From b8465755d7b8024fa4e1cc5b54556e46b10ddc29 Mon Sep 17 00:00:00 2001 From: m7pr Date: Wed, 28 Aug 2024 10:20:25 +0200 Subject: [PATCH 01/18] add teal.slice to rhub lookup-refs --- .github/workflows/scheduled.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/scheduled.yaml b/.github/workflows/scheduled.yaml index 398a2b6a..d149caa0 100644 --- a/.github/workflows/scheduled.yaml +++ b/.github/workflows/scheduled.yaml @@ -44,3 +44,4 @@ jobs: insightsengineering/teal.widgets insightsengineering/tern insightsengineering/teal.data + insightsengineering/teal.slice From c1afb40a934d650ba4b337ff490e5cb51782ffe4 Mon Sep 17 00:00:00 2001 From: m7pr Date: Wed, 28 Aug 2024 10:23:36 +0200 Subject: [PATCH 02/18] revert teal.slice from rhub lookups --- .github/workflows/scheduled.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/scheduled.yaml b/.github/workflows/scheduled.yaml index d149caa0..398a2b6a 100644 --- a/.github/workflows/scheduled.yaml +++ b/.github/workflows/scheduled.yaml @@ -44,4 +44,3 @@ jobs: insightsengineering/teal.widgets insightsengineering/tern insightsengineering/teal.data - insightsengineering/teal.slice From ad20538ddab4a4bc5e6ad8a826cdd3e03f77475d Mon Sep 17 00:00:00 2001 From: m7pr Date: Wed, 28 Aug 2024 10:30:28 +0200 Subject: [PATCH 03/18] do not run examples if nestcolor is not installed --- R/tm_g_ae_oview.R | 2 +- R/tm_g_butterfly.R | 2 +- R/tm_g_events_term_id.R | 2 +- R/tm_g_heat_bygrade.R | 2 +- R/tm_g_patient_profile.R | 2 +- R/tm_g_spiderplot.R | 2 +- R/tm_g_swimlane.R | 2 +- R/tm_g_waterfall.R | 2 +- man/tm_g_ae_oview.Rd | 3 ++- man/tm_g_butterfly.Rd | 7 ++++--- man/tm_g_events_term_id.Rd | 3 ++- man/tm_g_heat_bygrade.Rd | 3 ++- man/tm_g_patient_profile.Rd | 7 ++++--- man/tm_g_spiderplot.Rd | 7 ++++--- man/tm_g_swimlane.Rd | 7 ++++--- man/tm_g_waterfall.Rd | 7 ++++--- 16 files changed, 34 insertions(+), 26 deletions(-) diff --git a/R/tm_g_ae_oview.R b/R/tm_g_ae_oview.R index 776b113d..d58c8f29 100644 --- a/R/tm_g_ae_oview.R +++ b/R/tm_g_ae_oview.R @@ -15,7 +15,7 @@ #' #' @export #' -#' @examples +#' @examplesIf requireNamespace("nestcolor") #' data <- cdisc_data() |> #' within({ #' library(nestcolor) diff --git a/R/tm_g_butterfly.R b/R/tm_g_butterfly.R index f55b23c1..3eb60a2d 100644 --- a/R/tm_g_butterfly.R +++ b/R/tm_g_butterfly.R @@ -39,7 +39,7 @@ #' @template author_zhanc107 #' @template author_liaoc10 #' -#' @examples +#' @examplesIf requireNamespace("nestcolor") #' # Example using stream (ADaM) dataset #' data <- cdisc_data() |> #' within({ diff --git a/R/tm_g_events_term_id.R b/R/tm_g_events_term_id.R index 9b530aca..ff5dd513 100644 --- a/R/tm_g_events_term_id.R +++ b/R/tm_g_events_term_id.R @@ -17,7 +17,7 @@ #' @author Liming Li (lil128) \email{liming.li@roche.com} #' @author Molly He (hey59) \email{hey59@gene.com} #' -#' @examples +#' @examplesIf requireNamespace("nestcolor") #' data <- cdisc_data() |> #' within({ #' library(nestcolor) diff --git a/R/tm_g_heat_bygrade.R b/R/tm_g_heat_bygrade.R index 61d42c7a..8a40dcde 100644 --- a/R/tm_g_heat_bygrade.R +++ b/R/tm_g_heat_bygrade.R @@ -33,7 +33,7 @@ #' #' @export #' -#' @examples +#' @examplesIf requireNamespace("nestcolor") #' data <- cdisc_data() |> #' within({ #' library(dplyr) diff --git a/R/tm_g_patient_profile.R b/R/tm_g_patient_profile.R index 483b63eb..301c12d1 100644 --- a/R/tm_g_patient_profile.R +++ b/R/tm_g_patient_profile.R @@ -59,7 +59,7 @@ #' #' @export #' -#' @examples +#' @examplesIf requireNamespace("nestcolor") #' data <- cdisc_data() |> #' within({ #' library(nestcolor) diff --git a/R/tm_g_spiderplot.R b/R/tm_g_spiderplot.R index 7a0d26b0..1b38c862 100644 --- a/R/tm_g_spiderplot.R +++ b/R/tm_g_spiderplot.R @@ -24,7 +24,7 @@ #' @template author_zhanc107 #' @template author_liaoc10 #' -#' @examples +#' @examplesIf requireNamespace("nestcolor") #' # Example using stream (ADaM) dataset #' data <- cdisc_data() |> #' within({ diff --git a/R/tm_g_swimlane.R b/R/tm_g_swimlane.R index 9f5a44ce..0a8a19f5 100644 --- a/R/tm_g_swimlane.R +++ b/R/tm_g_swimlane.R @@ -34,7 +34,7 @@ #' #' @template author_qit3 #' -#' @examples +#' @examplesIf requireNamespace("nestcolor") #' # Example using stream (ADaM) dataset #' data <- cdisc_data() |> #' within(library(dplyr)) |> diff --git a/R/tm_g_waterfall.R b/R/tm_g_waterfall.R index 6d6c5b55..51b151f7 100644 --- a/R/tm_g_waterfall.R +++ b/R/tm_g_waterfall.R @@ -46,7 +46,7 @@ #' @template author_qit3 #' @author houx14 \email{houx14@gene.com} #' -#' @examples +#' @examplesIf requireNamespace("nestcolor") #' data <- cdisc_data() |> #' within({ #' library(nestcolor) diff --git a/man/tm_g_ae_oview.Rd b/man/tm_g_ae_oview.Rd index 621c211a..dd7c769a 100644 --- a/man/tm_g_ae_oview.Rd +++ b/man/tm_g_ae_oview.Rd @@ -51,6 +51,7 @@ the \code{\link[teal:teal_modules]{teal::module()}} object. Display the \code{AE} overview plot as a shiny module } \examples{ +\dontshow{if (requireNamespace("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} data <- cdisc_data() |> within({ library(nestcolor) @@ -107,5 +108,5 @@ app <- init( if (interactive()) { shinyApp(app$ui, app$server) } - +\dontshow{\}) # examplesIf} } diff --git a/man/tm_g_butterfly.Rd b/man/tm_g_butterfly.Rd index edef8704..ece439c8 100644 --- a/man/tm_g_butterfly.Rd +++ b/man/tm_g_butterfly.Rd @@ -59,10 +59,10 @@ vector to indicate default value, minimum and maximum values.} \item{plot_width}{(\code{numeric(3)})\cr vector to indicate default value, minimum and maximum values.} -\item{pre_output}{(\code{shiny.tag}) optional,\cr +\item{pre_output}{(\code{shiny.tag}, optional)\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} } \value{ @@ -86,6 +86,7 @@ used for subsequent analysis. Flag variables (from \code{ADaM} datasets) can be used directly as filter. } \examples{ +\dontshow{if (requireNamespace("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} # Example using stream (ADaM) dataset data <- cdisc_data() |> within({ @@ -149,7 +150,7 @@ app <- init( if (interactive()) { shinyApp(app$ui, app$server) } - +\dontshow{\}) # examplesIf} } \author{ Carolyn Zhang (zhanc107) \email{carolyn.zhang@duke.edu} diff --git a/man/tm_g_events_term_id.Rd b/man/tm_g_events_term_id.Rd index 915dab8a..72977d9e 100644 --- a/man/tm_g_events_term_id.Rd +++ b/man/tm_g_events_term_id.Rd @@ -50,6 +50,7 @@ the \code{\link[teal:teal_modules]{teal::module()}} object. Display Events by Term plot as a shiny module } \examples{ +\dontshow{if (requireNamespace("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} data <- cdisc_data() |> within({ library(nestcolor) @@ -84,7 +85,7 @@ app <- init( if (interactive()) { shinyApp(app$ui, app$server) } - +\dontshow{\}) # examplesIf} } \author{ Liming Li (lil128) \email{liming.li@roche.com} diff --git a/man/tm_g_heat_bygrade.Rd b/man/tm_g_heat_bygrade.Rd index d93e77d0..8e24d825 100644 --- a/man/tm_g_heat_bygrade.Rd +++ b/man/tm_g_heat_bygrade.Rd @@ -76,6 +76,7 @@ the \code{\link[teal:teal_modules]{teal::module()}} object. Display the heatmap by grade as a shiny module } \examples{ +\dontshow{if (requireNamespace("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} data <- cdisc_data() |> within({ library(dplyr) @@ -159,5 +160,5 @@ app <- init( if (interactive()) { shinyApp(app$ui, app$server) } - +\dontshow{\}) # examplesIf} } diff --git a/man/tm_g_patient_profile.Rd b/man/tm_g_patient_profile.Rd index a53152f0..79390ea4 100644 --- a/man/tm_g_patient_profile.Rd +++ b/man/tm_g_patient_profile.Rd @@ -82,10 +82,10 @@ vector to indicate default value, minimum and maximum values.} \item{plot_width}{(\code{numeric(3)})\cr vector to indicate default value, minimum and maximum values.} -\item{pre_output}{(\code{shiny.tag}) optional,\cr +\item{pre_output}{(\code{shiny.tag}, optional)\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} } \value{ @@ -108,6 +108,7 @@ the start date } } \examples{ +\dontshow{if (requireNamespace("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} data <- cdisc_data() |> within({ library(nestcolor) @@ -180,7 +181,7 @@ app <- init( if (interactive()) { shinyApp(app$ui, app$server) } - +\dontshow{\}) # examplesIf} } \author{ Xuefeng Hou (houx14) \email{houx14@gene.com} diff --git a/man/tm_g_spiderplot.Rd b/man/tm_g_spiderplot.Rd index b4fe33d9..521950b2 100644 --- a/man/tm_g_spiderplot.Rd +++ b/man/tm_g_spiderplot.Rd @@ -62,10 +62,10 @@ vector to indicate default value, minimum and maximum values.} \item{plot_width}{(\code{numeric(3)})\cr vector to indicate default value, minimum and maximum values.} -\item{pre_output}{(\code{shiny.tag}) optional,\cr +\item{pre_output}{(\code{shiny.tag}, optional)\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} } \value{ @@ -77,6 +77,7 @@ the \code{\link[teal:teal_modules]{teal::module()}} object. Display spider plot as a shiny module } \examples{ +\dontshow{if (requireNamespace("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} # Example using stream (ADaM) dataset data <- cdisc_data() |> within({ @@ -130,7 +131,7 @@ app <- init( if (interactive()) { shinyApp(app$ui, app$server) } - +\dontshow{\}) # examplesIf} } \author{ Carolyn Zhang (zhanc107) \email{carolyn.zhang@duke.edu} diff --git a/man/tm_g_swimlane.Rd b/man/tm_g_swimlane.Rd index 8429e65a..2da6a81c 100644 --- a/man/tm_g_swimlane.Rd +++ b/man/tm_g_swimlane.Rd @@ -64,10 +64,10 @@ vector to indicate default value, minimum and maximum values.} \item{plot_width}{(\code{numeric(3)})\cr vector to indicate default value, minimum and maximum values.} -\item{pre_output}{(\code{shiny.tag}) optional,\cr +\item{pre_output}{(\code{shiny.tag}, optional)\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} \item{x_label}{the label of the x axis} @@ -81,6 +81,7 @@ the \code{\link[teal:teal_modules]{teal::module()}} object. This is teal module that generates a \code{swimlane} plot (bar plot with markers) for \code{ADaM} data } \examples{ +\dontshow{if (requireNamespace("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} # Example using stream (ADaM) dataset data <- cdisc_data() |> within(library(dplyr)) |> @@ -149,7 +150,7 @@ app <- init( if (interactive()) { shinyApp(app$ui, app$server) } - +\dontshow{\}) # examplesIf} } \author{ Ting Qi (qit3) \email{qit3@gene.com} diff --git a/man/tm_g_waterfall.Rd b/man/tm_g_waterfall.Rd index 36815938..f2fbe390 100644 --- a/man/tm_g_waterfall.Rd +++ b/man/tm_g_waterfall.Rd @@ -85,10 +85,10 @@ vector to indicate default value, minimum and maximum values.} \item{plot_width}{(\code{numeric(3)})\cr vector to indicate default value, minimum and maximum values.} -\item{pre_output}{(\code{shiny.tag}) optional,\cr +\item{pre_output}{(\code{shiny.tag}, optional)\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} } \value{ @@ -100,6 +100,7 @@ the \code{\link[teal:teal_modules]{teal::module()}} object. This is teal module that generates a waterfall plot for \code{ADaM} data } \examples{ +\dontshow{if (requireNamespace("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} data <- cdisc_data() |> within({ library(nestcolor) @@ -136,7 +137,7 @@ app <- init( if (interactive()) { shinyApp(app$ui, app$server) } - +\dontshow{\}) # examplesIf} } \author{ Ting Qi (qit3) \email{qit3@gene.com} From 3f1240ad12b6d2583e9d6df6f1764168d7f2b78c Mon Sep 17 00:00:00 2001 From: m7pr Date: Wed, 28 Aug 2024 10:38:08 +0200 Subject: [PATCH 04/18] add teal.slice to Config/Needs/verdepcheck --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index ad530bff..4cf737b4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -48,7 +48,7 @@ Suggests: testthat (>= 3.1.5), withr (>= 2.0.0) Config/Needs/verdepcheck: insightsengineering/osprey, rstudio/shiny, - insightsengineering/teal, insightsengineering/teal.transform, + insightsengineering/teal, insightsengineering/teal.slice, insightsengineering/teal.transform, mllg/checkmate, tidyverse/dplyr, insightsengineering/formatters, tidyverse/ggplot2, r-lib/lifecycle, daroczig/logger, rstudio/shinyvalidate, insightsengineering/teal.code, From ba57bea75e2c25127e9d1de458a09f04616af436 Mon Sep 17 00:00:00 2001 From: Marcin <133694481+m7pr@users.noreply.github.com> Date: Thu, 29 Aug 2024 16:19:35 +0200 Subject: [PATCH 05/18] Update DESCRIPTION Signed-off-by: Marcin <133694481+m7pr@users.noreply.github.com> --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 4cf737b4..ad530bff 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -48,7 +48,7 @@ Suggests: testthat (>= 3.1.5), withr (>= 2.0.0) Config/Needs/verdepcheck: insightsengineering/osprey, rstudio/shiny, - insightsengineering/teal, insightsengineering/teal.slice, insightsengineering/teal.transform, + insightsengineering/teal, insightsengineering/teal.transform, mllg/checkmate, tidyverse/dplyr, insightsengineering/formatters, tidyverse/ggplot2, r-lib/lifecycle, daroczig/logger, rstudio/shinyvalidate, insightsengineering/teal.code, From 350750a282f64ffcd3e44443535bd83ff26efcf2 Mon Sep 17 00:00:00 2001 From: m7pr Date: Fri, 30 Aug 2024 10:55:28 +0200 Subject: [PATCH 06/18] replace requireNamespace("nestcolor") with require("nestcolor") --- R/tm_g_ae_oview.R | 2 +- R/tm_g_butterfly.R | 2 +- R/tm_g_events_term_id.R | 2 +- R/tm_g_heat_bygrade.R | 2 +- R/tm_g_patient_profile.R | 2 +- R/tm_g_spiderplot.R | 2 +- R/tm_g_swimlane.R | 2 +- R/tm_g_waterfall.R | 2 +- 8 files changed, 8 insertions(+), 8 deletions(-) diff --git a/R/tm_g_ae_oview.R b/R/tm_g_ae_oview.R index d58c8f29..f4fc0fcc 100644 --- a/R/tm_g_ae_oview.R +++ b/R/tm_g_ae_oview.R @@ -15,7 +15,7 @@ #' #' @export #' -#' @examplesIf requireNamespace("nestcolor") +#' @examplesIf require("nestcolor") #' data <- cdisc_data() |> #' within({ #' library(nestcolor) diff --git a/R/tm_g_butterfly.R b/R/tm_g_butterfly.R index 3eb60a2d..51c84702 100644 --- a/R/tm_g_butterfly.R +++ b/R/tm_g_butterfly.R @@ -39,7 +39,7 @@ #' @template author_zhanc107 #' @template author_liaoc10 #' -#' @examplesIf requireNamespace("nestcolor") +#' @examplesIf require("nestcolor") #' # Example using stream (ADaM) dataset #' data <- cdisc_data() |> #' within({ diff --git a/R/tm_g_events_term_id.R b/R/tm_g_events_term_id.R index ff5dd513..438a1c41 100644 --- a/R/tm_g_events_term_id.R +++ b/R/tm_g_events_term_id.R @@ -17,7 +17,7 @@ #' @author Liming Li (lil128) \email{liming.li@roche.com} #' @author Molly He (hey59) \email{hey59@gene.com} #' -#' @examplesIf requireNamespace("nestcolor") +#' @examplesIf require("nestcolor") #' data <- cdisc_data() |> #' within({ #' library(nestcolor) diff --git a/R/tm_g_heat_bygrade.R b/R/tm_g_heat_bygrade.R index 8a40dcde..059386c5 100644 --- a/R/tm_g_heat_bygrade.R +++ b/R/tm_g_heat_bygrade.R @@ -33,7 +33,7 @@ #' #' @export #' -#' @examplesIf requireNamespace("nestcolor") +#' @examplesIf require("nestcolor") #' data <- cdisc_data() |> #' within({ #' library(dplyr) diff --git a/R/tm_g_patient_profile.R b/R/tm_g_patient_profile.R index 301c12d1..c60b5680 100644 --- a/R/tm_g_patient_profile.R +++ b/R/tm_g_patient_profile.R @@ -59,7 +59,7 @@ #' #' @export #' -#' @examplesIf requireNamespace("nestcolor") +#' @examplesIf require("nestcolor") #' data <- cdisc_data() |> #' within({ #' library(nestcolor) diff --git a/R/tm_g_spiderplot.R b/R/tm_g_spiderplot.R index 1b38c862..37722740 100644 --- a/R/tm_g_spiderplot.R +++ b/R/tm_g_spiderplot.R @@ -24,7 +24,7 @@ #' @template author_zhanc107 #' @template author_liaoc10 #' -#' @examplesIf requireNamespace("nestcolor") +#' @examplesIf require("nestcolor") #' # Example using stream (ADaM) dataset #' data <- cdisc_data() |> #' within({ diff --git a/R/tm_g_swimlane.R b/R/tm_g_swimlane.R index 0a8a19f5..29bc9808 100644 --- a/R/tm_g_swimlane.R +++ b/R/tm_g_swimlane.R @@ -34,7 +34,7 @@ #' #' @template author_qit3 #' -#' @examplesIf requireNamespace("nestcolor") +#' @examplesIf require("nestcolor") #' # Example using stream (ADaM) dataset #' data <- cdisc_data() |> #' within(library(dplyr)) |> diff --git a/R/tm_g_waterfall.R b/R/tm_g_waterfall.R index 51b151f7..6d04e3c7 100644 --- a/R/tm_g_waterfall.R +++ b/R/tm_g_waterfall.R @@ -46,7 +46,7 @@ #' @template author_qit3 #' @author houx14 \email{houx14@gene.com} #' -#' @examplesIf requireNamespace("nestcolor") +#' @examplesIf require("nestcolor") #' data <- cdisc_data() |> #' within({ #' library(nestcolor) From 883e4a237f9a380c0b14603324cc0bf55aed637e Mon Sep 17 00:00:00 2001 From: Franciszek Walkowiak Date: Fri, 20 Sep 2024 13:47:04 +0200 Subject: [PATCH 07/18] chore: use revdepcheck.yaml@r-revdepcheck-action-fix_non_cran --- .github/workflows/scheduled.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/scheduled.yaml b/.github/workflows/scheduled.yaml index c8f21304..56e9eb5c 100644 --- a/.github/workflows/scheduled.yaml +++ b/.github/workflows/scheduled.yaml @@ -55,7 +55,7 @@ jobs: inputs.chosen-workflow == 'revdepcheck' ) name: revdepcheck ↩️ - uses: insightsengineering/r.pkg.template/.github/workflows/revdepcheck.yaml@main + uses: insightsengineering/r.pkg.template/.github/workflows/revdepcheck.yaml@r-revdepcheck-action-fix_non_cran rhub: if: > github.event_name == 'schedule' || ( From c28c02ccf4b71551e149d8122e7fd2f133a42671 Mon Sep 17 00:00:00 2001 From: "27856297+dependabot-preview[bot]@users.noreply.github.com" <27856297+dependabot-preview[bot]@users.noreply.github.com> Date: Thu, 3 Oct 2024 07:02:07 +0000 Subject: [PATCH 08/18] [skip roxygen] [skip vbump] Roxygen Man Pages Auto Update --- man/tm_g_ae_oview.Rd | 2 +- man/tm_g_butterfly.Rd | 6 +++--- man/tm_g_events_term_id.Rd | 2 +- man/tm_g_heat_bygrade.Rd | 2 +- man/tm_g_patient_profile.Rd | 6 +++--- man/tm_g_spiderplot.Rd | 6 +++--- man/tm_g_swimlane.Rd | 6 +++--- man/tm_g_waterfall.Rd | 6 +++--- 8 files changed, 18 insertions(+), 18 deletions(-) diff --git a/man/tm_g_ae_oview.Rd b/man/tm_g_ae_oview.Rd index dd7c769a..1e4b4f50 100644 --- a/man/tm_g_ae_oview.Rd +++ b/man/tm_g_ae_oview.Rd @@ -51,7 +51,7 @@ the \code{\link[teal:teal_modules]{teal::module()}} object. Display the \code{AE} overview plot as a shiny module } \examples{ -\dontshow{if (requireNamespace("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} +\dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} data <- cdisc_data() |> within({ library(nestcolor) diff --git a/man/tm_g_butterfly.Rd b/man/tm_g_butterfly.Rd index ece439c8..36a995f4 100644 --- a/man/tm_g_butterfly.Rd +++ b/man/tm_g_butterfly.Rd @@ -59,10 +59,10 @@ vector to indicate default value, minimum and maximum values.} \item{plot_width}{(\code{numeric(3)})\cr vector to indicate default value, minimum and maximum values.} -\item{pre_output}{(\code{shiny.tag}, optional)\cr +\item{pre_output}{(\code{shiny.tag}) optional,\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} } \value{ @@ -86,7 +86,7 @@ used for subsequent analysis. Flag variables (from \code{ADaM} datasets) can be used directly as filter. } \examples{ -\dontshow{if (requireNamespace("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} +\dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} # Example using stream (ADaM) dataset data <- cdisc_data() |> within({ diff --git a/man/tm_g_events_term_id.Rd b/man/tm_g_events_term_id.Rd index 72977d9e..aa1b5939 100644 --- a/man/tm_g_events_term_id.Rd +++ b/man/tm_g_events_term_id.Rd @@ -50,7 +50,7 @@ the \code{\link[teal:teal_modules]{teal::module()}} object. Display Events by Term plot as a shiny module } \examples{ -\dontshow{if (requireNamespace("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} +\dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} data <- cdisc_data() |> within({ library(nestcolor) diff --git a/man/tm_g_heat_bygrade.Rd b/man/tm_g_heat_bygrade.Rd index 8e24d825..cb9b3500 100644 --- a/man/tm_g_heat_bygrade.Rd +++ b/man/tm_g_heat_bygrade.Rd @@ -76,7 +76,7 @@ the \code{\link[teal:teal_modules]{teal::module()}} object. Display the heatmap by grade as a shiny module } \examples{ -\dontshow{if (requireNamespace("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} +\dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} data <- cdisc_data() |> within({ library(dplyr) diff --git a/man/tm_g_patient_profile.Rd b/man/tm_g_patient_profile.Rd index 79390ea4..26c18bd7 100644 --- a/man/tm_g_patient_profile.Rd +++ b/man/tm_g_patient_profile.Rd @@ -82,10 +82,10 @@ vector to indicate default value, minimum and maximum values.} \item{plot_width}{(\code{numeric(3)})\cr vector to indicate default value, minimum and maximum values.} -\item{pre_output}{(\code{shiny.tag}, optional)\cr +\item{pre_output}{(\code{shiny.tag}) optional,\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} } \value{ @@ -108,7 +108,7 @@ the start date } } \examples{ -\dontshow{if (requireNamespace("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} +\dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} data <- cdisc_data() |> within({ library(nestcolor) diff --git a/man/tm_g_spiderplot.Rd b/man/tm_g_spiderplot.Rd index 521950b2..53e9ba9e 100644 --- a/man/tm_g_spiderplot.Rd +++ b/man/tm_g_spiderplot.Rd @@ -62,10 +62,10 @@ vector to indicate default value, minimum and maximum values.} \item{plot_width}{(\code{numeric(3)})\cr vector to indicate default value, minimum and maximum values.} -\item{pre_output}{(\code{shiny.tag}, optional)\cr +\item{pre_output}{(\code{shiny.tag}) optional,\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} } \value{ @@ -77,7 +77,7 @@ the \code{\link[teal:teal_modules]{teal::module()}} object. Display spider plot as a shiny module } \examples{ -\dontshow{if (requireNamespace("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} +\dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} # Example using stream (ADaM) dataset data <- cdisc_data() |> within({ diff --git a/man/tm_g_swimlane.Rd b/man/tm_g_swimlane.Rd index 2da6a81c..019b7b54 100644 --- a/man/tm_g_swimlane.Rd +++ b/man/tm_g_swimlane.Rd @@ -64,10 +64,10 @@ vector to indicate default value, minimum and maximum values.} \item{plot_width}{(\code{numeric(3)})\cr vector to indicate default value, minimum and maximum values.} -\item{pre_output}{(\code{shiny.tag}, optional)\cr +\item{pre_output}{(\code{shiny.tag}) optional,\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} \item{x_label}{the label of the x axis} @@ -81,7 +81,7 @@ the \code{\link[teal:teal_modules]{teal::module()}} object. This is teal module that generates a \code{swimlane} plot (bar plot with markers) for \code{ADaM} data } \examples{ -\dontshow{if (requireNamespace("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} +\dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} # Example using stream (ADaM) dataset data <- cdisc_data() |> within(library(dplyr)) |> diff --git a/man/tm_g_waterfall.Rd b/man/tm_g_waterfall.Rd index f2fbe390..cdb00195 100644 --- a/man/tm_g_waterfall.Rd +++ b/man/tm_g_waterfall.Rd @@ -85,10 +85,10 @@ vector to indicate default value, minimum and maximum values.} \item{plot_width}{(\code{numeric(3)})\cr vector to indicate default value, minimum and maximum values.} -\item{pre_output}{(\code{shiny.tag}, optional)\cr +\item{pre_output}{(\code{shiny.tag}) optional,\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} } \value{ @@ -100,7 +100,7 @@ the \code{\link[teal:teal_modules]{teal::module()}} object. This is teal module that generates a waterfall plot for \code{ADaM} data } \examples{ -\dontshow{if (requireNamespace("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} +\dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} data <- cdisc_data() |> within({ library(nestcolor) From 689e71e66f17838731c9e7c334e7c3dccc833c59 Mon Sep 17 00:00:00 2001 From: m7pr Date: Thu, 3 Oct 2024 09:50:35 +0200 Subject: [PATCH 09/18] add teal.slice to lookup-refs for revdepcheck --- .github/workflows/scheduled.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/scheduled.yaml b/.github/workflows/scheduled.yaml index 398a2b6a..46bc371a 100644 --- a/.github/workflows/scheduled.yaml +++ b/.github/workflows/scheduled.yaml @@ -39,6 +39,7 @@ jobs: insightsengineering/teal.transform insightsengineering/formatters insightsengineering/teal.code + insightsengineering/teal.slice insightsengineering/teal.logger insightsengineering/teal.reporter insightsengineering/teal.widgets From 2b5a86b7fdf0c2721c43cfcd7318a05c4000f40c Mon Sep 17 00:00:00 2001 From: m7pr Date: Tue, 8 Oct 2024 10:59:07 +0200 Subject: [PATCH 10/18] change examples to teal_data --- R/tm_g_ae_oview.R | 2 +- R/tm_g_ae_sub.R | 2 +- R/tm_g_butterfly.R | 2 +- R/tm_g_events_term_id.R | 2 +- R/tm_g_heat_bygrade.R | 2 +- R/tm_g_patient_profile.R | 2 +- R/tm_g_spiderplot.R | 2 +- R/tm_g_swimlane.R | 2 +- R/tm_g_waterfall.R | 2 +- man/tm_g_ae_oview.Rd | 4 ++-- man/tm_g_ae_sub.Rd | 2 +- man/tm_g_butterfly.Rd | 2 +- man/tm_g_events_term_id.Rd | 2 +- man/tm_g_heat_bygrade.Rd | 2 +- man/tm_g_patient_profile.Rd | 2 +- man/tm_g_spiderplot.Rd | 2 +- man/tm_g_swimlane.Rd | 2 +- man/tm_g_waterfall.Rd | 2 +- 18 files changed, 19 insertions(+), 19 deletions(-) diff --git a/R/tm_g_ae_oview.R b/R/tm_g_ae_oview.R index f4fc0fcc..364bbd5c 100644 --- a/R/tm_g_ae_oview.R +++ b/R/tm_g_ae_oview.R @@ -16,7 +16,7 @@ #' @export #' #' @examplesIf require("nestcolor") -#' data <- cdisc_data() |> +#' data <- teal_data() |> #' within({ #' library(nestcolor) #' ADSL <- rADSL diff --git a/R/tm_g_ae_sub.R b/R/tm_g_ae_sub.R index f4333a3c..37c7f523 100644 --- a/R/tm_g_ae_sub.R +++ b/R/tm_g_ae_sub.R @@ -18,7 +18,7 @@ #' #' @examples #' # Example using stream (ADaM) dataset -#' data <- cdisc_data() |> +#' data <- teal_data() |> #' within({ #' ADSL <- rADSL #' ADAE <- rADAE diff --git a/R/tm_g_butterfly.R b/R/tm_g_butterfly.R index 51c84702..8e6e965c 100644 --- a/R/tm_g_butterfly.R +++ b/R/tm_g_butterfly.R @@ -41,7 +41,7 @@ #' #' @examplesIf require("nestcolor") #' # Example using stream (ADaM) dataset -#' data <- cdisc_data() |> +#' data <- teal_data() |> #' within({ #' library(dplyr) #' library(nestcolor) diff --git a/R/tm_g_events_term_id.R b/R/tm_g_events_term_id.R index 438a1c41..aac7751f 100644 --- a/R/tm_g_events_term_id.R +++ b/R/tm_g_events_term_id.R @@ -18,7 +18,7 @@ #' @author Molly He (hey59) \email{hey59@gene.com} #' #' @examplesIf require("nestcolor") -#' data <- cdisc_data() |> +#' data <- teal_data() |> #' within({ #' library(nestcolor) #' ADSL <- rADSL diff --git a/R/tm_g_heat_bygrade.R b/R/tm_g_heat_bygrade.R index 059386c5..01cc6052 100644 --- a/R/tm_g_heat_bygrade.R +++ b/R/tm_g_heat_bygrade.R @@ -34,7 +34,7 @@ #' @export #' #' @examplesIf require("nestcolor") -#' data <- cdisc_data() |> +#' data <- teal_data() |> #' within({ #' library(dplyr) #' library(nestcolor) diff --git a/R/tm_g_patient_profile.R b/R/tm_g_patient_profile.R index c60b5680..dc64b393 100644 --- a/R/tm_g_patient_profile.R +++ b/R/tm_g_patient_profile.R @@ -60,7 +60,7 @@ #' @export #' #' @examplesIf require("nestcolor") -#' data <- cdisc_data() |> +#' data <- teal_data() |> #' within({ #' library(nestcolor) #' ADSL <- rADSL diff --git a/R/tm_g_spiderplot.R b/R/tm_g_spiderplot.R index 37722740..8e9238a1 100644 --- a/R/tm_g_spiderplot.R +++ b/R/tm_g_spiderplot.R @@ -26,7 +26,7 @@ #' #' @examplesIf require("nestcolor") #' # Example using stream (ADaM) dataset -#' data <- cdisc_data() |> +#' data <- teal_data() |> #' within({ #' library(nestcolor) #' ADSL <- rADSL diff --git a/R/tm_g_swimlane.R b/R/tm_g_swimlane.R index 29bc9808..ff81e2e9 100644 --- a/R/tm_g_swimlane.R +++ b/R/tm_g_swimlane.R @@ -36,7 +36,7 @@ #' #' @examplesIf require("nestcolor") #' # Example using stream (ADaM) dataset -#' data <- cdisc_data() |> +#' data <- teal_data() |> #' within(library(dplyr)) |> #' within(library(nestcolor)) |> #' within(ADSL <- rADSL %>% diff --git a/R/tm_g_waterfall.R b/R/tm_g_waterfall.R index 6d04e3c7..04b9a2eb 100644 --- a/R/tm_g_waterfall.R +++ b/R/tm_g_waterfall.R @@ -47,7 +47,7 @@ #' @author houx14 \email{houx14@gene.com} #' #' @examplesIf require("nestcolor") -#' data <- cdisc_data() |> +#' data <- teal_data() |> #' within({ #' library(nestcolor) #' ADSL <- rADSL diff --git a/man/tm_g_ae_oview.Rd b/man/tm_g_ae_oview.Rd index 1e4b4f50..30aede55 100644 --- a/man/tm_g_ae_oview.Rd +++ b/man/tm_g_ae_oview.Rd @@ -51,8 +51,8 @@ the \code{\link[teal:teal_modules]{teal::module()}} object. Display the \code{AE} overview plot as a shiny module } \examples{ -\dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} -data <- cdisc_data() |> +\dontshow{if (requireNamespace("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} +data <- teal_data() |> within({ library(nestcolor) ADSL <- rADSL diff --git a/man/tm_g_ae_sub.Rd b/man/tm_g_ae_sub.Rd index 925ef6d0..06b4cc4c 100644 --- a/man/tm_g_ae_sub.Rd +++ b/man/tm_g_ae_sub.Rd @@ -50,7 +50,7 @@ Display the \code{AE} by subgroups plot as a teal module } \examples{ # Example using stream (ADaM) dataset -data <- cdisc_data() |> +data <- teal_data() |> within({ ADSL <- rADSL ADAE <- rADAE diff --git a/man/tm_g_butterfly.Rd b/man/tm_g_butterfly.Rd index 36a995f4..1daeeaae 100644 --- a/man/tm_g_butterfly.Rd +++ b/man/tm_g_butterfly.Rd @@ -88,7 +88,7 @@ used directly as filter. \examples{ \dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} # Example using stream (ADaM) dataset -data <- cdisc_data() |> +data <- teal_data() |> within({ library(dplyr) library(nestcolor) diff --git a/man/tm_g_events_term_id.Rd b/man/tm_g_events_term_id.Rd index aa1b5939..fb8141ce 100644 --- a/man/tm_g_events_term_id.Rd +++ b/man/tm_g_events_term_id.Rd @@ -51,7 +51,7 @@ Display Events by Term plot as a shiny module } \examples{ \dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} -data <- cdisc_data() |> +data <- teal_data() |> within({ library(nestcolor) ADSL <- rADSL diff --git a/man/tm_g_heat_bygrade.Rd b/man/tm_g_heat_bygrade.Rd index cb9b3500..5aeb1537 100644 --- a/man/tm_g_heat_bygrade.Rd +++ b/man/tm_g_heat_bygrade.Rd @@ -77,7 +77,7 @@ Display the heatmap by grade as a shiny module } \examples{ \dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} -data <- cdisc_data() |> +data <- teal_data() |> within({ library(dplyr) library(nestcolor) diff --git a/man/tm_g_patient_profile.Rd b/man/tm_g_patient_profile.Rd index 26c18bd7..b86e870a 100644 --- a/man/tm_g_patient_profile.Rd +++ b/man/tm_g_patient_profile.Rd @@ -109,7 +109,7 @@ the start date } \examples{ \dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} -data <- cdisc_data() |> +data <- teal_data() |> within({ library(nestcolor) ADSL <- rADSL diff --git a/man/tm_g_spiderplot.Rd b/man/tm_g_spiderplot.Rd index 53e9ba9e..fa780522 100644 --- a/man/tm_g_spiderplot.Rd +++ b/man/tm_g_spiderplot.Rd @@ -79,7 +79,7 @@ Display spider plot as a shiny module \examples{ \dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} # Example using stream (ADaM) dataset -data <- cdisc_data() |> +data <- teal_data() |> within({ library(nestcolor) ADSL <- rADSL diff --git a/man/tm_g_swimlane.Rd b/man/tm_g_swimlane.Rd index 019b7b54..367bb1b8 100644 --- a/man/tm_g_swimlane.Rd +++ b/man/tm_g_swimlane.Rd @@ -83,7 +83,7 @@ This is teal module that generates a \code{swimlane} plot (bar plot with markers \examples{ \dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} # Example using stream (ADaM) dataset -data <- cdisc_data() |> +data <- teal_data() |> within(library(dplyr)) |> within(library(nestcolor)) |> within(ADSL <- rADSL \%>\% diff --git a/man/tm_g_waterfall.Rd b/man/tm_g_waterfall.Rd index cdb00195..b7b5de12 100644 --- a/man/tm_g_waterfall.Rd +++ b/man/tm_g_waterfall.Rd @@ -101,7 +101,7 @@ This is teal module that generates a waterfall plot for \code{ADaM} data } \examples{ \dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} -data <- cdisc_data() |> +data <- teal_data() |> within({ library(nestcolor) ADSL <- rADSL From 48ca633636374a534e08c1d8f0e12dc2bbc4ff47 Mon Sep 17 00:00:00 2001 From: m7pr Date: Tue, 8 Oct 2024 11:02:40 +0200 Subject: [PATCH 11/18] Revert "change examples to teal_data" This reverts commit 2b5a86b7fdf0c2721c43cfcd7318a05c4000f40c. --- R/tm_g_ae_oview.R | 2 +- R/tm_g_ae_sub.R | 2 +- R/tm_g_butterfly.R | 2 +- R/tm_g_events_term_id.R | 2 +- R/tm_g_heat_bygrade.R | 2 +- R/tm_g_patient_profile.R | 2 +- R/tm_g_spiderplot.R | 2 +- R/tm_g_swimlane.R | 2 +- R/tm_g_waterfall.R | 2 +- man/tm_g_ae_oview.Rd | 4 ++-- man/tm_g_ae_sub.Rd | 2 +- man/tm_g_butterfly.Rd | 2 +- man/tm_g_events_term_id.Rd | 2 +- man/tm_g_heat_bygrade.Rd | 2 +- man/tm_g_patient_profile.Rd | 2 +- man/tm_g_spiderplot.Rd | 2 +- man/tm_g_swimlane.Rd | 2 +- man/tm_g_waterfall.Rd | 2 +- 18 files changed, 19 insertions(+), 19 deletions(-) diff --git a/R/tm_g_ae_oview.R b/R/tm_g_ae_oview.R index 364bbd5c..f4fc0fcc 100644 --- a/R/tm_g_ae_oview.R +++ b/R/tm_g_ae_oview.R @@ -16,7 +16,7 @@ #' @export #' #' @examplesIf require("nestcolor") -#' data <- teal_data() |> +#' data <- cdisc_data() |> #' within({ #' library(nestcolor) #' ADSL <- rADSL diff --git a/R/tm_g_ae_sub.R b/R/tm_g_ae_sub.R index 37c7f523..f4333a3c 100644 --- a/R/tm_g_ae_sub.R +++ b/R/tm_g_ae_sub.R @@ -18,7 +18,7 @@ #' #' @examples #' # Example using stream (ADaM) dataset -#' data <- teal_data() |> +#' data <- cdisc_data() |> #' within({ #' ADSL <- rADSL #' ADAE <- rADAE diff --git a/R/tm_g_butterfly.R b/R/tm_g_butterfly.R index 8e6e965c..51c84702 100644 --- a/R/tm_g_butterfly.R +++ b/R/tm_g_butterfly.R @@ -41,7 +41,7 @@ #' #' @examplesIf require("nestcolor") #' # Example using stream (ADaM) dataset -#' data <- teal_data() |> +#' data <- cdisc_data() |> #' within({ #' library(dplyr) #' library(nestcolor) diff --git a/R/tm_g_events_term_id.R b/R/tm_g_events_term_id.R index aac7751f..438a1c41 100644 --- a/R/tm_g_events_term_id.R +++ b/R/tm_g_events_term_id.R @@ -18,7 +18,7 @@ #' @author Molly He (hey59) \email{hey59@gene.com} #' #' @examplesIf require("nestcolor") -#' data <- teal_data() |> +#' data <- cdisc_data() |> #' within({ #' library(nestcolor) #' ADSL <- rADSL diff --git a/R/tm_g_heat_bygrade.R b/R/tm_g_heat_bygrade.R index 01cc6052..059386c5 100644 --- a/R/tm_g_heat_bygrade.R +++ b/R/tm_g_heat_bygrade.R @@ -34,7 +34,7 @@ #' @export #' #' @examplesIf require("nestcolor") -#' data <- teal_data() |> +#' data <- cdisc_data() |> #' within({ #' library(dplyr) #' library(nestcolor) diff --git a/R/tm_g_patient_profile.R b/R/tm_g_patient_profile.R index dc64b393..c60b5680 100644 --- a/R/tm_g_patient_profile.R +++ b/R/tm_g_patient_profile.R @@ -60,7 +60,7 @@ #' @export #' #' @examplesIf require("nestcolor") -#' data <- teal_data() |> +#' data <- cdisc_data() |> #' within({ #' library(nestcolor) #' ADSL <- rADSL diff --git a/R/tm_g_spiderplot.R b/R/tm_g_spiderplot.R index 8e9238a1..37722740 100644 --- a/R/tm_g_spiderplot.R +++ b/R/tm_g_spiderplot.R @@ -26,7 +26,7 @@ #' #' @examplesIf require("nestcolor") #' # Example using stream (ADaM) dataset -#' data <- teal_data() |> +#' data <- cdisc_data() |> #' within({ #' library(nestcolor) #' ADSL <- rADSL diff --git a/R/tm_g_swimlane.R b/R/tm_g_swimlane.R index ff81e2e9..29bc9808 100644 --- a/R/tm_g_swimlane.R +++ b/R/tm_g_swimlane.R @@ -36,7 +36,7 @@ #' #' @examplesIf require("nestcolor") #' # Example using stream (ADaM) dataset -#' data <- teal_data() |> +#' data <- cdisc_data() |> #' within(library(dplyr)) |> #' within(library(nestcolor)) |> #' within(ADSL <- rADSL %>% diff --git a/R/tm_g_waterfall.R b/R/tm_g_waterfall.R index 04b9a2eb..6d04e3c7 100644 --- a/R/tm_g_waterfall.R +++ b/R/tm_g_waterfall.R @@ -47,7 +47,7 @@ #' @author houx14 \email{houx14@gene.com} #' #' @examplesIf require("nestcolor") -#' data <- teal_data() |> +#' data <- cdisc_data() |> #' within({ #' library(nestcolor) #' ADSL <- rADSL diff --git a/man/tm_g_ae_oview.Rd b/man/tm_g_ae_oview.Rd index 30aede55..1e4b4f50 100644 --- a/man/tm_g_ae_oview.Rd +++ b/man/tm_g_ae_oview.Rd @@ -51,8 +51,8 @@ the \code{\link[teal:teal_modules]{teal::module()}} object. Display the \code{AE} overview plot as a shiny module } \examples{ -\dontshow{if (requireNamespace("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} -data <- teal_data() |> +\dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} +data <- cdisc_data() |> within({ library(nestcolor) ADSL <- rADSL diff --git a/man/tm_g_ae_sub.Rd b/man/tm_g_ae_sub.Rd index 06b4cc4c..925ef6d0 100644 --- a/man/tm_g_ae_sub.Rd +++ b/man/tm_g_ae_sub.Rd @@ -50,7 +50,7 @@ Display the \code{AE} by subgroups plot as a teal module } \examples{ # Example using stream (ADaM) dataset -data <- teal_data() |> +data <- cdisc_data() |> within({ ADSL <- rADSL ADAE <- rADAE diff --git a/man/tm_g_butterfly.Rd b/man/tm_g_butterfly.Rd index 1daeeaae..36a995f4 100644 --- a/man/tm_g_butterfly.Rd +++ b/man/tm_g_butterfly.Rd @@ -88,7 +88,7 @@ used directly as filter. \examples{ \dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} # Example using stream (ADaM) dataset -data <- teal_data() |> +data <- cdisc_data() |> within({ library(dplyr) library(nestcolor) diff --git a/man/tm_g_events_term_id.Rd b/man/tm_g_events_term_id.Rd index fb8141ce..aa1b5939 100644 --- a/man/tm_g_events_term_id.Rd +++ b/man/tm_g_events_term_id.Rd @@ -51,7 +51,7 @@ Display Events by Term plot as a shiny module } \examples{ \dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} -data <- teal_data() |> +data <- cdisc_data() |> within({ library(nestcolor) ADSL <- rADSL diff --git a/man/tm_g_heat_bygrade.Rd b/man/tm_g_heat_bygrade.Rd index 5aeb1537..cb9b3500 100644 --- a/man/tm_g_heat_bygrade.Rd +++ b/man/tm_g_heat_bygrade.Rd @@ -77,7 +77,7 @@ Display the heatmap by grade as a shiny module } \examples{ \dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} -data <- teal_data() |> +data <- cdisc_data() |> within({ library(dplyr) library(nestcolor) diff --git a/man/tm_g_patient_profile.Rd b/man/tm_g_patient_profile.Rd index b86e870a..26c18bd7 100644 --- a/man/tm_g_patient_profile.Rd +++ b/man/tm_g_patient_profile.Rd @@ -109,7 +109,7 @@ the start date } \examples{ \dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} -data <- teal_data() |> +data <- cdisc_data() |> within({ library(nestcolor) ADSL <- rADSL diff --git a/man/tm_g_spiderplot.Rd b/man/tm_g_spiderplot.Rd index fa780522..53e9ba9e 100644 --- a/man/tm_g_spiderplot.Rd +++ b/man/tm_g_spiderplot.Rd @@ -79,7 +79,7 @@ Display spider plot as a shiny module \examples{ \dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} # Example using stream (ADaM) dataset -data <- teal_data() |> +data <- cdisc_data() |> within({ library(nestcolor) ADSL <- rADSL diff --git a/man/tm_g_swimlane.Rd b/man/tm_g_swimlane.Rd index 367bb1b8..019b7b54 100644 --- a/man/tm_g_swimlane.Rd +++ b/man/tm_g_swimlane.Rd @@ -83,7 +83,7 @@ This is teal module that generates a \code{swimlane} plot (bar plot with markers \examples{ \dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} # Example using stream (ADaM) dataset -data <- teal_data() |> +data <- cdisc_data() |> within(library(dplyr)) |> within(library(nestcolor)) |> within(ADSL <- rADSL \%>\% diff --git a/man/tm_g_waterfall.Rd b/man/tm_g_waterfall.Rd index b7b5de12..cdb00195 100644 --- a/man/tm_g_waterfall.Rd +++ b/man/tm_g_waterfall.Rd @@ -101,7 +101,7 @@ This is teal module that generates a waterfall plot for \code{ADaM} data } \examples{ \dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} -data <- teal_data() |> +data <- cdisc_data() |> within({ library(nestcolor) ADSL <- rADSL From 13ac85a102ef9fe3c7c0ed5c39644002dfae654c Mon Sep 17 00:00:00 2001 From: m7pr Date: Tue, 8 Oct 2024 11:11:28 +0200 Subject: [PATCH 12/18] move teal.data to Imports and change exmaples --- DESCRIPTION | 2 +- NEWS.md | 1 + R/tm_g_ae_oview.R | 2 +- R/tm_g_ae_sub.R | 2 +- R/tm_g_butterfly.R | 2 +- R/tm_g_events_term_id.R | 2 +- R/tm_g_heat_bygrade.R | 2 +- R/tm_g_patient_profile.R | 2 +- R/tm_g_spiderplot.R | 2 +- R/tm_g_swimlane.R | 2 +- R/tm_g_waterfall.R | 2 +- man/tm_g_ae_oview.Rd | 2 +- man/tm_g_ae_sub.Rd | 2 +- man/tm_g_butterfly.Rd | 2 +- man/tm_g_events_term_id.Rd | 2 +- man/tm_g_heat_bygrade.Rd | 2 +- man/tm_g_patient_profile.Rd | 2 +- man/tm_g_spiderplot.Rd | 2 +- man/tm_g_swimlane.Rd | 2 +- man/tm_g_waterfall.Rd | 2 +- 20 files changed, 20 insertions(+), 19 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 3a313744..a6c31385 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -34,6 +34,7 @@ Imports: lifecycle (>= 0.2.0), shinyvalidate, teal.code (>= 0.4.1.9009), + teal.data (>= 0.3.0.9018), teal.logger (>= 0.2.0.9004), teal.reporter (>= 0.2.0), teal.widgets (>= 0.4.0), @@ -44,7 +45,6 @@ Suggests: logger (>= 0.2.2), nestcolor (>= 0.1.0), rmarkdown (>= 2.23), - teal.data (>= 0.3.0.9018), testthat (>= 3.1.5), withr (>= 2.0.0) Config/Needs/verdepcheck: insightsengineering/osprey, rstudio/shiny, diff --git a/NEWS.md b/NEWS.md index f0afe4f8..79de4f64 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,7 @@ # teal.osprey 0.1.16.9028 * Removed `Show Warnings` modals from modules. +* Moved `teal_data` from `Suggests` to `Imports` as it was used in `tm_g_swimlane`. Changed examples from `cdisc_data()` to `teal_data()`. ### Breaking Changes * Adapted all modules to use `teal_data` objects. diff --git a/R/tm_g_ae_oview.R b/R/tm_g_ae_oview.R index f4fc0fcc..364bbd5c 100644 --- a/R/tm_g_ae_oview.R +++ b/R/tm_g_ae_oview.R @@ -16,7 +16,7 @@ #' @export #' #' @examplesIf require("nestcolor") -#' data <- cdisc_data() |> +#' data <- teal_data() |> #' within({ #' library(nestcolor) #' ADSL <- rADSL diff --git a/R/tm_g_ae_sub.R b/R/tm_g_ae_sub.R index f4333a3c..37c7f523 100644 --- a/R/tm_g_ae_sub.R +++ b/R/tm_g_ae_sub.R @@ -18,7 +18,7 @@ #' #' @examples #' # Example using stream (ADaM) dataset -#' data <- cdisc_data() |> +#' data <- teal_data() |> #' within({ #' ADSL <- rADSL #' ADAE <- rADAE diff --git a/R/tm_g_butterfly.R b/R/tm_g_butterfly.R index 51c84702..8e6e965c 100644 --- a/R/tm_g_butterfly.R +++ b/R/tm_g_butterfly.R @@ -41,7 +41,7 @@ #' #' @examplesIf require("nestcolor") #' # Example using stream (ADaM) dataset -#' data <- cdisc_data() |> +#' data <- teal_data() |> #' within({ #' library(dplyr) #' library(nestcolor) diff --git a/R/tm_g_events_term_id.R b/R/tm_g_events_term_id.R index 438a1c41..aac7751f 100644 --- a/R/tm_g_events_term_id.R +++ b/R/tm_g_events_term_id.R @@ -18,7 +18,7 @@ #' @author Molly He (hey59) \email{hey59@gene.com} #' #' @examplesIf require("nestcolor") -#' data <- cdisc_data() |> +#' data <- teal_data() |> #' within({ #' library(nestcolor) #' ADSL <- rADSL diff --git a/R/tm_g_heat_bygrade.R b/R/tm_g_heat_bygrade.R index 059386c5..01cc6052 100644 --- a/R/tm_g_heat_bygrade.R +++ b/R/tm_g_heat_bygrade.R @@ -34,7 +34,7 @@ #' @export #' #' @examplesIf require("nestcolor") -#' data <- cdisc_data() |> +#' data <- teal_data() |> #' within({ #' library(dplyr) #' library(nestcolor) diff --git a/R/tm_g_patient_profile.R b/R/tm_g_patient_profile.R index c60b5680..dc64b393 100644 --- a/R/tm_g_patient_profile.R +++ b/R/tm_g_patient_profile.R @@ -60,7 +60,7 @@ #' @export #' #' @examplesIf require("nestcolor") -#' data <- cdisc_data() |> +#' data <- teal_data() |> #' within({ #' library(nestcolor) #' ADSL <- rADSL diff --git a/R/tm_g_spiderplot.R b/R/tm_g_spiderplot.R index 37722740..8e9238a1 100644 --- a/R/tm_g_spiderplot.R +++ b/R/tm_g_spiderplot.R @@ -26,7 +26,7 @@ #' #' @examplesIf require("nestcolor") #' # Example using stream (ADaM) dataset -#' data <- cdisc_data() |> +#' data <- teal_data() |> #' within({ #' library(nestcolor) #' ADSL <- rADSL diff --git a/R/tm_g_swimlane.R b/R/tm_g_swimlane.R index 29bc9808..ff81e2e9 100644 --- a/R/tm_g_swimlane.R +++ b/R/tm_g_swimlane.R @@ -36,7 +36,7 @@ #' #' @examplesIf require("nestcolor") #' # Example using stream (ADaM) dataset -#' data <- cdisc_data() |> +#' data <- teal_data() |> #' within(library(dplyr)) |> #' within(library(nestcolor)) |> #' within(ADSL <- rADSL %>% diff --git a/R/tm_g_waterfall.R b/R/tm_g_waterfall.R index 6d04e3c7..04b9a2eb 100644 --- a/R/tm_g_waterfall.R +++ b/R/tm_g_waterfall.R @@ -47,7 +47,7 @@ #' @author houx14 \email{houx14@gene.com} #' #' @examplesIf require("nestcolor") -#' data <- cdisc_data() |> +#' data <- teal_data() |> #' within({ #' library(nestcolor) #' ADSL <- rADSL diff --git a/man/tm_g_ae_oview.Rd b/man/tm_g_ae_oview.Rd index 1e4b4f50..310d39f5 100644 --- a/man/tm_g_ae_oview.Rd +++ b/man/tm_g_ae_oview.Rd @@ -52,7 +52,7 @@ Display the \code{AE} overview plot as a shiny module } \examples{ \dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} -data <- cdisc_data() |> +data <- teal_data() |> within({ library(nestcolor) ADSL <- rADSL diff --git a/man/tm_g_ae_sub.Rd b/man/tm_g_ae_sub.Rd index 925ef6d0..06b4cc4c 100644 --- a/man/tm_g_ae_sub.Rd +++ b/man/tm_g_ae_sub.Rd @@ -50,7 +50,7 @@ Display the \code{AE} by subgroups plot as a teal module } \examples{ # Example using stream (ADaM) dataset -data <- cdisc_data() |> +data <- teal_data() |> within({ ADSL <- rADSL ADAE <- rADAE diff --git a/man/tm_g_butterfly.Rd b/man/tm_g_butterfly.Rd index 36a995f4..1daeeaae 100644 --- a/man/tm_g_butterfly.Rd +++ b/man/tm_g_butterfly.Rd @@ -88,7 +88,7 @@ used directly as filter. \examples{ \dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} # Example using stream (ADaM) dataset -data <- cdisc_data() |> +data <- teal_data() |> within({ library(dplyr) library(nestcolor) diff --git a/man/tm_g_events_term_id.Rd b/man/tm_g_events_term_id.Rd index aa1b5939..fb8141ce 100644 --- a/man/tm_g_events_term_id.Rd +++ b/man/tm_g_events_term_id.Rd @@ -51,7 +51,7 @@ Display Events by Term plot as a shiny module } \examples{ \dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} -data <- cdisc_data() |> +data <- teal_data() |> within({ library(nestcolor) ADSL <- rADSL diff --git a/man/tm_g_heat_bygrade.Rd b/man/tm_g_heat_bygrade.Rd index cb9b3500..5aeb1537 100644 --- a/man/tm_g_heat_bygrade.Rd +++ b/man/tm_g_heat_bygrade.Rd @@ -77,7 +77,7 @@ Display the heatmap by grade as a shiny module } \examples{ \dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} -data <- cdisc_data() |> +data <- teal_data() |> within({ library(dplyr) library(nestcolor) diff --git a/man/tm_g_patient_profile.Rd b/man/tm_g_patient_profile.Rd index 26c18bd7..b86e870a 100644 --- a/man/tm_g_patient_profile.Rd +++ b/man/tm_g_patient_profile.Rd @@ -109,7 +109,7 @@ the start date } \examples{ \dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} -data <- cdisc_data() |> +data <- teal_data() |> within({ library(nestcolor) ADSL <- rADSL diff --git a/man/tm_g_spiderplot.Rd b/man/tm_g_spiderplot.Rd index 53e9ba9e..fa780522 100644 --- a/man/tm_g_spiderplot.Rd +++ b/man/tm_g_spiderplot.Rd @@ -79,7 +79,7 @@ Display spider plot as a shiny module \examples{ \dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} # Example using stream (ADaM) dataset -data <- cdisc_data() |> +data <- teal_data() |> within({ library(nestcolor) ADSL <- rADSL diff --git a/man/tm_g_swimlane.Rd b/man/tm_g_swimlane.Rd index 019b7b54..367bb1b8 100644 --- a/man/tm_g_swimlane.Rd +++ b/man/tm_g_swimlane.Rd @@ -83,7 +83,7 @@ This is teal module that generates a \code{swimlane} plot (bar plot with markers \examples{ \dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} # Example using stream (ADaM) dataset -data <- cdisc_data() |> +data <- teal_data() |> within(library(dplyr)) |> within(library(nestcolor)) |> within(ADSL <- rADSL \%>\% diff --git a/man/tm_g_waterfall.Rd b/man/tm_g_waterfall.Rd index cdb00195..b7b5de12 100644 --- a/man/tm_g_waterfall.Rd +++ b/man/tm_g_waterfall.Rd @@ -101,7 +101,7 @@ This is teal module that generates a waterfall plot for \code{ADaM} data } \examples{ \dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} -data <- cdisc_data() |> +data <- teal_data() |> within({ library(nestcolor) ADSL <- rADSL From 8e7b32ac5f210a33f020a291efbce1226ac24993 Mon Sep 17 00:00:00 2001 From: m7pr Date: Tue, 8 Oct 2024 11:17:42 +0200 Subject: [PATCH 13/18] remove nestcolor from DEPENDENCIES to simplify examples --- DESCRIPTION | 6 ++---- R/tm_g_ae_oview.R | 3 +-- R/tm_g_butterfly.R | 3 +-- R/tm_g_events_term_id.R | 3 +-- R/tm_g_heat_bygrade.R | 3 +-- R/tm_g_patient_profile.R | 3 +-- R/tm_g_spiderplot.R | 3 +-- R/tm_g_swimlane.R | 15 ++++++++------- R/tm_g_waterfall.R | 3 +-- man/tm_g_ae_oview.Rd | 4 +--- man/tm_g_butterfly.Rd | 4 +--- man/tm_g_events_term_id.Rd | 4 +--- man/tm_g_heat_bygrade.Rd | 4 +--- man/tm_g_patient_profile.Rd | 4 +--- man/tm_g_spiderplot.Rd | 4 +--- man/tm_g_swimlane.Rd | 16 ++++++++-------- man/tm_g_waterfall.Rd | 4 +--- staged_dependencies.yaml | 3 --- 18 files changed, 32 insertions(+), 57 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index a6c31385..824d04fd 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -43,7 +43,6 @@ Imports: Suggests: knitr (>= 1.42), logger (>= 0.2.2), - nestcolor (>= 0.1.0), rmarkdown (>= 2.23), testthat (>= 3.1.5), withr (>= 2.0.0) @@ -54,9 +53,8 @@ Config/Needs/verdepcheck: insightsengineering/osprey, rstudio/shiny, rstudio/shinyvalidate, insightsengineering/teal.code, insightsengineering/teal.logger, insightsengineering/teal.reporter, insightsengineering/teal.widgets, insightsengineering/tern, - tidyverse/tidyr, yihui/knitr, insightsengineering/nestcolor, - rstudio/rmarkdown, insightsengineering/teal.data, r-lib/testthat, - r-lib/withr + tidyverse/tidyr, yihui/knitr, rstudio/rmarkdown, + insightsengineering/teal.data, r-lib/testthat, r-lib/withr Config/Needs/website: insightsengineering/nesttemplate Encoding: UTF-8 Language: en-US diff --git a/R/tm_g_ae_oview.R b/R/tm_g_ae_oview.R index 364bbd5c..bcb2a73f 100644 --- a/R/tm_g_ae_oview.R +++ b/R/tm_g_ae_oview.R @@ -15,10 +15,9 @@ #' #' @export #' -#' @examplesIf require("nestcolor") +#' @examples #' data <- teal_data() |> #' within({ -#' library(nestcolor) #' ADSL <- rADSL #' ADAE <- rADAE #' add_event_flags <- function(dat) { diff --git a/R/tm_g_butterfly.R b/R/tm_g_butterfly.R index 8e6e965c..c8bfe47f 100644 --- a/R/tm_g_butterfly.R +++ b/R/tm_g_butterfly.R @@ -39,12 +39,11 @@ #' @template author_zhanc107 #' @template author_liaoc10 #' -#' @examplesIf require("nestcolor") +#' @examples #' # Example using stream (ADaM) dataset #' data <- teal_data() |> #' within({ #' library(dplyr) -#' library(nestcolor) #' set.seed(23) #' ADSL <- rADSL #' ADAE <- rADAE diff --git a/R/tm_g_events_term_id.R b/R/tm_g_events_term_id.R index aac7751f..98d67451 100644 --- a/R/tm_g_events_term_id.R +++ b/R/tm_g_events_term_id.R @@ -17,10 +17,9 @@ #' @author Liming Li (lil128) \email{liming.li@roche.com} #' @author Molly He (hey59) \email{hey59@gene.com} #' -#' @examplesIf require("nestcolor") +#' @examples #' data <- teal_data() |> #' within({ -#' library(nestcolor) #' ADSL <- rADSL #' ADAE <- rADAE #' }) diff --git a/R/tm_g_heat_bygrade.R b/R/tm_g_heat_bygrade.R index 01cc6052..ec423241 100644 --- a/R/tm_g_heat_bygrade.R +++ b/R/tm_g_heat_bygrade.R @@ -33,11 +33,10 @@ #' #' @export #' -#' @examplesIf require("nestcolor") +#' @examples #' data <- teal_data() |> #' within({ #' library(dplyr) -#' library(nestcolor) #' ADSL <- rADSL %>% slice(1:30) #' ADEX <- rADEX %>% filter(USUBJID %in% ADSL$USUBJID) #' ADAE <- rADAE %>% filter(USUBJID %in% ADSL$USUBJID) diff --git a/R/tm_g_patient_profile.R b/R/tm_g_patient_profile.R index dc64b393..6f064abd 100644 --- a/R/tm_g_patient_profile.R +++ b/R/tm_g_patient_profile.R @@ -59,10 +59,9 @@ #' #' @export #' -#' @examplesIf require("nestcolor") +#' @examples #' data <- teal_data() |> #' within({ -#' library(nestcolor) #' ADSL <- rADSL #' ADAE <- rADAE %>% mutate(ASTDT = as.Date(ASTDTM), AENDT = as.Date(AENDTM)) #' ADCM <- rADCM %>% mutate(ASTDT = as.Date(ASTDTM), AENDT = as.Date(AENDTM)) diff --git a/R/tm_g_spiderplot.R b/R/tm_g_spiderplot.R index 8e9238a1..ac0495f5 100644 --- a/R/tm_g_spiderplot.R +++ b/R/tm_g_spiderplot.R @@ -24,11 +24,10 @@ #' @template author_zhanc107 #' @template author_liaoc10 #' -#' @examplesIf require("nestcolor") +#' @examples #' # Example using stream (ADaM) dataset #' data <- teal_data() |> #' within({ -#' library(nestcolor) #' ADSL <- rADSL #' ADTR <- rADTR #' }) diff --git a/R/tm_g_swimlane.R b/R/tm_g_swimlane.R index ff81e2e9..ccc2df64 100644 --- a/R/tm_g_swimlane.R +++ b/R/tm_g_swimlane.R @@ -34,19 +34,20 @@ #' #' @template author_qit3 #' -#' @examplesIf require("nestcolor") +#' @examples #' # Example using stream (ADaM) dataset #' data <- teal_data() |> -#' within(library(dplyr)) |> -#' within(library(nestcolor)) |> -#' within(ADSL <- rADSL %>% +#' within({ +#' library(dplyr) +#' ADSL <- rADSL %>% #' mutate(TRTDURD = as.integer(TRTEDTM - TRTSDTM) + 1) %>% -#' filter(STRATA1 == "A" & ARMCD == "ARM A")) |> -#' within(ADRS <- rADRS %>% +#' filter(STRATA1 == "A" & ARMCD == "ARM A") +#' ADRS <- rADRS %>% #' filter(PARAMCD == "LSTASDI" & DCSREAS == "Death") %>% #' mutate(AVALC = DCSREAS, ADY = EOSDY) %>% #' rbind(rADRS %>% filter(PARAMCD == "OVRINV" & AVALC != "NE")) %>% -#' arrange(USUBJID)) +#' arrange(USUBJID) +#' }) #' #' datanames(data) <- c("ADSL", "ADRS") #' join_keys(data) <- default_cdisc_join_keys[datanames(data)] diff --git a/R/tm_g_waterfall.R b/R/tm_g_waterfall.R index 04b9a2eb..5a5c7129 100644 --- a/R/tm_g_waterfall.R +++ b/R/tm_g_waterfall.R @@ -46,10 +46,9 @@ #' @template author_qit3 #' @author houx14 \email{houx14@gene.com} #' -#' @examplesIf require("nestcolor") +#' @examples #' data <- teal_data() |> #' within({ -#' library(nestcolor) #' ADSL <- rADSL #' ADRS <- rADRS #' ADTR <- rADTR diff --git a/man/tm_g_ae_oview.Rd b/man/tm_g_ae_oview.Rd index 310d39f5..5c21df9d 100644 --- a/man/tm_g_ae_oview.Rd +++ b/man/tm_g_ae_oview.Rd @@ -51,10 +51,8 @@ the \code{\link[teal:teal_modules]{teal::module()}} object. Display the \code{AE} overview plot as a shiny module } \examples{ -\dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} data <- teal_data() |> within({ - library(nestcolor) ADSL <- rADSL ADAE <- rADAE add_event_flags <- function(dat) { @@ -108,5 +106,5 @@ app <- init( if (interactive()) { shinyApp(app$ui, app$server) } -\dontshow{\}) # examplesIf} + } diff --git a/man/tm_g_butterfly.Rd b/man/tm_g_butterfly.Rd index 1daeeaae..4b25ab2b 100644 --- a/man/tm_g_butterfly.Rd +++ b/man/tm_g_butterfly.Rd @@ -86,12 +86,10 @@ used for subsequent analysis. Flag variables (from \code{ADaM} datasets) can be used directly as filter. } \examples{ -\dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} # Example using stream (ADaM) dataset data <- teal_data() |> within({ library(dplyr) - library(nestcolor) set.seed(23) ADSL <- rADSL ADAE <- rADAE @@ -150,7 +148,7 @@ app <- init( if (interactive()) { shinyApp(app$ui, app$server) } -\dontshow{\}) # examplesIf} + } \author{ Carolyn Zhang (zhanc107) \email{carolyn.zhang@duke.edu} diff --git a/man/tm_g_events_term_id.Rd b/man/tm_g_events_term_id.Rd index fb8141ce..5a49b307 100644 --- a/man/tm_g_events_term_id.Rd +++ b/man/tm_g_events_term_id.Rd @@ -50,10 +50,8 @@ the \code{\link[teal:teal_modules]{teal::module()}} object. Display Events by Term plot as a shiny module } \examples{ -\dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} data <- teal_data() |> within({ - library(nestcolor) ADSL <- rADSL ADAE <- rADAE }) @@ -85,7 +83,7 @@ app <- init( if (interactive()) { shinyApp(app$ui, app$server) } -\dontshow{\}) # examplesIf} + } \author{ Liming Li (lil128) \email{liming.li@roche.com} diff --git a/man/tm_g_heat_bygrade.Rd b/man/tm_g_heat_bygrade.Rd index 5aeb1537..93057df0 100644 --- a/man/tm_g_heat_bygrade.Rd +++ b/man/tm_g_heat_bygrade.Rd @@ -76,11 +76,9 @@ the \code{\link[teal:teal_modules]{teal::module()}} object. Display the heatmap by grade as a shiny module } \examples{ -\dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} data <- teal_data() |> within({ library(dplyr) - library(nestcolor) ADSL <- rADSL \%>\% slice(1:30) ADEX <- rADEX \%>\% filter(USUBJID \%in\% ADSL$USUBJID) ADAE <- rADAE \%>\% filter(USUBJID \%in\% ADSL$USUBJID) @@ -160,5 +158,5 @@ app <- init( if (interactive()) { shinyApp(app$ui, app$server) } -\dontshow{\}) # examplesIf} + } diff --git a/man/tm_g_patient_profile.Rd b/man/tm_g_patient_profile.Rd index b86e870a..393b0e2d 100644 --- a/man/tm_g_patient_profile.Rd +++ b/man/tm_g_patient_profile.Rd @@ -108,10 +108,8 @@ the start date } } \examples{ -\dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} data <- teal_data() |> within({ - library(nestcolor) ADSL <- rADSL ADAE <- rADAE \%>\% mutate(ASTDT = as.Date(ASTDTM), AENDT = as.Date(AENDTM)) ADCM <- rADCM \%>\% mutate(ASTDT = as.Date(ASTDTM), AENDT = as.Date(AENDTM)) @@ -181,7 +179,7 @@ app <- init( if (interactive()) { shinyApp(app$ui, app$server) } -\dontshow{\}) # examplesIf} + } \author{ Xuefeng Hou (houx14) \email{houx14@gene.com} diff --git a/man/tm_g_spiderplot.Rd b/man/tm_g_spiderplot.Rd index fa780522..35011035 100644 --- a/man/tm_g_spiderplot.Rd +++ b/man/tm_g_spiderplot.Rd @@ -77,11 +77,9 @@ the \code{\link[teal:teal_modules]{teal::module()}} object. Display spider plot as a shiny module } \examples{ -\dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} # Example using stream (ADaM) dataset data <- teal_data() |> within({ - library(nestcolor) ADSL <- rADSL ADTR <- rADTR }) @@ -131,7 +129,7 @@ app <- init( if (interactive()) { shinyApp(app$ui, app$server) } -\dontshow{\}) # examplesIf} + } \author{ Carolyn Zhang (zhanc107) \email{carolyn.zhang@duke.edu} diff --git a/man/tm_g_swimlane.Rd b/man/tm_g_swimlane.Rd index 367bb1b8..718de623 100644 --- a/man/tm_g_swimlane.Rd +++ b/man/tm_g_swimlane.Rd @@ -81,19 +81,19 @@ the \code{\link[teal:teal_modules]{teal::module()}} object. This is teal module that generates a \code{swimlane} plot (bar plot with markers) for \code{ADaM} data } \examples{ -\dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} # Example using stream (ADaM) dataset data <- teal_data() |> - within(library(dplyr)) |> - within(library(nestcolor)) |> - within(ADSL <- rADSL \%>\% + within({ + library(dplyr) + ADSL <- rADSL \%>\% mutate(TRTDURD = as.integer(TRTEDTM - TRTSDTM) + 1) \%>\% - filter(STRATA1 == "A" & ARMCD == "ARM A")) |> - within(ADRS <- rADRS \%>\% + filter(STRATA1 == "A" & ARMCD == "ARM A") + ADRS <- rADRS \%>\% filter(PARAMCD == "LSTASDI" & DCSREAS == "Death") \%>\% mutate(AVALC = DCSREAS, ADY = EOSDY) \%>\% rbind(rADRS \%>\% filter(PARAMCD == "OVRINV" & AVALC != "NE")) \%>\% - arrange(USUBJID)) + arrange(USUBJID) + }) datanames(data) <- c("ADSL", "ADRS") join_keys(data) <- default_cdisc_join_keys[datanames(data)] @@ -150,7 +150,7 @@ app <- init( if (interactive()) { shinyApp(app$ui, app$server) } -\dontshow{\}) # examplesIf} + } \author{ Ting Qi (qit3) \email{qit3@gene.com} diff --git a/man/tm_g_waterfall.Rd b/man/tm_g_waterfall.Rd index b7b5de12..a1ebdd12 100644 --- a/man/tm_g_waterfall.Rd +++ b/man/tm_g_waterfall.Rd @@ -100,10 +100,8 @@ the \code{\link[teal:teal_modules]{teal::module()}} object. This is teal module that generates a waterfall plot for \code{ADaM} data } \examples{ -\dontshow{if (require("nestcolor")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} data <- teal_data() |> within({ - library(nestcolor) ADSL <- rADSL ADRS <- rADRS ADTR <- rADTR @@ -137,7 +135,7 @@ app <- init( if (interactive()) { shinyApp(app$ui, app$server) } -\dontshow{\}) # examplesIf} + } \author{ Ting Qi (qit3) \email{qit3@gene.com} diff --git a/staged_dependencies.yaml b/staged_dependencies.yaml index e6641518..d04bf594 100644 --- a/staged_dependencies.yaml +++ b/staged_dependencies.yaml @@ -33,7 +33,4 @@ upstream_repos: insightsengineering/formatters: repo: insightsengineering/formatters host: https://github.com - insightsengineering/nestcolor: - repo: insightsengineering/nestcolor - host: https://github.com downstream_repos: From 58395b86247a24c045f7f034fe7cc59f261a84d3 Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Tue, 8 Oct 2024 09:20:03 +0000 Subject: [PATCH 14/18] [skip style] [skip vbump] Restyle files --- R/tm_g_swimlane.R | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/R/tm_g_swimlane.R b/R/tm_g_swimlane.R index ccc2df64..55dcb42c 100644 --- a/R/tm_g_swimlane.R +++ b/R/tm_g_swimlane.R @@ -40,14 +40,14 @@ #' within({ #' library(dplyr) #' ADSL <- rADSL %>% -#' mutate(TRTDURD = as.integer(TRTEDTM - TRTSDTM) + 1) %>% -#' filter(STRATA1 == "A" & ARMCD == "ARM A") +#' mutate(TRTDURD = as.integer(TRTEDTM - TRTSDTM) + 1) %>% +#' filter(STRATA1 == "A" & ARMCD == "ARM A") #' ADRS <- rADRS %>% -#' filter(PARAMCD == "LSTASDI" & DCSREAS == "Death") %>% -#' mutate(AVALC = DCSREAS, ADY = EOSDY) %>% -#' rbind(rADRS %>% filter(PARAMCD == "OVRINV" & AVALC != "NE")) %>% -#' arrange(USUBJID) -#' }) +#' filter(PARAMCD == "LSTASDI" & DCSREAS == "Death") %>% +#' mutate(AVALC = DCSREAS, ADY = EOSDY) %>% +#' rbind(rADRS %>% filter(PARAMCD == "OVRINV" & AVALC != "NE")) %>% +#' arrange(USUBJID) +#' }) #' #' datanames(data) <- c("ADSL", "ADRS") #' join_keys(data) <- default_cdisc_join_keys[datanames(data)] From f2cedbe772efca54d0205280f3f64de8b1f57516 Mon Sep 17 00:00:00 2001 From: "27856297+dependabot-preview[bot]@users.noreply.github.com" <27856297+dependabot-preview[bot]@users.noreply.github.com> Date: Tue, 8 Oct 2024 09:24:14 +0000 Subject: [PATCH 15/18] [skip roxygen] [skip vbump] Roxygen Man Pages Auto Update --- man/tm_g_swimlane.Rd | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/man/tm_g_swimlane.Rd b/man/tm_g_swimlane.Rd index 718de623..6dd578b8 100644 --- a/man/tm_g_swimlane.Rd +++ b/man/tm_g_swimlane.Rd @@ -86,14 +86,14 @@ data <- teal_data() |> within({ library(dplyr) ADSL <- rADSL \%>\% - mutate(TRTDURD = as.integer(TRTEDTM - TRTSDTM) + 1) \%>\% - filter(STRATA1 == "A" & ARMCD == "ARM A") + mutate(TRTDURD = as.integer(TRTEDTM - TRTSDTM) + 1) \%>\% + filter(STRATA1 == "A" & ARMCD == "ARM A") ADRS <- rADRS \%>\% - filter(PARAMCD == "LSTASDI" & DCSREAS == "Death") \%>\% - mutate(AVALC = DCSREAS, ADY = EOSDY) \%>\% - rbind(rADRS \%>\% filter(PARAMCD == "OVRINV" & AVALC != "NE")) \%>\% - arrange(USUBJID) - }) + filter(PARAMCD == "LSTASDI" & DCSREAS == "Death") \%>\% + mutate(AVALC = DCSREAS, ADY = EOSDY) \%>\% + rbind(rADRS \%>\% filter(PARAMCD == "OVRINV" & AVALC != "NE")) \%>\% + arrange(USUBJID) + }) datanames(data) <- c("ADSL", "ADRS") join_keys(data) <- default_cdisc_join_keys[datanames(data)] From 01e241ddbe3e09eade7478031f9922f50562e04c Mon Sep 17 00:00:00 2001 From: Marcin <133694481+m7pr@users.noreply.github.com> Date: Tue, 8 Oct 2024 11:34:48 +0200 Subject: [PATCH 16/18] Update NEWS.md Co-authored-by: Pawel Rucki <12943682+pawelru@users.noreply.github.com> Signed-off-by: Marcin <133694481+m7pr@users.noreply.github.com> --- NEWS.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index 79de4f64..933d9341 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,7 +1,8 @@ # teal.osprey 0.1.16.9028 * Removed `Show Warnings` modals from modules. -* Moved `teal_data` from `Suggests` to `Imports` as it was used in `tm_g_swimlane`. Changed examples from `cdisc_data()` to `teal_data()`. +* Moved `teal_data` from `Suggests` to `Imports` as it was used in `tm_g_swimlane`. +* Changed examples from `cdisc_data()` to `teal_data()`. ### Breaking Changes * Adapted all modules to use `teal_data` objects. From 800726c2aad4c31e054ec770fcc41951d9069032 Mon Sep 17 00:00:00 2001 From: Pawel Rucki <12943682+pawelru@users.noreply.github.com> Date: Tue, 8 Oct 2024 14:27:36 +0200 Subject: [PATCH 17/18] Update NEWS.md Signed-off-by: Pawel Rucki <12943682+pawelru@users.noreply.github.com> --- NEWS.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index 933d9341..6b413e6d 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,7 +1,7 @@ # teal.osprey 0.1.16.9028 * Removed `Show Warnings` modals from modules. -* Moved `teal_data` from `Suggests` to `Imports` as it was used in `tm_g_swimlane`. +* Moved `teal.data` from `Suggests` to `Imports` as it was used in `tm_g_swimlane`. * Changed examples from `cdisc_data()` to `teal_data()`. ### Breaking Changes From 5a2c8c63793ad74304cf8aa91417ef0ac04afc90 Mon Sep 17 00:00:00 2001 From: Pawel Rucki <12943682+pawelru@users.noreply.github.com> Date: Tue, 8 Oct 2024 14:28:16 +0200 Subject: [PATCH 18/18] Update NEWS.md Signed-off-by: Pawel Rucki <12943682+pawelru@users.noreply.github.com> --- NEWS.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index 6b413e6d..4758b7b7 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,7 +1,7 @@ # teal.osprey 0.1.16.9028 * Removed `Show Warnings` modals from modules. -* Moved `teal.data` from `Suggests` to `Imports` as it was used in `tm_g_swimlane`. +* Moved `teal.data` from `Suggests` to `Imports`. * Changed examples from `cdisc_data()` to `teal_data()`. ### Breaking Changes