Comments (2)
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The visualization module has been ported to bctpy. Check under utils. Certain functions were changed since the matlab plot3D had no straightforward equivalent so I implemented it with mayavi.
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I have no strong opinion about the naming convention. Conservatively I copied the names in BCT. I would be open to changing them. For backwards compatiblity, it might be good to set up aliases for the old function names, after the new naming convention is established.
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Adhering to various different style guidelines is not a high priority for me. I am open to PRs addressing style issues. I will happily receive any style changes that don't negatively affect the readability of the code at a glance.
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Noted.
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There are five functions that compute the clustering coefficient:
clustering_coef_bd(A) clustering_coef_bu(G) clustering_coef_wd(W) clustering_coef_wu(W) clustering_coef_wu_sign(W, coef_type='default')
I propose defining just one dispatcher function, which can easily handle
the first four cases.clustering_coef(A, weighted=False, directed=False)
This function would just switch over its arguments and call the correct
version ofclustering_coef
.In this way, we don't touch the current functions so we have full backwards
compatibility, but we can expose and encourage the use of the new
dispatcher in the future.The fifth case,
clustering_coef_wu_sign(W, coef_type='default')
can be
supported by the dispatcher with one more optional parameter,clustering_coef(A, weighted=False, directed=False, coef_type='default')
which will only be used in case
weighted
anddirected
areTrue
. A
little less clear than I would have hoped, but I think it still works.I propose this scheme for all other measures too. There are also four
versions fortransitivity
, two foragreement
, etc. -
I'm sure by adhering to PEP8 we won't incur in any readability blunders, all the contrary. I'll prepare an example PR soon.
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Related Issues (20)
- bct.randomize_graph_partial_und does not converge? HOT 1
- NBS incorrectly(?) lumps positive and negative effects together
- B symmetrization inside if statement in community_louvain
- IndexError: index 2278 is out of bounds for axis 0 with size 2278 HOT 3
- bug: findwalks's for loop index is wrong at it's onset HOT 1
- Wrong description in `kcoreness_centrality_bu` HOT 1
- Update `get_rng` to return Generator instances
- Different implementations to compute global efficiency using bct.charpath and bct.efficiency_wei unclear HOT 1
- Does bct.efficiency_wei also work for directed networks? HOT 1
- Improve generalizability of partition_distance()
- No fucntion get_components.py inside module .algorithms? HOT 1
- Autofix(): Indexing error
- Issue with weighted transitivity and clustering coefficient? HOT 1
- Problem to run bct.modularity_dir with latest numpy HOT 1
- bct.charpath does not exclude 'Infs' in the distance matrix as mentioned in the documentation HOT 1
- Permutation max = 0 at stringent t-thresholds
- Official `bctpy` on `conda-forge` HOT 7
- local_assortativity_wu_sign not separating signs properly
- NBS covariates
- NBS parallel
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