3 PERMANOVA: Permutation Analysis of Variance

PERMANOVA (Permutational Multivariate Analysis of Variance) is a statistical test used to assess the significance of differences between groups of microbial communities. Particularly suited for analyzing multivariate data like microbiome composition, PERMANOVA offers valuable insights into how different experimental conditions or treatments impact microbial community structure.

Use PERMANOVA to assess the significance of differences between groups based on multivariate data. PERMANOVA is a flexible and robust method that accounts for various data characteristics and can provide valuable insights into the factors driving variation in the data.Permutational Multivariate Analysis of Variance {#permanova}

suppressPackageStartupMessages(library(microViz))
library(dplyr) 

bray_perm <- psextra_log10p_asin_bray_dist %>%
  dist_permanova(
    seed = 1234, # for set.seed to ensure reproducibility of random process
    n_processes = 1, n_perms = 99, # you should use at least 999!
    variables = "bmi_group"
  )

perm_get(bray_perm) %>% as.data.frame()
           Df  SumOfSqs         R2        F Pr(>F)
bmi_group   2 0.1233611 0.04544245 5.212833   0.01
Residual  219 2.5913059 0.95455755       NA     NA
Total     221 2.7146670 1.00000000       NA     NA


info_get(bray_perm)
psExtra info:
tax_agg = "Genus" tax_trans = "log10p" dist_method = "bray"