From 2c9b6fae2468d8067765ae39689a17c0dad153b4 Mon Sep 17 00:00:00 2001
From: RevBayes analysis <1695515+ms609@users.noreply.github.com>
Date: Wed, 5 Feb 2025 16:26:35 +0000
Subject: [PATCH 1/7] Functionalize existing (erroneous) behaviour

---
 R/AdditionTree.R                   | 10 +++++++---
 tests/testthat/test-AdditionTree.R | 18 ++++++++++++++++++
 2 files changed, 25 insertions(+), 3 deletions(-)

diff --git a/R/AdditionTree.R b/R/AdditionTree.R
index 29139ec1d..ef973774c 100644
--- a/R/AdditionTree.R
+++ b/R/AdditionTree.R
@@ -31,7 +31,7 @@ AdditionTree <- function (dataset, concavity = Inf, constraint, sequence) {
   # Initialize missing parameters
   taxa <- names(dataset)
   if (missing(sequence)) {
-    sequence <- taxa[1]
+    sequence <- taxa[[1]]
   } else if (is.numeric(sequence)) {
     sequence <- taxa[sequence]
   }
@@ -78,7 +78,7 @@ AdditionTree <- function (dataset, concavity = Inf, constraint, sequence) {
         constraint <- MatrixToPhyDat(t(as.matrix(constraint)))
       }
       thisConstr <- constraint[theseTaxa]
-      if (length(thisConstr[[1]]) && min(table(unlist(thisConstr))) > 1) {
+      if (.ConstraintConstrains(thisConstr)) {
         # Constraint constrains theseTaxa
         
         morphyConstr <- PhyDat2Morphy(thisConstr)
@@ -114,6 +114,10 @@ AdditionTree <- function (dataset, concavity = Inf, constraint, sequence) {
   tree
 }
 
-.Recompress <- function (dataset) {
+.ConstraintConstrains <- function(constraint) {
+  length(constraint[[1]]) && min(table(unlist(constraint))) > 1
+}
+
+.Recompress <- function(dataset) {
   MatrixToPhyDat(PhyDatToMatrix(dataset))
 }
diff --git a/tests/testthat/test-AdditionTree.R b/tests/testthat/test-AdditionTree.R
index 3c943504a..dd7846e11 100644
--- a/tests/testthat/test-AdditionTree.R
+++ b/tests/testthat/test-AdditionTree.R
@@ -20,6 +20,24 @@ test_that("Addition tree is more parsimonious", {
   expect_lt(Score(pr, "pr"), Score(nj10, "pr"))
 })
 
+test_that(".ConstraintConstrains() succeeds", {
+  expect_false(.ConstraintConstrains(
+    structure(list(A = 1L, B = 2L, C = 1L, D = 1L, E = 3L), weight = 1L, nr = 1L,
+              nc = 2L, index = 1L, levels = 0:1,
+              allLevels = c("0", "1", "?"), type = "USER",
+              contrast = structure(c(1, 0, 1, 0, 1, 1), dim = 3:2,
+                                   dimnames = list(NULL, 0:1)),
+              class = "phyDat")
+  ))
+  expect_true(.ConstraintConstrains(structure(
+    list(A = 1L, B = 2L, C = 1L, D = 1L, E = 3L, F = 2L), weight = 1L, nr = 1L,
+    nc = 2L, index = 1L, levels = 0:1, allLevels = c("0", "1", "?"),
+    type = "USER", contrast = structure(c(1, 0, 1, 0, 1, 1), dim = 3:2,
+                                        dimnames = list(NULL, 0:1)),
+    class = "phyDat")
+  ))
+})
+
 test_that("Addition tree obeys constraints", {
   dataset <- MatrixToPhyDat(matrix(
     c(0, 1, 1, 1, 0, 1,

From d57f0c84c84204f50116552629972fa85ff23056 Mon Sep 17 00:00:00 2001
From: RevBayes analysis <1695515+ms609@users.noreply.github.com>
Date: Wed, 5 Feb 2025 16:27:06 +0000
Subject: [PATCH 2/7] Check NULL

---
 tests/testthat/test-AdditionTree.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/testthat/test-AdditionTree.R b/tests/testthat/test-AdditionTree.R
index dd7846e11..16fe416df 100644
--- a/tests/testthat/test-AdditionTree.R
+++ b/tests/testthat/test-AdditionTree.R
@@ -21,6 +21,7 @@ test_that("Addition tree is more parsimonious", {
 })
 
 test_that(".ConstraintConstrains() succeeds", {
+  expect_false(.ConstraintConstrains(NULL))
   expect_false(.ConstraintConstrains(
     structure(list(A = 1L, B = 2L, C = 1L, D = 1L, E = 3L), weight = 1L, nr = 1L,
               nc = 2L, index = 1L, levels = 0:1,

From cb07ec4584db7975d22cc7fd74df13422c0d651b Mon Sep 17 00:00:00 2001
From: RevBayes analysis <1695515+ms609@users.noreply.github.com>
Date: Wed, 5 Feb 2025 16:58:56 +0000
Subject: [PATCH 3/7] .ConstraintConstrains implementation

---
 DESCRIPTION                        |  2 +-
 NEWS.md                            |  5 +++++
 R/AdditionTree.R                   | 16 +++++++++++++++-
 tests/testthat/test-AdditionTree.R | 15 +++++++++++++++
 4 files changed, 36 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f688aa6b6..dd8cc1a7d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: TreeSearch
 Title: Phylogenetic Analysis with Discrete Character Data
-Version: 1.5.1.9002
+Version: 1.5.1.9003
 Authors@R: c(
     person(
       "Martin R.", 'Smith',
diff --git a/NEWS.md b/NEWS.md
index 471dfabfc..a9a91ffd6 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,8 @@
+# TreeSearch 1.5.1.9003 (2025-02)
+
+- Improve support for constraints in `AdditionTree()`
+  (#173)[https://github.com/ms609/TreeSearch/issues/173]
+
 # TreeSearch 1.5.1.9002 (2025-01)
 
 - Buttons to download consensus trees in app
diff --git a/R/AdditionTree.R b/R/AdditionTree.R
index ef973774c..05191cfc8 100644
--- a/R/AdditionTree.R
+++ b/R/AdditionTree.R
@@ -115,7 +115,21 @@ AdditionTree <- function (dataset, concavity = Inf, constraint, sequence) {
 }
 
 .ConstraintConstrains <- function(constraint) {
-  length(constraint[[1]]) && min(table(unlist(constraint))) > 1
+  if (length(constraint[[1]]) < 1) {
+    FALSE
+  } else {
+    cont <- `mode<-`(attr(constraint, "contrast"), "logical")
+    nLevel <- dim(cont)[[1]]
+    # Could be > 2× more efficient using lower.tri
+    exclude <- vapply(seq_len(nLevel), function(i) {
+      colSums(apply(cont, 1, `&`, cont[i, ])) == 0
+    }, logical(nLevel))
+    
+    # TODO Not sure about this; passes tests but not proven to 
+    # work for all odd edge cases, e.g. 02 03 1 1
+    splits <- exclude * tabulate(unlist(constraint), nLevel)
+    any(splits[lower.tri(splits)] > 1 & t(splits)[lower.tri(splits)] > 1)
+  }
 }
 
 .Recompress <- function(dataset) {
diff --git a/tests/testthat/test-AdditionTree.R b/tests/testthat/test-AdditionTree.R
index 16fe416df..91b863cbe 100644
--- a/tests/testthat/test-AdditionTree.R
+++ b/tests/testthat/test-AdditionTree.R
@@ -37,6 +37,21 @@ test_that(".ConstraintConstrains() succeeds", {
                                         dimnames = list(NULL, 0:1)),
     class = "phyDat")
   ))
+  expect_false(.ConstraintConstrains(structure(
+    list(A = 1L, B = 2L, C = 1L, D = 1L, E = 3L, F = 2L), weight = 1L, nr = 1L,
+    nc = 2L, index = 1L,
+    levels = 0:2, allLevels = c("0", "1", "2", "?"), type = "USER",
+    contrast = structure(c(1, 1, 0, 1, 0, 1, 0, 1, 0, 0, 1, 1),
+                         dim = c(4, 3), dimnames = list(NULL, 0:2)),
+    class = "phyDat")
+  ))
+  expect_true(.ConstraintConstrains(structure(
+    list(A = 1L, B = 2L, C = 1L, D = 1L, E = 3L, F = 2L), weight = 1L, nr = 1L,
+    nc = 2L, index = 1L, levels = 0:2, allLevels = c("0", "1", "2", "?"),
+    type = "USER", contrast = structure(c(1, 0, 1, 1, 0, 1, 0, 1, 1),
+                                        dim = c(3, 3), dimnames = list(NULL, 0:2)),
+    class = "phyDat")
+  ))
 })
 
 test_that("Addition tree obeys constraints", {

From 38a8208deec5e05d92615fd9da26177c81507807 Mon Sep 17 00:00:00 2001
From: RevBayes analysis <1695515+ms609@users.noreply.github.com>
Date: Wed, 5 Feb 2025 17:00:29 +0000
Subject: [PATCH 4/7] Comment

---
 R/AdditionTree.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/AdditionTree.R b/R/AdditionTree.R
index 05191cfc8..3290406b9 100644
--- a/R/AdditionTree.R
+++ b/R/AdditionTree.R
@@ -125,8 +125,8 @@ AdditionTree <- function (dataset, concavity = Inf, constraint, sequence) {
       colSums(apply(cont, 1, `&`, cont[i, ])) == 0
     }, logical(nLevel))
     
-    # TODO Not sure about this; passes tests but not proven to 
-    # work for all odd edge cases, e.g. 02 03 1 1
+    # TODO Validate; passes existing tests, but these do not include all 
+    # edge cases, e.g. 02 03 1 1
     splits <- exclude * tabulate(unlist(constraint), nLevel)
     any(splits[lower.tri(splits)] > 1 & t(splits)[lower.tri(splits)] > 1)
   }

From 1091ee224f2b331efa515ecbac1d8e10abe0e949 Mon Sep 17 00:00:00 2001
From: RevBayes analysis <1695515+ms609@users.noreply.github.com>
Date: Wed, 5 Feb 2025 17:05:54 +0000
Subject: [PATCH 5/7] 1-col constraints

---
 R/AdditionTree.R                   | 29 ++++++++++++++++++-----------
 tests/testthat/test-AdditionTree.R | 10 ++++++++++
 2 files changed, 28 insertions(+), 11 deletions(-)

diff --git a/R/AdditionTree.R b/R/AdditionTree.R
index 3290406b9..d8cb340d4 100644
--- a/R/AdditionTree.R
+++ b/R/AdditionTree.R
@@ -114,24 +114,31 @@ AdditionTree <- function (dataset, concavity = Inf, constraint, sequence) {
   tree
 }
 
+
 .ConstraintConstrains <- function(constraint) {
   if (length(constraint[[1]]) < 1) {
     FALSE
   } else {
-    cont <- `mode<-`(attr(constraint, "contrast"), "logical")
-    nLevel <- dim(cont)[[1]]
-    # Could be > 2× more efficient using lower.tri
-    exclude <- vapply(seq_len(nLevel), function(i) {
-      colSums(apply(cont, 1, `&`, cont[i, ])) == 0
-    }, logical(nLevel))
-    
-    # TODO Validate; passes existing tests, but these do not include all 
-    # edge cases, e.g. 02 03 1 1
-    splits <- exclude * tabulate(unlist(constraint), nLevel)
-    any(splits[lower.tri(splits)] > 1 & t(splits)[lower.tri(splits)] > 1)
+    contrast <- attr(constraint, "contrast")
+    if (dim(contrast)[[2]] < 2) {
+      FALSE
+    } else {
+      cont <- `mode<-`(contrast, "logical")
+      nLevel <- dim(contrast)[[1]]
+      # Could be > 2× more efficient using lower.tri
+      exclude <- vapply(seq_len(nLevel), function(i) {
+        colSums(apply(cont, 1, `&`, cont[i, ])) == 0
+      }, logical(nLevel))
+      
+      # TODO Validate; passes existing tests, but these do not include all 
+      # edge cases, e.g. 02 03 1 1
+      splits <- exclude * tabulate(unlist(constraint), nLevel)
+      any(splits[lower.tri(splits)] > 1 & t(splits)[lower.tri(splits)] > 1)
+    }
   }
 }
 
+
 .Recompress <- function(dataset) {
   MatrixToPhyDat(PhyDatToMatrix(dataset))
 }
diff --git a/tests/testthat/test-AdditionTree.R b/tests/testthat/test-AdditionTree.R
index 91b863cbe..395e472cf 100644
--- a/tests/testthat/test-AdditionTree.R
+++ b/tests/testthat/test-AdditionTree.R
@@ -22,6 +22,16 @@ test_that("Addition tree is more parsimonious", {
 
 test_that(".ConstraintConstrains() succeeds", {
   expect_false(.ConstraintConstrains(NULL))
+  
+  # Single level
+  expect_false(.ConstraintConstrains(
+    structure(list(A = 1L, B = 2L, C = 2L, D = 2L), weight = 1L, nr = 1L,
+              nc = 1L, index = 1L, levels = 0, allLevels = c("0", "?"),
+              type = "USER", contrast = 
+                structure(c(1, 1), dim = 2:1, dimnames = list(NULL, 0)),
+              class = "phyDat")
+  ))
+  
   expect_false(.ConstraintConstrains(
     structure(list(A = 1L, B = 2L, C = 1L, D = 1L, E = 3L), weight = 1L, nr = 1L,
               nc = 2L, index = 1L, levels = 0:1,

From 3f7971941917930749f3f5117b15b42e107fd276 Mon Sep 17 00:00:00 2001
From: RevBayes analysis <1695515+ms609@users.noreply.github.com>
Date: Wed, 5 Feb 2025 18:57:03 +0000
Subject: [PATCH 6/7] link format

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

diff --git a/NEWS.md b/NEWS.md
index a9a91ffd6..333889154 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,7 +1,7 @@
 # TreeSearch 1.5.1.9003 (2025-02)
 
 - Improve support for constraints in `AdditionTree()`
-  (#173)[https://github.com/ms609/TreeSearch/issues/173]
+  [#173](https://github.com/ms609/TreeSearch/issues/173)
 
 # TreeSearch 1.5.1.9002 (2025-01)
 

From eb1422feda30278a1f4747ae9ef21192c0d3947f Mon Sep 17 00:00:00 2001
From: RevBayes analysis <1695515+ms609@users.noreply.github.com>
Date: Wed, 5 Feb 2025 19:02:49 +0000
Subject: [PATCH 7/7] +pandoc

for pandoc-citeproc
---
 .github/workflows/coverage.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
index 8c68f5464..e02d360ca 100644
--- a/.github/workflows/coverage.yml
+++ b/.github/workflows/coverage.yml
@@ -54,6 +54,9 @@ jobs:
           needs: |
             coverage
 
+      - name: Set up pandoc
+        uses: r-lib/actions/setup-pandoc@v2
+
       - name: Code coverage
         run: |
           covr::package_coverage(quiet = FALSE) # https://github.com/r-lib/covr/issues/252