From d79796ea97757c117a8188f33f856fb86416e1bb Mon Sep 17 00:00:00 2001
From: Martin Smith <martins@gmail.com>
Date: Mon, 21 Jan 2019 10:41:21 +0000
Subject: [PATCH 01/27] Don't use int64_t

---
 DESCRIPTION               |  4 ++--
 NEWS.md                   |  4 ++++
 src/HDTFactory.cpp        | 10 +++++-----
 src/RootedTreeFactory.cpp |  6 +++---
 src/hdt_factory.h         |  2 +-
 src/rooted_tree_factory.h |  2 +-
 6 files changed, 16 insertions(+), 12 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 628e839b..6c97b74f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Quartet
-Version: 1.0.0
-Date: 2019-01-09
+Version: 1.0.0.9000
+Date: 2019-01-21
 Title: Comparison of Phylogenetic Trees Using Quartet and Bipartition Measures
 Description: Calculates the number of four-taxon subtrees consistent with a pair
   of cladograms, calculating the symmetric quartet distance of Bandelt & Dress (1986),
diff --git a/NEWS.md b/NEWS.md
index 2d0656ee..f4400a2c 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,7 @@
+# Quartet v1.0.0.9000
+## Portability
+ - Improved portability of C++ code.
+
 # Quartet v1.0.0
 ## New features
  - Add functions to generate ternary plots from tree similarity measures.
diff --git a/src/HDTFactory.cpp b/src/HDTFactory.cpp
index 59fa47de..1c463ac3 100644
--- a/src/HDTFactory.cpp
+++ b/src/HDTFactory.cpp
@@ -179,9 +179,9 @@ TemplatedLinkedList<HDT*>* HDTFactory::getTemplatedLinkedList()
 	return returnMe;
 }
 
-int64_t HDTFactory::getSizeInRam()
+INTTYPE_N4 HDTFactory::getSizeInRam()
 {
-	int64_t resultHDT = 0;
+  INTTYPE_N4 resultHDT = 0;
 	{
 		HDT *current = createdHDTs;
 		while (current != NULL)
@@ -191,7 +191,7 @@ int64_t HDTFactory::getSizeInRam()
 		}
 	}
 
-	int64_t resultLL = 0;
+	INTTYPE_N4 resultLL = 0;
 	{
 		CountingLinkedList *current = createdLL;
 		while (current != NULL)
@@ -201,7 +201,7 @@ int64_t HDTFactory::getSizeInRam()
 		}
 	}
 
-	int64_t resultLLNO = 0;
+	INTTYPE_N4 resultLLNO = 0;
 	{
 		CountingLinkedListNumOnly *current = createdLLNO;
 		while (current != NULL)
@@ -211,7 +211,7 @@ int64_t HDTFactory::getSizeInRam()
 		}
 	}
 
-	int64_t resultTLL = 0;
+	INTTYPE_N4 resultTLL = 0;
 	{
 		TemplatedLinkedList<HDT*> *current = createdTLL;
 		while (current != NULL)
diff --git a/src/RootedTreeFactory.cpp b/src/RootedTreeFactory.cpp
index 8f292f0c..a5a9dd20 100644
--- a/src/RootedTreeFactory.cpp
+++ b/src/RootedTreeFactory.cpp
@@ -88,9 +88,9 @@ TemplatedLinkedList<RootedTree*>* RootedTreeFactory::getTemplatedLinkedList()
 	return returnMe;
 }
 
-int64_t RootedTreeFactory::getSizeInRam()
+INTTYPE_N4 RootedTreeFactory::getSizeInRam()
 {
-  int64_t resultRT = 0;
+  INTTYPE_N4 resultRT = 0;
 	{
 		RootedTree *current = createdRT;
 		while (current != NULL)
@@ -100,7 +100,7 @@ int64_t RootedTreeFactory::getSizeInRam()
 		}
 	}
 
-	int64_t resultTLL = 0;
+	INTTYPE_N4 resultTLL = 0;
 	{
 		TemplatedLinkedList<RootedTree*> *current = createdTLL;
 		while (current != NULL)
diff --git a/src/hdt_factory.h b/src/hdt_factory.h
index afd9c6a8..bc2edbe8 100644
--- a/src/hdt_factory.h
+++ b/src/hdt_factory.h
@@ -31,7 +31,7 @@ class HDTFactory
 		CountingLinkedListNumOnly* getLLNO();
 		TemplatedLinkedList<HDT*>* getTemplatedLinkedList();
 		void deleteTemplatedLinkedList();
-		int64_t getSizeInRam();
+		INTTYPE_N4 getSizeInRam();
 };
 
 #endif
\ No newline at end of file
diff --git a/src/rooted_tree_factory.h b/src/rooted_tree_factory.h
index b357eda7..61725d50 100644
--- a/src/rooted_tree_factory.h
+++ b/src/rooted_tree_factory.h
@@ -20,7 +20,7 @@ class RootedTreeFactory
 		~RootedTreeFactory();
 		RootedTree* getRootedTree(string name = "");
 		TemplatedLinkedList<RootedTree*>* getTemplatedLinkedList();
-		int64_t getSizeInRam();
+		INTTYPE_N4 getSizeInRam();
 };
 
 #endif
\ No newline at end of file

From eed1e2345ed65173dcd2d68882fb200c628f5b4b Mon Sep 17 00:00:00 2001
From: Martin Smith <martins@gmail.com>
Date: Mon, 21 Jan 2019 10:58:10 +0000
Subject: [PATCH 02/27] Do not include <io***>

---
 src/hdt.h           | 1 -
 src/int_stuff.cpp   | 2 --
 src/rooted_tree.h   | 1 -
 src/unrooted_tree.h | 1 -
 4 files changed, 5 deletions(-)

diff --git a/src/hdt.h b/src/hdt.h
index 4e05de02..5527a280 100644
--- a/src/hdt.h
+++ b/src/hdt.h
@@ -1,7 +1,6 @@
 #ifndef HDT_H
 #define HDT_H
 
-#include <iostream>
 #include <string>
 #include "int_stuff.h"
 #include "util.h"
diff --git a/src/int_stuff.cpp b/src/int_stuff.cpp
index 91e22e63..3eac7d8b 100644
--- a/src/int_stuff.cpp
+++ b/src/int_stuff.cpp
@@ -1,3 +1 @@
 #include "int_stuff.h"
-#include <iostream>
-#include <iomanip>
diff --git a/src/rooted_tree.h b/src/rooted_tree.h
index 46f8e959..bf91e9b2 100644
--- a/src/rooted_tree.h
+++ b/src/rooted_tree.h
@@ -1,7 +1,6 @@
 #ifndef ROOTED_TREE_H
 #define ROOTED_TREE_H
 
-#include <iostream>
 #include <vector>
 #include <map>
 #include <string>
diff --git a/src/unrooted_tree.h b/src/unrooted_tree.h
index e989468e..9af43f56 100644
--- a/src/unrooted_tree.h
+++ b/src/unrooted_tree.h
@@ -1,7 +1,6 @@
 #ifndef UNROOTED_TREE_H
 #define UNROOTED_TREE_H
 
-#include <iostream>
 #include <vector>
 #include <string>
 #include <algorithm>

From 6ef43ba8eab1f5a67ff461a4643f07bbc2f3470f Mon Sep 17 00:00:00 2001
From: Martin Smith <martins@gmail.com>
Date: Mon, 21 Jan 2019 10:58:52 +0000
Subject: [PATCH 03/27] Use int_fast64_t on all platforms

Requires C++11
---
 src/Makevars    |  1 +
 src/int_stuff.h | 14 ++++----------
 2 files changed, 5 insertions(+), 10 deletions(-)
 create mode 100644 src/Makevars

diff --git a/src/Makevars b/src/Makevars
new file mode 100644
index 00000000..260d08c6
--- /dev/null
+++ b/src/Makevars
@@ -0,0 +1 @@
+PKG_CXXFLAGS = -std=c++11
diff --git a/src/int_stuff.h b/src/int_stuff.h
index 6ed20b3b..214fdb03 100644
--- a/src/int_stuff.h
+++ b/src/int_stuff.h
@@ -2,15 +2,9 @@
   
   #define INT_STUFF_H
   
-  #include <iostream>
-  #include <stdint.h>
-  
-  #ifdef _WIN32
-    #define INTTYPE_N4 __int64 //previously long long, which fails -pedantic
-    #define INTTYPE_REST __int64 //previously long long, which fails -pedantic
-  #else
-    #define INTTYPE_N4 __int64_t //previously long long, which fails -pedantic
-    #define INTTYPE_REST __int64_t //previously long long, which fails -pedantic
-  #endif
+  #include <cstdint>
   
+  #define INTTYPE_N4 int_fast64_t // long long fails -pedantic
+  #define INTTYPE_REST int_fast64_t // long long fails -pedantic
+
 #endif
\ No newline at end of file

From 6c9f540afa97f9e117b372490cfd2594ec7ff929 Mon Sep 17 00:00:00 2001
From: Martin Smith <martins@gmail.com>
Date: Mon, 21 Jan 2019 10:59:49 +0000
Subject: [PATCH 04/27] Don't include <iostream>

---
 src/templated_linked_list.h | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/templated_linked_list.h b/src/templated_linked_list.h
index a3ccffd8..58db15eb 100644
--- a/src/templated_linked_list.h
+++ b/src/templated_linked_list.h
@@ -1,8 +1,6 @@
 #ifndef TEMPLATED_LINKED_LIST
 #define TEMPLATED_LINKED_LIST
 
-#include <iostream>
-
 using namespace std;
 
 template <class dataType>

From 12df27e41d662a08081f81c49dc2d34156a96106 Mon Sep 17 00:00:00 2001
From: Martin Smith <martins@gmail.com>
Date: Mon, 21 Jan 2019 11:01:26 +0000
Subject: [PATCH 05/27] Don't include <algorithm>

---
 src/NewickParser.cpp | 1 -
 src/unrooted_tree.h  | 1 -
 2 files changed, 2 deletions(-)

diff --git a/src/NewickParser.cpp b/src/NewickParser.cpp
index d4575f09..cbd5e44a 100644
--- a/src/NewickParser.cpp
+++ b/src/NewickParser.cpp
@@ -4,7 +4,6 @@
 #include <fstream>
 #include <sstream>
 #include <cstdlib>
-#include <algorithm> 
 #include <functional> 
 #include <cctype>
 #include <locale>
diff --git a/src/unrooted_tree.h b/src/unrooted_tree.h
index 9af43f56..68b49455 100644
--- a/src/unrooted_tree.h
+++ b/src/unrooted_tree.h
@@ -3,7 +3,6 @@
 
 #include <vector>
 #include <string>
-#include <algorithm>
 
 #include "rooted_tree.h"
 #include "rooted_tree_factory.h"

From 71ffcfdac5d07463e3ea7aa4022aff86fe3d3daa Mon Sep 17 00:00:00 2001
From: Martin Smith <martins@gmail.com>
Date: Mon, 21 Jan 2019 11:03:41 +0000
Subject: [PATCH 06/27] Don't include unused <sstream> or <functional>

---
 src/NewickParser.cpp | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/NewickParser.cpp b/src/NewickParser.cpp
index cbd5e44a..5ec3d7c0 100644
--- a/src/NewickParser.cpp
+++ b/src/NewickParser.cpp
@@ -2,9 +2,8 @@
 
 #include <Rcpp.h>
 #include <fstream>
-#include <sstream>
 #include <cstdlib>
-#include <functional> 
+
 #include <cctype>
 #include <locale>
 

From 3ae2bbafd57806124ad7785e3ce0be10e9755ca1 Mon Sep 17 00:00:00 2001
From: Martin Smith <martins@gmail.com>
Date: Mon, 21 Jan 2019 11:30:38 +0000
Subject: [PATCH 07/27] #if __cplusplus <= 199711L

---
 src/int_stuff.h | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/int_stuff.h b/src/int_stuff.h
index 214fdb03..cd4fbc99 100644
--- a/src/int_stuff.h
+++ b/src/int_stuff.h
@@ -2,9 +2,13 @@
   
   #define INT_STUFF_H
   
+#if __cplusplus <= 199711L
+  #define INTTYPE_N4 long long // fails -pedantic
+  #define INTTYPE_REST long long // fails -pedantic
+#else 
   #include <cstdint>
-  
   #define INTTYPE_N4 int_fast64_t // long long fails -pedantic
   #define INTTYPE_REST int_fast64_t // long long fails -pedantic
 
+#endif
 #endif
\ No newline at end of file

From 9b2ab8307bdaadd03c2569c233439ba80a28f44e Mon Sep 17 00:00:00 2001
From: Martin Smith <martins@gmail.com>
Date: Mon, 21 Jan 2019 11:37:08 +0000
Subject: [PATCH 08/27] Allow no c++11

and don't warn re. long longs
---
 src/Makevars | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Makevars b/src/Makevars
index 260d08c6..8515e47a 100644
--- a/src/Makevars
+++ b/src/Makevars
@@ -1 +1 @@
-PKG_CXXFLAGS = -std=c++11
+PKG_CXXFLAGS = -Wno-long-long

From 7fee8b9b203815ff2ea2fe4038ae8b255f9ec302 Mon Sep 17 00:00:00 2001
From: Martin Smith <martins@gmail.com>
Date: Mon, 21 Jan 2019 11:46:50 +0000
Subject: [PATCH 09/27] Include int_stuff first

---
 src/rTripletDist.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/rTripletDist.cpp b/src/rTripletDist.cpp
index a0b776bc..7883f2ba 100644
--- a/src/rTripletDist.cpp
+++ b/src/rTripletDist.cpp
@@ -1,8 +1,8 @@
 #include <Rcpp.h>
 using namespace Rcpp;
+#include "int_stuff.h"
 
 #include "TripletDistanceCalculator.h"
-#include "int_stuff.h"
 
 #include <R.h>
 #include <Rdefines.h>

From 5d9177d07479ab19f8aef21719906dae133b6dbe Mon Sep 17 00:00:00 2001
From: Martin Smith <martins@gmail.com>
Date: Mon, 21 Jan 2019 11:53:01 +0000
Subject: [PATCH 10/27] Triplets: Use CharacterVector instead of SEXP

---
 src/RcppExports.cpp  | 16 ++++++++--------
 src/rTripletDist.cpp | 28 +++++++++++++++++++++-------
 2 files changed, 29 insertions(+), 15 deletions(-)

diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
index ab6354de..bbad59d7 100644
--- a/src/RcppExports.cpp
+++ b/src/RcppExports.cpp
@@ -76,36 +76,36 @@ BEGIN_RCPP
 END_RCPP
 }
 // tqdist_TripletDistance
-IntegerVector tqdist_TripletDistance(SEXP file1, SEXP file2);
+IntegerVector tqdist_TripletDistance(CharacterVector file1, CharacterVector file2);
 RcppExport SEXP _Quartet_tqdist_TripletDistance(SEXP file1SEXP, SEXP file2SEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< SEXP >::type file1(file1SEXP);
-    Rcpp::traits::input_parameter< SEXP >::type file2(file2SEXP);
+    Rcpp::traits::input_parameter< CharacterVector >::type file1(file1SEXP);
+    Rcpp::traits::input_parameter< CharacterVector >::type file2(file2SEXP);
     rcpp_result_gen = Rcpp::wrap(tqdist_TripletDistance(file1, file2));
     return rcpp_result_gen;
 END_RCPP
 }
 // tqdist_PairsTripletDistance
-IntegerVector tqdist_PairsTripletDistance(SEXP file1, SEXP file2);
+IntegerVector tqdist_PairsTripletDistance(CharacterVector file1, CharacterVector file2);
 RcppExport SEXP _Quartet_tqdist_PairsTripletDistance(SEXP file1SEXP, SEXP file2SEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< SEXP >::type file1(file1SEXP);
-    Rcpp::traits::input_parameter< SEXP >::type file2(file2SEXP);
+    Rcpp::traits::input_parameter< CharacterVector >::type file1(file1SEXP);
+    Rcpp::traits::input_parameter< CharacterVector >::type file2(file2SEXP);
     rcpp_result_gen = Rcpp::wrap(tqdist_PairsTripletDistance(file1, file2));
     return rcpp_result_gen;
 END_RCPP
 }
 // tqdist_AllPairsTripletDistance
-IntegerMatrix tqdist_AllPairsTripletDistance(SEXP file);
+IntegerMatrix tqdist_AllPairsTripletDistance(CharacterVector file);
 RcppExport SEXP _Quartet_tqdist_AllPairsTripletDistance(SEXP fileSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< SEXP >::type file(fileSEXP);
+    Rcpp::traits::input_parameter< CharacterVector >::type file(fileSEXP);
     rcpp_result_gen = Rcpp::wrap(tqdist_AllPairsTripletDistance(file));
     return rcpp_result_gen;
 END_RCPP
diff --git a/src/rTripletDist.cpp b/src/rTripletDist.cpp
index 7883f2ba..c09ca3e5 100644
--- a/src/rTripletDist.cpp
+++ b/src/rTripletDist.cpp
@@ -13,7 +13,12 @@ using namespace Rcpp;
 //' @describeIn tqdist_QuartetDistance Triplet distance between two trees
 //' @export
 // [[Rcpp::export]]
-IntegerVector tqdist_TripletDistance(SEXP file1, SEXP file2) {
+IntegerVector tqdist_TripletDistance(CharacterVector file1, CharacterVector file2) {
+  int n1 = file1.size(), n2 = file2.size();
+  if (n1 != 1 || n2 != 1) {
+    Rcpp::stop("file1 and file2 must be character vectors of length 1");
+  }
+  
   const char *filename1;
   const char *filename2;
 
@@ -25,14 +30,19 @@ IntegerVector tqdist_TripletDistance(SEXP file1, SEXP file2) {
   INTTYPE_REST res = tripletCalc.calculateTripletDistance(filename1, filename2);
   
   IntegerVector IV_res(1);
-  IV_res = res;
+  IV_res[0] = res;
   return IV_res;
 }
 
 //' @describeIn tqdist_QuartetDistance Triplet distance between pairs
 //' @export
 // [[Rcpp::export]]
-IntegerVector tqdist_PairsTripletDistance(SEXP file1, SEXP file2) {
+IntegerVector tqdist_PairsTripletDistance(CharacterVector file1, CharacterVector file2) {
+  int n1 = file1.size(), n2 = file2.size();
+  if (n1 != 1 || n2 != 1) {
+    Rcpp::stop("file1 and file2 must be character vectors of length 1");
+  }
+  
   const char * filename1;
   const char * filename2;
   
@@ -40,6 +50,7 @@ IntegerVector tqdist_PairsTripletDistance(SEXP file1, SEXP file2) {
   filename2 = CHAR(STRING_ELT(file2, 0));
   
   TripletDistanceCalculator tripletCalc;
+  
   std::vector<INTTYPE_REST> res = tripletCalc.pairs_triplet_distance(filename1, filename2);
   
   IntegerVector IV_res(res.size());
@@ -52,16 +63,19 @@ IntegerVector tqdist_PairsTripletDistance(SEXP file1, SEXP file2) {
 //' @describeIn tqdist_QuartetDistance Triplet distance between all pairs
 //' @export
 // [[Rcpp::export]]
-IntegerMatrix tqdist_AllPairsTripletDistance(SEXP file) {
-  const char * filename;
+IntegerMatrix tqdist_AllPairsTripletDistance(CharacterVector file) {
+  int n = file.size();
+  if (n != 1) {
+    Rcpp::stop("file must be a character vector of length 1");
+  }
   
+  const char *filename;
   filename = CHAR(STRING_ELT(file, 0));
-
   TripletDistanceCalculator tripletCalc;
+
   std::vector<std::vector<INTTYPE_REST> > res = tripletCalc.calculateAllPairsTripletDistance(filename);
 
   IntegerMatrix IM_res(res.size(), res.size());
-  //  int *ians = INTEGER(res_sexp);
   
   for (size_t r = 0; r < res.size(); ++r) {
     for (size_t c = 0; c < r; ++c) {

From 19459108cb5ae3236912442e05b5f95268f3ede6 Mon Sep 17 00:00:00 2001
From: Martin Smith <martins@gmail.com>
Date: Mon, 21 Jan 2019 11:53:11 +0000
Subject: [PATCH 11/27] Unnecessary comment

---
 src/rQuartetDist.cpp | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/rQuartetDist.cpp b/src/rQuartetDist.cpp
index 8bfce3fa..834700fa 100644
--- a/src/rQuartetDist.cpp
+++ b/src/rQuartetDist.cpp
@@ -134,7 +134,6 @@ IntegerMatrix tqdist_AllPairsQuartetDistance(CharacterVector file) {
   std::vector<std::vector<INTTYPE_N4> > res = quartetCalc.calculateAllPairsQuartetDistance(filename);
   
   IntegerMatrix IM_res(res.size(), res.size());
-//  int *ians = INTEGER(res_sexp);
   
   for (size_t r = 0; r < res.size(); r++) {
     for (size_t c = 0; c < r; c++) {

From 8ead11f68af21f63522a4026bbe8773832681aab Mon Sep 17 00:00:00 2001
From: Martin Smith <martins@gmail.com>
Date: Mon, 21 Jan 2019 12:00:53 +0000
Subject: [PATCH 12/27] Remove unnecessary incldes

---
 src/hdt.h                      | 2 +-
 src/rooted_tree.h              | 1 -
 tests/testthat/test-1-tqdist.R | 2 +-
 3 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/hdt.h b/src/hdt.h
index 5527a280..4e4eb2c6 100644
--- a/src/hdt.h
+++ b/src/hdt.h
@@ -5,7 +5,7 @@
 #include "int_stuff.h"
 #include "util.h"
 #include "rooted_tree_factory.h"
-//#include "counting_linked_list.h"
+
 class RootedTree; // forward declaration
 class HDTFactory; // forward declaration
 class CountingLinkedList; // forward declaration
diff --git a/src/rooted_tree.h b/src/rooted_tree.h
index bf91e9b2..2596a824 100644
--- a/src/rooted_tree.h
+++ b/src/rooted_tree.h
@@ -2,7 +2,6 @@
 #define ROOTED_TREE_H
 
 #include <vector>
-#include <map>
 #include <string>
 
 #include "int_stuff.h"
diff --git a/tests/testthat/test-1-tqdist.R b/tests/testthat/test-1-tqdist.R
index 02595dff..dd61e659 100644
--- a/tests/testthat/test-1-tqdist.R
+++ b/tests/testthat/test-1-tqdist.R
@@ -1,4 +1,4 @@
-context("tqDist")
+context("tqDist tests")
 
 test_that("tqDist returns correct quartet distances", {
   expect_true(file.exists("../trees/quartet1.new"))

From 5fb41682545cfd9a0c6a31128d4c6777f44133e8 Mon Sep 17 00:00:00 2001
From: Martin Smith <martins@gmail.com>
Date: Mon, 21 Jan 2019 12:01:04 +0000
Subject: [PATCH 13/27] Remove -Wno-long-long

Non-portable...
---
 src/Makevars | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/Makevars b/src/Makevars
index 8515e47a..e69de29b 100644
--- a/src/Makevars
+++ b/src/Makevars
@@ -1 +0,0 @@
-PKG_CXXFLAGS = -Wno-long-long

From fea07fac0afcbfd0e51cc52e2cf93647a4705c3d Mon Sep 17 00:00:00 2001
From: Martin Smith <martins@gmail.com>
Date: Mon, 21 Jan 2019 12:06:00 +0000
Subject: [PATCH 14/27] doExtractAndContract is def'd; remove comments

---
 src/AbstractDistanceCalculator.cpp | 22 ++++------------------
 1 file changed, 4 insertions(+), 18 deletions(-)

diff --git a/src/AbstractDistanceCalculator.cpp b/src/AbstractDistanceCalculator.cpp
index 812e69e7..be879671 100644
--- a/src/AbstractDistanceCalculator.cpp
+++ b/src/AbstractDistanceCalculator.cpp
@@ -12,10 +12,8 @@ void AbstractDistanceCalculator::count(RootedTree *v) {
     // This will make sure the entire subtree has color 0!
     v->colorSubtree(0);
     
-/*#ifdef doExtractAndContract*/
     delete hdt->factory;
-/*#endif*/
-    
+
     return;
   }
 
@@ -52,7 +50,6 @@ void AbstractDistanceCalculator::count(RootedTree *v) {
   hdt->updateCounters();
   updateCounters();
   
-/*#ifdef doExtractAndContract*/
   // Extract
   RootedTree** extractedVersions = new RootedTree*[v->numChildren - 1];
   c = 0;
@@ -68,7 +65,6 @@ void AbstractDistanceCalculator::count(RootedTree *v) {
     }
     c++;
   }
-/*#endif*/
 
   // Color to 0
   for(TemplatedLinkedList<RootedTree*> *current = v->children->next;
@@ -80,16 +76,11 @@ void AbstractDistanceCalculator::count(RootedTree *v) {
   RootedTree *firstChild = v->children->data;
   if (firstChild->isLeaf() || firstChild->n <= 2) {
     // Do "nothing" (except clean up and possibly color!)
-/*#ifdef doExtractAndContract*/
     // Notice no recoloring here... It's not neccesary as it is extracted and contracted away,
     // and will actually cause an error if called with firstChild->colorSubtree(0) as t2 is linked
     // to a non-existing hdt (as we just deleted it) (we could wait with deleting it, but as we don't need the coloring why bother)
     delete hdt->factory;
-/*#else
-    firstChild->colorSubtree(0);
-#endif*/
   } else {
-/*#ifdef doExtractAndContract*/
     bool hdtTooBig = firstChild->n * CONTRACT_MAX_EXTRA_SIZE < hdt->leafCount();
     if (hdtTooBig) {
       HDT *newHDT;
@@ -103,9 +94,8 @@ void AbstractDistanceCalculator::count(RootedTree *v) {
       delete hdt->factory;
       hdt = newHDT;
     }
-/*#endif*/
     count(firstChild);
-    // HDT is deleted in recursive call!
+    // HDT is deleted in recursive call
   }
   
   // Color 1 and recurse
@@ -113,22 +103,18 @@ void AbstractDistanceCalculator::count(RootedTree *v) {
   for(TemplatedLinkedList<RootedTree*> *current = v->children->next;
       current != NULL; current = current->next) {
     if (!current->data->isLeaf() && current->data->n > 2) {
-/*#ifdef doExtractAndContract*/
       hdt = HDT::constructHDT(extractedVersions[c], t1->maxDegree, dummyHDTFactory, true);
       delete extractedVersions[c]->factory;
-/*#endif*/
-      
+
       current->data->colorSubtree(1);
       
       count(current->data);
     }
     c++;
-    // HDT is deleted on recursive calls!
+    // HDT is deleted on recursive call
   }
   
-/*#ifdef doExtractAndContract*/
   delete[] extractedVersions;
-/*#endif*/
 }
 
 void AbstractDistanceCalculator::countChildren(RootedTree *t) {

From 1a0b4945aab18d9aa5c298427ab5c71f448cd330 Mon Sep 17 00:00:00 2001
From: Martin Smith <martins@gmail.com>
Date: Mon, 21 Jan 2019 12:11:19 +0000
Subject: [PATCH 15/27] Remove unnecessary include <cstdlib>

---
 src/rQuartetDist.cpp | 1 -
 src/rooted_tree.h    | 4 ++--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/rQuartetDist.cpp b/src/rQuartetDist.cpp
index 834700fa..c17b1b07 100644
--- a/src/rQuartetDist.cpp
+++ b/src/rQuartetDist.cpp
@@ -7,7 +7,6 @@ using namespace Rcpp;
 #include <R.h>
 #include <Rdefines.h>
 #include <Rinternals.h>
-#include <cstdlib>
 #include <vector>
 
 //' Triplet and quartet distances with tqDist
diff --git a/src/rooted_tree.h b/src/rooted_tree.h
index 2596a824..b5b1b56a 100644
--- a/src/rooted_tree.h
+++ b/src/rooted_tree.h
@@ -7,8 +7,8 @@
 #include "int_stuff.h"
 #include "templated_linked_list.h"
 
-class HDT;// Forward declaration...
-class RootedTreeFactory; // Forward declaration...
+class HDT;// Forward declaration
+class RootedTreeFactory; // Forward declaration
 
 using namespace std;
 

From aaa7993d0f408f5397d941511dd6e46412d91ea9 Mon Sep 17 00:00:00 2001
From: Martin Smith <martins@gmail.com>
Date: Mon, 21 Jan 2019 12:15:54 +0000
Subject: [PATCH 16/27] Delete Makevars

---
 src/Makevars | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 src/Makevars

diff --git a/src/Makevars b/src/Makevars
deleted file mode 100644
index e69de29b..00000000

From 53ab126370c90acb0b85cf617297a9ba1390d5d8 Mon Sep 17 00:00:00 2001
From: Martin Smith <martins@gmail.com>
Date: Mon, 21 Jan 2019 12:18:59 +0000
Subject: [PATCH 17/27] Installation from CRAN

---
 README.md | 21 ++++++++++-----------
 1 file changed, 10 insertions(+), 11 deletions(-)

diff --git a/README.md b/README.md
index 9a29eff1..25f69706 100644
--- a/README.md
+++ b/README.md
@@ -19,21 +19,20 @@ function `SplitStatus`).
 
 
 ## Using the package
-The package will soon be compiled and uploaded to the CRAN repository.  
-Meanwhile, you can install the latest version of the package into R thus:
+Install and load the library from CRAN as follows:
+```
+install.packages('Quartet')
+library('Quartet')
+```
 
+If you're feeling brave, you can install the development version thus:
 ```r
-# Install the devtools package from CRAN
-install.packages('devtools')
-
-# Install the package from github
-devtools::install_github('ms609/Quartet', args='--no-multiarch')
-
-# Load the package into R
-library('Quartet')
+if(!require(devtools)) install.packages("devtools")
+devtools::install_github('ms609/Quartet')
 ```
 
-You will need [Rtools](https://cran.r-project.org/bin/windows/Rtools/) installed to allow R to build the package.
+You will need [Rtools](https://cran.r-project.org/bin/windows/Rtools/) installed 
+in order to build the development version from source.
 
 ## References
 - Brodal G.S., Fagerberg R., Pedersen C.N.S. 2004. Computing the quartet 

From 2643d2ee41729f0d3a94212b6610ff7289468114 Mon Sep 17 00:00:00 2001
From: Martin Smith <martins@gmail.com>
Date: Mon, 21 Jan 2019 12:30:27 +0000
Subject: [PATCH 18/27] Remove unnecessary comments

---
 src/HDT.cpp                       | 43 ++++++-------------------------
 src/HDTCountingCCToC.cpp          | 26 +++++--------------
 src/HDTCountingCTransform.cpp     | 20 +++-----------
 src/HDTCountingG.cpp              | 20 --------------
 src/HDTCountingIGToC.cpp          |  4 ---
 src/HDTCountingLeaf.cpp           |  4 ---
 src/HDTListUtils.cpp              |  4 ---
 src/QuartetDistanceCalculator.cpp |  7 +----
 src/TripletDistanceCalculator.cpp |  7 ++---
 src/counting_linked_list.h        |  9 +------
 src/hdt.h                         |  8 ++----
 11 files changed, 24 insertions(+), 128 deletions(-)

diff --git a/src/HDT.cpp b/src/HDT.cpp
index bdaaf46b..b73fb133 100644
--- a/src/HDT.cpp
+++ b/src/HDT.cpp
@@ -19,13 +19,12 @@ void HDT::initialize(CountingLinkedList *countingVars, NodeType type, int numD,
 	goBackVariable = NULL;
 	tripResolved = 0;
 	tripUnresolved = 0;
-/*#ifdef quartetsToo*/
 	quartResolvedAgree = 0;
 	quartResolvedAgreeDiag = 0;
 	quartResolvedAgreeUpper = 0;
 	// New sum for calculating E
 	quartSumE = 0;
-/*#endif*/
+
 	up2date = altMarked = false;
 
 	this->type = type;
@@ -200,10 +199,7 @@ RootedTree* HDT::extractAndGoBackImpl(RootedTree *addToMe, RootedTreeFactory *fa
 
 void HDT::toDot()
 {
-	// cout << "digraph g {" << endl;
-	//  << "node[shape=circle];" << endl;
 	toDotImpl();
-	//  << "}" << endl;
 }
 
 void HDT::updateCounters()
@@ -294,10 +290,11 @@ HDT* HDT::preFirstRound(RootedTree *t, int numD, bool doLink, HDTFactory *factor
 
 HDT* HDT::round(HDTFactory *factory)
 {
-	// NOTE: C -> G when parent I etc is moved down!!
+	// NOTE: C -> G when parent I etc is moved down.
 
 	// Composition 3: If we're a C we only have 1 child.
-	// If that's a C, use CC->C, skip the child and go directly to that-one's child (if exists)
+	// If that's a C, use CC->C, skip the child and go directly to that-one's 
+	// child (if it exists)
 	if (type == C && children != NULL && children->next == NULL /*children.size() == 1*/)
 	{
 		HDT *child = children->data;
@@ -310,7 +307,8 @@ HDT* HDT::round(HDTFactory *factory)
 			newC->right = child;
 			newC->right->parent = newC;
 
-			// If there's children, there's only 1. We recurse on that one and add the result to our children list.
+			// If there's children, there's only 1. 
+			// We recurse on that one and add the result to our children list.
 			if (child->children != NULL)
 			{
 				child = child->children->data;
@@ -346,7 +344,8 @@ HDT* HDT::round(HDTFactory *factory)
 			// We found 2 G's
 			if (lastG != NULL)
 			{
-				// Merge the two G's by removing one and replaceing the other with the new G that points to the two old ones
+				// Merge the two G's by removing one and replacing the other with the 
+				// new G that points to the two old ones
 
 				// Replace one with a new one with left, right and parent pointers set
 				HDT *newG = factory->getHDT(G, NULL, false);
@@ -409,38 +408,12 @@ bool HDT::isDownwardsClosed()
 
 void HDT::toDotImpl()
 {
-  /*
-	cout << "n" << this << "[label=\"";
-	if (convertedFrom != NotConverted)
-	{
-		switch(convertedFrom)
-		{
-			case I: cout << "I"; break;
-			case C: cout << "C"; break;
-			case G: cout << "G"; break;
-			case NotConverted: cout << "NotConverted"; break; // Shouldn't happen!
-		}
-		cout << " -> ";
-	}
-	switch(type)
-	{
-		case I: cout << "I"; break;
-		case C: cout << "C"; break;
-		case G: cout << "G"; break;
-		case NotConverted: cout << "NotConverted"; break; // Shouldn't happen!
-	}
-	if (link != NULL) cout << "; " << link->name;
-	if (type == G && convertedFrom == C && left == NULL && right == NULL) cout << "; 0's: " << numZeroes;
-	cout << "\"];" << endl;
-  */
 	if (left != NULL)
 	{
 		left->toDotImpl();
-		// cout << "n" << this << " -> n" << left << ";" << endl;
 	}
 	if (right != NULL)
 	{
 		right->toDotImpl();
-		// cout << "n" << this << " -> n" << right << ";" << endl;
 	}
 }
diff --git a/src/HDTCountingCCToC.cpp b/src/HDTCountingCCToC.cpp
index 897c0e93..33df022b 100644
--- a/src/HDTCountingCCToC.cpp
+++ b/src/HDTCountingCCToC.cpp
@@ -21,7 +21,6 @@ void HDT::handleCCToC()
 	n_circ_square = 0;
 
 	// Quartets
-/*#ifdef quartetsToo*/
 	// Initialize sums to 0 so we can increment it in the loop
 	n_circ_circ = 0;
 	n_square_paren_circ_circ = 0;
@@ -35,7 +34,7 @@ void HDT::handleCCToC()
 	n_0_circ = c1->n_0_circ + c2->n_0_circ;
 	n_paren_0_circ = c1->n_paren_0_circ + c2->n_paren_0_circ;
 
-	// Added by us for filling out tables (initialize)
+	// Added by Sand et al. (2014) for filling out tables (initialize)
 	n_bracket_circ_circ = 0;
 	n_paren_circ_paren_square_square = 0;
 	n_circ_arrow_circ = 0;
@@ -65,7 +64,6 @@ void HDT::handleCCToC()
 
 	// Fetch sum for calculating E from children
 	quartSumE = c1->quartSumE + c2->quartSumE;
-/*#endif*/
 
 	// Fetch the childrens "result counting data"
 	tripResolved = c1->tripResolved + c2->tripResolved;
@@ -79,7 +77,6 @@ void HDT::handleCCToC()
 	CountingLinkedList *ourCount = countingVars;
 
 	// Quartets
-/*#ifdef quartetsToo*/
 	INTTYPE_REST c1Zero = 0;
 	INTTYPE_REST c2Zero = 0;
 
@@ -97,7 +94,6 @@ void HDT::handleCCToC()
 	n_0_arrow_circ_circ = c1->n_0_arrow_circ_circ + c2->n_0_arrow_circ_circ +
 		c1Zero * c2->n_circ_circ;
 	// Not dependent on i (end)
-/*#endif*/
 
 	while (c1Next != NULL || c2Next != NULL)
 	{
@@ -158,7 +154,6 @@ void HDT::handleCCToC()
 			c1Count->n_i * (c2->n_circ - c2Count->n_i);
 
 		// Quartets
-/*#ifdef quartetsToo*/
 		// 2nd group in figure 12 (quartets only)
 		ourCount->n_0_i = c1Count->n_0_i + c2Count->n_0_i;
 		ourCount->n_ii = c1Count->n_ii + c2Count->n_ii;
@@ -258,7 +253,7 @@ void HDT::handleCCToC()
 			(c1->n_circ - c1Count->n_i) * c2Count->n_i_arrow_i +
 			c1Count->n_circ_arrow_i * c2Count->n_i;
 
-		// Added by us!
+		// Added by Sand et al. (2014)
 		ourCount->n_i_arrow_paren_circ_circ = c1Count->n_i_arrow_paren_circ_circ + c2Count->n_i_arrow_paren_circ_circ +
 			c1Count->n_i * (c2->n_paren_circ_circ - c2Count->n_paren_ii);
 
@@ -281,7 +276,7 @@ void HDT::handleCCToC()
 		if (ourCount->n_j_arrow_i != NULL) ourCount->n_j_arrow_i->type = CountingLinkedListNumOnly::SkipAndEnd;
 		if (ourCount->n_i_arrow_j != NULL) ourCount->n_i_arrow_j->type = CountingLinkedListNumOnly::SkipAndEnd;
 
-		// Added by us for filling out tables
+		// Added by Sand et al. (2014) for filling out tables
 		// A
 		ourCount->n_bracket_i_paren_circ_circ = c1Count->n_bracket_i_paren_circ_circ + c2Count->n_bracket_i_paren_circ_circ + 
 			(c1->n_bracket_circ_circ - Util::binom2(c1Count->n_i)) * c2Count->n_i + c1Count->n_i * (c2->n_paren_circ_circ - c2Count->n_paren_ii);
@@ -349,7 +344,7 @@ void HDT::handleCCToC()
 				ourCount->n_bracket_i_circ_square += addThis;
 				// E end
 
-				// Added by us for filling out tables
+				// Added by Sand et al. (2014) for filling out tables
 				ourCount->n_bracket_i_paren_circ_circ += c1->countingVars->getIteratorValue(j)->n_i * getIteratorValueForNumList(c2Count->n_j_arrow_i, j);
 				ourCount->n_bracket_i_paren_circ_square += c1->countingVars->getIteratorValue(j)->n_i * (c2Count->n_circ_arrow_i - getIteratorValueForNumList(c2Count->n_j_arrow_i, j));
 				ourCount->n_i_arrow_circ_arrow_circ += getIteratorValueForNumList(c1Count->n_i_arrow_j, j) * c2->countingVars->getIteratorValue(j)->n_i;
@@ -361,7 +356,7 @@ void HDT::handleCCToC()
 		ourCount->n_0_arrow_i_circ = c1Count->n_0_arrow_i_circ + c2Count->n_0_arrow_i_circ +
 			c1Zero * c2Count->n_i_circ;
 
-		// Added by us for filling out tables
+		// Added by Sand et al. (2014) for filling out tables
 		ourCount->n_paren_i_paren_circ_circ = c1Count->n_paren_i_paren_circ_circ + c2Count->n_paren_i_paren_circ_circ;
 
 		ourCount->n_paren_i_paren_circ_square = c1Count->n_paren_i_paren_circ_square + c2Count->n_paren_i_paren_circ_square;
@@ -394,13 +389,11 @@ void HDT::handleCCToC()
 			c1Zero * c2Count->n_i_circ + 
 			c1Count->n_i * (c2->n_0_circ - c2Count->n_0_i) +
 			(c1->n_circ - c1Count->n_i) * c2Count->n_0_i;
-/*#endif*/
 
 		// Sums and stuff
 		n_circ_square += ourCount->n_i_circ;
 				
 		// Quartets
-/*#ifdef quartetsToo*/
 		n_circ_circ += ourCount->n_ii;
 		n_square_paren_circ_circ += ourCount->n_i_paren_circ_circ;
 		n_paren_circ_circ += ourCount->n_paren_ii;
@@ -408,10 +401,10 @@ void HDT::handleCCToC()
 		n_circ_arrow_paren_square_square += ourCount->n_circ_arrow_paren_ii; // FIXED!!
 		n_bracket_circ_square += ourCount->n_bracket_i_circ;
 
-		// Added by us
+		// Added by Sand et al. (2014)
 		n_circ_arrow_square_square += ourCount->n_i_arrow_circ_circ;
 
-		// Added by us for filling out tables
+		// Added by Sand et al. (2014) for filling out tables
 		// A
 		n_bracket_circ_circ += Util::binom2(ourCount->n_i);
 		n_paren_circ_paren_square_square += ourCount->n_paren_i_paren_circ_circ;
@@ -432,7 +425,6 @@ void HDT::handleCCToC()
 
 		n_bracket_circ_square_triangle += ourCount->n_bracket_i_circ_square;
 		n_bracket_0_circ_square += ourCount->n_bracket_0_i_circ;
-/*#endif*/
 
 		// Update resolved/resolved and unresolved/unresolved
 		// (Figure 10)
@@ -442,7 +434,6 @@ void HDT::handleCCToC()
 		tripUnresolved += c1Count->n_i * (c2->n_circ_square - c2Count->n_i_circ);
 
 		// Quartets
-/*#ifdef quartetsToo*/
 		//quartResolvedAgree & quartResolvedDisagree
 
 		// alpha & alpha
@@ -562,7 +553,6 @@ void HDT::handleCCToC()
 		quartSumE += (INTTYPE_N4) c1Count->n_i * (c2->n_0_circ_arrow_square - c2Count->n_0_i_arrow_circ - c2Count->n_0_circ_arrow_i);
 		quartSumE += (INTTYPE_N4) (c1->n_bracket_0_circ_square - c1Count->n_bracket_0_i_circ) * c2Count->n_i;
 		quartSumE += (INTTYPE_N4) c1Count->n_i * (c2->n_paren_0_circ_square - c2Count->n_paren_0_i_circ);
-/*#endif*/
 
 		// Go to next on children unless we're done
 		if (c1Next == NULL && c2Next == NULL)
@@ -578,7 +568,6 @@ void HDT::handleCCToC()
 	n_circ_square /= 2;
 
 	// Quartets
-/*#ifdef quartetsToo*/
 	n_paren_circ_square /= 2;
 	n_bracket_circ_square /= 2;
 
@@ -617,5 +606,4 @@ void HDT::handleCCToC()
 	  Rcpp::warning("n_0_arrow_circ_square mod 2 check failed");
 	}
 	n_0_arrow_circ_square /= 2;
-/*#endif*/
 }
diff --git a/src/HDTCountingCTransform.cpp b/src/HDTCountingCTransform.cpp
index 77109eb6..741a7835 100644
--- a/src/HDTCountingCTransform.cpp
+++ b/src/HDTCountingCTransform.cpp
@@ -10,7 +10,6 @@ void HDT::handleCTransform()
 	n_circ_square = 0;
 
 	// Quartets
-/*#ifdef quartetsToo*/
 	// Sums initialized to 0, summed in loop below
 	n_paren_circ_circ = 0;
 	n_paren_circ_square = 0;
@@ -27,15 +26,7 @@ void HDT::handleCTransform()
 	n_paren_0_circ = gZero * n_circ;
 
 
-	/*
-	// Added by us for filling out tables (Actually undefined!)
-	n_circ_arrow_circ = 0;
-	n_circ_arrow_square = 0;
-	n_paren_circ_circ_arrow_square = 0;
-	n_circ_arrow_square_arrow_square = 0;
-	*/
-
-	// Added by us for filling out tables (initialize)
+	// Added by Sand et al. (2014) for filling out tables (initialize)
 	n_paren_circ_paren_square_square = 0;
 
 	// Reset sums and stuff for calculating E
@@ -43,7 +34,6 @@ void HDT::handleCTransform()
 	n_0_circ_square = 0;
 	n_paren_circ_square_triangle = 0;
 	n_paren_0_circ_square = 0;
-/*#endif*/
 
 	CountingLinkedList *current = countingVars;
 	if (current->num == 0)
@@ -60,7 +50,6 @@ void HDT::handleCTransform()
 		current->n_paren_ii = Util::binom2(current->n_i);
 
 		// Quartets
-/*#ifdef quartetsToo*/
 		// 2nd group in figure 12 (quartets only)
 		current->n_0_i = 0;
 		current->n_ii = 0;
@@ -84,12 +73,12 @@ void HDT::handleCTransform()
 		// Figure 15 counters (part 1)
 		if (current->n_i_j != NULL) current->n_i_j->type = CountingLinkedListNumOnly::SkipAndEnd;
 
-		// Added by us for filling out tables
+		// Added by Sand et al. (2014) for filling out tables
 		// A
 		current->n_paren_i_paren_circ_circ = current->n_bracket_i_paren_circ_circ;
 		current->n_paren_i_paren_circ_square = current->n_bracket_i_paren_circ_square;
 
-		// Added by us for filling out tables (sum)
+		// Added by Sand et al. (2014) for filling out tables (sum)
 		// A
 		n_paren_circ_paren_square_square += current->n_paren_i_paren_circ_circ;
 		
@@ -102,7 +91,6 @@ void HDT::handleCTransform()
 		// New sums for E
 		n_paren_circ_square_triangle += current->n_paren_i_circ_square;
 		n_paren_0_circ_square += current->n_paren_0_i_circ;
-/*#endif*/
 
 		// Go to next on children unless we're done
 		if (current->type != CountingLinkedList::End)
@@ -113,7 +101,6 @@ void HDT::handleCTransform()
 		else current = NULL;
 	}
 
-/*#ifdef quartetsToo*/
 	// These are all based on stuff that is reset to 0
 	n_circ_circ = 0;
 	n_square_paren_circ_circ = 0;
@@ -134,5 +121,4 @@ void HDT::handleCTransform()
 	  Rcpp::stop("n_paren_0_circ_square mod 2 test... FAIL!!!");
 	}
 	n_paren_0_circ_square /= 2;
-/*#endif*/
 }
diff --git a/src/HDTCountingG.cpp b/src/HDTCountingG.cpp
index 5314e4c7..846b8ecd 100644
--- a/src/HDTCountingG.cpp
+++ b/src/HDTCountingG.cpp
@@ -30,7 +30,6 @@ void HDT::handleG()
 	CountingLinkedList *g2Count = NULL;
 	CountingLinkedList *ourCount = countingVars;
 
-/*#ifdef quartetsToo*/
 	INTTYPE_REST g1Zero = 0;
 	INTTYPE_REST g2Zero = 0;
 
@@ -73,7 +72,6 @@ void HDT::handleG()
 
 	// Fetch sum for calculating E from children
 	quartSumE = g1->quartSumE + g2->quartSumE;
-/*#endif*/
 
 	while (g1Next != NULL || g2Next != NULL)
 	{
@@ -138,7 +136,6 @@ void HDT::handleG()
 		//ourCount->n_i_arrow_circ = 0; // undefined actually!
 
 		// Quartets
-/*#ifdef quartetsToo*/
 		// 2nd group in figure 12 (quartets only)
 		ourCount->n_0_i = g1Count->n_0_i + g2Count->n_0_i + 
 			g1Zero * g2Count->n_i +
@@ -280,14 +277,6 @@ void HDT::handleG()
 			g1Count->n_i * (g2->n_paren_circ_square - g2Count->n_paren_i_circ) +
 			g2Count->n_i * (g1->n_paren_circ_square - g1Count->n_paren_i_circ);
 
-		/*
-		// Undefined :)
-		ourCount->n_i_arrow_circ_arrow_circ = 0;
-		ourCount->n_i_arrow_circ_arrow_square = 0;
-		ourCount->n_paren_circ_square_arrow_i = 0;
-		if (ourCount->n_i_arrow_j != NULL) ourCount->n_i_arrow_j->type = CountingLinkedListNumOnly::SkipAndEnd;
-		*/
-
 		// New counters for calculating E
 		ourCount->n_paren_i_circ_square = g1Count->n_paren_i_circ_square + g2Count->n_paren_i_circ_square;
 
@@ -300,13 +289,11 @@ void HDT::handleG()
 		ourCount->n_bracket_0_i_circ = g1Count->n_bracket_0_i_circ + g2Count->n_bracket_0_i_circ +
 			g1Count->n_0_i * (g2->n_circ - g2Count->n_i) + g1Count->n_i * (g2->n_0_circ - g2Count->n_0_i) + g1Count->n_i_circ * g2Zero + 
 			g2Count->n_0_i * (g1->n_circ - g1Count->n_i) + g2Count->n_i * (g1->n_0_circ - g1Count->n_0_i) + g2Count->n_i_circ * g1Zero;
-/*#endif*/
 
 		// Sums and stuff
 		n_circ_square += ourCount->n_i_circ;
 
 		// Quartets
-/*#ifdef quartetsToo*/
 		n_circ_circ += ourCount->n_ii;
 		n_square_paren_circ_circ += ourCount->n_i_paren_circ_circ;
 		n_paren_circ_circ += ourCount->n_paren_ii;
@@ -324,7 +311,6 @@ void HDT::handleG()
 	
 		n_bracket_circ_square_triangle += ourCount->n_bracket_i_circ_square;
 		n_bracket_0_circ_square += ourCount->n_bracket_0_i_circ;
-/*#endif*/
 
 		// Update resolved/resolved and unresolved/unresolved
 		// (Figure 10)
@@ -335,7 +321,6 @@ void HDT::handleG()
 		tripUnresolved += g2Count->n_i * (g1->n_circ_square - g1Count->n_i_circ);
 
 		// Quartets
-/*#ifdef quartetsToo*/
 		//quartResolvedAgree & quartResolvedDisagree
 
 		// alpha & alpha
@@ -436,7 +421,6 @@ void HDT::handleG()
 		// epsilon & epsilon (part 2)
 		quartSumE += (INTTYPE_N4) (g1->n_paren_0_circ_square - g1Count->n_paren_0_i_circ) * g2Count->n_i;
 		quartSumE += (INTTYPE_N4) (g2->n_paren_0_circ_square - g2Count->n_paren_0_i_circ) * g1Count->n_i;
-/*#endif*/
 
 		// Go to next on children unless we're done
 		if (g1Next == NULL && g2Next == NULL)
@@ -450,16 +434,13 @@ void HDT::handleG()
 		}
 	}
 
-/*#ifdef quartetsToo*/
 	//gamma & beta (part 1) (continued from inside the loop) (figure 13)
 	quartResolvedAgree += (INTTYPE_N4) g1Zero * g2->n_square_paren_circ_circ;
 	quartResolvedAgree += (INTTYPE_N4) g2Zero * g1->n_square_paren_circ_circ;
-/*#endif*/
 
 	n_circ_square /= 2;
 
 	// Quartets
-/*#ifdef quartetsToo*/
 	n_paren_circ_square /= 2;
 	n_bracket_circ_square /= 2;
 
@@ -497,5 +478,4 @@ void HDT::handleG()
 	  Rcpp::stop("n_bracket_0_circ_square mod 2 check failed");
 	}
 	n_bracket_0_circ_square /= 2;
-/*#endif*/
 }
diff --git a/src/HDTCountingIGToC.cpp b/src/HDTCountingIGToC.cpp
index 8510b15c..38542651 100644
--- a/src/HDTCountingIGToC.cpp
+++ b/src/HDTCountingIGToC.cpp
@@ -18,7 +18,6 @@ void HDT::handleIGToC()
 	n_circ_square = right->n_circ_square;
 
 	// Quartets
-/*#ifdef quartetsToo*/
 	// Fetch the childrens "result counting data"
 	quartResolvedAgree = right->quartResolvedAgree;
 	quartResolvedAgreeDiag = right->quartResolvedAgreeDiag;
@@ -71,7 +70,6 @@ void HDT::handleIGToC()
 
 	// Fetch sum for calculating E from children
 	quartSumE = right->quartSumE;
-/*#endif*/
 
 	CountingLinkedList *current = right->countingVars;
 	CountingLinkedList *ourCount = countingVars;
@@ -103,7 +101,6 @@ void HDT::handleIGToC()
 		ourCount->n_i_arrow_circ = 0; // Not actually defined in G! IN G!!! (i.e. it *should* in fact be 0)
 
 		// Quartets
-/*#ifdef quartetsToo*/
 		// 2nd group in figure 12 (quartets only)
 		ourCount->n_0_i = current->n_0_i;
 		ourCount->n_ii = current->n_ii;
@@ -199,7 +196,6 @@ void HDT::handleIGToC()
 		ourCount->n_paren_0_i_circ = current->n_paren_0_i_circ;
 		ourCount->n_bracket_i_circ_square = current->n_bracket_i_circ_square;
 		ourCount->n_bracket_0_i_circ = current->n_bracket_0_i_circ;
-/*#endif*/
 
 		// Go to next on children unless we're done
 		if (ourCount->type != CountingLinkedList::End)
diff --git a/src/HDTCountingLeaf.cpp b/src/HDTCountingLeaf.cpp
index 64812d5c..f85b29c5 100644
--- a/src/HDTCountingLeaf.cpp
+++ b/src/HDTCountingLeaf.cpp
@@ -22,7 +22,6 @@ void HDT::handleLeaf()
 	countingVars->n_i_arrow_circ = 0;
 
 	// Quartets
-/*#ifdef quartetsToo*/
 	countingVars->n_0_i = 0;
 	countingVars->n_ii = 0;
 	countingVars->n_0_paren_ii = 0;
@@ -92,7 +91,6 @@ void HDT::handleLeaf()
 	countingVars->n_paren_0_i_circ = 0;
 	countingVars->n_bracket_i_circ_square = 0;
 	countingVars->n_bracket_0_i_circ = 0;
-/*#endif*/
 
 	countingVars->type = CountingLinkedList::End;
 
@@ -102,7 +100,6 @@ void HDT::handleLeaf()
 	n_circ_square = 0;
 
 	// Sums (quartets)
-/* ifdef quartetsToo*/
 	n_0_circ = 0;
 	n_circ_circ = 0;
 	n_square_paren_circ_circ = 0;
@@ -141,5 +138,4 @@ void HDT::handleLeaf()
 	n_paren_0_circ_square = 0;
 	n_bracket_circ_square_triangle = 0;
 	n_bracket_0_circ_square = 0;
-/*#endif */
 }
diff --git a/src/HDTListUtils.cpp b/src/HDTListUtils.cpp
index 91dfb1c3..2e5b992d 100644
--- a/src/HDTListUtils.cpp
+++ b/src/HDTListUtils.cpp
@@ -5,8 +5,6 @@
 #include "counting_linked_list.h"
 #include "counting_linked_list_num_only.h"
 
-/*#ifdef quartetsToo*/
-
 bool HDT::gotoIteratorValueForList(CountingLinkedList *list, unsigned int num)
 {
 	if (list == NULL || list->iteratorHasEnded()) return false;
@@ -62,5 +60,3 @@ void HDT::addToNumList(CountingLinkedList *parent, AddToType list, unsigned int
 	theList->num = num;
 	theList->value = value;
 }
-
-/*#endif*/
diff --git a/src/QuartetDistanceCalculator.cpp b/src/QuartetDistanceCalculator.cpp
index 33c3b221..ef0239b5 100644
--- a/src/QuartetDistanceCalculator.cpp
+++ b/src/QuartetDistanceCalculator.cpp
@@ -228,18 +228,13 @@ AE QuartetDistanceCalculator::calculateQuartetAgreement(UnrootedTree *t1, Unroot
   
   count(this->t1);
 
-/*#ifndef doExtractAndContract
-// factory deleted in count if def.
-  delete hdt->factory;
-#endif*/
-
   n = this->t1->n;
   
   res.a = resolvedQuartetsAgree + resolvedQuartetsAgreeDiag + resolvedQuartetsAgreeUpper;
   res.e = unresolvedQuartets;
   res.noQuartets = Util::binom4(n);
   
-  // HDT is deleted in count!
+  // HDT is deleted in count
   delete this->t1->factory;
   delete this->t2->factory;
   
diff --git a/src/TripletDistanceCalculator.cpp b/src/TripletDistanceCalculator.cpp
index 7f39ac12..40993d96 100644
--- a/src/TripletDistanceCalculator.cpp
+++ b/src/TripletDistanceCalculator.cpp
@@ -140,11 +140,8 @@ INTTYPE_REST TripletDistanceCalculator::calculateTripletDistance(RootedTree *t1,
   totalNoTriplets = Util::binom3(n);
 
   count(t1);
-  // HDT is deleted in count if extracting and contracting!
-/*#ifndef doExtractAndContract
-  delete hdt->factory;
-#endif*/
-	
+  // HDT is deleted in count if extracting and contracting.
+
   return totalNoTriplets - resolvedTriplets - unresolvedTriplets;
 }
 
diff --git a/src/counting_linked_list.h b/src/counting_linked_list.h
index fa09444f..122e3b09 100644
--- a/src/counting_linked_list.h
+++ b/src/counting_linked_list.h
@@ -12,7 +12,7 @@ class CountingLinkedList
 		INTTYPE_REST n_i, n_i_circ, n_paren_ii, n_i_arrow_circ;
 
 		// For quartets
-/*#ifdef quartetsToo*/
+
 		INTTYPE_REST n_0_i, n_ii, n_0_paren_ii, n_circ_paren_ii, n_i_paren_0_circ, n_i_paren_circ_circ, n_i_paren_circ_square;
 		INTTYPE_REST n_bracket_i_circ;
 		INTTYPE_REST n_paren_0_i, n_paren_i_circ, n_paren_0_paren_ii, n_paren_circ_paren_ii, n_paren_i_paren_0_circ;
@@ -53,7 +53,6 @@ class CountingLinkedList
 		INTTYPE_REST n_paren_0_i_circ;
 		INTTYPE_REST n_bracket_i_circ_square;
 		INTTYPE_REST n_bracket_0_i_circ;
-/*#endif*/
 
 		// More general stuff
 		unsigned int num;
@@ -70,10 +69,8 @@ class CountingLinkedList
 		void initialize()
 		{
 			next = NULL;
-/*#ifdef quartetsToo*/
 			n_i_j = NULL;
 			n_j_arrow_i = n_i_arrow_j = NULL;
-/*#endif*/
 		}
 
 		CountingLinkedList(bool dummy)
@@ -87,7 +84,6 @@ class CountingLinkedList
 			n_i_arrow_circ = 0;
 
 			// Quartets
-/*#ifdef quartetsToo*/
 			n_0_i = 0;
 			n_ii = 0;
 			n_0_paren_ii = 0;
@@ -155,10 +151,8 @@ class CountingLinkedList
 			n_paren_0_i_circ = 0;
 			n_bracket_i_circ_square = 0;
 			n_bracket_0_i_circ = 0;
-/*#endif*/
 		}
 
-/*#ifdef quartetsToo*/
 		void resetIterator()
 		{
 			iterator = this;
@@ -199,7 +193,6 @@ class CountingLinkedList
 			else iterator = iterator->next;
 			return result;
 		}
-/*#endif*/
 };
 
 #endif
diff --git a/src/hdt.h b/src/hdt.h
index 4e4eb2c6..a93e57a8 100644
--- a/src/hdt.h
+++ b/src/hdt.h
@@ -80,7 +80,6 @@ class HDT
 		INTTYPE_REST n_circ_square;
 
 		// Quartets
-/*#ifdef quartetsToo*/
 		INTTYPE_REST n_0_circ;
 		INTTYPE_REST n_paren_0_circ;
 		INTTYPE_REST n_circ_circ;
@@ -93,10 +92,10 @@ class HDT
 		INTTYPE_REST n_circ_arrow_0;
 		INTTYPE_REST n_0_arrow_circ_circ;
 
-		// Added by us
+		// Added by Sand et al. (2014)
 		INTTYPE_REST n_circ_arrow_square_square;
 
-		// Added by us for filling out tables
+		// Added by Sand et al. (2014) for filling out tables
 		INTTYPE_REST n_bracket_circ_circ;
 		INTTYPE_REST n_paren_circ_paren_square_square;
 		INTTYPE_REST n_circ_arrow_circ;
@@ -117,7 +116,6 @@ class HDT
 		INTTYPE_REST n_paren_0_circ_square;
 		INTTYPE_REST n_bracket_circ_square_triangle;
 		INTTYPE_REST n_bracket_0_circ_square;
-/*#endif*/
 
 		// Summing resolved/resolved and unresolved/unresolved
 		INTTYPE_REST tripResolved;
@@ -137,14 +135,12 @@ class HDT
 		void handleCTransform();
 		void handleG();
 		
-/*#ifdef quartetsToo*/
 		bool gotoIteratorValueForList(CountingLinkedList *list, unsigned int num);
 		enum AddToType {i_j, paren_i_j, j_arrow_i, i_arrow_j, i_paren_i_j, paren_i_paren_i_j, bracket_i_paren_i_j};
 		INTTYPE_REST getIteratorValueForNumList(CountingLinkedListNumOnly *list, unsigned int num);
 		bool gotoIteratorValueForNumList(CountingLinkedListNumOnly *list, unsigned int num);
 		bool hasIteratorForNumListEnded(CountingLinkedListNumOnly *list);
 		void addToNumList(CountingLinkedList *parent, AddToType list, unsigned int num, INTTYPE_REST value);
-/*#endif*/
 };
 
 #endif

From 62684180c53148fb15aeb2a8b8c9fb3f43c30208 Mon Sep 17 00:00:00 2001
From: Martin Smith <martins@gmail.com>
Date: Mon, 21 Jan 2019 12:37:21 +0000
Subject: [PATCH 19/27] Added by Sand et al.

Clarify "us".  Resolves #29: yes, it is necessary
---
 src/HDTCountingCCToC.cpp   |  6 +++---
 src/HDTCountingG.cpp       | 12 ++++++------
 src/HDTCountingIGToC.cpp   |  8 ++++----
 src/HDTCountingLeaf.cpp    |  8 ++++----
 src/counting_linked_list.h |  6 +++---
 5 files changed, 20 insertions(+), 20 deletions(-)

diff --git a/src/HDTCountingCCToC.cpp b/src/HDTCountingCCToC.cpp
index 33df022b..cae4bb6d 100644
--- a/src/HDTCountingCCToC.cpp
+++ b/src/HDTCountingCCToC.cpp
@@ -28,7 +28,7 @@ void HDT::handleCCToC()
 	n_paren_circ_square = 0;
 	n_circ_arrow_paren_square_square = 0;
 	n_bracket_circ_square = 0;
-	n_circ_arrow_square_square = 0; // Added by us
+	n_circ_arrow_square_square = 0; // Added by Sand et al. (2014)
 
 	// Not dependent on i
 	n_0_circ = c1->n_0_circ + c2->n_0_circ;
@@ -499,7 +499,7 @@ void HDT::handleCCToC()
 
 		//
 		// +------------------------------------------+
-		// | New sums for calculating A (Added by us) |
+		// | New sums for calculating A (Added by Sand et al. (2014)) |
 		// +------------------------------------------+
 		//
 
@@ -531,7 +531,7 @@ void HDT::handleCCToC()
 
 		//
 		// +------------------------------------------+
-		// | New sums for calculating E (Added by us) |
+		// | New sums for calculating E (Added by Sand et al. (2014)) |
 		// +------------------------------------------+
 		//
 
diff --git a/src/HDTCountingG.cpp b/src/HDTCountingG.cpp
index 846b8ecd..7c118e62 100644
--- a/src/HDTCountingG.cpp
+++ b/src/HDTCountingG.cpp
@@ -52,7 +52,7 @@ void HDT::handleG()
 	n_paren_circ_square = 0;
 	n_bracket_circ_square = 0;
 
-	// Added by us for filling out tables (initialize)
+	// Added by Sand et al. (2014) for filling out tables (initialize)
 	n_bracket_circ_circ = 0;
 	n_paren_circ_paren_square_square = 0;
 	n_bracket_circ_paren_square_square = 0;
@@ -248,7 +248,7 @@ void HDT::handleG()
 				// j > i
 				//
 				// +------------------------------------------+
-				// | New sums for calculating E (Added by us) |
+				// | New sums for calculating E (Added by Sand et al. (2014)) |
 				// +------------------------------------------+
 				//
 
@@ -261,7 +261,7 @@ void HDT::handleG()
 			lastJPlus1 = j+1;
 		}
 
-		// Added by us for filling out tables
+		// Added by Sand et al. (2014) for filling out tables
 		// A
 		ourCount->n_paren_i_paren_circ_circ = g1Count->n_paren_i_paren_circ_circ + g2Count->n_paren_i_paren_circ_circ;
 
@@ -300,7 +300,7 @@ void HDT::handleG()
 		n_paren_circ_square += ourCount->n_paren_i_circ;
 		n_bracket_circ_square += ourCount->n_bracket_i_circ;
 
-		// Added by us for filling out tables (initialize)
+		// Added by Sand et al. (2014) for filling out tables (initialize)
 		n_bracket_circ_circ += Util::binom2(ourCount->n_i);
 		n_paren_circ_paren_square_square += ourCount->n_paren_i_paren_circ_circ;
 		n_bracket_circ_paren_square_square += ourCount->n_bracket_i_paren_circ_circ;
@@ -373,7 +373,7 @@ void HDT::handleG()
 
 		//
 		// +------------------------------------------+
-		// | New sums for calculating A (Added by us) |
+		// | New sums for calculating A (Added by Sand et al. (2014)) |
 		// +------------------------------------------+
 		//
 
@@ -397,7 +397,7 @@ void HDT::handleG()
 
 		//
 		// +------------------------------------------+
-		// | New sums for calculating E (Added by us) |
+		// | New sums for calculating E (Added by Sand et al. (2014)) |
 		// +------------------------------------------+
 		//
 
diff --git a/src/HDTCountingIGToC.cpp b/src/HDTCountingIGToC.cpp
index 38542651..e9e0f19e 100644
--- a/src/HDTCountingIGToC.cpp
+++ b/src/HDTCountingIGToC.cpp
@@ -33,7 +33,7 @@ void HDT::handleIGToC()
 	// Sums
 	// Not actually defined in G! IN G!!! (i.e. it *should* in fact be 0)
 	n_circ_arrow_paren_square_square = 0;
-	n_circ_arrow_square_square = 0; // Added by us
+	n_circ_arrow_square_square = 0; // Added by Sand et al. (2014)
 
 	// Not dependent on i
 	n_0_circ = right->n_0_circ;
@@ -45,7 +45,7 @@ void HDT::handleIGToC()
 	n_circ_arrow_0 = 0;
 	n_0_arrow_circ_circ = 0;
 		
-	// Added by us for filling out tables
+	// Added by Sand et al. (2014) for filling out tables
 	n_bracket_circ_circ = right->n_bracket_circ_circ;
 	n_paren_circ_paren_square_square = right->n_paren_circ_paren_square_square;
 	n_circ_arrow_circ = 0;
@@ -146,7 +146,7 @@ void HDT::handleIGToC()
 		ourCount->n_i_arrow_0_arrow_circ = 0;
 		ourCount->n_circ_arrow_i_arrow_i = 0;
 
-		// Added by us
+		// Added by Sand et al. (2014)
 		ourCount->n_i_arrow_paren_circ_circ = 0;
 		ourCount->n_0_arrow_ii = 0;
 		ourCount->n_paren_0_circ_arrow_i = 0;
@@ -172,7 +172,7 @@ void HDT::handleIGToC()
 		ourCount->n_0_arrow_i_circ = 0;
 
 		
-		// Added by us for filling out tables
+		// Added by Sand et al. (2014) for filling out tables
 		// A
 		ourCount->n_paren_i_paren_circ_circ = current->n_paren_i_paren_circ_circ;
 		ourCount->n_bracket_i_paren_circ_circ = current->n_bracket_i_paren_circ_circ;
diff --git a/src/HDTCountingLeaf.cpp b/src/HDTCountingLeaf.cpp
index f85b29c5..91232a28 100644
--- a/src/HDTCountingLeaf.cpp
+++ b/src/HDTCountingLeaf.cpp
@@ -61,7 +61,7 @@ void HDT::handleLeaf()
 	countingVars->n_i_arrow_0_arrow_circ = 0;
 	countingVars->n_circ_arrow_i_arrow_i = 0;
 	
-	// Added by us
+	// Added by Sand et al. (2014)
 	countingVars->n_i_arrow_paren_circ_circ = 0;
 	countingVars->n_0_arrow_ii = 0;
 	countingVars->n_paren_0_circ_arrow_i = 0;
@@ -69,7 +69,7 @@ void HDT::handleLeaf()
 	//countingVars->n_i_j = NULL; // it already is!
 	countingVars->n_0_arrow_i_circ = 0;
 
-	// Added by us for filling out tables
+	// Added by Sand et al. (2014) for filling out tables
 	// A
 	countingVars->n_paren_i_paren_circ_circ = 0;
 	countingVars->n_bracket_i_paren_circ_circ = 0;
@@ -113,10 +113,10 @@ void HDT::handleLeaf()
 	n_circ_arrow_0 = 0;
 	n_0_arrow_circ_circ = 0;
 
-	// Added by us
+	// Added by Sand et al. (2014)
 	n_circ_arrow_square_square = 0;
 
-	// Added by us for filling out tables
+	// Added by Sand et al. (2014) for filling out tables
 	n_bracket_circ_circ = 0;
 	n_paren_circ_paren_square_square = 0;
 	n_circ_arrow_circ = 0;
diff --git a/src/counting_linked_list.h b/src/counting_linked_list.h
index 122e3b09..f63d50e2 100644
--- a/src/counting_linked_list.h
+++ b/src/counting_linked_list.h
@@ -22,14 +22,14 @@ class CountingLinkedList
 			n_i_arrow_circ_square, n_circ_arrow_ii, n_paren_ii_arrow_0, n_paren_ii_arrow_circ, n_paren_circ_circ_arrow_i,
 			n_0_arrow_i_arrow_i, n_i_arrow_circ_arrow_0, n_i_arrow_0_arrow_circ, n_circ_arrow_i_arrow_i;
 
-		// Added by us
+		// Added by Sand et al. (2014)
 		INTTYPE_REST n_i_arrow_paren_circ_circ, n_0_arrow_ii, n_paren_0_circ_arrow_i;
 
 		// Figure 15 counters (part 1)
 		CountingLinkedListNumOnly *n_i_j; // also used for E calculation
 		INTTYPE_REST n_0_arrow_i_circ; // also used for E calculation
 
-		// Added by us for filling out tables
+		// Added by Sand et al. (2014) for filling out tables
 		// A
 		INTTYPE_REST n_paren_i_paren_circ_circ;
 		INTTYPE_REST n_bracket_i_paren_circ_circ;
@@ -129,7 +129,7 @@ class CountingLinkedList
 
 			n_0_arrow_i_circ = 0;
 
-			// Added by us for filling out tables
+			// Added by Sand et al. (2014) for filling out tables
 			// A
 			n_paren_i_paren_circ_circ = 0;
 			n_bracket_i_paren_circ_circ = 0;

From 601bbb21491204bd2795a8c6ad0f3d8ce8392d03 Mon Sep 17 00:00:00 2001
From: Martin Smith <martins@gmail.com>
Date: Mon, 21 Jan 2019 14:01:56 +0000
Subject: [PATCH 20/27] Try long int

---
 src/int_stuff.h | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/int_stuff.h b/src/int_stuff.h
index cd4fbc99..428c8e3a 100644
--- a/src/int_stuff.h
+++ b/src/int_stuff.h
@@ -3,8 +3,8 @@
   #define INT_STUFF_H
   
 #if __cplusplus <= 199711L
-  #define INTTYPE_N4 long long // fails -pedantic
-  #define INTTYPE_REST long long // fails -pedantic
+  #define INTTYPE_N4 long int // long long fails -pedantic
+  #define INTTYPE_REST long int // long long fails -pedantic
 #else 
   #include <cstdint>
   #define INTTYPE_N4 int_fast64_t // long long fails -pedantic

From 94b4f740d5b96bdb75e3065015db57d301c53279 Mon Sep 17 00:00:00 2001
From: Martin Smith <martins@gmail.com>
Date: Mon, 21 Jan 2019 14:02:06 +0000
Subject: [PATCH 21/27] Update cran-comments.md

---
 cran-comments.md | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/cran-comments.md b/cran-comments.md
index 74267b1e..d18a97ca 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -2,25 +2,25 @@
 * local Windows 10 install, R 3.5.2
 * win-builder, with `check_win_devel()`
 * Ubuntu 14.04.5 LTS, R 3.4 and devel, via [Travis CI](https://travis-ci.org/ms609/Quartet)
-* R-hub, with `check_rhub()`
+* R-hub, with `check_rhub(platforms = platforms())`
 
   * Installation failed with PREPERROR on rhub/ubuntu-gcc-release and
-    rhub/fedora-clang-devel, on account of failures to install the required 
-    packages (`phangorn`; `git2r`).  This seems to be an issue outside
+    rhub/fedora-clang-devel, on account of failures to install a required 
+    dependency (`phangorn`).  This seems to be an issue outside
     of my control; the Debian rhub installation reports success.
 
-
 ## R CMD check results
 There were no ERRORs or WARNINGs.
 
-There was 1 NOTE:
+There was one NOTE:
+
+ > Days since last update: 5
 
-* checking CRAN incoming feasibility ... NOTE
-  Maintainer: 'Smith Martin R. <martin.smith@durham.ac.uk>'
-  
-  New submission
-  
-This package is a new submission.
+This release comes soon after the release of v1.0.0 on 2019-01-16, which failed
+certain CRAN package checks -- Brian Ripley requested that these be fixed 
+immediately.  After following Prof. Ripley's suggestions and testing the 
+errant platforms using `check_rhub`, it appears that the issues have been 
+resolved.
 
 ## Downstream dependencies
 There are currently no downstream dependencies for this package.

From 2b660be14d03a28cd69825613b7798d8f8b113fb Mon Sep 17 00:00:00 2001
From: Martin Smith <martins@gmail.com>
Date: Mon, 21 Jan 2019 16:55:32 +0000
Subject: [PATCH 22/27] v1.0.0.9001

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 6c97b74f..8e996383 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: Quartet
-Version: 1.0.0.9000
+Version: 1.0.0.9001
 Date: 2019-01-21
 Title: Comparison of Phylogenetic Trees Using Quartet and Bipartition Measures
 Description: Calculates the number of four-taxon subtrees consistent with a pair

From a38929cc47e9212675ad1d514e8a1f078e40b512 Mon Sep 17 00:00:00 2001
From: Martin Smith <martins@gmail.com>
Date: Tue, 22 Jan 2019 08:57:36 +0000
Subject: [PATCH 23/27] Update cran-comments.md

---
 cran-comments.md | 21 +++++++++++++--------
 1 file changed, 13 insertions(+), 8 deletions(-)

diff --git a/cran-comments.md b/cran-comments.md
index d18a97ca..281fb8d0 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -5,22 +5,27 @@
 * R-hub, with `check_rhub(platforms = platforms())`
 
   * Installation failed with PREPERROR on rhub/ubuntu-gcc-release and
-    rhub/fedora-clang-devel, on account of failures to install a required 
-    dependency (`phangorn`).  This seems to be an issue outside
-    of my control; the Debian rhub installation reports success.
+    rhub/fedora-clang-devel (and other platforms), on account of failures 
+    to install a required dependency (`phangorn`).  
+    This seems to be an issue outside of my control.
+  * Installation failed with ERROR on x86_64-pc-linux-gnu:
+    > "there is no package called `lattice`"
+    The failure to install the dependency `lattice` seems to be outwith my 
+    control.
 
 ## R CMD check results
 There were no ERRORs or WARNINGs.
 
 There was one NOTE:
 
- > Days since last update: 5
+ > Days since last update: 6
 
-This release comes soon after the release of v1.0.0 on 2019-01-16, which failed
+This release comes on the heels of v1.0.0 on 2019-01-16, which failed
 certain CRAN package checks -- Brian Ripley requested that these be fixed 
-immediately.  After following Prof. Ripley's suggestions and testing the 
-errant platforms using `check_rhub`, it appears that the issues have been 
-resolved.
+immediately and kindly proposed some suggestions for how portability could be
+improved.
+After implementing these and testing the relevant platforms using `check_rhub`, 
+I believe that the issues have been resolved.
 
 ## Downstream dependencies
 There are currently no downstream dependencies for this package.

From 36d7229fb9fc593e6147bf3e5e86170d2b90139f Mon Sep 17 00:00:00 2001
From: Martin Smith <martins@gmail.com>
Date: Tue, 22 Jan 2019 12:14:10 +0000
Subject: [PATCH 24/27] Use https:

---
 README.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 25f69706..75b67aa5 100644
--- a/README.md
+++ b/README.md
@@ -1,8 +1,8 @@
-[![Project Status: Inactive.](http://www.repostatus.org/badges/latest/inactive.svg)](http://www.repostatus.org/#inactive)
+[![Project Status: Inactive.](https://www.repostatus.org/badges/latest/inactive.svg)](https://www.repostatus.org/#inactive)
 [![Build Status](https://travis-ci.org/ms609/Quartet.svg?branch=master)](https://travis-ci.org/ms609/Quartet)
 [![codecov](https://codecov.io/gh/ms609/Quartet/branch/master/graph/badge.svg)](https://codecov.io/gh/ms609/Quartet)
-[![CRAN Status Badge](http://www.r-pkg.org/badges/version/Quartet)](https://cran.r-project.org/package=Quartet)
-[![CRAN Downloads](http://cranlogs.r-pkg.org/badges/Quartet)](https://cran.r-project.org/package=Quartet)
+[![CRAN Status Badge](https://www.r-pkg.org/badges/version/Quartet)](https://cran.r-project.org/package=Quartet)
+[![CRAN Downloads](https://cranlogs.r-pkg.org/badges/Quartet)](https://cran.r-project.org/package=Quartet)
 [![DOI](https://zenodo.org/badge/80424189.svg)](https://zenodo.org/badge/latestdoi/80424189)
 
 # Quartet

From 8bbe6b70c088252a2040cfd9b9c249708ea5475c Mon Sep 17 00:00:00 2001
From: Martin Smith <martins@gmail.com>
Date: Tue, 22 Jan 2019 12:32:54 +0000
Subject: [PATCH 25/27] Platform detail

---
 cran-comments.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cran-comments.md b/cran-comments.md
index 281fb8d0..052782e4 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -8,7 +8,7 @@
     rhub/fedora-clang-devel (and other platforms), on account of failures 
     to install a required dependency (`phangorn`).  
     This seems to be an issue outside of my control.
-  * Installation failed with ERROR on x86_64-pc-linux-gnu:
+  * Installation failed with ERROR on ubuntu-gcc-devel and debian-gcc-patched:
     > "there is no package called `lattice`"
     The failure to install the dependency `lattice` seems to be outwith my 
     control.

From bcabec5f49d3bea7668141d7b12b95285c202123 Mon Sep 17 00:00:00 2001
From: Martin Smith <martins@gmail.com>
Date: Tue, 22 Jan 2019 12:33:15 +0000
Subject: [PATCH 26/27] Remove unnecessary includes

---
 src/rQuartetDist.cpp | 5 +----
 src/rTripletDist.cpp | 6 +-----
 2 files changed, 2 insertions(+), 9 deletions(-)

diff --git a/src/rQuartetDist.cpp b/src/rQuartetDist.cpp
index c17b1b07..a04131dc 100644
--- a/src/rQuartetDist.cpp
+++ b/src/rQuartetDist.cpp
@@ -1,12 +1,9 @@
 #include <Rcpp.h>
 using namespace Rcpp;
-#include "int_stuff.h"
 
+#include "int_stuff.h"
 #include "QuartetDistanceCalculator.h"
 
-#include <R.h>
-#include <Rdefines.h>
-#include <Rinternals.h>
 #include <vector>
 
 //' Triplet and quartet distances with tqDist
diff --git a/src/rTripletDist.cpp b/src/rTripletDist.cpp
index c09ca3e5..a8c82e02 100644
--- a/src/rTripletDist.cpp
+++ b/src/rTripletDist.cpp
@@ -1,13 +1,9 @@
 #include <Rcpp.h>
 using namespace Rcpp;
-#include "int_stuff.h"
 
+#include "int_stuff.h"
 #include "TripletDistanceCalculator.h"
 
-#include <R.h>
-#include <Rdefines.h>
-#include <Rinternals.h>
-#include <cstdlib>
 #include <vector>
 
 //' @describeIn tqdist_QuartetDistance Triplet distance between two trees

From 70385f87b0c119a4fc40db3742f637aa8f6dd971 Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <martins@gmail.com>
Date: Tue, 22 Jan 2019 15:03:31 +0000
Subject: [PATCH 27/27] Discuss alternative metrics

Fixes #28
---
 .zenodo.json                        |  2 +-
 DESCRIPTION                         |  4 +-
 NEWS.md                             |  2 +-
 R/TreeManipulation.R                |  2 +-
 inst/REFERENCES.bib                 | 68 +++++++++++++++++++++++++++++
 man/UnshiftTree.Rd                  |  2 +-
 src/Quartet-init.c                  |  2 +-
 vignettes/Tree-distance-metrics.Rmd | 30 +++++++++++++
 8 files changed, 105 insertions(+), 7 deletions(-)

diff --git a/.zenodo.json b/.zenodo.json
index c4ef2f05..7f396558 100644
--- a/.zenodo.json
+++ b/.zenodo.json
@@ -2,7 +2,7 @@
     "description": "An R package that calculates distances between phylogenetic topologies, integrating the tqDist algorithm for quartet distances", 
     "license": "gpl-3.0", 
     "title": "Quartet: Comparison of Phylogenetic Trees Using Quartet and Bipartition Measures", 
-    "version": "v1.0.0", 
+    "version": "v1.0.1", 
     "upload_type": "software", 
     "creators": [
         {
diff --git a/DESCRIPTION b/DESCRIPTION
index 8d52cf56..9d3f7971 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Quartet
-Version: 1.0.0.9001
-Date: 2019-01-21
+Version: 1.0.1
+Date: 2019-01-22
 Title: Comparison of Phylogenetic Trees Using Quartet and Bipartition Measures
 Description: Calculates the number of four-taxon subtrees consistent with a pair
   of cladograms, calculating the symmetric quartet distance of Bandelt & Dress (1986),
diff --git a/NEWS.md b/NEWS.md
index f4400a2c..b95458e4 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# Quartet v1.0.0.9000
+# Quartet v1.0.1
 ## Portability
  - Improved portability of C++ code.
 
diff --git a/R/TreeManipulation.R b/R/TreeManipulation.R
index b4f3f364..9dd89f60 100644
--- a/R/TreeManipulation.R
+++ b/R/TreeManipulation.R
@@ -1,4 +1,4 @@
-#' Unshift Tree
+#' Add Tree to Start of List
 #' 
 #' Add a tree to the start of a list of trees
 #' 
diff --git a/inst/REFERENCES.bib b/inst/REFERENCES.bib
index 1178ad16..9c0f6d7d 100644
--- a/inst/REFERENCES.bib
+++ b/inst/REFERENCES.bib
@@ -1,3 +1,60 @@
+@article{Bluis2003,
+  author = {Bluis, John and Shin, Dong Guk},
+  doi = {10.1109/BIBE.2003.1188933},
+  journal = {Proceedings - 3rd IEEE Symposium on BioInformatics and BioEngineering, BIBE 2003},
+  pages = {87--94},
+  publisher = {IEEE},
+  title = {{Nodal distance algorithm: Calculating a phylogenetic tree comparison metric}},
+  year = {2003}
+}
+
+@incollection{Bocker2013,
+  address = {Berlin, Heidelberg},
+  author = {B{\"{o}}cker, Sebastian and Canzar, Stefan and Klau, Gunnar W.},
+  booktitle = {Algorithms in Bioinformatics. WABI 2013. Lecture Notes in Computer Science, vol 8126},
+  doi = {10.1007/978-3-642-40453-5_13},
+  editor = {Darling, A. and Stoye, J.},
+  pages = {156--169},
+  publisher = {Springer},
+  title = {{The generalized Robinson-Foulds metric}},
+  year = {2013}
+}
+
+
+@article{Bogdanowicz2012,
+  author = {Bogdanowicz, Damian and Giaro, Krzysztof},
+  doi = {10.1109/TCBB.2011.48},
+  issn = {15455963},
+  journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics},
+  number = {1},
+  pages = {150--160},
+  title = {{Matching split distance for unrooted binary phylogenetic trees}},
+  volume = {9},
+  year = {2012}
+}
+
+@article{Bogdanowicz2013,
+  author = {Bogdanowicz, Damian and Giaro, Krzysztof},
+  doi = {10.2478/amcs-2013-0050},
+  journal = {International Journal of Applied Mathematics and Computer Science},
+  number = {3},
+  pages = {669--684},
+  title = {{On a matching distance between rooted phylogenetic trees}},
+  volume = {23},
+  year = {2013}
+}
+
+@article{Bogdanowicz2017,
+  author = {Bogdanowicz, Damian and Giaro, Krzysztof},
+  doi = {10.1089/cmb.2016.0204},
+  journal = {Journal of Computational Biology},
+  number = {5},
+  pages = {422--435},
+  title = {{Comparing phylogenetic trees by matching nodes using the transfer distance between partitions}},
+  volume = {24},
+  year = {2017}
+}
+
 @article{Brodal2013,
   author = {Brodal, Gerth St{\o}lting and Fagerberg, Rolf and Mailund, Thomas and Pedersen, Christian N. S. and Sand, Andreas},
   doi = {10.1137/1.9781611973105.130},
@@ -61,6 +118,17 @@ @article{Marczewski1958
   year = {1958}
 }
 
+@article{Nye2006,
+  author = {Nye, Tom M W and Li{\`{o}}, Pietro and Gilks, Walter R.},
+  doi = {10.1093/bioinformatics/bti720},
+  journal = {Bioinformatics},
+  number = {1},
+  pages = {117--119},
+  title = {{A novel algorithm and web-based tool for comparing two alternative phylogenetic trees}},
+  volume = {22},
+  year = {2006}
+}
+
 @article{Penny1985,
   author = {Penny, David and Hendy, M. D.},
   doi = {10.2307/2413347},
diff --git a/man/UnshiftTree.Rd b/man/UnshiftTree.Rd
index 2191d2ce..d2ca7e9f 100644
--- a/man/UnshiftTree.Rd
+++ b/man/UnshiftTree.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/TreeManipulation.R
 \name{UnshiftTree}
 \alias{UnshiftTree}
-\title{Unshift Tree}
+\title{Add Tree to Start of List}
 \usage{
 UnshiftTree(add, treeList)
 }
diff --git a/src/Quartet-init.c b/src/Quartet-init.c
index 893f9f4d..7d5f27ce 100644
--- a/src/Quartet-init.c
+++ b/src/Quartet-init.c
@@ -1,5 +1,5 @@
 #include <R.h>
-#include <Rinternals.h>
+#include <Rinternals.h> /* for SEXP */
 #include <stdlib.h> /* for NULL */
 #include <R_ext/Rdynload.h>
 
diff --git a/vignettes/Tree-distance-metrics.Rmd b/vignettes/Tree-distance-metrics.Rmd
index 9d711d53..54c13d82 100644
--- a/vignettes/Tree-distance-metrics.Rmd
+++ b/vignettes/Tree-distance-metrics.Rmd
@@ -74,6 +74,8 @@ each pair of tips.
 The path difference metric [@Steel1993; `r Phangorn('path.dist')`] is the 
 square root of the sum of squares of each of these differences.
 
+The related nodal distance [@Bluis2003] is not considered further here.
+
 ## Partition metric
 The Robinson-Foulds (RF or 'partition') metric [@Robinson1981; @Steel1993;
 phangorn's `r Phangorn('RF.dist')` or this package's `RobinsonFoulds`]
@@ -372,5 +374,33 @@ all of the following desiderata:
  - Identifies pairs of trees that are more random than expected by chance
  - Does not reach its maximum value after relatively trivial rearrangements
  
+# Improvements to partition metrics
+
+The primary issue with the Robinson-Foulds distance is its conservative 
+pairing of clades: a grouping is either identical in both trees, or is 
+treated as different.  
+This makes no account for the possibility that one tree contains a grouping that
+is similar (though not quite identical) to a grouping in another.
+
+In order to incorporate some measure of similar-but-not-quite-identical clades,
+it is necessary to construct an optimal matching that pairs each clade in each
+tree with either a suitable clade in the other, or with no clade at all.
+
+Various approaches to this problem have been proposed; these typically search
+for a matching that minimises the total dissimilarity summed for all pairings.
+Approaches differ in how they penalize differences between paired groups.
+Bogdanowicz and Giaro [-@Bogdanowicz2012;-@Bogdanowicz2013;-@Bogdanowicz2017]
+calculate the size
+of the largest bipartition that is consistent with both input groups; 
+Nye _et al_. [-@Nye2006] normalize this number using the Jaccard index;
+Böcker _et al_. [-@Bocker2013] raise this value to an arbitrary exponent, and
+add a constraint that prohibits pairings that comprise contradictory groups.
+
+These approaches represent a refinement of the Robinson-Foulds metric,
+circumventing many of the issues raised above.  They are, however, more 
+computationally expensive, and lack an objective measure of clade similarity.
+I am not presently aware of an R implementation of any of these measures,
+though a related metric is planned for a future version of this package.
+
 # References
  
\ No newline at end of file