From 86b0ca5518729dd04097caf259113e9e467e4321 Mon Sep 17 00:00:00 2001
From: sdgamboa <samuel.gamboa.tuz@gmail.com>
Date: Wed, 4 Oct 2023 11:49:22 -0400
Subject: [PATCH] add "estimated" to fitMk

---
 inst/scripts/phytools2.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/inst/scripts/phytools2.R b/inst/scripts/phytools2.R
index ca2f4cf..1390a13 100644
--- a/inst/scripts/phytools2.R
+++ b/inst/scripts/phytools2.R
@@ -107,7 +107,7 @@ input_matrix <- input_matrix[tree$tip.label,]
 ## ------------------------------------------------------------------------------------------------------------------------
 system.time({
     fit <- fitMk(
-        tree = tree, x = input_matrix, model = 'ER', pi = 'fitzjohn',
+        tree = tree, x = input_matrix, model = 'ER', pi = 'estimated',
         lik.func = 'pruning', logscale = TRUE
     )
 })