rarefaction

Tools for analyzing changes in diversity across scales

Spatial analysis and simulation of ecological communities

R package for bootstrapping indices of bipartite ecological networks

A small R script for generating pangenome accumulation curves

q2-boots: bootstrapped and rarefaction-based alpha and beta diversity analyses 🥾

R package for building turnover saturation curves via bootstrapping

Easy testing of rarefaction thresholds on microbial abundance data

Evaluación del impacto del proceso de rarefacción en la detección de comunidades microbianas en datos de amplicones ARNr 16S

SaSii is a R script for estimating genetic parameters from genotypic data for inferring sample size effects on genetic analysis. Applications of this package include planning the number of samples necessary to obtain robust population genetic estimates and evaluating if obtained sample size is large enough.

Ordin: An open-source cross-platform electron desktop application for community ecology analysis.

Analysis of existing line-point-intercept data to learn whether fewer samples can return similar results

R function that resamples randomly and without replacement counts, and calculates rarefied richness (N0), diversity (N1, N2) and evenness (N2/N0) (after Hill (1973) and Birks et al. (2016))

Compare repertoire diversity fairly across samples sequenced to different depths. Subsamples each library at a series of depths and plots how many unique sequences appear, producing rarefaction curves whose shape tells you whether you have captured a library's diversity or only scratched it.