| line |
!l |
l&&!r |
l&&r |
condition |
|
224
|
5 |
0 |
0 |
$options{'threads'} > 1 and not $Bio::Phylo::EvolutionaryModels::Config{'useithreads'}
|
|
251
|
5 |
0 |
0 |
defined $options{'incomplete_sampling'} and $options{'incomplete_sampling'}
|
|
|
0 |
0 |
0 |
defined $options{'incomplete_sampling'} and $options{'incomplete_sampling'} and not defined $options{'algorithm_options'}{'sampling_probability'}
|
|
306
|
0 |
0 |
0 |
defined $options{'output_format'} and $options{'output_format'} eq 'newick'
|
|
325
|
1 |
4 |
0 |
defined $options{'output_format'} and $options{'output_format'} eq 'newick'
|
|
|
1 |
0 |
4 |
defined $options{'output_format'} and $options{'output_format'} eq 'forest'
|
|
615
|
0 |
1 |
0 |
ref $sampling_probability and scalar @{$sampling_probability;} != $mstar - $options{'tree_size'} + 1
|
|
1068
|
0 |
75 |
20 |
defined $options{'death_rate'} and $options{'death_rate'} == 0
|
|
1085
|
95 |
0 |
0 |
defined $options{'root_edge'} and $options{'root_edge'}
|
|
1107
|
0 |
47 |
5423 |
$tree_size > 0 and $tree_size < $options{'tree_size'}
|
|
|
47 |
0 |
5423 |
$tree_size > 0 and $tree_size < $options{'tree_size'} and $time < $options{'tree_age'}
|
|
1226
|
0 |
0 |
0 |
defined $options{'death_rate'} and $options{'death_rate'} == 0
|
|
1247
|
0 |
0 |
0 |
defined $options{'root_edge'} and $options{'root_edge'}
|
|
1269
|
0 |
0 |
0 |
$tree_size > 0 and $tree_size < $options{'tree_size'}
|
|
|
0 |
0 |
0 |
$tree_size > 0 and $tree_size < $options{'tree_size'} and $time < $options{'tree_age'}
|
|
1405
|
0 |
0 |
0 |
defined $options{'root_edge'} and $options{'root_edge'}
|
|
1423
|
0 |
0 |
0 |
$tree_size > 0 and $tree_size < $options{'tree_size'}
|
|
|
0 |
0 |
0 |
$tree_size > 0 and $tree_size < $options{'tree_size'} and $time < $options{'tree_age'}
|
|
1565
|
0 |
0 |
0 |
defined $options{'root_edge'} and $options{'root_edge'}
|
|
1577
|
0 |
0 |
0 |
$tree_size < $options{'tree_size'} and $time < $options{'tree_age'}
|
|
1594
|
0 |
0 |
0 |
$selected < scalar @terminals and $rand_select > $birth_rates[$selected]
|
|
1740
|
0 |
0 |
0 |
defined $options{'root_edge'} and $options{'root_edge'}
|
|
1772
|
0 |
0 |
0 |
$tree_size > 0 and $tree_size < $options{'tree_size'}
|
|
|
0 |
0 |
0 |
$tree_size > 0 and $tree_size < $options{'tree_size'} and $time < $options{'tree_age'}
|
|
1830
|
0 |
0 |
0 |
$selected < scalar @terminals and $rand_select > $birth_rates[$selected]
|
|
1842
|
0 |
0 |
0 |
$selected < scalar @terminals and $rand_select > $death_rates[$selected]
|
|
1984
|
0 |
0 |
0 |
defined $options{'root_edge'} and $options{'root_edge'}
|
|
1996
|
0 |
0 |
0 |
$tree_size < $options{'tree_size'} and $time < $options{'tree_age'}
|
|
2013
|
0 |
0 |
0 |
$selected < scalar @terminals and $rand_select > $birth_rates[$selected]
|
|
2333
|
14 |
75 |
998 |
scalar @extinction and ($end_time - $extinction[-1]) / $end_time < 1e-06
|
|
2339
|
89 |
2117 |
2879 |
scalar @speciation and $speciation[0] < $extinction[0]
|
| line |
l |
!l&&r |
!l&&!r |
condition |
|
261
|
4 |
1 |
0 |
defined $options{'model'} or $options{'algorithm'} eq 'constant_rate_bd'
|
|
442
|
2 |
3 |
11 |
$expected_samples > 1 or rand 1 < $expected_samples
|
|
536
|
1 |
4 |
16 |
$expected_samples > 1 or rand 1 < $expected_samples
|
|
711
|
0 |
5 |
5 |
$expected_samples > 1 or rand 1 < $expected_samples
|
|
1055
|
95 |
0 |
0 |
defined $options{'tree_size'} or defined $options{'tree_age'}
|
|
1133
|
3169 |
0 |
2254 |
$next_speciation < $next_extinction or not defined $next_extinction
|
|
1208
|
0 |
0 |
0 |
defined $options{'tree_size'} or defined $options{'tree_age'}
|
|
1295
|
0 |
0 |
0 |
$next_speciation < $next_extinction or not defined $next_extinction
|
|
1371
|
0 |
0 |
0 |
defined $options{'tree_size'} or defined $options{'tree_age'}
|
|
1463
|
0 |
0 |
0 |
$next_speciation < $next_extinction or not defined $next_extinction
|
|
1534
|
0 |
0 |
0 |
defined $options{'tree_size'} or defined $options{'tree_age'}
|
|
1684
|
0 |
0 |
0 |
defined $options{'tree_size'} or defined $options{'tree_age'}
|
|
1866
|
0 |
0 |
0 |
$next_speciation < $next_extinction or not defined $next_extinction
|
|
1953
|
0 |
0 |
0 |
defined $options{'tree_size'} or defined $options{'tree_age'}
|
|
2339
|
236 |
2879 |
2206 |
scalar @extinction == 0 or scalar @speciation and $speciation[0] < $extinction[0]
|
|
2448
|
0 |
0 |
0 |
$k > $n or $k < 0
|