Merge pull request #170 from pharmaverse/devel

PR for {admiralophtha} v0.2.0

.Rprofile

@@ -1,4 +1,14 @@
-if (Sys.getenv("GITHUB_ACTIONS") == "" || (Sys.getenv("GITHUB_ACTIONS") == "true" && getRversion()$major == 3 && getRversion()$minor == 6)) {
+# Set renv profile base on R version.
+if ((Sys.getenv("GITHUB_ACTIONS") == "") && (Sys.getenv("DOCKER_CONTAINER_CONTEXT") == "")) {
+  renv_profile <- paste(R.version$major, substr(R.version$minor, 1, 1), sep = ".")
+  if (file.exists("./renv/profile")) {
+    message("Using renv profile from `renv/profile` file.")
+  } else if (renv_profile %in% c("4.1", "4.2", "4.3")) {
+    message("Set renv profile to `", renv_profile, "`")
+    Sys.setenv("RENV_PROFILE" = renv_profile)
+  } else {
+    message("This repository do not contains the renv profile for your R version.")
+  }
   source("renv/activate.R")
 } else {
   options(repos = c(CRAN = "https://cran.rstudio.com"))

.github/workflows/common.yml

@@ -41,25 +41,25 @@ jobs:
     uses: pharmaverse/admiralci/.github/workflows/style.yml@main
     if: github.event_name == 'pull_request'
     with:
-      r-version: "4.0"
+      r-version: "4.1"
   spellcheck:
     name: Spelling
     uses: pharmaverse/admiralci/.github/workflows/spellcheck.yml@main
     if: github.event_name == 'pull_request'
     with:
-      r-version: "4.0"
+      r-version: "4.1"
   readme:
     name: Render README
     uses: pharmaverse/admiralci/.github/workflows/readme-render.yml@main
     if: github.event_name == 'push'
     with:
-      r-version: "4.0"
+      r-version: "4.1"
   validation:
     name: Validation
     uses: pharmaverse/admiralci/.github/workflows/r-pkg-validation.yml@main
     if: github.event_name == 'release'
     with:
-      r-version: "4.0"
+      r-version: "4.1"
   check:
     name: Check
     uses: pharmaverse/admiralci/.github/workflows/r-cmd-check.yml@main
@@ -69,7 +69,7 @@ jobs:
     uses: pharmaverse/admiralci/.github/workflows/pkgdown.yml@main
     if: github.event_name == 'push'
     with:
-      r-version: "4.0"
+      r-version: "4.1"
       # Whether to skip multiversion docs
       # Note that if you have multiple versions of docs,
       # your URL links are likely to break due to path changes
@@ -79,7 +79,7 @@ jobs:
     uses: pharmaverse/admiralci/.github/workflows/lintr.yml@main
     if: github.event_name == 'pull_request'
     with:
-      r-version: "4.0"
+      r-version: "4.1"
   links:
     name: Links
     uses: pharmaverse/admiralci/.github/workflows/links.yml@main
@@ -91,7 +91,7 @@ jobs:
     if: >
       github.event_name == 'push' || github.event_name == 'pull_request'
     with:
-      r-version: "4.0"
+      r-version: "4.1"
       # Whether to skip code coverage badge creation
       # Setting to 'false' will require you to create
       # an orphan branch called 'badges' in your repository
@@ -102,10 +102,10 @@ jobs:
     if: >
       github.event_name == 'push' || github.event_name == 'pull_request'
     with:
-      r-version: "4.0"
+      r-version: "4.1"
   man-pages:
     name: Man Pages
     uses: pharmaverse/admiralci/.github/workflows/man-pages.yml@main
     if: github.event_name == 'pull_request'
     with:
-      r-version: "4.0"
+      r-version: "4.1"

.gitignore

@@ -26,7 +26,6 @@ vignettes/*.pdf
 *.knit.md
 # Web Documentation files
 /docs/*
-!/docs/pkgdown.yml
 # R Environment Variables
 .Renviron
 # MacOS

DESCRIPTION

@@ -1,16 +1,20 @@
 Package: admiralophtha
 Type: Package
 Title: ADaM in R Asset Library - Ophthalmology
-Version: 0.1.0
+Version: 0.2.0
 Authors@R: c(
     person("Edoardo", "Mancini", email = "[email protected]", role = c("aut", "cre")),
+    person("Ritika", "Aggarwal", email = "[email protected]", role = c("aut")),
+    person("Jane", "Gao", email = "[email protected]",role = c("aut")),
+    person("William", "Holmes", email = "[email protected]", role = c("aut")),
+    person("Josie", "Jackson", email = "[email protected]", role = c("aut")),
+    person("Sonali", "Jain", email = "[email protected]", role = c("aut")),
+    person("Yuki", "Matsunaga", email = "[email protected]", role = c("aut")),
     person("Gordon", "Miller", email = "[email protected]", role = c("aut")),
-    person("Ritika", "Aggarwal", role = "aut", email = "[email protected]"),
-    person("Jane", "Gao", role = "aut", email = "[email protected]"),
-    person("William", "Holmes", role = "aut", email = "[email protected]"),
-    person("Rachel", "Linacre", role = "aut", email = "[email protected]"),
-    person("Lucy", "Palmen", role = "aut", email = "[email protected]"),
-    person("Nandini", "R Thampi", role = "aut", email = "[email protected]")
+    person("Rachel", "Linacre", email = "[email protected]", role = c("aut")),
+    person("Lucy", "Palmen", email = "[email protected]", role = c("aut")),
+    person("Nandini", "R Thampi", email = "[email protected]", role = c("aut")),
+    person("Aldrich", "Salva", email = "[email protected]", role = c("aut"))
     )
 Description: Aids the programming of Clinical Data Standards Interchange Consortium
     (CDISC) compliant Ophthalmology Analysis Data Model (ADaM) datasets in R. ADaM datasets are a
@@ -19,17 +23,17 @@ Description: Aids the programming of Clinical Data Standards Interchange Consort
     implemented in accordance with the "Analysis Data Model Implementation Guide"
     (CDISC Analysis Data Model Team, 2021, <https://www.cdisc.org/standards/foundational/adam/adamig-v1-3-release-package>).
 License: Apache License (>= 2)
+BugReports: https://github.com/pharmaverse/admiralophtha/issues
 URL: https://pharmaverse.github.io/admiralophtha/, https://github.com/pharmaverse/admiralophtha/
 Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 Depends: R (>= 3.5)
 Imports:
     admiral,
     admiraldev,
-    assertthat,
     dplyr,
     lubridate,
     magrittr,
@@ -53,7 +57,6 @@ Suggests:
     rmarkdown,
     roxygen2,
     spelling,
-    styler,
     tibble,
     usethis,
     covr,

NAMESPACE

@@ -4,7 +4,6 @@ export(convert_etdrs_to_logmar)
 export(convert_logmar_to_etdrs)
 export(derive_var_afeye)
 export(derive_var_bcvacritxfl)
-export(derive_var_bcvacritxfl_util)
 export(derive_var_studyeye)
 importFrom(admiral,derive_param_computed)
 importFrom(admiral,derive_var_merged_cat)
@@ -19,9 +18,6 @@ importFrom(admiraldev,assert_symbol)
 importFrom(admiraldev,expect_dfs_equal)
 importFrom(admiraldev,expr_c)
 importFrom(admiraldev,quo_c)
-importFrom(assertthat,"on_failure<-")
-importFrom(assertthat,assert_that)
-importFrom(assertthat,is.number)
 importFrom(dplyr,arrange)
 importFrom(dplyr,bind_cols)
 importFrom(dplyr,bind_rows)

NEWS.md

@@ -1,3 +1,23 @@
+# admiralophtha 0.2.0
+
+## Updates to Functions
+
+- Added new parameter `loc_vals` to function `derive_var_afeye()` to allow users to specify values of `xxLOC` for which `AFEYE` is derived (issue #163).
+- Updated function `derive_var_afeye()` to resolve bug when `STUDYEYE` is 'Bilateral' (issue #134).
+
+## Updates to Templates
+
+- Updated `ADOE` to refer to `OESTRESU` for `AVALU` creation (issue #139).
+- Updated `ADOE` and `ADBCVA` `PARAM` mapping to include units where applicable (issue #139).
+- Updated `ADOE`, `ADVFQ` and `ADBCVA` for the unique intermediate dataset name to avoid overwriting, corrected the link for Visit and Period variables Vignette in `ADVFQ` (issue #128).
+- Corrected values of `DTYPE`, `VISIT`, `VISITNUM`, `OEDY`, `OEDTC` for derived parameters in `ADBCVA` template (issue #137).
+- Updated `ADBCVA` and `ADOE` templates to include `AFEYE` (issue #133).
+
+## Updates to Site
+
+- Added a "Report a bug" link to `{admiralophtha}` website (issue #127).
+- Fixed bug where the search bar didn't work for some searches (issue #141).
+
 # admiralophtha 0.1.0
 
 ## New Features
@@ -10,4 +30,3 @@
 - Created ophthalmology-specific test data for the `EX` SDTM domain, stored in `{admiralophtha}` package and accessible by calling `data(admiralophtha_ex)` (issue #36).
 - Created ophthalmology-specific test data for the `SC` and `OE` SDTM domains, stored in `{admiral}` package and accessible by calling `data(admiral_sc)` or `data(admiral_oe)` (issues #11 and #13).
 - Updated `AE` and `QS` test datasets in `{admiral}` to include ophthalmology-specific variables and records, such as laterality variables in `AE` and VFQ records in `QS` (issues #12 and #52).
-

R/admiralophtha-package.R

@@ -17,7 +17,6 @@
 #'             flatten every modify_at modify_if reduce compose
 #' @importFrom stringr str_c str_detect str_extract str_remove str_remove_all
 #'             str_replace str_trim str_to_lower str_to_title str_to_upper str_glue
-#' @importFrom assertthat assert_that is.number on_failure<-
 #' @importFrom lubridate as_datetime ceiling_date date days duration floor_date is.Date is.instant
 #'             time_length %--% ymd ymd_hms weeks years hours minutes
 #' @importFrom tidyr drop_na nest pivot_longer pivot_wider unnest

R/data.R

@@ -4,7 +4,7 @@
 #' @keywords datasets
 #' @family datasets
 #' @source
-#' Constructed using `ex` from the `{admiral` package
+#' Constructed using `ex` from the `{admiral}` package
 #'
 "admiralophtha_ex"
 
@@ -14,7 +14,7 @@
 #' @keywords datasets
 #' @family datasets
 #' @source
-#' Derived from the `oe` and `ADSL` datasets using `{admiral`, `{admiralophtha}` and
+#' Derived from the `oe` and `ADSL` datasets using `{admiral}`, `{admiralophtha}` and
 #' (\url{https://github.com/pharmaverse/admiralophtha/blob/main/inst/templates/ad_adbcva.R})
 #'
 "admiralophtha_adbcva"
@@ -25,7 +25,7 @@
 #' @keywords datasets
 #' @family datasets
 #' @source
-#' Derived from the `ADSL` and `qs` datasets using `{admiral`, `{admiralophtha}` and
+#' Derived from the `ADSL` and `qs` datasets using `{admiral}`, `{admiralophtha}` and
 #' (\url{https://github.com/pharmaverse/admiralophtha/blob/main/inst/templates/ad_advfq.R})
 #'
 "admiralophtha_advfq"
@@ -36,7 +36,17 @@
 #' @keywords datasets
 #' @family datasets
 #' @source
-#' Derived from the `oe` and `ADSL` datasets using `{admiral`, `{admiralophtha}` and
+#' Derived from the `oe` and `ADSL` datasets using `{admiral}`, `{admiralophtha}` and
 #' (\url{https://github.com/pharmaverse/admiralophtha/blob/main/inst/templates/ad_adoe.R})
 #'
 "admiralophtha_adoe"
+
+#' Ophthalmology Questionnaires SDTM Dataset
+#'
+#' An example Questionnaires SDTM dataset with ophthalmology-specific questionnaire of NEI VFQ-25
+#' @keywords datasets
+#' @family datasets
+#' @source
+#' Constructed using `qs` from the `{admiral}` package
+#'
+"admiralophtha_qs"

R/derive_var_afeye.R

@@ -5,6 +5,7 @@
 #' @param dataset_occ Input Occurence dataset
 #' @param loc_var Location variable
 #' @param lat_var Laterality variable
+#' @param loc_vals `xxLOC`values for which `AFEYE` is derived
 #'
 #' @details
 #' Affected Eye is derived in the occurrence dataset using laterality and Study
@@ -24,24 +25,36 @@
 #'   ~STUDYID, ~USUBJID, ~STUDYEYE, ~AELOC, ~AELAT,
 #'   "XXX001", "P01", "RIGHT", "EYE", "RIGHT",
 #'   "XXX001", "P01", "RIGHT", "EYE", "LEFT",
+#'   "XXX001", "P01", "RIGHT", "EYE", "",
+#'   "XXX001", "P01", "RIGHT", "", "RIGHT",
 #'   "XXX001", "P02", "LEFT", "", "",
 #'   "XXX001", "P02", "LEFT", "EYE", "LEFT",
 #'   "XXX001", "P04", "BILATERAL", "EYE", "RIGHT",
-#'   "XXX001", "P05", "RIGHT", "EYE", "RIGHT"
+#'   "XXX001", "P05", "RIGHT", "EYE", "RIGHT",
+#'   "XXX001", "P05", "RIGHT", "EYE", "BILATERAL",
+#'   "XXX001", "P06", "BILATERAL", "", "",
+#'   "XXX001", "P06", "BILATERAL", "", "RIGHT",
+#'   "XXX001", "P07", "BILATERAL", "EYE", "BILATERAL",
+#'   "XXX001", "P08", "", "EYE", "BILATERAL",
 #' )
 #'
-#' derive_var_afeye(adae, AELOC, AELAT)
-derive_var_afeye <- function(dataset_occ, loc_var, lat_var) {
+#' adae <- derive_var_afeye(adae, AELOC, AELAT)
+derive_var_afeye <- function(dataset_occ, loc_var, lat_var, loc_vals = "EYE") {
   loc_var <- assert_symbol(enexpr(loc_var))
   lat_var <- assert_symbol(enexpr(lat_var))
-  assert_data_frame(dataset_occ, required_vars = expr_c(loc_var, lat_var))
+  assert_character_vector(loc_vals)
+  assert_data_frame(dataset_occ, required_vars = expr_c(loc_var, lat_var, exprs(STUDYEYE)))
 
   dataset_occ %>%
     mutate(AFEYE = case_when(
-      !!loc_var == "" ~ "",
-      toupper(STUDYEYE) == "BILATERAL" ~ "Study Eye",
-      toupper(!!lat_var) == toupper(STUDYEYE) ~ "Study Eye",
-      toupper(!!lat_var) != toupper(STUDYEYE) ~ "Fellow Eye",
-      TRUE ~ ""
+      STUDYEYE != "" & !!lat_var == "BILATERAL" &
+        !!loc_var %in% loc_vals ~ "Both Eyes",
+      toupper(STUDYEYE) == "BILATERAL" & !!lat_var != "" &
+        !!loc_var %in% loc_vals ~ "Study Eye",
+      toupper(!!lat_var) == toupper(STUDYEYE) & STUDYEYE != "" & !!lat_var != "" &
+        !!loc_var %in% loc_vals ~ "Study Eye",
+      toupper(!!lat_var) != toupper(STUDYEYE) & STUDYEYE != "" & !!lat_var != "" &
+        !!loc_var %in% loc_vals ~ "Fellow Eye",
+      TRUE ~ NA_character_
     ))
 }

R/derive_var_bcvacritxfl.R

@@ -30,8 +30,7 @@
 #' @author Edoardo Mancini
 #'
 #' @return The input ADBCVA dataset with additional columns `CRITx`, `CRITxFL`.
-#' @keywords der_ophtha
-#' @export
+#' @keywords internal
 
 derive_var_bcvacritxfl_util <- function(dataset,
                                         critx_text,

README.md

@@ -41,7 +41,7 @@ remotes::install_github("pharmaverse/admiralophtha", ref = "devel")
 ## References and Documentation
 
 * Please refer to the [{admiral} References and
-  Documentation](https://pharmaverse.github.io/admiral/pre-release/).
+  Documentation](https://pharmaverse.github.io/admiral/devel/).
 
 ## R Versions
 

_pkgdown.yml

@@ -1,4 +1,4 @@
-url: https://pharmaverse.github.io/admiralophtha/main
+url: https://pharmaverse.github.io/admiralophtha
 
 template:
   bootstrap: 5
@@ -8,7 +8,7 @@ search:
   exclude: ['news/index.html']
 repo:
   url:
-    home: https://github.com/pharmaverse/admiralophtha/main
+    home: https://github.com/pharmaverse/admiralophtha
     source: https://github.com/pharmaverse/admiralophtha/blob/main/
     issue: https://github.com/pharmaverse/admiralophtha/issues/
     user: https://github.com/
@@ -101,7 +101,7 @@ navbar:
     articles:
       text: User Guides
       menu:
-      - text: Ophthalomology Standards
+      - text: Ophthalmology Standards
         href: articles/standards.html
       - text: Creating ADOE
         href: articles/adoe.html