent.
 
-Please check off each taskbox as an acknowledgment that you completed the task or check off that it is not relevant to your Pull Request. This checklist is part of the Github Action workflows and the Pull Request will not be merged into the `devel` branch until you have checked off each task.
+Please check off each taskbox as an acknowledgment that you completed the task or check off that it is not relevant to your Pull Request. This checklist is part of the Github Action workflows and the Pull Request will not be merged into the `main` branch until you have checked off each task.
 
 - [ ] Place Closes #<insert_issue_number> into the beginning of your Pull Request Title (Use Edit button in top-right if you need to update)
 - [ ] Code is formatted according to the [tidyverse style guide](https://style.tidyverse.org/). Run `styler::style_file()` to style R and Rmd files
@@ -10,7 +10,7 @@ Please check off each taskbox as an acknowledgment that you completed the task o
 - [ ] Run `devtools::document()` so all `.Rd` files in the `man` folder and the `NAMESPACE` file in the project root are updated appropriately
 - [ ] Address any updates needed for vignettes and/or templates
 - [ ] Update `NEWS.md` if the changes pertain to a user-facing function (i.e. it has an `@export` tag) or documentation aimed at users (rather than developers)
-- [ ] Build admiral site `pkgdown::build_site()` and check that all affected examples are displayed correctly and that all new functions occur on the "[Reference](https://pharmaverse.github.io/admiral/cran-release/reference/index.html)" page.
+- [ ] Build admiralophtha site `pkgdown::build_site()` and check that all affected examples are displayed correctly and that all new functions occur on the "[Reference](https://pharmaverse.github.io/admiralophtha/reference/index.html)" page.
 - [ ] Address or fix all lintr warnings and errors - `lintr::lint_package()`
 - [ ] Run `R CMD check` locally and address all errors and warnings - `devtools::check()`
 - [ ] Link the issue so that it closes after successful merging.

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: admiralophtha
 Type: Package
 Title: ADaM in R Asset Library - Ophthalmology
-Version: 0.3.0.9004
+Version: 1.0.0
 Authors@R: c(
     person("Edoardo", "Mancini", email = "[email protected]", role = c("aut", "cre")),
     person("Ritika", "Aggarwal", email = "[email protected]", role = c("aut")),

NEWS.md

@@ -1,4 +1,4 @@
-# admiralophtha (development version)
+# admiralophtha 1.0.0
 
 ## Updates to Templates
 

README.md

@@ -38,7 +38,7 @@ remotes::install_github("pharmaverse/admiralophtha", ref = "devel")
 ## References and Documentation
 
 * Please refer to the [{admiral} References and
-  Documentation](https://pharmaverse.github.io/admiral/cran-release/).
+  Documentation](https://pharmaverse.github.io/admiral/).
 
 ## R Versions
 

vignettes/adbcva.Rmd

@@ -18,7 +18,7 @@ library(admiraldev)
 
 # Introduction
 
-This article describes creating an ADBCVA ADaM with Best-Corrected Visual Acuity (BCVA) 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/cran-release/articles/bds_finding.html). As such, derivations and processes that are not specific to ADBCVA are absent, and the user is invited to consult the aforementioned article for guidance.
+This article describes creating an ADBCVA ADaM with Best-Corrected Visual Acuity (BCVA) 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 ADBCVA are absent, and the user is invited to consult the aforementioned article for guidance.
 
 **Note**: *All examples assume CDISC SDTM and/or ADaM format as input unless
 otherwise specified.*
@@ -167,7 +167,7 @@ adbcva <- adbcva %>%
 
 ## Further Derivations of Standard BDS Variables {#further}
 
-The user is invited to consult the article on [creating a BDS dataset from SDTM](https://pharmaverse.github.io/admiral/cran-release/articles/bds_finding.html) to learn how to add standard BDS variables to ADBCVA. Henceforth, for the purposes of this article, the following sections use the ADBCVA dataset generated by the corresponding `{admiralophtha}` template program as a starting point.
+The user is invited to consult the article on [creating a BDS dataset from SDTM](https://pharmaverse.github.io/admiral/articles/bds_finding.html) to learn how to add standard BDS variables to ADBCVA. Henceforth, for the purposes of this article, the following sections use the ADBCVA dataset generated by the corresponding `{admiralophtha}` template program as a starting point.
 
 **Note**: This dataset already comes with some criterion flags and analysis value categorisation variables, so for illustration purposes these are removed.
 

vignettes/adoe.Rmd

@@ -18,7 +18,7 @@ library(admiraldev)
 
 # Introduction
 
-This article describes creating an ADOE ADaM with Ophthalmology Exam Analysis 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/cran-release/articles/bds_finding.html). As such, derivations and processes that are not specific to ADOE are absent, and the user is invited to consult the aforementioned article for guidance.
+This article describes creating an ADOE ADaM with Ophthalmology Exam Analysis 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 ADOE are absent, and the user is invited to consult the aforementioned article for guidance.
 
 As the current release of `{admiralophtha}` does not contain any functionality specific to ADOE, this article only showcases how to map parameters from OE in order to set up the basic structure of ADOE. For the following steps, the user is invited to consult the above-linked article on BDS datasets. This article will be updated for future releases to showcase and explain any `{admiralophtha}`-specific functionality.
 
@@ -110,7 +110,7 @@ adoe <- adoe %>%
 ```
 ## Further Derivations of Standard BDS Variables {#further}
 
-The user is invited to consult the article on [creating a BDS dataset from SDTM](https://pharmaverse.github.io/admiral/cran-release/articles/bds_finding.html) to learn how to add standard BDS variables to ADOE. 
+The user is invited to consult the article on [creating a BDS dataset from SDTM](https://pharmaverse.github.io/admiral/articles/bds_finding.html) to learn how to add standard BDS variables to ADOE. 
 
 ## Example Script {#example}
 

vignettes/advfq.Rmd

@@ -18,7 +18,7 @@ knitr::opts_chunk$set(
 # Introduction
 
 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/cran-release/articles/bds_finding.html). As such, derivations and processes that are not specific to ADVFQ are absent, and the user is invited to consult the aforementioned article for guidance.
+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 absent, and the user is invited to consult the aforementioned article for guidance.
 
  **Note**: *All examples assume CDISC SDTM and/or ADaM format as input unless
  otherwise specified.* 
@@ -80,7 +80,7 @@ param_lookup <- tibble::tribble(
   "QBCSCORE", "QBCSCORE", "Composite Score", "NEI VFQ-25", "Averaged Result"
 )
 ```
-Now the ADVFQ dataset can be constructed, merging the filtered QS dataset with ADSL. This is necessary because treatment start date `TRTSDT` is a prerequisite for the derivation of variables such as Analysis Day `ADY` which can be programmed by following the article on [creating a BDS dataset from SDTM](https://pharmaverse.github.io/admiral/cran-release/articles/bds_finding.html).
+Now the ADVFQ dataset can be constructed, merging the filtered QS dataset with ADSL. This is necessary because treatment start date `TRTSDT` is a prerequisite for the derivation of variables such as Analysis Day `ADY` which can be programmed by following the article on [creating a BDS dataset from SDTM](https://pharmaverse.github.io/admiral/articles/bds_finding.html).
 ```{r, eval=FALSE}
 adsl_vars <- exprs(TRTSDT, TRTEDT, TRT01A, TRT01P)