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create new generic converter#506

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thpral wants to merge 66 commits intodevelmicrobiome/mia:develfrom draft_convertersmicrobiome/mia:draft_convertersCopy head branch name to clipboard

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Commits on Mar 18, 2024

• new generic function convert

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• keep the original functions in their original files

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Commits on Mar 19, 2024

• up

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Commits on Mar 20, 2024

• convert documentation

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Commits on Mar 21, 2024

• correct documentation

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• correct internal functions naming

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Commits on Mar 22, 2024

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Commits on Mar 25, 2024

• correct convert man page

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Commits on Mar 26, 2024

• correct BiocCheck warnings

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Commits on Apr 3, 2024

• Merge branch 'devel' into draft_converters

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• change param tree_name to tree.name for convert

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• up

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

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• new parameter for choosing output type when converting SE and TSE

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Commits on Apr 4, 2024

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• merge devel and resolve conflicts

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Commits on Apr 10, 2024

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• changes after review

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• merge remote (resolve conflicts)

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• merge devel and resolve conflicts

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• correct arguments loadFromBiom

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Commits on Apr 15, 2024

• correct deprecate and NAMESPACE file

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Commits on Apr 17, 2024

• merge devel

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• correct importBIOM default arguments after merging devel

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• move loadFromBiom arguments (doc)

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Commits on Apr 25, 2024

• export loadFromBiom

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• export converters in deprecate file

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• update DESCRIPTION

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• merge devel

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Commits on Apr 26, 2024

• rename man page loadFromBiom to importBIOM to avoid duplicated aliases

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Commits on May 6, 2024

• resolve conflicts and merge devel

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• add import tags for phyloseq and dada classes

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Commits on May 9, 2024

• merge devel

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Commits on May 28, 2024

• merge devel and remove import tags for dada and phyloseq classes

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• fix lost braces

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Commits on May 29, 2024

• try to fix R CMD check note

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• up

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• reverse last 2 commits

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Commits on Jun 3, 2024

• Revert "fix lost braces"

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

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• merge devel

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Commits on Jun 5, 2024

• replace convert with new names in deprecate, biom and phyloseq

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Commits on Jun 10, 2024

• merge devel

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• replace convert with new functions

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• rename converters files

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• rearrange convert man page

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• Merge branch 'devel' into draft_converters

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Commits on Jun 12, 2024

• fix errors and warnings

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

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• fix convertToPhyloseq

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• try to fix R CMD check note

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Commits on Jun 19, 2024

• merge devel

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• merge devel

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• small fix

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Commits on Jun 20, 2024

• renaming files

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• renaming files

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• resolve R CMD check warning

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