Package: sprex 1.4.2

sprex:Species Richness and Extrapolation

Functions for calculating species richness for rarefaction and extrapolation, primarily non-parametric species richness such as jackknife, Chao1, and ACE. Also available are functions for plotting species richness and extrapolation curves, and computing standard diversity and entropy indices.

Authors:Eric Archer [aut, cre]

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sprex.pdf |sprex.html✨
sprex/json (API)

# Installsprex in R:

install.packages('sprex', repos = c('https://ericarcher.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ericarcher/sprex/issues

Uses libs:

jags– Just Another Gibbs Sampler for Bayesian MCMC
c++– GNU Standard C++ Library v3

Datasets:

osa.old.growth - Osa beetle species counts
osa.second.growth - Osa beetle species counts

On CRAN:

18 exports 1 stars 0.93 score 73 dependencies 208 downloads

Last updated 10 months agofrom:e91b438654

Exports:.s.ind.n.m ACE bootstrap.assemblage Chao1 Clench discovery.curve diversity expand.freqs expected.num.species f.stats iChao1 jack1 jack2 num.samples.required rarefaction.overlap sample.to.species.freq species.to.sample.freq Swor1

Dependencies:abind class classInt cli clue cluster coda colorspace cpp11 DBI deldir dplyr e1071 fansi farver fBasics generics ggplot2 ggrepel glue gss gtable HDInterval igraph isoband KernSmooth kknn labeling lattice lifecycle magrittr MASS Matrix mgcv modeest munsell nlme pillar pkgconfig polyclip proxy purrr R6 RColorBrewer Rcpp rlang rmutil rpart runjags s2 scales sf spatial spatstat.data spatstat.geom spatstat.utils stable stabledist statip stringi stringr swfscMisc tibble tidyr tidyselect timeDate timeSeries units utf8 vctrs viridisLite withr wk

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate species richness and extrapolation metrics	sprex-package sprex
Number of Unobserved Species	ACE Chao1 Clench f0 iChao1 jack1 jack2 Swor1
Bootstrap Assemblage of Species	bootstrap.assemblage
Discovery Curve	discovery.curve
Diversity Indices	diversity
Expand Frequency Matrix	expand.freqs
Expected Number of Species	expected.num.species
Frequency Vector Statistics	f.stats
Number of Samples Required	num.samples.required
Osa beetle species counts	osa.old.growth osa.second.growth
Rarefaction Overlap	rarefaction.overlap
Create Vector of Species Frequencies	sample.to.species.freq
Create Vector of Sample Frequencies	species.to.sample.freq