breakaway: Species Richness Estimation and Modeling

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Species richness estimation is an important problem in biodiversity analysis. This package provides methods for total species richness estimation (observed plus unobserved) and a method for modelling total diversity with covariates. breakaway() estimates total (observed plus unobserved) species richness. Microbial diversity datasets are characterized by a large number of rare species and a small number of highly abundant species. The class of models implemented by breakaway() is flexible enough to model both these features. breakaway_nof1() implements a similar procedure however does not require a singleton count. betta() provides a method for modelling total diversity with covariates in a way that accounts for its estimated nature and thus accounts for unobserved taxa, and betta_random() permits random effects modelling.

Author
Amy Willis and John Bunge
Date of publication
2016-03-30 08:14:27
Maintainer
Amy Willis <adw96@cornell.edu>
License
GPL-2
Version
3.0

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Man pages

apples
"apples" dataset
betta
modelling total diversity
betta_pic
function for plotting total diversity
betta_random
modelling total diversity with random effects
breakaway
function for species richness estimation
breakaway_nof1
species richness estimation without singletons
breakaway-package
Species richness estimation and modelling in the...
chao1
species richness lower bound
chao1_bc
species richness estimator under equal detection...
chao_bunge
function for species richness estimation
hawaii
"hawaii" dataset
wlrm_transformed
function for species richness estimation
wlrm_untransformed
function for species richness estimation

Files in this package

breakaway
breakaway/NAMESPACE
breakaway/R
breakaway/R/hawaii.R
breakaway/R/betta.R
breakaway/R/chao_bunge.R
breakaway/R/wlrm_untransformed.R
breakaway/R/breakaway_nof1.R
breakaway/R/apples.R
breakaway/R/betta_random.R
breakaway/R/chao1.R
breakaway/R/chao1_bc.R
breakaway/R/betta_pic.R
breakaway/R/wlrm_transformed.R
breakaway/R/breakaway.R
breakaway/MD5
breakaway/DESCRIPTION
breakaway/man
breakaway/man/chao1_bc.Rd
breakaway/man/breakaway.Rd
breakaway/man/apples.Rd
breakaway/man/betta_random.Rd
breakaway/man/betta.Rd
breakaway/man/chao_bunge.Rd
breakaway/man/breakaway-package.Rd
breakaway/man/breakaway_nof1.Rd
breakaway/man/chao1.Rd
breakaway/man/wlrm_transformed.Rd
breakaway/man/betta_pic.Rd
breakaway/man/wlrm_untransformed.Rd
breakaway/man/hawaii.Rd