patsy/patsy/test_build.py at master · Python-Repository-Hub/patsy · GitHub

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# This file is part of Patsy

# See file LICENSE.txt for license information.

# There are a number of unit tests in build.py, but this file contains more

# thorough tests of the overall design matrix building system. (These are

# still not exhaustive end-to-end tests, though -- for that see

# test_highlevel.py.)

from __future__ import print_function

import six

import numpy as np

import pytest

from patsy import PatsyError

from patsy.util import (atleast_2d_column_default,

have_pandas, have_pandas_categorical)

from patsy.desc import Term, INTERCEPT

from patsy.build import *

from patsy.categorical import C

from patsy.user_util import balanced, LookupFactor

from patsy.design_info import DesignMatrix, DesignInfo

if have_pandas:

import pandas

def assert_full_rank(m):

m = atleast_2d_column_default(m)

if m.shape[1] == 0:

return True

u, s, v = np.linalg.svd(m)

rank = np.sum(s > 1e-10)

assert rank == m.shape[1]

def test_assert_full_rank():

assert_full_rank(np.eye(10))

assert_full_rank([[1, 0], [1, 0], [1, 0], [1, 1]])

pytest.raises(AssertionError,

assert_full_rank, [[1, 0], [2, 0]])

pytest.raises(AssertionError,

assert_full_rank, [[1, 2], [2, 4]])

pytest.raises(AssertionError,

assert_full_rank, [[1, 2, 3], [1, 10, 100]])

# col1 + col2 = col3

pytest.raises(AssertionError,

assert_full_rank, [[1, 2, 3], [1, 5, 6], [1, 6, 7]])

def make_termlist(*entries):

terms = []

for entry in entries:

terms.append(Term([LookupFactor(name) for name in entry]))

return terms

def check_design_matrix(mm, expected_rank, termlist, column_names=None):

assert_full_rank(mm)

assert set(mm.design_info.terms) == set(termlist)

if column_names is not None:

assert mm.design_info.column_names == column_names

assert mm.ndim == 2

assert mm.shape[1] == expected_rank

def make_matrix(data, expected_rank, entries, column_names=None):

termlist = make_termlist(*entries)

def iter_maker():

yield data

design_infos = design_matrix_builders([termlist], iter_maker, eval_env=0)

matrices = build_design_matrices(design_infos, data)

matrix = matrices[0]

assert (design_infos[0].term_slices

== matrix.design_info.term_slices)

assert (design_infos[0].column_names

== matrix.design_info.column_names)

assert matrix.design_info is design_infos[0]

check_design_matrix(matrix, expected_rank, termlist,

column_names=column_names)

return matrix

def test_simple():

data = balanced(a=2, b=2)

x1 = data["x1"] = np.linspace(0, 1, len(data["a"]))

x2 = data["x2"] = data["x1"] ** 2

m = make_matrix(data, 2, [["a"]], column_names=["a[a1]", "a[a2]"])

assert np.allclose(m, [[1, 0], [1, 0], [0, 1], [0, 1]])

m = make_matrix(data, 2, [[], ["a"]], column_names=["Intercept", "a[T.a2]"])

assert np.allclose(m, [[1, 0], [1, 0], [1, 1], [1, 1]])

m = make_matrix(data, 4, [["a", "b"]],

column_names=["a[a1]:b[b1]", "a[a2]:b[b1]",

"a[a1]:b[b2]", "a[a2]:b[b2]"])

assert np.allclose(m, [[1, 0, 0, 0],

[0, 0, 1, 0],

[0, 1, 0, 0],

[0, 0, 0, 1]])

m = make_matrix(data, 4, [[], ["a"], ["b"], ["a", "b"]],

column_names=["Intercept", "a[T.a2]",

"b[T.b2]", "a[T.a2]:b[T.b2]"])

assert np.allclose(m, [[1, 0, 0, 0],

[1, 0, 1, 0],

[1, 1, 0, 0],

[1, 1, 1, 1]])

m = make_matrix(data, 4, [[], ["b"], ["a"], ["b", "a"]],

column_names=["Intercept", "b[T.b2]",

"a[T.a2]", "b[T.b2]:a[T.a2]"])

assert np.allclose(m, [[1, 0, 0, 0],

[1, 1, 0, 0],

[1, 0, 1, 0],

[1, 1, 1, 1]])

m = make_matrix(data, 4, [["a"], ["x1"], ["a", "x1"]],

column_names=["a[a1]", "a[a2]", "x1", "a[T.a2]:x1"])

assert np.allclose(m, [[1, 0, x1[0], 0],

[1, 0, x1[1], 0],

[0, 1, x1[2], x1[2]],

[0, 1, x1[3], x1[3]]])

m = make_matrix(data, 3, [["x1"], ["x2"], ["x2", "x1"]],

column_names=["x1", "x2", "x2:x1"])

assert np.allclose(m, np.column_stack((x1, x2, x1 * x2)))

def test_R_bugs():

data = balanced(a=2, b=2, c=2)

data["x"] = np.linspace(0, 1, len(data["a"]))

# For "1 + a:b", R produces a design matrix with too many columns (5

# instead of 4), because it can't tell that there is a redundancy between

# the two terms.

make_matrix(data, 4, [[], ["a", "b"]])

# For "0 + a:x + a:b", R produces a design matrix with too few columns (4

# instead of 6), because it thinks that there is a redundancy which

# doesn't exist.

make_matrix(data, 6, [["a", "x"], ["a", "b"]])

# This can be compared with "0 + a:c + a:b", where the redundancy does

# exist. Confusingly, adding another categorical factor increases the

# baseline dimensionality to 8, and then the redundancy reduces it to 6

# again, so the result is the same as before but for different reasons. (R

# does get this one right, but we might as well test it.)

make_matrix(data, 6, [["a", "c"], ["a", "b"]])

def test_redundancy_thoroughly():

# To make sure there aren't any lurking bugs analogous to the ones that R

# has (see above), we check that we get the correct matrix rank for every

# possible combination of 2 categorical and 2 numerical factors.

data = balanced(a=2, b=2, repeat=5)

data["x1"] = np.linspace(0, 1, len(data["a"]))

data["x2"] = data["x1"] ** 2

def all_subsets(l):

if not l:

yield tuple()

else:

obj = l[0]

for subset in all_subsets(l[1:]):

yield tuple(sorted(subset))

yield tuple(sorted((obj,) + subset))

all_terms = list(all_subsets(("a", "b", "x1", "x2")))

all_termlist_templates = list(all_subsets(all_terms))

print(len(all_termlist_templates))

# eliminate some of the symmetric versions to speed things up

redundant = [[("b",), ("a",)],

[("x2",), ("x1",)],

[("b", "x2"), ("a", "x1")],

[("a", "b", "x2"), ("a", "b", "x1")],

[("b", "x1", "x2"), ("a", "x1", "x2")]]

count = 0

import time

start = time.time()

for termlist_template in all_termlist_templates:

termlist_set = set(termlist_template)

for dispreferred, preferred in redundant:

if dispreferred in termlist_set and preferred not in termlist_set:

break

else:

expanded_terms = set()

for term_template in termlist_template:

numeric = tuple([t for t in term_template if t.startswith("x")])

rest = [t for t in term_template if not t.startswith("x")]

for subset_rest in all_subsets(rest):

expanded_terms.add(frozenset(subset_rest + numeric))

# Because our categorical variables have 2 levels, each expanded

# term corresponds to 1 unique dimension of variation

expected_rank = len(expanded_terms)

if termlist_template in [(), ((),)]:

# No data dependence, should fail

pytest.raises(PatsyError,

make_matrix,

data, expected_rank, termlist_template)

else:

make_matrix(data, expected_rank, termlist_template)

count += 1

if count % 100 == 0:

print("Completed:", count)

print("Took %0.2f seconds" % (time.time() - start,))

test_redundancy_thoroughly.slow = 1

def test_data_types():

basic_dict = {"a": ["a1", "a2", "a1", "a2"],

"x": [1, 2, 3, 4]}

# On Python 2, this is identical to basic_dict:

basic_dict_bytes = dict(basic_dict)

basic_dict_bytes["a"] = [s.encode("ascii") for s in basic_dict_bytes["a"]]

# On Python 3, this is identical to basic_dict:

basic_dict_unicode = {"a": ["a1", "a2", "a1", "a2"],

"x": [1, 2, 3, 4]}

basic_dict_unicode = dict(basic_dict)

basic_dict_unicode["a"] = [six.text_type(s) for s in basic_dict_unicode["a"]]

structured_array_bytes = np.array(list(zip(basic_dict["a"],

basic_dict["x"])),

dtype=[("a", "S2"), ("x", int)])

structured_array_unicode = np.array(list(zip(basic_dict["a"],

basic_dict["x"])),

dtype=[("a", "U2"), ("x", int)])

recarray_bytes = structured_array_bytes.view(np.recarray)

recarray_unicode = structured_array_unicode.view(np.recarray)

datas = [basic_dict, structured_array_bytes, structured_array_unicode,

recarray_bytes, recarray_unicode]

if have_pandas:

df_bytes = pandas.DataFrame(basic_dict_bytes)

datas.append(df_bytes)

df_unicode = pandas.DataFrame(basic_dict_unicode)

datas.append(df_unicode)

for data in datas:

m = make_matrix(data, 4, [["a"], ["a", "x"]],

column_names=["a[a1]", "a[a2]", "a[a1]:x", "a[a2]:x"])

assert np.allclose(m, [[1, 0, 1, 0],

[0, 1, 0, 2],

[1, 0, 3, 0],

[0, 1, 0, 4]])

def test_build_design_matrices_dtype():

data = {"x": [1, 2, 3]}

def iter_maker():

yield data

builder = design_matrix_builders([make_termlist("x")], iter_maker, 0)[0]

mat = build_design_matrices([builder], data)[0]

assert mat.dtype == np.dtype(np.float64)

mat = build_design_matrices([builder], data, dtype=np.float32)[0]

assert mat.dtype == np.dtype(np.float32)

if hasattr(np, "float128"):

mat = build_design_matrices([builder], data, dtype=np.float128)[0]

assert mat.dtype == np.dtype(np.float128)

def test_return_type():

data = {"x": [1, 2, 3]}

def iter_maker():

yield data

builder = design_matrix_builders([make_termlist("x")], iter_maker, 0)[0]

# Check explicitly passing return_type="matrix" works

mat = build_design_matrices([builder], data, return_type="matrix")[0]

assert isinstance(mat, DesignMatrix)

# Check that nonsense is detected

pytest.raises(PatsyError,

build_design_matrices, [builder], data,

return_type="asdfsadf")

def test_NA_action():

initial_data = {"x": [1, 2, 3], "c": ["c1", "c2", "c1"]}

def iter_maker():

yield initial_data

builder = design_matrix_builders([make_termlist("x", "c")], iter_maker, 0)[0]

# By default drops rows containing either NaN or None

mat = build_design_matrices([builder],

{"x": [10.0, np.nan, 20.0],

"c": np.asarray(["c1", "c2", None],

dtype=object)})[0]

assert mat.shape == (1, 3)

assert np.array_equal(mat, [[1.0, 0.0, 10.0]])

# NA_action="a string" also accepted:

mat = build_design_matrices([builder],

{"x": [10.0, np.nan, 20.0],

"c": np.asarray(["c1", "c2", None],

dtype=object)},

NA_action="drop")[0]

assert mat.shape == (1, 3)

assert np.array_equal(mat, [[1.0, 0.0, 10.0]])

# And objects

from patsy.missing import NAAction

# allows NaN's to pass through

NA_action = NAAction(NA_types=[])

mat = build_design_matrices([builder],

{"x": [10.0, np.nan],

"c": np.asarray(["c1", "c2"],

dtype=object)},

NA_action=NA_action)[0]

assert mat.shape == (2, 3)

# According to this (and only this) function, NaN == NaN.

np.testing.assert_array_equal(mat, [[1.0, 0.0, 10.0], [0.0, 1.0, np.nan]])

# NA_action="raise"

pytest.raises(PatsyError,

build_design_matrices,

[builder],

{"x": [10.0, np.nan, 20.0],

"c": np.asarray(["c1", "c2", None],

dtype=object)},

NA_action="raise")

def test_NA_drop_preserves_levels():

# Even if all instances of some level are dropped, we still include it in

# the output matrix (as an all-zeros column)

data = {"x": [1.0, np.nan, 3.0], "c": ["c1", "c2", "c3"]}

def iter_maker():

yield data

design_info = design_matrix_builders([make_termlist("x", "c")], iter_maker, 0)[0]

assert design_info.column_names == ["c[c1]", "c[c2]", "c[c3]", "x"]

mat, = build_design_matrices([design_info], data)

assert mat.shape == (2, 4)

assert np.array_equal(mat, [[1.0, 0.0, 0.0, 1.0],

[0.0, 0.0, 1.0, 3.0]])

def test_return_type_pandas():

if not have_pandas:

return

data = pandas.DataFrame({"x": [1, 2, 3],

"y": [4, 5, 6],

"a": ["a1", "a2", "a1"]},

index=[10, 20, 30])

def iter_maker():

yield data

int_builder, = design_matrix_builders([make_termlist([])], iter_maker, 0)

(y_builder, x_builder) = design_matrix_builders([make_termlist("y"),

make_termlist("x")],

iter_maker,

eval_env=0)

(x_a_builder,) = design_matrix_builders([make_termlist("x", "a")],

iter_maker,

eval_env=0)

(x_y_builder,) = design_matrix_builders([make_termlist("x", "y")],

iter_maker,

eval_env=0)

# Index compatibility is always checked for pandas input, regardless of

# whether we're producing pandas output

pytest.raises(PatsyError,

build_design_matrices,

[x_a_builder], {"x": data["x"], "a": data["a"][::-1]})

pytest.raises(PatsyError,

build_design_matrices,

[y_builder, x_builder],

{"x": data["x"], "y": data["y"][::-1]})

# And we also check consistency between data.index and value indexes

# Creating a mismatch between these is a bit tricky. We want a data object

# such that isinstance(data, DataFrame), but data["x"].index !=

# data.index.

class CheatingDataFrame(pandas.DataFrame):

def __getitem__(self, key):

if key == "x":

return pandas.DataFrame.__getitem__(self, key)[::-1]

else:

return pandas.DataFrame.__getitem__(self, key)

pytest.raises(PatsyError,

build_design_matrices,

[x_builder],

CheatingDataFrame(data))

# A mix of pandas input and unindexed input is fine

(mat,) = build_design_matrices([x_y_builder],

{"x": data["x"], "y": [40, 50, 60]})

assert np.allclose(mat, [[1, 40], [2, 50], [3, 60]])

# with return_type="dataframe", we get out DataFrames with nice indices

# and nice column names and design_info

y_df, x_df = build_design_matrices([y_builder, x_builder], data,

return_type="dataframe")

assert isinstance(y_df, pandas.DataFrame)

assert isinstance(x_df, pandas.DataFrame)

assert np.array_equal(y_df, [[4], [5], [6]])

assert np.array_equal(x_df, [[1], [2], [3]])

assert np.array_equal(y_df.index, [10, 20, 30])

assert np.array_equal(x_df.index, [10, 20, 30])

assert np.array_equal(y_df.columns, ["y"])

assert np.array_equal(x_df.columns, ["x"])

assert y_df.design_info.column_names == ["y"]

assert x_df.design_info.column_names == ["x"]

assert y_df.design_info.term_names == ["y"]

assert x_df.design_info.term_names == ["x"]

# Same with mix of pandas and unindexed info, even if in different

# matrices

y_df, x_df = build_design_matrices([y_builder, x_builder],

{"y": [7, 8, 9], "x": data["x"]},

return_type="dataframe")

assert isinstance(y_df, pandas.DataFrame)

assert isinstance(x_df, pandas.DataFrame)

assert np.array_equal(y_df, [[7], [8], [9]])

assert np.array_equal(x_df, [[1], [2], [3]])

assert np.array_equal(y_df.index, [10, 20, 30])

assert np.array_equal(x_df.index, [10, 20, 30])

assert np.array_equal(y_df.columns, ["y"])

assert np.array_equal(x_df.columns, ["x"])

assert y_df.design_info.column_names == ["y"]

assert x_df.design_info.column_names == ["x"]

assert y_df.design_info.term_names == ["y"]

assert x_df.design_info.term_names == ["x"]

# Check categorical works for carrying index too

(x_a_df,) = build_design_matrices([x_a_builder],

{"x": [-1, -2, -3], "a": data["a"]},

return_type="dataframe")

assert isinstance(x_a_df, pandas.DataFrame)

assert np.array_equal(x_a_df, [[1, 0, -1], [0, 1, -2], [1, 0, -3]])

assert np.array_equal(x_a_df.index, [10, 20, 30])

# And if we have no indexed input, then we let pandas make up an index as

# per its usual rules:

(x_y_df,) = build_design_matrices([x_y_builder],

{"y": [7, 8, 9], "x": [10, 11, 12]},

return_type="dataframe")

assert isinstance(x_y_df, pandas.DataFrame)

assert np.array_equal(x_y_df, [[10, 7], [11, 8], [12, 9]])

assert np.array_equal(x_y_df.index, [0, 1, 2])

# If 'data' is a DataFrame, then that suffices, even if no factors are

# available.

(int_df,) = build_design_matrices([int_builder], data,

return_type="dataframe")

assert isinstance(int_df, pandas.DataFrame)

assert np.array_equal(int_df, [[1], [1], [1]])

assert int_df.index.equals(pandas.Index([10, 20, 30]))

import patsy.build

had_pandas = patsy.build.have_pandas

try:

patsy.build.have_pandas = False

# return_type="dataframe" gives a nice error if pandas is not available

pytest.raises(PatsyError,

build_design_matrices,

[x_builder], {"x": [1, 2, 3]}, return_type="dataframe")

finally:

patsy.build.have_pandas = had_pandas

x_df, = build_design_matrices([x_a_builder],

{"x": [1.0, np.nan, 3.0],

"a": np.asarray([None, "a2", "a1"],

dtype=object)},

NA_action="drop",

return_type="dataframe")

assert x_df.index.equals(pandas.Index([2]))

def test_data_mismatch():

test_cases_twoway = [

# Data type mismatch

([1, 2, 3], [True, False, True]),

(C(["a", "b", "c"], levels=["c", "b", "a"]),

C(["a", "b", "c"], levels=["a", "b", "c"])),

# column number mismatches

([[1], [2], [3]], [[1, 1], [2, 2], [3, 3]]),

([[1, 1, 1], [2, 2, 2], [3, 3, 3]], [[1, 1], [2, 2], [3, 3]]),

]

test_cases_oneway = [

([1, 2, 3], ["a", "b", "c"]),

([1, 2, 3], C(["a", "b", "c"])),

([True, False, True], C(["a", "b", "c"])),

([True, False, True], ["a", "b", "c"]),

]

setup_predict_only = [

# This is not an error if both are fed in during make_builders, but it

# is an error to pass one to make_builders and the other to

# make_matrices.

(["a", "b", "c"], ["a", "b", "d"]),

]

termlist = make_termlist(["x"])

def t_incremental(data1, data2):

def iter_maker():

yield {"x": data1}

yield {"x": data2}

try:

builders = design_matrix_builders([termlist], iter_maker, 0)

build_design_matrices(builders, {"x": data1})

build_design_matrices(builders, {"x": data2})

except PatsyError:

pass

else:

raise AssertionError

def t_setup_predict(data1, data2):

def iter_maker():

yield {"x": data1}

builders = design_matrix_builders([termlist], iter_maker, 0)

pytest.raises(PatsyError,

build_design_matrices, builders, {"x": data2})

for (a, b) in test_cases_twoway:

t_incremental(a, b)

t_incremental(b, a)

t_setup_predict(a, b)

t_setup_predict(b, a)

for (a, b) in test_cases_oneway:

t_incremental(a, b)

t_setup_predict(a, b)

for (a, b) in setup_predict_only:

t_setup_predict(a, b)

t_setup_predict(b, a)

pytest.raises(PatsyError,

make_matrix, {"x": [1, 2, 3], "y": [1, 2, 3, 4]},

2, [["x"], ["y"]])

def test_data_independent_builder():

data = {"x": [1, 2, 3]}

def iter_maker():

yield data

# Trying to build a matrix that doesn't depend on the data at all is an

# error, if:

# - the index argument is not given

# - the data is not a DataFrame

# - there are no other matrices

null_builder = design_matrix_builders([make_termlist()], iter_maker, 0)[0]

pytest.raises(PatsyError, build_design_matrices, [null_builder], data)

intercept_builder = design_matrix_builders([make_termlist([])],

iter_maker,

eval_env=0)[0]

pytest.raises(PatsyError, build_design_matrices, [intercept_builder], data)

pytest.raises(PatsyError,

build_design_matrices,

[null_builder, intercept_builder], data)

# If data is a DataFrame, it sets the number of rows.

if have_pandas:

int_m, null_m = build_design_matrices([intercept_builder,

null_builder],

pandas.DataFrame(data))

assert np.allclose(int_m, [[1], [1], [1]])

assert null_m.shape == (3, 0)

# If there are other matrices that do depend on the data, we make the

# data-independent matrices have the same number of rows.

x_termlist = make_termlist(["x"])

builders = design_matrix_builders([x_termlist, make_termlist()],

iter_maker,

eval_env=0)

x_m, null_m = build_design_matrices(builders, data)

assert np.allclose(x_m, [[1], [2], [3]])

assert null_m.shape == (3, 0)

builders = design_matrix_builders([x_termlist, make_termlist([])],

iter_maker,

eval_env=0)

x_m, null_m = build_design_matrices(builders, data)

x_m, intercept_m = build_design_matrices(builders, data)

assert np.allclose(x_m, [[1], [2], [3]])

assert np.allclose(intercept_m, [[1], [1], [1]])

def test_same_factor_in_two_matrices():

data = {"x": [1, 2, 3], "a": ["a1", "a2", "a1"]}

def iter_maker():

yield data

t1 = make_termlist(["x"])

t2 = make_termlist(["x", "a"])

builders = design_matrix_builders([t1, t2], iter_maker, eval_env=0)

m1, m2 = build_design_matrices(builders, data)

check_design_matrix(m1, 1, t1, column_names=["x"])

assert np.allclose(m1, [[1], [2], [3]])

check_design_matrix(m2, 2, t2, column_names=["x:a[a1]", "x:a[a2]"])

assert np.allclose(m2, [[1, 0], [0, 2], [3, 0]])

def test_eval_env_type_builder():

data = {"x": [1, 2, 3]}

def iter_maker():

yield data

pytest.raises(TypeError, design_matrix_builders, [make_termlist("x")], iter_maker, "foo")

def test_categorical():

data_strings = {"a": ["a1", "a2", "a1"]}

data_categ = {"a": C(["a2", "a1", "a2"])}

datas = [data_strings, data_categ]

if have_pandas_categorical:

data_pandas = {"a": pandas.Categorical(["a1", "a2", "a2"])}

datas.append(data_pandas)

def t(data1, data2):

def iter_maker():

yield data1

builders = design_matrix_builders([make_termlist(["a"])],

iter_maker,

eval_env=0)

build_design_matrices(builders, data2)

for data1 in datas:

for data2 in datas:

t(data1, data2)

def test_contrast():

from patsy.contrasts import ContrastMatrix, Sum

values = ["a1", "a3", "a1", "a2"]

# No intercept in model, full-rank coding of 'a'

m = make_matrix({"a": C(values)}, 3, [["a"]],

column_names=["a[a1]", "a[a2]", "a[a3]"])

assert np.allclose(m, [[1, 0, 0],

[0, 0, 1],

[1, 0, 0],

[0, 1, 0]])

for s in (Sum, Sum()):

m = make_matrix({"a": C(values, s)}, 3, [["a"]],

column_names=["a[mean]", "a[S.a1]", "a[S.a2]"])

# Output from R

assert np.allclose(m, [[1, 1, 0],

[1,-1, -1],

[1, 1, 0],

[1, 0, 1]])

m = make_matrix({"a": C(values, Sum(omit=0))}, 3, [["a"]],

column_names=["a[mean]", "a[S.a2]", "a[S.a3]"])

# Output from R

assert np.allclose(m, [[1, -1, -1],

[1, 0, 1],

[1, -1, -1],

[1, 1, 0]])

# Intercept in model, non-full-rank coding of 'a'

m = make_matrix({"a": C(values)}, 3, [[], ["a"]],

column_names=["Intercept", "a[T.a2]", "a[T.a3]"])

assert np.allclose(m, [[1, 0, 0],

[1, 0, 1],

[1, 0, 0],

[1, 1, 0]])

for s in (Sum, Sum()):

m = make_matrix({"a": C(values, s)}, 3, [[], ["a"]],

column_names=["Intercept", "a[S.a1]", "a[S.a2]"])

# Output from R

assert np.allclose(m, [[1, 1, 0],

[1,-1, -1],

[1, 1, 0],

[1, 0, 1]])

m = make_matrix({"a": C(values, Sum(omit=0))}, 3, [[], ["a"]],

column_names=["Intercept", "a[S.a2]", "a[S.a3]"])

# Output from R

assert np.allclose(m, [[1, -1, -1],

[1, 0, 1],

[1, -1, -1],

[1, 1, 0]])

# Weird ad hoc less-than-full-rank coding of 'a'

m = make_matrix({"a": C(values, [[7, 12],

[2, 13],

[8, -1]])},

2, [["a"]],

column_names=["a[custom0]", "a[custom1]"])

assert np.allclose(m, [[7, 12],

[8, -1],

[7, 12],

[2, 13]])

m = make_matrix({"a": C(values, ContrastMatrix([[7, 12],

[2, 13],

[8, -1]],

["[foo]", "[bar]"]))},

2, [["a"]],

column_names=["a[foo]", "a[bar]"])

assert np.allclose(m, [[7, 12],

[8, -1],

[7, 12],

[2, 13]])

def test_DesignInfo_subset():

# For each combination of:

# formula, term names, term objects, mixed term name and term objects

# check that results match subset of full build

# and that removed variables don't hurt

all_data = {"x": [1, 2],

"y": [[3.1, 3.2],

[4.1, 4.2]],

"z": [5, 6]}

all_terms = make_termlist("x", "y", "z")

def iter_maker():

yield all_data

all_builder = design_matrix_builders([all_terms], iter_maker, 0)[0]

full_matrix = build_design_matrices([all_builder], all_data)[0]

def t(which_terms, variables, columns):

sub_design_info = all_builder.subset(which_terms)

sub_data = {}

for variable in variables:

sub_data[variable] = all_data[variable]

sub_matrix = build_design_matrices([sub_design_info], sub_data)[0]

sub_full_matrix = full_matrix[:, columns]

if not isinstance(which_terms, six.string_types):

assert len(which_terms) == len(sub_design_info.terms)

assert np.array_equal(sub_matrix, sub_full_matrix)

t("~ 0 + x + y + z", ["x", "y", "z"], slice(None))

t(["x", "y", "z"], ["x", "y", "z"], slice(None))

# Compatibility: six.PY2 wasn't added until 1.4.0, but six.PY3 exists in

# all versions.

if not six.PY3:

t([unicode("x"), unicode("y"), unicode("z")],

["x", "y", "z"], slice(None))

t(all_terms, ["x", "y", "z"], slice(None))

t([all_terms[0], "y", all_terms[2]], ["x", "y", "z"], slice(None))

t("~ 0 + x + z", ["x", "z"], [0, 3])

t(["x", "z"], ["x", "z"], [0, 3])

# Compatibility: six.PY2 wasn't added until 1.4.0, but six.PY3 exists in

# all versions.

if not six.PY3:

t([unicode("x"), unicode("z")], ["x", "z"], [0, 3])

t([all_terms[0], all_terms[2]], ["x", "z"], [0, 3])

t([all_terms[0], "z"], ["x", "z"], [0, 3])

t("~ 0 + z + x", ["x", "z"], [3, 0])

t(["z", "x"], ["x", "z"], [3, 0])

t([six.text_type("z"), six.text_type("x")], ["x", "z"], [3, 0])

t([all_terms[2], all_terms[0]], ["x", "z"], [3, 0])

t([all_terms[2], "x"], ["x", "z"], [3, 0])

t("~ 0 + y", ["y"], [1, 2])

t(["y"], ["y"], [1, 2])

t([six.text_type("y")], ["y"], [1, 2])

t([all_terms[1]], ["y"], [1, 2])

# Formula can't have a LHS

pytest.raises(PatsyError, all_builder.subset, "a ~ a")

# Term must exist

pytest.raises(KeyError, all_builder.subset, "~ asdf")

pytest.raises(KeyError, all_builder.subset, ["asdf"])

pytest.raises(KeyError,

all_builder.subset, [Term(["asdf"])])

# Also check for a minimal DesignInfo (column names only)

min_di = DesignInfo(["a", "b", "c"])

min_di_subset = min_di.subset(["c", "a"])

assert min_di_subset.column_names == ["c", "a"]

assert min_di_subset.terms is None

patsy/patsy/test_build.py at master · Python-Repository-Hub/patsy · GitHub

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