statsmodels.multivariate.pca.PCA¶

class
statsmodels.multivariate.pca.
PCA
(data, ncomp=None, standardize=True, demean=True, normalize=True, gls=False, weights=None, method='svd', missing=None, tol=5e08, max_iter=1000, tol_em=5e08, max_em_iter=100)[source]¶ Principal Component Analysis
 Parameters
data (arraylike) – Variables in columns, observations in rows
ncomp (int, optional) – Number of components to return. If None, returns the as many as the smaller of the number of rows or columns in data
standardize (bool, optional) – Flag indicating to use standardized data with mean 0 and unit variance. standardized being True implies demean. Using standardized data is equivalent to computing principal components from the correlation matrix of data
demean (bool, optional) – Flag indicating whether to demean data before computing principal components. demean is ignored if standardize is True. Demeaning data but not standardizing is equivalent to computing principal components from the covariance matrix of data
normalize (bool , optional) – Indicates whether th normalize the factors to have unit inner product. If False, the loadings will have unit inner product.
weights (array, optional) – Series weights to use after transforming data according to standardize or demean when computing the principal components.
gls (bool, optional) – Flag indicating to implement a twostep GLS estimator where in the first step principal components are used to estimate residuals, and then the inverse residual variance is used as a set of weights to estimate the final principal components. Setting gls to True requires ncomp to be less then the min of the number of rows or columns
method (str, optional) – Sets the linear algebra routine used to compute eigenvectors ‘svd’ uses a singular value decomposition (default). ‘eig’ uses an eigenvalue decomposition of a quadratic form ‘nipals’ uses the NIPALS algorithm and can be faster than SVD when ncomp is small and nvars is large. See notes about additional changes when using NIPALS
tol (float, optional) – Tolerance to use when checking for convergence when using NIPALS
max_iter (int, optional) – Maximum iterations when using NIPALS
missing (string) – Method for missing data. Choices are ‘droprow’  drop rows with missing values ‘dropcol’  drop columns with missing values ‘dropmin’  drop either rows or columns, choosing by data retention ‘fillem’  use EM algorithm to fill missing value. ncomp should be set to the number of factors required
tol_em (float) – Tolerance to use when checking for convergence of the EM algorithm
max_em_iter (int) – Maximum iterations for the EM algorithm

factors
¶ nobs by ncomp array of of principal components (scores)
 Type
array or DataFrame

scores
¶ nobs by ncomp array of of principal components  identical to factors
 Type
array or DataFrame

loadings
¶ ncomp by nvar array of principal component loadings for constructing the factors
 Type
array or DataFrame

coeff
¶ nvar by ncomp array of principal component loadings for constructing the projections
 Type
array or DataFrame

projection
¶ nobs by var array containing the projection of the data onto the ncomp estimated factors
 Type
array or DataFrame

rsquare
¶ ncomp array where the element in the ith position is the Rsquare of including the fist i principal components. Note: values are calculated on the transformed data, not the original data
 Type
array or Series

ic
¶ ncomp by 3 array containing the Bai and Ng (2003) Information criteria. Each column is a different criteria, and each row represents the number of included factors.
 Type
array or DataFrame

eigenvals
¶ nvar array of eigenvalues
 Type
array or Series

eigenvecs
¶ nvar by nvar array of eigenvectors
 Type
array or DataFrame

weights
¶ nvar array of weights used to compute the principal components, normalized to unit length
 Type
array

transformed_data
¶ Standardized, demeaned and weighted data used to compute principal components and related quantities
 Type
array

cols
¶ Array of indices indicating columns used in the PCA
 Type
array

rows
¶ Array of indices indicating rows used in the PCA
 Type
array
Examples
Basic PCA using the correlation matrix of the data
>>> import numpy as np >>> from statsmodels.multivariate.pca import PCA >>> x = np.random.randn(100)[:, None] >>> x = x + np.random.randn(100, 100) >>> pc = PCA(x)
Note that the principal components are computed using a SVD and so the correlation matrix is never constructed, unless method=’eig’.
PCA using the covariance matrix of the data
>>> pc = PCA(x, standardize=False)
Limiting the number of factors returned to 1 computed using NIPALS
>>> pc = PCA(x, ncomp=1, method='nipals') >>> pc.factors.shape (100, 1)
Notes
The default options perform principal component analysis on the demeaned, unit variance version of data. Setting standardize to False will instead only demean, and setting both standardized and demean to False will not alter the data.
Once the data have been transformed, the following relationships hold when the number of components (ncomp) is the same as tne minimum of the number of observation or the number of variables.
where X is the data, F is the array of principal components (factors or scores), and V is the array of eigenvectors (loadings) and V’ is the array of factor coefficients (coeff).
When weights are provided, the principal components are computed from the modified data
where \(\Omega\) is a diagonal matrix composed of the weights. For example, when using the GLS version of PCA, the elements of \(\Omega\) will be the inverse of the variances of the residuals from
where the number of factors is less than the rank of X
 *
J. Bai and S. Ng, “Determining the number of factors in approximate factor models,” Econometrica, vol. 70, number 1, pp. 191221, 2002
Methods
plot_rsquare
([ncomp, ax])Box plots of the individual series Rsquare against the number of PCs
plot_scree
([ncomp, log_scale, cumulative, ax])Plot of the ordered eigenvalues
project
([ncomp, transform, unweight])Project series onto a specific number of factors