From c3a4f7e126730be90a0e45c2f6be3e5ed2fdd804 Mon Sep 17 00:00:00 2001
From: Kuenzel <kuenzelt@emea.roche.com>
Date: Fri, 17 May 2024 10:46:14 +0200
Subject: [PATCH 1/8] fixed bug in generate_data and adapted tests

---
 R/generate_data.R                            | 21 ++++++++++++++------
 tests/testthat/test-aalen_johansen.R         |  4 ++--
 tests/testthat/test-inc_prop.R               |  2 +-
 tests/testthat/test-one_minus_kaplan_meier.R |  2 +-
 tests/testthat/test-prop_trans_inc_dens.R    |  2 +-
 tests/testthat/test-prop_trans_inc_dens_ce.R |  2 +-
 6 files changed, 21 insertions(+), 12 deletions(-)

diff --git a/R/generate_data.R b/R/generate_data.R
index df9a53b..c1dadca 100644
--- a/R/generate_data.R
+++ b/R/generate_data.R
@@ -39,7 +39,14 @@ generate_data <- function(n,
                           haz_death,
                           haz_soft) {
   assert_count(n, positive = TRUE)
-  assert_numeric(cens, lower = 0, finite = TRUE, any.missing = FALSE, len = 2L, unique = TRUE, sorted = TRUE)
+  assert_numeric(
+    cens,
+    lower = 0,
+    finite = TRUE,
+    any.missing = FALSE,
+    len = 2L,
+    unique = TRUE,
+    sorted = TRUE)
   assert_number(haz_ae, finite = TRUE)
   assert_number(haz_death, finite = TRUE)
   assert_number(haz_soft, finite = TRUE)
@@ -52,11 +59,13 @@ generate_data <- function(n,
   )
   haz_all <- sum(haz)
   result$time_to_event <- stats::rexp(n = n, rate = haz_all)
-  result$type_of_event <- 1L + stats::rbinom(
-    n = n,
-    size = 2,
-    prob = haz / haz_all
-  )
+
+  result$type_of_event <- sample(
+    1:3,
+    size = n,
+    prob = haz / haz_all,
+    replace = TRUE)
+
   result$cens <- stats::runif(n = n, min = cens[1L], max = cens[2L])
   result$type_of_event <- ifelse(
     result$time_to_event <= result$cens,
diff --git a/tests/testthat/test-aalen_johansen.R b/tests/testthat/test-aalen_johansen.R
index 971dad6..64cf2ac 100644
--- a/tests/testthat/test-aalen_johansen.R
+++ b/tests/testthat/test-aalen_johansen.R
@@ -8,7 +8,7 @@ test_that("Aalen Johansen works as expected", {
     haz_soft = 0.5
   )
   result <- aalen_johansen(data = df, ce = 2, tau = 4)
-  expected <- c(ae_prob = 0.2719, ae_prob_var = 0.0119, ce_prob = 0.7281, ce_prob_var = 0.0119)
+  expected <- c(ae_prob = 0.4792, ae_prob_var = 0.0266, ce_prob = 0.5208, ce_prob_var = 0.0266)
   expect_equal(result, expected, tolerance = 1e-4)
 })
 
@@ -39,7 +39,7 @@ test_that("Aalen Johansen works without competing events", {
   df <- df[df$type_of_event != 2, ]
   df <- df[df$type_of_event != 3, ]
   result <- aalen_johansen(data = df, ce = 2, tau = 4)
-  expected <- c(ae_prob = 0.5897, ae_prob_var = 0.0404, ce_prob = 0, ce_prob_var = 0)
+  expected <- c(ae_prob = 0.7643, ae_prob_var = 0.0363, ce_prob = 0, ce_prob_var = 0)
   expect_equal(result, expected, tolerance = 1e-4)
 })
 
diff --git a/tests/testthat/test-inc_prop.R b/tests/testthat/test-inc_prop.R
index e12fd11..d632cf0 100644
--- a/tests/testthat/test-inc_prop.R
+++ b/tests/testthat/test-inc_prop.R
@@ -8,6 +8,6 @@ test_that("inc_prop works as expected", {
     haz_soft = 0.5
   )
   result <- inc_prop(data = df, tau = 4)
-  expected <- c(ae_prob = 0.2, ae_prob_var = 0.0064)
+  expected <- c(ae_prob = 0.24, ae_prob_var = 0.0073)
   expect_equal(result, expected, tolerance = 1e-4)
 })
diff --git a/tests/testthat/test-one_minus_kaplan_meier.R b/tests/testthat/test-one_minus_kaplan_meier.R
index 92e78de..06bed4d 100644
--- a/tests/testthat/test-one_minus_kaplan_meier.R
+++ b/tests/testthat/test-one_minus_kaplan_meier.R
@@ -8,7 +8,7 @@ test_that("one_minus_kaplan_meier works as expected", {
     haz_soft = 0.5
   )
   result <- one_minus_kaplan_meier(data = df, tau = 4)
-  expected <- c(ae_prob = 0.3771350, ae_prob_var = 0.0260535)
+  expected <- c(ae_prob = 0.5865, ae_prob_var = 0.0394)
   expect_equal(result, expected, tolerance = 1e-4)
 })
 
diff --git a/tests/testthat/test-prop_trans_inc_dens.R b/tests/testthat/test-prop_trans_inc_dens.R
index e870379..8b28e0d 100644
--- a/tests/testthat/test-prop_trans_inc_dens.R
+++ b/tests/testthat/test-prop_trans_inc_dens.R
@@ -8,6 +8,6 @@ test_that("prop_trans_inc_dens works as expected", {
     haz_soft = 1.2
   )
   result <- prop_trans_inc_dens(data = df, tau = 0.1)
-  expected <- c(ae_prob = 0.33325, ae_prob_var = 0.0365)
+  expected <- c(ae_prob = 0.5554, ae_prob_var = 0.0325)
   expect_equal(result, expected, tolerance = 1e-4)
 })
diff --git a/tests/testthat/test-prop_trans_inc_dens_ce.R b/tests/testthat/test-prop_trans_inc_dens_ce.R
index da730b2..973aa5c 100644
--- a/tests/testthat/test-prop_trans_inc_dens_ce.R
+++ b/tests/testthat/test-prop_trans_inc_dens_ce.R
@@ -8,6 +8,6 @@ test_that("prop_trans_inc_dens_ce works as expected", {
     haz_soft = 1.2
   )
   result <- prop_trans_inc_dens_ce(data = df, ce = 2, tau = 0.1)
-  expected <- c(ae_prob = 0.296148137, ae_prob_var = 0.002755189)
+  expected <- c(ae_prob = 0.18114, ae_prob_var = 0.00205)
   expect_equal(result, expected, tolerance = 1e-4)
 })

From 7cf7a2f7bd6083ebc0bde8c79ab19795002d5937 Mon Sep 17 00:00:00 2001
From: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Date: Fri, 17 May 2024 08:50:03 +0000
Subject: [PATCH 2/8] [skip style] [skip vbump] Restyle files

---
 R/generate_data.R | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/R/generate_data.R b/R/generate_data.R
index c1dadca..c7189c7 100644
--- a/R/generate_data.R
+++ b/R/generate_data.R
@@ -46,7 +46,8 @@ generate_data <- function(n,
     any.missing = FALSE,
     len = 2L,
     unique = TRUE,
-    sorted = TRUE)
+    sorted = TRUE
+  )
   assert_number(haz_ae, finite = TRUE)
   assert_number(haz_death, finite = TRUE)
   assert_number(haz_soft, finite = TRUE)
@@ -64,7 +65,8 @@ generate_data <- function(n,
     1:3,
     size = n,
     prob = haz / haz_all,
-    replace = TRUE)
+    replace = TRUE
+  )
 
   result$cens <- stats::runif(n = n, min = cens[1L], max = cens[2L])
   result$type_of_event <- ifelse(

From 5700e1834bcde51f6aef7f77030771906daccb09 Mon Sep 17 00:00:00 2001
From: Kuenzel <kuenzelt@emea.roche.com>
Date: Fri, 17 May 2024 17:28:21 +0200
Subject: [PATCH 3/8] added test to show old version of generate_data fails

---
 tests/testthat/test-generate_data.R | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/tests/testthat/test-generate_data.R b/tests/testthat/test-generate_data.R
index 9b0ac63..70aaea2 100644
--- a/tests/testthat/test-generate_data.R
+++ b/tests/testthat/test-generate_data.R
@@ -12,3 +12,18 @@ test_that("generate_data works as expected", {
   expect_identical(result$id, 1:10)
   expect_integer(result$type_of_event, lower = 0, upper = 3, any.missing = FALSE)
 })
+
+test_that("show bug in v1 of generate_data", {
+  set.seed(123)
+  df <- generate_data(
+    n = 10^6,
+    cens = c(1000, 1001),
+    haz_ae = 0.2,
+    haz_death = 0.3,
+    haz_soft = 0.5
+  )
+  result <- inc_prop(data = df, tau = 4)
+  expected <- c(ae_prob = 0.2)
+  expect_equal(result["ae_prob"], expected, tolerance = 0.1)
+
+})

From 53a1f902cbc02ae62768ccbc88c10177c5b529d1 Mon Sep 17 00:00:00 2001
From: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Date: Fri, 17 May 2024 15:30:24 +0000
Subject: [PATCH 4/8] [skip style] [skip vbump] Restyle files

---
 tests/testthat/test-generate_data.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/testthat/test-generate_data.R b/tests/testthat/test-generate_data.R
index 70aaea2..4485815 100644
--- a/tests/testthat/test-generate_data.R
+++ b/tests/testthat/test-generate_data.R
@@ -25,5 +25,4 @@ test_that("show bug in v1 of generate_data", {
   result <- inc_prop(data = df, tau = 4)
   expected <- c(ae_prob = 0.2)
   expect_equal(result["ae_prob"], expected, tolerance = 0.1)
-
 })

From 65cec4f4bce53877017aab486c5e71d5b9f32ac3 Mon Sep 17 00:00:00 2001
From: kuenzelt <122105979+kuenzelt@users.noreply.github.com>
Date: Wed, 5 Jun 2024 15:08:46 +0200
Subject: [PATCH 5/8] Update tests/testthat/test-generate_data.R

Co-authored-by: Daniel Sabanes Bove <danielinteractive@users.noreply.github.com>
---
 tests/testthat/test-generate_data.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-generate_data.R b/tests/testthat/test-generate_data.R
index 4485815..9bbed67 100644
--- a/tests/testthat/test-generate_data.R
+++ b/tests/testthat/test-generate_data.R
@@ -13,7 +13,7 @@ test_that("generate_data works as expected", {
   expect_integer(result$type_of_event, lower = 0, upper = 3, any.missing = FALSE)
 })
 
-test_that("show bug in v1 of generate_data", {
+test_that("generate_data correctly ... ", {
   set.seed(123)
   df <- generate_data(
     n = 10^6,

From a12a9396424855e59ddf9dbcd38bef20129a1051 Mon Sep 17 00:00:00 2001
From: Kuenzel <kuenzelt@emea.roche.com>
Date: Wed, 5 Jun 2024 15:25:59 +0200
Subject: [PATCH 6/8] updated NEWS.md

---
 NEWS.md | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index 405c792..196a701 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -7,3 +7,14 @@
 
 - Estimators that do not account for competing events (incidence proportion, incidence density, Inverse Kaplan Meier).
 - Estimators accounting for competing events (incidence proportion accounting for competing events and Aalen-Johansen, both first with death only as hard competing event, or using all competing events).
+
+
+### bug fixes
+
+- changed the way data is generated in function generate_data:
+
+  result$type_of_event <- 1L + stats::rbinom(n = n, size = 2, prob = haz/haz_all)
+
+  was replaced with
+
+  result$type_of_event <- sample(1:3, size = n, prob = haz / haz_all, replace =      TRUE).

From cd36249620dba79015cfa83d1696ba157e36e466 Mon Sep 17 00:00:00 2001
From: Kuenzel <kuenzelt@emea.roche.com>
Date: Wed, 5 Jun 2024 15:25:59 +0200
Subject: [PATCH 7/8] updated NEWS.md

---
 NEWS.md | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index 405c792..efb5ef9 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,12 @@
 # savvyr 0.1.0
 
+### Bug Fixes
+
+- changed the way data is generated in function "generate_data":
+  variable "type_event" is now generated using the sample function which accurately 
+  reflects the specified hazard for AE, death and soft competing events.
+
+
 - First CRAN version of the package.
 - The package provides functions to easily conduct the improved AE analyses proposed by the SAVVY framework.
 
@@ -7,3 +14,6 @@
 
 - Estimators that do not account for competing events (incidence proportion, incidence density, Inverse Kaplan Meier).
 - Estimators accounting for competing events (incidence proportion accounting for competing events and Aalen-Johansen, both first with death only as hard competing event, or using all competing events).
+
+
+

From b8b9db05a9e28bde86b2ff4a879e05933b064098 Mon Sep 17 00:00:00 2001
From: Daniel Sabanes Bove <daniel.sabanes_bove@roche.com>
Date: Thu, 6 Jun 2024 11:28:12 +0200
Subject: [PATCH 8/8] bump up version, polish NEWS file

---
 DESCRIPTION | 4 ++--
 NEWS.md     | 9 ++++-----
 2 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 8606c5c..8fc2adb 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Type: Package
 Package: savvyr
 Title: Survival Analysis for AdVerse Events with VarYing Follow-Up Times
-Version: 0.1.0
-Date: 2024-02-20
+Version: 0.1.1
+Date: 2024-06-06
 Authors@R: c(
     person("Thomas", "Kuenzel", email = "thomas.kuenzel@roche.com", role = c("aut", "cre")),
     person("Kaspar", "Rufibach", email = "kaspar.rufibach@roche.com", role = "aut"),
diff --git a/NEWS.md b/NEWS.md
index efb5ef9..9c33d1f 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,11 +1,10 @@
-# savvyr 0.1.0
+# savvyr 0.1.1
 
 ### Bug Fixes
 
-- changed the way data is generated in function "generate_data":
-  variable "type_event" is now generated using the sample function which accurately 
-  reflects the specified hazard for AE, death and soft competing events.
-
+- Changed the way data is generated in function 'generate_data': The variable 'type_event' is now generated such that it accurately reflects the specified hazards for AE, death and soft competing events.
+  
+# savvyr 0.1.0
 
 - First CRAN version of the package.
 - The package provides functions to easily conduct the improved AE analyses proposed by the SAVVY framework.