1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
|
#! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this work or any portion thereof in published work,
## please cite it as:
##
## Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library
## for phylogenetic computing. Bioinformatics 26: 1569-1571.
##
##############################################################################
"""
DEPRECATED IN DENDROPY 4: USE `dendropy.model.continuous` instead.
"""
from dendropy.model import continuous
from dendropy.utility import deprecate
def simulate_continuous(node, rng=None, **kwargs):
deprecate.dendropy_deprecation_warning(
preamble="The 'dendropy.continuous' module has moved to 'dendropy.model.continuous', and this function has been renamed 'evolve_continuous_char()'.",
old_construct="from dendropy import continuous\ncontinuous.simulate_continuous(...)",
new_construct="from dendropy.model import continuous\ncontinuous.evolve_continuous_char(...)",
epilog="Note that this function is also available through 'dendropy.simulate.charsim.evolve_continuous_char(...)'.")
return continuous.evolve_continuous_char(node, rng, **kwargs)
class PhylogeneticIndependentConstrasts(continuous.PhylogeneticIndependentConstrasts):
def __init__(self,
tree,
char_matrix,
polytomy_strategy=None):
deprecate.dendropy_deprecation_warning(
preamble="The 'dendropy.continuous' module has moved to 'dendropy.model.continuous'.",
old_construct="from dendropy import continuous\ncontinuous.PhylogeneticIndependentConstrasts(...)",
new_construct="from dendropy.model import continuous\ncontinuous.PhylogeneticIndependentConstrasts(...)",
)
continuous.PhylogeneticIndependentConstrasts.__init__(self,
tree=tree,
char_matrix=char_matrix,
polytomy_strategy=polytomy_strategy)
|
