Issues

• Add Smith-Wilson evenness

  enhancement
  microbiome/mia#852 · Filter by author antagomir opened on Sep 8, 2026

• How to perform a pairwise adonis test with unifrac distance?

  microbiome/mia#851 · Filter by author antagomir opened on Sep 8, 2026
  2

• Distance decay plots

  microbiome/mia#850 · Filter by author antagomir opened on Sep 8, 2026

• Problem with hotplot

  microbiome/mia#849 · Filter by author antagomir opened on Sep 8, 2026

• addAlpha

  microbiome/mia#845 · Filter by author antagomir opened on Aug 22, 2026
  

• getNMF acceleration

  G1: performance
  microbiome/mia#843 · Filter by author antagomir opened on Aug 11, 2026
  1

• Dataset from environmental samples

  microbiome/mia#833 · Filter by author TuomasBorman opened on Jun 16, 2026
  1

• Joint-RPCA improvement

  G1: performance
  microbiome/mia#827 · Filter by author antagomir opened on May 12, 2026
  2

  

• convertToPhyloseq: row order is different between input TreeSE and output phyloseq

  microbiome/mia#821 · Filter by author RiboRings opened on Apr 14, 2026
  3

• getDominance?

  microbiome/mia#819 · Filter by author antagomir opened on Apr 10, 2026
  1

• agglomerateByPrevalence name is misleading?

  microbiome/mia#816 · Filter by author antagomir opened on Apr 9, 2026

• Transformations non consistent

  microbiome/mia#813 · Filter by author antagomir opened on Mar 23, 2026
  3

• Implement ENBI

  microbiome/mia#807 · Filter by author antagomir opened on Mar 2, 2026

• Simplify examples

  G4: adoption
  microbiome/mia#806 · Filter by author antagomir opened on Mar 1, 2026
  1

  

• verbose argument for transformAssay (.apply_pseudocount) (and maybe other functions?)

  microbiome/mia#788 · Filter by author nr0cinu opened on Oct 22, 2025
  6

• Clarification: getDissimilarity overlap metric appears to measure similarity

  microbiome/mia#787 · Filter by author ShivangPB opened on Oct 22, 2025
  5

• ecodive: A new, dependency-free package for diversity metrics (from rbiom dev)

  microbiome/mia#783 · Filter by author dansmith01 opened on Sep 23, 2025
  10

  

• Give warning when overwriting tables during normalization

  microbiome/mia#782 · Filter by author 0xMuluh opened on Sep 8, 2025
  1

• parseTaxonomy

  microbiome/mia#769 · Filter by author TuomasBorman opened on Aug 27, 2025
  

• getTop(rank = "genus", ...)

  microbiome/mia#768 · Filter by author TuomasBorman opened on Aug 27, 2025

• Allow method = "lmm" in mia::getCrossAssociation with parameter for random effects

  microbiome/mia#765 · Filter by author xec-cm opened on Aug 18, 2025
  2

• (db)RDA vs PERMANOVA

  microbiome/mia#763 · Filter by author antagomir opened on Aug 18, 2025
  1

• Tengeler2020 rowData has some families and genera with number suffix

  microbiome/mia#761 · Filter by author RiboRings opened on Aug 16, 2025
  1

• Add agglomerateByModule support for mixed ranks and multiple annotations

  microbiome/mia#760 · Filter by author RiboRings opened on Aug 8, 2025

• rbiom::unifrac deprecated

  microbiome/mia#756 · Filter by author RiboRings opened on Jul 29, 2025
  20