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Implements integrated constant coalescent prior #2

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1,075 changes: 1,075 additions & 0 deletions examples/fluA/fluA.trees

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1,730 changes: 904 additions & 826 deletions phylostan/generate_script.py

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4 changes: 2 additions & 2 deletions phylostan/phylostan.py
Original file line number Diff line number Diff line change
Expand Up @@ -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""")
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1 change: 0 additions & 1 deletion phylostan/utils.py
Original file line number Diff line number Diff line change
@@ -1,5 +1,4 @@
import numpy
import math

def get_peeling_order(tree):
peeling = []
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156 changes: 0 additions & 156 deletions src/GTR-coalescent.stan

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119 changes: 0 additions & 119 deletions src/GTR-uniform.stan

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