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a/development/graphs/efficacy/kmg01.html b/development/graphs/efficacy/kmg01.html index b614375928..35ab9e8a93 100644 --- a/development/graphs/efficacy/kmg01.html +++ b/development/graphs/efficacy/kmg01.html @@ -1473,216 +1473,199 @@ xlab = "Time (Days)", ylim = c(0, 1), annot_coxph = TRUE -) +) +plot
-

+

-
Code
plot
-
-
gTree[GRID.gTree.155]
-
-
Code
plot <- g_km(
-  df = anl,
-  variables = variables,
-  xlab = "Time (Days)",
-  yval = "Failure",
-  ylim = c(0, 1),
-  annot_surv_med = TRUE,
-  annot_coxph = TRUE,
-  font_size = 7.5,
-  position_coxph = c(0.3, 0),
-  position_surv_med = c(0.9, 0.3)
-)
+
Code
plot <- g_km(
+  df = anl,
+  variables = variables,
+  xlab = "Time (Days)",
+  yval = "Failure",
+  ylim = c(0, 1),
+  font_size = 8,
+  annot_coxph = TRUE
+)
+plot
-

+

-
Code
plot
-
-
gTree[GRID.gTree.298]
-
-
Code
plot <- g_km(
-  df = anl,
-  variables = variables,
-  xlab = "Time (Days)",
-  ylim = c(0, 1),
-  annot_surv_med = TRUE
-)
+
Code
plot <- g_km(
+  df = anl,
+  variables = variables,
+  xlab = "Time (Days)",
+  ylim = c(0, 1)
+)
+plot
-

+

-
Code
plot
-
-
gTree[GRID.gTree.415]
-
-
Code
plot <- g_km(
-  df = anl,
-  variables = variables,
-  censor_show = FALSE,
-  xlab = "Time (Days)",
-  ylim = c(0, 1),
-  annot_coxph = TRUE
-)
+
Code
plot <- g_km(
+  df = anl,
+  variables = variables,
+  censor_show = FALSE,
+  xlab = "Time (Days)",
+  ylim = c(0, 1),
+  annot_coxph = TRUE
+)
+plot
-

+

-
Code
plot
-
-
gTree[GRID.gTree.546]
-
-
Code
plot <- g_km(
-  df = anl,
-  variables = variables,
-  pch = 1,
-  size = 2,
-  xlab = "Time (Days)",
-  ylim = c(0, 1),
-  annot_coxph = TRUE
-)
+
Code
plot <- g_km(
+  df = anl,
+  variables = variables,
+  pch = 1,
+  size = 2,
+  xlab = "Time (Days)",
+  ylim = c(0, 1),
+  annot_coxph = TRUE
+)
+plot
-

+

-
Code
plot
-
-
gTree[GRID.gTree.689]
-
-
Code
variables$strata <- c("STRATA1", "STRATA2")
-plot <- g_km(
-  df = anl,
-  variables = variables,
-  control_surv = control_surv_timepoint(conf_level = 0.8),
-  xlab = "Time (Days)",
-  ylim = c(0, 1),
-  annot_coxph = TRUE,
-  control_coxph_pw = control_coxph(
-    pval_method = "wald",
-    ties = "breslow",
-    conf_level = 0.8
-  )
-)
+
Code
variables$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
-

+

-
Code
plot
-
-
gTree[GRID.gTree.832]
-
-
Code
if (exists("tenv")) {
-  filename <- paste0(gsub("\\.rmarkdown$", "", knitr::current_input(dir = TRUE)), ".rds")
-  filepath <- gsub(normalizePath(Sys.getenv("QUARTO_PROJECT_DIR")), file.path(Sys.getenv("QUARTO_TESTTHAT_DATA_PATH"), Sys.getenv("QUARTO_PROFILE")), filename)
-  if (!dir.exists(dirname(filepath))) {
-    dir.create(dirname(filepath), recursive = TRUE)
-  }
-  saveRDS(tenv, filepath)
-}
+
Code
if (exists("tenv")) {
+  filename <- paste0(gsub("\\.rmarkdown$", "", knitr::current_input(dir = TRUE)), ".rds")
+  filepath <- gsub(normalizePath(Sys.getenv("QUARTO_PROJECT_DIR")), file.path(Sys.getenv("QUARTO_TESTTHAT_DATA_PATH"), Sys.getenv("QUARTO_PROFILE")), filename)
+  if (!dir.exists(dirname(filepath))) {
+    dir.create(dirname(filepath), recursive = TRUE)
+  }
+  saveRDS(tenv, filepath)
+}
-
Code
library(teal.modules.clinical)
-
-## Data reproducible code
-data <- teal_data()
-data <- within(data, {
-  library(scda)
-  ADSL <- synthetic_cdisc_dataset("latest", "adsl")
-  ADTTE <- synthetic_cdisc_dataset("latest", "adtte")
-})
-datanames <- c("ADSL", "ADTTE")
-datanames(data) <- datanames
-join_keys(data) <- default_cdisc_join_keys[datanames]
-
-arm_ref_comp <- list(
-  ACTARMCD = list(
-    ref = "ARM B",
-    comp = c("ARM A", "ARM C")
-  ),
-  ARM = list(
-    ref = "B: Placebo",
-    comp = c("A: Drug X", "C: Combination")
-  )
-)
-
-## Reusable Configuration For Modules
-ADSL <- data[["ADSL"]]
-ADTTE <- data[["ADTTE"]]
-
-## Setup App
-app <- init(
-  data = data,
-  modules = modules(
-    tm_g_km(
-      label = "KM PLOT",
-      plot_height = c(600, 100, 2000),
-      dataname = "ADTTE",
-      arm_var = choices_selected(
-        variable_choices(ADSL, c("ARM", "ARMCD", "ACTARMCD")),
-        "ARM"
-      ),
-      paramcd = choices_selected(
-        value_choices(ADTTE, "PARAMCD", "PARAM"),
-        "OS"
-      ),
-      arm_ref_comp = arm_ref_comp,
-      strata_var = choices_selected(
-        variable_choices(ADSL, c("SEX", "BMRKR2")),
-        "SEX"
-      ),
-      facet_var = choices_selected(
-        variable_choices(ADSL, c("SEX", "BMRKR2")),
-        NULL
-      )
-    )
-  )
-)
-
-shinyApp(app$ui, app$server)
-
+
Code
library(teal.modules.clinical)
+
+## Data reproducible code
+data <- teal_data()
+data <- within(data, {
+  library(scda)
+  ADSL <- synthetic_cdisc_dataset("latest", "adsl")
+  ADTTE <- synthetic_cdisc_dataset("latest", "adtte")
+})
+datanames <- c("ADSL", "ADTTE")
+datanames(data) <- datanames
+join_keys(data) <- default_cdisc_join_keys[datanames]
+
+arm_ref_comp <- list(
+  ACTARMCD = list(
+    ref = "ARM B",
+    comp = c("ARM A", "ARM C")
+  ),
+  ARM = list(
+    ref = "B: Placebo",
+    comp = c("A: Drug X", "C: Combination")
+  )
+)
+
+## Reusable Configuration For Modules
+ADSL <- data[["ADSL"]]
+ADTTE <- data[["ADTTE"]]
+
+## Setup App
+app <- init(
+  data = data,
+  modules = modules(
+    tm_g_km(
+      label = "KM PLOT",
+      plot_height = c(600, 100, 2000),
+      dataname = "ADTTE",
+      arm_var = choices_selected(
+        variable_choices(ADSL, c("ARM", "ARMCD", "ACTARMCD")),
+        "ARM"
+      ),
+      paramcd = choices_selected(
+        value_choices(ADTTE, "PARAMCD", "PARAM"),
+        "OS"
+      ),
+      arm_ref_comp = arm_ref_comp,
+      strata_var = choices_selected(
+        variable_choices(ADSL, c("SEX", "BMRKR2")),
+        "SEX"
+      ),
+      facet_var = choices_selected(
+        variable_choices(ADSL, c("SEX", "BMRKR2")),
+        NULL
+      )
+    )
+  )
+)
+
+shinyApp(app$ui, app$server)
+
+
Warning: Error in : Assertion on 'all(vapply(grobs, grid::is.grob, logical(1)))' failed: Must be TRUE. 
+ when evaluating qenv code:
+plot <- tern::stack_grobs(grobs = plot_list)
+
+

@@ -1693,18 +1676,18 @@

Timestamp

-
Code
Sys.time()
+
Code
Sys.time()
-
[1] "2024-03-20 17:57:34 UTC"
+
[1] "2024-03-22 18:17:21 UTC"

Session Info

-
Code
sessionInfo()
+
Code
sessionInfo()
R version 4.3.3 (2024-02-29)
 Platform: x86_64-pc-linux-gnu (64-bit)
-Running under: Ubuntu 22.04.3 LTS
+Running under: Ubuntu 22.04.4 LTS
 
 Matrix products: default
 BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
@@ -1726,76 +1709,76 @@
 
 other attached packages:
  [1] teal.modules.clinical_0.9.0.9012 teal.transform_0.5.0.9004       
- [3] teal_0.15.2.9012                 teal.slice_0.5.0.9008           
+ [3] teal_0.15.2.9016                 teal.slice_0.5.0.9009           
  [5] teal.data_0.5.0.9005             teal.code_0.5.0.9004            
  [7] shiny_1.8.0                      nestcolor_0.1.2.9009            
  [9] dplyr_1.1.4                      scda_0.1.6.9017                 
-[11] tern_0.9.3.9025                  rtables_0.6.6.9011              
+[11] tern_0.9.3.9028                  rtables_0.6.6.9011              
 [13] magrittr_2.0.3                   formatters_0.5.5.9016           
 
 loaded via a namespace (and not attached):
- [1] Rdpack_2.6               gridExtra_2.3            formatR_1.14            
- [4] tern.gee_0.1.3.9004      logger_0.3.0             testthat_3.2.1          
- [7] sandwich_3.1-0           rlang_1.1.3              multcomp_1.4-25         
-[10] compiler_4.3.3           systemfonts_1.0.6        callr_3.7.5             
-[13] vctrs_0.6.5              pkgconfig_2.0.3          fastmap_1.1.1           
-[16] backports_1.4.1          ellipsis_0.3.2           fontawesome_0.5.2       
-[19] labeling_0.4.3           utf8_1.2.4               promises_1.2.1          
-[22] rmarkdown_2.26           ps_1.7.6                 ragg_1.2.7              
-[25] purrr_1.0.2              xfun_0.42                shinyvalidate_0.1.3     
-[28] cachem_1.0.8             teal.reporter_0.3.1.9001 jsonlite_1.8.8          
-[31] later_1.3.2              broom_1.0.5              R6_2.5.1                
-[34] bslib_0.6.1              brio_1.1.4               jquerylib_0.1.4         
-[37] estimability_1.5         Rcpp_1.0.12              knitr_1.45              
-[40] zoo_1.8-12               teal.logger_0.1.3.9013   httpuv_1.6.14           
-[43] Matrix_1.6-5             splines_4.3.3            tidyselect_1.2.0        
-[46] yaml_2.3.8               codetools_0.2-19         websocket_1.4.1         
-[49] processx_3.8.3           teal.widgets_0.4.2.9009  lattice_0.22-5          
-[52] tibble_3.2.1             withr_3.0.0              coda_0.19-4.1           
-[55] evaluate_0.23            survival_3.5-8           pillar_1.9.0            
-[58] shinycssloaders_1.0.0    checkmate_2.3.1          shinyjs_2.1.0           
-[61] generics_0.1.3           chromote_0.2.0           ggplot2_3.5.0           
-[64] munsell_0.5.0            scales_1.3.0             xtable_1.8-4            
-[67] glue_1.7.0               emmeans_1.10.0           tools_4.3.3             
-[70] webshot2_0.1.1           webshot_0.5.5            mvtnorm_1.2-4           
-[73] grid_4.3.3               tidyr_1.3.1              rbibutils_2.2.16        
-[76] colorspace_2.1-0         nlme_3.1-164             cli_3.6.2               
-[79] textshaping_0.3.7        fansi_1.0.6              geepack_1.3.10          
-[82] gtable_0.3.4             sass_0.4.8               digest_0.6.34           
-[85] TH.data_1.1-2            htmlwidgets_1.6.4        farver_2.1.1            
-[88] memoise_2.0.1            htmltools_0.5.7          lifecycle_1.0.4         
-[91] shinyWidgets_0.8.2       mime_0.12                MASS_7.3-60.0.1
+ [1] Rdpack_2.6 formatR_1.14 tern.gee_0.1.3.9004 + [4] logger_0.3.0 testthat_3.2.1 sandwich_3.1-0 + [7] rlang_1.1.3 multcomp_1.4-25 compiler_4.3.3 +[10] callr_3.7.5 vctrs_0.6.5 pkgconfig_2.0.3 +[13] crayon_1.5.2 fastmap_1.1.1 backports_1.4.1 +[16] ellipsis_0.3.2 fontawesome_0.5.2 labeling_0.4.3 +[19] utf8_1.2.4 promises_1.2.1 rmarkdown_2.26 +[22] ps_1.7.6 purrr_1.0.2 xfun_0.42 +[25] shinyvalidate_0.1.3 cachem_1.0.8 teal.reporter_0.3.1.9001 +[28] jsonlite_1.8.8 later_1.3.2 broom_1.0.5 +[31] R6_2.5.1 bslib_0.6.1 brio_1.1.4 +[34] jquerylib_0.1.4 estimability_1.5 Rcpp_1.0.12 +[37] knitr_1.45 zoo_1.8-12 teal.logger_0.1.3.9013 +[40] httpuv_1.6.14 Matrix_1.6-5 splines_4.3.3 +[43] tidyselect_1.2.1 yaml_2.3.8 codetools_0.2-19 +[46] websocket_1.4.1 processx_3.8.4 teal.widgets_0.4.2.9009 +[49] lattice_0.22-6 tibble_3.2.1 withr_3.0.0 +[52] coda_0.19-4.1 evaluate_0.23 survival_3.5-8 +[55] pillar_1.9.0 shinycssloaders_1.0.0 checkmate_2.3.1 +[58] shinyjs_2.1.0 generics_0.1.3 chromote_0.2.0 +[61] ggplot2_3.5.0 munsell_0.5.0 scales_1.3.0 +[64] xtable_1.8-4 glue_1.7.0 emmeans_1.10.0 +[67] tools_4.3.3 webshot2_0.1.1 webshot_0.5.5 +[70] mvtnorm_1.2-4 cowplot_1.1.3 grid_4.3.3 +[73] tidyr_1.3.1 rbibutils_2.2.16 colorspace_2.1-0 +[76] nlme_3.1-164 cli_3.6.2 fansi_1.0.6 +[79] geepack_1.3.10 gtable_0.3.4 sass_0.4.9 +[82] digest_0.6.35 TH.data_1.1-2 htmlwidgets_1.6.4 +[85] farver_2.1.1 memoise_2.0.1 htmltools_0.5.7 +[88] lifecycle_1.0.4 shinyWidgets_0.8.2 mime_0.12 +[91] MASS_7.3-60.0.1

.lock file

Download the .lock file and use renv::restore() on it to recreate environment used to generate this website.

-
Code
parent_file_path <- knitr::current_input(dir = TRUE)
-
-book_root_dir <- parent_file_path
-while (!file.exists(file.path(book_root_dir, "_quarto.yml"))) book_root_dir <- dirname(book_root_dir)
-
-lock_path <- file.path(
-  "../../assets/www/lock",
-  paste0(
-    gsub(
-      file.path(book_root_dir, ""),
-      "",
-      gsub(
-        "\\.rmarkdown$",
-        "",
-        knitr::current_input(dir = TRUE)
-      )
-    ),
-    ".lock"
-  )
-)
-
-withr::with_options(
-  list(renv.verbose = FALSE),
-  renv::snapshot(parent_file_path, lockfile = lock_path, prompt = FALSE, force = TRUE)
-)
+
Code
parent_file_path <- knitr::current_input(dir = TRUE)
+
+book_root_dir <- parent_file_path
+while (!file.exists(file.path(book_root_dir, "_quarto.yml"))) book_root_dir <- dirname(book_root_dir)
+
+lock_path <- file.path(
+  "../../assets/www/lock",
+  paste0(
+    gsub(
+      file.path(book_root_dir, ""),
+      "",
+      gsub(
+        "\\.rmarkdown$",
+        "",
+        knitr::current_input(dir = TRUE)
+      )
+    ),
+    ".lock"
+  )
+)
+
+withr::with_options(
+  list(renv.verbose = FALSE),
+  renv::snapshot(parent_file_path, lockfile = lock_path, prompt = FALSE, force = TRUE)
+)

Download

@@ -2423,199 +2406,313 @@