def test02PCAScaleOnly(self):
'''
This is the R result.
Standard deviations:
[1] 1.5649625 0.7209789 0.1762999
Rotation:
PC1 PC2 PC3
[1,] 0.6261964 -0.2060872 -0.7519349
[2,] -0.5082884 -0.8392166 -0.1932835
[3,] -0.5912030 0.5032332 -0.6302661
Scale:
[1] 1.415300 2.449408 2.032120
'''
stdev,rot,scale = pv.prcomp(self.data,center=False,scale=True)
r_stdev = [1.5649625, 0.7209789, 0.1762999]
r_rot = [0.6261964, -0.2060872, -0.7519349, -0.5082884, -0.8392166, -0.1932835, -0.5912030, 0.5032332, -0.6302661]
r_scale = [1.415300, 2.449408, 2.032120]
self.assertLess(np.abs(stdev - r_stdev).max(), 0.0001)
self.assertLess(np.abs(rot.flatten() - r_rot).max(), 0.0001)
self.assertLess(np.abs(scale.flatten() - r_scale).max(), 0.0001)
def test01PCACenterOnly(self):
'''
This is the R result.
Standard deviations:
[1] 2.9519567 1.5879939 0.2839961
Rotation:
PC1 PC2 PC3
[1,] 0.4204812 0.2913070 0.8592647
[2,] -0.7281257 0.6733826 0.1280189
[3,] -0.5413211 -0.6794822 0.4952529
center:
[1] -0.4235626 0.4724063 0.6102422
'''
stdev,rot,center = pv.prcomp(self.data,center=True,scale=False)
r_stdev = [2.9519567, 1.5879939, 0.2839961]
r_rot = [0.4204812, 0.2913070, 0.8592647, -0.7281257, 0.6733826, 0.1280189, -0.5413211, -0.6794822, 0.4952529]
r_center = [-0.4235626, 0.4724063, 0.6102422]
self.assertLess(np.abs(stdev - r_stdev).max(), 0.0001)
self.assertLess(np.abs(rot.flatten() - r_rot).max(), 0.0001)
self.assertLess(np.abs(center - r_center).max(), 0.0001)
def test02PCAAll(self):
'''
This is the R result.
Standard deviations:
[1] 1.5550735 0.7399330 0.1850559
Rotation:
PC1 PC2 PC3
[1,] 0.6297830 -0.1983517 -0.7510193
[2,] -0.5027915 -0.8410733 -0.1994906
[3,] -0.5920929 0.5032419 -0.6294232
Center:
[1] -0.4235626 0.4724063 0.6102422
Scale
[1] 1.346932 2.400976 1.933266
'''
stdev,rot,center,scale = pv.prcomp(self.data,center=True,scale=True)
r_stdev = [1.5550735, 0.7399330, 0.1850559]
r_rot = [0.6297830, -0.1983517, -0.7510193, -0.5027915, -0.8410733, -0.1994906, -0.5920929, 0.5032419, -0.6294232]
r_scale = [1.346932, 2.400976, 1.933266]
r_center = [-0.4235626, 0.4724063, 0.6102422]
self.assertLess(np.abs(stdev - r_stdev).max(), 0.0001)
self.assertLess(np.abs(rot.flatten() - r_rot).max(), 0.0001)
self.assertLess(np.abs(scale.flatten() - r_scale).max(), 0.0001)
self.assertLess(np.abs(center - r_center).max(), 0.0001)
def test01PCACenterOnly(self):
'''
This is the R result.
Standard deviations:
[1] 2.9519567 1.5879939 0.2839961
Rotation:
PC1 PC2 PC3
[1,] 0.4204812 0.2913070 0.8592647
[2,] -0.7281257 0.6733826 0.1280189
[3,] -0.5413211 -0.6794822 0.4952529
center:
[1] -0.4235626 0.4724063 0.6102422
'''
stdev, rot, center = pv.prcomp(self.data, center=True, scale=False)
r_stdev = [2.9519567, 1.5879939, 0.2839961]
r_rot = [
0.4204812, 0.2913070, 0.8592647, -0.7281257, 0.6733826, 0.1280189,
-0.5413211, -0.6794822, 0.4952529
]
r_center = [-0.4235626, 0.4724063, 0.6102422]
self.assertLess(np.abs(stdev - r_stdev).max(), 0.0001)
self.assertLess(np.abs(rot.flatten() - r_rot).max(), 0.0001)
self.assertLess(np.abs(center - r_center).max(), 0.0001)
def test02PCAAll(self):
'''
This is the R result.
Standard deviations:
[1] 1.5550735 0.7399330 0.1850559
Rotation:
PC1 PC2 PC3
[1,] 0.6297830 -0.1983517 -0.7510193
[2,] -0.5027915 -0.8410733 -0.1994906
[3,] -0.5920929 0.5032419 -0.6294232
Center:
[1] -0.4235626 0.4724063 0.6102422
Scale
[1] 1.346932 2.400976 1.933266
'''
stdev, rot, center, scale = pv.prcomp(self.data,
center=True,
scale=True)
r_stdev = [1.5550735, 0.7399330, 0.1850559]
r_rot = [
0.6297830, -0.1983517, -0.7510193, -0.5027915, -0.8410733,
-0.1994906, -0.5920929, 0.5032419, -0.6294232
]
r_scale = [1.346932, 2.400976, 1.933266]
r_center = [-0.4235626, 0.4724063, 0.6102422]
self.assertLess(np.abs(stdev - r_stdev).max(), 0.0001)
self.assertLess(np.abs(rot.flatten() - r_rot).max(), 0.0001)
self.assertLess(np.abs(scale.flatten() - r_scale).max(), 0.0001)
self.assertLess(np.abs(center - r_center).max(), 0.0001)
def test02PCAScaleOnly(self):
'''
This is the R result.
Standard deviations:
[1] 1.5649625 0.7209789 0.1762999
Rotation:
PC1 PC2 PC3
[1,] 0.6261964 -0.2060872 -0.7519349
[2,] -0.5082884 -0.8392166 -0.1932835
[3,] -0.5912030 0.5032332 -0.6302661
Scale:
[1] 1.415300 2.449408 2.032120
'''
stdev, rot, scale = pv.prcomp(self.data, center=False, scale=True)
r_stdev = [1.5649625, 0.7209789, 0.1762999]
r_rot = [
0.6261964, -0.2060872, -0.7519349, -0.5082884, -0.8392166,
-0.1932835, -0.5912030, 0.5032332, -0.6302661
]
r_scale = [1.415300, 2.449408, 2.032120]
self.assertLess(np.abs(stdev - r_stdev).max(), 0.0001)
self.assertLess(np.abs(rot.flatten() - r_rot).max(), 0.0001)
self.assertLess(np.abs(scale.flatten() - r_scale).max(), 0.0001)
def test02PCAAllOff(self):
'''
This is the R result.
Standard deviations:
[1] 3.0796955 1.6021872 0.2839987
Rotation:
PC1 PC2 PC3
[1,] 0.4287266 0.2792776 0.8591842
[2,] -0.7085966 0.6939010 0.1280322
[3,] -0.5604323 -0.6637058 0.4953890
'''
stdev,rot = pv.prcomp(self.data,center=False,scale=False)
r_stdev = [3.0796955, 1.6021872, 0.2839987]
r_rot = [0.4287266, 0.2792776, 0.8591842,-0.7085966, 0.6939010, 0.1280322, -0.5604323, -0.6637058, 0.4953890]
self.assertLess(np.abs(stdev - r_stdev).max(), 0.0001)
self.assertLess(np.abs(rot.flatten() - r_rot).max(), 0.0001)
def test02PCAAllOff(self):
'''
This is the R result.
Standard deviations:
[1] 3.0796955 1.6021872 0.2839987
Rotation:
PC1 PC2 PC3
[1,] 0.4287266 0.2792776 0.8591842
[2,] -0.7085966 0.6939010 0.1280322
[3,] -0.5604323 -0.6637058 0.4953890
'''
stdev, rot = pv.prcomp(self.data, center=False, scale=False)
r_stdev = [3.0796955, 1.6021872, 0.2839987]
r_rot = [
0.4287266, 0.2792776, 0.8591842, -0.7085966, 0.6939010, 0.1280322,
-0.5604323, -0.6637058, 0.4953890
]
self.assertLess(np.abs(stdev - r_stdev).max(), 0.0001)
self.assertLess(np.abs(rot.flatten() - r_rot).max(), 0.0001)
def testPCATraspose(self):
'''
Test the prcomp function when pca rows < cols
Standard deviations:
[1] 8.331994e+00 4.825577e+00 1.501489e-15
Rotation:
PC1 PC2 PC3
[1,] 0.120344086 0.09556545 -0.936538815
[2,] 0.252861085 0.10623090 0.315668331
[3,] 0.024271246 -0.04690261 -0.005344113
[4,] 0.299257461 0.16307696 0.018798443
[5,] 0.382358959 0.28156629 0.028963283
[6,] -0.156277263 0.15979575 0.031295934
[7,] -0.074892351 0.03402898 0.014440886
[8,] -0.113677717 -0.40901126 -0.025021991
[9,] 0.101972797 0.03267545 0.003185637
[10,] 0.018748487 0.50967727 -0.025423314
[11,] -0.009698747 0.12256309 0.034447390
[12,] 0.186645947 -0.06658096 0.014372061
[13,] 0.299222477 0.09675674 0.048910786
[14,] 0.268436630 -0.01164026 0.079693297
[15,] -0.057854438 0.07654372 -0.064354215
[16,] -0.020516392 0.01883692 0.004268303
[17,] 0.297578045 -0.59552725 -0.054518114
[18,] -0.504587911 0.06186216 -0.004543222
[19,] 0.213855451 -0.14782261 -0.047011001
[20,] -0.205779238 -0.03449968 -0.007623901
Center:
[1] 0.70935633 1.04780400 -0.06950500 0.90656600 1.00758200 -0.91922167 0.09474133 -0.05085167 0.00192200 -0.35097200 -0.34026333 0.95575633 0.91019200 0.87737233 -0.43181900 -0.02607167
[17] 1.75353700 -1.85199600 0.88335000 -0.71357333
'''
stdev,rot,center = pv.prcomp(self.data.T,center=True,scale=False)
r_stdev = [8.331994e+00, 4.825577e+00, 1.501489e-15]
r_rot = [0.120344086, 0.09556545, -0.936538815,
0.252861085, 0.10623090, 0.315668331,
0.024271246, -0.04690261, -0.005344113,
0.299257461, 0.16307696, 0.018798443,
0.382358959, 0.28156629, 0.028963283,
-0.156277263, 0.15979575, 0.031295934,
-0.074892351, 0.03402898, 0.014440886,
-0.113677717, -0.40901126, -0.025021991,
0.101972797, 0.03267545, 0.003185637,
0.018748487, 0.50967727, -0.025423314,
-0.009698747, 0.12256309, 0.034447390,
0.186645947, -0.06658096, 0.014372061,
0.299222477, 0.09675674, 0.048910786,
0.268436630, -0.01164026, 0.079693297,
-0.057854438, 0.07654372, -0.064354215,
-0.020516392, 0.01883692, 0.004268303,
0.297578045, -0.59552725, -0.054518114,
-0.504587911, 0.06186216, -0.004543222,
0.213855451, -0.14782261, -0.047011001,
-0.205779238, -0.03449968, -0.007623901]
r_rot = np.array(r_rot).reshape(20,3)
r_center = [0.70935633, 1.04780400, -0.06950500, 0.90656600,
1.00758200, -0.91922167, 0.09474133, -0.05085167,
0.00192200, -0.35097200, -0.34026333, 0.95575633,
0.91019200, 0.87737233, -0.43181900, -0.02607167,
1.75353700, -1.85199600, 0.88335000, -0.71357333]
self.assertLess(np.abs(stdev - r_stdev).max(), 0.0001)
self.assertLess(np.abs(rot[:,:2].flatten() - r_rot[:,:2].flatten()).max(), 0.0001)
self.assertLess(np.abs(center.flatten() - r_center).max(), 0.0001)
def testPCATraspose(self):
'''
Test the prcomp function when pca rows < cols
Standard deviations:
[1] 8.331994e+00 4.825577e+00 1.501489e-15
Rotation:
PC1 PC2 PC3
[1,] 0.120344086 0.09556545 -0.936538815
[2,] 0.252861085 0.10623090 0.315668331
[3,] 0.024271246 -0.04690261 -0.005344113
[4,] 0.299257461 0.16307696 0.018798443
[5,] 0.382358959 0.28156629 0.028963283
[6,] -0.156277263 0.15979575 0.031295934
[7,] -0.074892351 0.03402898 0.014440886
[8,] -0.113677717 -0.40901126 -0.025021991
[9,] 0.101972797 0.03267545 0.003185637
[10,] 0.018748487 0.50967727 -0.025423314
[11,] -0.009698747 0.12256309 0.034447390
[12,] 0.186645947 -0.06658096 0.014372061
[13,] 0.299222477 0.09675674 0.048910786
[14,] 0.268436630 -0.01164026 0.079693297
[15,] -0.057854438 0.07654372 -0.064354215
[16,] -0.020516392 0.01883692 0.004268303
[17,] 0.297578045 -0.59552725 -0.054518114
[18,] -0.504587911 0.06186216 -0.004543222
[19,] 0.213855451 -0.14782261 -0.047011001
[20,] -0.205779238 -0.03449968 -0.007623901
Center:
[1] 0.70935633 1.04780400 -0.06950500 0.90656600 1.00758200 -0.91922167 0.09474133 -0.05085167 0.00192200 -0.35097200 -0.34026333 0.95575633 0.91019200 0.87737233 -0.43181900 -0.02607167
[17] 1.75353700 -1.85199600 0.88335000 -0.71357333
'''
stdev, rot, center = pv.prcomp(self.data.T, center=True, scale=False)
r_stdev = [8.331994e+00, 4.825577e+00, 1.501489e-15]
r_rot = [
0.120344086, 0.09556545, -0.936538815, 0.252861085, 0.10623090,
0.315668331, 0.024271246, -0.04690261, -0.005344113, 0.299257461,
0.16307696, 0.018798443, 0.382358959, 0.28156629, 0.028963283,
-0.156277263, 0.15979575, 0.031295934, -0.074892351, 0.03402898,
0.014440886, -0.113677717, -0.40901126, -0.025021991, 0.101972797,
0.03267545, 0.003185637, 0.018748487, 0.50967727, -0.025423314,
-0.009698747, 0.12256309, 0.034447390, 0.186645947, -0.06658096,
0.014372061, 0.299222477, 0.09675674, 0.048910786, 0.268436630,
-0.01164026, 0.079693297, -0.057854438, 0.07654372, -0.064354215,
-0.020516392, 0.01883692, 0.004268303, 0.297578045, -0.59552725,
-0.054518114, -0.504587911, 0.06186216, -0.004543222, 0.213855451,
-0.14782261, -0.047011001, -0.205779238, -0.03449968, -0.007623901
]
r_rot = np.array(r_rot).reshape(20, 3)
r_center = [
0.70935633, 1.04780400, -0.06950500, 0.90656600, 1.00758200,
-0.91922167, 0.09474133, -0.05085167, 0.00192200, -0.35097200,
-0.34026333, 0.95575633, 0.91019200, 0.87737233, -0.43181900,
-0.02607167, 1.75353700, -1.85199600, 0.88335000, -0.71357333
]
self.assertLess(np.abs(stdev - r_stdev).max(), 0.0001)
self.assertLess(
np.abs(rot[:, :2].flatten() - r_rot[:, :2].flatten()).max(),
0.0001)
self.assertLess(np.abs(center.flatten() - r_center).max(), 0.0001)
