def test_apply(self, lung_X, lung_y):
tree = RangerTreeSurvival()
tree.fit(lung_X, lung_y)
leaves = tree.apply(lung_X)
assert isinstance(leaves, np.ndarray)
assert np.all(leaves > 0)
assert len(leaves) == len(lung_X)
def test_split_rule(self, lung_X, lung_y, split_rule):
tree = RangerTreeSurvival(split_rule=split_rule)
assert tree.criterion == split_rule
if split_rule not in [
"logrank", "extratrees", "C", "C_ignore_ties", "maxstat"
]:
with pytest.raises(ValueError):
tree.fit(lung_X, lung_y)
return
tree.fit(lung_X, lung_y)
if split_rule == "logrank":
assert tree.split_rule_ == 1
elif split_rule == "extratrees":
assert tree.split_rule_ == 5
elif split_rule == "C":
assert tree.split_rule_ == 2
elif split_rule == "C_ignore_ties":
assert tree.split_rule_ == 3
elif split_rule == "maxstat":
assert tree.split_rule_ == 4
if split_rule != "extratrees":
tree = RangerTreeSurvival(split_rule=split_rule,
num_random_splits=2)
with pytest.raises(ValueError):
tree.fit(lung_X, lung_y)
def test_verbose(self, lung_X, lung_y, verbose, capfd):
tree = RangerTreeSurvival(verbose=verbose)
tree.fit(lung_X, lung_y)
captured = capfd.readouterr()
if verbose:
assert len(captured.out) > 0
else:
assert len(captured.out) == 0
def test_sample_fraction_replace(self, lung_X, lung_y, replace):
tree = RangerTreeSurvival(replace=replace)
tree.fit(lung_X, lung_y)
if replace:
assert tree.sample_fraction_ == [1.0]
else:
assert tree.sample_fraction_ == [0.632]
def test_serialize(self, lung_X, lung_y):
tf = tempfile.TemporaryFile()
tree = RangerTreeSurvival()
tree.fit(lung_X, lung_y)
pickle.dump(tree, tf)
tf.seek(0)
new_tree = pickle.load(tf)
pred = new_tree.predict(lung_X)
assert len(pred) == lung_X.shape[0]
def test_sample_fraction(self, lung_X, lung_y):
tree = RangerTreeSurvival(sample_fraction=0.69)
tree.fit(lung_X, lung_y)
assert tree.sample_fraction_ == [0.69]
# test with single record
lung_X_record = lung_X.values[0:1, :]
pred = tree.predict(lung_X_record)
assert len(pred) == 1
def test_fit(self, lung_X, lung_y):
tree = RangerTreeSurvival()
with pytest.raises(NotFittedError):
check_is_fitted(tree)
tree.fit(lung_X, lung_y)
check_is_fitted(tree)
assert hasattr(tree, "event_times_")
assert hasattr(tree, "cumulative_hazard_function_")
assert hasattr(tree, "ranger_forest_")
assert hasattr(tree, "n_features_in_")
def test_sample_weight(self, lung_X, lung_y):
forest_w = RangerTreeSurvival()
forest_w.fit(lung_X, lung_y, sample_weight=[1] * len(lung_y))
tree = RangerTreeSurvival()
tree.fit(lung_X, lung_y)
pred_w = forest_w.predict(lung_X)
pred = tree.predict(lung_X)
np.testing.assert_array_equal(pred.reshape(-1, 1),
pred_w.reshape(-1, 1))
def test_tree_interface(self, lung_X, lung_y):
tree = RangerTreeSurvival()
tree.fit(lung_X, lung_y)
# access attributes the way we would expect to in sklearn
tree_ = tree.tree_
children_left = tree_.children_left
children_right = tree_.children_right
feature = tree_.feature
threshold = tree_.threshold
max_depth = tree_.max_depth
n_node_samples = tree_.n_node_samples
weighted_n_node_samples = tree_.weighted_n_node_samples
node_count = tree_.node_count
capacity = tree_.capacity
n_outputs = tree_.n_outputs
n_classes = tree_.n_classes
def get_estimator(self, idx):
"""Extract a single estimator tree from the forest.
:param int idx: The index of the tree to extract.
"""
check_is_fitted(self)
if not self.enable_tree_details:
raise ValueError(
"enable_tree_details must be True prior to training")
return RangerTreeSurvival.from_forest(self, idx=idx)
def test_importance(self, lung_X, lung_y, importance,
scale_permutation_importance, local_importance):
tree = RangerTreeSurvival(
importance=importance,
scale_permutation_importance=scale_permutation_importance,
local_importance=local_importance,
)
if importance not in [
"none", "impurity", "impurity_corrected", "permutation"
]:
with pytest.raises(ValueError):
tree.fit(lung_X, lung_y)
return
tree.fit(lung_X, lung_y)
if importance == "none":
assert tree.importance_mode_ == 0
elif importance == "impurity":
assert tree.importance_mode_ == 1
elif importance == "impurity_corrected":
assert tree.importance_mode_ == 5
elif importance == "permutation":
if local_importance:
assert tree.importance_mode_ == 6
elif scale_permutation_importance:
assert tree.importance_mode_ == 2
else:
assert tree.importance_mode_ == 3
def estimators_(self):
try:
check_is_fitted(self)
except NotFittedError:
raise AttributeError(
f"{self.__class__.__name__} object has no attribute 'estimators_'"
) from None
if not self.enable_tree_details:
raise ValueError(
"enable_tree_details must be True prior to training")
return [
RangerTreeSurvival.from_forest(self, idx=idx)
for idx in range(self.n_estimators)
]
def test_mtry(self, lung_X, lung_y, mtry):
tree = RangerTreeSurvival(mtry=mtry)
if callable(mtry) and mtry(5) > 5:
with pytest.raises(ValueError):
tree.fit(lung_X, lung_y)
return
elif not callable(mtry) and (mtry < 0 or mtry > lung_X.shape[0]):
with pytest.raises(ValueError):
tree.fit(lung_X, lung_y)
return
tree.fit(lung_X, lung_y)
if callable(mtry):
assert tree.mtry_ == mtry(lung_X.shape[1])
else:
assert tree.mtry_ == mtry
def test_predict(self, lung_X, lung_y):
tree = RangerTreeSurvival()
tree.fit(lung_X, lung_y)
pred = tree.predict(lung_X)
assert len(pred) == lung_X.shape[0]
# test with single record
lung_X_record = lung_X.values[0:1, :]
pred = tree.predict(lung_X_record)
assert len(pred) == 1
def test_categorical_features(self, lung_X, lung_y,
respect_categorical_features):
# add a categorical feature
categorical_col = np.atleast_2d(
np.array([random.choice([0, 1]) for _ in range(lung_X.shape[0])]))
lung_X_c = np.hstack((lung_X, categorical_col.transpose()))
categorical_features = [lung_X.shape[1]]
tree = RangerTreeSurvival(
respect_categorical_features=respect_categorical_features, )
if respect_categorical_features not in [
"partition", "ignore", "order"
]:
with pytest.raises(ValueError):
tree.fit(lung_X_c,
lung_y,
categorical_features=categorical_features)
return
tree.fit(lung_X_c, lung_y, categorical_features=categorical_features)
tree.predict(lung_X_c)
def test_get_depth(self, lung_X, lung_y):
tree = RangerTreeSurvival()
tree.fit(lung_X, lung_y)
depth = tree.get_depth()
assert isinstance(depth, int)
assert depth > 0
def test_init(self):
_ = RangerTreeSurvival()
def test_split_select_weights(self, lung_X, lung_y):
n_trees = 1
weights = [0.1] * lung_X.shape[1]
tree = RangerTreeSurvival()
tree.fit(lung_X, lung_y, split_select_weights=weights)
weights = [0.1] * (lung_X.shape[1] - 1)
tree = RangerTreeSurvival()
with pytest.raises(RuntimeError):
tree.fit(lung_X, lung_y, split_select_weights=weights)
weights = [[0.1] * (lung_X.shape[1])] * n_trees
tree = RangerTreeSurvival()
tree.fit(lung_X, lung_y, split_select_weights=weights)
weights = [[0.1] * (lung_X.shape[1])] * (n_trees + 1)
tree = RangerTreeSurvival()
with pytest.raises(RuntimeError):
tree.fit(lung_X, lung_y, split_select_weights=weights)
def test_clone(self, lung_X, lung_y):
tree = RangerTreeSurvival()
tree.fit(lung_X, lung_y)
clone(tree)
def test_regularization(self, lung_X, lung_y):
tree = RangerTreeSurvival()
tree.fit(lung_X, lung_y)
assert tree.regularization_factor_ == []
assert not tree.use_regularization_factor_
# vector must be between 0 and 1 and length matching feature num
for r in [[1.1], [-0.1], [1, 1]]:
tree = RangerTreeSurvival(regularization_factor=r)
with pytest.raises(ValueError):
tree.fit(lung_X, lung_y)
# vector of ones isn't applied
tree = RangerTreeSurvival(regularization_factor=[1] * lung_X.shape[1])
tree.fit(lung_X, lung_y)
assert tree.regularization_factor_ == []
assert not tree.use_regularization_factor_
# regularization vector is used
reg = [0.5]
tree = RangerTreeSurvival(regularization_factor=reg, )
tree.fit(lung_X, lung_y)
assert tree.regularization_factor_ == reg
assert tree.use_regularization_factor_
def test_predict_survival_function(self, lung_X, lung_y):
tree = RangerTreeSurvival()
tree.fit(lung_X, lung_y)
pred = tree.predict_survival_function(lung_X)
assert len(pred) == lung_X.shape[0]
def test_always_split_features(self, lung_X, lung_y):
tree = RangerTreeSurvival()
tree.fit(lung_X, lung_y, always_split_features=[0])
# feature 0 is in every tree split
for tree in tree.ranger_forest_["forest"]["split_var_ids"]:
assert 0 in tree
def test_decision_path(self, lung_X, lung_y):
tree = RangerTreeSurvival()
tree.fit(lung_X, lung_y)
paths = tree.decision_path(lung_X)
assert isinstance(paths, csr_matrix)
assert paths.shape[0] == len(lung_X)
def test_get_tags(self):
tree = RangerTreeSurvival()
tags = tree._get_tags()
assert tags["requires_y"]
def test_get_n_leaves(self, lung_X, lung_y):
tree = RangerTreeSurvival()
tree.fit(lung_X, lung_y)
leaves = tree.get_n_leaves()
assert isinstance(leaves, int)
assert np.all(leaves > 0)
def test_inbag(self, lung_X, lung_y):
inbag = [[1, 2, 3]]
tree = RangerTreeSurvival(inbag=inbag)
tree.fit(lung_X, lung_y)
# can't use inbag with sample weight
tree = RangerTreeSurvival(inbag=inbag)
with pytest.raises(ValueError):
tree.fit(lung_X, lung_y, sample_weight=[1] * len(lung_y))
# can't use class sampling and inbag
tree = RangerTreeSurvival(inbag=inbag, sample_fraction=[1, 1])
with pytest.raises(ValueError):
tree.fit(lung_X, lung_y)