From 3ab7dd3f74b4b98984f7a89491b37925a51937d0 Mon Sep 17 00:00:00 2001
From: Ryan O'Dea <70209371+ryan-odea@users.noreply.github.com>
Date: Mon, 27 Oct 2025 19:15:51 +0100
Subject: [PATCH 1/2] set deviation as WIP

---
 SEQTaRget/R/SEQopts.R                     |  3 +++
 SEQTaRget/tests/testthat/test_deviation.R | 12 ++++++++++++
 2 files changed, 15 insertions(+)
 create mode 100644 SEQTaRget/tests/testthat/test_deviation.R

diff --git a/SEQTaRget/R/SEQopts.R b/SEQTaRget/R/SEQopts.R
index 1e8d390..5997298 100644
--- a/SEQTaRget/R/SEQopts.R
+++ b/SEQTaRget/R/SEQopts.R
@@ -86,6 +86,9 @@ SEQopts <- function(bootstrap = FALSE, bootstrap.nboot = 100, bootstrap.sample =
   weight.upper <- as.numeric(weight.upper)
   weight.eligible_cols <- as.list(weight.eligible_cols)
   
+  # Temporarily disabling deviation - work in progress method
+  if (deviation) stop("Deviation is currently under further development and is currently not suitable for analysis.
+                      We apologize for this inconvenience")
   deviation.col <- as.character(deviation.col)
   deviation.conditions <- as.list(deviation.conditions)
   deviation.excused_cols <- as.list(deviation.excused_cols)
diff --git a/SEQTaRget/tests/testthat/test_deviation.R b/SEQTaRget/tests/testthat/test_deviation.R
new file mode 100644
index 0000000..c1c2a10
--- /dev/null
+++ b/SEQTaRget/tests/testthat/test_deviation.R
@@ -0,0 +1,12 @@
+test_that("Post-Expansion Excused Censoring", {
+  data <- copy(SEQdata)
+  data[N > 10, deviation := TRUE]
+  model <- expect_error(SEQuential(data, "ID", "time", "eligible", "tx_init", "outcome",
+                                       list("N", "L", "P"), list("sex"),
+                                       method = "censoring",
+                                       options = SEQopts(
+                                         weighted = TRUE, deviation = TRUE,
+                                         deviation.col = "deviation",
+                                         weight.preexpansion = FALSE)
+  ))
+})

From 70ccca92d0640a62c9ba65e7c6abb99bfca8b027 Mon Sep 17 00:00:00 2001
From: Ryan O'Dea <70209371+ryan-odea@users.noreply.github.com>
Date: Mon, 27 Oct 2025 19:16:34 +0100
Subject: [PATCH 2/2] bump version

---
 SEQTaRget/DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/SEQTaRget/DESCRIPTION b/SEQTaRget/DESCRIPTION
index a2bd9d4..78b6737 100644
--- a/SEQTaRget/DESCRIPTION
+++ b/SEQTaRget/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: SEQTaRget
 Type: Package
 Title: Sequential Trial Emulation
-Version: 1.1.0
+Version: 1.1.1
 Authors@R: c(person(given = "Ryan",
                     family = "O'Dea",
                     role = c("aut", "cre"),