From 33f1938b4961b910adb561f2f92c33b1a53ff57d Mon Sep 17 00:00:00 2001
From: daijiang <daijianglee@gmail.com>
Date: Wed, 21 Feb 2024 15:00:07 -0600
Subject: [PATCH] In case of dist object for site cov

---
 DESCRIPTION     | 2 +-
 R/pglmm-utils.R | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index b323ba8..302b436 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -34,7 +34,7 @@ Imports:
     latticeExtra,
     tidyr
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 LinkingTo:
     Rcpp, RcppArmadillo
 Suggests: 
diff --git a/R/pglmm-utils.R b/R/pglmm-utils.R
index 0f51c0e..f483f77 100755
--- a/R/pglmm-utils.R
+++ b/R/pglmm-utils.R
@@ -32,6 +32,8 @@ parse_conv_ranef = function(x, df){
       Vphy = Vphy[spl, spl] # same order as species levels
     }
     
+    if(inherits(xx, "dist")) xx = as.matrix(xx)
+    
     if(inherits(xx, c("matrix", "Matrix"))){
       # already a cov matrix
       if(length(setdiff(spl, row.names(xx))))