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/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

@@ -54,3 +54,5 @@ admiralvaccine*.tar.gz
 admiralvaccine*.tgz
 
 .Rproj.user
+/doc/
+/Meta/

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

inst/templates/ad_adce.R

@@ -7,6 +7,7 @@ library(admiral)
 library(dplyr)
 library(lubridate)
 library(admiralvaccine)
+library(pharmaversesdtm)
 
 
 # Load source datasets
@@ -15,12 +16,12 @@ library(admiralvaccine)
 # as needed and assign to the variables below.
 # For illustration purposes read in admiral test data
 
-data("vx_ce")
-data("vx_adsl")
+data("ce_vaccine")
+data("admiralvaccine_adsl")
 
 
-adsl <- vx_adsl
-ce <- vx_ce
+adsl <- admiralvaccine_adsl
+ce <- ce_vaccine
 
 
 # When SAS datasets are imported into R using haven::read_sas(), missing
@@ -84,7 +85,8 @@ adce03 <-
     adce02,
     dataset_add = adperiods,
     by_vars = exprs(STUDYID, USUBJID),
-    filter_join = ASTDT >= APERSDT & ASTDT <= APEREDT
+    filter_join = ASTDT >= APERSDT & ASTDT <= APEREDT,
+    join_type = "all"
   ) %>%
   mutate(
     APERSTDY = as.integer(ASTDT - APERSDT) + 1,
@@ -148,7 +150,14 @@ adce <- adce05 %>%
   )
 
 
-# Save output
+admiralvaccine_adce <- adce
 
-dir <- tempdir() # Change to whichever directory you want to save the dataset in
-saveRDS(adce, file = file.path(dir, "adce.rds"), compress = "bzip2")
+# Save output ----
+
+dir <- tools::R_user_dir("admiralvaccine_templates_data", which = "cache")
+# Change to whichever directory you want to save the dataset in
+if (!file.exists(dir)) {
+  # Create the folder
+  dir.create(dir, recursive = TRUE, showWarnings = FALSE)
+}
+save(admiralvaccine_adce, file = file.path(dir, "adce.rda"), compress = "bzip2")