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zetadiv (version 1.2.0)

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

267

Version

1.2.0

License

GPL-3

Last Published

July 2nd, 2020

Functions in zetadiv (1.2.0)

Predict.msgdm

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

Plotting of zeta diversity scaling with sample grain using hierarchical increases in grain size
Plot.ispline

Plots I-splines for Multi-Site Generalised Dissimilarity Modelling
Plot.zeta.decline

Zeta diversity decline plotting
Marion.env

Marion Island Environmental Dataset
Plot.zeta.scale.min.dist

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

Perform an I-spline regression
Zeta.ddecay

Zeta distance decay for a specific number of assemblages or sites
Zeta.ddecays

Zeta distance decay for a range of numbers of assemblages or sites
Zeta.order.ex

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

Multi-site generalised dissimilarity modelling for a set of environmental variables and distances
bird.env.fine

South-East Australia Environmental Dataset at Fine Scale
Zeta.order.mc

Zeta diversity for a specific number of assemblages or sites using Monte Carlo sampling
Zeta.order.mc.mult

Number of species in common between a specific number of assemblages or sites using Monte Carlo sampling, for multiple combinations and several groups of taxa
bird.env.coarse

South-East Australia Environmental Dataset at Coarse Scale
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
Return.ispline

Computing splines coordinates from I-spline-based multi-site generalised dissimilarity modelling
bird.spec.coarse

Australia Bird Atlas Species Occurrence Dataset at Coarse Scale over South-East Australia
pie.neg

Pie Chart, considering negative values as zeros
rescale.min.dist

Rescaling of data based on the minimum distance between sites
Zeta.decline.ex

Expectation of zeta diversity decline
Zeta.decline.mc

Zeta diversity decline using Monte Carlo sampling
Zeta.scale.regular

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

Rescaling of data following a hierarchical increase in grain size
Zeta.varpart

Variation partitioning for zeta diversity
glm.fit.cons

Generalized Linear Models fitting method with negative coefficients constraint
glm.cons

Fitting Generalized Linear Models with constraint on the coefficients signs
bird.spec.fine

Australia Bird Atlas Species Occurrence Dataset at Fine Scale over South-East Australia