From 1d51d3f18ac49629fc0b9ad448ddc9d8448a8a18 Mon Sep 17 00:00:00 2001 From: ayogasekaram Date: Tue, 14 May 2024 14:05:03 +0000 Subject: [PATCH] reverse any layout changes --- book/_quarto.yml | 4 +- book/graphs/efficacy/fstg01.qmd | 24 +++++------ book/graphs/efficacy/fstg02.qmd | 19 +++++---- book/graphs/efficacy/kmg01.qmd | 25 ++++++------ book/graphs/efficacy/mmrmg01.qmd | 5 +-- book/graphs/efficacy/mmrmg02.qmd | 1 + book/graphs/other/brg01.qmd | 32 +++++++++------ book/graphs/other/bwg01.qmd | 30 +++++++++----- book/graphs/other/cig01.qmd | 20 +++++----- book/graphs/other/ippg01.qmd | 9 +++-- book/graphs/other/ltg01.qmd | 28 +++++++------ book/graphs/other/mng01.qmd | 29 +++++++------- book/graphs/pharmacokinetic/pkcg01.qmd | 9 +++-- book/graphs/pharmacokinetic/pkcg02.qmd | 9 +++-- book/graphs/pharmacokinetic/pkcg03.qmd | 9 +++-- book/graphs/pharmacokinetic/pkpg01.qmd | 9 +++-- book/graphs/pharmacokinetic/pkpg02.qmd | 9 +++-- book/graphs/pharmacokinetic/pkpg03.qmd | 5 ++- book/graphs/pharmacokinetic/pkpg04.qmd | 5 ++- book/graphs/pharmacokinetic/pkpg06.qmd | 17 ++++---- book/listings/ADA/adal02.qmd | 4 +- book/listings/ECG/egl01.qmd | 4 +- book/listings/adverse-events/ael01.qmd | 4 +- book/listings/adverse-events/ael01_nollt.qmd | 4 +- book/listings/adverse-events/ael02.qmd | 4 +- book/listings/adverse-events/ael02_ed.qmd | 4 +- book/listings/adverse-events/ael03.qmd | 4 +- book/listings/adverse-events/ael04.qmd | 4 +- .../concomitant-medications/cml01.qmd | 4 +- .../concomitant-medications/cml02a_gl.qmd | 4 +- .../concomitant-medications/cml02b_gl.qmd | 4 +- .../dsur4.qmd | 4 +- book/listings/disposition/dsl01.qmd | 4 +- book/listings/disposition/dsl02.qmd | 4 +- book/listings/efficacy/oncl01.qmd | 4 +- book/listings/exposure/exl01.qmd | 4 +- book/listings/lab-results/lbl01.qmd | 4 +- book/listings/lab-results/lbl01_rls.qmd | 4 +- book/listings/lab-results/lbl02a.qmd | 4 +- book/listings/lab-results/lbl02a_rls.qmd | 4 +- book/listings/lab-results/lbl02b.qmd | 4 +- book/listings/medical-history/mhl01.qmd | 4 +- book/listings/pharmacokinetic/pkcl01.qmd | 4 +- book/listings/pharmacokinetic/pkcl02.qmd | 4 +- book/listings/pharmacokinetic/pkpl01.qmd | 4 +- book/listings/pharmacokinetic/pkpl02.qmd | 4 +- book/listings/pharmacokinetic/pkpl04.qmd | 4 +- book/listings/vital-signs/vsl01.qmd | 4 +- book/tables/ADA/adat01.qmd | 5 ++- book/tables/ADA/adat02.qmd | 4 +- book/tables/ADA/adat03.qmd | 4 +- book/tables/ADA/adat04a.qmd | 5 ++- book/tables/ADA/adat04b.qmd | 5 ++- book/tables/ECG/egt01.qmd | 4 +- book/tables/ECG/egt02.qmd | 7 +++- book/tables/ECG/egt03.qmd | 7 +++- book/tables/ECG/egt04.qmd | 4 +- book/tables/ECG/egt05_qtcat.qmd | 4 +- book/tables/adverse-events/aet01.qmd | 14 ++++--- book/tables/adverse-events/aet01_aesi.qmd | 13 ++++-- book/tables/adverse-events/aet02.qmd | 40 +++++++++++++------ book/tables/adverse-events/aet02_smq.qmd | 7 +++- book/tables/adverse-events/aet03.qmd | 4 +- book/tables/adverse-events/aet04.qmd | 22 ++++++---- book/tables/adverse-events/aet04_pi.qmd | 25 ++++++++---- book/tables/adverse-events/aet05.qmd | 7 +++- book/tables/adverse-events/aet05_all.qmd | 7 +++- book/tables/adverse-events/aet06.qmd | 16 +++++--- book/tables/adverse-events/aet06_smq.qmd | 10 +++-- book/tables/adverse-events/aet07.qmd | 7 +++- book/tables/adverse-events/aet09.qmd | 7 +++- book/tables/adverse-events/aet09_smq.qmd | 7 +++- book/tables/adverse-events/aet10.qmd | 7 +++- book/tables/concomitant-medications/cmt01.qmd | 13 ++++-- .../tables/concomitant-medications/cmt01a.qmd | 13 ++++-- .../tables/concomitant-medications/cmt01b.qmd | 10 +++-- .../concomitant-medications/cmt02_pt.qmd | 4 +- book/tables/deaths/dtht01.qmd | 13 ++++-- book/tables/demography/dmt01.qmd | 16 +++++--- book/tables/disclosures/disclosurest01.qmd | 19 ++++++--- book/tables/disclosures/eudrat01.qmd | 4 +- book/tables/disclosures/eudrat02.qmd | 4 +- book/tables/disposition/dst01.qmd | 10 +++-- book/tables/disposition/pdt01.qmd | 4 +- book/tables/disposition/pdt02.qmd | 4 +- book/tables/efficacy/aovt01.qmd | 4 +- book/tables/efficacy/aovt02.qmd | 4 +- book/tables/efficacy/aovt03.qmd | 4 +- book/tables/efficacy/cfbt01.qmd | 4 +- book/tables/efficacy/cmht01.qmd | 9 +++-- book/tables/efficacy/coxt01.qmd | 13 ++++-- book/tables/efficacy/coxt02.qmd | 7 +++- book/tables/efficacy/dort01.qmd | 13 ++++-- book/tables/efficacy/lgrt02.qmd | 13 ++++-- book/tables/efficacy/mmrmt01.qmd | 4 +- book/tables/efficacy/onct05.qmd | 17 ++++---- book/tables/efficacy/ratet01.qmd | 4 +- book/tables/efficacy/rspt01.qmd | 20 ++++++---- book/tables/efficacy/ttet01.qmd | 19 ++++++--- book/tables/exposure/ext01.qmd | 10 +++-- book/tables/lab-results/lbt01.qmd | 4 +- book/tables/lab-results/lbt02.qmd | 4 +- book/tables/lab-results/lbt03.qmd | 7 +++- book/tables/lab-results/lbt04.qmd | 4 +- book/tables/lab-results/lbt05.qmd | 10 +++-- book/tables/lab-results/lbt06.qmd | 7 +++- book/tables/lab-results/lbt07.qmd | 4 +- book/tables/lab-results/lbt08.qmd | 4 +- book/tables/lab-results/lbt09.qmd | 7 +++- book/tables/lab-results/lbt10.qmd | 7 +++- book/tables/lab-results/lbt10_bl.qmd | 7 +++- book/tables/lab-results/lbt11.qmd | 10 +++-- book/tables/lab-results/lbt11_bl.qmd | 10 +++-- book/tables/lab-results/lbt12.qmd | 4 +- book/tables/lab-results/lbt12_bl.qmd | 4 +- book/tables/lab-results/lbt13.qmd | 16 +++++--- book/tables/lab-results/lbt14.qmd | 16 +++++--- book/tables/lab-results/lbt15.qmd | 7 +++- book/tables/medical-history/mht01.qmd | 13 ++++-- book/tables/pharmacokinetic/pkct01.qmd | 10 +++-- book/tables/pharmacokinetic/pkpt02.qmd | 9 +++-- book/tables/pharmacokinetic/pkpt03.qmd | 11 +++-- book/tables/pharmacokinetic/pkpt04.qmd | 9 +++-- book/tables/pharmacokinetic/pkpt05.qmd | 9 +++-- book/tables/pharmacokinetic/pkpt06.qmd | 9 +++-- book/tables/pharmacokinetic/pkpt07.qmd | 9 +++-- book/tables/pharmacokinetic/pkpt08.qmd | 5 ++- book/tables/pharmacokinetic/pkpt11.qmd | 5 ++- book/tables/risk-management-plan/rmpt01.qmd | 4 +- book/tables/risk-management-plan/rmpt03.qmd | 7 +++- book/tables/risk-management-plan/rmpt04.qmd | 4 +- book/tables/risk-management-plan/rmpt05.qmd | 4 +- book/tables/risk-management-plan/rmpt06.qmd | 13 ++++-- book/tables/safety/enrollment01.qmd | 13 ++++-- book/tables/vital-signs/vst01.qmd | 4 +- book/tables/vital-signs/vst02.qmd | 7 +++- 136 files changed, 775 insertions(+), 413 deletions(-) diff --git a/book/_quarto.yml b/book/_quarto.yml index 84a893b240..1bb7bd4fee 100644 --- a/book/_quarto.yml +++ b/book/_quarto.yml @@ -43,7 +43,7 @@ execute: engine: knitr webr: channel-type: "post-message" - packages: ["tern", "random.cdisc.data", "dplyr"] + packages: ["tern", "scda", "scda.2022", "dplyr"] show-startup-message: false autoload-packages: false @@ -118,4 +118,4 @@ website: profile: group: - [stable, development] - default: stable + default: stable \ No newline at end of file diff --git a/book/graphs/efficacy/fstg01.qmd b/book/graphs/efficacy/fstg01.qmd index 41f14a2707..452eba2681 100644 --- a/book/graphs/efficacy/fstg01.qmd +++ b/book/graphs/efficacy/fstg01.qmd @@ -47,9 +47,7 @@ var_labels(anl_rsp_arms_ab) <- c(anl_labels, is_rsp = "Is Responder") ## {{< fa regular file-lines sm fw >}} Preview - - ```{r plot1, test = list(plot_v1 = "plot"), fig.width = 20, fig.height = 5, opts.label = ifelse(packageVersion("survival") < "3.5-8" || packageVersion("tern") < "0.9.3.9018", "skip_test_strict", "")} df <- extract_rsp_subgroups( variables = list( @@ -69,7 +67,8 @@ plot <- g_forest(tbl = result) plot ``` -`r webr_code_labels <- c("setup", "plot1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot Specifying Class Variables and
Options for the Treatment Variable @@ -78,9 +77,7 @@ plot ## {{< fa regular file-lines sm fw >}} Preview - - ```{r plot2, test = list(plot_v2 = "plot"), fig.width = 20, fig.height = 5, opts.label = ifelse(packageVersion("survival") < "3.5-8" || packageVersion("tern") < "0.9.3.9018", "skip_test_strict", "")} anl_rsp_comb_arms_ac <- anl %>% mutate(is_rsp = AVALC %in% c("CR", "PR")) %>% @@ -118,7 +115,8 @@ plot <- g_forest(tbl = result) plot ``` -`r webr_code_labels <- c("setup", "plot2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot Selecting Columns and
Changing the Alpha Level @@ -127,9 +125,7 @@ plot ## {{< fa regular file-lines sm fw >}} Preview - - ```{r plot3, test = list(plot_v3 = "plot"), fig.width = 10, fig.height = 4, opts.label = ifelse(packageVersion("survival") < "3.5-8" || packageVersion("tern") < "0.9.3.9018", "skip_test_strict", "")} df <- extract_rsp_subgroups( variables = list( @@ -149,7 +145,8 @@ plot <- g_forest(tbl = result) plot ``` -`r webr_code_labels <- c("setup", "plot3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot3")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot with Fixed
Symbol Size @@ -183,7 +180,8 @@ plot <- g_forest( plot ``` -`r webr_code_labels <- c("setup", "plot4")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot4")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot of CR Only, Setting
Values Indicating Response @@ -192,9 +190,7 @@ plot ## {{< fa regular file-lines sm fw >}} Preview - - ```{r plot5, test = list(plot_v5 = "plot"), fig.width = 20, fig.height = 5, opts.label = ifelse(packageVersion("survival") < "3.5-8" || packageVersion("tern") < "0.9.3.9018", "skip_test_strict", "")} anl_cr_arms_ab <- anl %>% mutate(is_rsp = AVALC == "CR") %>% @@ -231,7 +227,8 @@ width <- 20 height <- 5 ``` -`r webr_code_labels <- c("setup", "plot5")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot5")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -306,4 +303,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/graphs/efficacy/fstg02.qmd b/book/graphs/efficacy/fstg02.qmd index 39c89e93fb..5d7af619dd 100644 --- a/book/graphs/efficacy/fstg02.qmd +++ b/book/graphs/efficacy/fstg02.qmd @@ -1,8 +1,6 @@ --- title: FSTG02 subtitle: Subgroup Analysis of Survival Duration -editor_options: - chunk_output_type: console --- ------------------------------------------------------------------------ @@ -61,7 +59,6 @@ anl <- random.cdisc.data::cadtte %>% ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot1, test = list(plot_v1 = "plot"), fig.width = 15, fig.height = 4, opts.label = ifelse(packageVersion("rtables") < "0.6.6.9011", "skip_test_strict", "")} anl1 <- anl @@ -83,7 +80,8 @@ plot <- g_forest(tbl = result) plot ``` -`r webr_code_labels <- c("setup", "plot1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot Specifying Class Variables and
Options for the Treatment Variable @@ -92,7 +90,6 @@ plot ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot2, test = list(plot_v2 = "plot"), fig.width = 15, fig.height = 4, opts.label = ifelse(packageVersion("rtables") < "0.6.6.9011", "skip_test_strict", "")} anl2 <- anl %>% mutate( @@ -125,7 +122,8 @@ plot <- g_forest(tbl = result) plot ``` -`r webr_code_labels <- c("setup", "plot2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot Selecting Columns and
Changing the Alpha Level @@ -134,7 +132,6 @@ plot ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot3, test = list(plot_v3 = "plot"), fig.width = 8, fig.height = 4, opts.label = ifelse(packageVersion("rtables") < "0.6.6.9011", "skip_test_strict", "")} anl3 <- anl @@ -156,7 +153,8 @@ plot <- g_forest(tbl = result) plot ``` -`r webr_code_labels <- c("setup", "plot3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot3")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot with Fixed
Symbol Size @@ -165,7 +163,6 @@ plot ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot4, test = list(plot_v4 = "plot"), fig.width = 15, fig.height = 4, opts.label = ifelse(packageVersion("rtables") < "0.6.6.9011", "skip_test_strict", "")} anl4 <- anl @@ -196,7 +193,8 @@ height <- 4 plot_v3.width <- 8 # nolint: object_name. ``` -`r webr_code_labels <- c("setup", "plot4")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot4")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -280,4 +278,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/graphs/efficacy/kmg01.qmd b/book/graphs/efficacy/kmg01.qmd index 6060f16e50..925cd81322 100644 --- a/book/graphs/efficacy/kmg01.qmd +++ b/book/graphs/efficacy/kmg01.qmd @@ -30,7 +30,6 @@ variables <- list(tte = "AVAL", is_event = "is_event", arm = "ARMCD") ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot1, fig.width = 9, fig.height = 6, test = list(plot_v1 = "plot"), opts.label = "skip_test_strict"} plot <- g_km( df = anl, @@ -42,7 +41,8 @@ plot <- g_km( plot ``` -`r webr_code_labels <- c("setup", "plot1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot of Failures @@ -51,7 +51,6 @@ plot ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot2, fig.width = 9, fig.height = 6, test = list(plot_v2 = "plot"), opts.label = "skip_test_strict"} plot <- g_km( df = anl, @@ -65,7 +64,8 @@ plot <- g_km( plot ``` -`r webr_code_labels <- c("setup", "plot2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot Without
Comparative Statistics @@ -74,7 +74,6 @@ plot ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot3, fig.width = 9, fig.height = 6, test = list(plot_v3 = "plot"), opts.label = "skip_test_strict"} plot <- g_km( df = anl, @@ -85,7 +84,8 @@ plot <- g_km( plot ``` -`r webr_code_labels <- c("setup", "plot3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot3")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot Without
Censoring Marks @@ -94,7 +94,6 @@ plot ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot4, fig.width = 9, fig.height = 6, test = list(plot_v4 = "plot"), opts.label = "skip_test_strict"} plot <- g_km( df = anl, @@ -107,7 +106,8 @@ plot <- g_km( plot ``` -`r webr_code_labels <- c("setup", "plot4")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot4")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot Modifying
Censoring Marks @@ -116,7 +116,6 @@ plot ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot5, fig.width = 9, fig.height = 6, test = list(plot_v5 = "plot"), opts.label = "skip_test_strict"} plot <- g_km( df = anl, @@ -130,7 +129,8 @@ plot <- g_km( plot ``` -`r webr_code_labels <- c("setup", "plot5")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot5")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot Modifying Options for Statistics,
Tie Handling, Stratification, etc. @@ -139,7 +139,6 @@ plot ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot6, fig.width = 9, fig.height = 6, test = list(plot_v6 = "plot"), opts.label = "skip_test_strict"} variables$strata <- c("STRATA1", "STRATA2") plot <- g_km( @@ -158,7 +157,8 @@ plot <- g_km( plot ``` -`r webr_code_labels <- c("setup", "plot6")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot6")` +{{< include ../../_utils/webr.qmd >}} ::: ::: {.content-visible when-profile="development"} @@ -239,4 +239,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/graphs/efficacy/mmrmg01.qmd b/book/graphs/efficacy/mmrmg01.qmd index 04e6792e97..fdca815b70 100644 --- a/book/graphs/efficacy/mmrmg01.qmd +++ b/book/graphs/efficacy/mmrmg01.qmd @@ -46,7 +46,6 @@ mmrm_results <- fit_mmrm( ### Considering the treatment variable in the model - ```{r plot1, dev.args = list(pointsize = 6), test = list(plot_v1 = "plot"), opts.label = "skip_test_strict"} plot <- g_mmrm_lsmeans( mmrm_results, @@ -59,7 +58,6 @@ plot ### Considering the treatment variable in the model, with lines - ```{r plot2, dev.args = list(pointsize = 6), test = list(plot_v2 = "plot"), opts.label = "skip_test_strict"} plot <- g_mmrm_lsmeans( mmrm_results, @@ -73,7 +71,6 @@ plot ### Considering the treatment variable in the model, with statistics table - ```{r plot3, dev.args = list(pointsize = 6), fig.height = 7, test = list(plot_v3 = "plot"), opts.label = "skip_test_strict"} plot <- g_mmrm_lsmeans( mmrm_results, @@ -91,7 +88,6 @@ plot Users can choose to display both estimates and contrasts together by running `g_mmrm_lsmeans(mmrm_results)`. - ```{r plot4, dev.args = list(pointsize = 6), test = list(plot_v4 = "plot"), opts.label = "skip_test_strict"} plot <- g_mmrm_lsmeans( mmrm_results, @@ -180,4 +176,5 @@ shinyApp(app$ui, app$server) ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/graphs/efficacy/mmrmg02.qmd b/book/graphs/efficacy/mmrmg02.qmd index 7c4e1abdd6..ffee055d0d 100644 --- a/book/graphs/efficacy/mmrmg02.qmd +++ b/book/graphs/efficacy/mmrmg02.qmd @@ -137,4 +137,5 @@ height <- 4 {{< include ../../_utils/save_results.qmd >}} {{< include ../../repro.qmd >}} + :::: diff --git a/book/graphs/other/brg01.qmd b/book/graphs/other/brg01.qmd index 384fd6cb4c..df5682f837 100644 --- a/book/graphs/other/brg01.qmd +++ b/book/graphs/other/brg01.qmd @@ -58,7 +58,8 @@ plot <- ggplot(anl, aes(x = .data[["ACTARM"]])) + plot ``` -`r webr_code_labels <- c("setup", "plot1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot of Percentage @@ -88,7 +89,8 @@ plot <- ggplot(anl, aes(x = .data[["ACTARM"]])) + plot ``` -`r webr_code_labels <- c("setup", "plot2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot of Frequency with
Total Number of Subjects @@ -115,7 +117,8 @@ plot <- ggplot(anl, aes(x = .data[["xvarlabel"]])) + plot ``` -`r webr_code_labels <- c("setup", "plot3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot3")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot of Frequency
with Horizontal Bars @@ -138,7 +141,8 @@ plot <- ggplot(anl, aes(x = .data[["ACTARM"]])) + plot ``` -`r webr_code_labels <- c("setup", "plot4")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot4")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot of Percentage
and Confidence Intervals @@ -147,7 +151,6 @@ plot ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot5, test = list(plot_v5 = "plot"), opts.label = "skip_test_strict"} anl <- adlb %>% filter(PARAMCD == "ALT" & ANRIND == "HIGH") @@ -189,7 +192,8 @@ plot <- ggplot(anl) + plot ``` -`r webr_code_labels <- c("setup", "plot5")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot5")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot of Percentage by
Treatment and Covariate @@ -198,7 +202,6 @@ plot ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot6, test = list(plot_v6 = "plot"), opts.label = "skip_test_strict"} anl <- adae %>% filter(AESER == "Y") @@ -222,7 +225,8 @@ plot <- ggplot(anl, aes(x = .data[["ACTARM"]], fill = .data[["SEX"]])) + plot ``` -`r webr_code_labels <- c("setup", "plot6")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot6")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot of Percentage by
Covariate and Treatment @@ -231,7 +235,6 @@ plot ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot7, test = list(plot_v7 = "plot"), opts.label = "skip_test_strict"} anl <- adae %>% filter(AESER == "Y") @@ -254,7 +257,8 @@ plot <- ggplot(anl, aes(x = .data[["SEX"]], fill = .data[["ACTARM"]])) + plot ``` -`r webr_code_labels <- c("setup", "plot7")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot7")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot of Percentage
with Mean and Median @@ -323,7 +327,8 @@ plot <- cowplot::plot_grid(graph, tbl, plot ``` -`r webr_code_labels <- c("setup", "plot8")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot8")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot of Categorical
Variable @@ -332,7 +337,6 @@ plot ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot9, test = list(plot_v9 = "plot"), opts.label = "skip_test_strict"} anl <- adae @@ -360,7 +364,8 @@ plot <- ggplot(anl, aes(x = .data[["ACTARM"]], fill = .data[["AETOXGRC"]])) + plot ``` -`r webr_code_labels <- c("setup", "plot9")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot9")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -374,4 +379,5 @@ plot ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/graphs/other/bwg01.qmd b/book/graphs/other/bwg01.qmd index ea8556ac04..fa1b1ffa61 100644 --- a/book/graphs/other/bwg01.qmd +++ b/book/graphs/other/bwg01.qmd @@ -105,7 +105,8 @@ plot <- bp_annos(bp_1, oc) plot ``` -`r webr_code_labels <- c("setup", "plot1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot Changing
Whiskers @@ -133,7 +134,8 @@ plot <- bp_annos(bp_3, oc) plot ``` -`r webr_code_labels <- c("setup", "plot2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot Adding
Outliers @@ -162,7 +164,8 @@ plot <- bp_annos(bp_4, oc) plot ``` -`r webr_code_labels <- c("setup", "plot3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot3")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot Specifying Marker
for Outliers and
Adding Patient ID @@ -202,7 +205,8 @@ plot <- bp_annos(bp_5, oc) plot ``` -`r webr_code_labels <- c("setup", "plot4")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot4")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot Specifying
Marker for Mean @@ -227,7 +231,8 @@ plot <- bp_annos(bp_6, oc) plot ``` -`r webr_code_labels <- c("setup", "plot5")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot5")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot by Treatment
and Timepoint @@ -236,7 +241,6 @@ plot ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot6, test = list(plot_v6 = "plot"), opts.label = "skip_test_strict"} adsl <- random.cdisc.data::cadsl adlb <- random.cdisc.data::cadlb @@ -271,7 +275,8 @@ plot <- bp_annos(bp_7, oc, 2) plot ``` -`r webr_code_labels <- c("setup", "plot6")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot6")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot by Timepoint
and Treatment @@ -280,7 +285,6 @@ plot ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot7, test = list(plot_v7 = "plot"), opts.label = "skip_test_strict"} bp_8 <- ggplot(adlb_v, aes(x = ARMCD, y = AVAL)) + stat_summary( @@ -309,7 +313,8 @@ plot <- bp_annos(bp_8, oc, 2) plot ``` -`r webr_code_labels <- c("setup", "plot7")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot7")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot with
Table Section @@ -382,7 +387,8 @@ plot <- cowplot::plot_grid(bp_annos(bp_9, oc), tbl_1, plot ``` -`r webr_code_labels <- c("setup", "plot8")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot8")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot with Number of Patients
only in Table Section @@ -408,7 +414,8 @@ plot <- cowplot::plot_grid(bp_annos(bp_9, oc), tbl_2, plot ``` -`r webr_code_labels <- c("setup", "plot8", "plot9")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot8", "plot9")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -520,4 +527,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/graphs/other/cig01.qmd b/book/graphs/other/cig01.qmd index 77aa0b6249..85c9b04665 100644 --- a/book/graphs/other/cig01.qmd +++ b/book/graphs/other/cig01.qmd @@ -30,7 +30,6 @@ adlb <- random.cdisc.data::cadlb %>% The function `stat_mean_ci` from the `tern` package can be used with default values to draw the 95% confidence interval around the mean. - ```{r plot1and2, test = list(plot_v1_and_v2 = "plot"), opts.label = "skip_test_strict"} plot <- ggplot( data = adlb, @@ -59,7 +58,8 @@ plot <- ggplot( plot ``` -`r webr_code_labels <- c("setup", "plot1and2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot1and2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot of Confidence Interval Using
a Different Stratification Variable @@ -68,7 +68,6 @@ plot ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot3, test = list(plot_v3 = "plot"), opts.label = "skip_test_strict"} plot <- ggplot( data = adlb, @@ -97,7 +96,8 @@ plot <- ggplot( plot ``` -`r webr_code_labels <- c("setup", "plot3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot3")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot of Median and
95% CIs for Median @@ -108,7 +108,6 @@ plot The function `stat_median_ci` from the `tern` package works similarly to `stat_mean_ci`. - ```{r plot4, test = list(plot_v4 = "plot"), opts.label = "skip_test_strict"} plot <- ggplot( data = adlb, @@ -137,7 +136,8 @@ plot <- ggplot( plot ``` -`r webr_code_labels <- c("setup", "plot4")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot4")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot of Median and 95% CIs for
Median Using Different Alpha Level @@ -148,7 +148,6 @@ plot To modify the confidence level for the estimation of the confidence interval, the call to `stat_mean_ci` (or `stat_median_ci`) can be slightly modified. - ```{r plot5, test = list(plot_v5 = "plot"), opts.label = "skip_test_strict"} plot <- ggplot( data = adlb, @@ -177,7 +176,8 @@ plot <- ggplot( plot ``` -`r webr_code_labels <- c("setup", "plot5")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot5")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table of Mean
and Median @@ -195,7 +195,8 @@ table <- build_table(lyt = lyt, df = adlb) table ``` -`r webr_code_labels <- c("setup", "table6")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "table6")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -287,4 +288,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/graphs/other/ippg01.qmd b/book/graphs/other/ippg01.qmd index b7e67ce05f..ad5ed720c4 100644 --- a/book/graphs/other/ippg01.qmd +++ b/book/graphs/other/ippg01.qmd @@ -46,7 +46,6 @@ The user can select different `plotting_choices` depending on their preference. To demonstrate, separate plots are produced with a maximum of 3 observations each. - ```{r plots1, test = list(plots_v1 = "plots"), opts.label = "skip_test_strict"} plots <- g_ipp( df = adlb_f, @@ -63,7 +62,8 @@ plots <- g_ipp( plots ``` -`r webr_code_labels <- c("setup", "plots1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plots1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot with Patient Baselines as Reference @@ -75,7 +75,6 @@ Here, patients' individual baseline values will be shown for reference. Note that users can provide their own custom theme to the function via the `ggtheme` argument. - ```{r plots2, test = list(plots_v2 = "plots"), opts.label = "skip_test_strict"} plots <- g_ipp( df = adlb_f, @@ -95,7 +94,8 @@ plots <- g_ipp( plots ``` -`r webr_code_labels <- c("setup", "plots2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plots2")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -180,4 +180,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/graphs/other/ltg01.qmd b/book/graphs/other/ltg01.qmd index 72e7cb139f..0fa0d47fa0 100644 --- a/book/graphs/other/ltg01.qmd +++ b/book/graphs/other/ltg01.qmd @@ -54,7 +54,6 @@ pch <- c( ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot1, test = list(plot_v1 = "plot"), opts.label = "skip_test_strict"} # General mapping and "lattice" ("facet" in ggplot2 nomenclature). g1 <- { @@ -73,7 +72,8 @@ plot <- g1 plot ``` -`r webr_code_labels <- c("setup", "plot1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot1")` +{{< include ../../_utils/webr.qmd >}} ::: #### Modifying Facets @@ -84,7 +84,6 @@ plot The units describing rows of panes and the number of patients under each arm is specified by modifying `facet_grid()`: - ```{r plot2, test = list(plot_v2 = "plot"), opts.label = "skip_test_strict"} # Include the units and the sample size N. g2 <- g1 + facet_grid( @@ -96,7 +95,8 @@ plot <- g2 plot ``` -`r webr_code_labels <- c("setup", "plot1", "plot2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot1", "plot2")` +{{< include ../../_utils/webr.qmd >}} ::: #### Modifying X-Axis @@ -108,7 +108,6 @@ The graphic elements are modified through usual `ggplot2` functions. For instance, the x-axis could be improved as follows: - ```{r plot3, test = list(plot_v3 = "g3"), opts.label = "skip_test_strict"} g3 <- g2 + theme( axis.text.x = element_text(angle = 45, hjust = 1), @@ -119,7 +118,8 @@ plot <- g3 plot ``` -`r webr_code_labels <- c("setup", "plot1", "plot2", "plot3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot1", "plot2", "plot3")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot of Liver Function Tests
Including Mean, Median, and 95% CIs @@ -189,7 +189,8 @@ plot <- g4 plot ``` -`r webr_code_labels <- c("setup", "pre-processing", "plot4")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "pre-processing", "plot4")` +{{< include ../../_utils/webr.qmd >}} ::: #### Adding Mean @@ -198,7 +199,6 @@ plot ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot51, test = list(plot_v51 = "plot"), opts.label = "skip_test_strict"} # Add the mean along with the 95% CI at every visit. g51 <- g4 + stat_summary( @@ -213,7 +213,8 @@ plot <- g51 + guides(linetype = guide_legend(title = NULL)) plot ``` -`r webr_code_labels <- c("setup", "pre-processing", "plot4", "plot51")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "pre-processing", "plot4", "plot51")` +{{< include ../../_utils/webr.qmd >}} ::: #### Adding Median @@ -222,7 +223,6 @@ plot ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot52, test = list(plot_v52 = "plot"), opts.label = "skip_test_strict"} # Instead of a mean, the median could be more relevant. g52 <- g51 + stat_summary( @@ -237,7 +237,8 @@ plot <- g52 + guides(linetype = guide_legend(title = "Aggregate")) plot ``` -`r webr_code_labels <- c("setup", "pre-processing", "plot4", "plot51", "plot52")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "pre-processing", "plot4", "plot51", "plot52")` +{{< include ../../_utils/webr.qmd >}} ::: #### Changing Confidence Level @@ -246,7 +247,6 @@ plot ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot53, test = list(plot_v53 = "plot"), opts.label = "skip_test_strict"} # Change the confidence level of interval for the median. # Note: check `?stat_mean_ci()` and `?stat_median_ci()` for further fine tuning. @@ -262,7 +262,8 @@ plot <- g53 + guides(linetype = guide_legend(title = NULL)) plot ``` -`r webr_code_labels <- c("setup", "pre-processing", "plot4", "plot53")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "pre-processing", "plot4", "plot53")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -276,4 +277,5 @@ plot ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/graphs/other/mng01.qmd b/book/graphs/other/mng01.qmd index 75d498d44c..b461e85a6c 100644 --- a/book/graphs/other/mng01.qmd +++ b/book/graphs/other/mng01.qmd @@ -55,7 +55,6 @@ advs_f <- advs %>% ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot1, test = list(plot_v1 = "plot"), opts.label = "skip_test_strict"} plot <- g_lineplot( df = adlb_f, @@ -65,7 +64,8 @@ plot <- g_lineplot( plot ``` -`r webr_code_labels <- c("setup", "plot1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot of Mean and CIs of Change
from Baseline (Changing the Input
Analysis Data Set and Analysis Variable) @@ -74,7 +74,6 @@ plot ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot2, test = list(plot_v2 = "plot"), opts.label = "skip_test_strict"} plot <- g_lineplot( df = advs_f, @@ -86,7 +85,8 @@ plot <- g_lineplot( plot ``` -`r webr_code_labels <- c("setup", "plot2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot of Mean (+/-SD)
(Changing the Statistics) @@ -95,7 +95,6 @@ plot ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot3, test = list(plot_v3 = "plot"), opts.label = "skip_test_strict"} plot <- g_lineplot( df = adlb_f, @@ -108,7 +107,8 @@ plot <- g_lineplot( plot ``` -`r webr_code_labels <- c("setup", "plot3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot3")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot of Mean and CI
(Modify Alpha Level) @@ -117,7 +117,6 @@ plot ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot4, test = list(plot_v4 = "plot"), opts.label = "skip_test_strict"} plot <- g_lineplot( df = adlb_f, @@ -129,7 +128,8 @@ plot <- g_lineplot( plot ``` -`r webr_code_labels <- c("setup", "plot4")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot4")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot of Mean and CI (with Number
of Patients only in Table Section) @@ -138,7 +138,6 @@ plot ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot5, test = list(plot_v5 = "plot"), opts.label = "skip_test_strict"} plot <- g_lineplot( df = adlb_f, @@ -149,7 +148,8 @@ plot <- g_lineplot( plot ``` -`r webr_code_labels <- c("setup", "plot5")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot5")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot of Mean and CI
(with Table Section) @@ -158,7 +158,6 @@ plot ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot6, fig.height = 8, test = list(plot_v6 = "plot"), opts.label = "skip_test_strict"} plot <- g_lineplot( df = adlb_f, @@ -169,7 +168,8 @@ plot <- g_lineplot( plot ``` -`r webr_code_labels <- c("setup", "plot6")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot6")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot of Median and CI (Visits
Condensed in Table Section) @@ -182,7 +182,6 @@ This option is not supported. ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot7, test = list(plot_v7 = "plot"), opts.label = "skip_test_strict"} plot <- g_lineplot( df = adlb_f, @@ -193,7 +192,8 @@ plot <- g_lineplot( plot ``` -`r webr_code_labels <- c("setup", "plot7")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot7")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -254,4 +254,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/graphs/pharmacokinetic/pkcg01.qmd b/book/graphs/pharmacokinetic/pkcg01.qmd index 9cf75914c0..c8f5294b52 100644 --- a/book/graphs/pharmacokinetic/pkcg01.qmd +++ b/book/graphs/pharmacokinetic/pkcg01.qmd @@ -27,7 +27,6 @@ adpc <- random.cdisc.data::cadpc ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot1, test = list(plot_v1 = "plot"), opts.label = "skip_test_strict"} adpc_a <- adpc %>% filter( @@ -58,7 +57,8 @@ plot <- result[[1]] # only show the first subject plot ``` -`r webr_code_labels <- c("setup", "plot1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot in Log Scale @@ -67,7 +67,6 @@ plot ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot2, test = list(plot_v2 = "plot"), opts.label = "skip_test_strict"} adpc_a <- adpc %>% filter( @@ -99,7 +98,8 @@ plot <- result[[1]] + ggplot2::scale_y_log10(breaks = c(0.001, 0.01, 0.1, 1, 10) plot ``` -`r webr_code_labels <- c("setup", "plot2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot2")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -113,4 +113,5 @@ plot ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/graphs/pharmacokinetic/pkcg02.qmd b/book/graphs/pharmacokinetic/pkcg02.qmd index 169a39c2cc..30376889f7 100644 --- a/book/graphs/pharmacokinetic/pkcg02.qmd +++ b/book/graphs/pharmacokinetic/pkcg02.qmd @@ -27,7 +27,6 @@ adpc <- random.cdisc.data::cadpc ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot1, test = list(plot_v1 = "plot"), opts.label = "skip_test_strict"} adpc_a <- adpc %>% filter( @@ -58,7 +57,8 @@ plot <- g_ipp( plot ``` -`r webr_code_labels <- c("setup", "plot1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot in Log Scale @@ -67,7 +67,6 @@ plot ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot2, test = list(plot_v2 = "plot"), opts.label = "skip_test_strict"} adpc_a <- adpc %>% filter( @@ -100,7 +99,8 @@ plot <- result + ggplot2::scale_y_log10(breaks = c(0.001, 0.01, 0.1, 1, 10), lab plot ``` -`r webr_code_labels <- c("setup", "plot2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot2")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -114,4 +114,5 @@ plot ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/graphs/pharmacokinetic/pkcg03.qmd b/book/graphs/pharmacokinetic/pkcg03.qmd index 241e5ee1de..6303bc2770 100644 --- a/book/graphs/pharmacokinetic/pkcg03.qmd +++ b/book/graphs/pharmacokinetic/pkcg03.qmd @@ -35,7 +35,6 @@ adpc <- random.cdisc.data::cadpc %>% ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot1, test = list(plot_v1 = "plot"), opts.label = "skip_test_strict"} use_title <- "Plot of Mean (+/- SD) Plasma Concentrations Over Time by Treatment, \nPK Evaluable Patients" use_subtitle <- "Analyte:" @@ -67,7 +66,8 @@ plot <- result + theme(plot.caption = element_text(hjust = 0)) plot ``` -`r webr_code_labels <- c("setup", "plot1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot in Log Scale @@ -76,7 +76,6 @@ plot ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot2, warning = FALSE, test = list(plot_v2 = "plot"), opts.label = "skip_test_strict"} use_title <- "Plot of Mean (+/- SD) Log-Scale Plasma Concentrations Over Time by Treatment, \nPK Evaluable Patients" use_subtitle <- "Analyte:" @@ -112,7 +111,8 @@ plot <- result + theme(plot.caption = element_text(hjust = 0)) + plot ``` -`r webr_code_labels <- c("setup", "plot2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot2")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -126,4 +126,5 @@ plot ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/graphs/pharmacokinetic/pkpg01.qmd b/book/graphs/pharmacokinetic/pkpg01.qmd index 9a8701a1e2..c0c1282a9f 100644 --- a/book/graphs/pharmacokinetic/pkpg01.qmd +++ b/book/graphs/pharmacokinetic/pkpg01.qmd @@ -47,7 +47,6 @@ levels(adpp$ARM) <- c( ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot1, test = list(plot_v1 = "plot"), opts.label = "skip_test_strict"} use_title <- "Plot of Mean (+/- SD) Cummulative Percentage (%) of Recovered Drug in Urine \nby Analyte, Visit: PK Evaluable Patients" # nolint: line_length. use_subtitle <- "Analyte: Plasma Drug X \nVisit: CYCLE 1 DAY 1 \nPK Parameter:" @@ -83,7 +82,8 @@ plot <- result + theme(plot.caption = element_text(hjust = 0)) + plot ``` -`r webr_code_labels <- c("setup", "plot1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot with Six Cohorts @@ -95,7 +95,6 @@ In this case we need to process the data further by artificially adding more ran Of course this step is not necessary in the case that data already has more cohorts. - ```{r plot2, test = list(plot_v2 = "plot"), opts.label = "skip_test_strict"} adpp_hck <- adpp %>% mutate(AVAL + 1 * rnorm(nrow(adpp), mean = 1, sd = 1)) %>% @@ -147,7 +146,8 @@ plot <- result + theme(plot.caption = element_text(hjust = 0)) + plot ``` -`r webr_code_labels <- c("setup", "plot2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot2")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -161,4 +161,5 @@ plot ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/graphs/pharmacokinetic/pkpg02.qmd b/book/graphs/pharmacokinetic/pkpg02.qmd index c35db2e924..0b9fc3ca12 100644 --- a/book/graphs/pharmacokinetic/pkpg02.qmd +++ b/book/graphs/pharmacokinetic/pkpg02.qmd @@ -54,7 +54,6 @@ y_var <- "AUCinf" ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot1, test = list(plot_v1 = "plot"), opts.label = "skip_test_strict"} # calculate Summary Statistics (mean and sd) for each group SummaryStat <- adpp_adex %>% # nolint: object_name. @@ -115,7 +114,8 @@ plot <- ggplot(adpp_adex, aes(x = .data[[x_var]], y = .data[[y_var]])) + plot ``` -`r webr_code_labels <- c("setup", "plot1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Summary of Plasma Pharmacokinetic
Parameters with Median Points @@ -124,7 +124,6 @@ plot ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot2, test = list(plot_v2 = "plot"), opts.label = "skip_test_strict"} # calculate median for each group if preferred SummaryStat <- adpp_adex %>% # nolint: object_name. @@ -163,7 +162,8 @@ plot <- ggplot(adpp_adex, aes(x = .data[[x_var]], y = .data[[y_var]])) + plot ``` -`r webr_code_labels <- c("setup", "plot2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot2")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -177,4 +177,5 @@ plot ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/graphs/pharmacokinetic/pkpg03.qmd b/book/graphs/pharmacokinetic/pkpg03.qmd index b5111d0d58..ecaf98cbe7 100644 --- a/book/graphs/pharmacokinetic/pkpg03.qmd +++ b/book/graphs/pharmacokinetic/pkpg03.qmd @@ -27,7 +27,6 @@ adpp <- random.cdisc.data::cadpp ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot1, test = list(plot_v1 = "plot"), opts.label = "skip_test_strict"} # filtered parameter adpp <- adpp %>% filter(PARAMCD == "CMAX", PPSPEC == "Plasma") @@ -64,10 +63,12 @@ plot <- ggplot(adpp, aes(x = AVISIT, y = AVAL, fill = ACTARM)) + plot ``` -`r webr_code_labels <- c("setup", "plot1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot1")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} {{< include ../../repro.qmd >}} + :::: diff --git a/book/graphs/pharmacokinetic/pkpg04.qmd b/book/graphs/pharmacokinetic/pkpg04.qmd index 04a5fd32ef..ace4c1e0a6 100644 --- a/book/graphs/pharmacokinetic/pkpg04.qmd +++ b/book/graphs/pharmacokinetic/pkpg04.qmd @@ -28,7 +28,6 @@ adpp <- random.cdisc.data::cadpp ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot1, test = list(plot_v1 = "plot"), opts.label = "skip_test_strict"} # filtered parameter adpp <- adpp %>% filter(toupper(PARAMCD) == "CMAX" & toupper(PPSPEC) == "PLASMA") @@ -66,10 +65,12 @@ plot <- p + geom_point(aes(fill = ACTARM), size = 2, shape = 21, position = posi plot ``` -`r webr_code_labels <- c("setup", "plot1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot1")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} {{< include ../../repro.qmd >}} + :::: diff --git a/book/graphs/pharmacokinetic/pkpg06.qmd b/book/graphs/pharmacokinetic/pkpg06.qmd index 1ed84590f0..1743df26c6 100644 --- a/book/graphs/pharmacokinetic/pkpg06.qmd +++ b/book/graphs/pharmacokinetic/pkpg06.qmd @@ -67,7 +67,6 @@ outliers <- function(x) { ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot1, test = list(plot_v1 = "plot"), opts.label = "skip_test_strict"} plot <- ggplot(anl_x, aes(x = PARAMCD, y = ratio, fill = ACTARM)) + geom_boxplot(outlier.size = 2) + @@ -108,7 +107,8 @@ plot <- ggplot(anl_x, aes(x = PARAMCD, y = ratio, fill = ACTARM)) + plot ``` -`r webr_code_labels <- c("setup", "plot1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot1")` +{{< include ../../_utils/webr.qmd >}} ::: #### Drug Y Boxplot @@ -117,7 +117,6 @@ plot ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot2, test = list(plot_v2 = "plot"), opts.label = "skip_test_strict"} plot <- ggplot(anl_y, aes(x = PARAMCD, y = ratio, fill = ACTARM)) + geom_boxplot(outlier.size = 2) + @@ -158,7 +157,8 @@ plot <- ggplot(anl_y, aes(x = PARAMCD, y = ratio, fill = ACTARM)) + plot ``` -`r webr_code_labels <- c("setup", "plot2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot with Whiskers at
Minimum and Maximum Values @@ -167,7 +167,6 @@ plot ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot3, test = list(plot_v3 = "plot"), opts.label = "skip_test_strict"} # whiskers are formed with the minimum and maximum values plot <- ggplot(anl_x, aes(x = PARAMCD, y = ratio, fill = ACTARM)) + @@ -194,7 +193,8 @@ plot <- ggplot(anl_x, aes(x = PARAMCD, y = ratio, fill = ACTARM)) + plot ``` -`r webr_code_labels <- c("setup", "plot3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot3")` +{{< include ../../_utils/webr.qmd >}} ::: ## Plot with Whiskers at
5th and 95th Percentiles @@ -203,7 +203,6 @@ plot ## {{< fa regular file-lines sm fw >}} Preview - ```{r plot4, test = list(plot_v4 = "plot"), opts.label = "skip_test_strict"} anl_x_without_outliers <- anl_x %>% dplyr::group_by(PARAMCD, ACTARM) %>% @@ -263,7 +262,8 @@ plot <- ggplot(anl_x, aes(PARAMCD, ratio, fill = ACTARM, label = USUBJID)) + plot ``` -`r webr_code_labels <- c("setup", "plot4")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "plot4")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -277,4 +277,5 @@ plot ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/listings/ADA/adal02.qmd b/book/listings/ADA/adal02.qmd index 85c16189a8..46578f921f 100644 --- a/book/listings/ADA/adal02.qmd +++ b/book/listings/ADA/adal02.qmd @@ -129,10 +129,12 @@ Asterisk denotes sample that tested positive for Neutralizing Antibodies." head(lsting, 20) ``` -`r webr_code_labels <- c("setup", "lsting")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lsting")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} {{< include ../../repro.qmd >}} + :::: diff --git a/book/listings/ECG/egl01.qmd b/book/listings/ECG/egl01.qmd index 0032f10bef..a091274338 100644 --- a/book/listings/ECG/egl01.qmd +++ b/book/listings/ECG/egl01.qmd @@ -96,10 +96,12 @@ lsting <- as_listing( head(lsting, 20) ``` -`r webr_code_labels <- c("setup", "lsting")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lsting")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} {{< include ../../repro.qmd >}} + :::: diff --git a/book/listings/adverse-events/ael01.qmd b/book/listings/adverse-events/ael01.qmd index 0cfbcdb9c1..7d8f661f03 100644 --- a/book/listings/adverse-events/ael01.qmd +++ b/book/listings/adverse-events/ael01.qmd @@ -46,10 +46,12 @@ lsting <- as_listing( head(lsting, 20) ``` -`r webr_code_labels <- c("setup", "lsting")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lsting")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} {{< include ../../repro.qmd >}} + :::: diff --git a/book/listings/adverse-events/ael01_nollt.qmd b/book/listings/adverse-events/ael01_nollt.qmd index 29e793bcaa..e466002412 100644 --- a/book/listings/adverse-events/ael01_nollt.qmd +++ b/book/listings/adverse-events/ael01_nollt.qmd @@ -45,10 +45,12 @@ lsting <- as_listing( head(lsting, 20) ``` -`r webr_code_labels <- c("setup", "lsting")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lsting")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} {{< include ../../repro.qmd >}} + :::: diff --git a/book/listings/adverse-events/ael02.qmd b/book/listings/adverse-events/ael02.qmd index c17153e593..a34a7d928d 100644 --- a/book/listings/adverse-events/ael02.qmd +++ b/book/listings/adverse-events/ael02.qmd @@ -88,10 +88,12 @@ lsting <- as_listing( head(lsting, 20) ``` -`r webr_code_labels <- c("setup", "lsting")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lsting")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} {{< include ../../repro.qmd >}} + :::: diff --git a/book/listings/adverse-events/ael02_ed.qmd b/book/listings/adverse-events/ael02_ed.qmd index 4a385aa002..3d61a04d82 100644 --- a/book/listings/adverse-events/ael02_ed.qmd +++ b/book/listings/adverse-events/ael02_ed.qmd @@ -106,10 +106,12 @@ lsting <- as_listing( head(lsting, 20) ``` -`r webr_code_labels <- c("setup", "lsting")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lsting")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} {{< include ../../repro.qmd >}} + :::: diff --git a/book/listings/adverse-events/ael03.qmd b/book/listings/adverse-events/ael03.qmd index d98911439e..c67586b467 100644 --- a/book/listings/adverse-events/ael03.qmd +++ b/book/listings/adverse-events/ael03.qmd @@ -102,10 +102,12 @@ lsting <- as_listing( head(lsting, 20) ``` -`r webr_code_labels <- c("setup", "lsting")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lsting")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} {{< include ../../repro.qmd >}} + :::: diff --git a/book/listings/adverse-events/ael04.qmd b/book/listings/adverse-events/ael04.qmd index 02a0859a00..5ac3561416 100644 --- a/book/listings/adverse-events/ael04.qmd +++ b/book/listings/adverse-events/ael04.qmd @@ -56,10 +56,12 @@ lsting <- as_listing( head(lsting, 20) ``` -`r webr_code_labels <- c("setup", "lsting")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lsting")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} {{< include ../../repro.qmd >}} + :::: diff --git a/book/listings/concomitant-medications/cml01.qmd b/book/listings/concomitant-medications/cml01.qmd index cbb78dd6d2..884f26e9eb 100644 --- a/book/listings/concomitant-medications/cml01.qmd +++ b/book/listings/concomitant-medications/cml01.qmd @@ -67,10 +67,12 @@ lsting <- as_listing( head(lsting, 20) ``` -`r webr_code_labels <- c("setup", "lsting")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lsting")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} {{< include ../../repro.qmd >}} + :::: diff --git a/book/listings/concomitant-medications/cml02a_gl.qmd b/book/listings/concomitant-medications/cml02a_gl.qmd index c422ccac02..cd0beeb48c 100644 --- a/book/listings/concomitant-medications/cml02a_gl.qmd +++ b/book/listings/concomitant-medications/cml02a_gl.qmd @@ -45,10 +45,12 @@ lsting <- as_listing( head(lsting, 20) ``` -`r webr_code_labels <- c("setup", "lsting")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lsting")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} {{< include ../../repro.qmd >}} + :::: diff --git a/book/listings/concomitant-medications/cml02b_gl.qmd b/book/listings/concomitant-medications/cml02b_gl.qmd index a87a283287..4631107316 100644 --- a/book/listings/concomitant-medications/cml02b_gl.qmd +++ b/book/listings/concomitant-medications/cml02b_gl.qmd @@ -48,10 +48,12 @@ lsting <- as_listing( head(lsting, 20) ``` -`r webr_code_labels <- c("setup", "lsting")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lsting")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} {{< include ../../repro.qmd >}} + :::: diff --git a/book/listings/development-safety-update-report/dsur4.qmd b/book/listings/development-safety-update-report/dsur4.qmd index fe26ec7f42..8b4d72a9cd 100644 --- a/book/listings/development-safety-update-report/dsur4.qmd +++ b/book/listings/development-safety-update-report/dsur4.qmd @@ -47,10 +47,12 @@ lsting <- as_listing( head(lsting, 20) ``` -`r webr_code_labels <- c("setup", "lsting")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lsting")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} {{< include ../../repro.qmd >}} + :::: diff --git a/book/listings/disposition/dsl01.qmd b/book/listings/disposition/dsl01.qmd index c0bf0cbd13..97c325141d 100644 --- a/book/listings/disposition/dsl01.qmd +++ b/book/listings/disposition/dsl01.qmd @@ -55,10 +55,12 @@ lsting <- as_listing( head(lsting, 20) ``` -`r webr_code_labels <- c("setup", "lsting")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lsting")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} {{< include ../../repro.qmd >}} + :::: diff --git a/book/listings/disposition/dsl02.qmd b/book/listings/disposition/dsl02.qmd index cc5794eead..73f625ee1d 100644 --- a/book/listings/disposition/dsl02.qmd +++ b/book/listings/disposition/dsl02.qmd @@ -63,10 +63,12 @@ lsting <- as_listing( head(lsting, 20) ``` -`r webr_code_labels <- c("setup", "lsting")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lsting")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} {{< include ../../repro.qmd >}} + :::: diff --git a/book/listings/efficacy/oncl01.qmd b/book/listings/efficacy/oncl01.qmd index 019506b998..990458e483 100644 --- a/book/listings/efficacy/oncl01.qmd +++ b/book/listings/efficacy/oncl01.qmd @@ -107,10 +107,12 @@ lsting <- as_listing( head(lsting, 20) ``` -`r webr_code_labels <- c("setup", "lsting")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lsting")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} {{< include ../../repro.qmd >}} + :::: diff --git a/book/listings/exposure/exl01.qmd b/book/listings/exposure/exl01.qmd index 49f91cc21b..474b0b9fc3 100644 --- a/book/listings/exposure/exl01.qmd +++ b/book/listings/exposure/exl01.qmd @@ -55,10 +55,12 @@ lsting <- as_listing( head(lsting, 20) ``` -`r webr_code_labels <- c("setup", "lsting")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lsting")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} {{< include ../../repro.qmd >}} + :::: diff --git a/book/listings/lab-results/lbl01.qmd b/book/listings/lab-results/lbl01.qmd index 5dcd383d8c..6520665a6e 100644 --- a/book/listings/lab-results/lbl01.qmd +++ b/book/listings/lab-results/lbl01.qmd @@ -80,10 +80,12 @@ lsting <- as_listing( head(lsting, 20) ``` -`r webr_code_labels <- c("setup", "lsting")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lsting")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} {{< include ../../repro.qmd >}} + :::: diff --git a/book/listings/lab-results/lbl01_rls.qmd b/book/listings/lab-results/lbl01_rls.qmd index 180a9aac98..2c412d8367 100644 --- a/book/listings/lab-results/lbl01_rls.qmd +++ b/book/listings/lab-results/lbl01_rls.qmd @@ -85,10 +85,12 @@ lsting <- as_listing( head(lsting, 20) ``` -`r webr_code_labels <- c("setup", "lsting")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lsting")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} {{< include ../../repro.qmd >}} + :::: diff --git a/book/listings/lab-results/lbl02a.qmd b/book/listings/lab-results/lbl02a.qmd index 81bbacb88d..1e96462acb 100644 --- a/book/listings/lab-results/lbl02a.qmd +++ b/book/listings/lab-results/lbl02a.qmd @@ -80,10 +80,12 @@ lsting <- as_listing( head(lsting, 20) ``` -`r webr_code_labels <- c("setup", "lsting")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lsting")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} {{< include ../../repro.qmd >}} + :::: diff --git a/book/listings/lab-results/lbl02a_rls.qmd b/book/listings/lab-results/lbl02a_rls.qmd index 6c6382a5d2..c163e56bb0 100644 --- a/book/listings/lab-results/lbl02a_rls.qmd +++ b/book/listings/lab-results/lbl02a_rls.qmd @@ -100,10 +100,12 @@ lsting <- as_listing( head(lsting, 20) ``` -`r webr_code_labels <- c("setup", "lsting")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lsting")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} {{< include ../../repro.qmd >}} + :::: diff --git a/book/listings/lab-results/lbl02b.qmd b/book/listings/lab-results/lbl02b.qmd index 52e55b3b39..ad4cf493ed 100644 --- a/book/listings/lab-results/lbl02b.qmd +++ b/book/listings/lab-results/lbl02b.qmd @@ -81,10 +81,12 @@ lsting <- as_listing( head(lsting, 20) ``` -`r webr_code_labels <- c("setup", "lsting")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lsting")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} {{< include ../../repro.qmd >}} + :::: diff --git a/book/listings/medical-history/mhl01.qmd b/book/listings/medical-history/mhl01.qmd index 530e72ae7c..6000330ce0 100644 --- a/book/listings/medical-history/mhl01.qmd +++ b/book/listings/medical-history/mhl01.qmd @@ -59,10 +59,12 @@ lsting <- as_listing( head(lsting, 20) ``` -`r webr_code_labels <- c("setup", "lsting")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lsting")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} {{< include ../../repro.qmd >}} + :::: diff --git a/book/listings/pharmacokinetic/pkcl01.qmd b/book/listings/pharmacokinetic/pkcl01.qmd index af73cfd648..6f0b8f2045 100644 --- a/book/listings/pharmacokinetic/pkcl01.qmd +++ b/book/listings/pharmacokinetic/pkcl01.qmd @@ -55,10 +55,12 @@ lsting <- as_listing( head(lsting, 20) ``` -`r webr_code_labels <- c("setup", "lsting")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lsting")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} {{< include ../../repro.qmd >}} + :::: diff --git a/book/listings/pharmacokinetic/pkcl02.qmd b/book/listings/pharmacokinetic/pkcl02.qmd index cbcfa930cf..93435872d0 100644 --- a/book/listings/pharmacokinetic/pkcl02.qmd +++ b/book/listings/pharmacokinetic/pkcl02.qmd @@ -88,10 +88,12 @@ lsting <- as_listing( head(lsting, 20) ``` -`r webr_code_labels <- c("setup", "lsting")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lsting")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} {{< include ../../repro.qmd >}} + :::: diff --git a/book/listings/pharmacokinetic/pkpl01.qmd b/book/listings/pharmacokinetic/pkpl01.qmd index fd36a09fe0..62e320802d 100644 --- a/book/listings/pharmacokinetic/pkpl01.qmd +++ b/book/listings/pharmacokinetic/pkpl01.qmd @@ -59,10 +59,12 @@ lsting <- as_listing( head(lsting, 20) ``` -`r webr_code_labels <- c("setup", "lsting")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lsting")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} {{< include ../../repro.qmd >}} + :::: diff --git a/book/listings/pharmacokinetic/pkpl02.qmd b/book/listings/pharmacokinetic/pkpl02.qmd index 5bf56661d7..357cd844df 100644 --- a/book/listings/pharmacokinetic/pkpl02.qmd +++ b/book/listings/pharmacokinetic/pkpl02.qmd @@ -60,10 +60,12 @@ lsting <- as_listing( head(lsting, 20) ``` -`r webr_code_labels <- c("setup", "lsting")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lsting")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} {{< include ../../repro.qmd >}} + :::: diff --git a/book/listings/pharmacokinetic/pkpl04.qmd b/book/listings/pharmacokinetic/pkpl04.qmd index 05da58b95b..ec1c8cc84e 100644 --- a/book/listings/pharmacokinetic/pkpl04.qmd +++ b/book/listings/pharmacokinetic/pkpl04.qmd @@ -75,10 +75,12 @@ lsting <- as_listing( head(lsting, 20) ``` -`r webr_code_labels <- c("setup", "lsting")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lsting")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} {{< include ../../repro.qmd >}} + :::: diff --git a/book/listings/vital-signs/vsl01.qmd b/book/listings/vital-signs/vsl01.qmd index 8b3ed7947a..5e2e04086f 100644 --- a/book/listings/vital-signs/vsl01.qmd +++ b/book/listings/vital-signs/vsl01.qmd @@ -129,10 +129,12 @@ lsting <- as_listing( head(lsting, 20) ``` -`r webr_code_labels <- c("setup", "lsting")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lsting")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/ADA/adat01.qmd b/book/tables/ADA/adat01.qmd index a75fc0975a..3dc546483f 100644 --- a/book/tables/ADA/adat01.qmd +++ b/book/tables/ADA/adat01.qmd @@ -133,7 +133,6 @@ adab_pb <- df_explicit_na(adab) %>% ## {{< fa regular file-lines sm fw >}} Preview - ```{r variant1, test = list(result_v1 = "result"), opts.label = ifelse(packageVersion("rtables") < "0.6.6.9011", "skip_test_strict", "")} # Layout for Baseline Prevalence of NAbs lyt_bl <- basic_table(show_colcounts = TRUE) %>% @@ -240,7 +239,8 @@ main_footer(result) <- "ADA = Anti-Drug Antibodies (is also referred to as ATA, result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -254,4 +254,5 @@ result ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/ADA/adat02.qmd b/book/tables/ADA/adat02.qmd index d1496747bc..7a6696876f 100644 --- a/book/tables/ADA/adat02.qmd +++ b/book/tables/ADA/adat02.qmd @@ -139,7 +139,8 @@ main_footer(result) <- paste( result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -153,4 +154,5 @@ result ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/ADA/adat03.qmd b/book/tables/ADA/adat03.qmd index 0b512da583..ef46a4457e 100644 --- a/book/tables/ADA/adat03.qmd +++ b/book/tables/ADA/adat03.qmd @@ -116,7 +116,8 @@ fnotes_at_path(result, rowpath = NULL, colpath = c("multivars", "AVAL_LT")) <- " result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -130,4 +131,5 @@ result ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/ADA/adat04a.qmd b/book/tables/ADA/adat04a.qmd index c953a00669..e68f044831 100644 --- a/book/tables/ADA/adat04a.qmd +++ b/book/tables/ADA/adat04a.qmd @@ -160,7 +160,6 @@ adab_pb <- df_explicit_na(adab) %>% ## {{< fa regular file-lines sm fw >}} Preview - ```{r variant1, test = list(result_v1 = "result"), opts.label = ifelse(packageVersion("rtables") < "0.6.6.9011", "skip_test_strict", "")} # Layout for Baseline Prevalence of NAbs lyt_bl <- basic_table(show_colcounts = TRUE) %>% @@ -266,7 +265,8 @@ Treatment unaffected = A post-baseline evaluable patient with a positive result result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -280,4 +280,5 @@ result ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/ADA/adat04b.qmd b/book/tables/ADA/adat04b.qmd index 57d60aa526..89a6573063 100644 --- a/book/tables/ADA/adat04b.qmd +++ b/book/tables/ADA/adat04b.qmd @@ -140,7 +140,6 @@ adab_pb <- left_join(adab_pb_ada, adab_pb_adap, by = mergecol) %>% ## {{< fa regular file-lines sm fw >}} Preview - ```{r variant1, test = list(result_v1 = "result"), opts.label = ifelse(packageVersion("rtables") < "0.6.6.9011", "skip_test_strict", "")} # Layout for Baseline Prevalence of NAbs lyt_bl <- basic_table(show_colcounts = TRUE) %>% @@ -225,7 +224,8 @@ Number of patients positive for NAb = the number (and percentage) of post-baseli result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -239,4 +239,5 @@ result ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/ECG/egt01.qmd b/book/tables/ECG/egt01.qmd index cebbbd4302..bcb087f16a 100644 --- a/book/tables/ECG/egt01.qmd +++ b/book/tables/ECG/egt01.qmd @@ -81,7 +81,8 @@ result <- build_table(lyt, adeg_f, alt_counts_df = adsl) result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -151,4 +152,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/ECG/egt02.qmd b/book/tables/ECG/egt02.qmd index 4e50ac7e66..e0b2382e62 100644 --- a/book/tables/ECG/egt02.qmd +++ b/book/tables/ECG/egt02.qmd @@ -57,7 +57,8 @@ result <- build_table(lyt = lyt, df = adeg_f, alt_counts_df = adsl) result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## ECG Abnormalities Among Subjects
Without Abnormality at Baseline @@ -83,7 +84,8 @@ result <- build_table(lyt = lyt, df = adeg_f, alt_counts_df = adsl) result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -144,4 +146,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/ECG/egt03.qmd b/book/tables/ECG/egt03.qmd index 4bbead525b..9cdfa1affe 100644 --- a/book/tables/ECG/egt03.qmd +++ b/book/tables/ECG/egt03.qmd @@ -93,7 +93,8 @@ result <- build_table( result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table of Baseline Versus
Maximum Post-Baseline @@ -146,7 +147,8 @@ result <- build_table( result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -220,4 +222,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/ECG/egt04.qmd b/book/tables/ECG/egt04.qmd index c1eb452712..bbd5d49dd9 100644 --- a/book/tables/ECG/egt04.qmd +++ b/book/tables/ECG/egt04.qmd @@ -87,7 +87,8 @@ result <- build_table(lyt, adeg_f) result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -101,4 +102,5 @@ result ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/ECG/egt05_qtcat.qmd b/book/tables/ECG/egt05_qtcat.qmd index f6a3a72c4c..9d41494db0 100644 --- a/book/tables/ECG/egt05_qtcat.qmd +++ b/book/tables/ECG/egt05_qtcat.qmd @@ -105,7 +105,8 @@ result <- build_table(lyt = lyt, df = adeg_f, alt_counts_df = adsl) %>% result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -220,4 +221,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/adverse-events/aet01.qmd b/book/tables/adverse-events/aet01.qmd index 3fdaa13846..0163f3f44a 100644 --- a/book/tables/adverse-events/aet01.qmd +++ b/book/tables/adverse-events/aet01.qmd @@ -80,7 +80,6 @@ adae <- adae %>% ## {{< fa regular file-lines sm fw >}} Preview - ```{r variant1, test = list(result_v1 = "result"), opts.label = ifelse(packageVersion("rtables") < "0.6.6.9011", "skip_test_strict", "")} aesi_vars <- c("FATAL", "SER", "SERWD", "SERDSM", "RELSER", "WD", "DSM", "REL", "RELWD", "RELDSM", "SEV") @@ -137,7 +136,8 @@ result <- rbind( result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with Medical
Concepts Section @@ -210,7 +210,8 @@ result <- rbind( result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with
Modified Rows @@ -278,7 +279,8 @@ result <- rbind( result ``` -`r webr_code_labels <- c("setup", "variant3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant3")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with Rows Counting
Events & Additional Sections @@ -362,7 +364,8 @@ result <- rbind( result ``` -`r webr_code_labels <- c("setup", "variant4")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant4")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -451,4 +454,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/adverse-events/aet01_aesi.qmd b/book/tables/adverse-events/aet01_aesi.qmd index c3e10dee3e..e74a9212ce 100644 --- a/book/tables/adverse-events/aet01_aesi.qmd +++ b/book/tables/adverse-events/aet01_aesi.qmd @@ -169,7 +169,8 @@ result <- build_table(lyt_adae, df = adae, alt_counts_df = adsl) result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with
Optional Lines @@ -241,7 +242,8 @@ result <- build_table(lyt_adae, df = adae, alt_counts_df = adsl) result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table For Studies
with Multiple Drugs @@ -529,7 +531,8 @@ result -`r webr_code_labels <- c("variant3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("variant3")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table of AEs
by SMQ @@ -709,7 +712,8 @@ result <- build_table(lyt_adae, df = adae_smq, alt_counts_df = adsl) result ``` -`r webr_code_labels <- c("setup", "variant4")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant4")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -840,4 +844,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/adverse-events/aet02.qmd b/book/tables/adverse-events/aet02.qmd index e2f5203847..00ee72ecda 100644 --- a/book/tables/adverse-events/aet02.qmd +++ b/book/tables/adverse-events/aet02.qmd @@ -75,7 +75,8 @@ result <- build_table(lyt, df = adae, alt_counts_df = adsl) result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: The variable `result` corresponds to the adverse events table. @@ -100,7 +101,8 @@ result <- result %>% result ``` -`r webr_code_labels <- c("setup", "variant1", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with
Event Totals @@ -159,7 +161,8 @@ result <- build_table(lyt, df = adae, alt_counts_df = adsl) %>% result ``` -`r webr_code_labels <- c("setup", "variant3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant3")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with
High-Level Term @@ -232,7 +235,8 @@ result <- build_table(lyt, df = adae, alt_counts_df = adsl) %>% result ``` -`r webr_code_labels <- c("setup", "variant4")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant4")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with Preferred
Terms Only @@ -264,7 +268,8 @@ result <- build_table(lyt, df = adae, alt_counts_df = adsl) %>% result ``` -`r webr_code_labels <- c("setup", "variant5")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant5")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with Fill-In of
Treatment Groups @@ -318,7 +323,8 @@ result <- build_table(lyt, df = adae_5, alt_counts_df = adsl) %>% result ``` -`r webr_code_labels <- c("setup", "variant6")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant6")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table of AEs with an Incidence Rate
$\geq$ 5% in Any Treatment Group (subsetting
preferred terms based on frequency) @@ -372,7 +378,8 @@ result <- prune_table(result, keep_rows(row_condition)) result ``` -`r webr_code_labels <- c("setup", "variant7")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant7")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table of AEs with an Incidence Rate $\geq$ 5% in
Any Treatment Group (subsetting preferred terms
based on frequency with high-level terms) @@ -442,7 +449,8 @@ result <- prune_table(result, keep_rows(row_condition)) result ``` -`r webr_code_labels <- c("setup", "variant8")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant8")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table of AEs with an Incidence Rate $\geq$ 10%
in Any Treatment Group (subsetting
preferred terms based on frequency) @@ -496,7 +504,8 @@ result <- prune_table(result, keep_rows(row_condition)) result ``` -`r webr_code_labels <- c("setup", "variant9")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant9")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table of AEs with an Incidence Rate $\geq$ 3
Patients in Any Treatment Group (subsetting
preferred terms based on number of patients) @@ -550,7 +559,8 @@ result <- prune_table(result, keep_rows(row_condition)) result ``` -`r webr_code_labels <- c("setup", "variant10")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant10")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table of AEs with a Difference in Incidence Rate $\geq$ 5%
Between Any Treatment (subsetting preferred terms based
on difference in percentage between treatment groups) @@ -604,7 +614,8 @@ result <- prune_table(result, keep_rows(row_condition)) result ``` -`r webr_code_labels <- c("setup", "variant11")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant11")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table of AEs with an Incidence Rate $\geq$ 5%
in B: Placebo (subsetting preferred terms based
on frequency for a particular treatment group) @@ -658,7 +669,8 @@ result <- prune_table(result, keep_rows(row_condition)) result ``` -`r webr_code_labels <- c("setup", "variant12")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant12")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table of AEs with a Difference in Incidence Rate $\geq$ 5% Between
Arm A and Arm B or Arm C (displaying preferred terms with a
difference of at least x% between selected treatment groups) @@ -711,7 +723,8 @@ result <- prune_table(result, keep_rows(row_condition)) result ``` -`r webr_code_labels <- c("setup", "variant13")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant13")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -770,4 +783,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/adverse-events/aet02_smq.qmd b/book/tables/adverse-events/aet02_smq.qmd index 55d897f730..ec543006bb 100644 --- a/book/tables/adverse-events/aet02_smq.qmd +++ b/book/tables/adverse-events/aet02_smq.qmd @@ -119,7 +119,8 @@ result <- build_table( result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with Customized Queries @@ -181,7 +182,8 @@ result <- build_table( result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -249,4 +251,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/adverse-events/aet03.qmd b/book/tables/adverse-events/aet03.qmd index 93cd5dd939..2d73306a7a 100644 --- a/book/tables/adverse-events/aet03.qmd +++ b/book/tables/adverse-events/aet03.qmd @@ -106,7 +106,8 @@ result -`r webr_code_labels <- c("setup", "pre-processing", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "pre-processing", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -163,4 +164,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/adverse-events/aet04.qmd b/book/tables/adverse-events/aet04.qmd index 6b3d43ef2c..7fdc82cf89 100644 --- a/book/tables/adverse-events/aet04.qmd +++ b/book/tables/adverse-events/aet04.qmd @@ -190,7 +190,8 @@ result <- lyt %>% result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with Fill-In
of Treatment Groups @@ -265,7 +266,8 @@ result <- lyt %>% result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with Fill-In
of Grades @@ -337,7 +339,8 @@ result <- lyt %>% result ``` -`r webr_code_labels <- c("setup", "variant3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant3")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with Collapsing
of Grades @@ -415,7 +418,8 @@ result <- lyt %>% result ``` -`r webr_code_labels <- c("setup", "variant4")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant4")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Using Worst Grade
Flags from ADAE @@ -531,7 +535,8 @@ result <- lyt %>% result ``` -`r webr_code_labels <- c("setup", "variant6")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant6")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with an Incidence Rate
$\geq$ X%, Totals Unrestricted @@ -570,7 +575,8 @@ result <- prune_table(raw_table, keep_content_rows(my_row_condition(row_conditio result ``` -`r webr_code_labels <- c("setup", "variant9")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant9")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with an Incidence Rate
$\geq$ 5%, SOCs \< 5% Removed @@ -591,7 +597,8 @@ result <- prune_table(raw_table, keep_content_rows(my_row_condition(row_conditio result ``` -`r webr_code_labels <- c("setup", "variant11")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant11")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -648,4 +655,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/adverse-events/aet04_pi.qmd b/book/tables/adverse-events/aet04_pi.qmd index 7f1e837948..90b3e63924 100644 --- a/book/tables/adverse-events/aet04_pi.qmd +++ b/book/tables/adverse-events/aet04_pi.qmd @@ -99,7 +99,8 @@ result <- full_table %>% result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with Patients Treated with a Particular Treatment by Highest NCI
CTCAE Grade (specifying a treatment for selecting preferred terms) @@ -133,7 +134,8 @@ result <- full_table %>% result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Adverse Events Reported in $\geq$ 5% of Patients by
Highest NCI CTCAE Grade (changing the threshold) @@ -167,7 +169,8 @@ result <- full_table %>% result ``` -`r webr_code_labels <- c("setup", "variant3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant3")` +{{< include ../../_utils/webr.qmd >}} ::: ## Adverse Events Reported in $\geq$ 5% of Patients and
$\geq$ 2% Difference Between Treatments by Highest
NCI CTCAE Grade (using more than one condition) @@ -202,7 +205,8 @@ result <- full_table %>% result ``` -`r webr_code_labels <- c("setup", "variant4")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant4")` +{{< include ../../_utils/webr.qmd >}} ::: ## Adverse Events Reported in $\geq$ 10% of Patients for Any Grade
or $\geq$ 5% of Patients for Grade 3-4 by Highest NCI CTCAE
Grade (using different condition depending on the grade) @@ -238,7 +242,8 @@ result <- full_table %>% result ``` -`r webr_code_labels <- c("setup", "variant5")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant5")` +{{< include ../../_utils/webr.qmd >}} ::: ## Standard Table with
Modified Grade Grouping @@ -302,7 +307,8 @@ result <- full_table %>% result ``` -`r webr_code_labels <- c("setup", "variant6")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant6")` +{{< include ../../_utils/webr.qmd >}} ::: ## Standard Table with
Overlapping Grade Groupings @@ -365,7 +371,8 @@ result <- full_table %>% result ``` -`r webr_code_labels <- c("setup", "variant7")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant7")` +{{< include ../../_utils/webr.qmd >}} ::: ## Standard Table without SOCs @@ -412,7 +419,8 @@ result <- full_table %>% result ``` -`r webr_code_labels <- c("setup", "variant8")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant8")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -476,4 +484,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/adverse-events/aet05.qmd b/book/tables/adverse-events/aet05.qmd index b95fab5394..b7562b561f 100644 --- a/book/tables/adverse-events/aet05.qmd +++ b/book/tables/adverse-events/aet05.qmd @@ -48,7 +48,8 @@ result <- build_table(lyt, anl, alt_counts_df = adsl) result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Setting Type of Confidence Interval @@ -76,7 +77,8 @@ result <- build_table(lyt, anl, alt_counts_df = adsl) result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -145,4 +147,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/adverse-events/aet05_all.qmd b/book/tables/adverse-events/aet05_all.qmd index 52f891cc10..d0f40f851e 100644 --- a/book/tables/adverse-events/aet05_all.qmd +++ b/book/tables/adverse-events/aet05_all.qmd @@ -54,7 +54,8 @@ result <- build_table(lyt, anl, alt_counts_df = adsl) result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Setting Type of Confidence Interval @@ -77,7 +78,8 @@ result <- build_table(lyt, anl, alt_counts_df = adsl) result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -153,4 +155,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/adverse-events/aet06.qmd b/book/tables/adverse-events/aet06.qmd index dd35a93bc9..f0aea4caa1 100644 --- a/book/tables/adverse-events/aet06.qmd +++ b/book/tables/adverse-events/aet06.qmd @@ -126,7 +126,8 @@ result <- build_table( result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Adverse Events by Other Baseline
Characteristics (e.g. Biomarker Group) @@ -186,7 +187,8 @@ result <- build_table( result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Adverse Events by Baseline Characteristic
from ADSUB (e.g. BMI Category) @@ -246,7 +248,8 @@ result <- build_table( result ``` -`r webr_code_labels <- c("setup", "variant3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant3")` +{{< include ../../_utils/webr.qmd >}} ::: ## Adverse Events by Regrouped Baseline
Characteristics (e.g. Race) @@ -307,7 +310,8 @@ result <- build_table( result ``` -`r webr_code_labels <- c("setup", "variant4")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant4")` +{{< include ../../_utils/webr.qmd >}} ::: ## Adverse Events by Baseline Characteristics
(e.g. Sex) Including High-Level Terms @@ -387,7 +391,8 @@ result <- build_table( result ``` -`r webr_code_labels <- c("setup", "variant5")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant5")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -446,4 +451,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/adverse-events/aet06_smq.qmd b/book/tables/adverse-events/aet06_smq.qmd index f827c6fa79..6a06499be2 100644 --- a/book/tables/adverse-events/aet06_smq.qmd +++ b/book/tables/adverse-events/aet06_smq.qmd @@ -141,7 +141,8 @@ result <- build_table( result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Adverse Events by Sex, by SMQ and
Preferred Term (with Customized Queries) @@ -199,7 +200,8 @@ result <- build_table( result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Adverse Events by Other Baseline
Characteristics (e.g. Age Group) @@ -249,7 +251,8 @@ result <- build_table( result ``` -`r webr_code_labels <- c("setup", "variant3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant3")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -340,4 +343,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/adverse-events/aet07.qmd b/book/tables/adverse-events/aet07.qmd index e0e8b7c6fd..4f2f7a9040 100644 --- a/book/tables/adverse-events/aet07.qmd +++ b/book/tables/adverse-events/aet07.qmd @@ -76,7 +76,8 @@ result <- build_table( result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with Fill-In of Treatment Groups without Deaths @@ -113,7 +114,8 @@ result <- build_table( result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -199,4 +201,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/adverse-events/aet09.qmd b/book/tables/adverse-events/aet09.qmd index 0d728db94c..90844025ee 100644 --- a/book/tables/adverse-events/aet09.qmd +++ b/book/tables/adverse-events/aet09.qmd @@ -94,7 +94,8 @@ result <- tbl1 %>% result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Including High-Level Terms @@ -177,7 +178,8 @@ result <- tbl2 %>% result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -237,4 +239,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/adverse-events/aet09_smq.qmd b/book/tables/adverse-events/aet09_smq.qmd index 149dfff305..56cd31a0d9 100644 --- a/book/tables/adverse-events/aet09_smq.qmd +++ b/book/tables/adverse-events/aet09_smq.qmd @@ -123,7 +123,8 @@ result <- build_table( result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with Customized Queries @@ -185,7 +186,8 @@ result <- build_table( result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -259,4 +261,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/adverse-events/aet10.qmd b/book/tables/adverse-events/aet10.qmd index 2ff77b0895..0f8f3ad253 100644 --- a/book/tables/adverse-events/aet10.qmd +++ b/book/tables/adverse-events/aet10.qmd @@ -64,7 +64,8 @@ result <- sort_at_path( result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Most Common ($\geq$ 35%) Adverse Events (setting threshold) @@ -105,7 +106,8 @@ result <- sort_at_path( result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -168,4 +170,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/concomitant-medications/cmt01.qmd b/book/tables/concomitant-medications/cmt01.qmd index 9dc30888da..2107e43848 100644 --- a/book/tables/concomitant-medications/cmt01.qmd +++ b/book/tables/concomitant-medications/cmt01.qmd @@ -89,7 +89,8 @@ result <- build_table( result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Showing Medications Prior
to the Start of the Study @@ -140,7 +141,8 @@ result <- build_table( result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with Subtotal Per
Medication Class Suppressed @@ -187,7 +189,8 @@ result <- build_table( result ``` -`r webr_code_labels <- c("setup", "variant3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant3")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Sorted by Total Column Showing
Additional "All Patients" Column @@ -246,7 +249,8 @@ result <- build_table( result ``` -`r webr_code_labels <- c("setup", "variant4")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant4")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -314,4 +318,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/concomitant-medications/cmt01a.qmd b/book/tables/concomitant-medications/cmt01a.qmd index 759e7c4a31..3bde3747c0 100644 --- a/book/tables/concomitant-medications/cmt01a.qmd +++ b/book/tables/concomitant-medications/cmt01a.qmd @@ -83,7 +83,8 @@ result <- build_table(lyt = lyt, df = adcm, alt_counts_df = adsl) %>% result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Changing
ATC Class Level @@ -136,7 +137,8 @@ result <- build_table(lyt = lyt, df = adcm, alt_counts_df = adsl) %>% result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with Classes
Sorted by Frequency @@ -186,7 +188,8 @@ result <- build_table(lyt = lyt, df = adcm, alt_counts_df = adsl) %>% result ``` -`r webr_code_labels <- c("setup", "variant3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant3")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with Total Number of Treatments
per Medication Class Suppressed @@ -238,7 +241,8 @@ result <- build_table(lyt = lyt, df = adcm, alt_counts_df = adsl) %>% result ``` -`r webr_code_labels <- c("setup", "variant4")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant4")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -305,4 +309,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/concomitant-medications/cmt01b.qmd b/book/tables/concomitant-medications/cmt01b.qmd index e01ca1424d..4aa20e3bfe 100644 --- a/book/tables/concomitant-medications/cmt01b.qmd +++ b/book/tables/concomitant-medications/cmt01b.qmd @@ -110,7 +110,8 @@ result <- build_table( result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Changing
Class Levels @@ -175,7 +176,8 @@ result <- build_table( result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with Classes
Sorted by Frequency @@ -263,7 +265,8 @@ result <- build_table( result ``` -`r webr_code_labels <- c("setup", "variant4")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant4")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -329,4 +332,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/concomitant-medications/cmt02_pt.qmd b/book/tables/concomitant-medications/cmt02_pt.qmd index 6a58faf063..5b71ca787b 100644 --- a/book/tables/concomitant-medications/cmt02_pt.qmd +++ b/book/tables/concomitant-medications/cmt02_pt.qmd @@ -67,7 +67,8 @@ result <- build_table(lyt = lyt, df = adcm, alt_counts_df = adsl) %>% result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -134,4 +135,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/deaths/dtht01.qmd b/book/tables/deaths/dtht01.qmd index 3e5be0b55d..924be2b8d7 100644 --- a/book/tables/deaths/dtht01.qmd +++ b/book/tables/deaths/dtht01.qmd @@ -45,7 +45,8 @@ result <- build_table(lyt, df = adsl) result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Selecting
Sections to Display @@ -89,7 +90,8 @@ result <- build_table(lyt, df = adsl) %>% prune_table() result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table for Studies Collecting Death
Information from Public Records @@ -140,7 +142,8 @@ result <- build_table(lyt, df = adsl) result ``` -`r webr_code_labels <- c("setup", "variant3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant3")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Adding Details for "All other causes"
Category for Studies Collecting Death
Information from Public Records @@ -201,7 +204,8 @@ result <- build_table(lyt, df = adsl) result ``` -`r webr_code_labels <- c("setup", "variant4")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant4")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -215,4 +219,5 @@ result ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/demography/dmt01.qmd b/book/tables/demography/dmt01.qmd index 0ec470d8af..8c436023ff 100644 --- a/book/tables/demography/dmt01.qmd +++ b/book/tables/demography/dmt01.qmd @@ -112,7 +112,8 @@ result <- basic_table(show_colcounts = TRUE) %>% result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with an Additional
Study-Specific Categorical Variable @@ -142,7 +143,8 @@ result <- basic_table(show_colcounts = TRUE) %>% result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with Subgrouping
for Some Analyses @@ -168,7 +170,8 @@ result <- basic_table(show_colcounts = TRUE) %>% result ``` -`r webr_code_labels <- c("setup", "variant3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant3")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with Additional Vital
Signs Baseline Values @@ -194,7 +197,8 @@ result <- basic_table(show_colcounts = TRUE) %>% result ``` -`r webr_code_labels <- c("setup", "variant4")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant4")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with Additional
Values from ADSUB @@ -219,7 +223,8 @@ result <- basic_table(show_colcounts = TRUE) %>% result ``` -`r webr_code_labels <- c("setup", "variant5")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant5")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -271,4 +276,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/disclosures/disclosurest01.qmd b/book/tables/disclosures/disclosurest01.qmd index e1dcb283a3..ab278ef102 100644 --- a/book/tables/disclosures/disclosurest01.qmd +++ b/book/tables/disclosures/disclosurest01.qmd @@ -125,7 +125,8 @@ result <- build_table(lyt = lyt, df = adsl0) result ``` -`r webr_code_labels <- c("setup1", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup1", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Demographic Table
(CTgov & EudraCT) @@ -182,7 +183,8 @@ result <- build_table(lyt = lyt, df = adsl) result ``` -`r webr_code_labels <- c("setup2", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup2", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Enrollment by Country
Table (EudraCT only) @@ -222,7 +224,8 @@ result <- build_table(lyt, adsl) result ``` -`r webr_code_labels <- c("setup3", "variant3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup3", "variant3")` +{{< include ../../_utils/webr.qmd >}} ::: ## Non-Serious Adverse Events
Reported in $\geq$ 5% of Patients in Any
Treatment Group (CTgov & EudraCT) @@ -309,7 +312,8 @@ result <- build_table(lyt, adae_trim) result ``` -`r webr_code_labels <- c("setup4", "variant4")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup4", "variant4")` +{{< include ../../_utils/webr.qmd >}} ::: ## Serious Adverse Events, Fatal SAEs
and SAEs Related to Study Medication,
by Treatment Group (CTgov & EudraCT) @@ -373,7 +377,8 @@ result <- build_table(lyt, adae_serious_arm) result ``` -`r webr_code_labels <- c("setup5", "variant5")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup5", "variant5")` +{{< include ../../_utils/webr.qmd >}} ::: ## Death Table
(EudraCT only) @@ -407,10 +412,12 @@ result <- build_table(lyt, adae, alt_counts_df = adsl) result ``` -`r webr_code_labels <- c("setup6", "variant6")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup6", "variant6")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/disclosures/eudrat01.qmd b/book/tables/disclosures/eudrat01.qmd index e4386a9ee5..7389bca359 100644 --- a/book/tables/disclosures/eudrat01.qmd +++ b/book/tables/disclosures/eudrat01.qmd @@ -92,7 +92,8 @@ result <- build_table(lyt, adae_trim) result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -106,4 +107,5 @@ result ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/disclosures/eudrat02.qmd b/book/tables/disclosures/eudrat02.qmd index 7c90a442f0..fb827a2bb1 100644 --- a/book/tables/disclosures/eudrat02.qmd +++ b/book/tables/disclosures/eudrat02.qmd @@ -69,7 +69,8 @@ result <- build_table(lyt, adae_serious_arm) result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -83,4 +84,5 @@ result ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/disposition/dst01.qmd b/book/tables/disposition/dst01.qmd index 38c17e6646..1d7ede383d 100644 --- a/book/tables/disposition/dst01.qmd +++ b/book/tables/disposition/dst01.qmd @@ -67,7 +67,8 @@ result1 <- build_table(lyt = lyt, df = adsl) result1 ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with Grouping of Reasons @@ -99,7 +100,8 @@ result2 <- prune_table(tbl) # remove rows containing all zeros result2 ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Adding Optional Rows @@ -128,7 +130,8 @@ result3 <- rbind(result2, tbl) result3 ``` -`r webr_code_labels <- c("setup", "variant3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant3")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -201,4 +204,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/disposition/pdt01.qmd b/book/tables/disposition/pdt01.qmd index 6c3207057d..8a979b1551 100644 --- a/book/tables/disposition/pdt01.qmd +++ b/book/tables/disposition/pdt01.qmd @@ -64,7 +64,8 @@ result <- build_table(lyt = lyt, df = addv, alt_counts_df = adsl) %>% result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -123,4 +124,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/disposition/pdt02.qmd b/book/tables/disposition/pdt02.qmd index d322d282f7..6158be2c6b 100644 --- a/book/tables/disposition/pdt02.qmd +++ b/book/tables/disposition/pdt02.qmd @@ -65,7 +65,8 @@ result <- build_table(lyt, addv_pan, alt_counts_df = adsl) result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -79,4 +80,5 @@ result ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/efficacy/aovt01.qmd b/book/tables/efficacy/aovt01.qmd index 2f37c39849..ff38cf4c20 100644 --- a/book/tables/efficacy/aovt01.qmd +++ b/book/tables/efficacy/aovt01.qmd @@ -61,7 +61,8 @@ result <- build_table( result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -141,4 +142,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/efficacy/aovt02.qmd b/book/tables/efficacy/aovt02.qmd index 1ee7513973..af4a12ea32 100644 --- a/book/tables/efficacy/aovt02.qmd +++ b/book/tables/efficacy/aovt02.qmd @@ -68,7 +68,8 @@ result <- build_table( result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -147,4 +148,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/efficacy/aovt03.qmd b/book/tables/efficacy/aovt03.qmd index c22df6e52a..89fe145996 100644 --- a/book/tables/efficacy/aovt03.qmd +++ b/book/tables/efficacy/aovt03.qmd @@ -69,7 +69,8 @@ result <- basic_table(show_colcounts = TRUE) %>% result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -83,4 +84,5 @@ result ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/efficacy/cfbt01.qmd b/book/tables/efficacy/cfbt01.qmd index e63ce35861..9ffc7dc4b8 100644 --- a/book/tables/efficacy/cfbt01.qmd +++ b/book/tables/efficacy/cfbt01.qmd @@ -89,7 +89,8 @@ result <- build_table(lyt, adqs) result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -161,4 +162,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/efficacy/cmht01.qmd b/book/tables/efficacy/cmht01.qmd index 62db974c3b..89d1680c0f 100644 --- a/book/tables/efficacy/cmht01.qmd +++ b/book/tables/efficacy/cmht01.qmd @@ -30,7 +30,6 @@ adqs <- df_explicit_na(adqs) ## {{< fa regular file-lines sm fw >}} Preview - ```{r variant1, test = list(result_v1 = "result"), opts.label = ifelse(packageVersion("survival") < "3.5-8", "skip_test_strict", "")} anl_01 <- adqs %>% filter(PARAMCD == "FKSI-FWB" & AVISIT == "WEEK 1 DAY 8") %>% @@ -78,7 +77,8 @@ result <- build_table( result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table of Multiple Parameters @@ -87,7 +87,6 @@ result ## {{< fa regular file-lines sm fw >}} Preview - ```{r variant2, test = list(result_v2 = "result"), opts.label = ifelse(packageVersion("survival") < "3.5-8", "skip_test_strict", "")} anl_02 <- adqs %>% filter(AVISIT == "WEEK 1 DAY 8") %>% @@ -146,7 +145,8 @@ result <- build_table( result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -207,4 +207,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/efficacy/coxt01.qmd b/book/tables/efficacy/coxt01.qmd index 84809607b0..02e6063cde 100644 --- a/book/tables/efficacy/coxt01.qmd +++ b/book/tables/efficacy/coxt01.qmd @@ -75,7 +75,8 @@ result <- build_table(lyt = lyt, df = anl) result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Cox Regression
with Interaction Term @@ -107,7 +108,8 @@ result <- build_table(lyt = lyt, df = anl) result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Cox Regression
Specifying Covariates @@ -141,7 +143,8 @@ result <- build_table(lyt = lyt, df = anl) result ``` -`r webr_code_labels <- c("setup", "variant3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant3")` +{{< include ../../_utils/webr.qmd >}} ::: ## Cox Regression Setting
Strata, Ties, Alpha Level @@ -181,7 +184,8 @@ result <- build_table(lyt = lyt, df = anl) result ``` -`r webr_code_labels <- c("setup", "variant4")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant4")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -251,4 +255,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/efficacy/coxt02.qmd b/book/tables/efficacy/coxt02.qmd index 592666455f..aa90f00e51 100644 --- a/book/tables/efficacy/coxt02.qmd +++ b/book/tables/efficacy/coxt02.qmd @@ -76,7 +76,8 @@ result <- build_table(lyt = lyt, df = anl) result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Multivariable Cox Regression
with Interaction Term @@ -136,7 +137,8 @@ result <- build_table(lyt = lyt, df = anl) result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Multivariable Cox Regression
with Selection Process for Covariates @@ -205,4 +207,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/efficacy/dort01.qmd b/book/tables/efficacy/dort01.qmd index b6797803da..23ee1b27bc 100644 --- a/book/tables/efficacy/dort01.qmd +++ b/book/tables/efficacy/dort01.qmd @@ -96,7 +96,8 @@ result <- build_table(lyt, df = adtte_f, alt_counts_df = adsl) %>% result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Selecting
Sections to Display @@ -157,7 +158,8 @@ result <- build_table(lyt, df = adtte_f, alt_counts_df = adsl) %>% result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Modifying Analysis Details
like Conf. Type and Alpha Level @@ -218,7 +220,8 @@ result <- build_table(lyt, df = adtte_f, alt_counts_df = adsl) %>% result ``` -`r webr_code_labels <- c("setup", "variant3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant3")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Modifying Time Point for
the "XX Months duration" Analysis @@ -277,7 +280,8 @@ result <- build_table(lyt, df = adtte_f, alt_counts_df = adsl) %>% result ``` -`r webr_code_labels <- c("setup", "variant4")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant4")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -355,4 +359,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/efficacy/lgrt02.qmd b/book/tables/efficacy/lgrt02.qmd index 210866a72f..35a2f03e43 100644 --- a/book/tables/efficacy/lgrt02.qmd +++ b/book/tables/efficacy/lgrt02.qmd @@ -68,7 +68,8 @@ result <- basic_table() %>% result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Multi-Variable Logistic Regression
with Interaction Term @@ -102,7 +103,8 @@ result <- basic_table() %>% result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Multi-Variable Logistic Regression
Specifying Covariates @@ -135,7 +137,8 @@ result <- basic_table() %>% result ``` -`r webr_code_labels <- c("setup", "variant3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant3")` +{{< include ../../_utils/webr.qmd >}} ::: ## Multi-Variable Logistic Regression Setting
an Event, Alpha Level, and Level for Interaction @@ -170,7 +173,8 @@ result <- basic_table() %>% result ``` -`r webr_code_labels <- c("setup", "variant4")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant4")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -240,4 +244,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/efficacy/mmrmt01.qmd b/book/tables/efficacy/mmrmt01.qmd index 0efca49f3c..e60ab4fd5a 100644 --- a/book/tables/efficacy/mmrmt01.qmd +++ b/book/tables/efficacy/mmrmt01.qmd @@ -182,7 +182,6 @@ result #### Considering the treatment variable in the model - ```{r, opts.label = ifelse(packageVersion("rtables") < "0.6.6.9011", "skip_test_strict", "")} as.rtable(mmrm_results, type = "fixed") ``` @@ -190,7 +189,6 @@ as.rtable(mmrm_results, type = "fixed") #### Not considering the treatment variable in the model - ```{r, opts.label = ifelse(packageVersion("rtables") < "0.6.6.9011", "skip_test_strict", "")} as.rtable(mmrm_results_no_arm, type = "fixed") ``` @@ -198,7 +196,6 @@ as.rtable(mmrm_results_no_arm, type = "fixed") ## Covariance Matrix - ```{r, opts.label = ifelse(packageVersion("rtables") < "0.6.6.9011", "skip_test_strict", "")} as.rtable(mmrm_results, type = "cov") ``` @@ -275,4 +272,5 @@ shinyApp(app$ui, app$server) ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/efficacy/onct05.qmd b/book/tables/efficacy/onct05.qmd index b6f2837ee4..2e077cfa85 100644 --- a/book/tables/efficacy/onct05.qmd +++ b/book/tables/efficacy/onct05.qmd @@ -52,7 +52,6 @@ var_labels(anl) <- c(anl_labels, rsp = "Is Response") ## {{< fa regular file-lines sm fw >}} Preview - ```{r variant1, test = list(result_v1 = "result"), opts.label = ifelse(packageVersion("rtables") < "0.6.6.9011", "skip_test_strict", "")} df <- extract_rsp_subgroups( variables = list( @@ -69,7 +68,8 @@ result <- basic_table() %>% result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Specifying
Class Variables @@ -81,7 +81,6 @@ Here, the levels of subgroup variables `SEX` and `STRATA1` are reordered. `STRATA1` is reordered by frequency. - ```{r variant2, test = list(result_v2 = "result"), opts.label = ifelse(packageVersion("rtables") < "0.6.6.9011", "skip_test_strict", "")} anl_reorder <- anl %>% mutate( @@ -100,7 +99,8 @@ result <- basic_table() %>% result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Selecting Columns
and Changing the Alpha Level @@ -109,7 +109,6 @@ result ## {{< fa regular file-lines sm fw >}} Preview - ```{r variant3, test = list(result_v3 = "result"), opts.label = ifelse(packageVersion("rtables") < "0.6.6.9011", "skip_test_strict", "")} df <- extract_rsp_subgroups( variables = list( @@ -128,7 +127,8 @@ result <- basic_table() %>% result ``` -`r webr_code_labels <- c("setup", "variant3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant3")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Setting Values
Indicating Response @@ -139,7 +139,6 @@ result Create a new variable `new_rsp` in `anl` data that uses new criteria for responder. - ```{r variant4, test = list(result_v4 = "result"), opts.label = ifelse(packageVersion("rtables") < "0.6.6.9011", "skip_test_strict", "")} anl_new <- anl %>% mutate(new_rsp = AVALC == "CR") @@ -159,7 +158,8 @@ result <- basic_table() %>% result ``` -`r webr_code_labels <- c("setup", "variant4")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant4")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -237,4 +237,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/efficacy/ratet01.qmd b/book/tables/efficacy/ratet01.qmd index acd8f2b261..e9edddef10 100644 --- a/book/tables/efficacy/ratet01.qmd +++ b/book/tables/efficacy/ratet01.qmd @@ -90,7 +90,8 @@ result <- build_table( result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -104,4 +105,5 @@ result ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/efficacy/rspt01.qmd b/book/tables/efficacy/rspt01.qmd index f462547106..e9d68fc297 100644 --- a/book/tables/efficacy/rspt01.qmd +++ b/book/tables/efficacy/rspt01.qmd @@ -81,7 +81,8 @@ result <- build_table(lyt = lyt_01, df = anl) result ``` -`r webr_code_labels <- c("setup", "pre-processing", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "pre-processing", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Selecting
Sections to Display @@ -115,7 +116,8 @@ result <- build_table(lyt = lyt_02, df = anl) result ``` -`r webr_code_labels <- c("setup", "pre-processing", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "pre-processing", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Modifying Analysis Details like Type of
Confidence Interval, Alpha Level, Test Statistic @@ -164,7 +166,8 @@ result <- build_table(lyt = lyt_03, df = anl) result ``` -`r webr_code_labels <- c("setup", "pre-processing", "variant3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "pre-processing", "variant3")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with
Stratified Analysis @@ -175,7 +178,6 @@ result The stratified analysis section can be added by defining the analyses needed with `control_binary_comparison` for the argument `strat_analysis` and identifying the stratification variables to use. - ```{r variant4, test = list(result_v4 = "result"), opts.label = ifelse(packageVersion("survival") < "3.5-8", "skip_test_strict", "")} strata <- "STRATA1" lyt_04 <- basic_table(show_colcounts = TRUE) %>% @@ -223,7 +225,8 @@ result <- build_table(lyt = lyt_04, df = anl) result ``` -`r webr_code_labels <- c("setup", "pre-processing", "variant4")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "pre-processing", "variant4")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Modifying the Definition
of Overall Response @@ -246,7 +249,8 @@ result <- build_table(lyt = lyt_01, df = anl) result ``` -`r webr_code_labels <- c("setup", "pre-processing", "variant5")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "pre-processing", "variant5")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Defining New
Sections to Display @@ -276,7 +280,8 @@ result <- build_table(lyt = lyt_01, df = anl) result ``` -`r webr_code_labels <- c("setup", "pre-processing", "variant6")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "pre-processing", "variant6")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -355,4 +360,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/efficacy/ttet01.qmd b/book/tables/efficacy/ttet01.qmd index 69ad05a673..1d3b234ce9 100644 --- a/book/tables/efficacy/ttet01.qmd +++ b/book/tables/efficacy/ttet01.qmd @@ -99,7 +99,8 @@ result <- build_table(lyt, df = adtte_f, alt_counts_df = adsl) %>% result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Selecting
Sections to Display @@ -147,7 +148,8 @@ result <- build_table(lyt, df = adtte_f, alt_counts_df = adsl) result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Modifying Analysis Details
like Conf. Type, Ties, Alpha Level @@ -221,7 +223,8 @@ result <- build_table(lyt, df = adtte_f, alt_counts_df = adsl) %>% result ``` -`r webr_code_labels <- c("setup", "variant3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant3")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with
Stratified Analysis @@ -286,7 +289,8 @@ result <- build_table(lyt, df = adtte_f, alt_counts_df = adsl) %>% result ``` -`r webr_code_labels <- c("setup", "variant4")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant4")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Modifying Time Point for
the "XX Months" Analysis @@ -345,7 +349,8 @@ result <- build_table(lyt, df = adtte_f, alt_counts_df = adsl) %>% result ``` -`r webr_code_labels <- c("setup", "variant5")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant5")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Requesting
\> 1 p-value @@ -422,7 +427,8 @@ result <- build_table(lyt, df = adtte_f, alt_counts_df = adsl) %>% result ``` -`r webr_code_labels <- c("setup", "variant6")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant6")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -500,4 +506,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/exposure/ext01.qmd b/book/tables/exposure/ext01.qmd index ae7b41e036..883b0b1074 100644 --- a/book/tables/exposure/ext01.qmd +++ b/book/tables/exposure/ext01.qmd @@ -98,7 +98,8 @@ result <- build_table(lyt = lyt, df = adex, alt_counts_df = adsl) result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with Optional Analyses @@ -151,7 +152,8 @@ result <- build_table(lyt = lyt, df = anl, alt_counts_df = adsl) result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with User-Specified
Categories for Missed Doses @@ -209,7 +211,8 @@ result <- build_table(lyt = lyt, df = anl, alt_counts_df = adsl) result ``` -`r webr_code_labels <- c("setup", "variant3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant3")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -291,4 +294,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/lab-results/lbt01.qmd b/book/tables/lab-results/lbt01.qmd index 787e5748e7..bc5401b18c 100644 --- a/book/tables/lab-results/lbt01.qmd +++ b/book/tables/lab-results/lbt01.qmd @@ -85,7 +85,8 @@ result <- build_table(lyt, adlb_f) result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -155,4 +156,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/lab-results/lbt02.qmd b/book/tables/lab-results/lbt02.qmd index 0ae37d76bf..aa0a1827df 100644 --- a/book/tables/lab-results/lbt02.qmd +++ b/book/tables/lab-results/lbt02.qmd @@ -60,7 +60,8 @@ result <- build_table(l, result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -127,4 +128,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/lab-results/lbt03.qmd b/book/tables/lab-results/lbt03.qmd index 5944f3d80a..53dd01b912 100644 --- a/book/tables/lab-results/lbt03.qmd +++ b/book/tables/lab-results/lbt03.qmd @@ -71,7 +71,8 @@ result <- build_table( result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: In the final step, a new variable is derived from `AVISIT` that can specify the method of estimation of the evaluated change. @@ -114,7 +115,8 @@ result <- build_table( result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -205,4 +207,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/lab-results/lbt04.qmd b/book/tables/lab-results/lbt04.qmd index 1b35a2e659..3ced64cfb0 100644 --- a/book/tables/lab-results/lbt04.qmd +++ b/book/tables/lab-results/lbt04.qmd @@ -56,7 +56,8 @@ result <- build_table(lyt = lyt, df = adlb_f, alt_counts_df = adsl) result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -118,4 +119,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/lab-results/lbt05.qmd b/book/tables/lab-results/lbt05.qmd index 975cd59b18..08cb7a7a28 100644 --- a/book/tables/lab-results/lbt05.qmd +++ b/book/tables/lab-results/lbt05.qmd @@ -108,7 +108,8 @@ result <- prune_table(result, keep_rows(has_lbl("Any Abnormality"))) result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Showing
All Categories @@ -137,7 +138,8 @@ result <- build_table(lyt, df = adlb_f, alt_counts_df = adsl) result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with
Study-Specific
MLAs @@ -182,10 +184,12 @@ result # this is an a posteriori approach, though. ``` -`r webr_code_labels <- c("setup", "variant4")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant4")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/lab-results/lbt06.qmd b/book/tables/lab-results/lbt06.qmd index 778ce04dcc..d8e8da9fd4 100644 --- a/book/tables/lab-results/lbt06.qmd +++ b/book/tables/lab-results/lbt06.qmd @@ -64,7 +64,8 @@ result <- build_table( result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Standard Table for
Multiple Lab Tests @@ -98,7 +99,8 @@ result <- build_table( result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -112,4 +114,5 @@ result ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/lab-results/lbt07.qmd b/book/tables/lab-results/lbt07.qmd index 1df655535c..13181ed552 100644 --- a/book/tables/lab-results/lbt07.qmd +++ b/book/tables/lab-results/lbt07.qmd @@ -105,7 +105,8 @@ result <- result %>% prune_table() result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -168,4 +169,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/lab-results/lbt08.qmd b/book/tables/lab-results/lbt08.qmd index e9d33e6c09..9c7879bb9f 100644 --- a/book/tables/lab-results/lbt08.qmd +++ b/book/tables/lab-results/lbt08.qmd @@ -71,7 +71,8 @@ result <- basic_table(show_colcounts = TRUE) %>% result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -85,4 +86,5 @@ result ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/lab-results/lbt09.qmd b/book/tables/lab-results/lbt09.qmd index 7c9da24af0..43ed28277b 100644 --- a/book/tables/lab-results/lbt09.qmd +++ b/book/tables/lab-results/lbt09.qmd @@ -132,7 +132,8 @@ result <- result %>% trim_rows(criteria = criteria_fun) result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Selecting Sections @@ -172,7 +173,8 @@ result <- result %>% trim_rows(criteria = criteria_fun) result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -186,4 +188,5 @@ result ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/lab-results/lbt10.qmd b/book/tables/lab-results/lbt10.qmd index b810024045..b0ff0d4b8d 100644 --- a/book/tables/lab-results/lbt10.qmd +++ b/book/tables/lab-results/lbt10.qmd @@ -67,7 +67,8 @@ result <- tbl %>% trim_rows(criteria = criteria_fun) result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Selecting Sections @@ -97,7 +98,8 @@ result <- tbl2 %>% trim_rows(criteria = criteria_fun) result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -111,4 +113,5 @@ result ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/lab-results/lbt10_bl.qmd b/book/tables/lab-results/lbt10_bl.qmd index bb531c0ca2..5ea93fdc62 100644 --- a/book/tables/lab-results/lbt10_bl.qmd +++ b/book/tables/lab-results/lbt10_bl.qmd @@ -67,7 +67,8 @@ result <- tbl %>% trim_rows(criteria = criteria_fun) result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Selecting Sections @@ -97,7 +98,8 @@ result <- tbl2 %>% trim_rows(criteria = criteria_fun) result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -111,4 +113,5 @@ result ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/lab-results/lbt11.qmd b/book/tables/lab-results/lbt11.qmd index d074e5319b..89b371fde5 100644 --- a/book/tables/lab-results/lbt11.qmd +++ b/book/tables/lab-results/lbt11.qmd @@ -82,7 +82,8 @@ result <- build_table(lyt, df = anl, alt_counts_df = adsl_safl) result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Time-To-Event Summary
Selecting Sections to Display @@ -105,7 +106,8 @@ result <- build_table(lyt, df = anl, alt_counts_df = adsl_safl) result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Time-To-Event Summary
with Stratified Analysis @@ -144,7 +146,8 @@ result <- build_table(lyt, df = anl, alt_counts_df = adsl_safl) result ``` -`r webr_code_labels <- c("setup", "variant3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant3")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -223,4 +226,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/lab-results/lbt11_bl.qmd b/book/tables/lab-results/lbt11_bl.qmd index e528271083..b1f8feba3a 100644 --- a/book/tables/lab-results/lbt11_bl.qmd +++ b/book/tables/lab-results/lbt11_bl.qmd @@ -82,7 +82,8 @@ result <- build_table(lyt, df = anl, alt_counts_df = adsl_safl) result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Time-To-Event Summary
Selecting Sections to Display @@ -105,7 +106,8 @@ result <- build_table(lyt, df = anl, alt_counts_df = adsl_safl) result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Time-To-Event Summary
with Stratified Analysis @@ -144,7 +146,8 @@ result <- build_table(lyt, df = anl, alt_counts_df = adsl_safl) result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -223,4 +226,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/lab-results/lbt12.qmd b/book/tables/lab-results/lbt12.qmd index 77a4fcf589..a866393f3d 100644 --- a/book/tables/lab-results/lbt12.qmd +++ b/book/tables/lab-results/lbt12.qmd @@ -72,7 +72,8 @@ result <- result %>% trim_rows(criteria = criteria_fun) result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -86,4 +87,5 @@ result ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/lab-results/lbt12_bl.qmd b/book/tables/lab-results/lbt12_bl.qmd index c0265e02a4..d22d6bb67a 100644 --- a/book/tables/lab-results/lbt12_bl.qmd +++ b/book/tables/lab-results/lbt12_bl.qmd @@ -72,7 +72,8 @@ result <- result %>% trim_rows(criteria = criteria_fun) result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -86,4 +87,5 @@ result ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/lab-results/lbt13.qmd b/book/tables/lab-results/lbt13.qmd index a25d1020ad..ebc0325c89 100644 --- a/book/tables/lab-results/lbt13.qmd +++ b/book/tables/lab-results/lbt13.qmd @@ -112,7 +112,8 @@ result <- basic_table(show_colcounts = TRUE) %>% result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Standard Table (High) @@ -194,7 +195,8 @@ result <- basic_table(show_colcounts = TRUE) %>% result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Without Patients with
Missing Baseline (Low) @@ -275,7 +277,8 @@ result <- basic_table(show_colcounts = TRUE) %>% result ``` -`r webr_code_labels <- c("setup", "variant3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant3")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with Missing Baseline
Considered as Grade 0 (High) @@ -355,7 +358,8 @@ result <- basic_table(show_colcounts = TRUE) %>% result ``` -`r webr_code_labels <- c("setup", "variant4")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant4")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with Fill-In
of Grades (High) @@ -438,7 +442,8 @@ result <- basic_table(show_colcounts = TRUE) %>% result ``` -`r webr_code_labels <- c("setup", "variant5")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant5")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -511,4 +516,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/lab-results/lbt14.qmd b/book/tables/lab-results/lbt14.qmd index 2a64519b15..0accd9f0d0 100644 --- a/book/tables/lab-results/lbt14.qmd +++ b/book/tables/lab-results/lbt14.qmd @@ -93,7 +93,8 @@ result <- basic_table(show_colcounts = TRUE) %>% result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Standard Table (Low) @@ -156,7 +157,8 @@ result <- basic_table(show_colcounts = TRUE) %>% result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Without Patients with
Missing Baseline (High) @@ -218,7 +220,8 @@ result <- basic_table(show_colcounts = TRUE) %>% result ``` -`r webr_code_labels <- c("setup", "variant3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant3")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with Missing Baseline
Considered as Grade 0 (Low) @@ -279,7 +282,8 @@ result <- basic_table(show_colcounts = TRUE) %>% result ``` -`r webr_code_labels <- c("setup", "variant4")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant4")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with Fill-In of Grades @@ -340,7 +344,8 @@ result <- basic_table(show_colcounts = TRUE) %>% result ``` -`r webr_code_labels <- c("setup", "variant5")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant5")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -413,4 +418,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/lab-results/lbt15.qmd b/book/tables/lab-results/lbt15.qmd index dcb476f0eb..8f8e649711 100644 --- a/book/tables/lab-results/lbt15.qmd +++ b/book/tables/lab-results/lbt15.qmd @@ -100,7 +100,8 @@ result <- build_table(lyt, adlb, alt_counts_df = adsl) result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Modifying Cut Point @@ -113,7 +114,8 @@ result <- build_table(lyt, adlb_alt_cut, alt_counts_df = adsl) result ``` -`r webr_code_labels <- c("setup", "variant1", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -198,4 +200,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/medical-history/mht01.qmd b/book/tables/medical-history/mht01.qmd index f0e4527028..9710a95a41 100644 --- a/book/tables/medical-history/mht01.qmd +++ b/book/tables/medical-history/mht01.qmd @@ -71,7 +71,8 @@ result <- build_table(lyt, admh_f, alt_counts_df = adsl_f) %>% result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table of History
Prior to Study @@ -89,7 +90,8 @@ result <- build_table(lyt, admh_f_prior, alt_counts_df = adsl_f) %>% result ``` -`r webr_code_labels <- c("setup", "variant1", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with Total Number
of Conditions Suppressed @@ -128,7 +130,8 @@ result <- build_table(lyt, admh_f, alt_counts_df = adsl) %>% result ``` -`r webr_code_labels <- c("setup", "variant3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant3")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with Total Number of Conditions Per Body
System After The Summary of Patients @@ -180,7 +183,8 @@ result <- build_table(lyt, admh_f, alt_counts_df = adsl_f) %>% result ``` -`r webr_code_labels <- c("setup", "variant4")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant4")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -239,4 +243,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/pharmacokinetic/pkct01.qmd b/book/tables/pharmacokinetic/pkct01.qmd index d44f92f6a7..a7009bbc5b 100644 --- a/book/tables/pharmacokinetic/pkct01.qmd +++ b/book/tables/pharmacokinetic/pkct01.qmd @@ -95,7 +95,8 @@ main_footer(result) <- "NE: Not Estimable" result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Implementing 1/3 Imputation Rule @@ -134,7 +135,8 @@ main_footer(result) <- c("NE: Not Estimable", "ND: Not Derived") result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Implementing 1/2 Imputation Rule @@ -173,7 +175,8 @@ main_footer(result) <- "ND: Not Derived" result ``` -`r webr_code_labels <- c("setup", "variant3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant3")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -187,4 +190,5 @@ result ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/pharmacokinetic/pkpt02.qmd b/book/tables/pharmacokinetic/pkpt02.qmd index 67dfb66bc0..fbc6be681d 100644 --- a/book/tables/pharmacokinetic/pkpt02.qmd +++ b/book/tables/pharmacokinetic/pkpt02.qmd @@ -56,7 +56,6 @@ lyt <- basic_table() %>% ## {{< fa regular file-lines sm fw >}} Preview - ```{r variant1, test = list(result_v1 = "result"), opts.label = ifelse(packageVersion("tern") < "0.9.3.9020", "skip_test_strict", "")} adpp0 <- adpp %>% filter(PPCAT == "Plasma Drug X") %>% @@ -70,7 +69,8 @@ subtitles(result) <- paste("Analyte:", unique(adpp0$PPCAT), "\nVisit:", unique(a result ``` -`r webr_code_labels <- c("setup", "lyt", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lyt", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: #### Plasma Drug Y @@ -79,7 +79,6 @@ result ## {{< fa regular file-lines sm fw >}} Preview - ```{r variant2, test = list(result_v2 = "result"), opts.label = ifelse(packageVersion("tern") < "0.9.3.9020", "skip_test_strict", "")} adpp1 <- adpp %>% filter(PPCAT == "Plasma Drug Y") %>% @@ -93,7 +92,8 @@ subtitles(result) <- paste("Analyte:", unique(adpp1$PPCAT), "\nVisit:", unique(a result ``` -`r webr_code_labels <- c("setup", "lyt", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lyt", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -107,4 +107,5 @@ result ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/pharmacokinetic/pkpt03.qmd b/book/tables/pharmacokinetic/pkpt03.qmd index 3f8752d433..42c4168a8b 100644 --- a/book/tables/pharmacokinetic/pkpt03.qmd +++ b/book/tables/pharmacokinetic/pkpt03.qmd @@ -11,7 +11,6 @@ subtitle: Pharmacokinetic Parameter Summary of Plasma by Treatment (Stats in Col ## Data Setup - ```{r setup, message = FALSE, opts.label = ifelse(packageVersion("tern") < "0.9.3.9020", "skip_test_strict", "")} #| code-fold: show @@ -142,7 +141,8 @@ result <- paginate_table(result, landscape = TRUE) result ``` -`r webr_code_labels <- c("setup", "lyt", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lyt", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: #### Plasma Drug X: Remove Rows with 0s @@ -160,7 +160,8 @@ result <- paginate_table(result, landscape = TRUE) result ``` -`r webr_code_labels <- c("setup", "lyt", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lyt", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: #### Plasma Drug Y @@ -176,7 +177,8 @@ result <- paginate_table(result, landscape = TRUE) result ``` -`r webr_code_labels <- c("setup", "lyt", "variant3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lyt", "variant3")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -190,4 +192,5 @@ result ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/pharmacokinetic/pkpt04.qmd b/book/tables/pharmacokinetic/pkpt04.qmd index 16b134cc0f..32657c0b22 100644 --- a/book/tables/pharmacokinetic/pkpt04.qmd +++ b/book/tables/pharmacokinetic/pkpt04.qmd @@ -56,7 +56,6 @@ lyt <- basic_table() %>% ## {{< fa regular file-lines sm fw >}} Preview - ```{r variant1, test = list(result_v1 = "result"), opts.label = ifelse(packageVersion("tern") < "0.9.3.9020", "skip_test_strict", "")} adpp0 <- adpp %>% filter(PPCAT == "Plasma Drug X") %>% @@ -70,7 +69,8 @@ subtitles(result) <- paste("Analyte:", unique(adpp0$PPCAT), "\nVisit:", unique(a result ``` -`r webr_code_labels <- c("setup", "lyt", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lyt", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: #### Plasma Drug Y @@ -79,7 +79,6 @@ result ## {{< fa regular file-lines sm fw >}} Preview - ```{r variant2, test = list(result_v2 = "result"), opts.label = ifelse(packageVersion("tern") < "0.9.3.9020", "skip_test_strict", "")} adpp1 <- adpp %>% filter(PPCAT == "Plasma Drug Y") %>% @@ -93,7 +92,8 @@ subtitles(result) <- paste("Analyte:", unique(adpp1$PPCAT), "\nVisit:", unique(a result ``` -`r webr_code_labels <- c("setup", "lyt", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lyt", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -107,4 +107,5 @@ result ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/pharmacokinetic/pkpt05.qmd b/book/tables/pharmacokinetic/pkpt05.qmd index d5e28d4721..5a7c558ec7 100644 --- a/book/tables/pharmacokinetic/pkpt05.qmd +++ b/book/tables/pharmacokinetic/pkpt05.qmd @@ -75,7 +75,6 @@ lyt <- basic_table() %>% ## {{< fa regular file-lines sm fw >}} Preview - ```{r variant1, test = list(result_v1 = "result"), opts.label = ifelse(packageVersion("tern") < "0.9.3.9020", "skip_test_strict", "")} adpp0 <- adpp %>% filter(PPCAT == "Plasma Drug X") %>% @@ -89,7 +88,8 @@ subtitles(result) <- paste("Analyte:", unique(adpp0$PPCAT), "\nVisit:", unique(a result ``` -`r webr_code_labels <- c("setup", "lyt", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lyt", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: #### Plasma Drug Y @@ -98,7 +98,6 @@ result ## {{< fa regular file-lines sm fw >}} Preview - ```{r variant2, test = list(result_v2 = "result"), opts.label = ifelse(packageVersion("tern") < "0.9.3.9020", "skip_test_strict", "")} adpp1 <- adpp %>% filter(PPCAT == "Plasma Drug Y") %>% @@ -112,7 +111,8 @@ subtitles(result) <- paste("Analyte:", unique(adpp1$PPCAT), "\nVisit:", unique(a result ``` -`r webr_code_labels <- c("setup", "lyt", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lyt", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -126,4 +126,5 @@ result ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/pharmacokinetic/pkpt06.qmd b/book/tables/pharmacokinetic/pkpt06.qmd index 5f7ae9553e..63ea19583b 100644 --- a/book/tables/pharmacokinetic/pkpt06.qmd +++ b/book/tables/pharmacokinetic/pkpt06.qmd @@ -58,7 +58,6 @@ lyt <- basic_table() %>% ## {{< fa regular file-lines sm fw >}} Preview - ```{r variant1, test = list(result_v1 = "result"), opts.label = ifelse(packageVersion("tern") < "0.9.3.9020", "skip_test_strict", "")} adpp0 <- adpp %>% filter(PPCAT == "Plasma Drug X") %>% @@ -72,7 +71,8 @@ subtitles(result) <- paste("Analyte:", unique(adpp0$PPCAT), "\nVisit:", unique(a result ``` -`r webr_code_labels <- c("setup", "lyt", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lyt", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: #### Plasma Drug Y @@ -81,7 +81,6 @@ result ## {{< fa regular file-lines sm fw >}} Preview - ```{r variant2, test = list(result_v2 = "result"), opts.label = ifelse(packageVersion("tern") < "0.9.3.9020", "skip_test_strict", "")} adpp1 <- adpp %>% filter(PPCAT == "Plasma Drug Y") %>% @@ -95,7 +94,8 @@ subtitles(result) <- paste("Analyte:", unique(adpp1$PPCAT), "\nVisit:", unique(a result ``` -`r webr_code_labels <- c("setup", "lyt", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lyt", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -109,4 +109,5 @@ result ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/pharmacokinetic/pkpt07.qmd b/book/tables/pharmacokinetic/pkpt07.qmd index baee4abdce..a4076dc049 100644 --- a/book/tables/pharmacokinetic/pkpt07.qmd +++ b/book/tables/pharmacokinetic/pkpt07.qmd @@ -77,7 +77,6 @@ lyt <- basic_table() %>% ## {{< fa regular file-lines sm fw >}} Preview - ```{r variant1, test = list(result_v1 = "result"), opts.label = ifelse(packageVersion("tern") < "0.9.3.9020", "skip_test_strict", "")} adpp0 <- adpp %>% filter(PPCAT == "Plasma Drug X") %>% @@ -91,7 +90,8 @@ subtitles(result) <- paste("Analyte:", unique(adpp0$PPCAT), "\nVisit:", unique(a result ``` -`r webr_code_labels <- c("setup", "lyt", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lyt", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: #### Plasma Drug Y @@ -100,7 +100,6 @@ result ## {{< fa regular file-lines sm fw >}} Preview - ```{r variant2, test = list(result_v2 = "result"), opts.label = ifelse(packageVersion("tern") < "0.9.3.9020", "skip_test_strict", "")} adpp1 <- adpp %>% filter(PPCAT == "Plasma Drug Y") %>% @@ -114,7 +113,8 @@ subtitles(result) <- paste("Analyte:", unique(adpp1$PPCAT), "\nVisit:", unique(a result ``` -`r webr_code_labels <- c("setup", "lyt", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "lyt", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -128,4 +128,5 @@ result ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/pharmacokinetic/pkpt08.qmd b/book/tables/pharmacokinetic/pkpt08.qmd index 5ddf07c88a..5d0dcd0fbe 100644 --- a/book/tables/pharmacokinetic/pkpt08.qmd +++ b/book/tables/pharmacokinetic/pkpt08.qmd @@ -29,7 +29,6 @@ adpp <- adpp %>% ## {{< fa regular file-lines sm fw >}} Preview - ```{r variant1, test = list(result_v1 = "result"), opts.label = ifelse(packageVersion("tern") < "0.9.3.9020", "skip_test_strict", "")} # create layout lyt <- basic_table() %>% @@ -89,7 +88,8 @@ subtitles(result) <- paste("Analyte:", unique(adpp0$PPCAT), "\nVisit:", unique(a cat(rtables::toString(result, indent_size = 10)) ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -103,4 +103,5 @@ cat(rtables::toString(result, indent_size = 10)) ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/pharmacokinetic/pkpt11.qmd b/book/tables/pharmacokinetic/pkpt11.qmd index 39ce5d8ba3..3b01076de1 100644 --- a/book/tables/pharmacokinetic/pkpt11.qmd +++ b/book/tables/pharmacokinetic/pkpt11.qmd @@ -11,7 +11,6 @@ subtitle: Pharmacokinetic Parameter Estimated Ratios of Geometric Means and 90% ## Data Setup - ```{r setup, message = FALSE, opts.label = ifelse(packageVersion("tern") < "0.9.3.9020", "skip_test_strict", "")} #| code-fold: show @@ -162,7 +161,8 @@ subtitles(result) <- paste("Analyte:", unique(adpp0$PPCAT)) result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -176,4 +176,5 @@ result ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/risk-management-plan/rmpt01.qmd b/book/tables/risk-management-plan/rmpt01.qmd index 036eaab154..b72be95051 100644 --- a/book/tables/risk-management-plan/rmpt01.qmd +++ b/book/tables/risk-management-plan/rmpt01.qmd @@ -80,7 +80,8 @@ result <- build_table(lyt, df = anl, alt_counts_df = adsl_f) result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -168,4 +169,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/risk-management-plan/rmpt03.qmd b/book/tables/risk-management-plan/rmpt03.qmd index 9a5a3168fe..eae5ba8f06 100644 --- a/book/tables/risk-management-plan/rmpt03.qmd +++ b/book/tables/risk-management-plan/rmpt03.qmd @@ -89,7 +89,8 @@ result <- build_table(lyt, df = anl, alt_counts_df = adsl_f) result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Excluding Empty Age Groups @@ -119,7 +120,8 @@ result <- build_table(lyt, df = anl, alt_counts_df = adsl_f) %>% result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -220,4 +222,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/risk-management-plan/rmpt04.qmd b/book/tables/risk-management-plan/rmpt04.qmd index bbada4b9ce..0ef9ab109f 100644 --- a/book/tables/risk-management-plan/rmpt04.qmd +++ b/book/tables/risk-management-plan/rmpt04.qmd @@ -69,7 +69,8 @@ result <- build_table(lyt, df = anl, alt_counts_df = adsl_f) result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -149,4 +150,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/risk-management-plan/rmpt05.qmd b/book/tables/risk-management-plan/rmpt05.qmd index 687717140c..272ab66b65 100644 --- a/book/tables/risk-management-plan/rmpt05.qmd +++ b/book/tables/risk-management-plan/rmpt05.qmd @@ -71,7 +71,8 @@ result <- build_table(lyt, df = anl, alt_counts_df = adsl_f) result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -151,4 +152,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/risk-management-plan/rmpt06.qmd b/book/tables/risk-management-plan/rmpt06.qmd index 262788fc83..66ced68d95 100644 --- a/book/tables/risk-management-plan/rmpt06.qmd +++ b/book/tables/risk-management-plan/rmpt06.qmd @@ -129,7 +129,8 @@ result <- rbind( result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Selecting
Sections to Display @@ -185,7 +186,8 @@ result <- rbind( result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table with Differences @@ -257,7 +259,8 @@ result <- rbind( result ``` -`r webr_code_labels <- c("setup", "variant3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant3")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table Modifying Alpha Level and
Type of Confidence Interval @@ -332,7 +335,8 @@ result <- rbind( result ``` -`r webr_code_labels <- c("setup", "variant4")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant4")` +{{< include ../../_utils/webr.qmd >}} ::: ## Table by SMQ @@ -354,4 +358,5 @@ result ``` {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/safety/enrollment01.qmd b/book/tables/safety/enrollment01.qmd index 45bdba271c..2dcf6745c7 100644 --- a/book/tables/safety/enrollment01.qmd +++ b/book/tables/safety/enrollment01.qmd @@ -68,7 +68,8 @@ result <- build_table(lyt, adsl) %>% result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## ENT01A -- Enrollment by Country
and Investigator Number @@ -91,7 +92,8 @@ result <- build_table(lyt, adsl) %>% result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: ## ENT02 -- Enrollment by Region, Country,
and Investigator Number/Name @@ -116,7 +118,8 @@ result <- build_table(lyt, adsl) %>% result ``` -`r webr_code_labels <- c("setup", "variant3")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant3")` +{{< include ../../_utils/webr.qmd >}} ::: ## ENT02A -- Enrollment by Country
and Investigator Number/Name @@ -139,7 +142,8 @@ result <- build_table(lyt, adsl) %>% result ``` -`r webr_code_labels <- c("setup", "variant4")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant4")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -229,4 +233,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/vital-signs/vst01.qmd b/book/tables/vital-signs/vst01.qmd index 4e8afc1f35..c019fcdf3e 100644 --- a/book/tables/vital-signs/vst01.qmd +++ b/book/tables/vital-signs/vst01.qmd @@ -122,7 +122,8 @@ result <- build_table(lyt = lyt, df = advs_f, alt_counts_df = adsl) result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -229,4 +230,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + :::: diff --git a/book/tables/vital-signs/vst02.qmd b/book/tables/vital-signs/vst02.qmd index 46bada24e2..06a1e06d91 100644 --- a/book/tables/vital-signs/vst02.qmd +++ b/book/tables/vital-signs/vst02.qmd @@ -57,7 +57,8 @@ result <- build_table(lyt = lyt, df = advs_f, alt_counts_df = adsl) result ``` -`r webr_code_labels <- c("setup", "variant1")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant1")` +{{< include ../../_utils/webr.qmd >}} ::: ## VST02_2 -- Table of Abnormalities Among
Subjects Without Abnormality at Baseline @@ -82,7 +83,8 @@ result <- build_table(lyt = lyt, df = advs_f, alt_counts_df = adsl) result ``` -`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} +`r webr_code_labels <- c("setup", "variant2")` +{{< include ../../_utils/webr.qmd >}} ::: {{< include ../../_utils/save_results.qmd >}} @@ -147,4 +149,5 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} + ::::