From e884c223f4230cf00ffabe075b99a103d935137a Mon Sep 17 00:00:00 2001
From: Jari Oksanen <jhoksane@gmail.com>
Date: Tue, 28 May 2024 14:56:29 +0300
Subject: [PATCH 1/2] dist2xy: keep/set attributes of input dissimilarities

---
 R/dist2xy.R | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/R/dist2xy.R b/R/dist2xy.R
index 4f5952518..761f44e6d 100644
--- a/R/dist2xy.R
+++ b/R/dist2xy.R
@@ -51,6 +51,7 @@
     type <- match.arg(type)
     if (!inherits(dist, "dist"))
         stop("'dist' must be a dissimilarity object of class 'dist'")
+    att <- attributes(dist)
     dist <- as.matrix(dist)
     n <- nrow(dist)
     ## make up the selection vector
@@ -59,9 +60,13 @@
     if (invert)
         k <- !k
     ## make compartments
-    if (type == "xy")
-        dist[k, !k, drop = FALSE]
-    else
-        as.dist(dist[k, k, drop = FALSE])
+    dist <- if (type == "xy")
+                dist[k, !k, drop = FALSE]
+            else
+                as.dist(dist[k, k, drop = FALSE])
+    attr(dist, "call") <- match.call()
+    attr(dist, "method") <- att$method
+    attr(dist, "maxdist") <- att$maxdist
+    dist
 }
 

From bb8b7079528db4964a790d736c9310b9d978216f Mon Sep 17 00:00:00 2001
From: Jari Oksanen <jhoksane@gmail.com>
Date: Tue, 28 May 2024 14:58:17 +0300
Subject: [PATCH 2/2] update tests/Examples

---
 tests/Examples/vegan-Ex.Rout.save | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tests/Examples/vegan-Ex.Rout.save b/tests/Examples/vegan-Ex.Rout.save
index b75c69ff7..ef5e9a63f 100644
--- a/tests/Examples/vegan-Ex.Rout.save
+++ b/tests/Examples/vegan-Ex.Rout.save
@@ -187,17 +187,17 @@ adj. RDA R squares -0.12553 -0.0250
 > MDSaddpoints(mod3, dist2xy(d, 3))
 $points
          MDS1       MDS2
-3 -0.04351138 -0.2040447
+3 -0.09726945 -0.4560911
 
 $seed
-            [,1]       [,2]
-[1,] 0.005468615 -0.1947698
+           [,1]      [,2]
+[1,] 0.01222408 -0.435372
 
 $deltastress
 [1] 0.001811369
 
 $iters
-[1] 16
+[1] 18
 
 $cause
 [1] 4
@@ -8948,7 +8948,7 @@ Procrustes sum of squares:
 > cleanEx()
 > options(digits = 7L)
 > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed:  8.578 0.271 8.874 0 0 
+Time elapsed:  8.559 0.295 8.885 0 0 
 > grDevices::dev.off()
 null device 
           1