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randomized svd draft #3008

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1f45245
randomized svd draft
hanbin973 Oct 3, 2024
e408ab3
modified api remove scipy
hanbin973 Oct 4, 2024
a176132
remove scipy
hanbin973 Oct 7, 2024
8c662c8
correct docstring and comments
hanbin973 Oct 7, 2024
aa13613
space remove
hanbin973 Oct 7, 2024
5bf405a
rng to random seed
hanbin973 Oct 8, 2024
6e415e5
add windows feature
hanbin973 Oct 8, 2024
45ac61e
output shape change when windows=wholegnome
hanbin973 Oct 11, 2024
2cdb9dd
make centre work with nodes
hanbin973 Oct 11, 2024
1f194aa
remove redundant options from internal functions
hanbin973 Oct 11, 2024
fdc5842
start at testing
petrelharp Oct 13, 2024
c0a2854
change variable name to n_* to num_*
hanbin973 Oct 13, 2024
667d60f
return range sketch matrix Q
hanbin973 Oct 13, 2024
36c10e9
fix random sketch option to handle None
hanbin973 Oct 13, 2024
0ac88b8
random_sketch needs windows specified
hanbin973 Oct 13, 2024
a6fa8ab
input checking for range_sketch to align with windows
hanbin973 Oct 13, 2024
791c7da
docstring change to reflect range_sketch
hanbin973 Oct 13, 2024
2f4ce2b
linting has a bug; when converting lambda to ordinary function defini…
hanbin973 Oct 14, 2024
be2f736
now output is a dataclass
hanbin973 Oct 17, 2024
bcbbcf6
docstring change
hanbin973 Oct 17, 2024
1a8ff7a
change variable name of PCAResult class
hanbin973 Oct 18, 2024
af16340
move internal function of PCA out
hanbin973 Oct 18, 2024
e81db15
function rearrangement
hanbin973 Oct 22, 2024
277cfc2
terminology change loaindgs -> factor
hanbin973 Nov 15, 2024
be715de
time resolved feature
hanbin973 Nov 16, 2024
d3e6c89
Update python/tskit/trees.py
hanbin973 Nov 17, 2024
49fe716
Update python/tskit/trees.py
hanbin973 Nov 17, 2024
d217fc7
Update python/tskit/trees.py
hanbin973 Nov 17, 2024
89e3b27
Update python/tskit/trees.py
hanbin973 Nov 17, 2024
81cbecf
remove comments; eigen_values -> eigenvalues
hanbin973 Nov 18, 2024
7ca6452
support for subset of samples and individuals in a tree
hanbin973 Nov 20, 2024
587409b
add time assertion
hanbin973 Dec 18, 2024
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7 changes: 5 additions & 2 deletions python/tskit/trees.py
Original file line number Diff line number Diff line change
Expand Up @@ -8637,8 +8637,11 @@ def pca(
be automatically generated. Valid random seeds must be between 1 and
:math:`2^32 − 1`.
:param np.ndarray range_sketch: Sketch matrix for each window. Default is None.
:return: A tuple (U, D, Q) of ndarrays, with the principal component loadings in U
and the principal values in D. Q is the range sketch array for each window.
:return: A class object with attributes U, D, Q and E.
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The principal component loadings are in U
and the principal values are in D.
Q is the range sketch array for each window.
E is the error bound of the singular values..
"""

if samples is None and individuals is None:
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