From ea1a0d60a16aa51163480c9ac38de76fa9ab9ea2 Mon Sep 17 00:00:00 2001 From: "Mancini, Edoardo {MDBB~Welwyn}" Date: Wed, 25 Oct 2023 11:44:35 +0200 Subject: [PATCH 1/2] #207 updates to `derive_param_computed()` calls in vignette and template --- DESCRIPTION | 2 +- NEWS.md | 10 ++++++++++ inst/templates/ad_adbcva.R | 4 ++-- vignettes/adbcva.Rmd | 12 ++++++------ 4 files changed, 19 insertions(+), 9 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index c0a274fc..4d9f0c18 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: admiralophtha Type: Package Title: ADaM in R Asset Library - Ophthalmology -Version: 0.3.0 +Version: 0.3.0.9000 Authors@R: c( person("Edoardo", "Mancini", email = "edoardo.mancini@roche.com", role = c("aut", "cre")), person("Ritika", "Aggarwal", email = "ritika.aggarwal@novartis.com", role = c("aut")), diff --git a/NEWS.md b/NEWS.md index cb19d81c..f6ba03b4 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,13 @@ +# 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 + +- 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/inst/templates/ad_adbcva.R b/inst/templates/ad_adbcva.R index 1dfafcee..dc5aa594 100644 --- 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 index ed1b15ec..c43561cb 100644 --- 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" ) ) %>% From 5b250f5740e7c55d0c3d2998c90495d6323579c5 Mon Sep 17 00:00:00 2001 From: "Mancini, Edoardo {MDBB~Welwyn}" Date: Wed, 25 Oct 2023 11:54:00 +0200 Subject: [PATCH 2/2] #207 updated common.yml file to note about high version number --- .github/workflows/common.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/common.yml b/.github/workflows/common.yml index 3f96431d..ca7b8612 100644 --- a/.github/workflows/common.yml +++ b/.github/workflows/common.yml @@ -13,7 +13,6 @@ on: push: branches: - main - - devel - pre-release - test # 'pull_request' events are triggered when PRs are @@ -21,7 +20,6 @@ on: 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