From 88fa224b5153b5194b6b3f677af7170a7f867853 Mon Sep 17 00:00:00 2001
From: Klaus Schliep <klaus.schliep@gmail.com>
Date: Wed, 14 Feb 2024 16:52:25 +0100
Subject: [PATCH] bugfix

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

diff --git a/NAMESPACE b/NAMESPACE
index 60295801..09225936 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -79,7 +79,6 @@ S3method(unique,dist)
 S3method(unique,phyDat)
 S3method(unique,splits)
 S3method(update,pml)
-S3method(vcov,pml)
 export(AICc)
 export(Ancestors)
 export(CI)
@@ -161,7 +160,7 @@ export(h2st)
 export(h4st)
 export(hadamard)
 export(hash)
-export(keep.as.tip)
+export(keep_as_tip)
 export(ldfactorial)
 export(lento)
 export(lli)
@@ -231,6 +230,7 @@ export(tidy)
 export(transferBootstrap)
 export(treedist)
 export(upgma)
+export(vcov.pml)
 export(wRF.dist)
 export(wpgma)
 export(write.nexus.dist)
diff --git a/R/pmlPart.R b/R/pmlPart.R
index b1350405..1d59c3a9 100644
--- a/R/pmlPart.R
+++ b/R/pmlPart.R
@@ -251,7 +251,7 @@ makePart <- function(fit, rooted, weight = ~index + genes) {
 multiphyDat2pmlPart <- function(x, method="unrooted", tip.dates=NULL, ...) {
   if(is.list(x) && all(sapply(x,inherits, "phyDat"))) seq  <- x
   else if(inherits(x, "multiphyDat")) seq <- x@seq
-  else stop("x must be of class 'multiphyDat' or a list of 'phyDat' objects")
+  else stop("x must be of class multiphyDat or a list of phyDat objects")
   shared_tree <- TRUE
   if (shared_tree) {
     concatenate_x <- do.call(cbind.phyDat, seq)