estimateAbundance {alakazam} | R Documentation |
estimateAbundance
estimates the complete clonal relative abundance distribution
and confidence intervals on clone sizes using bootstrapping.
estimateAbundance( data, clone = "clone_id", copy = NULL, group = NULL, min_n = 30, max_n = NULL, uniform = TRUE, ci = 0.95, nboot = 200, progress = FALSE )
data |
data.frame with Change-O style columns containing clonal assignments. |
clone |
name of the |
copy |
name of the |
group |
name of the |
min_n |
minimum number of observations to sample. A group with less observations than the minimum is excluded. |
max_n |
maximum number of observations to sample. If |
uniform |
if |
ci |
confidence interval to calculate; the value must be between 0 and 1. |
nboot |
number of bootstrap realizations to generate. |
progress |
if |
A AbundanceCurve object summarizing the abundances.
Chao A. Nonparametric Estimation of the Number of Classes in a Population. Scand J Stat. 1984 11, 265270.
Chao A, et al. Rarefaction and extrapolation with Hill numbers: A framework for sampling and estimation in species diversity studies. Ecol Monogr. 2014 84:45-67.
Chao A, et al. Unveiling the species-rank abundance distribution by generalizing the Good-Turing sample coverage theory. Ecology. 2015 96, 11891201.
See plotAbundanceCurve for plotting of the abundance distribution. See alphaDiversity for a similar application to clonal diversity.
abund <- estimateAbundance(ExampleDb, group="sample_id", nboot=100)