From 5387af551ef2e3d99736cf589d28a19beb69ba02 Mon Sep 17 00:00:00 2001 From: "Zhao, Yujie" Date: Tue, 7 Feb 2023 10:23:32 -0500 Subject: [PATCH 1/7] address comments from CRAN --- .Rbuildignore | 1 + DESCRIPTION | 11 ++++++++++- R/outdata.R | 2 +- cran-comments.md | 9 +++++++++ man/metalite-package.Rd | 2 +- man/outdata.Rd | 2 +- 6 files changed, 23 insertions(+), 4 deletions(-) create mode 100644 cran-comments.md diff --git a/.Rbuildignore b/.Rbuildignore index f1df76f..7304f04 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -9,3 +9,4 @@ ^codecov\.yml$ ^tests/testthat/_snaps$ ^\.github$ +^cran-comments\.md$ diff --git a/DESCRIPTION b/DESCRIPTION index 456374c..1d344f2 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -15,7 +15,16 @@ Authors@R: c( person("Merck Sharp & Dohme Corp", role = c("cph")) ) Description: A metadata structure for clinical data analysis - and reporting based on Analysis Data Model (ADaM) datasets. + and reporting based on Analysis Data Model (ADaM) datasets. + It offers a foundation to simplify tool development and + create standard engineering workflows. For example, + metalite can be used to: standardize input and output for + A&R functions, create analysis and reporting planning grid; + create mock table, create and validate A&R results, and + trace analysis records. It offers an unified data structure + for metadata information in clinical analysis & reporting (A&R), + leveraging the ADaM datasets for consistent and accurate + metadata representation. License: GPL-3 URL: https://merck.github.io/metalite/, https://github.com/Merck/metalite BugReports: https://github.com/Merck/metalite/issues diff --git a/R/outdata.R b/R/outdata.R index abfdbf4..5a7ef0d 100644 --- a/R/outdata.R +++ b/R/outdata.R @@ -43,7 +43,7 @@ #' @export #' #' @examples -#' metalite:::outdata( +#' outdata( #' meta = meta_example(), #' population = "apat", #' observation = "wk12", diff --git a/cran-comments.md b/cran-comments.md new file mode 100644 index 0000000..b1db2b0 --- /dev/null +++ b/cran-comments.md @@ -0,0 +1,9 @@ +This is a new release that fixed the issue in v0.1.1 identified by CRAN. + +## R CMD check results + +0 errors | 0 warnings | 0 note + +- Update DESCRIPTION by adding rich text in the Description section +- Skip adding reference in DESCRIPTION since no reference is cited +- Omit the usage of `:::` diff --git a/man/metalite-package.Rd b/man/metalite-package.Rd index 5fd849d..aa443dd 100644 --- a/man/metalite-package.Rd +++ b/man/metalite-package.Rd @@ -8,7 +8,7 @@ \description{ \if{html}{\figure{logo.png}{options: style='float: right' alt='logo' width='120'}} -A metadata structure for clinical data analysis and reporting based on Analysis Data Model (ADaM) datasets. +A metadata structure for clinical data analysis and reporting based on Analysis Data Model (ADaM) datasets. It offers a foundation to simplify tool development and create standard engineering workflows. For example, metalite can be used to: standardize input and output for A&R functions, create analysis and reporting planning grid; create mock table, create and validate A&R results, and trace analysis records. It offers an unified data structure for metadata information in clinical analysis & reporting (A&R), leveraging the ADaM datasets for consistent and accurate metadata representation. } \seealso{ Useful links: diff --git a/man/outdata.Rd b/man/outdata.Rd index 6d0aa32..2fdfa77 100644 --- a/man/outdata.Rd +++ b/man/outdata.Rd @@ -51,7 +51,7 @@ analysis and reporting. The design is inspired by \code{ggplot2::aes()}. } \examples{ -metalite:::outdata( +outdata( meta = meta_example(), population = "apat", observation = "wk12", From 4d9f153045472ef740af1ec0d1d905c1405426cb Mon Sep 17 00:00:00 2001 From: "Zhao, Yujie" Date: Tue, 7 Feb 2023 11:41:12 -0500 Subject: [PATCH 2/7] update the version number in DESCRIPTION --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 1d344f2..d254541 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: metalite Title: ADaM Metadata Structure -Version: 0.1.0 +Version: 0.1.1 Authors@R: c( person("Yilong", "Zhang", role = c("aut")), person("Yujie", "Zhao", email = "yujie.zhao@merck.com", role = c("aut", "cre")), From 3bf0b5e9ebac3417f674f07ed988c8e2baf53324 Mon Sep 17 00:00:00 2001 From: "Zhao, Yujie" Date: Tue, 7 Feb 2023 11:43:29 -0500 Subject: [PATCH 3/7] update NEWS --- NEWS.md | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index 1247485..5dbddc0 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,10 @@ +# metalite 0.1.1 + +- This is the version after addressing CRAN comments +- Update DESCRIPTION by adding rich text in the Description section +- Omit the usage of `:::` in `./man` folder + # metalite 0.1.0 -- Initial version. +- Initial version submitted to CRAN - Added a `NEWS.md` file to track changes to the package. From c1ac011087c212258996c6650b000cc9639365b1 Mon Sep 17 00:00:00 2001 From: "Zhao, Yujie" Date: Tue, 7 Feb 2023 11:44:53 -0500 Subject: [PATCH 4/7] update Description in DESCRIPTION with Yilong's suggestions --- DESCRIPTION | 15 +++++---------- 1 file changed, 5 insertions(+), 10 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index d254541..4dad590 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -15,16 +15,11 @@ Authors@R: c( person("Merck Sharp & Dohme Corp", role = c("cph")) ) Description: A metadata structure for clinical data analysis - and reporting based on Analysis Data Model (ADaM) datasets. - It offers a foundation to simplify tool development and - create standard engineering workflows. For example, - metalite can be used to: standardize input and output for - A&R functions, create analysis and reporting planning grid; - create mock table, create and validate A&R results, and - trace analysis records. It offers an unified data structure - for metadata information in clinical analysis & reporting (A&R), - leveraging the ADaM datasets for consistent and accurate - metadata representation. + and reporting based on Analysis Data Model (ADaM) datasets. + The package simplify clinical analysis and reporting tool development + by defining standardized input, output and workflow. For example, + the package can be used to create analysis and reporting planning grid; + mock table, and validated A&R results based on consistent input. License: GPL-3 URL: https://merck.github.io/metalite/, https://github.com/Merck/metalite BugReports: https://github.com/Merck/metalite/issues From a15e11b3d16c2b46c4afa36ed18b362b45c568ff Mon Sep 17 00:00:00 2001 From: Nan Xiao Date: Tue, 7 Feb 2023 12:22:27 -0500 Subject: [PATCH 5/7] Update description --- DESCRIPTION | 9 +++++---- man/metalite-package.Rd | 2 +- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 4dad590..cf992dc 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -16,10 +16,11 @@ Authors@R: c( ) Description: A metadata structure for clinical data analysis and reporting based on Analysis Data Model (ADaM) datasets. - The package simplify clinical analysis and reporting tool development - by defining standardized input, output and workflow. For example, - the package can be used to create analysis and reporting planning grid; - mock table, and validated A&R results based on consistent input. + The package simplifies clinical analysis and reporting tool development + by defining standardized inputs, outputs, and workflow. + The package can be used to create analysis and reporting planning grid, + mock table, and validated analysis and reporting results based on + consistent inputs. License: GPL-3 URL: https://merck.github.io/metalite/, https://github.com/Merck/metalite BugReports: https://github.com/Merck/metalite/issues diff --git a/man/metalite-package.Rd b/man/metalite-package.Rd index aa443dd..6925e14 100644 --- a/man/metalite-package.Rd +++ b/man/metalite-package.Rd @@ -8,7 +8,7 @@ \description{ \if{html}{\figure{logo.png}{options: style='float: right' alt='logo' width='120'}} -A metadata structure for clinical data analysis and reporting based on Analysis Data Model (ADaM) datasets. It offers a foundation to simplify tool development and create standard engineering workflows. For example, metalite can be used to: standardize input and output for A&R functions, create analysis and reporting planning grid; create mock table, create and validate A&R results, and trace analysis records. It offers an unified data structure for metadata information in clinical analysis & reporting (A&R), leveraging the ADaM datasets for consistent and accurate metadata representation. +A metadata structure for clinical data analysis and reporting based on Analysis Data Model (ADaM) datasets. The package simplifies clinical analysis and reporting tool development by defining standardized inputs, outputs, and workflow. The package can be used to create analysis and reporting planning grid, mock table, and validated analysis and reporting results based on consistent inputs. } \seealso{ Useful links: From 5d27f5dd49f3e252fddd43b96140464c49a950a6 Mon Sep 17 00:00:00 2001 From: Nan Xiao Date: Tue, 7 Feb 2023 12:22:36 -0500 Subject: [PATCH 6/7] Update `cran-comments.md` --- cran-comments.md | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/cran-comments.md b/cran-comments.md index b1db2b0..4975094 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,9 +1,7 @@ -This is a new release that fixed the issue in v0.1.1 identified by CRAN. +## Resubmission -## R CMD check results +This is a resubmission. In this version, I have fixed the issues identified in v0.1.0: -0 errors | 0 warnings | 0 note - -- Update DESCRIPTION by adding rich text in the Description section -- Skip adding reference in DESCRIPTION since no reference is cited -- Omit the usage of `:::` +* Updated DESCRIPTION to add more details to the Description field. +* Skipped adding references to the Description field for now, as after evaluation, no appropriate publications or links were identified. +* Removed the usage of `:::` in documentation. From 18473419db61d9dd28747277c9eaf4c074e2a6c3 Mon Sep 17 00:00:00 2001 From: Nan Xiao Date: Tue, 7 Feb 2023 12:22:43 -0500 Subject: [PATCH 7/7] Update news --- NEWS.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/NEWS.md b/NEWS.md index 5dbddc0..605fcc2 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,8 +1,7 @@ # metalite 0.1.1 -- This is the version after addressing CRAN comments -- Update DESCRIPTION by adding rich text in the Description section -- Omit the usage of `:::` in `./man` folder +- Updated `DESCRIPTION` file to add more details to the `Description` field. +- Removed the usage of `:::` in documentation. # metalite 0.1.0