kassambara#578 update tests and replace a few select and as.tibbles

R/ggsurvplot_combine.R

@@ -162,7 +162,7 @@ ggsurvplot_combine <- function(fit, data,
         factor(levels = strata.levels)
       survtable %>%
         dplyr::select(strata, time, n.risk, pct.risk, n.event, cum.n.event,
-                      n.censor, cum.n.censor, strata_size)))
+                      n.censor, cum.n.censor, strata_size)
     }
 
     grouped.d <- grouped.d %>%
@@ -198,8 +198,8 @@ ggsurvplot_combine <- function(fit, data,
     #::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 
     if(keep.data){
-    res$data.survplot <- tibble::as.tibble(all.survsummary)
-    res$data.survtable <- tibble::as.tibble(all.survtable)
+    res$data.survplot <- tibble::as_tibble(all.survsummary)
+    res$data.survtable <- tibble::as_tibble(all.survtable)
     }
 
 

R/ggsurvplot_facet.R

@@ -179,10 +179,10 @@ ggsurvplot_facet <- function(fit, data, facet.by,
     pvalue <- surv_pvalue(grouped.d$fit, grouped.d$data, pval.coord = pval.coord,
                           pval.method.coord = pval.method.coord,...) %>%
       dplyr::bind_rows() %>%
-      tibble::as.tibble()
+      tibble::as_tibble()
     # Select the grouping variable columns and cbind the corresponding pvalue
     pvals.df <- grouped.d %>%
-      dplyr::select_( .dots = facet.by) %>%
+      dplyr::select(!!!syms(facet.by)) %>%
       dplyr::bind_cols(pvalue)
     pval.x <- pval.y <- pval.txt <- method.x <- method.y <- method <-  NULL
     p <- p +

tests/testthat/test-ggsurvplot_combine.R

@@ -1,11 +1,6 @@
-context("test-ggsurvplot_combine")
-
-library(dplyr)
-library(survival)
-data("lung")
 start_time <- 250
 fit1 <- survfit(Surv(time, status) ~ sex, data = lung)
-fit2 <- survfit(Surv(time, status) ~ sex, data = lung, start.time=start_time)
+fit2 <- survfit(Surv(time, status) ~ sex, data = lung, start.time = start_time)
 
 test_that("survplot_combine plots successfully into 4 lines; second 2 fits have only (0,1) before start_time", {
   p <- ggsurvplot_combine(list(
@@ -14,5 +9,13 @@ test_that("survplot_combine plots successfully into 4 lines; second 2 fits have
   .build <- ggplot_build(p$plot)
   .build_data <- .build$data[[1]]
   expect_equal(length(unique(.build_data[['group']])), 4)
-  expect_lt(nrow(.build_data[(.build_data[['group']] >= 3) & (.build_data[['x']] < start_time), ]), 3)
+  expect_lt(nrow(.build_data[(.build_data[['group']] >= 3) &
+                               (.build_data[['x']] < start_time), ]), 3)
+})
+
+test_that("survplot_combine includes dataframes when keep.data==TRUE", {
+  p <- ggsurvplot_combine(list(
+    original=fit1, conditional=fit2
+  ), data = lung, keep.data = TRUE)
+  expect_equal(length(names(p)), 3)
 })

tests/testthat/test-ggsurvplot_facet.R

@@ -0,0 +1,21 @@
+test_that("ggsurvplot_facet creates the correct quanitty of subplots", {
+  fit <- survfit(Surv(time, status) ~ sex, data=kidney)
+  p <- ggsurvplot_facet(fit, kidney, facet.by='disease')
+  .build <- ggplot_build(p)
+  expect_equal(nrow(.build$data[[2]]),
+               length(unique(kidney[['disease']])))
+
+  fit <- survfit(Surv(time, status) ~ disease, data=kidney)
+  p <- ggsurvplot_facet(fit, kidney, facet.by='sex')
+  .build <- ggplot_build(p)
+  expect_equal(nrow(.build$data[[2]]),
+               length(unique(kidney[['sex']])))
+})
+
+test_that("ggsurvplot_facet calculates pvalue for each facet", {
+  fit <- survfit(Surv(time, status) ~ sex, data=kidney)
+  p <- ggsurvplot_facet(fit, kidney, facet.by='disease', pval = TRUE)
+  .build <- ggplot_build(p)
+  expect_equal(nrow(.build$plot$layer[[4]][['data']]),
+               length(unique(kidney[['disease']])))
+})