def test_stratified_table_cube():
# Test that we can pass a rank 3 ndarray or a list of rank 2
# ndarrays to StratifiedTable and get the same results.
tab1 = [[[8, 9], [6, 7]], [[4, 9], [5, 5]], [[8, 8], [9, 11]]]
tab2 = np.asarray(tab1).T
ct1 = ctab.StratifiedTable(tab1)
ct2 = ctab.StratifiedTable(tab2)
assert_allclose(ct1.oddsratio_pooled, ct2.oddsratio_pooled)
assert_allclose(ct1.logodds_pooled, ct2.logodds_pooled)
def test_from_data(self):
np.random.seed(241)
df = pd.DataFrame(index=range(100), columns=("v1", "v2", "strat"))
df["v1"] = np.random.randint(0, 2, 100)
df["v2"] = np.random.randint(0, 2, 100)
df["strat"] = np.kron(np.arange(10), np.ones(10))
tables = []
for k in range(10):
ii = np.arange(10 * k, 10 * (k + 1))
tables.append(pd.crosstab(df.loc[ii, "v1"], df.loc[ii, "v2"]))
rslt1 = ctab.StratifiedTable(tables)
rslt2 = ctab.StratifiedTable.from_data("v1", "v2", "strat", df)
assert_equal(rslt1.summary().as_text(), rslt2.summary().as_text())
def initialize(cls, tables):
cls.rslt = ctab.StratifiedTable(tables)
cls.rslt_0 = ctab.StratifiedTable(tables, shift_zeros=True)
tables_pandas = [pd.DataFrame(x) for x in tables]
cls.rslt_pandas = ctab.StratifiedTable(tables_pandas)
def initialize(cls, tables, use_arr=False):
tables1 = tables if not use_arr else np.dstack(tables)
cls.rslt = ctab.StratifiedTable(tables1)
cls.rslt_0 = ctab.StratifiedTable(tables, shift_zeros=True)
tables_pandas = [pd.DataFrame(x) for x in tables]
cls.rslt_pandas = ctab.StratifiedTable(tables_pandas)
def initialize(self, tables):
self.rslt = ctab.StratifiedTable(tables)
self.rslt_0 = ctab.StratifiedTable(tables, shift_zeros=True)
tables_pandas = [pd.DataFrame(x) for x in tables]
self.rslt_pandas = ctab.StratifiedTable(tables_pandas)
#
if ((matchindex - currRow) == number_of_elements_of_stratified_table):
ctable = np.zeros(shape=(2, 2, sk))
ict = currRow
for k in range(0, sk):
# print("=======================================")
# print("strata :" + str(k+1))
# print("=======================================")
for i in range(0, 2):
for j in range(0, 2):
ctable[i, j, k] = data.iloc[ict, 12]
# print(" c(" + str(i+1) + "," + str(j+1) + "," + str(k+1) + ") = " + str(ctable[i,j,k]), end = '')
ict = ict + 1
# print("\n", end = '')
# print(ctable[:,:,k])
cmh = sm.StratifiedTable(ctable)
t = cmh.test_null_odds()
print(currTemp + " " + currDay + " " + currMapping + " " +
currPosition + "\t" + currRef + "\t" + currAllele + "\t" +
str(t.pvalue) + "\t" + str(t.statistic))
# print(cmh.test_null_odds())
# print(cmh.test_equal_odds())
# print(cmh.summary())
# while loop check
currRow = matchindex
if (currRow < nrow):
currTemp = data.iloc[currRow, 0]
currDay = data.iloc[currRow, 1]
currPop = data.iloc[currRow, 2]
currMapping = data.iloc[currRow, 3]
currPosition = data.iloc[currRow, 4]
