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'
])
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'])
class TestRDAResults(object):
# STATUS: L&L only shows results with scaling 1, and they agree
# with vegan's (module multiplying by a constant). I can also
# compute scaling 2, agreeing with vegan, but there are no written
# results in L&L.
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'
])
def test_scaling1(self):
scores = self.ordination.scores(1)
# Load data as computed with vegan 2.0-8
vegan_species = np.loadtxt(
get_data_path('example2_species_scaling1_from_vegan'))
npt.assert_almost_equal(scores.species, vegan_species, decimal=6)
vegan_site = np.loadtxt(
get_data_path('example2_site_scaling1_from_vegan'))
npt.assert_almost_equal(scores.site, vegan_site, decimal=6)
def test_scaling2(self):
scores = self.ordination.scores(2)
# Load data as computed with vegan 2.0-8
vegan_species = np.loadtxt(
get_data_path('example2_species_scaling2_from_vegan'))
npt.assert_almost_equal(scores.species, vegan_species, decimal=6)
vegan_site = np.loadtxt(
get_data_path('example2_site_scaling2_from_vegan'))
npt.assert_almost_equal(scores.site, vegan_site, decimal=6)
class TestRDAResults(object):
# STATUS: L&L only shows results with scaling 1, and they agree
# with vegan's (module multiplying by a constant). I can also
# compute scaling 2, agreeing with vegan, but there are no written
# results in L&L.
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'])
def test_scaling1(self):
scores = self.ordination.scores(1)
# Load data as computed with vegan 2.0-8
vegan_species = np.loadtxt(get_data_path(
'example2_species_scaling1_from_vegan'))
npt.assert_almost_equal(scores.species, vegan_species, decimal=6)
vegan_site = np.loadtxt(get_data_path(
'example2_site_scaling1_from_vegan'))
npt.assert_almost_equal(scores.site, vegan_site, decimal=6)
def test_scaling2(self):
scores = self.ordination.scores(2)
# Load data as computed with vegan 2.0-8
vegan_species = np.loadtxt(get_data_path(
'example2_species_scaling2_from_vegan'))
npt.assert_almost_equal(scores.species, vegan_species, decimal=6)
vegan_site = np.loadtxt(get_data_path(
'example2_site_scaling2_from_vegan'))
npt.assert_almost_equal(scores.site, vegan_site, decimal=6)
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()