How to add CI whiskers to a rarefaction curve

Question

I need to make some rarefaction curves and I wish them to display the whiskers at the edges of the confidence interval bars, whereas the default is to simply display the bars without whiskers:

library(vegan) 
data("dune")
result <- specaccum(dune)
plot(result, lwd=2)

Default rarefaction curve

I've tried to add some whiskers using the arrows function, but the results from the specaccum function only include the standard deviation. So I ended up with half the job done:

samples <- result$sites
error <- result$sd
richness <- result$richness
arrows(samples, richness-error, samples, richness+error, angle=90, code=3, length=0.05)

Rarefaction curve with sd whiskers

From what I've searched, the most common approach would be to convert the confidence intervals into a shaded area (by using the argument ci.type="polygon") and then add a boxplot to the plotted curve. However, this leads to a very busy image that I'd rather avoid.

Does anyone have a more elegant solution?

Answer 1

You forgot the multiplier (see argument ci in ?plot.specaccum). What you drew were for a ~68% confidence interval. Multiplying by 2 (ci = 2) gives an approximate 95% confidence interval, which is what plot.specaccum draws by default.

Including the (default) multiplier in a modification of the code you used

plot(result)
with(result, arrows(sites, richness - (2 * sd), sites, richness + (2 * sd),
                    angle = 90, code = 3, length = 0.05))

we get:

You can ignore the warning; the standard error of the last data point drawn is zero

> result$sd
 [1] 2.3510636 1.8763851 1.5722711 1.4469584 1.3901594 1.3530349 1.3164796
 [8] 1.2749034 1.2282010 1.1763410 1.1193437 1.0564537 0.9874094 0.9115998
[15] 0.8286890 0.7380921 0.6333903 0.5139710 0.3570714 0.0000000

and arrow() is just warning you that it won't draw a length 0 arrow.