From e6ed2f9244da5d5c6721ad33cdb9fd77c3376795 Mon Sep 17 00:00:00 2001
From: Michael McCarthy <51542091+mccarthy-m-g@users.noreply.github.com>
Date: Sat, 3 Jun 2023 16:39:00 -0700
Subject: [PATCH 1/3] return standard errors for the survival probability, not
 the cumulative hazard

---
 R/survival-survfit-tidiers.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/survival-survfit-tidiers.R b/R/survival-survfit-tidiers.R
index 1bbf8c547..f685d78b2 100644
--- a/R/survival-survfit-tidiers.R
+++ b/R/survival-survfit-tidiers.R
@@ -65,7 +65,7 @@ tidy.survfit <- function(x, ...) {
       n.event = c(x$n.event),
       n.censor = c(x$n.censor),
       estimate = c(x$pstate),
-      std.error = c(x$std.err),
+      std.error = c(summary(x)$std.err),
       conf.high = c(x$upper),
       conf.low = c(x$lower),
       state = rep(x$states, each = nrow(x$pstate))
@@ -79,7 +79,7 @@ tidy.survfit <- function(x, ...) {
       n.event = x$n.event,
       n.censor = x$n.censor,
       estimate = x$surv,
-      std.error = x$std.err,
+      std.error = summary(x)$std.err,
       conf.high = x$upper,
       conf.low = x$lower
     )

From 03a4662da40ae34d07597a319d46d0514cba3fa8 Mon Sep 17 00:00:00 2001
From: Michael McCarthy <51542091+mccarthy-m-g@users.noreply.github.com>
Date: Sun, 4 Jun 2023 16:47:04 -0700
Subject: [PATCH 2/3] compute std.error manually instead of using `summary()`
 for compatibility with objects reformulated by `survfit0()`

---
 R/survival-survfit-tidiers.R | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/R/survival-survfit-tidiers.R b/R/survival-survfit-tidiers.R
index f685d78b2..235357474 100644
--- a/R/survival-survfit-tidiers.R
+++ b/R/survival-survfit-tidiers.R
@@ -65,7 +65,9 @@ tidy.survfit <- function(x, ...) {
       n.event = c(x$n.event),
       n.censor = c(x$n.censor),
       estimate = c(x$pstate),
-      std.error = c(summary(x)$std.err),
+      # A survfit object may contain std(log S) or std(S), tidy/summary should
+      # always be std(S).
+      std.error = c(x$std.err * x$surv),
       conf.high = c(x$upper),
       conf.low = c(x$lower),
       state = rep(x$states, each = nrow(x$pstate))
@@ -79,7 +81,9 @@ tidy.survfit <- function(x, ...) {
       n.event = x$n.event,
       n.censor = x$n.censor,
       estimate = x$surv,
-      std.error = summary(x)$std.err,
+      # A survfit object may contain std(log S) or std(S), tidy/summary should
+      # always be std(S).
+      std.error = x$std.err * x$surv,
       conf.high = x$upper,
       conf.low = x$lower
     )

From 73638a76130eab585da0b1835926d753cb302007 Mon Sep 17 00:00:00 2001
From: Michael McCarthy <51542091+mccarthy-m-g@users.noreply.github.com>
Date: Sun, 4 Jun 2023 16:47:04 -0700
Subject: [PATCH 3/3] compute std.error manually instead of using `summary()`
 for compatibility with objects reformulated by `survfit0()`

---
 R/survival-survfit-tidiers.R | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/R/survival-survfit-tidiers.R b/R/survival-survfit-tidiers.R
index f685d78b2..208a8e712 100644
--- a/R/survival-survfit-tidiers.R
+++ b/R/survival-survfit-tidiers.R
@@ -58,6 +58,10 @@
 #'
 tidy.survfit <- function(x, ...) {
   if (inherits(x, "survfitms")) {
+    # A survfit object may contain std(log S) or std(S), tidy/summary should
+    # always be std(S).
+    if (!is.null(x$std.err) && x$logse) x$std.err <- x$std.err * x$pstate 
+    
     # c() coerces to vector
     ret <- data.frame(
       time = x$time,
@@ -65,7 +69,7 @@ tidy.survfit <- function(x, ...) {
       n.event = c(x$n.event),
       n.censor = c(x$n.censor),
       estimate = c(x$pstate),
-      std.error = c(summary(x)$std.err),
+      std.error = c(x$std.err),
       conf.high = c(x$upper),
       conf.low = c(x$lower),
       state = rep(x$states, each = nrow(x$pstate))
@@ -73,13 +77,17 @@ tidy.survfit <- function(x, ...) {
 
     ret <- ret[ret$state != "", ]
   } else {
+    # A survfit object may contain std(log S) or std(S), tidy/summary should
+    # always be std(S).
+    if (!is.null(x$std.err) && x$logse) x$std.err <- x$std.err * x$surv 
+    
     ret <- data.frame(
       time = x$time,
       n.risk = x$n.risk,
       n.event = x$n.event,
       n.censor = x$n.censor,
       estimate = x$surv,
-      std.error = summary(x)$std.err,
+      std.error = x$std.err,
       conf.high = x$upper,
       conf.low = x$lower
     )