From faec65d8e3b641a7c6a159da3c793b1dfff54291 Mon Sep 17 00:00:00 2001
From: Klaus Schliep <klaus.schliep@gmail.com>
Date: Tue, 19 Nov 2024 14:07:26 +0100
Subject: [PATCH] small improvements

---
 R/pml_generics.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/pml_generics.R b/R/pml_generics.R
index 700de768..60d800f5 100644
--- a/R/pml_generics.R
+++ b/R/pml_generics.R
@@ -162,7 +162,8 @@ write.pml <- function(x, file="pml", save_rds=TRUE, ...){
   }
   else {
     call <- x$call
-    call$data <- "align"
+    call$data <- quote(align)
+    call$tree <- quote(tree)
     cat("tree <- read.tree(\"", file, "_tree.nwk\")\n", sep="")
     cat("align <- read.phyDat(\"", file, "_align.fasta\", format=\"fasta\")",
         sep="")