Merge pull request #226 from pharmaverse/225_navbar_update_and_descri…

…ption

Closes #225, Closes #228, Closes #229: Updates on Navbar Description and admiral core impacts

.Rbuildignore

@@ -32,3 +32,4 @@
 ^admiralvaccine\.Rcheck$
 ^admiralvaccine.*\.tar\.gz$
 ^admiralvaccine.*\.tgz$
+^doc$

.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
@@ -33,7 +33,7 @@ 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 - Question/Comments, Community Meeting
         - label: Given write access to Github Repository
         - label: Slack channel invites to admiral

.github/pull_request_template.md

@@ -1,16 +1,16 @@
-Thank you for your Pull Request! We have developed this task checklist from the [Development Process Guide](https://pharmaverse.github.io/admiraldev/main/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#detailed-development-process) 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.
 
 - [ ] 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
-- [ ] Updated relevant unit tests or have written new unit tests - See [Unit Test Guide](https://pharmaverse.github.io/admiraldev/main/articles/unit_test_guidance.html#writing-unit-tests-in-admiral)
-- [ ] If you removed/replaced any function and/or function parameters, did you fully follow the [deprecation guidance](https://pharmaverse.github.io/admiraldev/main/articles/programming_strategy.html#deprecation)?
+- [ ] Updated relevant unit tests or have written new unit tests - See [Unit Test Guide](https://pharmaverse.github.io/admiraldev/articles/unit_test_guidance.html#writing-unit-tests-in-admiral)
+- [ ] If you removed/replaced any function and/or function parameters, did you fully follow the [deprecation guidance](https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html#deprecation)?
 - [ ] Update to all relevant roxygen headers and examples.
 - [ ] 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 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/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.

.github/workflows/templates.yml

@@ -0,0 +1,18 @@
+---
+name: Check Templates
+
+on:
+  workflow_dispatch:
+  pull_request:
+    branches:
+      - main
+      - devel
+
+jobs:
+  templates:
+    name: Check Templates
+    uses: pharmaverse/admiralci/.github/workflows/check-templates.yml@main
+    secrets: inherit
+    with:
+      r-version: "4.1"
+      push-templates-data: true

.gitignore

@@ -1,56 +1,44 @@
 # History files
 .Rhistory
 .Rapp.history
-
 # Session Data files
 .RData
-
 # User-specific files
 .Ruserdata
-
 # Example code in package build process
 *-Ex.R
-
 # Output files from R CMD build
 /*.tar.gz
-
 # Output files from R CMD check
 /*.Rcheck/
-
 # RStudio files
 .Rproj.user/
-
 # produced vignettes
 vignettes/*.html
 vignettes/*.pdf
-
 # OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
 .httr-oauth
-
 # knitr and R markdown default cache directories
 *_cache/
 /cache/
-
 # Temporary files created by R markdown
 *.utf8.md
 *.knit.md
-
 # Web Documentation files
 /docs/*
 !/docs/pkgdown.yml
-
 # R Environment Variables
 .Renviron
 admiralext.Rcheck/
 admiralext*.tar.gz
 admiralext*.tgz
-
 # MacOS
 .DS_Store
-
 inst/doc
 admiralvaccine.Rcheck/
 admiralvaccine*.tar.gz
 admiralvaccine*.tgz
-
 .Rproj.user
+/doc/
+/Meta/
+docs

DESCRIPTION

@@ -4,9 +4,9 @@ Title: Vaccine Extension Package for ADaM in 'R' Asset Library
 Version: 0.1.0
 Authors@R: c(
     person("Sukalpo", "Saha", email = "[email protected]", role = c("aut", "cre")),
-    person("Vikram", "S", email = "vikram.s@pfizer.com", role = "aut"),
+    person("Arjun", "Rubalingam", email = "arjun.rubalingam@pfizer.com", role = "aut"),
     person("Ben", "Straub", email = "[email protected]", role = "aut"),
-    person("Arjun", "Rubalingam", role = "aut"),
+    person("Vikram", "S", role = "aut"),
     person("Dhivya", "Kanagaraj", role = "aut"),
     person("Federico", "Baratin", role = "aut"),
     person("Yamini", "Purna Bollu", role = "aut"),
@@ -18,6 +18,7 @@ Authors@R: c(
     person("Ankur", "Jindal", role = "ctb"),
     person("Jayashree", "V", role = "ctb"),
     person("Jagadish", "Katam", role = "ctb"),
+    person("Lee", "Armishaw", role = "ctb"),
     person("Andrea", "Pammolli", role = "ctb"),
     person("Daniele", "Bottigliengo", role = "ctb"),
     person("Ranya", "Ben Hsain", role = "ctb"),
@@ -49,8 +50,8 @@ BugReports: https://github.com/pharmaverse/admiralvaccine/issues/
 Depends: 
     R (>= 3.5)
 Imports:
-    admiral (>= 0.10.2),
-    admiraldev (>= 0.4.0),
+    admiral (>= 1.0.0),
+    admiraldev (>= 1.0.0),
     assertthat (>= 0.2.1),
     dplyr (>= 0.8.4),
     hms (>= 0.5.3),
@@ -64,7 +65,6 @@ Imports:
     tidyr (>= 1.0.2),
     tidyselect (>= 1.0.0)
 Suggests:
-    admiral.test,
     covr,
     devtools,
     diffdf,
@@ -73,6 +73,7 @@ Suggests:
     lintr,
     methods,
     miniUI,
+    pharmaversesdtm,
     pkgdown,
     rmarkdown,
     roxygen2,

R/data.R

@@ -1,118 +1,39 @@
-#' Immunogenicity Specimen
+#' Subject Level Analysis Dataset - Vaccine Specific
 #'
-#' A SDTM IS dataset
-#'
-#' @keywords dataset
-#' @family dataset
-#' @source
-#' (\url{https://github.com/pharmaverse/admiralvaccine/tree/main/inst/create_vx_data/vx_is.R})
-"vx_is"
-
-#' Clinical Events
-#'
-#' A SDTM CE dataset
-#'
-#' @keywords dataset
-#' @family dataset
-#' @source
-#' (\url{https://github.com/pharmaverse/admiralvaccine/tree/main/inst/create_vx_data/vx_ce.R})
-"vx_ce"
-
-#' Demographics
-#'
-#' A SDTM DM dataset
-#'
-#' @keywords dataset
-#' @family dataset
-#' @source
-#' (\url{https://github.com/pharmaverse/admiralvaccine/tree/main/inst/create_vx_data/vx_dm.R})
-"vx_dm"
-
-#' Exposure
-#'
-#' A SDTM EX dataset
-#'
-#' @keywords dataset
-#' @family dataset
-#' @source
-#' (\url{https://github.com/pharmaverse/admiralvaccine/tree/main/inst/create_vx_data/vx_ex.R})
-"vx_ex"
-
-#' Findings About Clinical Events
-#'
-#' A SDTM FACE dataset
-#'
-#' @keywords dataset
-#' @family dataset
-#' @source
-#' (\url{https://github.com/pharmaverse/admiralvaccine/tree/main/inst/create_vx_data/vx_face.R})
-"vx_face"
-
-#' Vital Signs
-#'
-#' A SDTM VS dataset
-#'
-#' @keywords dataset
-#' @family dataset
-#' @source
-#' (\url{https://github.com/pharmaverse/admiralvaccine/tree/main/inst/create_vx_data/vx_vs.R})
-"vx_vs"
-
-#' Subject Level Analysis - Vaccine Specific
-#'
-#' A subject level analysis dataset
+#' An example Subject Level analysis dataset
 #'
 #' @keywords dataset
 #' @family dataset
 #' @source
 #' (\url{https://github.com/pharmaverse/admiralvaccine/tree/main/inst/templates/ad_adsl.R})
-"vx_adsl"
+"admiralvaccine_adsl"
 
-#' Supplemental Immunogenicity Specimen
+#' Clinical Events Analysis Dataset - Vaccine Specific
 #'
-#' A SDTM Supplementary IS dataset
+#' An example Clinical Events analysis dataset
 #'
 #' @keywords dataset
 #' @family dataset
 #' @source
-#' (\url{https://github.com/pharmaverse/admiralvaccine/tree/main/inst/create_vx_data/vx_suppis.R})
-"vx_suppis"
+#' (\url{https://github.com/pharmaverse/admiralvaccine/tree/main/inst/templates/ad_adce.R})
+"admiralvaccine_adce"
 
-#' Supplemental Clinical Events
+#' Findings About Clinical Events Analysis Dataset - Vaccine Specific
 #'
-#' A SDTM Supplementary CE dataset
-#'
-#' @keywords dataset
-#' @family dataset
-#' @source
-#' (\url{https://github.com/pharmaverse/admiralvaccine/tree/main/inst/create_vx_data/vx_suppce.R})
-"vx_suppce"
-
-#' Supplemental Demographics
-#'
-#' A SDTM Supplementary DM dataset
-#'
-#' @keywords dataset
-#' @family dataset
-#' @source
-#' (\url{https://github.com/pharmaverse/admiralvaccine/tree/main/inst/create_vx_data/vx_suppdm.R})
-"vx_suppdm"
-
-#' Supplemental Exposure
-#' A SDTM Supplementary EX dataset
+#' An example Findings About Clinical Events analysis dataset
 #'
 #' @keywords dataset
 #' @family dataset
 #' @source
-#' (\url{https://github.com/pharmaverse/admiralvaccine/tree/main/inst/create_vx_data/vx_suppex.R})
-"vx_suppex"
+#' (\url{https://github.com/pharmaverse/admiralvaccine/tree/main/inst/templates/ad_adface.R})
+"admiralvaccine_adface"
 
-#' Supplemental Findings About Clinical Events
+#' Immunogenicity Specimen Assessments Analysis Dataset - Vaccine Specific
 #'
-#' A SDTM Supplementary FACE dataset
+#' An example Immunogenicity Specimen Assessments analysis dataset
 #'
 #' @keywords dataset
 #' @family dataset
 #' @source
-#' (\url{https://github.com/pharmaverse/admiralvaccine/tree/main/inst/create_vx_data/vx_suppface.R})
-"vx_suppface"
+#' (\url{https://github.com/pharmaverse/admiralvaccine/tree/main/inst/templates/ad_adis.R})
+"admiralvaccine_adis"

R/derive_fever_records.R

@@ -124,7 +124,7 @@ derive_fever_records <- function(dataset,
         ),
         FASTRESC = FAORRES
       ) %>%
-      select(-(starts_with("VS")), VSSTRESN)
+      select(-(starts_with("VS")), VSSTRESN) # nolint
 
     bind_rows(dataset, fev_rec)
   } else if (row_rec > 0) {

R/derive_vars_merged_vaccine.R

@@ -61,10 +61,11 @@
 #' library(tibble)
 #' library(admiral)
 #' library(dplyr)
+#' library(pharmaversesdtm)
 #'
 #' derive_vars_merged_vaccine(
-#'   dataset = vx_face,
-#'   dataset_ex = vx_ex,
+#'   dataset = face_vaccine,
+#'   dataset_ex = ex_vaccine,
 #'   dataset_supp = NULL,
 #'   dataset_suppex = NULL,
 #'   by_vars_sys = exprs(USUBJID, FATPTREF = EXLNKGRP),
@@ -75,10 +76,10 @@
 #'   head(10)
 #'
 #' derive_vars_merged_vaccine(
-#'   dataset = vx_face,
-#'   dataset_ex = vx_ex,
-#'   dataset_supp = vx_suppface,
-#'   dataset_suppex = vx_suppex,
+#'   dataset = face_vaccine,
+#'   dataset_ex = ex_vaccine,
+#'   dataset_supp = suppface_vaccine,
+#'   dataset_suppex = suppex_vaccine,
 #'   by_vars_sys = exprs(USUBJID, FATPTREF = EXLNKGRP),
 #'   by_vars_adms = exprs(USUBJID, FATPTREF = EXLNKGRP, FALOC = EXLOC, FALAT = EXLAT),
 #'   ex_vars = exprs(EXTRT, EXDOSE, EXDOSU, EXSTDTC, EXENDTC)

R/post_process_reacto.R

@@ -46,7 +46,7 @@ post_process_reacto <- function(dataset,
   favars <- names(dataset %>% select(starts_with("FA"), FATESTCD))
 
   dataset %>% mutate(across(
-    favars,
+    all_of(favars),
     function(x) ifelse(!!filter_dataset, NA, x)
   ))
 }

README.md

@@ -64,7 +64,7 @@ for vaccine ADaMs.
 ## References and Documentation
 
 -   Please refer to the [{admiral} References and
-    Documentation](https://pharmaverse.github.io/admiral/main/)
+    Documentation](https://pharmaverse.github.io/admiral/)
 
 ## R Versions
 

_pkgdown.yml

@@ -44,6 +44,7 @@ reference:
 navbar:
   structure:
     left: [getstarted, reference, articles, news]
+    right: [search, slack, newissue, github]
   components:
     getstarted:
       text: Get Started
@@ -62,3 +63,11 @@ navbar:
         href: articles/adce.html
       - text: Creating ADFACE
         href: articles/adface.html
+    slack:
+      icon: fa-slack
+      href: https://app.slack.com/client/T028PB489D3/C02M8KN8269
+      aria-label: Slack
+    newissue:
+      icon: fa-bug
+      href: https://github.com/pharmaverse/admiralvaccine/issues/new/choose
+      aria-label: New Issue