def test_continous(self):
exp_basis = pd.read_csv(
self.get_data_path('expected/numeric_basis.tsv'), sep='\t')
exp_data = pd.read_csv(self.get_data_path('expected/numeric_data.tsv'),
sep='\t')
exp_groups = pd.read_csv(
self.get_data_path('expected/numeric_groups.tsv'), sep='\t')
exp_factors = pd.read_csv(
self.get_data_path('expected/numeric_factors.tsv'), sep='\t')
exp_tree = (TreeNode.read(
self.get_data_path('expected/numeric_tree.nwk')))
pf = phylofactor(self.table,
self.phylogeny,
self.metadata,
formula='Continuous~Data',
nfactors=3,
family='poisson')
data, basis, out_tree, groups, factors = pf
assert_frame_equal(basis, exp_basis)
assert_frame_equal(groups, exp_groups)
assert_frame_equal(factors, exp_factors)
assert_frame_equal(data, exp_data)
self.assertEqual(TreeNode.compare_rfd(exp_tree, out_tree), 0)
def test_defaults(self):
exp_basis = pd.read_csv(
self.get_data_path('expected/categorical_basis.tsv'), sep='\t')
exp_data = pd.read_csv(
self.get_data_path('expected/categorical_data.tsv'), sep='\t')
exp_groups = pd.read_csv(
self.get_data_path('expected/categorical_groups.tsv'), sep='\t')
exp_factors = pd.read_csv(
self.get_data_path('expected/categorical_factors.tsv'), sep='\t')
exp_tree = TreeNode.read(
self.get_data_path('expected/categorical_tree.nwk'))
pf = phylofactor(self.table,
self.phylogeny,
self.metadata,
formula='Categorical~Data',
nfactors=3,
family='binomial')
data, basis, out_tree, groups, factors = pf
assert_frame_equal(basis, exp_basis)
assert_frame_equal(groups, exp_groups)
assert_frame_equal(factors, exp_factors)
assert_frame_equal(data, exp_data)
self.assertEqual(TreeNode.compare_rfd(exp_tree, out_tree), 0)
