rarefy: Calculate rarefaction using boostrapping

In sherrillmix/dnar: Miscellaneous functions to deal with bioinformatic analyses

Calculate rarefaction using boostrapping

Description

Calculate rarefaction using boostrapping

Usage

rarefy(
  counts,
  samples = unique(round(sum(counts) * seq(0.1, 1, 0.1))),
  reps = 1000,
  chaoAdjust = FALSE,
  replace = FALSE,
  minObs = 1,
  statFunc = stats::quantile,
  ...
)

Arguments

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

Value

Dataframe of calculated quantiles with rownames of the number of samples drawn

See Also

rareEquation, chao, link{rarefyCounts}

Examples

rarefy(1:20,reps=100)
rarefy(1:20,reps=100,chaoAdjust=TRUE)

sherrillmix/dnar documentation built on July 18, 2022, 10:07 p.m.