From f8e3434ae94b47c0692f9a94a1875ab4a8aa54c2 Mon Sep 17 00:00:00 2001
From: Oskar Gauffin <Oskar.Gauffin@who-umc.org>
Date: Wed, 14 Feb 2024 12:57:03 +0100
Subject: [PATCH 1/2] expanded news 0.0.3

---
 NEWS.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/NEWS.md b/NEWS.md
index e5c8928..12cc276 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -5,5 +5,5 @@ This is the first version of the package.
 Fixing a minor bug discovered by the CRAN checks. 
 
 # version 0.0.3
-Fixing a bug where the group_by-variable was hard-coded as "group". From now, any group_by column name should work. 
+Fixing a bug where the group_by-variable was hard-coded as "group". From now, any group_by column name should work. Removed the export tag from a few internal functions for a cleaner reference manual.
 

From 6e14170825948dadef6f8e4f90579c69dd5fcfb4 Mon Sep 17 00:00:00 2001
From: Oskar Gauffin <Oskar.Gauffin@who-umc.org>
Date: Fri, 16 Feb 2024 14:21:02 +0100
Subject: [PATCH 2/2] Added quality check on the IC025, unit test nr 19

---
 tests/testthat/test-disprop_analysis.R | 61 ++++++++++++++++++++++++++
 1 file changed, 61 insertions(+)

diff --git a/tests/testthat/test-disprop_analysis.R b/tests/testthat/test-disprop_analysis.R
index 2df72de..23d1f00 100644
--- a/tests/testthat/test-disprop_analysis.R
+++ b/tests/testthat/test-disprop_analysis.R
@@ -186,3 +186,64 @@ test_that("18. It's possible to name the group_by something else than 'group'",
 
   expect_equal(2L, ncol(summary_output))
 })
+
+test_that("19. The IC values match manually calculated IC-values", {
+
+  report_dt <-
+    data.table::as.data.table(pvda::drug_event_df) |>
+    dplyr::select(report_id, drug, event)
+
+  counts_dt <-
+    report_dt |>
+    dplyr::group_by(drug) |>
+    dplyr::mutate(n_drugs = dplyr::n_distinct(report_id)) |>
+    dplyr::group_by(event) |>
+    dplyr::mutate(n_events = dplyr::n_distinct(report_id)) |>
+    dplyr::distinct(drug, event, report_id, .keep_all = TRUE) |>
+    dplyr::group_by(drug, event, n_drugs, n_events) |> # Setting n_drugs and n_pts in the group_by preserves them in the count-step
+    dplyr::count(name="obs")
+
+  # Need a total count, probably easiest to do it separately
+  n_tot <-
+    report_dt |>
+    dplyr::distinct(report_id) |>
+    dplyr::count() |>
+    dplyr::pull(n)
+
+  # Calculate the 2.5th percentiles of the posterior
+  ic_dt <-
+    counts_dt |>
+    dplyr::mutate(n_tot = n_tot) |>
+    dplyr::mutate(exp = as.numeric(n_drugs)*as.numeric(n_events)/as.numeric(n_tot)) |>
+    dplyr::mutate(ic025 = log2(qgamma(0.025, obs + 0.5, exp + 0.5)))
+
+  ic_dt |>
+    dplyr::mutate(sign = ifelse(ic025>0, TRUE, FALSE)) |>
+    dplyr::group_by(sign) |>
+    dplyr::count()
+
+  ic_dt <-
+    ic_dt |>
+    dplyr::ungroup() |>
+    dplyr::select(drug, event, ic025)
+
+  ##############################################
+  da1 <- pvda::drug_event_df |> pvda::da()
+  output_pvda <- da1$da_df |> dplyr::select(drug, event, ic2.5)
+
+  compare_pvda_to_manual <-
+    ic_dt |>
+    dplyr::left_join(output_pvda, dplyr::join_by(drug==drug, event==event)) |>
+    dplyr::mutate(same = ifelse(round(ic025,2) == round(ic2.5,2), TRUE, FALSE))
+
+  all_the_same <- all(compare_pvda_to_manual$same)
+
+
+
+
+
+  expect_equal(all_the_same, TRUE)
+})
+
+
+