From 91b8908433c84b7aa88e15c319288e0e4b43a7fa Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Wed, 12 Jun 2024 19:01:32 +0200
Subject: [PATCH 1/7] stable
---
.../_snaps/stable/tables-efficacy-mmrmt01.md | 29 ++++++++++++++++
.../_snaps/stable/tables-efficacy-rbmit01.md | 34 +++++++++----------
.../_snaps/stable/tables-lab-results-lbt11.md | 6 ++--
.../stable/tables-lab-results-lbt11_bl.md | 6 ++--
4 files changed, 52 insertions(+), 23 deletions(-)
diff --git a/package/tests/testthat/_snaps/stable/tables-efficacy-mmrmt01.md b/package/tests/testthat/_snaps/stable/tables-efficacy-mmrmt01.md
index 7651df082f..138240e761 100644
--- a/package/tests/testthat/_snaps/stable/tables-efficacy-mmrmt01.md
+++ b/package/tests/testthat/_snaps/stable/tables-efficacy-mmrmt01.md
@@ -149,3 +149,32 @@
Relative Increase (%) 8.7% 4.3%
p-value (MMRM) 0.0324 0.2924
+# tables/efficacy/mmrmt01.qmd result_baseline stable
+
+ Code
+ print(data_snap[[i]])
+ Output
+ Visit All Patients
+ Statistics (N=400)
+ ———————————————————————————————————————
+ WEEK 1 DAY 8
+ n 400
+ Adjusted Mean (SE) 3.615 (0.620)
+ 95% CI (2.396, 4.834)
+ WEEK 2 DAY 15
+ n 400
+ Adjusted Mean (SE) 8.870 (0.602)
+ 95% CI (7.687, 10.053)
+ WEEK 3 DAY 22
+ n 400
+ Adjusted Mean (SE) 15.094 (0.683)
+ 95% CI (13.751, 16.437)
+ WEEK 4 DAY 29
+ n 400
+ Adjusted Mean (SE) 19.009 (0.717)
+ 95% CI (17.599, 20.418)
+ WEEK 5 DAY 36
+ n 400
+ Adjusted Mean (SE) 24.028 (0.747)
+ 95% CI (22.560, 25.496)
+
diff --git a/package/tests/testthat/_snaps/stable/tables-efficacy-rbmit01.md b/package/tests/testthat/_snaps/stable/tables-efficacy-rbmit01.md
index 4242c9d782..7e93ad6359 100644
--- a/package/tests/testthat/_snaps/stable/tables-efficacy-rbmit01.md
+++ b/package/tests/testthat/_snaps/stable/tables-efficacy-rbmit01.md
@@ -13,24 +13,24 @@
Relative Reduction (%) 5.7%
p-value (RBMI) 0.8932
5
- Adjusted Mean (SE) -4.241 (0.646) -2.814 (0.643)
- 95% CI (-5.537, -2.984) (-4.084, -1.545)
- Difference in Adjusted Means (SE) 1.447 (0.915)
- 95% CI (-0.360, 3.254)
- Relative Reduction (%) -34.0%
- p-value (RBMI) 0.1159
+ Adjusted Mean (SE) -4.256 (0.649) -2.822 (0.646)
+ 95% CI (-5.538, -2.974) (-4.098, -1.545)
+ Difference in Adjusted Means (SE) 1.434 (0.920)
+ 95% CI (-0.383, 3.252)
+ Relative Reduction (%) -33.7%
+ p-value (RBMI) 0.1211
6
- Adjusted Mean (SE) -6.365 (0.721) -4.123 (0.689)
- 95% CI (-7.791, -4.939) (-5.484, -2.761)
- Difference in Adjusted Means (SE) 2.242 (0.998)
- 95% CI (0.269, 4.216)
- Relative Reduction (%) -35.2%
- p-value (RBMI) 0.0262
+ Adjusted Mean (SE) -6.373 (0.716) -4.164 (0.689)
+ 95% CI (-7.789, -4.956) (-5.524, -2.803)
+ Difference in Adjusted Means (SE) 2.209 (0.990)
+ 95% CI (0.253, 4.165)
+ Relative Reduction (%) -34.7%
+ p-value (RBMI) 0.0271
7
- Adjusted Mean (SE) -7.665 (0.831) -4.802 (0.762)
- 95% CI (-9.314, -6.017) (-6.308, -3.296)
- Difference in Adjusted Means (SE) 2.863 (1.120)
- 95% CI (0.645, 5.082)
- Relative Reduction (%) -37.4%
+ Adjusted Mean (SE) -7.640 (0.822) -4.823 (0.767)
+ 95% CI (-9.270, -6.010) (-6.341, -3.306)
+ Difference in Adjusted Means (SE) 2.816 (1.103)
+ 95% CI (0.634, 4.999)
+ Relative Reduction (%) -36.9%
p-value (RBMI) 0.0118
diff --git a/package/tests/testthat/_snaps/stable/tables-lab-results-lbt11.md b/package/tests/testthat/_snaps/stable/tables-lab-results-lbt11.md
index 32c8a8d526..7a4c838705 100644
--- a/package/tests/testthat/_snaps/stable/tables-lab-results-lbt11.md
+++ b/package/tests/testthat/_snaps/stable/tables-lab-results-lbt11.md
@@ -66,9 +66,9 @@
Hazard Ratio 0.43 0.58
95% CI (0.19, 0.94) (0.26, 1.27)
Stratified By: RACE, SEX
- p-value (log-rank) 0.0295 0.1687
- Hazard Ratio 0.43 0.58
- 95% CI (0.19, 0.94) (0.26, 1.27)
+ p-value (log-rank) 0.0858 0.1605
+ Hazard Ratio 0.51 0.57
+ 95% CI (0.23, 1.12) (0.26, 1.26)
———————————————————————————————————————————————————————————————————————————————————————
{1} - Censored observations: range minimum & maximum
diff --git a/package/tests/testthat/_snaps/stable/tables-lab-results-lbt11_bl.md b/package/tests/testthat/_snaps/stable/tables-lab-results-lbt11_bl.md
index 23e0c6119b..513d6f6e2f 100644
--- a/package/tests/testthat/_snaps/stable/tables-lab-results-lbt11_bl.md
+++ b/package/tests/testthat/_snaps/stable/tables-lab-results-lbt11_bl.md
@@ -64,9 +64,9 @@
Hazard Ratio 1.27 0.84
95% CI (0.63, 2.56) (0.40, 1.75)
Stratified By: RACE, SEX
- p-value (log-rank) 0.0858 0.1605
- Hazard Ratio 0.51 0.57
- 95% CI (0.23, 1.12) (0.26, 1.26)
+ p-value (log-rank) 0.3886 0.7970
+ Hazard Ratio 1.39 0.91
+ 95% CI (0.65, 2.97) (0.43, 1.93)
———————————————————————————————————————————————————————————————————————————————————————
{1} - Censored observations: range minimum & maximum
From a132848f78210863c4781c80604cc39c0cb4730c Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Wed, 12 Jun 2024 19:04:58 +0200
Subject: [PATCH 2/7] devel
---
.../development/tables-efficacy-mmrmt01.md | 33 +++++++++++++++--
.../development/tables-efficacy-rbmit01.md | 36 +++++++++----------
2 files changed, 49 insertions(+), 20 deletions(-)
diff --git a/package/tests/testthat/_snaps/development/tables-efficacy-mmrmt01.md b/package/tests/testthat/_snaps/development/tables-efficacy-mmrmt01.md
index 3f35fd0afa..7efad52641 100644
--- a/package/tests/testthat/_snaps/development/tables-efficacy-mmrmt01.md
+++ b/package/tests/testthat/_snaps/development/tables-efficacy-mmrmt01.md
@@ -13,7 +13,7 @@
Difference in Adjusted Means (SE) 0.759 (0.973) -0.325 (0.976)
95% CI (-1.155, 2.672) (-2.243, 1.593)
Relative Increase (%) 21.8% -9.3%
- p-value (MMRM) 0.4362 0.7394
+ p-value (MMRM) 0.4362 0.7393
WEEK 2 DAY 15
n 134 134 132
Adjusted Mean (SE) 9.135 (0.768) 9.018 (0.767) 8.509 (0.773)
@@ -21,7 +21,7 @@
Difference in Adjusted Means (SE) -0.117 (1.087) -0.626 (1.090)
95% CI (-2.253, 2.020) (-2.768, 1.517)
Relative Increase (%) -1.3% -6.8%
- p-value (MMRM) 0.9146 0.5662
+ p-value (MMRM) 0.9147 0.5662
WEEK 3 DAY 22
n 134 134 132
Adjusted Mean (SE) 13.547 (0.871) 16.014 (0.871) 15.789 (0.877)
@@ -149,3 +149,32 @@
Relative Increase (%) 8.7% 4.3%
p-value (MMRM) 0.0324 0.2924
+# tables/efficacy/mmrmt01.qmd result_baseline development
+
+ Code
+ print(data_snap[[i]])
+ Output
+ Visit All Patients
+ Statistics (N=400)
+ ———————————————————————————————————————
+ WEEK 1 DAY 8
+ n 400
+ Adjusted Mean (SE) 3.615 (0.620)
+ 95% CI (2.396, 4.834)
+ WEEK 2 DAY 15
+ n 400
+ Adjusted Mean (SE) 8.870 (0.602)
+ 95% CI (7.687, 10.053)
+ WEEK 3 DAY 22
+ n 400
+ Adjusted Mean (SE) 15.094 (0.683)
+ 95% CI (13.751, 16.437)
+ WEEK 4 DAY 29
+ n 400
+ Adjusted Mean (SE) 19.009 (0.717)
+ 95% CI (17.599, 20.418)
+ WEEK 5 DAY 36
+ n 400
+ Adjusted Mean (SE) 24.028 (0.747)
+ 95% CI (22.560, 25.496)
+
diff --git a/package/tests/testthat/_snaps/development/tables-efficacy-rbmit01.md b/package/tests/testthat/_snaps/development/tables-efficacy-rbmit01.md
index 6d60b03535..cf4408adc8 100644
--- a/package/tests/testthat/_snaps/development/tables-efficacy-rbmit01.md
+++ b/package/tests/testthat/_snaps/development/tables-efficacy-rbmit01.md
@@ -13,24 +13,24 @@
Relative Reduction (%) 5.7%
p-value (RBMI) 0.8932
5
- Adjusted Mean (SE) -4.247 (0.649) -2.815 (0.646)
- 95% CI (-5.527, -2.966) (-4.091, -1.540)
- Difference in Adjusted Means (SE) 1.431 (0.915)
- 95% CI (-0.377, 3.239)
- Relative Reduction (%) -33.7%
- p-value (RBMI) 0.1200
+ Adjusted Mean (SE) -4.253 (0.651) -2.812 (0.645)
+ 95% CI (-5.539, -2.968) (-4.087, -1.537)
+ Difference in Adjusted Means (SE) 1.442 (0.921)
+ 95% CI (-0.377, 3.261)
+ Relative Reduction (%) -33.9%
+ p-value (RBMI) 0.1195
6
- Adjusted Mean (SE) -6.388 (0.724) -4.115 (0.692)
- 95% CI (-7.820, -4.956) (-5.481, -2.748)
- Difference in Adjusted Means (SE) 2.274 (1.005)
- 95% CI (0.287, 4.261)
- Relative Reduction (%) -35.6%
- p-value (RBMI) 0.0252
+ Adjusted Mean (SE) -6.359 (0.724) -4.126 (0.696)
+ 95% CI (-7.791, -4.927) (-5.502, -2.749)
+ Difference in Adjusted Means (SE) 2.234 (1.000)
+ 95% CI (0.258, 4.210)
+ Relative Reduction (%) -35.1%
+ p-value (RBMI) 0.0270
7
- Adjusted Mean (SE) -7.649 (0.792) -4.812 (0.764)
- 95% CI (-9.217, -6.081) (-6.323, -3.301)
- Difference in Adjusted Means (SE) 2.836 (1.121)
- 95% CI (0.617, 5.056)
- Relative Reduction (%) -37.1%
- p-value (RBMI) 0.0127
+ Adjusted Mean (SE) -7.612 (0.822) -4.819 (0.767)
+ 95% CI (-9.242, -5.982) (-6.335, -3.302)
+ Difference in Adjusted Means (SE) 2.793 (1.110)
+ 95% CI (0.597, 4.989)
+ Relative Reduction (%) -36.7%
+ p-value (RBMI) 0.0131
From 73d1fc24a130de1f8bb41c32ff043d9fe2b47530 Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Wed, 12 Jun 2024 19:06:45 +0200
Subject: [PATCH 3/7] rm unused snap files
---
.../graphs-efficacy-fstg01/fstg01-plot_v1.svg | 147 -
.../graphs-efficacy-fstg01/fstg01-plot_v2.svg | 147 -
.../graphs-efficacy-fstg01/fstg01-plot_v3.svg | 101 -
.../graphs-efficacy-fstg01/fstg01-plot_v4.svg | 147 -
.../graphs-efficacy-fstg01/fstg01-plot_v5.svg | 147 -
.../graphs-efficacy-fstg02/fstg02-plot_v1.svg | 133 -
.../graphs-efficacy-fstg02/fstg02-plot_v2.svg | 133 -
.../graphs-efficacy-fstg02/fstg02-plot_v3.svg | 101 -
.../graphs-efficacy-fstg02/fstg02-plot_v4.svg | 133 -
.../graphs-efficacy-kmg01/kmg01-plot_v1.svg | 612 -
.../graphs-efficacy-kmg01/kmg01-plot_v2.svg | 612 -
.../graphs-efficacy-kmg01/kmg01-plot_v3.svg | 590 -
.../graphs-efficacy-kmg01/kmg01-plot_v4.svg | 178 -
.../graphs-efficacy-kmg01/kmg01-plot_v5.svg | 396 -
.../graphs-efficacy-kmg01/kmg01-plot_v6.svg | 612 -
.../mmrmg01-plot_v1.svg | 166 -
.../mmrmg01-plot_v2.svg | 172 -
.../mmrmg01-plot_v3.svg | 332 -
.../mmrmg01-plot_v4.svg | 137 -
.../mmrmg01-plot_v5.svg | 2740 ---
.../mmrmg01-plot_v6.svg | 2686 ---
.../mmrmg02-plot_v1.svg | 103 -
.../mmrmg02-plot_v2.svg | 103 -
.../graphs-other-brg01/brg01-plot_v1.svg | 73 -
.../graphs-other-brg01/brg01-plot_v2.svg | 74 -
.../graphs-other-brg01/brg01-plot_v3.svg | 73 -
.../graphs-other-brg01/brg01-plot_v4.svg | 70 -
.../graphs-other-brg01/brg01-plot_v5.svg | 72 -
.../graphs-other-brg01/brg01-plot_v6.svg | 81 -
.../graphs-other-brg01/brg01-plot_v7.svg | 77 -
.../graphs-other-brg01/brg01-plot_v8.svg | 107 -
.../graphs-other-brg01/brg01-plot_v9.svg | 96 -
.../graphs-other-bwg01/bwg01-plot_v1.svg | 100 -
.../graphs-other-bwg01/bwg01-plot_v2.svg | 93 -
.../graphs-other-bwg01/bwg01-plot_v3.svg | 142 -
.../graphs-other-bwg01/bwg01-plot_v4.svg | 124 -
.../graphs-other-bwg01/bwg01-plot_v5.svg | 91 -
.../graphs-other-bwg01/bwg01-plot_v6.svg | 216 -
.../graphs-other-bwg01/bwg01-plot_v7.svg | 219 -
.../graphs-other-bwg01/bwg01-plot_v8.svg | 145 -
.../graphs-other-bwg01/bwg01-plot_v9.svg | 125 -
.../cig01-plot_v1_and_v2.svg | 103 -
.../graphs-other-cig01/cig01-plot_v3.svg | 99 -
.../graphs-other-cig01/cig01-plot_v4.svg | 111 -
.../graphs-other-cig01/cig01-plot_v5.svg | 98 -
.../graphs-other-ltg01/ltg01-plot_v1.svg | 754 -
.../graphs-other-ltg01/ltg01-plot_v2.svg | 757 -
.../graphs-other-ltg01/ltg01-plot_v3.svg | 3248 ----
.../graphs-other-ltg01/ltg01-plot_v4.svg | 14601 ---------------
.../graphs-other-ltg01/ltg01-plot_v51.svg | 14822 ---------------
.../graphs-other-ltg01/ltg01-plot_v52.svg | 15025 ----------------
.../graphs-other-ltg01/ltg01-plot_v53.svg | 14822 ---------------
.../graphs-other-mng01/mng01-plot_v1.svg | 130 -
.../graphs-other-mng01/mng01-plot_v2.svg | 134 -
.../graphs-other-mng01/mng01-plot_v3.svg | 134 -
.../graphs-other-mng01/mng01-plot_v4.svg | 134 -
.../graphs-other-mng01/mng01-plot_v5.svg | 230 -
.../graphs-other-mng01/mng01-plot_v6.svg | 266 -
.../graphs-other-mng01/mng01-plot_v7.svg | 149 -
.../pkcg01-plot_v1.svg | 80 -
.../pkcg01-plot_v2.svg | 82 -
.../pkcg02-plot_v1.svg | 206 -
.../pkcg02-plot_v2.svg | 208 -
.../pkcg03-plot_v1.svg | 154 -
.../pkcg03-plot_v2.svg | 156 -
.../pkpg01-plot_v1.svg | 82 -
.../pkpg01-plot_v2.svg | 156 -
.../pkpg02-plot_v1.svg | 876 -
.../pkpg02-plot_v2.svg | 861 -
.../pkpg03-plot_v1.svg | 184 -
.../pkpg04-plot_v1.svg | 2575 ---
.../pkpg06-plot_v1.svg | 142 -
.../pkpg06-plot_v2.svg | 95 -
.../pkpg06-plot_v3.svg | 129 -
.../pkpg06-plot_v4.svg | 228 -
.../graphs-efficacy-fstg01/fstg01-plot_v1.svg | 135 -
.../graphs-efficacy-fstg01/fstg01-plot_v2.svg | 135 -
.../graphs-efficacy-fstg01/fstg01-plot_v3.svg | 88 -
.../graphs-efficacy-fstg01/fstg01-plot_v4.svg | 135 -
.../graphs-efficacy-fstg01/fstg01-plot_v5.svg | 135 -
.../graphs-efficacy-fstg02/fstg02-plot_v1.svg | 121 -
.../graphs-efficacy-fstg02/fstg02-plot_v2.svg | 121 -
.../graphs-efficacy-fstg02/fstg02-plot_v3.svg | 88 -
.../graphs-efficacy-fstg02/fstg02-plot_v4.svg | 121 -
.../graphs-efficacy-kmg01/kmg01-plot_v1.svg | 968 -
.../graphs-efficacy-kmg01/kmg01-plot_v2.svg | 968 -
.../graphs-efficacy-kmg01/kmg01-plot_v3.svg | 789 -
.../graphs-efficacy-kmg01/kmg01-plot_v4.svg | 535 -
.../graphs-efficacy-kmg01/kmg01-plot_v5.svg | 752 -
.../graphs-efficacy-kmg01/kmg01-plot_v6.svg | 968 -
.../mmrmg01-plot_v1.svg | 166 -
.../mmrmg01-plot_v2.svg | 172 -
.../mmrmg01-plot_v3.svg | 332 -
.../mmrmg01-plot_v4.svg | 137 -
.../mmrmg01-plot_v5.svg | 2740 ---
.../mmrmg01-plot_v6.svg | 2686 ---
.../mmrmg02-plot_v1.svg | 88 -
.../mmrmg02-plot_v2.svg | 88 -
.../graphs-other-brg01/brg01-plot_v1.svg | 73 -
.../graphs-other-brg01/brg01-plot_v2.svg | 74 -
.../graphs-other-brg01/brg01-plot_v3.svg | 73 -
.../graphs-other-brg01/brg01-plot_v4.svg | 70 -
.../graphs-other-brg01/brg01-plot_v5.svg | 72 -
.../graphs-other-brg01/brg01-plot_v6.svg | 81 -
.../graphs-other-brg01/brg01-plot_v7.svg | 77 -
.../graphs-other-brg01/brg01-plot_v8.svg | 107 -
.../graphs-other-brg01/brg01-plot_v9.svg | 96 -
.../graphs-other-bwg01/bwg01-plot_v1.svg | 100 -
.../graphs-other-bwg01/bwg01-plot_v2.svg | 93 -
.../graphs-other-bwg01/bwg01-plot_v3.svg | 142 -
.../graphs-other-bwg01/bwg01-plot_v4.svg | 124 -
.../graphs-other-bwg01/bwg01-plot_v5.svg | 91 -
.../graphs-other-bwg01/bwg01-plot_v6.svg | 216 -
.../graphs-other-bwg01/bwg01-plot_v7.svg | 219 -
.../graphs-other-bwg01/bwg01-plot_v8.svg | 145 -
.../graphs-other-bwg01/bwg01-plot_v9.svg | 125 -
.../cig01-plot_v1_and_v2.svg | 103 -
.../graphs-other-cig01/cig01-plot_v3.svg | 99 -
.../graphs-other-cig01/cig01-plot_v4.svg | 111 -
.../graphs-other-cig01/cig01-plot_v5.svg | 98 -
.../graphs-other-ltg01/ltg01-plot_v1.svg | 754 -
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.../graphs-other-ltg01/ltg01-plot_v3.svg | 3248 ----
.../graphs-other-ltg01/ltg01-plot_v4.svg | 14601 ---------------
.../graphs-other-ltg01/ltg01-plot_v51.svg | 14822 ---------------
.../graphs-other-ltg01/ltg01-plot_v52.svg | 15025 ----------------
.../graphs-other-ltg01/ltg01-plot_v53.svg | 14822 ---------------
.../graphs-other-mng01/mng01-plot_v1.svg | 130 -
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.../graphs-other-mng01/mng01-plot_v6.svg | 266 -
.../graphs-other-mng01/mng01-plot_v7.svg | 149 -
.../pkcg01-plot_v1.svg | 80 -
.../pkcg01-plot_v2.svg | 82 -
.../pkcg02-plot_v1.svg | 206 -
.../pkcg02-plot_v2.svg | 208 -
.../pkcg03-plot_v1.svg | 154 -
.../pkcg03-plot_v2.svg | 156 -
.../pkpg01-plot_v1.svg | 82 -
.../pkpg01-plot_v2.svg | 156 -
.../pkpg02-plot_v1.svg | 876 -
.../pkpg02-plot_v2.svg | 861 -
.../pkpg03-plot_v1.svg | 184 -
.../pkpg04-plot_v1.svg | 2575 ---
.../pkpg06-plot_v1.svg | 142 -
.../pkpg06-plot_v2.svg | 95 -
.../pkpg06-plot_v3.svg | 129 -
.../pkpg06-plot_v4.svg | 228 -
150 files changed, 170714 deletions(-)
delete mode 100644 package/tests/testthat/_snaps/development/graphs-efficacy-fstg01/fstg01-plot_v1.svg
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diff --git a/package/tests/testthat/_snaps/stable/graphs-other-mng01/mng01-plot_v2.svg b/package/tests/testthat/_snaps/stable/graphs-other-mng01/mng01-plot_v2.svg
deleted file mode 100644
index 3c6b190b16..0000000000
--- a/package/tests/testthat/_snaps/stable/graphs-other-mng01/mng01-plot_v2.svg
+++ /dev/null
@@ -1,134 +0,0 @@
-
-
diff --git a/package/tests/testthat/_snaps/stable/graphs-other-mng01/mng01-plot_v3.svg b/package/tests/testthat/_snaps/stable/graphs-other-mng01/mng01-plot_v3.svg
deleted file mode 100644
index 1f1f128eaa..0000000000
--- a/package/tests/testthat/_snaps/stable/graphs-other-mng01/mng01-plot_v3.svg
+++ /dev/null
@@ -1,134 +0,0 @@
-
-
diff --git a/package/tests/testthat/_snaps/stable/graphs-other-mng01/mng01-plot_v4.svg b/package/tests/testthat/_snaps/stable/graphs-other-mng01/mng01-plot_v4.svg
deleted file mode 100644
index a1e019cb6d..0000000000
--- a/package/tests/testthat/_snaps/stable/graphs-other-mng01/mng01-plot_v4.svg
+++ /dev/null
@@ -1,134 +0,0 @@
-
-
diff --git a/package/tests/testthat/_snaps/stable/graphs-other-mng01/mng01-plot_v5.svg b/package/tests/testthat/_snaps/stable/graphs-other-mng01/mng01-plot_v5.svg
deleted file mode 100644
index 5f62f27633..0000000000
--- a/package/tests/testthat/_snaps/stable/graphs-other-mng01/mng01-plot_v5.svg
+++ /dev/null
@@ -1,230 +0,0 @@
-
-
diff --git a/package/tests/testthat/_snaps/stable/graphs-other-mng01/mng01-plot_v6.svg b/package/tests/testthat/_snaps/stable/graphs-other-mng01/mng01-plot_v6.svg
deleted file mode 100644
index f6c46eaf2e..0000000000
--- a/package/tests/testthat/_snaps/stable/graphs-other-mng01/mng01-plot_v6.svg
+++ /dev/null
@@ -1,266 +0,0 @@
-
-
diff --git a/package/tests/testthat/_snaps/stable/graphs-other-mng01/mng01-plot_v7.svg b/package/tests/testthat/_snaps/stable/graphs-other-mng01/mng01-plot_v7.svg
deleted file mode 100644
index c2713a870b..0000000000
--- a/package/tests/testthat/_snaps/stable/graphs-other-mng01/mng01-plot_v7.svg
+++ /dev/null
@@ -1,149 +0,0 @@
-
-
diff --git a/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkcg01/pkcg01-plot_v1.svg b/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkcg01/pkcg01-plot_v1.svg
deleted file mode 100644
index cd7e5edb94..0000000000
--- a/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkcg01/pkcg01-plot_v1.svg
+++ /dev/null
@@ -1,80 +0,0 @@
-
-
diff --git a/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkcg01/pkcg01-plot_v2.svg b/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkcg01/pkcg01-plot_v2.svg
deleted file mode 100644
index 36c8f024f8..0000000000
--- a/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkcg01/pkcg01-plot_v2.svg
+++ /dev/null
@@ -1,82 +0,0 @@
-
-
diff --git a/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkcg02/pkcg02-plot_v1.svg b/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkcg02/pkcg02-plot_v1.svg
deleted file mode 100644
index e8e520eb99..0000000000
--- a/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkcg02/pkcg02-plot_v1.svg
+++ /dev/null
@@ -1,206 +0,0 @@
-
-
diff --git a/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkcg02/pkcg02-plot_v2.svg b/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkcg02/pkcg02-plot_v2.svg
deleted file mode 100644
index 5f7a8078e0..0000000000
--- a/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkcg02/pkcg02-plot_v2.svg
+++ /dev/null
@@ -1,208 +0,0 @@
-
-
diff --git a/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkcg03/pkcg03-plot_v1.svg b/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkcg03/pkcg03-plot_v1.svg
deleted file mode 100644
index af6069ed4e..0000000000
--- a/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkcg03/pkcg03-plot_v1.svg
+++ /dev/null
@@ -1,154 +0,0 @@
-
-
diff --git a/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkcg03/pkcg03-plot_v2.svg b/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkcg03/pkcg03-plot_v2.svg
deleted file mode 100644
index 4b9f455ff6..0000000000
--- a/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkcg03/pkcg03-plot_v2.svg
+++ /dev/null
@@ -1,156 +0,0 @@
-
-
diff --git a/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkpg01/pkpg01-plot_v1.svg b/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkpg01/pkpg01-plot_v1.svg
deleted file mode 100644
index f5049fbcc2..0000000000
--- a/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkpg01/pkpg01-plot_v1.svg
+++ /dev/null
@@ -1,82 +0,0 @@
-
-
diff --git a/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkpg01/pkpg01-plot_v2.svg b/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkpg01/pkpg01-plot_v2.svg
deleted file mode 100644
index a2d3676170..0000000000
--- a/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkpg01/pkpg01-plot_v2.svg
+++ /dev/null
@@ -1,156 +0,0 @@
-
-
diff --git a/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkpg02/pkpg02-plot_v1.svg b/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkpg02/pkpg02-plot_v1.svg
deleted file mode 100644
index 8249da5b01..0000000000
--- a/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkpg02/pkpg02-plot_v1.svg
+++ /dev/null
@@ -1,876 +0,0 @@
-
-
diff --git a/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkpg02/pkpg02-plot_v2.svg b/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkpg02/pkpg02-plot_v2.svg
deleted file mode 100644
index f89c5db8cb..0000000000
--- a/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkpg02/pkpg02-plot_v2.svg
+++ /dev/null
@@ -1,861 +0,0 @@
-
-
diff --git a/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkpg03/pkpg03-plot_v1.svg b/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkpg03/pkpg03-plot_v1.svg
deleted file mode 100644
index 4cdca4c7ae..0000000000
--- a/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkpg03/pkpg03-plot_v1.svg
+++ /dev/null
@@ -1,184 +0,0 @@
-
-
diff --git a/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkpg04/pkpg04-plot_v1.svg b/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkpg04/pkpg04-plot_v1.svg
deleted file mode 100644
index f412cf9b26..0000000000
--- a/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkpg04/pkpg04-plot_v1.svg
+++ /dev/null
@@ -1,2575 +0,0 @@
-
-
diff --git a/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkpg06/pkpg06-plot_v1.svg b/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkpg06/pkpg06-plot_v1.svg
deleted file mode 100644
index 343e9e4a4f..0000000000
--- a/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkpg06/pkpg06-plot_v1.svg
+++ /dev/null
@@ -1,142 +0,0 @@
-
-
diff --git a/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkpg06/pkpg06-plot_v2.svg b/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkpg06/pkpg06-plot_v2.svg
deleted file mode 100644
index 63cd8130ca..0000000000
--- a/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkpg06/pkpg06-plot_v2.svg
+++ /dev/null
@@ -1,95 +0,0 @@
-
-
diff --git a/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkpg06/pkpg06-plot_v3.svg b/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkpg06/pkpg06-plot_v3.svg
deleted file mode 100644
index dbfd87691a..0000000000
--- a/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkpg06/pkpg06-plot_v3.svg
+++ /dev/null
@@ -1,129 +0,0 @@
-
-
diff --git a/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkpg06/pkpg06-plot_v4.svg b/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkpg06/pkpg06-plot_v4.svg
deleted file mode 100644
index 95b880d95d..0000000000
--- a/package/tests/testthat/_snaps/stable/graphs-pharmacokinetic-pkpg06/pkpg06-plot_v4.svg
+++ /dev/null
@@ -1,228 +0,0 @@
-
-
From cae9864948e7a31d84206090793c7180924879b7 Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Wed, 12 Jun 2024 19:07:04 +0200
Subject: [PATCH 4/7] install devel deps for devel profile
---
.github/workflows/check.yml | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/.github/workflows/check.yml b/.github/workflows/check.yml
index ff02d81473..1a83975a67 100644
--- a/.github/workflows/check.yml
+++ b/.github/workflows/check.yml
@@ -27,6 +27,7 @@ jobs:
secrets:
REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
with:
+ install-deps-from-package-repositories: "R-universe=https://pharmaverse.r-universe.dev/,CRAN=https://cloud.r-project.org/"
package-subdirectory: package
additional-env-vars: |
_R_CHECK_CRAN_INCOMING_REMOTE_=false
@@ -43,7 +44,7 @@ jobs:
package-subdirectory: package
additional-env-vars: |
_R_CHECK_CRAN_INCOMING_REMOTE_=false
- QUARTO_PROFILE=stable
+ QUARTO_PROFILE=stable
concurrency-group: stable
linter:
if: github.event_name != 'push'
From 2a27831a958e261e38cbfa4585002413242b031e Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Thu, 13 Jun 2024 11:52:20 +0200
Subject: [PATCH 5/7] fix path of urlchecker workflow
---
.github/workflows/check.yml | 2 ++
1 file changed, 2 insertions(+)
diff --git a/.github/workflows/check.yml b/.github/workflows/check.yml
index 1a83975a67..c582f6311f 100644
--- a/.github/workflows/check.yml
+++ b/.github/workflows/check.yml
@@ -54,6 +54,8 @@ jobs:
if: github.event_name != 'push'
name: Check URLs 🌐
uses: insightsengineering/r.pkg.template/.github/workflows/links.yaml@main
+ with:
+ package-subdirectory: package
vbump:
name: Version Bump 🤜🤛
if: github.event_name == 'push'
From 4efab49d9772885bc7172bb3ae95ea00de4f5c5a Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Thu, 13 Jun 2024 15:43:22 +0200
Subject: [PATCH 6/7] add NOT_CRAN=true
---
.github/workflows/check.yml | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/.github/workflows/check.yml b/.github/workflows/check.yml
index c582f6311f..bf47198a4c 100644
--- a/.github/workflows/check.yml
+++ b/.github/workflows/check.yml
@@ -30,7 +30,7 @@ jobs:
install-deps-from-package-repositories: "R-universe=https://pharmaverse.r-universe.dev/,CRAN=https://cloud.r-project.org/"
package-subdirectory: package
additional-env-vars: |
- _R_CHECK_CRAN_INCOMING_REMOTE_=false
+ NOT_CRAN=true
QUARTO_PROFILE=development
concurrency-group: development
r-cmd-stable:
@@ -43,7 +43,7 @@ jobs:
install-deps-from-package-repositories: "R-universe=https://insightsengineering.r-universe.dev/,CRAN=https://cloud.r-project.org/"
package-subdirectory: package
additional-env-vars: |
- _R_CHECK_CRAN_INCOMING_REMOTE_=false
+ NOT_CRAN=true
QUARTO_PROFILE=stable
concurrency-group: stable
linter:
From 3eb378cc1b21d0cb100418f9320af18090c16bc3 Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Thu, 13 Jun 2024 16:34:24 +0200
Subject: [PATCH 7/7] copy values from CI results
---
.../development/tables-efficacy-rbmit01.md | 36 +++++++++----------
.../_snaps/stable/tables-efficacy-rbmit01.md | 36 +++++++++----------
2 files changed, 36 insertions(+), 36 deletions(-)
diff --git a/package/tests/testthat/_snaps/development/tables-efficacy-rbmit01.md b/package/tests/testthat/_snaps/development/tables-efficacy-rbmit01.md
index cf4408adc8..22d838ab26 100644
--- a/package/tests/testthat/_snaps/development/tables-efficacy-rbmit01.md
+++ b/package/tests/testthat/_snaps/development/tables-efficacy-rbmit01.md
@@ -13,24 +13,24 @@
Relative Reduction (%) 5.7%
p-value (RBMI) 0.8932
5
- Adjusted Mean (SE) -4.253 (0.651) -2.812 (0.645)
- 95% CI (-5.539, -2.968) (-4.087, -1.537)
- Difference in Adjusted Means (SE) 1.442 (0.921)
- 95% CI (-0.377, 3.261)
- Relative Reduction (%) -33.9%
- p-value (RBMI) 0.1195
+ Adjusted Mean (SE) -4.251 (0.647) -2.805 (0.644)
+ 95% CI (-5.528, -2.974) (-4.077, -1.533)
+ Difference in Adjusted Means (SE) 1.446 (0.914)
+ 95% CI (-0.358, 3.250)
+ Relative Reduction (%) -34.0%
+ p-value (RBMI) 0.1155
6
- Adjusted Mean (SE) -6.359 (0.724) -4.126 (0.696)
- 95% CI (-7.791, -4.927) (-5.502, -2.749)
- Difference in Adjusted Means (SE) 2.234 (1.000)
- 95% CI (0.258, 4.210)
- Relative Reduction (%) -35.1%
- p-value (RBMI) 0.0270
+ Adjusted Mean (SE) -6.366 (0.721) -4.095 (0.696)
+ 95% CI (-7.793, -4.939) (-5.471, -2.720)
+ Difference in Adjusted Means (SE) 2.270 (0.996)
+ 95% CI (0.301, 4.239)
+ Relative Reduction (%) -35.7%
+ p-value (RBMI) 0.0241
7
- Adjusted Mean (SE) -7.612 (0.822) -4.819 (0.767)
- 95% CI (-9.242, -5.982) (-6.335, -3.302)
- Difference in Adjusted Means (SE) 2.793 (1.110)
- 95% CI (0.597, 4.989)
- Relative Reduction (%) -36.7%
- p-value (RBMI) 0.0131
+ Adjusted Mean (SE) -7.689 (0.797) -4.776 (0.752)
+ 95% CI (-9.266, -6.112) (-6.261, -3.290)
+ Difference in Adjusted Means (SE) 2.913 (1.073)
+ 95% CI (0.792, 5.035)
+ Relative Reduction (%) -37.9%
+ p-value (RBMI) 0.0074
diff --git a/package/tests/testthat/_snaps/stable/tables-efficacy-rbmit01.md b/package/tests/testthat/_snaps/stable/tables-efficacy-rbmit01.md
index 7e93ad6359..d51404e2af 100644
--- a/package/tests/testthat/_snaps/stable/tables-efficacy-rbmit01.md
+++ b/package/tests/testthat/_snaps/stable/tables-efficacy-rbmit01.md
@@ -13,24 +13,24 @@
Relative Reduction (%) 5.7%
p-value (RBMI) 0.8932
5
- Adjusted Mean (SE) -4.256 (0.649) -2.822 (0.646)
- 95% CI (-5.538, -2.974) (-4.098, -1.545)
- Difference in Adjusted Means (SE) 1.434 (0.920)
- 95% CI (-0.383, 3.252)
- Relative Reduction (%) -33.7%
- p-value (RBMI) 0.1211
+ Adjusted Mean (SE) -4.251 (0.647) -2.805 (0.644)
+ 95% CI (-5.528, -2.974) (-4.077, -1.533)
+ Difference in Adjusted Means (SE) 1.446 (0.914)
+ 95% CI (-0.358, 3.250)
+ Relative Reduction (%) -34.0%
+ p-value (RBMI) 0.1155
6
- Adjusted Mean (SE) -6.373 (0.716) -4.164 (0.689)
- 95% CI (-7.789, -4.956) (-5.524, -2.803)
- Difference in Adjusted Means (SE) 2.209 (0.990)
- 95% CI (0.253, 4.165)
- Relative Reduction (%) -34.7%
- p-value (RBMI) 0.0271
+ Adjusted Mean (SE) -6.366 (0.721) -4.095 (0.696)
+ 95% CI (-7.793, -4.939) (-5.471, -2.720)
+ Difference in Adjusted Means (SE) 2.270 (0.996)
+ 95% CI (0.301, 4.239)
+ Relative Reduction (%) -35.7%
+ p-value (RBMI) 0.0241
7
- Adjusted Mean (SE) -7.640 (0.822) -4.823 (0.767)
- 95% CI (-9.270, -6.010) (-6.341, -3.306)
- Difference in Adjusted Means (SE) 2.816 (1.103)
- 95% CI (0.634, 4.999)
- Relative Reduction (%) -36.9%
- p-value (RBMI) 0.0118
+ Adjusted Mean (SE) -7.689 (0.797) -4.776 (0.752)
+ 95% CI (-9.266, -6.112) (-6.261, -3.290)
+ Difference in Adjusted Means (SE) 2.913 (1.073)
+ 95% CI (0.792, 5.035)
+ Relative Reduction (%) -37.9%
+ p-value (RBMI) 0.0074