tests/testthat/_snaps/tm_g_km.md

In teal.modules.clinical: 'teal' Modules for Standard Clinical Outputs

template_g_km works as expected with default arguments

Code
  res
Output
  $data
  {
      anl <- ANL %>% dplyr::mutate(ARM = droplevels(ARM)) %>% dplyr::mutate(is_event = CNSR == 
          0)
  }

  $variables
  variables <- list(tte = "AVAL", is_event = "is_event", arm = "ARM")

  $graph
  {
      facets <- droplevels(anl$SEX)
      anl <- split(anl, f = facets)
      g_km_counter_generator <- function() {
          plot_number <- 0L
          function(x) {
              plot_number <<- plot_number + 1L
              g_km(x, variables = variables, control_surv = control_surv_timepoint(conf_level = 0.95), 
                  xticks = NULL, xlab = sprintf("%s (%s)", "Survival time", 
                    gsub("(^|[[:space:]])([[:alpha:]])", "\\1\\U\\2", 
                      tolower(x$AVALU[1]), perl = TRUE)), yval = "Survival", 
                  ylim = NULL, title = sprintf("%s%s", sprintf("%s%s", 
                    "KM Plot", if (!is.null(facets)) {
                      sprintf(", %s = %s", as.character(quote(SEX)), 
                        unique(x[[as.character(quote(SEX))]]))
                    }
                    else {
                      ""
                    }), if (length(NULL) != 0) {
                    sprintf("\nStratified by %s", toString(NULL))
                  }
                  else {
                    ""
                  }), footnotes = if (TRUE) {
                    paste("Ties for Coxph (Hazard Ratio):", "efron", 
                      "\n", "p-value Method for Coxph (Hazard Ratio):", 
                      "log-rank")
                  }, font_size = 11, ci_ribbon = FALSE, annot_surv_med = TRUE, 
                  annot_coxph = TRUE, control_coxph_pw = control_coxph(conf_level = 0.95, 
                    pval_method = "log-rank", ties = "efron"), 
                  control_annot_surv_med = list(x = 0.8, y = 0.85, 
                    w = 0.32, h = 0.16, fill = TRUE), control_annot_coxph = list(x = 0.27, 
                    y = 0.35, w = 0.3, h = 0.125, fill = TRUE, 
                    ref_lbls = FALSE), legend_pos = NULL, rel_height_plot = 0.8)
          }
      }
      g_km_counter <- g_km_counter_generator()
      plot_list <- lapply(anl, g_km_counter)
      plot <- cowplot::plot_grid(plotlist = plot_list, ncol = 1)
  }

template_g_km gives correct data expression when we want to compare versus reference arms

Code
  res
Output
  $data
  {
      anl <- ANL %>% dplyr::filter(ARM %in% c("ARM C", "ARM D", 
          "ARM A", "ARM B")) %>% dplyr::mutate(ARM = combine_levels(ARM, 
          levels = c("ARM C", "ARM D"), new_level = "ARM C/ARM D")) %>% 
          dplyr::mutate(ARM = stats::relevel(ARM, ref = "ARM C/ARM D")) %>% 
          dplyr::mutate(ARM = droplevels(ARM)) %>% dplyr::mutate(is_event = CNSR == 
          0)
  }

  $variables
  variables <- list(tte = "AVAL", is_event = "is_event", arm = "ARM")

  $graph
  {
      facets <- droplevels(anl$SEX)
      anl <- split(anl, f = facets)
      g_km_counter_generator <- function() {
          plot_number <- 0L
          function(x) {
              plot_number <<- plot_number + 1L
              g_km(x, variables = variables, control_surv = control_surv_timepoint(conf_level = 0.95), 
                  xticks = NULL, xlab = sprintf("%s (%s)", "Survival time", 
                    gsub("(^|[[:space:]])([[:alpha:]])", "\\1\\U\\2", 
                      tolower(x$AVALU[1]), perl = TRUE)), yval = "Survival", 
                  ylim = NULL, title = sprintf("%s%s", sprintf("%s%s", 
                    "KM Plot", if (!is.null(facets)) {
                      sprintf(", %s = %s", as.character(quote(SEX)), 
                        unique(x[[as.character(quote(SEX))]]))
                    }
                    else {
                      ""
                    }), if (length(NULL) != 0) {
                    sprintf("\nStratified by %s", toString(NULL))
                  }
                  else {
                    ""
                  }), footnotes = if (TRUE) {
                    paste("Ties for Coxph (Hazard Ratio):", "efron", 
                      "\n", "p-value Method for Coxph (Hazard Ratio):", 
                      "log-rank")
                  }, font_size = 11, ci_ribbon = FALSE, annot_surv_med = TRUE, 
                  annot_coxph = TRUE, control_coxph_pw = control_coxph(conf_level = 0.95, 
                    pval_method = "log-rank", ties = "efron"), 
                  control_annot_surv_med = list(x = 0.8, y = 0.85, 
                    w = 0.32, h = 0.16, fill = TRUE), control_annot_coxph = list(x = 0.27, 
                    y = 0.35, w = 0.3, h = 0.125, fill = TRUE, 
                    ref_lbls = FALSE), legend_pos = NULL, rel_height_plot = 0.8)
          }
      }
      g_km_counter <- g_km_counter_generator()
      plot_list <- lapply(anl, g_km_counter)
      plot <- cowplot::plot_grid(plotlist = plot_list, ncol = 1)
  }

template_g_km gives correct data expression when we want to combine comparison arms

Code
  res
Output
  $data
  {
      anl <- ANL %>% dplyr::filter(ARM %in% c("ARM C", "ARM D", 
          "ARM A", "ARM B")) %>% dplyr::mutate(ARM = combine_levels(ARM, 
          levels = c("ARM C", "ARM D"), new_level = "ARM C/ARM D")) %>% 
          dplyr::mutate(ARM = stats::relevel(ARM, ref = "ARM C/ARM D")) %>% 
          dplyr::mutate(ARM = droplevels(ARM)) %>% dplyr::mutate(is_event = CNSR == 
          0) %>% dplyr::mutate(ARM = combine_levels(ARM, levels = c("ARM A", 
          "ARM B"), new_level = "ARM A/ARM B"))
  }

  $variables
  variables <- list(tte = "AVAL", is_event = "is_event", arm = "ARM")

  $graph
  {
      facets <- droplevels(anl$SEX)
      anl <- split(anl, f = facets)
      g_km_counter_generator <- function() {
          plot_number <- 0L
          function(x) {
              plot_number <<- plot_number + 1L
              g_km(x, variables = variables, control_surv = control_surv_timepoint(conf_level = 0.95), 
                  xticks = NULL, xlab = sprintf("%s (%s)", "Survival time", 
                    gsub("(^|[[:space:]])([[:alpha:]])", "\\1\\U\\2", 
                      tolower(x$AVALU[1]), perl = TRUE)), yval = "Survival", 
                  ylim = NULL, title = sprintf("%s%s", sprintf("%s%s", 
                    "KM Plot", if (!is.null(facets)) {
                      sprintf(", %s = %s", as.character(quote(SEX)), 
                        unique(x[[as.character(quote(SEX))]]))
                    }
                    else {
                      ""
                    }), if (length(NULL) != 0) {
                    sprintf("\nStratified by %s", toString(NULL))
                  }
                  else {
                    ""
                  }), footnotes = if (TRUE) {
                    paste("Ties for Coxph (Hazard Ratio):", "efron", 
                      "\n", "p-value Method for Coxph (Hazard Ratio):", 
                      "log-rank")
                  }, font_size = 11, ci_ribbon = FALSE, annot_surv_med = TRUE, 
                  annot_coxph = TRUE, control_coxph_pw = control_coxph(conf_level = 0.95, 
                    pval_method = "log-rank", ties = "efron"), 
                  control_annot_surv_med = list(x = 0.8, y = 0.85, 
                    w = 0.32, h = 0.16, fill = TRUE), control_annot_coxph = list(x = 0.27, 
                    y = 0.35, w = 0.3, h = 0.125, fill = TRUE, 
                    ref_lbls = FALSE), legend_pos = NULL, rel_height_plot = 0.8)
          }
      }
      g_km_counter <- g_km_counter_generator()
      plot_list <- lapply(anl, g_km_counter)
      plot <- cowplot::plot_grid(plotlist = plot_list, ncol = 1)
  }

teal.modules.clinical documentation built on April 4, 2025, 12:35 a.m.