Merge branch 'main' into issue_222

pharmaverse · Jan 23, 2025 · 50546f0 · 50546f0
2 parents 6a1fcd2 + 7d2ef50
commit 50546f0
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -31,8 +31,8 @@ jobs:
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}
           - {os: ubuntu-latest,   r: 'oldrel-2'}
-          - {os: ubuntu-latest,   r: 'oldrel-3'}
-          - {os: ubuntu-latest,   r: 'oldrel-4'}
+          # - {os: ubuntu-latest,   r: 'oldrel-3'}
+          # - {os: ubuntu-latest,   r: 'oldrel-4'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -53,4 +53,4 @@ Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
diff --git a/R/scale_ggsurvfit.R b/R/scale_ggsurvfit.R
@@ -7,6 +7,8 @@
 #' - `scale_y_continuous(expand = c(0.025, 0), limits = c(0, 1), label = scales::label_percent())`.
 #' - `scale_x_continuous(expand = c(0.015, 0), n.breaks = 8)`
 #'
+#' *NOTE*: The y-axis limits are only set for survival curves.
+#'
 #' If you use this function, you **must** include **all** scale specifications
 #' that would appear in `scale_x_continuous()` or `scale_y_continuous()`.
 #' For example, it's common you'll need to specify the x-axis break points.

diff --git a/ggsurvfit.Rproj b/ggsurvfit.Rproj
@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: bc923b98-5bad-45ab-b348-e227eecb86bc
 
 RestoreWorkspace: No
 SaveWorkspace: No

diff --git a/man/scale_ggsurvfit.Rd b/man/scale_ggsurvfit.Rd
diff --git a/tests/testthat/test-ggsurvfit.R b/tests/testthat/test-ggsurvfit.R
@@ -55,15 +55,6 @@ test_that("ggsurvfit() works", {
   vdiffr::expect_doppelganger("sf2-ggsurvfit_linetype", lst_survfit2_linetype[[1]])
   vdiffr::expect_doppelganger("sf3-ggsurvfit_linetype", lst_survfit2_linetype[[2]])
 
-  expect_error(
-    lst_survfit_KMunicate <-
-      list(sf1, sf2, sf3) %>%
-      lapply(function(x) ggsurvfit(x, theme = theme_ggsurvfit_KMunicate())),
-    NA
-  )
-  vdiffr::expect_doppelganger("sf1-ggsurvfit-KMunicate", lst_survfit_KMunicate[[1]])
-  vdiffr::expect_doppelganger("sf2-ggsurvfit-KMunicate", lst_survfit_KMunicate[[2]])
-  vdiffr::expect_doppelganger("sf3-ggsurvfit-KMunicate", lst_survfit_KMunicate[[3]])
 
   # test that the variable names are stripped when using transformations
   vdiffr::expect_doppelganger(
@@ -193,3 +184,30 @@ test_that("ggsurvfit() works with geoms with new data", {
   vdiffr::expect_doppelganger("sf2-ggsurvfit_new_data_geom1", p1)
   vdiffr::expect_doppelganger("sf2-ggsurvfit_new_data_geom2", p2)
 })
+
+test_that("KMunicate theme is working and reproducible", {
+
+  expect_no_error(
+    lst_survfit_KMunicate <-
+      list(sf1, sf2, sf3) %>%
+      lapply(function(x) ggsurvfit(x, theme = theme_ggsurvfit_KMunicate()))
+  )
+
+  vdiffr::expect_doppelganger("sf1-ggsurvfit-KMunicate", lst_survfit_KMunicate[[1]])
+  vdiffr::expect_doppelganger("sf2-ggsurvfit-KMunicate", lst_survfit_KMunicate[[2]])
+  vdiffr::expect_doppelganger("sf3-ggsurvfit-KMunicate", lst_survfit_KMunicate[[3]])
+
+  #plot from the documentation
+  p <- survfit2(Surv(time, status) ~ surg, data = df_colon) %>%
+    ggsurvfit(linetype_aes = TRUE) +
+    add_confidence_interval() +
+    add_risktable(
+      risktable_stats = c("n.risk", "cum.censor", "cum.event")
+    ) +
+    theme_ggsurvfit_KMunicate() +
+    scale_y_continuous(limits = c(0, 1)) +
+    scale_x_continuous(expand = c(0.02, 0)) +
+    theme(legend.position="inside", legend.position.inside = c(0.85, 0.85))
+  vdiffr::expect_doppelganger("vignette-ggsurvfit-KMunicate", p)
+})
+
diff --git a/vignettes/articles/gallery.Rmd b/vignettes/articles/gallery.Rmd
@@ -317,7 +317,7 @@ survfit2(Surv(time, status) ~ surg, data = df_colon) %>%
   theme_ggsurvfit_KMunicate() +
   scale_y_continuous(limits = c(0, 1)) +
   scale_x_continuous(expand = c(0.02, 0)) +
-  theme(legend.position.inside = c(0.85, 0.85))
+  theme(legend.position="inside", legend.position.inside = c(0.85, 0.85))
 ```
 
 ## Swap Line Type & Color Aesthetics