4ment · maxbiostat · Oct 2, 2019 · Oct 2, 2019 · Oct 2, 2019 · Oct 2, 2019
diff --git a/examples/fluA/fluA.trees b/examples/fluA/fluA.trees
diff --git a/phylostan/generate_script.py b/phylostan/generate_script.py
diff --git a/phylostan/phylostan.py b/phylostan/phylostan.py
@@ -76,8 +76,8 @@ def create_build_parser(subprasers, prog, help):
 	parser.add_argument('--clock', required=False, choices=['strict', 'autocorrelated', 'uncorrelated'], default=None,
 						help="""Type of clock""")
 	parser.add_argument('--estimate_rate', action='store_true', help="""Estimate substitution rate""")
-	parser.add_argument('-c', '--coalescent', choices=['constant', 'skyride', 'skygrid'], default=None,
-						help="""Type of coalescent (constant or skyride)""")
+	parser.add_argument('-c', '--coalescent', choices=['constant', 'integrated', 'skyride', 'skygrid'], default=None,
+						help="""Type of coalescent (constant, integrated, skyride or skygrid)""")
 	parser.add_argument('--grid', metavar='I', required=False, type=int, help="""Number of grid points in skygrid""")
 	parser.add_argument('--cutoff', metavar='G', required=False, type=float, help="""a cutoff for skygrid""")
 	parser.add_argument('--compile', action="store_true", help="""Compile Stan script""")

diff --git a/phylostan/utils.py b/phylostan/utils.py
@@ -1,5 +1,4 @@
 import numpy
-import math
 
 def get_peeling_order(tree):
     peeling = []

diff --git a/src/GTR-coalescent.stan b/src/GTR-coalescent.stan
diff --git a/src/GTR-uniform.stan b/src/GTR-uniform.stan