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Add network methods#235

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d-callan merged 41 commits intomainVEuPathDB/plot.data:mainfrom feature-232-network-methodsVEuPathDB/plot.data:feature-232-network-methodsCopy head branch name to clipboardJan 31, 2024

+1,405-221

Commits

Commits on Nov 2, 2023

• handle isolated nodes

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Commits on Nov 3, 2023

• Merge branch 'feature-229-add-network' into feature-232-network-methods

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Commits on Jan 22, 2024

• Merge branch 'feature-229-add-network' into feature-232-network-methods

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  553bce2

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• clean up

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• get tests passing again

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• draft methods to find and remove dup links

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• add some more documentation

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• test removing dup links

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• add link thresholding draft methods

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• more helpers for pruning links by weight

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• update documentation

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• test for pruning links by weight

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• draft some toJSON Network stuff

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• bug preventing toJSON methods loading

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• draft some toJSON stuff for Nodes and Links

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• update documentation

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• a test for writing networks to json

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Commits on Jan 23, 2024

• add config to Network toJSON

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• draft some constructors

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• some cleanup and get existing tests passing again

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• add test for generating Network from edgeList data.frame and get it passing

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• constructor and classes for kpartite networks from edgeLists

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• typo

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Commits on Jan 25, 2024

• clean up and get tests passing

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• clean up NodeIdList constructor

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• add toJSON methods and tests for KPartiteNetwork

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• update LinkList constructor to respect weights and colors from edgeList data.frames

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• update description

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Commits on Jan 26, 2024

• Merge branch 'feature-229-add-network' into feature-232-network-methods

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• clean up

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Commits on Jan 30, 2024

• Merge branch 'main' into feature-232-network-methods

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• wip: review feedback

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• move partitions class to own file

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• typo

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• update collation

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• get tests passing again

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• fix another case of poor use of isValidEdgeList

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• require kpartite networks have at min 2 partitions

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• update kpartitenetwork toJSON to match new data service api

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• get toJSON tests passing again

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Commits on Jan 31, 2024

• improve naming of helper fxn

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