r - How to add CI whiskers to a rarefaction curve -


i need make rarefaction curves , wish them display whiskers @ edges of confidence interval bars, whereas default display bars without whiskers:

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

default rarefaction curve default rarefaction curve

i've tried add whiskers using arrows function, results specaccum function include standard deviation. ended half 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 sd whiskers rarefaction curve sd whiskers

from i've searched, common approach convert confidence intervals shaded area (by using argument ci.type="polygon") , add boxplot plotted curve. however, leads busy image i'd rather avoid.

does have more elegant solution?

you forgot multiplier (see argument ci in ?plot.specaccum). drew ~68% confidence interval. multiplying 2 (ci = 2) gives approximate 95% confidence interval, plot.specaccum draws default.

including (default) multiplier in modification of code used

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

we get:

enter image description here

you can ignore warning; standard error of last data point drawn 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() warning won't draw length 0 arrow.


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