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zetadiv (version 1.1.1)

Functions to Compute Compositional Turnover Using Zeta Diversity

Description

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.

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Version

Install

install.packages('zetadiv')

Monthly Downloads

496

Version

1.1.1

License

GPL-3

Maintainer

Guillaume Latombe

Last Published

May 17th, 2018

Functions in zetadiv (1.1.1)

Zeta.order.ex

Expectation of zeta diversity for a specific number of assemblages or sites
Zeta.varpart

Variation partitioning for zeta diversity
rescale.min.dist

Rescaling of data based on the minimum distance between sites
bird.env.fine

South-East Australia Environmental Dataset at Fine Scale
bird.spec.coarse

Australia Bird Atlas Species Occurrence Dataset at Coarse Scale over South-East Australia
rescale.regular

Rescaling of data following a hierarchical increase in grain size
glm.cons

Fitting Generalized Linear Models with constraint on the coefficients signs
bird.env.coarse

South-East Australia Environmental Dataset at Coarse Scale
bird.spec.fine

Australia Bird Atlas Species Occurrence Dataset at Fine Scale over South-East Australia
glm.fit.cons

Generalized Linear Models fitting method with negative coefficients constraint
pie.neg

Pie Chart, considering negative values as zeros
Plot.zeta.decline

Zeta diversity decline plotting
Plot.ispline

Plotting splines from I-spline-based multi-site generalised dissimilarity modelling
Plot.zeta.scale.regular

Plotting of zeta diversity scaling with sample grain using hierarchical increases in grain size
Predict.msgdm

Predict zeta values for new environmental and distance data
Plot.zeta.scale.min.dist

Plotting of zeta diversity scaling with sample grain dependency based on the minimum distance between sites
Marion.species

Marion Island Species Presence-Absence Dataset
Plot.zeta.ddecay

Zeta distance-decay plotting
Ispline

Transform data using I-splines
Plot.zeta.ddecays

Zeta distance-decay plotting for multiple orders
Marion.env

Marion Island Environmental Dataset
Zeta.decline.ex

Expectation of zeta diversity decline
Zeta.order.mc

Zeta diversity for a specific number of assemblages or sites using Monte Carlo sampling
Zeta.sam.sensitivity

Sensitivity analysis for the sample size of zeta
Zeta.scale.min.dist

Zeta diversity scaling with sample grain dependency based on the minimum distance between sites
Zeta.decline.mc

Zeta diversity decline using Monte Carlo sampling
Zeta.ddecays

Zeta distance decay for a range of numbers of assemblages or sites
Zeta.scale.regular

Zeta diversity scaling with sample grain using hierarchical increases in grain size
Zeta.msgdm

Multi-site generalised dissimilarity modelling for a set of environmental variables and distances
Zeta.ddecay

Zeta distance decay for a specific number of assemblages or sites