From 441ceef118907ae6d63fc678853cc63715389532 Mon Sep 17 00:00:00 2001
From: joshwlambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Oct 2023 10:28:20 +0100
Subject: [PATCH] ensure correct parameter is changed for relaxed rate model

---
 R/run_daisie_ml.R | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/R/run_daisie_ml.R b/R/run_daisie_ml.R
index 8b37c4c..6a20b2c 100644
--- a/R/run_daisie_ml.R
+++ b/R/run_daisie_ml.R
@@ -109,7 +109,10 @@ run_daisie_ml <- function(daisie_data,
     # prevent initial parameters being greater than upper parameter limit
     pick <- which(c("cladogenesis", "extinction", "carrying_capacity",
                     "immigration", "anagenesis") == cs_version$relaxed_par)
-    initparsopt[initparsopt[pick] > par_upper_bound] <- par_upper_bound / 2
+    if (initparsopt[pick] > par_upper_bound) {
+      initparsopt[pick] <- par_upper_bound / 2
+    }
+
   }
 
   ##### ML Optimization ####