Fix tutorials/chromo and add a test.

Author: bredelings

tutorials/chromo/index.md

@@ -296,14 +296,14 @@ max_chromo = 26
 {% endsnippet %}
 
 Now we get the observed chromosome counts from a tab-delimited file.
-```
-chromo_data = readCharacterDataDelimited("data/aristolochia_chromosome_counts.tsv", stateLabels=(max_chromo + 1), type="NaturalNumbers", delimiter="\t", headers=FALSE)
-```
+{% snippet scripts/ChromEvol_simple.Rev %}
+chromo_data = readCharacterDataDelimited("data/aristolochia_chromosome_counts.tsv", stateLabels=(max_chromo + 1), type="NaturalNumbers", delimiter="\t", header=FALSE)
+{% endsnippet %}
 Finally, we initialize a variable for our vector of moves and monitors.
-```
+{% snippet scripts/ChromEvol_simple.Rev %}
 moves    = VectorMoves()
 monitors = VectorMonitors()
-```
+{% endsnippet %}
 
 ### The Chromosome Evolution Model
 

tutorials/chromo/scripts/BiChroM.Rev

@@ -52,7 +52,7 @@ phylogeny <- readBranchLengthTrees("data/aristolochia.tree")[1]
 max_chromo = 26
 
 # Get the chromosome counts from a tab-delimited file.
-chromo_data = readCharacterDataDelimited("data/aristolochia_bichrom_counts.tsv", stateLabels=2*(max_chromo + 1), type="NaturalNumbers", delimiter="\t", headers=FALSE)
+chromo_data = readCharacterDataDelimited("data/aristolochia_bichrom_counts.tsv", stateLabels=2*(max_chromo + 1), type="NaturalNumbers", delimiter="\t", header=FALSE)
 
 
 #########################

tutorials/chromo/scripts/ChromEvol_clado.Rev

@@ -37,7 +37,7 @@ phylogeny <- readBranchLengthTrees("data/aristolochia.tree")[1]
 max_chromo = 26
 
 # Get the chromosome counts from a tab-delimited file.
-chromo_data = readCharacterDataDelimited("data/aristolochia_chromosome_counts.tsv", stateLabels=(max_chromo + 1), type="NaturalNumbers", delimiter="\t", headers=FALSE)
+chromo_data = readCharacterDataDelimited("data/aristolochia_chromosome_counts.tsv", stateLabels=(max_chromo + 1), type="NaturalNumbers", delimiter="\t", header=FALSE)
 
 
 #########################

tutorials/chromo/scripts/ChromEvol_joint.Rev

@@ -35,7 +35,7 @@ monitors = VectorMonitors()
 max_chromo = 26
 
 # Get the chromosome counts from a tab-delimited file.
-chromo_data = readCharacterDataDelimited("data/aristolochia_chromosome_counts.tsv", stateLabels=(max_chromo + 1), type="NaturalNumbers", delimiter="\t", headers=FALSE)
+chromo_data = readCharacterDataDelimited("data/aristolochia_chromosome_counts.tsv", stateLabels=(max_chromo + 1), type="NaturalNumbers", delimiter="\t", header=FALSE)
 
 # Get the DNA sequence alignment for the matK chloroplast gene.
 dna_seq = readDiscreteCharacterData("data/aristolochia_matK.fasta")

tutorials/chromo/scripts/ChromEvol_simmap.Rev

@@ -34,7 +34,7 @@ phylogeny <- readBranchLengthTrees("data/aristolochia.tree")[1]
 max_chromo = 26
 
 # Get the chromosome counts from a tab-delimited file.
-chromo_data = readCharacterDataDelimited("data/aristolochia_chromosome_counts.tsv", stateLabels=(max_chromo + 1), type="NaturalNumbers", delimiter="\t", headers=FALSE)
+chromo_data = readCharacterDataDelimited("data/aristolochia_chromosome_counts.tsv", stateLabels=(max_chromo + 1), type="NaturalNumbers", delimiter="\t", header=FALSE)
 
 
 #########################

tutorials/chromo/scripts/ChromEvol_simple.Rev

@@ -35,7 +35,7 @@ phylogeny <- readBranchLengthTrees("data/aristolochia.tree")[1]
 max_chromo = 26
 
 # Get the chromosome counts from a tab-delimited file.
-chromo_data = readCharacterDataDelimited("data/aristolochia_chromosome_counts.tsv", stateLabels=(max_chromo + 1), type="NaturalNumbers", delimiter="\t", headers=FALSE)
+chromo_data = readCharacterDataDelimited("data/aristolochia_chromosome_counts.tsv", stateLabels=(max_chromo + 1), type="NaturalNumbers", delimiter="\t", header=FALSE)
 
 
 #########################

tutorials/chromo/scripts/ChromoSSE_simple.Rev

@@ -35,7 +35,7 @@ phylogeny <- readTrees("data/aristolochia-bd.tree")[1]
 max_chromo = 26
 
 # Get the chromosome counts from a tab-delimited file.
-chromo_data = readCharacterDataDelimited("data/aristolochia_chromosome_counts.tsv", stateLabels=(max_chromo + 1), type="NaturalNumbers", delimiter="\t", headers=FALSE)
+chromo_data = readCharacterDataDelimited("data/aristolochia_chromosome_counts.tsv", stateLabels=(max_chromo + 1), type="NaturalNumbers", delimiter="\t", header=FALSE)
 
 
 #########################

tutorials/chromo/tests.txt

@@ -0,0 +1 @@
+scripts/ChromEvol_simple.Rev