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Bring threshold inside BaseReconstructor class #290

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4907b2e
Bring threshold inside BaseReconstructor class
sdmccabe Feb 18, 2020
691a1c2
Remove CST from docs and correct typo
sdmccabe Feb 18, 2020
fdc0e1e
remove remove_self_loops parameter in to_graph
sdmccabe Feb 18, 2020
bb64353
access self.matrix through to_matrix in utility methods
sdmccabe Feb 18, 2020
bd10912
add draft docstrings to BaseReconstructor and associated methods
sdmccabe Feb 18, 2020
13f3e74
autoformatter, again
sdmccabe Feb 18, 2020
630640f
fix CCM test by adding remove_self_loops
sdmccabe Feb 19, 2020
985f30f
autoformatter, again
sdmccabe Feb 19, 2020
84efe18
Merge branch 'master' into threshold-feature
sdmccabe Feb 19, 2020
9efe813
remove update_graph, add sparse matrix operations
sdmccabe Feb 19, 2020
0d3e628
Merge branch 'threshold-feature' of https://github.com/sdmccabe/netrd…
sdmccabe Feb 19, 2020
eae49b8
make copies in non-fit BaseReconstructor methods
sdmccabe Feb 21, 2020
815cb14
Signal that graph and matrix attributes are private
sdmccabe Feb 25, 2020
46fc46f
Merge master, resolve PCI merge conflict
sdmccabe Mar 11, 2020
b95e7f8
doc tweaks
sdmccabe Mar 12, 2020
2683d8c
return MSTs directly
sdmccabe Mar 12, 2020
dedaca3
rename _sparse_allclose to _sparse_check_symmetric
sdmccabe Mar 12, 2020
6d516ca
correct out-of-date exception messages
sdmccabe Mar 12, 2020
ff6cc80
test for None rather than falseness
sdmccabe Mar 12, 2020
18f261c
add clarifying comment back to threshold_by_degree
sdmccabe Mar 12, 2020
46ac1bf
autoformatter
sdmccabe Mar 12, 2020
1d61eb5
Merge branch 'master' into threshold-feature
sdmccabe Oct 28, 2020
a59359f
refactor to_graph()
sdmccabe Oct 28, 2020
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3 changes: 1 addition & 2 deletions doc/source/reconstruction.rst
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Reconstruction
==============

Algorithms to recosntruct a graph from time series data.
Algorithms to reconstruct a graph from time series data.


Base class
Expand All @@ -20,7 +20,6 @@ the same general usage as above.

netrd.reconstruction.ConvergentCrossMapping
netrd.reconstruction.CorrelationMatrix
netrd.reconstruction.CorrelationSpanningTree
netrd.reconstruction.FreeEnergyMinimization
netrd.reconstruction.GrangerCausality
netrd.reconstruction.GraphicalLasso
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3 changes: 0 additions & 3 deletions doc/source/threshold.rst
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1 change: 0 additions & 1 deletion doc/source/utilities.rst
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Expand Up @@ -13,4 +13,3 @@ Common utilities for use within ``netrd``.
graph
read
standardize
threshold
2 changes: 0 additions & 2 deletions netrd/reconstruction/__init__.py
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Expand Up @@ -15,7 +15,6 @@
from .naive_transfer_entropy import NaiveTransferEntropy
from .granger_causality import GrangerCausality
from .optimal_causation_entropy import OptimalCausationEntropy
from .correlation_spanning_tree import CorrelationSpanningTree

__all__ = [
'RandomReconstructor',
Expand All @@ -34,5 +33,4 @@
'NaiveTransferEntropy',
'GrangerCausality',
'OptimalCausationEntropy',
'CorrelationSpanningTree',
]
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