From b45d0b6324d1ec9212a3fc7d52b39e2e07e43d18 Mon Sep 17 00:00:00 2001
From: Bill Denney <wdenney@humanpredictions.com>
Date: Wed, 6 Feb 2019 20:59:35 -0500
Subject: [PATCH 1/2] Test that assignment keeps the correct class

---
 tests/testthat/test-xpose_data.R | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/tests/testthat/test-xpose_data.R b/tests/testthat/test-xpose_data.R
index e95ef8e2..4e73b504 100644
--- a/tests/testthat/test-xpose_data.R
+++ b/tests/testthat/test-xpose_data.R
@@ -90,3 +90,8 @@ test_that('properly handles errors in files', {
   expect_error(grd_vs_iteration(xpdb_5), regex = 'No `files` slot could be found in this xpdb')
 })  
 
+test_that('Allow assignment within object while maintaining the class', {
+  xpdb <- xpdb_ex_pk
+  xpdb$options$quiet <- TRUE
+  expect_equal(class(xpdb), class(xpdb_ex_pk))
+})

From e113dff0896f3020cd2fb7fc4040d6fecf8f4a22 Mon Sep 17 00:00:00 2001
From: Bill Denney <wdenney@humanpredictions.com>
Date: Sun, 17 Mar 2019 15:25:46 -0400
Subject: [PATCH 2/2] Detect off-diagonal omega names

---
 R/xpdb_access.R | 19 +++++++++++++++----
 1 file changed, 15 insertions(+), 4 deletions(-)

diff --git a/R/xpdb_access.R b/R/xpdb_access.R
index ab9fadc6..ac860139 100644
--- a/R/xpdb_access.R
+++ b/R/xpdb_access.R
@@ -423,13 +423,24 @@ get_prm <- function(xpdb,
       }
       
       # Assign OMEGA labels
-      n_omega     <- sum(prms$type == 'ome' & prms$diagonal, na.rm = TRUE)
+      mask_omega <- prms$type == 'ome' & prms$diagonal
+      mask_omega_all <-
+        prms$type == 'ome' &
+        !is.nan(prms$value) &
+        (prms$diagonal |
+           !(prms$value == 0 & prms$fixed & !prms$diagonal)
+        )
+      n_omega     <- sum(mask_omega, na.rm = TRUE)
+      n_omega_all <- sum(mask_omega_all, na.rm = TRUE)
       omega_names <- data$prm_names$omega
-      if (n_omega != length(omega_names)) {
+      if (n_omega == length(omega_names)) {
+        prms$label[mask_omega] <- omega_names
+      } else if (n_omega_all == length(omega_names)) {
+        prms$label[mask_omega_all] <- omega_names
+      } else {
+        browser()
         warning('[$prob no.', data$problem, ', subprob no.', data$subprob, ', ', data$method, 
                 '] $OMEGA labels did not match the number of OMEGAs in the `.ext` file.', call. = FALSE)
-      } else {
-        prms$label[prms$type == 'ome' & prms$diagonal] <- omega_names
       }
       
       # Assign SIGMA labels