Euclidean_vs_Hellinger_vs_Bray

# Euclidean vs Hellinger vs Bray-Curtis distances and double zero problem
library (vegan)
library (pals)
vltava.spe <- read.delim ('https://raw.githubusercontent.com/zdealveindy/anadat-r/master/data/vltava-spe.txt', row.names = 1)

prop_dz <- function (com)
  (nrow (com)-designdist (x = com, method = "A+B-J", terms = "binary"))/nrow (com)  # calculates proportion of double zeros

D_eucl <- dist (vltava.spe, method = 'euclidean')
D_hell <- dist (decostand (vltava.spe, method = 'hell'), method = 'euclidean')
D_bray <- vegdist (vltava.spe, method = 'bray')
D_eucl_log <- dist (log1p (vltava.spe), method = 'euclidean')
D_hell_log <- dist (decostand (log1p (vltava.spe), method = 'hell'), method = 'euclidean')
D_bray_log <- vegdist (log1p (vltava.spe), method = 'bray')
D_eucl_pa <- dist (decostand (vltava.spe, 'pa'), method = 'euclidean')
D_hell_pa <- dist (decostand (decostand (vltava.spe, method = 'pa'), method = 'hell'), method = 'euclidean')
D_bray_pa <- vegdist (decostand (vltava.spe, method = 'pa'), method = 'bray')
double_zeros <- prop_dz (vltava.spe)

png ('dist_vs_doublezeros.png', width = 10, height = 10, res = 300, units = 'in', pointsize = 16)
par (mfrow = c(3,3))
plot (D_eucl ~ double_zeros, main = 'Raw data')
legend ('topright', bty = 'n', legend = '(a)')
plot (D_eucl_log ~ double_zeros, main = 'Log-transformed data')
legend ('topright', bty = 'n', legend = '(b)')
plot (D_eucl_pa ~ double_zeros, main = 'Presence-absence data')
legend ('topright', bty = 'n', legend = '(c)')
plot (D_hell ~ double_zeros)
legend ('topright', bty = 'n', legend = '(d)')
plot (D_hell_log ~ double_zeros)
legend ('topright', bty = 'n', legend = '(e)')
plot (D_hell_pa ~ double_zeros)
legend ('topright', bty = 'n', legend = '(f)')
plot (D_bray ~ double_zeros)
legend ('topright', bty = 'n', legend = '(g)')
plot (D_bray_log ~ double_zeros)
legend ('topright', bty = 'n', legend = '(h)')
plot (D_bray_pa ~ double_zeros)
legend ('topright', bty = 'n', legend = '(i)')
dev.off ()