Data Import: Load OTU/ASV/species count table + metadata.
Preprocessing: Filter low-abundance taxa, normalize (rarefaction/CSS/CLR), transform if needed.
Alpha Diversity: Compute within-sample richness/evenness indices.
Beta Diversity: Calculate between-sample dissimilarity matrix.
Ordination & Testing: Visualize patterns (NMDS/PCoA) and test group differences (PERMANOVA/ANOSIM).

library(vegan)

Load data

otu <- read.table("asv_table.tsv", header=T, row.names=1, sep="\t")
meta <- read.table("metadata.tsv", header=T, row.names=1, sep="\t")

Alpha diversity

alpha <- data.frame(
Shannon = diversity(t(otu), index="shannon"),
Richness = specnumber(t(otu))
)

dist_bc <- vegdist(t(otu), method="bray")
nmds <- metaMDS(dist_bc, k=2, trymax=100)

perm <- adonis2(dist_bc ~ Condition, data=meta, permutations=999)

plot(nmds, display="sites"); ordihull(nmds, meta$Condition, col=1:3)