Update KMG01 after g_km refactor

insightsengineering · Mar 21, 2024 · 12b2abd · 12b2abd
1 parent 5f881fc
commit 12b2abd
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diff --git a/book/graphs/efficacy/kmg01.qmd b/book/graphs/efficacy/kmg01.qmd
@@ -27,8 +27,9 @@ variables <- list(tte = "AVAL", is_event = "is_event", arm = "ARMCD")
 
 ## Standard Plot
 
+::: {.content-visible when-profile="development"}
 <!-- skip strict because of https://github.com/r-lib/gtable/pull/94 -->
-```{r plot1, fig.height = 8, test = list(plot_v1 = "plot"), opts.label = "skip_test_strict"}
+```{r plot1, fig.width = 9, fig.height = 6, test = list(plot_v1 = "plot"), opts.label = "skip_test_strict"}
 plot <- g_km(
   df = anl,
   variables = variables,
@@ -38,11 +39,44 @@ plot <- g_km(
 )
 plot
 ```
+:::
+
+::: {.content-visible when-profile="stable"}
+<!-- skip strict because of https://github.com/r-lib/gtable/pull/94 -->
+```{r plot1-stbl, fig.height = 8, test = list(plot_v1 = "plot"), opts.label = "skip_test_strict"}
+plot <- g_km(
+  df = anl,
+  variables = variables,
+  xlab = "Time (Days)",
+  ylim = c(0, 1),
+  annot_coxph = TRUE
+)
+plot
+```
+:::
 
 ## Plot of Failures
 
+::: {.content-visible when-profile="development"}
 <!-- skip strict because of https://github.com/r-lib/gtable/pull/94 -->
-```{r plot2, fig.height = 8, test = list(plot_v2 = "plot"), opts.label = "skip_test_strict"}
+```{r plot2, fig.width = 9, fig.height = 6, test = list(plot_v2 = "plot"), opts.label = "skip_test_strict"}
+plot <- g_km(
+  df = anl,
+  variables = variables,
+  xlab = "Time (Days)",
+  yval = "Failure",
+  ylim = c(0, 1),
+  font_size = 8,
+  annot_coxph = TRUE,
+  control_annot_coxph = control_coxph_annot(x = 0.25, y = 0.85, w = 0.3)
+)
+plot
+```
+:::
+
+::: {.content-visible when-profile="stable"}
+<!-- skip strict because of https://github.com/r-lib/gtable/pull/94 -->
+```{r plot2-stbl, fig.height = 8, test = list(plot_v2 = "plot"), opts.label = "skip_test_strict"}
 plot <- g_km(
   df = anl,
   variables = variables,
@@ -57,11 +91,26 @@ plot <- g_km(
 )
 plot
 ```
+:::
 
 ## Plot Without <br/> Comparative Statistics
 
+::: {.content-visible when-profile="development"}
+<!-- skip strict because of https://github.com/r-lib/gtable/pull/94 -->
+```{r plot3, fig.width = 9, fig.height = 6, test = list(plot_v3 = "plot"), opts.label = "skip_test_strict"}
+plot <- g_km(
+  df = anl,
+  variables = variables,
+  xlab = "Time (Days)",
+  ylim = c(0, 1)
+)
+plot
+```
+:::
+
+::: {.content-visible when-profile="stable"}
 <!-- skip strict because of https://github.com/r-lib/gtable/pull/94 -->
-```{r plot3, fig.height = 8, test = list(plot_v3 = "plot"), opts.label = "skip_test_strict"}
+```{r plot3-stbl, fig.height = 8, test = list(plot_v3 = "plot"), opts.label = "skip_test_strict"}
 plot <- g_km(
   df = anl,
   variables = variables,
@@ -71,11 +120,28 @@ plot <- g_km(
 )
 plot
 ```
+:::
 
 ## Plot Without <br/> Censoring Marks
 
+::: {.content-visible when-profile="development"}
+<!-- skip strict because of https://github.com/r-lib/gtable/pull/94 -->
+```{r plot4, fig.width = 9, fig.height = 6, test = list(plot_v4 = "plot"), opts.label = "skip_test_strict"}
+plot <- g_km(
+  df = anl,
+  variables = variables,
+  censor_show = FALSE,
+  xlab = "Time (Days)",
+  ylim = c(0, 1),
+  annot_coxph = TRUE
+)
+plot
+```
+:::
+
+::: {.content-visible when-profile="stable"}
 <!-- skip strict because of https://github.com/r-lib/gtable/pull/94 -->
-```{r plot4, fig.height = 8, test = list(plot_v4 = "plot"), opts.label = "skip_test_strict"}
+```{r plot4-stbl, fig.height = 8, test = list(plot_v4 = "plot"), opts.label = "skip_test_strict"}
 plot <- g_km(
   df = anl,
   variables = variables,
@@ -86,11 +152,13 @@ plot <- g_km(
 )
 plot
 ```
+:::
 
 ## Plot Modifying <br/> Censoring Marks
 
+::: {.content-visible when-profile="development"}
 <!-- skip strict because of https://github.com/r-lib/gtable/pull/94 -->
-```{r plot5, fig.height = 8, test = list(plot_v5 = "plot"), opts.label = "skip_test_strict"}
+```{r plot5, fig.width = 9, fig.height = 6, test = list(plot_v5 = "plot"), opts.label = "skip_test_strict"}
 plot <- g_km(
   df = anl,
   variables = variables,
@@ -102,11 +170,29 @@ plot <- g_km(
 )
 plot
 ```
+:::
+
+::: {.content-visible when-profile="stable"}
+<!-- skip strict because of https://github.com/r-lib/gtable/pull/94 -->
+```{r plot5-stbl, fig.height = 8, test = list(plot_v5 = "plot"), opts.label = "skip_test_strict"}
+plot <- g_km(
+  df = anl,
+  variables = variables,
+  pch = 1,
+  size = 2,
+  xlab = "Time (Days)",
+  ylim = c(0, 1),
+  annot_coxph = TRUE
+)
+plot
+```
+:::
 
 ## Plot Modifying Options for Statistics, <br/> Tie Handling, Stratification, etc.
 
+::: {.content-visible when-profile="development"}
 <!-- skip strict because of https://github.com/r-lib/gtable/pull/94 -->
-```{r plot6, test = list(plot_v6 = "plot"), opts.label = "skip_test_strict"}
+```{r plot6, fig.width = 9, fig.height = 6, test = list(plot_v6 = "plot"), opts.label = "skip_test_strict"}
 variables$strata <- c("STRATA1", "STRATA2")
 plot <- g_km(
   df = anl,
@@ -123,6 +209,35 @@ plot <- g_km(
 )
 plot
 ```
+:::
+
+::: {.content-visible when-profile="stable"}
+<!-- skip strict because of https://github.com/r-lib/gtable/pull/94 -->
+```{r plot6-stbl, test = list(plot_v6 = "plot"), opts.label = "skip_test_strict"}
+variables$strata <- c("STRATA1", "STRATA2")
+plot <- g_km(
+  df = anl,
+  variables = variables,
+  control_surv = control_surv_timepoint(conf_level = 0.8),
+  xlab = "Time (Days)",
+  ylim = c(0, 1),
+  annot_coxph = TRUE,
+  control_coxph_pw = control_coxph(
+    pval_method = "wald",
+    ties = "breslow",
+    conf_level = 0.8
+  )
+)
+plot
+```
+:::
+
+::: {.content-visible when-profile="development"}
+```{r test parameters, test = list(width = "width", height = "height"), echo=FALSE}
+width <- 9
+height <- 6
+```
+:::
 
 {{< include ../../test-utils/save_results.qmd >}}