def setup(self):
"""Data from table 11.3 in Legendre & Legendre 1998."""
Y = np.loadtxt(get_data_path('example2_Y'))
X = np.loadtxt(get_data_path('example2_X'))
self.ordination = RDA(Y, X, [
'Site0', 'Site1', 'Site2', 'Site3', 'Site4', 'Site5', 'Site6',
'Site7', 'Site8', 'Site9'
], [
'Species0', 'Species1', 'Species2', 'Species3', 'Species4',
'Species5'
])
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()
