Compare the effects of these transformations and standardizations on the ranges
and distributions of the scaled abundances.
Another way of comparing the effects of transformations on species abundances
is to plot them along the river course:
## Plot raw and transformed abundances along the upstream## downstream river gradient
par(mfrow = c(2, 2))
plot(env$dfs,
spe$Satr,
type = "l",
col = 4,
main = "Raw data",
xlab = "Distance from the source [km]",
ylab = "Raw abundance code"
)
lines(env$dfs, spe$Thth, col = 3)
lines(env$dfs, spe$Baba, col = "orange")
lines(env$dfs, spe$Abbr, col = 2)
lines(env$dfs, spe$Babl, col = 1, lty = "dotted")
plot(env$dfs,
spe.scal$Satr,
type = "l",
col = 4,
main = "Species abundances ranged
by maximum",
xlab = "Distance from the source [km]",
ylab = "Ranged abundance"
)
lines(env$dfs, spe.scal$Thth, col = 3)
lines(env$dfs, spe.scal$Baba, col = "orange")
lines(env$dfs, spe.scal$Abbr, col = 2)
lines(env$dfs, spe.scal$Babl, col = 1, lty = "dotted")
plot(env$dfs,
spe.hel$Satr,
type = "l",
col = 4,
main = "Hellinger-transformed abundances",
xlab = "Distance from the source [km]",
ylab = "Standardized abundance"
)
lines(env$dfs, spe.hel$Thth, col = 3)
lines(env$dfs, spe.hel$Baba, col = "orange")
lines(env$dfs, spe.hel$Abbr, col = 2)
lines(env$dfs, spe.hel$Babl, col = 1, lty = "dotted")
plot(env$dfs,
26
2 Exploratory Data Analysis