def setup(self):
"""Data from table 9.11 in Legendre & Legendre 1998."""
self.X = np.loadtxt(get_data_path('L&L_CA_data'))
self.ordination = CA(self.X, ['Site1', 'Site2', 'Site3'],
['Species1', 'Species2', 'Species3'])
def test_negative(self):
X = np.array([[1, 2], [-0.1, -2]])
with npt.assert_raises(ValueError):
CA(X, None, None)
import os
import numpy as np
from skbio.math.stats.ordination import CA, RDA, CCA
path = os.path.dirname(os.path.abspath(__file__))
def get_path(fn):
return os.path.join(path, os.pardir, 'math', 'stats', 'ordination',
'test', 'data', fn)
X = np.loadtxt(get_path('L&L_CA_data'))
ordint = CA(X)
ordint.biplot(1)
ordint.biplot(2)
Y = np.loadtxt(get_path('example2_Y'))
X = np.loadtxt(get_path('example2_X')).reshape(-1, 4, order='F')
ordint = RDA(Y, X)
ordint.biplot()
Y = np.loadtxt(get_path('example3_Y'))
X = np.loadtxt(get_path('example3_X')).reshape(-1, 4, order='F')
ordint = CCA(Y, X)
ordint.biplot()
