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Replace getPrevalence with addPrevalence #119

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Replace getPrevalence with addPrevalence #119

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thpralas
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After mia PR microbiome/mia#529 that renamed the following functions :

  • getPrevalence --> addPrevalence
  • getPrevalentAbundance --> addPrevalentAbundance

This PR replaces getPrevalence with addPrevalence in miaViz.

@antagomir
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imo OK to merge

@antagomir
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@thpralas still some failing checks?

@TuomasBorman
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Bioconductor devel does not still have latest changes. That is because there is a pending agglomerateByRank issue. The fixes are already merged in devel, so we have to solve the issue before pushing to Bioconductor

@thpralas
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The R CMD check warning should be solved when pushing mia current version to Bioc devel.

@thpralas
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This PR is linked to mia PR microbiome/mia#529 that was closed.

@thpralas thpralas closed this Jun 20, 2024
@thpralas thpralas deleted the rename_prevalence_functions branch July 1, 2024 10:53
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@TuomasBorman TuomasBorman TuomasBorman approved these changes

@antagomir antagomir antagomir approved these changes

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@thpralas @antagomir @TuomasBorman