def count_ecological_edges(methods, num_ees, ro):
'''Automates counting of ecological edges.
Inputs:
methods - list of strs. names of methods that weer used to generate the
engineered edges. must be formatted properly (e.g.
'amensally_related_1d_st_3' and in the same order as the num_ees list.
num_ees - list of ints. numbers of otus that are generated by each
method in the methods list.
ro - result object.
'''
starts = cumsum([0]+num_ees[:-1]) #add a 0 entry for start indices
stops = cumsum(num_ees)
method_names, strengths, dims = get_params_from_methods(methods)
edge_counts = [interacting_edges(starts[i], stops[i], dims[i], ro.edges,
ro.interactions) for i in range(len(num_ees))]
return (method_names, strengths, dims, edge_counts, len(ro.edges))
def count_ecological_edges(methods, num_ees, ro):
'''Automates counting of ecological edges.
Inputs:
methods - list of strs. names of methods that weer used to generate the
engineered edges. must be formatted properly (e.g.
'amensally_related_1d_st_3' and in the same order as the num_ees list.
num_ees - list of ints. numbers of otus that are generated by each
method in the methods list.
ro - result object.
'''
starts = cumsum([0] + num_ees[:-1]) #add a 0 entry for start indices
stops = cumsum(num_ees)
method_names, strengths, dims = get_params_from_methods(methods)
edge_counts = [
interacting_edges(starts[i], stops[i], dims[i], ro.edges,
ro.interactions) for i in range(len(num_ees))
]
return (method_names, strengths, dims, edge_counts, len(ro.edges))
def test_interacting_edges(self):
'''Test that interacting edges are calculated correctly.'''
edges = [\
('o0','o2'),
('o1','o2'),
('o0','o1'),
('o3','o2'),
('o3','o5'),
('o11','o25'),
('o0','o6'),
('o47','o50'),
('o6','o7')]
interactions = [\
'mutualExclusion',
'mutualExclusion',
'mutualExclusion',
'mutualExclusion',
'copresence',
'copresence',
'copresence',
'copresence',
'copresence']
# test with 1d relationships
start = 0
stop = 10
dim = 1
exp_total_detected = 3
exp_cis_edges = 0
exp_cis_cps = 0
exp_cis_mes = 0
exp_trans_edges = 3
exp_trans_cps = 1
exp_trans_mes = 2
self.assertEqual((exp_total_detected, exp_cis_edges, exp_cis_cps,
exp_cis_mes, exp_trans_edges, exp_trans_cps, exp_trans_mes),
interacting_edges(start, stop, dim, edges, interactions))
# test with 1d relationships, offset from last
start = 1
stop = 5
dim = 1
exp_total_detected = 1
exp_cis_edges = 0
exp_cis_cps = 0
exp_cis_mes = 0
exp_trans_edges = 1
exp_trans_cps = 0
exp_trans_mes = 1
self.assertEqual((exp_total_detected, exp_cis_edges, exp_cis_cps,
exp_cis_mes, exp_trans_edges, exp_trans_cps, exp_trans_mes),
interacting_edges(start, stop, dim, edges, interactions))
# test case with 2d relationships. inverted direction in some cases.
start = 0
stop = 6
dim = 2
exp_total_detected = 4
exp_cis_edges = 1
exp_cis_cps = 0
exp_cis_mes = 1
exp_trans_edges = 3
exp_trans_cps = 1
exp_trans_mes = 2
self.assertEqual((exp_total_detected, exp_cis_edges, exp_cis_cps,
exp_cis_mes, exp_trans_edges, exp_trans_cps, exp_trans_mes),
interacting_edges(start, stop, dim, edges, interactions))
# adjust start to make sure it handles non zero starts correctly
start = 3
stop = 9
dim = 2
exp_total_detected = 2
exp_cis_edges = 1
exp_cis_cps = 1
exp_cis_mes = 0
exp_trans_edges = 1
exp_trans_cps = 1
exp_trans_mes = 0
self.assertEqual((exp_total_detected, exp_cis_edges, exp_cis_cps,
exp_cis_mes, exp_trans_edges, exp_trans_cps, exp_trans_mes),
interacting_edges(start, stop, dim, edges, interactions))
# test with 4d relationships
start = 0
stop = 50
dim = 5
exp_total_detected = 6
exp_cis_edges = 5
exp_cis_cps = 1
exp_cis_mes = 4
exp_trans_edges = 1
exp_trans_cps = 1
exp_trans_mes = 0
self.assertEqual((exp_total_detected, exp_cis_edges, exp_cis_cps,
exp_cis_mes, exp_trans_edges, exp_trans_cps, exp_trans_mes),
interacting_edges(start, stop, dim, edges, interactions))
def test_interacting_edges(self):
'''Test that interacting edges are calculated correctly.'''
edges = [\
('o0','o2'),
('o1','o2'),
('o0','o1'),
('o3','o2'),
('o3','o5'),
('o11','o25'),
('o0','o6'),
('o47','o50'),
('o6','o7')]
interactions = [\
'mutualExclusion',
'mutualExclusion',
'mutualExclusion',
'mutualExclusion',
'copresence',
'copresence',
'copresence',
'copresence',
'copresence']
# test with 1d relationships
start = 0
stop = 10
dim = 1
exp_total_detected = 3
exp_cis_edges = 0
exp_cis_cps = 0
exp_cis_mes = 0
exp_trans_edges = 3
exp_trans_cps = 1
exp_trans_mes = 2
self.assertEqual(
(exp_total_detected, exp_cis_edges, exp_cis_cps, exp_cis_mes,
exp_trans_edges, exp_trans_cps, exp_trans_mes),
interacting_edges(start, stop, dim, edges, interactions))
# test with 1d relationships, offset from last
start = 1
stop = 5
dim = 1
exp_total_detected = 1
exp_cis_edges = 0
exp_cis_cps = 0
exp_cis_mes = 0
exp_trans_edges = 1
exp_trans_cps = 0
exp_trans_mes = 1
self.assertEqual(
(exp_total_detected, exp_cis_edges, exp_cis_cps, exp_cis_mes,
exp_trans_edges, exp_trans_cps, exp_trans_mes),
interacting_edges(start, stop, dim, edges, interactions))
# test case with 2d relationships. inverted direction in some cases.
start = 0
stop = 6
dim = 2
exp_total_detected = 4
exp_cis_edges = 1
exp_cis_cps = 0
exp_cis_mes = 1
exp_trans_edges = 3
exp_trans_cps = 1
exp_trans_mes = 2
self.assertEqual(
(exp_total_detected, exp_cis_edges, exp_cis_cps, exp_cis_mes,
exp_trans_edges, exp_trans_cps, exp_trans_mes),
interacting_edges(start, stop, dim, edges, interactions))
# adjust start to make sure it handles non zero starts correctly
start = 3
stop = 9
dim = 2
exp_total_detected = 2
exp_cis_edges = 1
exp_cis_cps = 1
exp_cis_mes = 0
exp_trans_edges = 1
exp_trans_cps = 1
exp_trans_mes = 0
self.assertEqual(
(exp_total_detected, exp_cis_edges, exp_cis_cps, exp_cis_mes,
exp_trans_edges, exp_trans_cps, exp_trans_mes),
interacting_edges(start, stop, dim, edges, interactions))
# test with 4d relationships
start = 0
stop = 50
dim = 5
exp_total_detected = 6
exp_cis_edges = 5
exp_cis_cps = 1
exp_cis_mes = 4
exp_trans_edges = 1
exp_trans_cps = 1
exp_trans_mes = 0
self.assertEqual(
(exp_total_detected, exp_cis_edges, exp_cis_cps, exp_cis_mes,
exp_trans_edges, exp_trans_cps, exp_trans_mes),
interacting_edges(start, stop, dim, edges, interactions))