From f66823d0635655d53316505f7cb0e8d383befd90 Mon Sep 17 00:00:00 2001
From: Fabio Morgante <fabiom@clemson.edu>
Date: Thu, 10 Oct 2024 12:07:08 -0400
Subject: [PATCH 1/3] Fix bug when kernel has only one positive eigenvalues

---
 R/BGLR.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/BGLR.R b/R/BGLR.R
index dbded8e..1a9c4a5 100644
--- a/R/BGLR.R
+++ b/R/BGLR.R
@@ -548,7 +548,7 @@ setLT.RKHS=function(LT,y,n,j,weights,saveAt,R2,nLT,rmExistingFiles,verbose)
     tmp= LT$d > LT$tolD
     LT$levelsU = sum(tmp)
     LT$d = LT$d[tmp]
-    LT$V = LT$V[, tmp]
+    LT$V = LT$V[, tmp, drop=FALSE]
     
     #Default degrees of freedom and scale parameter associated with the variance component for marker effect
     if (is.null(LT$df0)) 

From 93d80a4a6127799ab5dfb783c587ec29786f9805 Mon Sep 17 00:00:00 2001
From: fmorgante <fabiom@clemson.edu>
Date: Wed, 5 Mar 2025 12:08:48 -0500
Subject: [PATCH 2/3] Compute covariance matrix with flashier

---
 DESCRIPTION    | 2 +-
 R/Multitrait.R | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index c8fb832..768e1e9 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: BGLR
-Version: 1.1.3
+Version: 1.1.4
 Title: Bayesian Generalized Linear Regression
 Authors@R: c(person(given = "Gustavo",
                       family = "de los Campos",
diff --git a/R/Multitrait.R b/R/Multitrait.R
index 85e4aad..d8dabf5 100644
--- a/R/Multitrait.R
+++ b/R/Multitrait.R
@@ -1284,8 +1284,8 @@ Multitrait<-function(y,
 	
 	n<-nrow(y)
 	
-	#Compute sample variance covariance matrix
-	Sy<-cov(y,use="pairwise.complete.obs")
+	#Compute sample variance covariance matrix using flashier
+	Sy <- mr.mash.alpha:::compute_cov_flash(y)
 	Sy[is.na(Sy)]=0
 	
 	#Deep copy of y, DO NOT REPLACE with y.back<-y, it does not work, both objects 

From 414321469a0f526d40642bb3f3e38d75ff0befd5 Mon Sep 17 00:00:00 2001
From: fmorgante <fabiom@clemson.edu>
Date: Wed, 5 Mar 2025 12:22:46 -0500
Subject: [PATCH 3/3] Handle rows with all missing values

---
 R/Multitrait.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/Multitrait.R b/R/Multitrait.R
index d8dabf5..3de89fb 100644
--- a/R/Multitrait.R
+++ b/R/Multitrait.R
@@ -1284,8 +1284,8 @@ Multitrait<-function(y,
 	
 	n<-nrow(y)
 	
-	#Compute sample variance covariance matrix using flashier
-	Sy <- mr.mash.alpha:::compute_cov_flash(y)
+	#Compute sample variance covariance matrix using flashier (removing rows that have all NAs)
+	Sy <- mr.mash.alpha:::compute_cov_flash(y[rowSums(is.na(y)) != ncol(y), ])
 	Sy[is.na(Sy)]=0
 	
 	#Deep copy of y, DO NOT REPLACE with y.back<-y, it does not work, both objects