From 5bdb92855f0790119f8f91ce5d29f2eeb4b05be8 Mon Sep 17 00:00:00 2001
From: Klaus Schliep <klaus.schliep@gmail.com>
Date: Fri, 22 Nov 2024 13:15:56 +0100
Subject: [PATCH] bug fix

---
 R/pml_generics.R | 2 +-
 man/write.pml.Rd | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/pml_generics.R b/R/pml_generics.R
index 9c4e874d..cf33f496 100644
--- a/R/pml_generics.R
+++ b/R/pml_generics.R
@@ -141,7 +141,7 @@ print.pml <- function(x, ...) {
 #' data(woodmouse)
 #' fit <- pml_bb(woodmouse, "JC", rearrangement = "none")
 #' write.pml(fit, "woodmouse")
-#' unlink(c("woodmouse_pml.txt", "woodmouse_tree.nwk", "woodmouse.rds"))
+#' unlink(c("woodmouse.txt", "woodmouse_tree.nwk", "woodmouse_align.fasta"))
 #' @importFrom utils citation
 #' @export
 write.pml <- function(x, file="pml", save_rds=FALSE, ...){
diff --git a/man/write.pml.Rd b/man/write.pml.Rd
index 39f9b590..6b60697b 100644
--- a/man/write.pml.Rd
+++ b/man/write.pml.Rd
@@ -4,7 +4,7 @@
 \alias{write.pml}
 \title{Export pml objects}
 \usage{
-write.pml(x, file = "pml", save_rds = TRUE, ...)
+write.pml(x, file = "pml", save_rds = FALSE, ...)
 }
 \arguments{
 \item{x}{an object of class ancestral.}
@@ -26,7 +26,7 @@ otherwise the alignment is saved as a fasta file.}
 data(woodmouse)
 fit <- pml_bb(woodmouse, "JC", rearrangement = "none")
 write.pml(fit, "woodmouse")
-unlink(c("woodmouse_pml.txt", "woodmouse_tree.nwk", "woodmouse.rds"))
+unlink(c("woodmouse.txt", "woodmouse_tree.nwk", "woodmouse_align.fasta"))
 }
 \seealso{
 \code{\link{ancestral.pml}}, \code{\link{plotAnc}}