From c4a3de19724f7cd14f436b806410fb0dbe014744 Mon Sep 17 00:00:00 2001
From: "Baer, Travis" <tbaer@lmi.org>
Date: Fri, 1 Apr 2022 13:53:52 -0400
Subject: [PATCH 01/10] addresses #578 - use dplyr::select insstead of select_

---
 R/ggsurvplot_combine.R                   |  7 +++----
 tests/testthat/test-ggsurvplot_combine.R | 18 ++++++++++++++++++
 2 files changed, 21 insertions(+), 4 deletions(-)
 create mode 100644 tests/testthat/test-ggsurvplot_combine.R

diff --git a/R/ggsurvplot_combine.R b/R/ggsurvplot_combine.R
index 1ec7717..b8af1cf 100644
--- a/R/ggsurvplot_combine.R
+++ b/R/ggsurvplot_combine.R
@@ -114,7 +114,7 @@ ggsurvplot_combine <- function(fit, data,
       all.levels <- c(all.levels, .levels(ss$strata))
     # convert strata into character before binding
     # avoid this warning: Unequal factor levels: coercing to character
-    grouped.d$survsummary <- map(grouped.d$survsummary,
+    grouped.d$survsummary <- purrr::map(grouped.d$survsummary,
                                  function(x){
                                    x$strata <- as.character(x$strata)
                                    x
@@ -161,9 +161,8 @@ ggsurvplot_combine <- function(fit, data,
       survtable$strata <- paste(fitname, "::", survtable$strata, sep = "") %>%
         factor(levels = strata.levels)
       survtable %>%
-        dplyr::select_( .dots = c("strata", "time", "n.risk", "pct.risk",
-                                  "n.event", "cum.n.event", "n.censor",
-                                  "cum.n.censor", "strata_size"))
+        dplyr::select(strata, time, n.risk, pct.risk, n.event, cum.n.event,
+                      n.censor, cum.n.censor, strata_size)))
     }
 
     grouped.d <- grouped.d %>%
diff --git a/tests/testthat/test-ggsurvplot_combine.R b/tests/testthat/test-ggsurvplot_combine.R
new file mode 100644
index 0000000..f0814e8
--- /dev/null
+++ b/tests/testthat/test-ggsurvplot_combine.R
@@ -0,0 +1,18 @@
+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)
+
+test_that("survplot_combine plots successfully into 4 lines; second 2 fits have only (0,1) before start_time", {
+  p <- ggsurvplot_combine(list(
+      original=fit1, conditional=fit2
+    ), data = lung)
+  .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)
+})

From 359c0c0812133be80a119ec05fe740f0a2b03448 Mon Sep 17 00:00:00 2001
From: Baer <tbaer@lmi.org>
Date: Tue, 5 Apr 2022 18:53:11 -0400
Subject: [PATCH 02/10] #578 update tests and replace a few select and
 as.tibbles

---
 R/ggsurvplot_combine.R                   |  6 +++---
 R/ggsurvplot_facet.R                     |  4 ++--
 tests/testthat/test-ggsurvplot_combine.R | 17 ++++++++++-------
 tests/testthat/test-ggsurvplot_facet.R   | 21 +++++++++++++++++++++
 4 files changed, 36 insertions(+), 12 deletions(-)
 create mode 100644 tests/testthat/test-ggsurvplot_facet.R

diff --git a/R/ggsurvplot_combine.R b/R/ggsurvplot_combine.R
index b8af1cf..d634022 100644
--- a/R/ggsurvplot_combine.R
+++ b/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)
     }
 
 
diff --git a/R/ggsurvplot_facet.R b/R/ggsurvplot_facet.R
index e1f0f0d..4e00f82 100644
--- a/R/ggsurvplot_facet.R
+++ b/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 +
diff --git a/tests/testthat/test-ggsurvplot_combine.R b/tests/testthat/test-ggsurvplot_combine.R
index f0814e8..09e7c11 100644
--- a/tests/testthat/test-ggsurvplot_combine.R
+++ b/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)
 })
diff --git a/tests/testthat/test-ggsurvplot_facet.R b/tests/testthat/test-ggsurvplot_facet.R
new file mode 100644
index 0000000..dd88862
--- /dev/null
+++ b/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']])))
+})

From be678e68213d4c54d19468125f5b8b530c9ab9db Mon Sep 17 00:00:00 2001
From: Travis Baer <tbaer@lmi.org>
Date: Tue, 5 Apr 2022 18:57:42 -0400
Subject: [PATCH 03/10] #509 replace select_ with select in surv_median

---
 R/surv_median.R                   | 2 +-
 tests/testthat/test-surv_median.R | 6 ++++++
 2 files changed, 7 insertions(+), 1 deletion(-)
 create mode 100644 tests/testthat/test-surv_median.R

diff --git a/R/surv_median.R b/R/surv_median.R
index 6ec63f6..afc16e0 100644
--- a/R/surv_median.R
+++ b/R/surv_median.R
@@ -59,7 +59,7 @@ surv_median <- function(fit, combine = FALSE){
     .table$strata <- rownames(.table)
 
     .table <- .table %>%
-      dplyr::select_(.dots = c("strata",  "median", "`0.95LCL`", "`0.95UCL`"))
+      dplyr::select(strata, median, `0.95LCL`, `0.95UCL`)
     colnames(.table) <- c("strata", "median", "lower", "upper")
     rownames(.table) <- NULL
     .table
diff --git a/tests/testthat/test-surv_median.R b/tests/testthat/test-surv_median.R
new file mode 100644
index 0000000..560c310
--- /dev/null
+++ b/tests/testthat/test-surv_median.R
@@ -0,0 +1,6 @@
+test_that("surv_median calculates medians", {
+  df_medians <- surv_median(survfit(Surv(time, status) ~ sex,
+                                    data=lung))
+  expect_equal(df_medians[['median']], c(270,426))
+  expect_lt(df_medians[['lower']][2], 426)
+})

From b35b1cbab1a2bdf7dcf7c90275078d6b76b293fd Mon Sep 17 00:00:00 2001
From: Travis Baer <tbaer@lmi.org>
Date: Fri, 8 Apr 2022 18:29:06 -0400
Subject: [PATCH 04/10] #577 replace deprecated function with superceded
 function

---
 R/ggcoxdiagnostics.R                   |  6 +++---
 tests/testthat/setup-load_data.R       |  2 ++
 tests/testthat/test-ggcoxdiagnostics.R | 16 ++++++++++++++++
 3 files changed, 21 insertions(+), 3 deletions(-)
 create mode 100644 tests/testthat/setup-load_data.R
 create mode 100644 tests/testthat/test-ggcoxdiagnostics.R

diff --git a/R/ggcoxdiagnostics.R b/R/ggcoxdiagnostics.R
index 986ebc1..62d2c35 100644
--- a/R/ggcoxdiagnostics.R
+++ b/R/ggcoxdiagnostics.R
@@ -99,9 +99,9 @@ ggcoxdiagnostics <- function (fit,
   else col_names <- names(stats::coef(fit))
   colnames(res) <- col_names
   res$xval <- xval
-  data2plot <- tidyr::gather_(res,
-                              key_col = "covariate", value_col = "res",
-                              gather_col = col_names)
+  data2plot <- tidyr::gather(res,
+                              key = "covariate", value = "res",
+                              col_names)
 
   gplot <- ggplot(aes(xval, res), data = data2plot) +
            geom_point(col = point.col, shape = point.shape,
diff --git a/tests/testthat/setup-load_data.R b/tests/testthat/setup-load_data.R
new file mode 100644
index 0000000..175865c
--- /dev/null
+++ b/tests/testthat/setup-load_data.R
@@ -0,0 +1,2 @@
+library(survival)
+data('cancer')
diff --git a/tests/testthat/test-ggcoxdiagnostics.R b/tests/testthat/test-ggcoxdiagnostics.R
new file mode 100644
index 0000000..eb173f1
--- /dev/null
+++ b/tests/testthat/test-ggcoxdiagnostics.R
@@ -0,0 +1,16 @@
+test_that('ggcoxdiagnostics creates plot with all the observations', {
+  cph <- coxph(Surv(futime, fustat) ~ rx + age, data=ovarian)
+  p <- ggcoxdiagnostics(cph, type="deviance")
+  .build <- ggplot_build(p)
+  expect_equal(nrow(.build$data[[1]]), nrow(ovarian))
+})
+
+test_that('ggcoxdiagnostics with second type two rows for each observed event*term', {
+  cph <- coxph(Surv(futime, fustat) ~ rx + age, data=ovarian)
+  qty_terms <- length(attr(terms(cph$formula), "term.labels"))
+  qty_events <- sum(ovarian$fustat==1)
+  p <- ggcoxdiagnostics(cph, type="schoenfeld")
+  .build <- ggplot_build(p)
+  expect_equal(nrow(.build$data[[1]]), qty_terms*qty_events)
+})
+

From 68c99696c0114619b540f69c8988ebca886348a4 Mon Sep 17 00:00:00 2001
From: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Date: Mon, 13 Feb 2023 21:35:54 +0100
Subject: [PATCH 05/10] doc updated

---
 DESCRIPTION             |  4 ++--
 man/ggcoxdiagnostics.Rd |  4 ++--
 man/ggcoxfunctional.Rd  |  4 ++--
 man/ggcoxzph.Rd         |  4 ++--
 man/ggsurvplot_df.Rd    | 10 ++--------
 man/ggsurvtable.Rd      | 16 +++++-----------
 man/ggsurvtheme.Rd      |  6 +++---
 7 files changed, 18 insertions(+), 30 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 012539b..8cd2a59 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -43,9 +43,9 @@ Suggests:
     testthat,
     rmarkdown
 VignetteBuilder: knitr
-URL:  https://rpkgs.datanovia.com/survminer/index.html
+URL: https://rpkgs.datanovia.com/survminer/index.html
 BugReports: https://github.com/kassambara/survminer/issues
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.3
 Collate: 
     'BMT.R'
     'BRCAOV.survInfo.R'
diff --git a/man/ggcoxdiagnostics.Rd b/man/ggcoxdiagnostics.Rd
index 01579c6..ebe406e 100644
--- a/man/ggcoxdiagnostics.Rd
+++ b/man/ggcoxdiagnostics.Rd
@@ -79,9 +79,9 @@ can be calculated with \link{coxph} function.
 }
 \section{Functions}{
 \itemize{
-\item \code{ggcoxdiagnostics}: Diagnostic Plots for Cox Proportional Hazards Model with \pkg{ggplot2}
-}}
+\item \code{ggcoxdiagnostics()}: Diagnostic Plots for Cox Proportional Hazards Model with \pkg{ggplot2}
 
+}}
 \examples{
 
 library(survival)
diff --git a/man/ggcoxfunctional.Rd b/man/ggcoxfunctional.Rd
index c6f5e2f..e655d2b 100644
--- a/man/ggcoxfunctional.Rd
+++ b/man/ggcoxfunctional.Rd
@@ -67,9 +67,9 @@ should be linear to satisfy cox proportional hazards model assumptions.
 }
 \section{Functions}{
 \itemize{
-\item \code{ggcoxfunctional}: Functional Form of Continuous Variable in Cox Proportional Hazards Model.
-}}
+\item \code{ggcoxfunctional()}: Functional Form of Continuous Variable in Cox Proportional Hazards Model.
 
+}}
 \examples{
 
 library(survival)
diff --git a/man/ggcoxzph.Rd b/man/ggcoxzph.Rd
index b7bc53c..a967d64 100644
--- a/man/ggcoxzph.Rd
+++ b/man/ggcoxzph.Rd
@@ -74,9 +74,9 @@ Displays a graph of the scaled Schoenfeld residuals, along with a
 }
 \section{Functions}{
 \itemize{
-\item \code{ggcoxzph}: Graphical Test of Proportional Hazards using ggplot2.
-}}
+\item \code{ggcoxzph()}: Graphical Test of Proportional Hazards using ggplot2.
 
+}}
 \examples{
 
 library(survival)
diff --git a/man/ggsurvplot_df.Rd b/man/ggsurvplot_df.Rd
index a397f2f..1269947 100644
--- a/man/ggsurvplot_df.Rd
+++ b/man/ggsurvplot_df.Rd
@@ -111,15 +111,9 @@ censors. Default value is "+" (3), a sensible choice is "|" (124).}
 \item{censor.size}{numveric value specifying the point size of censors.
 Default is 4.5.}
 
-\item{title}{main title and axis labels}
+\item{title, xlab, ylab}{main title and axis labels}
 
-\item{xlab}{main title and axis labels}
-
-\item{ylab}{main title and axis labels}
-
-\item{xlim}{x and y axis limits e.g. xlim = c(0, 1000), ylim = c(0, 1).}
-
-\item{ylim}{x and y axis limits e.g. xlim = c(0, 1000), ylim = c(0, 1).}
+\item{xlim, ylim}{x and y axis limits e.g. xlim = c(0, 1000), ylim = c(0, 1).}
 
 \item{axes.offset}{logical value. Default is TRUE. If FALSE, set the plot axes
 to start at the origin.}
diff --git a/man/ggsurvtable.Rd b/man/ggsurvtable.Rd
index c3e7a7d..00eeb3e 100644
--- a/man/ggsurvtable.Rd
+++ b/man/ggsurvtable.Rd
@@ -97,8 +97,6 @@ function \link[grDevices]{palette}.}
 \item{break.time.by}{numeric value controlling time axis breaks. Default value
 is NULL.}
 
-\item{xlim}{x and y axis limits e.g. xlim = c(0, 1000), ylim = c(0, 1).}
-
 \item{xscale}{numeric or character value specifying x-axis scale. \itemize{
 \item If numeric, the value is used to divide the labels on the x axis. For
 example, a value of 365.25 will give labels in years instead of the original
@@ -107,10 +105,6 @@ days. \item If character, allowed options include one of c("d_m", "d_y",
 example, xscale = "d_m" will transform labels from days to months; xscale =
 "m_y", will transform labels from months to years.}}
 
-\item{xlab}{main title and axis labels}
-
-\item{ylab}{main title and axis labels}
-
 \item{xlog}{logical value. If TRUE, x axis is tansformed into log scale.}
 
 \item{legend}{character specifying legend position. Allowed values are one of
@@ -163,15 +157,15 @@ Normally, users don't need to use this function directly. Internally used by the
 }
 \section{Functions}{
 \itemize{
-\item \code{ggrisktable}: Plot the number at risk table.
+\item \code{ggrisktable()}: Plot the number at risk table.
 
-\item \code{ggcumevents}: Plot the cumulative number of events table
+\item \code{ggcumevents()}: Plot the cumulative number of events table
 
-\item \code{ggcumcensor}: Plot the cumulative number of censor table
+\item \code{ggcumcensor()}: Plot the cumulative number of censor table
 
-\item \code{ggsurvtable}: Generic function to plot survival tables: risk.table, cumevents and cumcensor
-}}
+\item \code{ggsurvtable()}: Generic function to plot survival tables: risk.table, cumevents and cumcensor
 
+}}
 \examples{
 # Fit survival curves
 #:::::::::::::::::::::::::::::::::::::::::::::::
diff --git a/man/ggsurvtheme.Rd b/man/ggsurvtheme.Rd
index e93236a..aa2f412 100644
--- a/man/ggsurvtheme.Rd
+++ b/man/ggsurvtheme.Rd
@@ -45,13 +45,13 @@ Default theme for plots generated with survminer.
 }
 \section{Functions}{
 \itemize{
-\item \code{theme_survminer}: Default theme for survminer plots. A theme similar to theme_classic() with large font size.
+\item \code{theme_survminer()}: Default theme for survminer plots. A theme similar to theme_classic() with large font size.
 
-\item \code{theme_cleantable}: theme for drawing a clean risk table and cumulative
+\item \code{theme_cleantable()}: theme for drawing a clean risk table and cumulative
 number of events table. A theme similar to theme_survminer() without i)
 axis lines and, ii) x axis ticks and title.
-}}
 
+}}
 \examples{
 
 # Fit survival curves

From 761a2e9fdfa60e4ec60463bdafdd6a6383df5b3b Mon Sep 17 00:00:00 2001
From: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Date: Thu, 16 Feb 2023 07:58:28 +0100
Subject: [PATCH 06/10] fix for dplyr:select()

---
 R/ggsurvplot_combine.R | 5 +++--
 R/surv_median.R        | 2 +-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/R/ggsurvplot_combine.R b/R/ggsurvplot_combine.R
index d634022..32aaca8 100644
--- a/R/ggsurvplot_combine.R
+++ b/R/ggsurvplot_combine.R
@@ -161,8 +161,9 @@ ggsurvplot_combine <- function(fit, data,
       survtable$strata <- paste(fitname, "::", survtable$strata, sep = "") %>%
         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)
+        dplyr::select( dplyr::all_of(c("strata", "time", "n.risk", "pct.risk",
+                                       "n.event", "cum.n.event", "n.censor",
+                                       "cum.n.censor", "strata_size")))
     }
 
     grouped.d <- grouped.d %>%
diff --git a/R/surv_median.R b/R/surv_median.R
index afc16e0..f1caee4 100644
--- a/R/surv_median.R
+++ b/R/surv_median.R
@@ -59,7 +59,7 @@ surv_median <- function(fit, combine = FALSE){
     .table$strata <- rownames(.table)
 
     .table <- .table %>%
-      dplyr::select(strata, median, `0.95LCL`, `0.95UCL`)
+      dplyr::select(dplyr::all_of(c("strata",  "median", "0.95LCL", "0.95UCL")))
     colnames(.table) <- c("strata", "median", "lower", "upper")
     rownames(.table) <- NULL
     .table

From 7c4ad1571a1aede654028685bf6cfb28451cc940 Mon Sep 17 00:00:00 2001
From: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Date: Thu, 16 Feb 2023 07:59:01 +0100
Subject: [PATCH 07/10] fix lung data not found in unit test

---
 tests/testthat/test-ggsurvtable.R | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/tests/testthat/test-ggsurvtable.R b/tests/testthat/test-ggsurvtable.R
index d7d6da9..d8566cd 100644
--- a/tests/testthat/test-ggsurvtable.R
+++ b/tests/testthat/test-ggsurvtable.R
@@ -1,11 +1,12 @@
 context("test-ggsurvtable")
 
-library(dplyr)
-library("survival")
-data("lung")
-fit <- survfit(Surv(time, status) ~ sex, data = lung)
+
 
 test_that("survtable y axis label colors work", {
+  library(dplyr)
+  library("survival")
+  #data("lung", package = "survival")
+  fit <- survfit(Surv(time, status) ~ sex, data = lung)
   p <- ggrisktable(fit, data = lung, color = "strata")
   .build <- ggplot_build(p)
   .build_data <- .build$data[[1]]

From eb7f42df2ac03f5b8cc7e91191937c7133760470 Mon Sep 17 00:00:00 2001
From: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Date: Tue, 29 Oct 2024 15:48:41 +0000
Subject: [PATCH 08/10] ggplot2 minimum version set to 3.4.0

---
 DESCRIPTION | 2 +-
 NEWS.md     | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f423982..866110a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -16,7 +16,7 @@ License: GPL-2
 LazyData: TRUE
 Encoding: UTF-8
 Depends:
-    ggplot2,
+    ggplot2(>= 3.4.0),
     ggpubr(>= 0.1.6)
 Imports:
     grid,
diff --git a/NEWS.md b/NEWS.md
index 2997f43..42721f4 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -7,6 +7,7 @@
 ## Minor changes
 
 - R-ADDICT website is no longer live, so updating links in README (#622)
+- ggplot2 minimum version is now 3.4.0
 
 ## Bug fixes
 

From c7ff6282b297da4a3070b334a68219ac53cf8873 Mon Sep 17 00:00:00 2001
From: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Date: Tue, 29 Oct 2024 15:49:13 +0000
Subject: [PATCH 09/10] gather replaced by pivot_longer()

---
 R/ggcoxdiagnostics.R | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/R/ggcoxdiagnostics.R b/R/ggcoxdiagnostics.R
index 8f5676f..62b64e7 100644
--- a/R/ggcoxdiagnostics.R
+++ b/R/ggcoxdiagnostics.R
@@ -99,19 +99,20 @@ ggcoxdiagnostics <- function (fit,
   else col_names <- names(stats::coef(fit))
   colnames(res) <- col_names
   res$xval <- xval
-  data2plot <- tidyr::gather(res,
-                              key = "covariate", value = "res",
-                              col_names)
+  data2plot <- tidyr::pivot_longer(
+    data = res, cols = dplyr::all_of(col_names),  
+    names_to = "covariate", values_to = "res"
+  )
 
   gplot <- ggplot(aes(xval, res), data = data2plot) +
            geom_point(col = point.col, shape = point.shape,
                        size = point.size, alpha = point.alpha)
 
   if (hline) gplot <- gplot + geom_hline(yintercept=hline.yintercept, col = hline.col,
-                                         size = hline.size, lty = hline.lty, alpha = hline.alpha)
+                                         linewidth = hline.size, lty = hline.lty, alpha = hline.alpha)
 
   if (sline) gplot <- gplot + geom_smooth(col = sline.col, se = sline.se, method = "loess",
-                                         size = sline.size, lty = sline.lty, alpha = sline.alpha)
+                                         linewidth = sline.size, lty = sline.lty, alpha = sline.alpha)
 
   gplot <- gplot + labs(x = xlabel, y = ylabel, title = title, subtitle = subtitle, caption = caption) + ggtheme
   # customization

From b7c4fae968640548253a0b81e3d278edf883b1af Mon Sep 17 00:00:00 2001
From: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Date: Tue, 29 Oct 2024 15:50:10 +0000
Subject: [PATCH 10/10] deprecated aes_string() replaced by aes()

---
 NAMESPACE            | 2 ++
 R/ggsurvplot_df.R    | 2 +-
 R/utilities.R        | 1 +
 man/ggsurvplot_df.Rd | 1 -
 4 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 66e0e14..3402bea 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -53,6 +53,8 @@ importFrom(grDevices,axisTicks)
 importFrom(magrittr,"%>%")
 importFrom(methods,is)
 importFrom(purrr,map)
+importFrom(rlang,"!!")
+importFrom(rlang,sym)
 importFrom(rlang,syms)
 importFrom(stats,anova)
 importFrom(stats,approx)
diff --git a/R/ggsurvplot_df.R b/R/ggsurvplot_df.R
index 1fb6a50..5f0eb64 100644
--- a/R/ggsurvplot_df.R
+++ b/R/ggsurvplot_df.R
@@ -176,7 +176,7 @@ ggsurvplot_df <- function(fit, fun = NULL,
   #::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
   df[, .strata.var] <- factor( df[, .strata.var], levels = .levels(.strata), labels = legend.labs)
 
-  p <- ggplot2::ggplot(df, ggplot2::aes_string("time", "surv")) +
+  p <- ggplot2::ggplot(df, ggplot2::aes(x = !!sym("time"), y = !!sym("surv"))) +
     ggpubr::geom_exec(surv.geom, data = df, size = size, color = color, linetype = linetype, ...) +
     ggplot2::scale_y_continuous(breaks = y.breaks, labels = scale_labels, limits = ylim, expand = .expand) +
     ggplot2::coord_cartesian(xlim = xlim)+
diff --git a/R/utilities.R b/R/utilities.R
index 9049585..ebd5818 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -10,6 +10,7 @@
 #' @importFrom stats pchisq
 #' @importFrom survMisc ten comp
 #' @importFrom utils capture.output
+#' @importFrom rlang !! sym
 
 
 # Count the number of ggplots in a list
diff --git a/man/ggsurvplot_df.Rd b/man/ggsurvplot_df.Rd
index f0e22eb..8d64341 100644
--- a/man/ggsurvplot_df.Rd
+++ b/man/ggsurvplot_df.Rd
@@ -111,7 +111,6 @@ censors. Default value is "+" (3), a sensible choice is "|" (124).}
 \item{censor.size}{numveric value specifying the point size of censors.
 Default is 4.5.}
 
-
 \item{title}{main title}
 
 \item{xlab}{x axis label}