Phyloseq 1.24.2
Call:
adonis(formula = dist ~ EnvType, data = metadata, permutations = 9999)
Permutation: free
Number of permutations: 9999
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
EnvType 7 7.6565 1.09379 13.699 0.63132 1e-04 ***
Residuals 56 4.4713 0.07984 0.36868
Total 63 12.1278 1.00000
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
library(vegan)
## if in new session
# library(phyloseq)
#
## load phyloseq object
# data <- path to Rdata file
# load(data)
# extract sample metadata in a dataframe
metadata <- as(sample_data(data), "data.frame")
## load beta distance matrix
beta_file <- # path to Beta diversity tsv file
A <- read.table(file=beta_file, row.names=1)
beta_dist <- as.dist(A)
## change experiment variable (currently EnvType )if you wish
## Multivariate ANOVA performed with adonis
adonis(beta_dist ~ EnvType, data = metadata, perm = 9999)