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alakazam (version 0.2.7)

DiversityCurve-class: S4 class defining diversity curve

Description

DiversityCurve defines diversity (\(D\)) scores over multiple diversity orders (\(Q\)).

Usage

# S4 method for DiversityCurve
print(x)
# S4 method for DiversityCurve,missing
plot(x, y, ...)

Arguments

x

DiversityCurve object

y

ignored.

...

arguments to pass to plotDiversityCurve.

Slots

data

data.frame defining the diversity curve with the following columns:

  • GROUP: group label.

  • Q: diversity order.

  • D: mean diversity index over all bootstrap realizations.

  • D_SD: standard deviation of the diversity index over all bootstrap realizations.

  • D_LOWER: diversity lower confidence inverval bound.

  • D_UPPER: diversity upper confidence interval bound.

  • E: evenness index calculated as D divided by D at Q=0.

  • E_LOWER: evenness lower confidence inverval bound.

  • E_UPPER: eveness upper confidence interval bound.

groups

character vector of groups retained in the diversity calculation.

n

numeric vector indication the number of sequences sampled from each group.

nboot

number of bootstrap realizations performed.

ci

confidence interval defining the upper and lower bounds (a value between 0 and 1).