rarefy | R Documentation |
Calculate rarefaction using boostrapping
rarefy( counts, samples = unique(round(sum(counts) * seq(0.1, 1, 0.1))), reps = 1000, chaoAdjust = FALSE, replace = FALSE, minObs = 1, statFunc = stats::quantile, ... )
counts |
Counts of species |
samples |
Vector of numbers of draws to calculate rarefaction at |
reps |
How many random samples to take at each step |
chaoAdjust |
If TRUE calculate chao-predicted species number on each random draw |
replace |
If TRUE sample with replacements. If FALSE sample without replacement. |
minObs |
Minimum number of counts to be counted as present e.g. minobs=2 discards singletons (ignored if chaoAdjust=TRUE) |
statFunc |
Function to apply to counts e.g. mean or median |
... |
Additional arguments to statFunc |
Dataframe of calculated quantiles with rownames of the number of samples drawn
rareEquation
, chao
, link{rarefyCounts}
rarefy(1:20,reps=100) rarefy(1:20,reps=100,chaoAdjust=TRUE)
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