Code

New dissimilarity functions#609

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TuomasBorman merged 66 commits intodevelmicrobiome/mia:develfrom getDissimilaritymicrobiome/mia:getDissimilarityCopy head branch name to clipboardAug 13, 2024

+913-846

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Commits on Jul 9, 2024

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Commits on Jul 12, 2024

• small fix

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• addDissimilarity function

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• fix addDissimilarity

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• rename JSD and overlap functions

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• man page getDissimilarity

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Commits on Jul 16, 2024

• rename unifrac functions

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• Merge branch 'devel' into getDissimilarity

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• fix R check warnings

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• Merge branch 'getDissimilarity' of https://github.com/microbiome/mia into getDissimilarity

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Commits on Jul 18, 2024

• fix getUnifrac SE method

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Commits on Jul 22, 2024

• Merge branch 'devel' into getDissimilarity

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• fix naming .get_jsd

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• remove generic methods for jsd, overlap and unifrac

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Commits on Jul 23, 2024

• Merge branch 'getDissimilarity' of https://github.com/microbiome/mia into getDissimilarity

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• fix argument types in documentation

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Commits on Jul 24, 2024

• merge devel

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• fix overlap tests with getDissimilarity

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• fix error in unifrac

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Commits on Jul 25, 2024

• update pckgdown

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Commits on Jul 29, 2024

• modify inheritance in man pages

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• fix documentation

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• try to fix unifrac node.label argument

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Commits on Jul 30, 2024

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Commits on Aug 1, 2024

• Merge branch 'devel' into getDissimilarity

  thpralas

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• add unifrac, overlap and jsd documentation in getDissimilarity manual page

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• merge devel

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• update doc getDissimilarity

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• deprecate dissimilarity functions

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• add check to .add_values_to_reducedDims

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Commits on Aug 2, 2024

• fix deprecated functions and .add_values_to_reducedDims

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Commits on Aug 5, 2024

• Merge branch 'devel' into getDissimilarity

  antagomir

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Commits on Aug 6, 2024

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• Merge branch 'devel' into getDissimilarity

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Commits on Aug 7, 2024

• address review comments

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• add tests for getDissimililarity

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• fix braces in .add_values_to_reducedDims

  thpralas

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• add missing argument to runDPCoA documentation

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Commits on Aug 8, 2024

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  TuomasBorman

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• Simplify. Add method for TreeSE.

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• address review comments

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• deprecate runUnifrac

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• add dis matrix to metadata instead of reducedDims

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• fix getDissimilarity examples and doc

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Commits on Aug 9, 2024

• Merge branch 'devel' into getDissimilarity

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• add rarefaction test

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Commits on Aug 10, 2024

• Merge branch 'devel' into getDissimilarity

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• address review comment

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• Merge branch 'getDissimilarity' of https://github.com/microbiome/mia into getDissimilarity

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• setting seed in rarefaction tests

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Commits on Aug 11, 2024

• merge devel

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Commits on Aug 13, 2024

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• fix rarefaction tests

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