From 566ac671ea54012779cb944bb6b02ad4d62ff494 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 15 Oct 2025 14:43:41 +0000
Subject: [PATCH 1/4] Initial plan


From 2092d0c3610b316460766328651c9e0dc3448429 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 15 Oct 2025 14:49:18 +0000
Subject: [PATCH 2/4] Add warning for combining objects from different
 hierarchies

Co-authored-by: rix133 <6965560+rix133@users.noreply.github.com>
---
 R/combineRDBESDataObjects.R                   | 33 +++++++++++++++++++
 tests/testthat/test-combineRDBESDataObjects.R | 26 +++++++++++++++
 2 files changed, 59 insertions(+)

diff --git a/R/combineRDBESDataObjects.R b/R/combineRDBESDataObjects.R
index e58831f6..865171e2 100644
--- a/R/combineRDBESDataObjects.R
+++ b/R/combineRDBESDataObjects.R
@@ -9,6 +9,13 @@
 #' @param strict (Optional) This function validates its input data - should
 #' the validation be strict? The default is TRUE.
 #'
+#' @details 
+#' When combining RDBESDataObjects from different hierarchies (e.g., H1 and H5),
+#' a warning is issued. The resulting combined object will have a mixed hierarchy,
+#' which may be structurally and statistically invalid for some analyses. However,
+#' such combinations can be useful for fisheries overviews, annual reports, or
+#' countries performing broader estimations.
+#'
 #' @return the combination of \code{RDBESDataObject1} and  \code{RDBESDataObject2}
 #' @seealso  \link[data.table]{rbindlist}
 #' @export
@@ -31,6 +38,32 @@ combineRDBESDataObjects <- function(RDBESDataObject1,
 
   validateRDBESDataObject(RDBESDataObject1, verbose = verbose, strict = strict)
   validateRDBESDataObject(RDBESDataObject2, verbose = verbose, strict = strict)
+  
+  # Check for multiple hierarchies
+  hierarchy1 <- NULL
+  hierarchy2 <- NULL
+  
+  if (!is.null(RDBESDataObject1$DE) && nrow(RDBESDataObject1$DE) > 0) {
+    hierarchy1 <- unique(RDBESDataObject1$DE$DEhierarchy)
+  }
+  
+  if (!is.null(RDBESDataObject2$DE) && nrow(RDBESDataObject2$DE) > 0) {
+    hierarchy2 <- unique(RDBESDataObject2$DE$DEhierarchy)
+  }
+  
+  # Warn if combining different hierarchies
+  if (!is.null(hierarchy1) && !is.null(hierarchy2) && 
+      length(hierarchy1) > 0 && length(hierarchy2) > 0) {
+    if (!all(hierarchy1 %in% hierarchy2) || !all(hierarchy2 %in% hierarchy1)) {
+      warning("Combining RDBESDataObjects from different hierarchies (", 
+              paste(hierarchy1, collapse = ", "), " and ", 
+              paste(hierarchy2, collapse = ", "), 
+              "). This creates a mixed hierarchy object that may be structurally ",
+              "and statistically invalid for some analyses.", 
+              call. = FALSE)
+    }
+  }
+  
   # Create an empty RDBESDataObject as the basis of what we will return
   myRDBESDataObject <- createRDBESDataObject()
 
diff --git a/tests/testthat/test-combineRDBESDataObjects.R b/tests/testthat/test-combineRDBESDataObjects.R
index 92425576..2c7c533a 100644
--- a/tests/testthat/test-combineRDBESDataObjects.R
+++ b/tests/testthat/test-combineRDBESDataObjects.R
@@ -40,4 +40,30 @@ test_that("combineRDBESDataObjects returns valid RDBESDataObject when supplied
   expect_error(validateRDBESDataObject(myCombinedObject), NA)
 })
 
+test_that("combineRDBESDataObjects warns when combining objects from different hierarchies",  {
+
+  myObject1 <- importRDBESDataCSV(rdbesExtractPath = "./h1_v_20250211")
+  myObject2 <- importRDBESDataCSV(rdbesExtractPath = "./h5_v_20250211")
+
+  # Check these are valid objects before we try and combine them
+  expect_error(validateRDBESDataObject(myObject1), NA)
+  expect_error(validateRDBESDataObject(myObject2), NA)
+
+  # Expect a warning about different hierarchies
+  expect_warning(combineRDBESDataObjects(RDBESDataObject1=myObject1,
+                                        RDBESDataObject2=myObject2),
+                 "Combining RDBESDataObjects from different hierarchies")
+})
+
+test_that("combineRDBESDataObjects does not warn when combining objects from same hierarchy",  {
+
+  myObject1 <- importRDBESDataCSV(rdbesExtractPath = "./h1_v_20250211")
+  myObject2 <- importRDBESDataCSV(rdbesExtractPath = "./h1_v_20250211")
+
+  # Expect no warning about different hierarchies (but will have duplicate rows error later)
+  expect_warning(combineRDBESDataObjects(RDBESDataObject1=myObject1,
+                                        RDBESDataObject2=myObject2),
+                 NA)
+})
+
 }) ## end capture.output

From af7946d10e5837ea5f1277db3315596fa8076ca6 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 15 Oct 2025 14:51:49 +0000
Subject: [PATCH 3/4] Add comprehensive tests for hierarchy warning edge cases

Co-authored-by: rix133 <6965560+rix133@users.noreply.github.com>
---
 tests/testthat/test-combineRDBESDataObjects.R | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/tests/testthat/test-combineRDBESDataObjects.R b/tests/testthat/test-combineRDBESDataObjects.R
index 2c7c533a..5cf38035 100644
--- a/tests/testthat/test-combineRDBESDataObjects.R
+++ b/tests/testthat/test-combineRDBESDataObjects.R
@@ -66,4 +66,15 @@ test_that("combineRDBESDataObjects does not warn when combining objects from sam
                  NA)
 })
 
+test_that("combineRDBESDataObjects does not warn when one object has no DE table",  {
+
+  myObject1 <- importRDBESDataCSV(rdbesExtractPath = "./h1_v_20250211")
+  myObject2 <- createRDBESDataObject()  # Empty object with no DE
+
+  # Expect no warning because one object has no hierarchy
+  expect_warning(combineRDBESDataObjects(RDBESDataObject1=myObject1,
+                                        RDBESDataObject2=myObject2),
+                 NA)
+})
+
 }) ## end capture.output

From b92ce853d100b34e0389fbb09c99ce1776cfc1a3 Mon Sep 17 00:00:00 2001
From: Richard Meitern <rix133@users.noreply.github.com>
Date: Wed, 15 Oct 2025 18:10:15 +0300
Subject: [PATCH 4/4] Add branch to pull request trigger in pkgdown.yaml

Only when main updates
---
 .github/workflows/pkgdown.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index bfc9f4db..3de2a835 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -4,6 +4,7 @@ on:
   push:
     branches: [main, master]
   pull_request:
+    branches: [ main ] 
   release:
     types: [published]
   workflow_dispatch: