Merge branch 'main' into patch-2

pharmaverse · Oct 25, 2023 · 46c53e0 · 46c53e0
2 parents 494a876 + d8f88fd
commit 46c53e0
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diff --git a/.github/workflows/common.yml b/.github/workflows/common.yml
@@ -13,15 +13,13 @@ on:
   push:
     branches:
       - main
-      - devel
       - pre-release
       - test
   # 'pull_request' events are triggered when PRs are
   # created against one of these target branches.
   pull_request:
     branches:
       - main
-      - devel
       - pre-release
       - test
   # 'release' events are triggered when...
@@ -64,6 +62,8 @@ jobs:
     name: Check
     uses: pharmaverse/admiralci/.github/workflows/r-cmd-check.yml@main
     if: github.event_name == 'pull_request'
+    with:
+      error-on: warning # TODO: find a way to ignore specific notes
   docs:
     name: Documentation
     uses: pharmaverse/admiralci/.github/workflows/pkgdown.yml@main

diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: admiralophtha
 Type: Package
 Title: ADaM in R Asset Library - Ophthalmology
-Version: 0.3.0
+Version: 0.3.0.9001
 Authors@R: c(
     person("Edoardo", "Mancini", email = "[email protected]", role = c("aut", "cre")),
     person("Ritika", "Aggarwal", email = "[email protected]", role = c("aut")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,14 @@
+# admiralophtha (development version)
+
+## Updates to Templates
+
+- Removed `analysis_value` argument in the calls to `derive_param_computed()` in ADBCVA template in line with the deprecation of this argument in the new version of `{admiral}`. Variable values for parameters of interest are now all populated through the `set_values_to` argument (#207). 
+
+## Updates to Documentation
+
+- Added release date for `{admiralophtha}` 1.0 to the front page (#203).
+- Removed `analysis_value` argument in the calls to `derive_param_computed()` in ADBCVA vignette in line with the deprecation of this argument in the new version of `{admiral}`. Variable values for parameters of interest are now all populated through the `set_values_to` argument (#207). 
+
 # admiralophtha 0.3.0
 
 ## Updates to Functions

diff --git a/README.md b/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/devel/).
+  Documentation](https://pharmaverse.github.io/admiral/cran-release/).
 
 ## R Versions
 
@@ -73,4 +73,4 @@ developer community:
 * The first release (v. 0.1.0) came out on 13th March 2023.
 * The second release (v. 0.2.0) came out on 12th June 2023.
 * The third release (v. 0.3.0) came out on 18th September 2023.
-* We are planning for a fourth release before the end of 2023.
+* We are planning for a fourth release (v.1.0) on December 11th 2023. The objective of the 1.0 release of `{admiralophtha}` is to provide a package that is mature enough to be used as it is as part of the ADaM work on any ophthalmology study.
diff --git a/cran-comments.md b/cran-comments.md
diff --git a/inst/templates/ad_adbcva.R b/inst/templates/ad_adbcva.R
@@ -139,8 +139,8 @@ adbcva_logparam <- adbcva_nlogparam %>%
   derive_param_computed(
     by_vars = c(exprs(STUDYID, USUBJID, VISIT, VISITNUM, OEDY, OEDTC, AFEYE), adsl_vars),
     parameters = c("SBCVA"),
-    analysis_value = convert_etdrs_to_logmar(AVAL.SBCVA),
     set_values_to = exprs(
+      AVAL = convert_etdrs_to_logmar(AVAL.SBCVA),
       PARAMCD = "SBCVALOG",
       PARAM = "Study Eye Visual Acuity LogMAR Score",
       DTYPE = NA_character_,
@@ -150,8 +150,8 @@ adbcva_logparam <- adbcva_nlogparam %>%
   derive_param_computed(
     by_vars = c(exprs(STUDYID, USUBJID, VISIT, OEDY, OEDTC, AFEYE), adsl_vars),
     parameters = c("FBCVA"),
-    analysis_value = convert_etdrs_to_logmar(AVAL.FBCVA),
     set_values_to = exprs(
+      AVAL = convert_etdrs_to_logmar(AVAL.FBCVA),
       PARAMCD = "FBCVALOG",
       PARAM = "Fellow Eye Visual Acuity LogMAR Score",
       DTYPE = NA_character_,

diff --git a/vignettes/adbcva.Rmd b/vignettes/adbcva.Rmd
@@ -150,24 +150,24 @@ Often ADBCVA datasets contain derived records for BCVA in LogMAR units. This can
 ```{r}
 adbcva <- adbcva %>%
   derive_param_computed(
-    by_vars = c(exprs(STUDYID, USUBJID, VISIT, VISITNUM, OEDY, OEDTC), adsl_vars),
+    by_vars = c(exprs(STUDYID, USUBJID, VISIT, VISITNUM, OEDY, OEDTC, AFEYE), adsl_vars),
     parameters = c("SBCVA"),
-    analysis_value = convert_etdrs_to_logmar(AVAL.SBCVA),
     set_values_to = exprs(
+      AVAL = convert_etdrs_to_logmar(AVAL.SBCVA),
       PARAMCD = "SBCVALOG",
       PARAM = "Study Eye Visual Acuity LogMAR Score",
-      DTYPE = "DERIVED",
+      DTYPE = NA_character_,
       AVALU = "LogMAR"
     )
   ) %>%
   derive_param_computed(
-    by_vars = c(exprs(STUDYID, USUBJID, VISIT, OEDY, OEDTC), adsl_vars),
+    by_vars = c(exprs(STUDYID, USUBJID, VISIT, OEDY, OEDTC, AFEYE), adsl_vars),
     parameters = c("FBCVA"),
-    analysis_value = convert_etdrs_to_logmar(AVAL.FBCVA),
     set_values_to = exprs(
+      AVAL = convert_etdrs_to_logmar(AVAL.FBCVA),
       PARAMCD = "FBCVALOG",
       PARAM = "Fellow Eye Visual Acuity LogMAR Score",
-      DTYPE = "DERIVED",
+      DTYPE = NA_character_,
       AVALU = "LogMAR"
     )
   ) %>%