zetadiv: Functions to Compute Compositional Turnover Using Zeta Diversity
Version 1.0

Functions to compute compositional turnover using zeta-diversity, the number of species shared by multiple assemblages. The package includes functions to compute zeta-diversity for a specific number of assemblages and to compute zeta-diversity for a range of numbers of assemblages. It also includes functions to explain how zeta-diversity varies with distance and with differences in environmental variables between assemblages, using generalised linear models, linear models with negative constraints, generalised additive models,shape constrained additive models, and I-splines.

AuthorGuillaume Latombe, Melodie A. McGeoch, David A. Nipperess, Cang Hui
Date of publication2016-12-09 08:58:59
MaintainerGuillaume Latombe <guillaume.latombe@monash.edu>
LicenseGPL-3
Version1.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("zetadiv")

Popular man pages

glm.fit.cons: Generalized Linear Models fitting method with negative...
Marion.species: Marion Island Species Presence-Absence Dataset
Plot.zeta.ddecay: Zeta distance-decay plotting
Plot.zeta.scale.min.dist: Plotting of zeta diversity scaling with sample grain...
Zeta.ddecay: Zeta distance decay for a specific number of assemblages or...
Zeta.scale.regular: Zeta diversity scaling with sample grain using hierarchical...
Zeta.varpart: Variation partitioning for zeta diversity
See all...

All man pages Function index File listing

Man pages

bird.env.coarse: South-East Australia Environmental Dataset at Coarse Scale
bird.env.fine: South-East Australia Environmental Dataset at Fine Scale
bird.spec.coarse: Australia Bird Atlas Species Occurrence Dataset at Coarse...
bird.spec.fine: Australia Bird Atlas Species Occurrence Dataset at Fine Scale...
glm.cons: Fitting Generalized Linear Models with constraint on the...
glm.fit.cons: Generalized Linear Models fitting method with negative...
Ispline: Transform data using I-splines
Marion.env: Marion Island Environmental Dataset
Marion.species: Marion Island Species Presence-Absence Dataset
pie.neg: Pie Chart, considering negative values as zeros
Plot.zeta.ddecay: Zeta distance-decay plotting
Plot.zeta.ddecays: Zeta distance-decay plotting for multiple orders
Plot.zeta.decline: Zeta diversity decline plotting
Plot.zeta.scale.min.dist: Plotting of zeta diversity scaling with sample grain...
Plot.zeta.scale.regular: Plotting of zeta diversity scaling with sample grain using...
Predict.msgdm: Predict zeta values for new environmental and distance data
rescale.min.dist: Rescaling of data based on the minimum distance between sites
rescale.regular: Rescaling of data following a hierarchical increase in grain...
Zeta.ddecay: Zeta distance decay for a specific number of assemblages or...
Zeta.ddecays: Zeta distance decay for a range of numbers of assemblages or...
Zeta.decline.ex: Expectation of zeta diversity decline
Zeta.decline.mc: Zeta diversity decline using Monte Carlo sampling
Zeta.msgdm: Multi-site generalised dissimilarity modelling for a set of...
Zeta.order.ex: Expectation of zeta diversity for a specific number of...
Zeta.order.mc: Zeta diversity for a specific number of assemblages or sites...
Zeta.sam.sensitivity: Sensitivity analysis for the sample size of zeta
Zeta.scale.min.dist: Zeta diversity scaling with sample grain dependency based on...
Zeta.scale.regular: Zeta diversity scaling with sample grain using hierarchical...
Zeta.varpart: Variation partitioning for zeta diversity

Functions

D2notExp Source code
D3notExp Source code
DnotExp Source code
Ii Source code
Ispline Man page Source code
Marion.env Man page
Marion.species Man page
Mi Source code
Plot.zeta.ddecay Man page Source code
Plot.zeta.ddecays Man page Source code
Plot.zeta.decline Man page Source code
Plot.zeta.scale.min.dist Man page Source code
Plot.zeta.scale.regular Man page Source code
Predict.msgdm Man page Source code
Scam.zeta Source code
Zeta.ddecay Man page Source code
Zeta.ddecays Man page Source code
Zeta.decline.ex Man page Source code
Zeta.decline.mc Man page Source code
Zeta.msgdm Man page Source code
Zeta.order.ex Man page Source code
Zeta.order.mc Man page Source code
Zeta.sam.sensitivity Man page Source code
Zeta.scale.min.dist Man page Source code
Zeta.scale.regular Man page Source code
Zeta.varpart Man page Source code
bfgs_gcv.ubre Source code
bird.env.coarse Man page
bird.env.fine Man page
bird.spec.coarse Man page
bird.spec.fine Man page
dgcv.ubre.nlm Source code
estimate.scam Source code
gcv.ubre Source code
gcv.ubre.derivative Source code
gdist_matrix Source code
glm.cons Man page Source code
glm.fit.cons Man page Source code
initial.sp.scam Source code
notExp Source code
onAttach Source code
penalty_pident Source code
pie.neg Man page Source code
rescale.min.dist Man page Source code
rescale.regular Man page Source code
scam.fit.post Source code

Files

NAMESPACE
data
data/bird.spec.coarse.RData
data/Marion.species.RData
data/bird.spec.fine.RData
data/bird.env.coarse.RData
data/bird.env.fine.RData
data/Marion.env.RData
R
R/zetadiv.R
R/unexported.functions.from.scam.1.2.R
MD5
DESCRIPTION
man
man/Plot.zeta.decline.Rd
man/Zeta.decline.ex.Rd
man/Plot.zeta.scale.min.dist.Rd
man/Zeta.sam.sensitivity.Rd
man/Zeta.ddecays.Rd
man/Zeta.order.mc.Rd
man/Zeta.scale.regular.Rd
man/rescale.regular.Rd
man/rescale.min.dist.Rd
man/Zeta.order.ex.Rd
man/Zeta.varpart.Rd
man/Plot.zeta.ddecay.Rd
man/bird.env.fine.Rd
man/bird.spec.fine.Rd
man/Marion.env.Rd
man/glm.fit.cons.Rd
man/pie.neg.Rd
man/Plot.zeta.scale.regular.Rd
man/Zeta.decline.mc.Rd
man/Plot.zeta.ddecays.Rd
man/Marion.species.Rd
man/bird.spec.coarse.Rd
man/bird.env.coarse.Rd
man/Zeta.scale.min.dist.Rd
man/Zeta.msgdm.Rd
man/Predict.msgdm.Rd
man/Zeta.ddecay.Rd
man/Ispline.Rd
man/glm.cons.Rd
zetadiv documentation built on May 20, 2017, 3:45 a.m.

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