From e582dab045b5358e72cde5333076088f7b2d9fc1 Mon Sep 17 00:00:00 2001
From: jjmccollum <jpmccollum05834@yahoo.com>
Date: Sat, 7 Sep 2024 17:45:11 +1000
Subject: [PATCH] :bug: Added rootFrequencies attribute (and, for convenience,
 value attribute) to loggers in BEAST template

---
 teiphy/templates/beast_template.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/teiphy/templates/beast_template.xml b/teiphy/templates/beast_template.xml
index 6c19be2..510f530 100644
--- a/teiphy/templates/beast_template.xml
+++ b/teiphy/templates/beast_template.xml
@@ -332,14 +332,14 @@
         <logger id="ancestralStateLogger" fileName="$(tree).ancestral.trees" logEvery="1000" mode="tree">
             <!-- Start character ancestral state loggers -->
             {%- for vu in variation_units %}
-            <log spec="beastlabs.evolution.likelihood.AncestralStateLogger" id="morphTreeLikelihood.character.{{ loop.index }}.anclogger" data="@filter.{{ loop.index }}" taxonset="@taxa" siteModel="@morphSiteModel.{{ loop.index }}" branchRateModel="@clock" tree="@tree" useAmbiguities="true" useTipLikelihoods="true"/>
+            <log spec="beastlabs.evolution.likelihood.AncestralStateLogger" id="morphTreeLikelihood.character.{{ loop.index }}.anclogger" value="site.{{ loop.index }}" data="@filter.{{ loop.index }}" taxonset="@taxa" siteModel="@morphSiteModel.{{ loop.index }}" rootFrequencies="@rootfreqs.{{loop.index}}" branchRateModel="@clock" tree="@tree" useAmbiguities="true" useTipLikelihoods="true"/>
             {%- endfor %}
         </logger>
         {%- elif ancestral_logger == "sequence" %}
         <logger id="ancestralSequenceLogger" fileName="$(tree).ancestral.trees" logEvery="1000" mode="tree">
             <!-- Start character ancestral sequence loggers -->
             {%- for vu in variation_units %}
-            <log spec="beastclassic.evolution.likelihood.AncestralSequenceLogger" id="morphTreeLikelihood.character.{{ loop.index }}.anclogger" tag="morphTreeLikelihood.character.{{ loop.index }}" data="@filter.{{ loop.index }}" siteModel="@morphSiteModel.{{ loop.index }}" branchRateModel="@clock" tree="@tree" useAmbiguities="true" useTipLikelihoods="true"/>
+            <log spec="beastclassic.evolution.likelihood.AncestralSequenceLogger" id="morphTreeLikelihood.character.{{ loop.index }}.anclogger" value="site.{{ loop.index }}" tag="morphTreeLikelihood.character.{{ loop.index }}" data="@filter.{{ loop.index }}" siteModel="@morphSiteModel.{{ loop.index }}" rootFrequencies="@rootfreqs.{{loop.index}}" branchRateModel="@clock" tree="@tree" useAmbiguities="true" useTipLikelihoods="true"/>
             {%- endfor %}
         </logger>
         {%- endif %}