From 9a853afce3f0ac99c0e1f4edf9ad0c8eb160448d Mon Sep 17 00:00:00 2001
From: Matthew Andres Moreno <mmore500.login+gpg@gmail.com>
Date: Mon, 26 Feb 2024 22:35:48 -0500
Subject: [PATCH 1/2] Implement, test GetSumDistance member for Systematics

---
 include/emp/Evolve/Systematics.hpp | 17 +++++++++++++++++
 tests/Evolve/Systematics.cpp       |  4 ++++
 2 files changed, 21 insertions(+)

diff --git a/include/emp/Evolve/Systematics.hpp b/include/emp/Evolve/Systematics.hpp
index 9286c68454..67b1fb3753 100644
--- a/include/emp/Evolve/Systematics.hpp
+++ b/include/emp/Evolve/Systematics.hpp
@@ -420,6 +420,7 @@ namespace emp {
     virtual int GetMaxDepth() = 0;
     virtual int GetPhylogeneticDiversity() const = 0;
     virtual double GetMeanPairwiseDistance(bool branch_only) const = 0;
+    virtual double GetSumDistance() const = 0;
     virtual double GetSumPairwiseDistance(bool branch_only) const = 0;
     virtual double GetVariancePairwiseDistance(bool branch_only) const = 0;
     virtual emp::vector<double> GetPairwiseDistances(bool branch_only) const = 0;
@@ -494,6 +495,7 @@ namespace emp {
     using parent_t::GetNumTaxa;
     using parent_t::GetPhylogeneticDiversity;
     using parent_t::GetMeanPairwiseDistance;
+    using parent_t::GetSumDistance;
     using parent_t::GetSumPairwiseDistance;
     using parent_t::GetVariancePairwiseDistance;
     using parent_t::GetPairwiseDistances;
@@ -1086,6 +1088,21 @@ namespace emp {
       return (double)Sum(dists)/dists.size();
     }
 
+    /** Calculates summed branch lengths of tree. Tucker et al 2017 points
+     *  out that this is a measure of phylogenetic richness.
+     */
+    double GetSumDistance() const {
+      const auto op = [](const double a, const Ptr<taxon_t>& t){
+        const auto branch = t->GetParent() ? t->GetOriginationTime() - t->GetParent()->GetOriginationTime(): 0.0;
+        return a + branch;
+      };
+      return std::accumulate(
+        std::begin(active_taxa), std::end(active_taxa), double{}, op
+      ) + std::accumulate(
+        std::begin(ancestor_taxa), std::end(ancestor_taxa), double{}, op
+      );
+    }
+
     /** Calculates summed pairwise distance between extant taxa. Tucker et al 2017 points
      *  out that this is a measure of phylogenetic richness.
      *
diff --git a/tests/Evolve/Systematics.cpp b/tests/Evolve/Systematics.cpp
index 3360340896..26e6cb5270 100644
--- a/tests/Evolve/Systematics.cpp
+++ b/tests/Evolve/Systematics.cpp
@@ -175,6 +175,10 @@ TEST_CASE("Test Systematics", "[Evolve]") {
   // std::cout << "MPD: " << mpd <<std::endl;
   CHECK(mpd == Approx(2.8));
 
+  double sd = sys.GetSumDistance();
+  // std::cout << "MPD: " << mpd <<std::endl;
+  CHECK(sd == Approx(74.0));
+
   // std::cout << "\nAddOrg 31 (id8; parent id7)\n";
   sys.SetUpdate(11);
   auto id8 = sys.AddOrg(31, id7);

From 915bc4cdf15103b49e18859ff2edab75e1683785 Mon Sep 17 00:00:00 2001
From: Emily Dolson <emilyldolson@gmail.com>
Date: Thu, 29 Feb 2024 03:38:29 -0500
Subject: [PATCH 2/2] Fix tests

---
 tests/Evolve/Systematics.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/Evolve/Systematics.cpp b/tests/Evolve/Systematics.cpp
index d6f4ae2d35..e80ac34c77 100644
--- a/tests/Evolve/Systematics.cpp
+++ b/tests/Evolve/Systematics.cpp
@@ -510,7 +510,7 @@ TEST_CASE("Test not tracking ancestors", "[Evolve]") {
   CHECK(sys.GetNumOutside() == 0);
 
   auto active = sys.GetActive();
-  emp::vector<emp::Ptr<emp::Taxon< active_vec(active.begin(), active.end());
+  emp::vector<emp::Ptr<emp::Taxon<int>>> active_vec(active.begin(), active.end());
   emp::Sort(active_vec, [](emp::Ptr<emp::Taxon<int>> & a, emp::Ptr<emp::Taxon<int>> & b){
     return a->GetID() < b->GetID();
   });