From 1d4dc459298118f3c1d5de644271ea0049c71707 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <211358+averissimo@users.noreply.github.com> Date: Fri, 25 Jul 2025 13:09:48 +0100 Subject: [PATCH 01/11] feat: build data references in site --- R/data.R | 67 ++++++++++++++++++---------------- R/dummy_function.R | 4 +- _pkgdown.yml | 14 +++++++ data-raw/data.R | 18 ++++----- man/default_cdisc_join_keys.Rd | 4 +- man/example_cdisc_data.Rd | 4 +- man/rADAE.Rd | 7 ++-- man/rADCM.Rd | 7 ++-- man/rADEX.Rd | 7 ++-- man/rADLB.Rd | 7 ++-- man/rADRS.Rd | 7 ++-- man/rADSL.Rd | 7 ++-- man/rADTR.Rd | 7 ++-- man/rADTTE.Rd | 3 +- man/rADVS.Rd | 7 ++-- 15 files changed, 90 insertions(+), 80 deletions(-) diff --git a/R/data.R b/R/data.R index 88d6abea5..c363ab7b8 100644 --- a/R/data.R +++ b/R/data.R @@ -1,65 +1,70 @@ -#' Random adverse events +#' Random adverse events analysis dataset #' #' @docType data #' @usage rADAE -#' @keywords datasets internal -#' @source internal +#' @inherit random.cdisc.data::cadae format +#' @keywords datasets +#' @source [random.cdisc.data::cadae] #' @name rADAE "rADAE" -#' Random concomitant medications +#' Random concomitant medications analysis dataset #' #' @docType data #' @usage rADCM -#' @keywords datasets internal -#' @source internal +#' @inherit random.cdisc.data::cadcm format +#' @keywords datasets +#' @source [random.cdisc.data::cadcm] #' @name rADCM "rADCM" -#' Random response -#' -#' Random exposure. +#' Random response analysis dataset #' #' @docType data #' @usage rADEX -#' @keywords datasets internal -#' @source internal +#' @inherit random.cdisc.data::cadex format +#' @keywords datasets +#' @source [random.cdisc.data::cadex] #' @name rADEX "rADEX" -#' Random lab analysis +#' Random laboratory data analysis dataset #' #' @docType data #' @usage rADLB -#' @keywords datasets internal -#' @source internal +#' @inherit random.cdisc.data::cadlb format +#' @keywords datasets +#' @source [random.cdisc.data::cadlb] #' @name rADLB "rADLB" -#' Random response +#' Random response analysis dataset #' #' @docType data #' @usage rADRS -#' @keywords datasets internal -#' @source internal +#' @inherit random.cdisc.data::cadrs format +#' @keywords datasets +#' @source [random.cdisc.data::cadrs] #' @name rADRS "rADRS" -#' Random patient listing +#' Random patient listing dataset #' #' @docType data #' @usage rADSL -#' @keywords datasets internal -#' @source internal +#' @keywords datasets +#' @inherit random.cdisc.data::cadsl format +#' @source [random.cdisc.data::cadsl] #' @name rADSL "rADSL" -#' Random data `rADTR` +#' Random tumor response analysis dataset #' #' @docType data #' @usage rADTR -#' @keywords datasets internal -#' @source internal +#' @keywords datasets +#' @inherit random.cdisc.data::cadtr format +#' @source [random.cdisc.data::cadtr] #' @name rADTR "rADTR" @@ -67,26 +72,26 @@ #' #' @docType data #' @usage rADTTE -#' @keywords datasets internal -#' @source internal +#' @inherit random.cdisc.data::cadtte format +#' @keywords datasets +#' @source [random.cdisc.data::cadtte] #' @name rADTTE "rADTTE" -#' Random data `rADVS` +#' Random vital signs analysis dataset #' #' @docType data #' @usage rADVS -#' @keywords datasets internal -#' @source internal +#' @inherit random.cdisc.data::cadvs format +#' @keywords datasets +#' @source [random.cdisc.data::cadvs] #' @name rADVS "rADVS" #' List containing default joining keys for `CDISC` datasets #' -#' This data object is created at loading time from `cdisc_datasets/cdisc_datasets.yaml`. -#' #' @name default_cdisc_join_keys #' @usage default_cdisc_join_keys #' @docType data -#' @source internal +#' @source internal. See `data-raw/cdisc_datasets.yaml` and `data-raw/data.R` for details. "default_cdisc_join_keys" diff --git a/R/dummy_function.R b/R/dummy_function.R index f35cd22b7..e2195c20d 100644 --- a/R/dummy_function.R +++ b/R/dummy_function.R @@ -3,9 +3,9 @@ #' Retrieves example CDISC datasets for use in examples and testing. #' #' This function returns a dummy dataset and should only be used within `teal.data`. -#' Note that the datasets are not created and maintained in `teal.data`, they are retrieved its dependencies. +#' Note that the datasets are not created and maintained in `teal.data`, they are retrieved from [`random.cdisc.data`][random.cdisc.data::random.cdisc.data-package] package. #' -#' @param dataname (`character(1)`) name of a CDISC dataset +#' @param dataname (`character(1)`) name of a CDISC dataset. #' #' @return A CDISC dataset as a `data.frame`. #' diff --git a/_pkgdown.yml b/_pkgdown.yml index 70c6032aa..6cb81eb9c 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -20,6 +20,7 @@ navbar: href: unit-test-report-non-cran/ github: icon: fa-github + aria-label: View on Github href: https://github.com/insightsengineering/teal.data articles: @@ -56,3 +57,16 @@ reference: - col_labels<- - col_relabel - example_cdisc_data + - title: Built-in datasets + desc: > + Random CDISC synthetic data generated from `{random.cdisc.data}` package. + contents: + - rADSL + - rADAE + - rADLB + - rADCM + - rADEX + - rADRS + - rADTR + - rADTTE + - rADVS diff --git a/data-raw/data.R b/data-raw/data.R index 829b343ee..75f5ba112 100644 --- a/data-raw/data.R +++ b/data-raw/data.R @@ -1,29 +1,29 @@ ## code to prepare `data` for testing examples -rADAE <- random.cdisc.data::cadae # nolint: object_name_linter. +rADAE <- random.cdisc.data::cadae # nolint: object_name. usethis::use_data(rADAE) -rADCM <- random.cdisc.data::cadcm # nolint: object_name_linter. +rADCM <- random.cdisc.data::cadcm # nolint: object_name. usethis::use_data(rADCM) -rADEX <- random.cdisc.data::cadex # nolint: object_name_linter. +rADEX <- random.cdisc.data::cadex # nolint: object_name. usethis::use_data(rADEX) -rADLB <- random.cdisc.data::cadlb # nolint: object_name_linter. +rADLB <- random.cdisc.data::cadlb # nolint: object_name. usethis::use_data(rADLB) -rADRS <- random.cdisc.data::cadrs # nolint: object_name_linter. +rADRS <- random.cdisc.data::cadrs # nolint: object_name. usethis::use_data(rADRS) -rADSL <- random.cdisc.data::cadsl # nolint: object_name_linter. +rADSL <- random.cdisc.data::cadsl # nolint: object_name. usethis::use_data(rADSL) -rADTR <- random.cdisc.data::cadtr # nolint: object_name_linter. +rADTR <- random.cdisc.data::cadtr # nolint: object_name. usethis::use_data(rADTR) -rADTTE <- random.cdisc.data::cadtte # nolint: object_name_linter. +rADTTE <- random.cdisc.data::cadtte # nolint: object_name. usethis::use_data(rADTTE) -rADVS <- random.cdisc.data::cadvs # nolint: object_name_linter. +rADVS <- random.cdisc.data::cadvs # nolint: object_name. usethis::use_data(rADVS) ## Code to prepare default CDISC datasets for `teal.data` diff --git a/man/default_cdisc_join_keys.Rd b/man/default_cdisc_join_keys.Rd index 266dd9d9c..d9b40aeaa 100644 --- a/man/default_cdisc_join_keys.Rd +++ b/man/default_cdisc_join_keys.Rd @@ -8,12 +8,12 @@ An object of class \code{join_keys} (inherits from \code{list}) of length 19. } \source{ -internal +internal. See \code{data-raw/cdisc_datasets.yaml} and \code{data-raw/data.R} for details. } \usage{ default_cdisc_join_keys } \description{ -This data object is created at loading time from \code{cdisc_datasets/cdisc_datasets.yaml}. +List containing default joining keys for \code{CDISC} datasets } \keyword{datasets} diff --git a/man/example_cdisc_data.Rd b/man/example_cdisc_data.Rd index 7e268f77b..3b00b842a 100644 --- a/man/example_cdisc_data.Rd +++ b/man/example_cdisc_data.Rd @@ -9,7 +9,7 @@ example_cdisc_data( ) } \arguments{ -\item{dataname}{(\code{character(1)}) name of a CDISC dataset} +\item{dataname}{(\code{character(1)}) name of a CDISC dataset.} } \value{ A CDISC dataset as a \code{data.frame}. @@ -19,5 +19,5 @@ Retrieves example CDISC datasets for use in examples and testing. } \details{ This function returns a dummy dataset and should only be used within \code{teal.data}. -Note that the datasets are not created and maintained in \code{teal.data}, they are retrieved its dependencies. +Note that the datasets are not created and maintained in \code{teal.data}, they are retrieved from \code{\link[random.cdisc.data:random.cdisc.data-package]{random.cdisc.data}} package. } diff --git a/man/rADAE.Rd b/man/rADAE.Rd index 6e57b7d7a..9bc58b25b 100644 --- a/man/rADAE.Rd +++ b/man/rADAE.Rd @@ -3,18 +3,17 @@ \docType{data} \name{rADAE} \alias{rADAE} -\title{Random adverse events} +\title{Random adverse events analysis dataset} \format{ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 1934 rows and 92 columns. } \source{ -internal +\link[random.cdisc.data:cadae]{random.cdisc.data::cadae} } \usage{ rADAE } \description{ -Random adverse events +Random adverse events analysis dataset } \keyword{datasets} -\keyword{internal} diff --git a/man/rADCM.Rd b/man/rADCM.Rd index 487916eff..721b3588a 100644 --- a/man/rADCM.Rd +++ b/man/rADCM.Rd @@ -3,18 +3,17 @@ \docType{data} \name{rADCM} \alias{rADCM} -\title{Random concomitant medications} +\title{Random concomitant medications analysis dataset} \format{ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 3685 rows and 83 columns. } \source{ -internal +\link[random.cdisc.data:cadcm]{random.cdisc.data::cadcm} } \usage{ rADCM } \description{ -Random concomitant medications +Random concomitant medications analysis dataset } \keyword{datasets} -\keyword{internal} diff --git a/man/rADEX.Rd b/man/rADEX.Rd index dbffbce48..e9c0e5287 100644 --- a/man/rADEX.Rd +++ b/man/rADEX.Rd @@ -3,18 +3,17 @@ \docType{data} \name{rADEX} \alias{rADEX} -\title{Random response} +\title{Random response analysis dataset} \format{ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 6400 rows and 79 columns. } \source{ -internal +\link[random.cdisc.data:cadex]{random.cdisc.data::cadex} } \usage{ rADEX } \description{ -Random exposure. +Random response analysis dataset } \keyword{datasets} -\keyword{internal} diff --git a/man/rADLB.Rd b/man/rADLB.Rd index a5430d325..1da7893b9 100644 --- a/man/rADLB.Rd +++ b/man/rADLB.Rd @@ -3,18 +3,17 @@ \docType{data} \name{rADLB} \alias{rADLB} -\title{Random lab analysis} +\title{Random laboratory data analysis dataset} \format{ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 8400 rows and 102 columns. } \source{ -internal +\link[random.cdisc.data:cadlb]{random.cdisc.data::cadlb} } \usage{ rADLB } \description{ -Random lab analysis +Random laboratory data analysis dataset } \keyword{datasets} -\keyword{internal} diff --git a/man/rADRS.Rd b/man/rADRS.Rd index b25c99888..6ff822b2e 100644 --- a/man/rADRS.Rd +++ b/man/rADRS.Rd @@ -3,18 +3,17 @@ \docType{data} \name{rADRS} \alias{rADRS} -\title{Random response} +\title{Random response analysis dataset} \format{ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 3200 rows and 65 columns. } \source{ -internal +\link[random.cdisc.data:cadrs]{random.cdisc.data::cadrs} } \usage{ rADRS } \description{ -Random response +Random response analysis dataset } \keyword{datasets} -\keyword{internal} diff --git a/man/rADSL.Rd b/man/rADSL.Rd index 1b09ee22a..0fb4abbe5 100644 --- a/man/rADSL.Rd +++ b/man/rADSL.Rd @@ -3,18 +3,17 @@ \docType{data} \name{rADSL} \alias{rADSL} -\title{Random patient listing} +\title{Random patient listing dataset} \format{ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 400 rows and 55 columns. } \source{ -internal +\link[random.cdisc.data:cadsl]{random.cdisc.data::cadsl} } \usage{ rADSL } \description{ -Random patient listing +Random patient listing dataset } \keyword{datasets} -\keyword{internal} diff --git a/man/rADTR.Rd b/man/rADTR.Rd index 176308a02..b697ab093 100644 --- a/man/rADTR.Rd +++ b/man/rADTR.Rd @@ -3,18 +3,17 @@ \docType{data} \name{rADTR} \alias{rADTR} -\title{Random data \code{rADTR}} +\title{Random tumor response analysis dataset} \format{ An object of class \code{data.frame} with 2800 rows and 76 columns. } \source{ -internal +\link[random.cdisc.data:cadtr]{random.cdisc.data::cadtr} } \usage{ rADTR } \description{ -Random data \code{rADTR} +Random tumor response analysis dataset } \keyword{datasets} -\keyword{internal} diff --git a/man/rADTTE.Rd b/man/rADTTE.Rd index 185d391d9..d04c795b2 100644 --- a/man/rADTTE.Rd +++ b/man/rADTTE.Rd @@ -8,7 +8,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 2000 rows and 67 columns. } \source{ -internal +\link[random.cdisc.data:cadtte]{random.cdisc.data::cadtte} } \usage{ rADTTE @@ -17,4 +17,3 @@ rADTTE Random time to event analysis dataset } \keyword{datasets} -\keyword{internal} diff --git a/man/rADVS.Rd b/man/rADVS.Rd index a567f538d..bed50a791 100644 --- a/man/rADVS.Rd +++ b/man/rADVS.Rd @@ -3,18 +3,17 @@ \docType{data} \name{rADVS} \alias{rADVS} -\title{Random data \code{rADVS}} +\title{Random vital signs analysis dataset} \format{ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 16800 rows and 87 columns. } \source{ -internal +\link[random.cdisc.data:cadvs]{random.cdisc.data::cadvs} } \usage{ rADVS } \description{ -Random data \code{rADVS} +Random vital signs analysis dataset } \keyword{datasets} -\keyword{internal} From 3640e91a0e0d23ae46608aa731818d659e2a758f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <211358+averissimo@users.noreply.github.com> Date: Fri, 25 Jul 2025 13:24:24 +0100 Subject: [PATCH 02/11] chore: last name that wasn't consistent --- R/data.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/data.R b/R/data.R index c363ab7b8..42f9d4679 100644 --- a/R/data.R +++ b/R/data.R @@ -48,7 +48,7 @@ #' @name rADRS "rADRS" -#' Random patient listing dataset +#' Random subject-level analysis dataset #' #' @docType data #' @usage rADSL From ed262bb1be729e28e161c2fbe26cc4f50e828f04 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <211358+averissimo@users.noreply.github.com> Date: Fri, 25 Jul 2025 13:33:01 +0100 Subject: [PATCH 03/11] chore: add 'random.cdisc.data' to Suggests --- DESCRIPTION | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index b8ad45a86..2c24c8519 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -39,6 +39,7 @@ Imports: utils Suggests: knitr (>= 1.42), + random.cdisc.data (>= 0.2.1), rmarkdown (>= 2.23), testthat (>= 3.2.2), withr (>= 2.0.0) @@ -51,7 +52,7 @@ Remotes: insightsengineering/teal.code@main Config/Needs/verdepcheck: insightsengineering/teal.code, mllg/checkmate, r-lib/lifecycle, r-lib/rlang, yihui/knitr, rstudio/rmarkdown, - r-lib/testthat, r-lib/withr + insightsengineering/random.cdisc.data, r-lib/testthat, r-lib/withr Config/Needs/website: insightsengineering/nesttemplate Encoding: UTF-8 Language: en-US From b3107905348f2f5c260d674a60bb5738c12a8bff Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <211358+averissimo@users.noreply.github.com> Date: Fri, 25 Jul 2025 13:40:30 +0100 Subject: [PATCH 04/11] chore: revert the internal keywords --- R/data.R | 18 +++++++++--------- _pkgdown.yml | 13 ------------- man/rADAE.Rd | 1 + man/rADCM.Rd | 1 + man/rADEX.Rd | 1 + man/rADLB.Rd | 1 + man/rADRS.Rd | 1 + man/rADSL.Rd | 5 +++-- man/rADTR.Rd | 1 + man/rADTTE.Rd | 1 + man/rADVS.Rd | 1 + 11 files changed, 20 insertions(+), 24 deletions(-) diff --git a/R/data.R b/R/data.R index 42f9d4679..a3589e281 100644 --- a/R/data.R +++ b/R/data.R @@ -3,7 +3,7 @@ #' @docType data #' @usage rADAE #' @inherit random.cdisc.data::cadae format -#' @keywords datasets +#' @keywords datasets internal #' @source [random.cdisc.data::cadae] #' @name rADAE "rADAE" @@ -13,7 +13,7 @@ #' @docType data #' @usage rADCM #' @inherit random.cdisc.data::cadcm format -#' @keywords datasets +#' @keywords datasets internal #' @source [random.cdisc.data::cadcm] #' @name rADCM "rADCM" @@ -23,7 +23,7 @@ #' @docType data #' @usage rADEX #' @inherit random.cdisc.data::cadex format -#' @keywords datasets +#' @keywords datasets internal #' @source [random.cdisc.data::cadex] #' @name rADEX "rADEX" @@ -33,7 +33,7 @@ #' @docType data #' @usage rADLB #' @inherit random.cdisc.data::cadlb format -#' @keywords datasets +#' @keywords datasets internal #' @source [random.cdisc.data::cadlb] #' @name rADLB "rADLB" @@ -43,7 +43,7 @@ #' @docType data #' @usage rADRS #' @inherit random.cdisc.data::cadrs format -#' @keywords datasets +#' @keywords datasets internal #' @source [random.cdisc.data::cadrs] #' @name rADRS "rADRS" @@ -52,7 +52,7 @@ #' #' @docType data #' @usage rADSL -#' @keywords datasets +#' @keywords datasets internal #' @inherit random.cdisc.data::cadsl format #' @source [random.cdisc.data::cadsl] #' @name rADSL @@ -62,7 +62,7 @@ #' #' @docType data #' @usage rADTR -#' @keywords datasets +#' @keywords datasets internal #' @inherit random.cdisc.data::cadtr format #' @source [random.cdisc.data::cadtr] #' @name rADTR @@ -73,7 +73,7 @@ #' @docType data #' @usage rADTTE #' @inherit random.cdisc.data::cadtte format -#' @keywords datasets +#' @keywords datasets internal #' @source [random.cdisc.data::cadtte] #' @name rADTTE "rADTTE" @@ -83,7 +83,7 @@ #' @docType data #' @usage rADVS #' @inherit random.cdisc.data::cadvs format -#' @keywords datasets +#' @keywords datasets internal #' @source [random.cdisc.data::cadvs] #' @name rADVS "rADVS" diff --git a/_pkgdown.yml b/_pkgdown.yml index 6cb81eb9c..0aeabb39a 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -57,16 +57,3 @@ reference: - col_labels<- - col_relabel - example_cdisc_data - - title: Built-in datasets - desc: > - Random CDISC synthetic data generated from `{random.cdisc.data}` package. - contents: - - rADSL - - rADAE - - rADLB - - rADCM - - rADEX - - rADRS - - rADTR - - rADTTE - - rADVS diff --git a/man/rADAE.Rd b/man/rADAE.Rd index 9bc58b25b..1f8a02567 100644 --- a/man/rADAE.Rd +++ b/man/rADAE.Rd @@ -17,3 +17,4 @@ rADAE Random adverse events analysis dataset } \keyword{datasets} +\keyword{internal} diff --git a/man/rADCM.Rd b/man/rADCM.Rd index 721b3588a..0d5c0a106 100644 --- a/man/rADCM.Rd +++ b/man/rADCM.Rd @@ -17,3 +17,4 @@ rADCM Random concomitant medications analysis dataset } \keyword{datasets} +\keyword{internal} diff --git a/man/rADEX.Rd b/man/rADEX.Rd index e9c0e5287..d7b03fb4c 100644 --- a/man/rADEX.Rd +++ b/man/rADEX.Rd @@ -17,3 +17,4 @@ rADEX Random response analysis dataset } \keyword{datasets} +\keyword{internal} diff --git a/man/rADLB.Rd b/man/rADLB.Rd index 1da7893b9..26b8ec081 100644 --- a/man/rADLB.Rd +++ b/man/rADLB.Rd @@ -17,3 +17,4 @@ rADLB Random laboratory data analysis dataset } \keyword{datasets} +\keyword{internal} diff --git a/man/rADRS.Rd b/man/rADRS.Rd index 6ff822b2e..2e59038fd 100644 --- a/man/rADRS.Rd +++ b/man/rADRS.Rd @@ -17,3 +17,4 @@ rADRS Random response analysis dataset } \keyword{datasets} +\keyword{internal} diff --git a/man/rADSL.Rd b/man/rADSL.Rd index 0fb4abbe5..75e4ca620 100644 --- a/man/rADSL.Rd +++ b/man/rADSL.Rd @@ -3,7 +3,7 @@ \docType{data} \name{rADSL} \alias{rADSL} -\title{Random patient listing dataset} +\title{Random subject-level analysis dataset} \format{ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 400 rows and 55 columns. } @@ -14,6 +14,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) w rADSL } \description{ -Random patient listing dataset +Random subject-level analysis dataset } \keyword{datasets} +\keyword{internal} diff --git a/man/rADTR.Rd b/man/rADTR.Rd index b697ab093..3cb7f75f7 100644 --- a/man/rADTR.Rd +++ b/man/rADTR.Rd @@ -17,3 +17,4 @@ rADTR Random tumor response analysis dataset } \keyword{datasets} +\keyword{internal} diff --git a/man/rADTTE.Rd b/man/rADTTE.Rd index d04c795b2..bc9e3bc3d 100644 --- a/man/rADTTE.Rd +++ b/man/rADTTE.Rd @@ -17,3 +17,4 @@ rADTTE Random time to event analysis dataset } \keyword{datasets} +\keyword{internal} diff --git a/man/rADVS.Rd b/man/rADVS.Rd index bed50a791..6992c73f0 100644 --- a/man/rADVS.Rd +++ b/man/rADVS.Rd @@ -17,3 +17,4 @@ rADVS Random vital signs analysis dataset } \keyword{datasets} +\keyword{internal} From 2a81258773e0621961e9b35b035fd41ad13d7f01 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <211358+averissimo@users.noreply.github.com> Date: Fri, 25 Jul 2025 15:25:39 +0100 Subject: [PATCH 05/11] Revert "chore: revert the internal keywords" This reverts commit b3107905348f2f5c260d674a60bb5738c12a8bff. --- R/data.R | 18 +++++++++--------- _pkgdown.yml | 13 +++++++++++++ man/rADAE.Rd | 1 - man/rADCM.Rd | 1 - man/rADEX.Rd | 1 - man/rADLB.Rd | 1 - man/rADRS.Rd | 1 - man/rADSL.Rd | 5 ++--- man/rADTR.Rd | 1 - man/rADTTE.Rd | 1 - man/rADVS.Rd | 1 - 11 files changed, 24 insertions(+), 20 deletions(-) diff --git a/R/data.R b/R/data.R index a3589e281..42f9d4679 100644 --- a/R/data.R +++ b/R/data.R @@ -3,7 +3,7 @@ #' @docType data #' @usage rADAE #' @inherit random.cdisc.data::cadae format -#' @keywords datasets internal +#' @keywords datasets #' @source [random.cdisc.data::cadae] #' @name rADAE "rADAE" @@ -13,7 +13,7 @@ #' @docType data #' @usage rADCM #' @inherit random.cdisc.data::cadcm format -#' @keywords datasets internal +#' @keywords datasets #' @source [random.cdisc.data::cadcm] #' @name rADCM "rADCM" @@ -23,7 +23,7 @@ #' @docType data #' @usage rADEX #' @inherit random.cdisc.data::cadex format -#' @keywords datasets internal +#' @keywords datasets #' @source [random.cdisc.data::cadex] #' @name rADEX "rADEX" @@ -33,7 +33,7 @@ #' @docType data #' @usage rADLB #' @inherit random.cdisc.data::cadlb format -#' @keywords datasets internal +#' @keywords datasets #' @source [random.cdisc.data::cadlb] #' @name rADLB "rADLB" @@ -43,7 +43,7 @@ #' @docType data #' @usage rADRS #' @inherit random.cdisc.data::cadrs format -#' @keywords datasets internal +#' @keywords datasets #' @source [random.cdisc.data::cadrs] #' @name rADRS "rADRS" @@ -52,7 +52,7 @@ #' #' @docType data #' @usage rADSL -#' @keywords datasets internal +#' @keywords datasets #' @inherit random.cdisc.data::cadsl format #' @source [random.cdisc.data::cadsl] #' @name rADSL @@ -62,7 +62,7 @@ #' #' @docType data #' @usage rADTR -#' @keywords datasets internal +#' @keywords datasets #' @inherit random.cdisc.data::cadtr format #' @source [random.cdisc.data::cadtr] #' @name rADTR @@ -73,7 +73,7 @@ #' @docType data #' @usage rADTTE #' @inherit random.cdisc.data::cadtte format -#' @keywords datasets internal +#' @keywords datasets #' @source [random.cdisc.data::cadtte] #' @name rADTTE "rADTTE" @@ -83,7 +83,7 @@ #' @docType data #' @usage rADVS #' @inherit random.cdisc.data::cadvs format -#' @keywords datasets internal +#' @keywords datasets #' @source [random.cdisc.data::cadvs] #' @name rADVS "rADVS" diff --git a/_pkgdown.yml b/_pkgdown.yml index 0aeabb39a..6cb81eb9c 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -57,3 +57,16 @@ reference: - col_labels<- - col_relabel - example_cdisc_data + - title: Built-in datasets + desc: > + Random CDISC synthetic data generated from `{random.cdisc.data}` package. + contents: + - rADSL + - rADAE + - rADLB + - rADCM + - rADEX + - rADRS + - rADTR + - rADTTE + - rADVS diff --git a/man/rADAE.Rd b/man/rADAE.Rd index 1f8a02567..9bc58b25b 100644 --- a/man/rADAE.Rd +++ b/man/rADAE.Rd @@ -17,4 +17,3 @@ rADAE Random adverse events analysis dataset } \keyword{datasets} -\keyword{internal} diff --git a/man/rADCM.Rd b/man/rADCM.Rd index 0d5c0a106..721b3588a 100644 --- a/man/rADCM.Rd +++ b/man/rADCM.Rd @@ -17,4 +17,3 @@ rADCM Random concomitant medications analysis dataset } \keyword{datasets} -\keyword{internal} diff --git a/man/rADEX.Rd b/man/rADEX.Rd index d7b03fb4c..e9c0e5287 100644 --- a/man/rADEX.Rd +++ b/man/rADEX.Rd @@ -17,4 +17,3 @@ rADEX Random response analysis dataset } \keyword{datasets} -\keyword{internal} diff --git a/man/rADLB.Rd b/man/rADLB.Rd index 26b8ec081..1da7893b9 100644 --- a/man/rADLB.Rd +++ b/man/rADLB.Rd @@ -17,4 +17,3 @@ rADLB Random laboratory data analysis dataset } \keyword{datasets} -\keyword{internal} diff --git a/man/rADRS.Rd b/man/rADRS.Rd index 2e59038fd..6ff822b2e 100644 --- a/man/rADRS.Rd +++ b/man/rADRS.Rd @@ -17,4 +17,3 @@ rADRS Random response analysis dataset } \keyword{datasets} -\keyword{internal} diff --git a/man/rADSL.Rd b/man/rADSL.Rd index 75e4ca620..0fb4abbe5 100644 --- a/man/rADSL.Rd +++ b/man/rADSL.Rd @@ -3,7 +3,7 @@ \docType{data} \name{rADSL} \alias{rADSL} -\title{Random subject-level analysis dataset} +\title{Random patient listing dataset} \format{ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 400 rows and 55 columns. } @@ -14,7 +14,6 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) w rADSL } \description{ -Random subject-level analysis dataset +Random patient listing dataset } \keyword{datasets} -\keyword{internal} diff --git a/man/rADTR.Rd b/man/rADTR.Rd index 3cb7f75f7..b697ab093 100644 --- a/man/rADTR.Rd +++ b/man/rADTR.Rd @@ -17,4 +17,3 @@ rADTR Random tumor response analysis dataset } \keyword{datasets} -\keyword{internal} diff --git a/man/rADTTE.Rd b/man/rADTTE.Rd index bc9e3bc3d..d04c795b2 100644 --- a/man/rADTTE.Rd +++ b/man/rADTTE.Rd @@ -17,4 +17,3 @@ rADTTE Random time to event analysis dataset } \keyword{datasets} -\keyword{internal} diff --git a/man/rADVS.Rd b/man/rADVS.Rd index 6992c73f0..bed50a791 100644 --- a/man/rADVS.Rd +++ b/man/rADVS.Rd @@ -17,4 +17,3 @@ rADVS Random vital signs analysis dataset } \keyword{datasets} -\keyword{internal} From 24b415518c320ba141d064e4717902d949251098 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <211358+averissimo@users.noreply.github.com> Date: Tue, 29 Jul 2025 13:42:07 +0100 Subject: [PATCH 06/11] chore: another reorganization of code for clean docs --- .pre-commit-config.yaml | 2 +- R/data.R | 131 +++++++++++++++++-------------- R/dummy_function.R | 3 +- man/default_cdisc_join_keys.Rd | 9 ++- man/example_cdisc_data.Rd | 3 +- man/rADAE.Rd | 19 ----- man/rADCM.Rd | 19 ----- man/rADEX.Rd | 19 ----- man/rADLB.Rd | 19 ----- man/rADRS.Rd | 19 ----- man/rADSL.Rd | 138 +++++++++++++++++++++++++++++++-- man/rADTR.Rd | 19 ----- man/rADTTE.Rd | 19 ----- man/rADVS.Rd | 19 ----- 14 files changed, 217 insertions(+), 221 deletions(-) delete mode 100644 man/rADAE.Rd delete mode 100644 man/rADCM.Rd delete mode 100644 man/rADEX.Rd delete mode 100644 man/rADLB.Rd delete mode 100644 man/rADRS.Rd delete mode 100644 man/rADTR.Rd delete mode 100644 man/rADTTE.Rd delete mode 100644 man/rADVS.Rd diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index d0ad77573..a3f8925ca 100755 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -20,7 +20,7 @@ repos: - methods - rlang - stats - - teal.code + - insightsengineering/teal.code - utils - yaml - id: spell-check diff --git a/R/data.R b/R/data.R index 42f9d4679..90e23a6cb 100644 --- a/R/data.R +++ b/R/data.R @@ -1,97 +1,108 @@ -#' Random adverse events analysis dataset +#' Simulated `CDISC` Data for Examples #' +#' @description +#' This package contains random datasets that are used for testing purposes in the `teal.data` package: +#' +#' - `rADSL` Random subject-level analysis dataset +#' +#' @name random_cdisc_data +#' @docType data +#' @keywords datasets +#' @source - `rADSL`: [random.cdisc.data::cadsl] +# nolint start: line_length. +#' @format - `rADSL`: An object of class `tbl_df` (inherits from `tbl`, `data.frame`) with `r nrow(rADSL)` rows and `r ncol(rADSL)` columns. +# nolint end: line_length. +#' @rdname rADSL +"rADSL" + +#' @description - `rADAE`: Random adverse events analysis dataset #' @docType data -#' @usage rADAE -#' @inherit random.cdisc.data::cadae format #' @keywords datasets -#' @source [random.cdisc.data::cadae] -#' @name rADAE +#' @source - `rADAE`: [random.cdisc.data::cadae] +# nolint start: line_length. +#' @format - `rADAE`: An object of class `tbl_df` (inherits from `tbl`, `data.frame`) with `r nrow(rADAE)` rows and `r ncol(rADAE)` columns. +# nolint end: line_length. +#' @rdname rADSL "rADAE" -#' Random concomitant medications analysis dataset -#' +#' @description - `rADCM`: Random concomitant medications analysis dataset #' @docType data -#' @usage rADCM -#' @inherit random.cdisc.data::cadcm format #' @keywords datasets -#' @source [random.cdisc.data::cadcm] -#' @name rADCM +#' @source - `rADCM`: [random.cdisc.data::cadcm] +# nolint start: line_length. +#' @format - `rADCM`: An object of class `tbl_df` (inherits from `tbl`, `data.frame`) with `r nrow(rADCM)` rows and `r ncol(rADCM)` columns. +# nolint end: line_length. +#' @rdname rADSL "rADCM" -#' Random response analysis dataset -#' +#' @description - `rADEX`: Random response analysis dataset #' @docType data -#' @usage rADEX -#' @inherit random.cdisc.data::cadex format -#' @keywords datasets -#' @source [random.cdisc.data::cadex] -#' @name rADEX +#' @keywords datasets +#' @source - `rADEX`: [random.cdisc.data::cadex] +# nolint start: line_length. +#' @format - `rADEX`: An object of class `tbl_df` (inherits from `tbl`, `data.frame`) with `r nrow(rADEX)` rows and `r ncol(rADEX)` columns. +# nolint end: line_length. +#' @rdname rADSL "rADEX" -#' Random laboratory data analysis dataset -#' +#' @description - `rADLB`: Random laboratory data analysis dataset #' @docType data -#' @usage rADLB -#' @inherit random.cdisc.data::cadlb format #' @keywords datasets -#' @source [random.cdisc.data::cadlb] -#' @name rADLB +#' @source - `rADLB`: [random.cdisc.data::cadlb] +# nolint start: line_length. +#' @format - `rADLB`: An object of class `tbl_df` (inherits from `tbl`, `data.frame`) with `r nrow(rADLB)` rows and `r ncol(rADLB)` columns. +# nolint end: line_length. +#' @rdname rADSL "rADLB" -#' Random response analysis dataset -#' +#' @description - `rADRS`: Random response analysis dataset #' @docType data -#' @usage rADRS -#' @inherit random.cdisc.data::cadrs format #' @keywords datasets -#' @source [random.cdisc.data::cadrs] -#' @name rADRS +#' @source - `rADRS`: [random.cdisc.data::cadrs] +# nolint start: line_length. +#' @format - `rADRS`: An object of class `tbl_df` (inherits from `tbl`, `data.frame`) with `r nrow(rADRS)` rows and `r ncol(rADRS)` columns. +# nolint end: line_length. +#' @rdname rADSL "rADRS" -#' Random subject-level analysis dataset -#' -#' @docType data -#' @usage rADSL -#' @keywords datasets -#' @inherit random.cdisc.data::cadsl format -#' @source [random.cdisc.data::cadsl] -#' @name rADSL -"rADSL" - -#' Random tumor response analysis dataset -#' +#' @description - `rADTR`: Random tumor response analysis dataset #' @docType data -#' @usage rADTR #' @keywords datasets -#' @inherit random.cdisc.data::cadtr format -#' @source [random.cdisc.data::cadtr] -#' @name rADTR +#' @source - `rADTR`: [random.cdisc.data::cadtr] +# nolint start: line_length. +#' @format - `rADTR`: An object of class `tbl_df` (inherits from `tbl`, `data.frame`) with `r nrow(rADTR)` rows and `r ncol(rADTR)` columns. +# nolint end: line_length. +#' @rdname rADSL "rADTR" -#' Random time to event analysis dataset -#' +#' @description - `rADTTE`: Random time to event analysis dataset #' @docType data -#' @usage rADTTE -#' @inherit random.cdisc.data::cadtte format #' @keywords datasets -#' @source [random.cdisc.data::cadtte] -#' @name rADTTE +#' @source - `rADTTE`: [random.cdisc.data::cadtte] +# nolint start: line_length. +#' @format - `rADTTE`: An object of class `tbl_df` (inherits from `tbl`, `data.frame`) with `r nrow(rADTTE)` rows and `r ncol(rADTTE)` columns. +# nolint end: line_length. +#' @rdname rADSL "rADTTE" -#' Random vital signs analysis dataset -#' +#' @description - `rADVS`: Random vital signs analysis dataset #' @docType data -#' @usage rADVS -#' @inherit random.cdisc.data::cadvs format #' @keywords datasets -#' @source [random.cdisc.data::cadvs] -#' @name rADVS +#' @source - `rADVS`: [random.cdisc.data::cadvs] +# nolint start: line_length. +#' @format - `rADVS`: An object of class `tbl_df` (inherits from `tbl`, `data.frame`) with `r nrow(rADVS)` rows and `r ncol(rADVS)` columns. +# nolint end: line_length. +#' @rdname rADSL "rADVS" #' List containing default joining keys for `CDISC` datasets #' -#' @name default_cdisc_join_keys -#' @usage default_cdisc_join_keys +#' These represent primary and foreign keys for joining `CDISC` datasets. +#' #' @docType data #' @source internal. See `data-raw/cdisc_datasets.yaml` and `data-raw/data.R` for details. +#' @seealso [join_keys()] +#' @examples +#' default_cdisc_join_keys +#' default_cdisc_join_keys[c("ADSL", "ADAE")] # Subset for ADSL and ADAE "default_cdisc_join_keys" diff --git a/R/dummy_function.R b/R/dummy_function.R index e2195c20d..6103f2757 100644 --- a/R/dummy_function.R +++ b/R/dummy_function.R @@ -3,7 +3,8 @@ #' Retrieves example CDISC datasets for use in examples and testing. #' #' This function returns a dummy dataset and should only be used within `teal.data`. -#' Note that the datasets are not created and maintained in `teal.data`, they are retrieved from [`random.cdisc.data`][random.cdisc.data::random.cdisc.data-package] package. +#' Note that the datasets are not created and maintained in `teal.data`, they are retrieved from +#' [`random.cdisc.data`][random.cdisc.data::random.cdisc.data-package] package. #' #' @param dataname (`character(1)`) name of a CDISC dataset. #' diff --git a/man/default_cdisc_join_keys.Rd b/man/default_cdisc_join_keys.Rd index d9b40aeaa..40a3df933 100644 --- a/man/default_cdisc_join_keys.Rd +++ b/man/default_cdisc_join_keys.Rd @@ -14,6 +14,13 @@ internal. See \code{data-raw/cdisc_datasets.yaml} and \code{data-raw/data.R} for default_cdisc_join_keys } \description{ -List containing default joining keys for \code{CDISC} datasets +These represent primary and foreign keys for joining \code{CDISC} datasets. +} +\examples{ +default_cdisc_join_keys +default_cdisc_join_keys[c("ADSL", "ADAE")] # Subset for ADSL and ADAE +} +\seealso{ +\code{\link[=join_keys]{join_keys()}} } \keyword{datasets} diff --git a/man/example_cdisc_data.Rd b/man/example_cdisc_data.Rd index 3b00b842a..059e96a1f 100644 --- a/man/example_cdisc_data.Rd +++ b/man/example_cdisc_data.Rd @@ -19,5 +19,6 @@ Retrieves example CDISC datasets for use in examples and testing. } \details{ This function returns a dummy dataset and should only be used within \code{teal.data}. -Note that the datasets are not created and maintained in \code{teal.data}, they are retrieved from \code{\link[random.cdisc.data:random.cdisc.data-package]{random.cdisc.data}} package. +Note that the datasets are not created and maintained in \code{teal.data}, they are retrieved from +\code{\link[random.cdisc.data:random.cdisc.data-package]{random.cdisc.data}} package. } diff --git a/man/rADAE.Rd b/man/rADAE.Rd deleted file mode 100644 index 9bc58b25b..000000000 --- a/man/rADAE.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/data.R -\docType{data} -\name{rADAE} -\alias{rADAE} -\title{Random adverse events analysis dataset} -\format{ -An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 1934 rows and 92 columns. -} -\source{ -\link[random.cdisc.data:cadae]{random.cdisc.data::cadae} -} -\usage{ -rADAE -} -\description{ -Random adverse events analysis dataset -} -\keyword{datasets} diff --git a/man/rADCM.Rd b/man/rADCM.Rd deleted file mode 100644 index 721b3588a..000000000 --- a/man/rADCM.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/data.R -\docType{data} -\name{rADCM} -\alias{rADCM} -\title{Random concomitant medications analysis dataset} -\format{ -An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 3685 rows and 83 columns. -} -\source{ -\link[random.cdisc.data:cadcm]{random.cdisc.data::cadcm} -} -\usage{ -rADCM -} -\description{ -Random concomitant medications analysis dataset -} -\keyword{datasets} diff --git a/man/rADEX.Rd b/man/rADEX.Rd deleted file mode 100644 index e9c0e5287..000000000 --- a/man/rADEX.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/data.R -\docType{data} -\name{rADEX} -\alias{rADEX} -\title{Random response analysis dataset} -\format{ -An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 6400 rows and 79 columns. -} -\source{ -\link[random.cdisc.data:cadex]{random.cdisc.data::cadex} -} -\usage{ -rADEX -} -\description{ -Random response analysis dataset -} -\keyword{datasets} diff --git a/man/rADLB.Rd b/man/rADLB.Rd deleted file mode 100644 index 1da7893b9..000000000 --- a/man/rADLB.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/data.R -\docType{data} -\name{rADLB} -\alias{rADLB} -\title{Random laboratory data analysis dataset} -\format{ -An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 8400 rows and 102 columns. -} -\source{ -\link[random.cdisc.data:cadlb]{random.cdisc.data::cadlb} -} -\usage{ -rADLB -} -\description{ -Random laboratory data analysis dataset -} -\keyword{datasets} diff --git a/man/rADRS.Rd b/man/rADRS.Rd deleted file mode 100644 index 6ff822b2e..000000000 --- a/man/rADRS.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/data.R -\docType{data} -\name{rADRS} -\alias{rADRS} -\title{Random response analysis dataset} -\format{ -An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 3200 rows and 65 columns. -} -\source{ -\link[random.cdisc.data:cadrs]{random.cdisc.data::cadrs} -} -\usage{ -rADRS -} -\description{ -Random response analysis dataset -} -\keyword{datasets} diff --git a/man/rADSL.Rd b/man/rADSL.Rd index 0fb4abbe5..2cb6efe4e 100644 --- a/man/rADSL.Rd +++ b/man/rADSL.Rd @@ -1,19 +1,147 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/data.R \docType{data} -\name{rADSL} +\name{random_cdisc_data} +\alias{random_cdisc_data} \alias{rADSL} -\title{Random patient listing dataset} +\alias{rADAE} +\alias{rADCM} +\alias{rADEX} +\alias{rADLB} +\alias{rADRS} +\alias{rADTR} +\alias{rADTTE} +\alias{rADVS} +\title{Simulated \code{CDISC} Data for Examples} \format{ -An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 400 rows and 55 columns. +\itemize{ +\item \code{rADSL}: An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 400 rows and 55 columns. +} + +\itemize{ +\item \code{rADAE}: An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 1934 rows and 92 columns. +} + +\itemize{ +\item \code{rADCM}: An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 3685 rows and 83 columns. +} + +\itemize{ +\item \code{rADEX}: An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 6400 rows and 79 columns. +} + +\itemize{ +\item \code{rADLB}: An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 8400 rows and 102 columns. +} + +\itemize{ +\item \code{rADRS}: An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 3200 rows and 65 columns. +} + +\itemize{ +\item \code{rADTR}: An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 2800 rows and 76 columns. +} + +\itemize{ +\item \code{rADTTE}: An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 2000 rows and 67 columns. +} + +\itemize{ +\item \code{rADVS}: An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 16800 rows and 87 columns. +} } \source{ -\link[random.cdisc.data:cadsl]{random.cdisc.data::cadsl} +\itemize{ +\item \code{rADSL}: \link[random.cdisc.data:cadsl]{random.cdisc.data::cadsl} +} + +\itemize{ +\item \code{rADAE}: \link[random.cdisc.data:cadae]{random.cdisc.data::cadae} +} + +\itemize{ +\item \code{rADCM}: \link[random.cdisc.data:cadcm]{random.cdisc.data::cadcm} +} + +\itemize{ +\item \code{rADEX}: \link[random.cdisc.data:cadex]{random.cdisc.data::cadex} +} + +\itemize{ +\item \code{rADLB}: \link[random.cdisc.data:cadlb]{random.cdisc.data::cadlb} +} + +\itemize{ +\item \code{rADRS}: \link[random.cdisc.data:cadrs]{random.cdisc.data::cadrs} +} + +\itemize{ +\item \code{rADTR}: \link[random.cdisc.data:cadtr]{random.cdisc.data::cadtr} +} + +\itemize{ +\item \code{rADTTE}: \link[random.cdisc.data:cadtte]{random.cdisc.data::cadtte} +} + +\itemize{ +\item \code{rADVS}: \link[random.cdisc.data:cadvs]{random.cdisc.data::cadvs} +} } \usage{ rADSL + +rADAE + +rADCM + +rADEX + +rADLB + +rADRS + +rADTR + +rADTTE + +rADVS } \description{ -Random patient listing dataset +This package contains random datasets that are used for testing purposes in the \code{teal.data} package: +\itemize{ +\item \code{rADSL} Random subject-level analysis dataset +} + +\itemize{ +\item \code{rADAE}: Random adverse events analysis dataset +} + +\itemize{ +\item \code{rADCM}: Random concomitant medications analysis dataset +} + +\itemize{ +\item \code{rADEX}: Random response analysis dataset +} + +\itemize{ +\item \code{rADLB}: Random laboratory data analysis dataset +} + +\itemize{ +\item \code{rADRS}: Random response analysis dataset +} + +\itemize{ +\item \code{rADTR}: Random tumor response analysis dataset +} + +\itemize{ +\item \code{rADTTE}: Random time to event analysis dataset +} + +\itemize{ +\item \code{rADVS}: Random vital signs analysis dataset +} } \keyword{datasets} diff --git a/man/rADTR.Rd b/man/rADTR.Rd deleted file mode 100644 index b697ab093..000000000 --- a/man/rADTR.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/data.R -\docType{data} -\name{rADTR} -\alias{rADTR} -\title{Random tumor response analysis dataset} -\format{ -An object of class \code{data.frame} with 2800 rows and 76 columns. -} -\source{ -\link[random.cdisc.data:cadtr]{random.cdisc.data::cadtr} -} -\usage{ -rADTR -} -\description{ -Random tumor response analysis dataset -} -\keyword{datasets} diff --git a/man/rADTTE.Rd b/man/rADTTE.Rd deleted file mode 100644 index d04c795b2..000000000 --- a/man/rADTTE.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/data.R -\docType{data} -\name{rADTTE} -\alias{rADTTE} -\title{Random time to event analysis dataset} -\format{ -An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 2000 rows and 67 columns. -} -\source{ -\link[random.cdisc.data:cadtte]{random.cdisc.data::cadtte} -} -\usage{ -rADTTE -} -\description{ -Random time to event analysis dataset -} -\keyword{datasets} diff --git a/man/rADVS.Rd b/man/rADVS.Rd deleted file mode 100644 index bed50a791..000000000 --- a/man/rADVS.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/data.R -\docType{data} -\name{rADVS} -\alias{rADVS} -\title{Random vital signs analysis dataset} -\format{ -An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 16800 rows and 87 columns. -} -\source{ -\link[random.cdisc.data:cadvs]{random.cdisc.data::cadvs} -} -\usage{ -rADVS -} -\description{ -Random vital signs analysis dataset -} -\keyword{datasets} From 760be4c4a548728e0e4f69923529c15389b8b9f5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <211358+averissimo@users.noreply.github.com> Date: Tue, 29 Jul 2025 13:51:04 +0100 Subject: [PATCH 07/11] docs: update wordlist and NEWS --- NEWS.md | 4 ++++ inst/WORDLIST | 1 + 2 files changed, 5 insertions(+) diff --git a/NEWS.md b/NEWS.md index c0e55fd88..16a3ec140 100644 --- a/NEWS.md +++ b/NEWS.md @@ -4,6 +4,10 @@ * Print of a `teal_data` object now shows "code (un)verified" instead of "(un)verified teal_data object". +### Miscellaneous + +* Documentation for random `CDISC` datasets was updated and placed in a single man page (#367). + # teal.data 0.7.0 ### Breaking changes diff --git a/inst/WORDLIST b/inst/WORDLIST index c0b8bc658..147bc2b76 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -8,3 +8,4 @@ formatters funder getter pre +un From 5cdc87dd93177ed5db37a77031b6764476cfdfd5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <211358+averissimo@users.noreply.github.com> Date: Fri, 8 Aug 2025 14:25:47 +0200 Subject: [PATCH 08/11] Update R/data.R MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Dony Unardi Signed-off-by: André Veríssimo <211358+averissimo@users.noreply.github.com> --- R/data.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/data.R b/R/data.R index 90e23a6cb..a6fdda006 100644 --- a/R/data.R +++ b/R/data.R @@ -12,7 +12,7 @@ # nolint start: line_length. #' @format - `rADSL`: An object of class `tbl_df` (inherits from `tbl`, `data.frame`) with `r nrow(rADSL)` rows and `r ncol(rADSL)` columns. # nolint end: line_length. -#' @rdname rADSL +#' @rdname random_cdisc_data "rADSL" #' @description - `rADAE`: Random adverse events analysis dataset From 585eea9dc110a8ac6594921094927d02fc0e0562 Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Fri, 8 Aug 2025 12:28:44 +0000 Subject: [PATCH 09/11] [skip roxygen] [skip vbump] Roxygen Man Pages Auto Update --- man/rADSL.Rd | 147 --------------------------------------- man/random_cdisc_data.Rd | 27 +++++++ 2 files changed, 27 insertions(+), 147 deletions(-) delete mode 100644 man/rADSL.Rd create mode 100644 man/random_cdisc_data.Rd diff --git a/man/rADSL.Rd b/man/rADSL.Rd deleted file mode 100644 index 2cb6efe4e..000000000 --- a/man/rADSL.Rd +++ /dev/null @@ -1,147 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/data.R -\docType{data} -\name{random_cdisc_data} -\alias{random_cdisc_data} -\alias{rADSL} -\alias{rADAE} -\alias{rADCM} -\alias{rADEX} -\alias{rADLB} -\alias{rADRS} -\alias{rADTR} -\alias{rADTTE} -\alias{rADVS} -\title{Simulated \code{CDISC} Data for Examples} -\format{ -\itemize{ -\item \code{rADSL}: An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 400 rows and 55 columns. -} - -\itemize{ -\item \code{rADAE}: An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 1934 rows and 92 columns. -} - -\itemize{ -\item \code{rADCM}: An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 3685 rows and 83 columns. -} - -\itemize{ -\item \code{rADEX}: An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 6400 rows and 79 columns. -} - -\itemize{ -\item \code{rADLB}: An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 8400 rows and 102 columns. -} - -\itemize{ -\item \code{rADRS}: An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 3200 rows and 65 columns. -} - -\itemize{ -\item \code{rADTR}: An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 2800 rows and 76 columns. -} - -\itemize{ -\item \code{rADTTE}: An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 2000 rows and 67 columns. -} - -\itemize{ -\item \code{rADVS}: An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 16800 rows and 87 columns. -} -} -\source{ -\itemize{ -\item \code{rADSL}: \link[random.cdisc.data:cadsl]{random.cdisc.data::cadsl} -} - -\itemize{ -\item \code{rADAE}: \link[random.cdisc.data:cadae]{random.cdisc.data::cadae} -} - -\itemize{ -\item \code{rADCM}: \link[random.cdisc.data:cadcm]{random.cdisc.data::cadcm} -} - -\itemize{ -\item \code{rADEX}: \link[random.cdisc.data:cadex]{random.cdisc.data::cadex} -} - -\itemize{ -\item \code{rADLB}: \link[random.cdisc.data:cadlb]{random.cdisc.data::cadlb} -} - -\itemize{ -\item \code{rADRS}: \link[random.cdisc.data:cadrs]{random.cdisc.data::cadrs} -} - -\itemize{ -\item \code{rADTR}: \link[random.cdisc.data:cadtr]{random.cdisc.data::cadtr} -} - -\itemize{ -\item \code{rADTTE}: \link[random.cdisc.data:cadtte]{random.cdisc.data::cadtte} -} - -\itemize{ -\item \code{rADVS}: \link[random.cdisc.data:cadvs]{random.cdisc.data::cadvs} -} -} -\usage{ -rADSL - -rADAE - -rADCM - -rADEX - -rADLB - -rADRS - -rADTR - -rADTTE - -rADVS -} -\description{ -This package contains random datasets that are used for testing purposes in the \code{teal.data} package: -\itemize{ -\item \code{rADSL} Random subject-level analysis dataset -} - -\itemize{ -\item \code{rADAE}: Random adverse events analysis dataset -} - -\itemize{ -\item \code{rADCM}: Random concomitant medications analysis dataset -} - -\itemize{ -\item \code{rADEX}: Random response analysis dataset -} - -\itemize{ -\item \code{rADLB}: Random laboratory data analysis dataset -} - -\itemize{ -\item \code{rADRS}: Random response analysis dataset -} - -\itemize{ -\item \code{rADTR}: Random tumor response analysis dataset -} - -\itemize{ -\item \code{rADTTE}: Random time to event analysis dataset -} - -\itemize{ -\item \code{rADVS}: Random vital signs analysis dataset -} -} -\keyword{datasets} diff --git a/man/random_cdisc_data.Rd b/man/random_cdisc_data.Rd new file mode 100644 index 000000000..6784fef3d --- /dev/null +++ b/man/random_cdisc_data.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{random_cdisc_data} +\alias{random_cdisc_data} +\alias{rADSL} +\title{Simulated \code{CDISC} Data for Examples} +\format{ +\itemize{ +\item \code{rADSL}: An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 400 rows and 55 columns. +} +} +\source{ +\itemize{ +\item \code{rADSL}: \link[random.cdisc.data:cadsl]{random.cdisc.data::cadsl} +} +} +\usage{ +rADSL +} +\description{ +This package contains random datasets that are used for testing purposes in the \code{teal.data} package: +\itemize{ +\item \code{rADSL} Random subject-level analysis dataset +} +} +\keyword{datasets} From 751a49c4a38a16bd7300cafdf2d8d0cc173ee190 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <211358+averissimo@users.noreply.github.com> Date: Fri, 8 Aug 2025 13:30:45 +0100 Subject: [PATCH 10/11] empty: trigger ci From 7c6c70d83fc428229ca18958d82c5d7a910d3651 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <211358+averissimo@users.noreply.github.com> Date: Fri, 8 Aug 2025 13:41:10 +0100 Subject: [PATCH 11/11] chore: update rdnames --- R/data.R | 16 +++--- man/random_cdisc_data.Rd | 120 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 128 insertions(+), 8 deletions(-) diff --git a/R/data.R b/R/data.R index a6fdda006..6204997e6 100644 --- a/R/data.R +++ b/R/data.R @@ -22,7 +22,7 @@ # nolint start: line_length. #' @format - `rADAE`: An object of class `tbl_df` (inherits from `tbl`, `data.frame`) with `r nrow(rADAE)` rows and `r ncol(rADAE)` columns. # nolint end: line_length. -#' @rdname rADSL +#' @rdname random_cdisc_data "rADAE" #' @description - `rADCM`: Random concomitant medications analysis dataset @@ -32,7 +32,7 @@ # nolint start: line_length. #' @format - `rADCM`: An object of class `tbl_df` (inherits from `tbl`, `data.frame`) with `r nrow(rADCM)` rows and `r ncol(rADCM)` columns. # nolint end: line_length. -#' @rdname rADSL +#' @rdname random_cdisc_data "rADCM" #' @description - `rADEX`: Random response analysis dataset @@ -42,7 +42,7 @@ # nolint start: line_length. #' @format - `rADEX`: An object of class `tbl_df` (inherits from `tbl`, `data.frame`) with `r nrow(rADEX)` rows and `r ncol(rADEX)` columns. # nolint end: line_length. -#' @rdname rADSL +#' @rdname random_cdisc_data "rADEX" #' @description - `rADLB`: Random laboratory data analysis dataset @@ -52,7 +52,7 @@ # nolint start: line_length. #' @format - `rADLB`: An object of class `tbl_df` (inherits from `tbl`, `data.frame`) with `r nrow(rADLB)` rows and `r ncol(rADLB)` columns. # nolint end: line_length. -#' @rdname rADSL +#' @rdname random_cdisc_data "rADLB" #' @description - `rADRS`: Random response analysis dataset @@ -62,7 +62,7 @@ # nolint start: line_length. #' @format - `rADRS`: An object of class `tbl_df` (inherits from `tbl`, `data.frame`) with `r nrow(rADRS)` rows and `r ncol(rADRS)` columns. # nolint end: line_length. -#' @rdname rADSL +#' @rdname random_cdisc_data "rADRS" #' @description - `rADTR`: Random tumor response analysis dataset @@ -72,7 +72,7 @@ # nolint start: line_length. #' @format - `rADTR`: An object of class `tbl_df` (inherits from `tbl`, `data.frame`) with `r nrow(rADTR)` rows and `r ncol(rADTR)` columns. # nolint end: line_length. -#' @rdname rADSL +#' @rdname random_cdisc_data "rADTR" #' @description - `rADTTE`: Random time to event analysis dataset @@ -82,7 +82,7 @@ # nolint start: line_length. #' @format - `rADTTE`: An object of class `tbl_df` (inherits from `tbl`, `data.frame`) with `r nrow(rADTTE)` rows and `r ncol(rADTTE)` columns. # nolint end: line_length. -#' @rdname rADSL +#' @rdname random_cdisc_data "rADTTE" #' @description - `rADVS`: Random vital signs analysis dataset @@ -92,7 +92,7 @@ # nolint start: line_length. #' @format - `rADVS`: An object of class `tbl_df` (inherits from `tbl`, `data.frame`) with `r nrow(rADVS)` rows and `r ncol(rADVS)` columns. # nolint end: line_length. -#' @rdname rADSL +#' @rdname random_cdisc_data "rADVS" #' List containing default joining keys for `CDISC` datasets diff --git a/man/random_cdisc_data.Rd b/man/random_cdisc_data.Rd index 6784fef3d..2cb6efe4e 100644 --- a/man/random_cdisc_data.Rd +++ b/man/random_cdisc_data.Rd @@ -4,24 +4,144 @@ \name{random_cdisc_data} \alias{random_cdisc_data} \alias{rADSL} +\alias{rADAE} +\alias{rADCM} +\alias{rADEX} +\alias{rADLB} +\alias{rADRS} +\alias{rADTR} +\alias{rADTTE} +\alias{rADVS} \title{Simulated \code{CDISC} Data for Examples} \format{ \itemize{ \item \code{rADSL}: An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 400 rows and 55 columns. } + +\itemize{ +\item \code{rADAE}: An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 1934 rows and 92 columns. +} + +\itemize{ +\item \code{rADCM}: An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 3685 rows and 83 columns. +} + +\itemize{ +\item \code{rADEX}: An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 6400 rows and 79 columns. +} + +\itemize{ +\item \code{rADLB}: An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 8400 rows and 102 columns. +} + +\itemize{ +\item \code{rADRS}: An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 3200 rows and 65 columns. +} + +\itemize{ +\item \code{rADTR}: An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 2800 rows and 76 columns. +} + +\itemize{ +\item \code{rADTTE}: An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 2000 rows and 67 columns. +} + +\itemize{ +\item \code{rADVS}: An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 16800 rows and 87 columns. +} } \source{ \itemize{ \item \code{rADSL}: \link[random.cdisc.data:cadsl]{random.cdisc.data::cadsl} } + +\itemize{ +\item \code{rADAE}: \link[random.cdisc.data:cadae]{random.cdisc.data::cadae} +} + +\itemize{ +\item \code{rADCM}: \link[random.cdisc.data:cadcm]{random.cdisc.data::cadcm} +} + +\itemize{ +\item \code{rADEX}: \link[random.cdisc.data:cadex]{random.cdisc.data::cadex} +} + +\itemize{ +\item \code{rADLB}: \link[random.cdisc.data:cadlb]{random.cdisc.data::cadlb} +} + +\itemize{ +\item \code{rADRS}: \link[random.cdisc.data:cadrs]{random.cdisc.data::cadrs} +} + +\itemize{ +\item \code{rADTR}: \link[random.cdisc.data:cadtr]{random.cdisc.data::cadtr} +} + +\itemize{ +\item \code{rADTTE}: \link[random.cdisc.data:cadtte]{random.cdisc.data::cadtte} +} + +\itemize{ +\item \code{rADVS}: \link[random.cdisc.data:cadvs]{random.cdisc.data::cadvs} +} } \usage{ rADSL + +rADAE + +rADCM + +rADEX + +rADLB + +rADRS + +rADTR + +rADTTE + +rADVS } \description{ This package contains random datasets that are used for testing purposes in the \code{teal.data} package: \itemize{ \item \code{rADSL} Random subject-level analysis dataset } + +\itemize{ +\item \code{rADAE}: Random adverse events analysis dataset +} + +\itemize{ +\item \code{rADCM}: Random concomitant medications analysis dataset +} + +\itemize{ +\item \code{rADEX}: Random response analysis dataset +} + +\itemize{ +\item \code{rADLB}: Random laboratory data analysis dataset +} + +\itemize{ +\item \code{rADRS}: Random response analysis dataset +} + +\itemize{ +\item \code{rADTR}: Random tumor response analysis dataset +} + +\itemize{ +\item \code{rADTTE}: Random time to event analysis dataset +} + +\itemize{ +\item \code{rADVS}: Random vital signs analysis dataset +} } \keyword{datasets}