From d838091a55ba279a0c0ab1f278e91dafd68d93b1 Mon Sep 17 00:00:00 2001
From: nfrerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Date: Mon, 13 Jan 2025 23:33:32 +0100
Subject: [PATCH] Fix condense() for ungrouped matrix

---
 R/condense.R                      |   3 ++-
 inst/tinytest/_snaps/condense.rds | Bin 499 -> 518 bytes
 inst/tinytest/test_condense.R     |  17 +++++++++++++----
 3 files changed, 15 insertions(+), 5 deletions(-)

diff --git a/R/condense.R b/R/condense.R
index dd2bda0..b5ca1da 100644
--- a/R/condense.R
+++ b/R/condense.R
@@ -10,7 +10,8 @@ setMethod(
   signature = "CompositionMatrix",
   definition = function(x, by, verbose = FALSE, ...) {
     x <- group(x, by = by)
-    methods::callGeneric(x = x, verbose = verbose, ...)
+    y <- methods::callGeneric(x = x, verbose = verbose, ...)
+    ungroup(y)
   }
 )
 
diff --git a/inst/tinytest/_snaps/condense.rds b/inst/tinytest/_snaps/condense.rds
index 615f982537a8b5b005a6571368c6e037b433b932..bbfa236aa6d52d4582f92d1f93dff8773eb90e8b 100644
GIT binary patch
delta 177
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zLAJuu#G;ZaD32>QGr1@~IVUqO6)M7Akdv662^2~!E`|!RCuQcBWR}2GaORd4C+C+T
z1laQn5(`UHVamDk^7Bwd*!0qi@=FWQoX1&|U#^GjL|AAsI>IR!PB4ZujNt-fxT1R&
f;$nzNFhQ=A#F9k4v?8D-K;Az9E4k;J1p@#8%BV^t

delta 158
zcmV;P0Ac@z1oH#1UIBlBG@~Po;RIti!x%0whARUDFm`|pr~qqTVs2_N)Fck5AX{N+
zVo^yIl*g5unOu~goRgWC3Kiil$Vp7k1PUb<7ej^ElQQ#5GD~18ICD#jlk>|E0_^z(
ziG`)9Fy&l%`FW@!Y<lTM`K1MD&f_e~FV{nMB4wV1xENv*Opq2UC9xz?FRch@36S>>
M02ehkzQh6m0DAR5D*ylh

diff --git a/inst/tinytest/test_condense.R b/inst/tinytest/test_condense.R
index 694b0eb..9a9c082 100644
--- a/inst/tinytest/test_condense.R
+++ b/inst/tinytest/test_condense.R
@@ -1,12 +1,21 @@
 data("slides")
-coda <- as_composition(slides, groups = 2)
+coda <- as_composition(slides)
 
-## Compositional mean by sample
+## Ungrouped
+flat <- condense(coda, by = slides$analyst)
+expect_false(is_grouped(flat))
+expect_identical(rownames(flat), paste0("A", 1:5))
+
+## Compositional mean by group
+coda <- group(coda, by = slides$analyst)
 flat <- condense(coda)
-expect_equal_to_reference(as.data.frame(flat), file = "_snaps/condense.rds")
+expect_identical(group_names(flat), paste0("A", 1:5))
 
 ## Override groups
-flat <- condense(coda, by = slides$analyst)
+flat <- condense(coda, by = slides$slide)
+expect_identical(rownames(flat), c("A", "B", "C", "D", "E"))
+expect_identical(group_names(flat), rep(paste0("A", 1:5, collapse = ":"), 5))
+expect_equal_to_reference(as.data.frame(flat), file = "_snaps/condense.rds")
 
 ## With zeros
 X1 <- data.frame(