def test_survdiff_entry_1():
# entry times = 0 is equivalent to no entry times
ti = np.r_[1, 3, 4, 2, 5, 4, 6, 7, 5, 9]
st = np.r_[1, 1, 0, 1, 1, 0, 1, 1, 0, 0]
gr = np.r_[0, 0, 0, 0, 0, 1, 1, 1, 1, 1]
entry = np.r_[0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
z1, p1 = survdiff(ti, st, gr, entry=entry)
z2, p2 = survdiff(ti, st, gr)
assert_allclose(z1, z2)
assert_allclose(p1, p2)
def test_survdiff_entry_1():
# entry times = 0 is equivalent to no entry times
ti = np.r_[1, 3, 4, 2, 5, 4, 6, 7, 5, 9]
st = np.r_[1, 1, 0, 1, 1, 0, 1, 1, 0, 0]
gr = np.r_[0, 0, 0, 0, 0, 1, 1, 1, 1, 1]
entry = np.r_[0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
z1, p1 = survdiff(ti, st, gr, entry=entry)
z2, p2 = survdiff(ti, st, gr)
assert_allclose(z1, z2)
assert_allclose(p1, p2)
def test_survdiff_basic():
# Constants taken from R, code above
ti = np.concatenate((ti1, ti2))
st = np.concatenate((st1, st2))
groups = np.ones(len(ti))
groups[0:len(ti1)] = 0
z, p = survdiff(ti, st, groups)
assert_allclose(z, 2.14673, atol=1e-4, rtol=1e-4)
assert_allclose(p, 0.14287, atol=1e-4, rtol=1e-4)
def test_survdiff_basic():
# Constants taken from R, code above
ti = np.concatenate((ti1, ti2))
st = np.concatenate((st1, st2))
groups = np.ones(len(ti))
groups[0:len(ti1)] = 0
z, p = survdiff(ti, st, groups)
assert_allclose(z, 2.14673, atol=1e-4, rtol=1e-4)
assert_allclose(p, 0.14287, atol=1e-4, rtol=1e-4)
def test_survdiff_entry_3():
# Tests against Stata:
#
# stset time, failure(status) entry(entry)
# sts test group, logrank
ti = np.r_[2, 1, 5, 8, 7, 8, 8, 9, 4, 9]
st = np.r_[1, 1, 1, 1, 1, 0, 1, 0, 0, 0]
gr = np.r_[0, 0, 0, 0, 0, 1, 1, 1, 1, 1]
entry = np.r_[1, 1, 2, 2, 3, 3, 2, 1, 2, 0]
# Check with no entry times
z, p = survdiff(ti, st, gr)
assert_allclose(z, 6.9543024)
assert_allclose(p, 0.008361789)
# Check with entry times
z, p = survdiff(ti, st, gr, entry=entry)
assert_allclose(z, 6.75082959)
assert_allclose(p, 0.00937041)
def test_survdiff_entry_2():
# Tests against Stata:
#
# stset time, failure(status) entry(entry)
# sts test group, logrank
ti = np.r_[5, 3, 4, 2, 5, 4, 6, 7, 5, 9]
st = np.r_[1, 1, 0, 1, 1, 0, 1, 1, 0, 0]
gr = np.r_[0, 0, 0, 0, 0, 1, 1, 1, 1, 1]
entry = np.r_[1, 2, 2, 1, 3, 3, 5, 4, 2, 5]
# Check with no entry times
z, p = survdiff(ti, st, gr)
assert_allclose(z, 6.694424)
assert_allclose(p, 0.00967149)
# Check with entry times
z, p = survdiff(ti, st, gr, entry=entry)
assert_allclose(z, 3.0)
assert_allclose(p, 0.083264516)
def test_survdiff_entry_3():
# Tests against Stata:
#
# stset time, failure(status) entry(entry)
# sts test group, logrank
ti = np.r_[2, 1, 5, 8, 7, 8, 8, 9, 4, 9]
st = np.r_[1, 1, 1, 1, 1, 0, 1, 0, 0, 0]
gr = np.r_[0, 0, 0, 0, 0, 1, 1, 1, 1, 1]
entry = np.r_[1, 1, 2, 2, 3, 3, 2, 1, 2, 0]
# Check with no entry times
z, p = survdiff(ti, st, gr)
assert_allclose(z, 6.9543024)
assert_allclose(p, 0.008361789)
# Check with entry times
z, p = survdiff(ti, st, gr, entry=entry)
assert_allclose(z, 6.75082959)
assert_allclose(p, 0.00937041)
def test_survdiff_entry_2():
# Tests against Stata:
#
# stset time, failure(status) entry(entry)
# sts test group, logrank
ti = np.r_[5, 3, 4, 2, 5, 4, 6, 7, 5, 9]
st = np.r_[1, 1, 0, 1, 1, 0, 1, 1, 0, 0]
gr = np.r_[0, 0, 0, 0, 0, 1, 1, 1, 1, 1]
entry = np.r_[1, 2, 2, 1, 3, 3, 5, 4, 2, 5]
# Check with no entry times
z, p = survdiff(ti, st, gr)
assert_allclose(z, 6.694424)
assert_allclose(p, 0.00967149)
# Check with entry times
z, p = survdiff(ti, st, gr, entry=entry)
assert_allclose(z, 3.0)
assert_allclose(p, 0.083264516)
def test_survdiff():
# Results come from R survival and survMisc packages (survMisc is
# used for non G-rho family tests but does not seem to support
# stratification)
full_df = bmt.copy()
df = bmt[bmt.Group != "ALL"].copy()
# Not stratified
stat, p = survdiff(df["T"], df.Status, df.Group)
assert_allclose(stat, 13.44556, atol=1e-4, rtol=1e-4)
stat, p = survdiff(df["T"], df.Status, df.Group, weight_type="gb")
assert_allclose(stat, 15.38787, atol=1e-4, rtol=1e-4)
stat, p = survdiff(df["T"], df.Status, df.Group, weight_type="tw")
assert_allclose(stat, 14.98382, atol=1e-4, rtol=1e-4)
stat, p = survdiff(df["T"],
df.Status,
df.Group,
weight_type="fh",
fh_p=0.5)
assert_allclose(stat, 14.46866, atol=1e-4, rtol=1e-4)
stat, p = survdiff(df["T"], df.Status, df.Group, weight_type="fh", fh_p=1)
assert_allclose(stat, 14.84500, atol=1e-4, rtol=1e-4)
# Not stratified, >2 groups
stat, p = survdiff(full_df["T"],
full_df.Status,
full_df.Group,
weight_type="fh",
fh_p=1)
assert_allclose(stat, 15.67247, atol=1e-4, rtol=1e-4)
# 5 strata
strata = np.arange(df.shape[0]) % 5
df["strata"] = strata
stat, p = survdiff(df["T"], df.Status, df.Group, strata=df.strata)
assert_allclose(stat, 11.97799, atol=1e-4, rtol=1e-4)
stat, p = survdiff(df["T"],
df.Status,
df.Group,
strata=df.strata,
weight_type="fh",
fh_p=0.5)
assert_allclose(stat, 12.6257, atol=1e-4, rtol=1e-4)
stat, p = survdiff(df["T"],
df.Status,
df.Group,
strata=df.strata,
weight_type="fh",
fh_p=1)
assert_allclose(stat, 12.73565, atol=1e-4, rtol=1e-4)
# 5 strata, >2 groups
full_strata = np.arange(full_df.shape[0]) % 5
full_df["strata"] = full_strata
stat, p = survdiff(full_df["T"],
full_df.Status,
full_df.Group,
strata=full_df.strata,
weight_type="fh",
fh_p=0.5)
assert_allclose(stat, 13.56793, atol=1e-4, rtol=1e-4)
# 8 strata
df["strata"] = np.arange(df.shape[0]) % 8
stat, p = survdiff(df["T"], df.Status, df.Group, strata=df.strata)
assert_allclose(stat, 12.12631, atol=1e-4, rtol=1e-4)
stat, p = survdiff(df["T"],
df.Status,
df.Group,
strata=df.strata,
weight_type="fh",
fh_p=0.5)
assert_allclose(stat, 12.9633, atol=1e-4, rtol=1e-4)
stat, p = survdiff(df["T"],
df.Status,
df.Group,
strata=df.strata,
weight_type="fh",
fh_p=1)
assert_allclose(stat, 13.35259, atol=1e-4, rtol=1e-4)
def test_survdiff():
# Results come from R survival and survMisc packages (survMisc is
# used for non G-rho family tests but does not seem to support
# stratification)
df = bmt[bmt.Group != "ALL"].copy()
# Not stratified
stat, p = survdiff(df["T"], df.Status, df.Group)
assert_allclose(stat, 13.44556, atol=1e-4, rtol=1e-4)
stat, p = survdiff(df["T"], df.Status, df.Group, weight_type="gb")
assert_allclose(stat, 15.38787, atol=1e-4, rtol=1e-4)
stat, p = survdiff(df["T"], df.Status, df.Group, weight_type="tw")
assert_allclose(stat, 14.98382, atol=1e-4, rtol=1e-4)
stat, p = survdiff(df["T"], df.Status, df.Group, weight_type="fh",
fh_p=0.5)
assert_allclose(stat, 14.46866, atol=1e-4, rtol=1e-4)
stat, p = survdiff(df["T"], df.Status, df.Group, weight_type="fh",
fh_p=1)
assert_allclose(stat, 14.84500, atol=1e-4, rtol=1e-4)
# 5 strata
strata = np.arange(df.shape[0]) % 5
df["strata"] = strata
stat, p = survdiff(df["T"], df.Status, df.Group, strata=df.strata)
assert_allclose(stat, 11.97799, atol=1e-4, rtol=1e-4)
stat, p = survdiff(df["T"], df.Status, df.Group, strata=df.strata,
weight_type="fh", fh_p=0.5)
assert_allclose(stat, 12.6257, atol=1e-4, rtol=1e-4)
stat, p = survdiff(df["T"], df.Status, df.Group, strata=df.strata,
weight_type="fh", fh_p=1)
assert_allclose(stat, 12.73565, atol=1e-4, rtol=1e-4)
# 8 strata
df["strata"] = np.arange(df.shape[0]) % 8
stat, p = survdiff(df["T"], df.Status, df.Group, strata=df.strata)
assert_allclose(stat, 12.12631, atol=1e-4, rtol=1e-4)
stat, p = survdiff(df["T"], df.Status, df.Group, strata=df.strata,
weight_type="fh", fh_p=0.5)
assert_allclose(stat, 12.9633, atol=1e-4, rtol=1e-4)
stat, p = survdiff(df["T"], df.Status, df.Group, strata=df.strata,
weight_type="fh", fh_p=1)
assert_allclose(stat, 13.35259, atol=1e-4, rtol=1e-4)
