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LDA ordination with feature loadings computation #598

Merged
merged 35 commits into from
Jul 23, 2024
Merged

LDA ordination with feature loadings computation #598

merged 35 commits into from
Jul 23, 2024

Commits on Jul 5, 2024

  1. new functions getLDA and addLDA

    @thpralas
    thpralas committed Jul 5, 2024
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  2. up

    @thpralas
    thpralas committed Jul 5, 2024
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  3. add topicmodels package to imports

    @thpralas
    thpralas committed Jul 5, 2024
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Commits on Jul 8, 2024

  1. Merge branch 'devel' into feature_loadings_methods

    @thpralas
    thpralas committed Jul 8, 2024
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  2. coding style and small modifications

    @thpralas
    thpralas committed Jul 8, 2024
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  3. Merge branch 'feature_loadings_methods' of https://github.com/microbi… 

    …ome/mia into feature_loadings_methods
    @thpralas
    thpralas committed Jul 8, 2024
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  4. new internal function add_values_to_reducedDims

    @thpralas
    thpralas committed Jul 8, 2024
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  5. move topicmodels package to suggests

    @thpralas
    thpralas committed Jul 8, 2024
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  6. simplify function

    @thpralas
    thpralas committed Jul 8, 2024
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Commits on Jul 9, 2024

  1. add comments to getLDA and addLDA

    @thpralas
    thpralas committed Jul 9, 2024
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  2. Merge branch 'devel' into feature_loadings_methods

    @thpralas
    thpralas committed Jul 9, 2024
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  3. add input checks

    @thpralas
    thpralas committed Jul 9, 2024
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  4. Merge branch 'feature_loadings_methods' of https://github.com/microbi… 

    …ome/mia into feature_loadings_methods
    @thpralas
    thpralas committed Jul 9, 2024
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  5. add tests for addLDA

    @thpralas
    thpralas committed Jul 9, 2024
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Commits on Jul 10, 2024

  1. review modifications

    @thpralas
    thpralas committed Jul 10, 2024
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Commits on Jul 11, 2024

  1. review modifs

    @thpralas
    thpralas committed Jul 11, 2024
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  2. call agglomerateByPrevalence without prevalence level in examples

    @thpralas
    thpralas committed Jul 11, 2024
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Commits on Jul 12, 2024

  1. merge devel 

    Merge branch 'devel' of https://github.com/microbiome/mia into feature_loadings_methods

# Conflicts:
#	NEWS
    @thpralas
    thpralas committed Jul 12, 2024
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Commits on Jul 16, 2024

  1. Merge branch 'devel' into feature_loadings_methods

    @thpralas
    thpralas committed Jul 16, 2024
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Commits on Jul 17, 2024

  1. address review comments

    @thpralas
    thpralas committed Jul 17, 2024
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Commits on Jul 22, 2024

  1. Update addLDA.R

    @TuomasBorman
    TuomasBorman committed Jul 22, 2024
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  2. Merge branch 'devel' into feature_loadings_methods

    @thpralas
    thpralas committed Jul 22, 2024
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Commits on Jul 23, 2024

  1. modify input check and indentation in .add_values_to_reducedDims

    @thpralas
    thpralas committed Jul 23, 2024
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  2. Merge branch 'feature_loadings_methods' of https://github.com/microbi… 

    …ome/mia into feature_loadings_methods
    @thpralas
    thpralas committed Jul 23, 2024
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  3. up

    @TuomasBorman
    TuomasBorman committed Jul 23, 2024
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  4. up

    @TuomasBorman
    TuomasBorman committed Jul 23, 2024
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  5. up

    @TuomasBorman
    TuomasBorman committed Jul 23, 2024
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  6. up

    @TuomasBorman
    TuomasBorman committed Jul 23, 2024
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  7. up

    @TuomasBorman
    TuomasBorman committed Jul 23, 2024
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  8. up

    @TuomasBorman
    TuomasBorman committed Jul 23, 2024
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  9. up

    @TuomasBorman
    TuomasBorman committed Jul 23, 2024
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  10. up

    @TuomasBorman
    TuomasBorman committed Jul 23, 2024
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  11. Merge branch 'devel' into feature_loadings_methods

    @TuomasBorman
    TuomasBorman committed Jul 23, 2024
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  12. up

    @TuomasBorman
    TuomasBorman committed Jul 23, 2024
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  13. up

    @TuomasBorman
    TuomasBorman committed Jul 23, 2024
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