From 57e075e479d51f403a8a9af8672c5f60c5422206 Mon Sep 17 00:00:00 2001 From: Kangjie Zhang Date: Thu, 30 May 2024 16:51:43 -0700 Subject: [PATCH] #104: address cran feedback 404 links --- DESCRIPTION | 2 +- R/data.R | 28 ++++++++++++++-------------- README.md | 2 +- cran-comments.md | 5 +++++ man/ae_ophtha.Rd | 2 +- man/ce_vaccine.Rd | 2 +- man/dm_vaccine.Rd | 2 +- man/ex_ophtha.Rd | 2 +- man/ex_vaccine.Rd | 2 +- man/face_vaccine.Rd | 2 +- man/is_vaccine.Rd | 2 +- man/pharmaversesdtm-package.Rd | 2 +- man/qs_ophtha.Rd | 2 +- man/suppce_vaccine.Rd | 2 +- man/suppdm_vaccine.Rd | 2 +- man/suppex_vaccine.Rd | 2 +- man/suppface_vaccine.Rd | 2 +- man/suppis_vaccine.Rd | 2 +- man/vs_vaccine.Rd | 2 +- 19 files changed, 36 insertions(+), 31 deletions(-) create mode 100644 cran-comments.md diff --git a/DESCRIPTION b/DESCRIPTION index 8832539..d08b61a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -18,7 +18,7 @@ Description: A set of Study Data Tabulation Model (SDTM) datasets from the Clini (2021) . Language: en-US License: Apache License (>= 2.0) -URL: https://pharmaverse.github.io/pharmaversesdtm/main/, https://github.com/pharmaverse/pharmaversesdtm +URL: https://pharmaverse.github.io/pharmaversesdtm, https://github.com/pharmaverse/pharmaversesdtm Depends: R (>= 3.5.0) Encoding: UTF-8 LazyData: true diff --git a/R/data.R b/R/data.R index c4ef5d7..1a3f2a0 100644 --- a/R/data.R +++ b/R/data.R @@ -9,7 +9,7 @@ #' #' An example Adverse Events SDTM dataset with ophthalmology-specific variable `AELAT` #' -#' @source Constructed using `ae` from the `{pharmaversesdtm}` package # nolint +#' @source Constructed using `ae` from the `{pharmaversesdtm}` package "ae_ophtha" #' Concomitant Medication @@ -51,7 +51,7 @@ #' #' An example Exposure SDTM dataset with ophthalmology-specific variables such as `EXLOC` and `EXLAT` #' -#' @source Constructed using `ex` from the `{pharmaversesdtm}` package #nolint +#' @source Constructed using `ex` from the `{pharmaversesdtm}` package "ex_ophtha" #' Laboratory Measurements @@ -97,7 +97,7 @@ #' #' An example Questionnaires SDTM dataset with ophthalmology-specific questionnaire of NEI VFQ-25 #' -#' @source Constructed using `qs` from the `{pharmaversesdtm}` package #nolint +#' @source Constructed using `qs` from the `{pharmaversesdtm}` package "qs_ophtha" #' Subject Characteristic for Ophthalmology @@ -244,75 +244,75 @@ #' #' An example SDTM DM dataset for vaccine studies #' -#' @source \url{https://github.com/pharmaverse/admiralvaccine/blob/main/data/vx_dm.rda} # nolint +#' @source Constructed by `{admiralvaccine}` developers "dm_vaccine" #' Vital Signs for Vaccine #' #' An example SDTM VS dataset for vaccine studies #' -#' @source \url{https://github.com/pharmaverse/admiralvaccine/blob/main/data/vx_vs.rda} # nolint +#' @source Constructed by `{admiralvaccine}` developers "vs_vaccine" #' Clinical Events for Vaccine #' #' An example SDTM CE dataset for vaccine studies #' -#' @source \url{https://github.com/pharmaverse/admiralvaccine/blob/main/data/vx_ce.rda} # nolint +#' @source Constructed by `{admiralvaccine}` developers "ce_vaccine" #' Exposures for Vaccine #' #' An example SDTM EX dataset for vaccine studies #' -#' @source \url{https://github.com/pharmaverse/admiralvaccine/blob/main/data/vx_ex.rda} # nolint +#' @source Constructed by `{admiralvaccine}` developers "ex_vaccine" #' Immunogenicity Specimen Assessments for Vaccine #' #' An example SDTM IS for vaccine studies #' -#' @source \url{https://github.com/pharmaverse/admiralvaccine/blob/main/data/vx_is.rda} # nolint +#' @source Constructed by `{admiralvaccine}` developers "is_vaccine" #' Findings About Clinical Events for Vaccine #' #' An example SDTM FACE for vaccine studies #' -#' @source \url{https://github.com/pharmaverse/admiralvaccine/blob/main/data/vx_face.rda} # nolint +#' @source Constructed by `{admiralvaccine}` developers "face_vaccine" #' Supplemental Qualifiers for Clinical Events for Vaccine #' #' An example SDTM SUPPCE for vaccine studies #' -#' @source \url{https://github.com/pharmaverse/admiralvaccine/blob/main/data/vx_suppce.rda} # nolint +#' @source Constructed by `{admiralvaccine}` developers "suppce_vaccine" #' Supplemental Qualifiers for Demographics for Vaccine #' #' An example SDTM SUPPDM dataset for vaccine studies #' -#' @source \url{https://github.com/pharmaverse/admiralvaccine/blob/main/data/vx_suppdm.rda} # nolint +#' @source Constructed by `{admiralvaccine}` developers "suppdm_vaccine" #' Supplemental Qualifiers for Exposures for Vaccine #' #' An example SDTM SUPPEX dataset for vaccine studies #' -#' @source \url{https://github.com/pharmaverse/admiralvaccine/blob/main/data/vx_suppex.rda} # nolint +#' @source Constructed by `{admiralvaccine}` developers "suppex_vaccine" #' Supplemental Qualifiers for Findings About for Clinical Events for Vaccine #' #' An example SDTM SUPPFACE dataset for vaccine studies #' -#' @source \url{https://github.com/pharmaverse/admiralvaccine/blob/main/data/vx_suppface.rda} # nolint +#' @source Constructed by `{admiralvaccine}` developers "suppface_vaccine" #' Supplemental Qualifiers for Immunogenicity Specimen Assessments for Vaccine #' #' An example SDTM SUPPIS dataset for vaccine studies #' -#' @source \url{https://github.com/pharmaverse/admiralvaccine/blob/main/data/vx_suppis.rda} # nolint +#' @source Constructed by `{admiralvaccine}` developers "suppis_vaccine" diff --git a/README.md b/README.md index e66af28..26f73d1 100644 --- a/README.md +++ b/README.md @@ -26,7 +26,7 @@ remotes::install_github("pharmaverse/pharmaversesdtm", ref = "main") # Data Sources -Some of the test datasets has been sourced from the [CDISC pilot project](https://github.com/cdisc-org/sdtm-adam-pilot-project), while other datasets have been constructed ad-hoc by the admiral team. Please check the [Reference page](https://pharmaverse.github.io/pharmaversesdtm/cran-release/reference/index.html) for detailed information regarding the source of specific datasets. +Some of the test datasets has been sourced from the [CDISC pilot project](https://github.com/cdisc-org/sdtm-adam-pilot-project), while other datasets have been constructed ad-hoc by the admiral team. Please check the [Reference page](https://pharmaverse.github.io/pharmaversesdtm/reference/index.html) for detailed information regarding the source of specific datasets. # Naming Conventions {#naming} diff --git a/cran-comments.md b/cran-comments.md new file mode 100644 index 0000000..858617d --- /dev/null +++ b/cran-comments.md @@ -0,0 +1,5 @@ +## R CMD check results + +0 errors | 0 warnings | 1 note + +* This is a new release. diff --git a/man/ae_ophtha.Rd b/man/ae_ophtha.Rd index 3fed60b..18b4699 100644 --- a/man/ae_ophtha.Rd +++ b/man/ae_ophtha.Rd @@ -8,7 +8,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 1191 rows and 36 columns. } \source{ -Constructed using \code{ae} from the \code{{pharmaversesdtm}} package # nolint +Constructed using \code{ae} from the \code{{pharmaversesdtm}} package } \usage{ ae_ophtha diff --git a/man/ce_vaccine.Rd b/man/ce_vaccine.Rd index 6813804..64d6216 100644 --- a/man/ce_vaccine.Rd +++ b/man/ce_vaccine.Rd @@ -8,7 +8,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 44 rows and 29 columns. } \source{ -\url{https://github.com/pharmaverse/admiralvaccine/blob/main/data/vx_ce.rda} # nolint +Constructed by \code{{admiralvaccine}} developers } \usage{ ce_vaccine diff --git a/man/dm_vaccine.Rd b/man/dm_vaccine.Rd index cd81706..d8dc344 100644 --- a/man/dm_vaccine.Rd +++ b/man/dm_vaccine.Rd @@ -8,7 +8,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 2 rows and 28 columns. } \source{ -\url{https://github.com/pharmaverse/admiralvaccine/blob/main/data/vx_dm.rda} # nolint +Constructed by \code{{admiralvaccine}} developers } \usage{ dm_vaccine diff --git a/man/ex_ophtha.Rd b/man/ex_ophtha.Rd index 7732d2a..b62c996 100644 --- a/man/ex_ophtha.Rd +++ b/man/ex_ophtha.Rd @@ -8,7 +8,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 591 rows and 19 columns. } \source{ -Constructed using \code{ex} from the \code{{pharmaversesdtm}} package #nolint +Constructed using \code{ex} from the \code{{pharmaversesdtm}} package } \usage{ ex_ophtha diff --git a/man/ex_vaccine.Rd b/man/ex_vaccine.Rd index 44c5e31..e88a179 100644 --- a/man/ex_vaccine.Rd +++ b/man/ex_vaccine.Rd @@ -8,7 +8,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 4 rows and 21 columns. } \source{ -\url{https://github.com/pharmaverse/admiralvaccine/blob/main/data/vx_ex.rda} # nolint +Constructed by \code{{admiralvaccine}} developers } \usage{ ex_vaccine diff --git a/man/face_vaccine.Rd b/man/face_vaccine.Rd index 06c84ab..dbdd7eb 100644 --- a/man/face_vaccine.Rd +++ b/man/face_vaccine.Rd @@ -8,7 +8,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 307 rows and 30 columns. } \source{ -\url{https://github.com/pharmaverse/admiralvaccine/blob/main/data/vx_face.rda} # nolint +Constructed by \code{{admiralvaccine}} developers } \usage{ face_vaccine diff --git a/man/is_vaccine.Rd b/man/is_vaccine.Rd index f8fc54e..106fba2 100644 --- a/man/is_vaccine.Rd +++ b/man/is_vaccine.Rd @@ -8,7 +8,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 16 rows and 24 columns. } \source{ -\url{https://github.com/pharmaverse/admiralvaccine/blob/main/data/vx_is.rda} # nolint +Constructed by \code{{admiralvaccine}} developers } \usage{ is_vaccine diff --git a/man/pharmaversesdtm-package.Rd b/man/pharmaversesdtm-package.Rd index 2d5802e..c5e7785 100644 --- a/man/pharmaversesdtm-package.Rd +++ b/man/pharmaversesdtm-package.Rd @@ -13,7 +13,7 @@ A set of Study Data Tabulation Model (SDTM) datasets from the Clinical Data Inte \seealso{ Useful links: \itemize{ - \item \url{https://pharmaverse.github.io/pharmaversesdtm/main/} + \item \url{https://pharmaverse.github.io/pharmaversesdtm} \item \url{https://github.com/pharmaverse/pharmaversesdtm} } diff --git a/man/qs_ophtha.Rd b/man/qs_ophtha.Rd index 43576c9..e27ee67 100644 --- a/man/qs_ophtha.Rd +++ b/man/qs_ophtha.Rd @@ -8,7 +8,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 75922 rows and 20 columns. } \source{ -Constructed using \code{qs} from the \code{{pharmaversesdtm}} package #nolint +Constructed using \code{qs} from the \code{{pharmaversesdtm}} package } \usage{ qs_ophtha diff --git a/man/suppce_vaccine.Rd b/man/suppce_vaccine.Rd index e99218a..0d11c82 100644 --- a/man/suppce_vaccine.Rd +++ b/man/suppce_vaccine.Rd @@ -8,7 +8,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 4 rows and 9 columns. } \source{ -\url{https://github.com/pharmaverse/admiralvaccine/blob/main/data/vx_suppce.rda} # nolint +Constructed by \code{{admiralvaccine}} developers } \usage{ suppce_vaccine diff --git a/man/suppdm_vaccine.Rd b/man/suppdm_vaccine.Rd index 655d833..a674524 100644 --- a/man/suppdm_vaccine.Rd +++ b/man/suppdm_vaccine.Rd @@ -8,7 +8,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 2 rows and 9 columns. } \source{ -\url{https://github.com/pharmaverse/admiralvaccine/blob/main/data/vx_suppdm.rda} # nolint +Constructed by \code{{admiralvaccine}} developers } \usage{ suppdm_vaccine diff --git a/man/suppex_vaccine.Rd b/man/suppex_vaccine.Rd index ea27a7f..8c5b086 100644 --- a/man/suppex_vaccine.Rd +++ b/man/suppex_vaccine.Rd @@ -8,7 +8,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 4 rows and 9 columns. } \source{ -\url{https://github.com/pharmaverse/admiralvaccine/blob/main/data/vx_suppex.rda} # nolint +Constructed by \code{{admiralvaccine}} developers } \usage{ suppex_vaccine diff --git a/man/suppface_vaccine.Rd b/man/suppface_vaccine.Rd index 022d731..5dc0c10 100644 --- a/man/suppface_vaccine.Rd +++ b/man/suppface_vaccine.Rd @@ -8,7 +8,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 4 rows and 9 columns. } \source{ -\url{https://github.com/pharmaverse/admiralvaccine/blob/main/data/vx_suppface.rda} # nolint +Constructed by \code{{admiralvaccine}} developers } \usage{ suppface_vaccine diff --git a/man/suppis_vaccine.Rd b/man/suppis_vaccine.Rd index 4521486..75b558d 100644 --- a/man/suppis_vaccine.Rd +++ b/man/suppis_vaccine.Rd @@ -8,7 +8,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 16 rows and 10 columns. } \source{ -\url{https://github.com/pharmaverse/admiralvaccine/blob/main/data/vx_suppis.rda} # nolint +Constructed by \code{{admiralvaccine}} developers } \usage{ suppis_vaccine diff --git a/man/vs_vaccine.Rd b/man/vs_vaccine.Rd index 9382de9..9934669 100644 --- a/man/vs_vaccine.Rd +++ b/man/vs_vaccine.Rd @@ -8,7 +8,7 @@ An object of class \code{grouped_df} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 28 rows and 23 columns. } \source{ -\url{https://github.com/pharmaverse/admiralvaccine/blob/main/data/vx_vs.rda} # nolint +Constructed by \code{{admiralvaccine}} developers } \usage{ vs_vaccine