zetadiv: Functions to Compute Compositional Turnover Using Zeta Diversity

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.

Install the latest version of this package by entering the following in R:
install.packages("zetadiv")
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

View on CRAN

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

bird.env.coarse Man page
bird.env.fine Man page
bird.spec.coarse Man page
bird.spec.fine Man page
glm.cons Man page
glm.fit.cons Man page
Ispline Man page
Marion.env Man page
Marion.species Man page
pie.neg Man page
Plot.zeta.ddecay Man page
Plot.zeta.ddecays Man page
Plot.zeta.decline Man page
Plot.zeta.scale.min.dist Man page
Plot.zeta.scale.regular Man page
Predict.msgdm Man page
rescale.min.dist Man page
rescale.regular Man page
Zeta.ddecay Man page
Zeta.ddecays Man page
Zeta.decline.ex Man page
Zeta.decline.mc Man page
Zeta.msgdm Man page
Zeta.order.ex Man page
Zeta.order.mc Man page
Zeta.sam.sensitivity Man page
Zeta.scale.min.dist Man page
Zeta.scale.regular Man page
Zeta.varpart Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.