Package: zetadiv 1.2.1

Guillaume Latombe

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.

Authors:Guillaume Latombe [aut, cre], Melodie A. McGeoch [aut], David A. Nipperess [aut], Cang Hui [aut]

zetadiv_1.2.1.tar.gz
zetadiv_1.2.1.tar.gz(r-4.5-noble)zetadiv_1.2.1.tar.gz(r-4.4-noble)
zetadiv_1.2.1.tgz(r-4.4-emscripten)zetadiv_1.2.1.tgz(r-4.3-emscripten)
zetadiv.pdf |zetadiv.html✨
zetadiv/json (API)

# Install 'zetadiv' in R:
install.packages('zetadiv', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • Marion.env - Marion Island Environmental Dataset
  • Marion.species - Marion Island Species Presence-Absence Dataset
  • 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 Scale over South-East Australia
  • bird.spec.fine - Australia Bird Atlas Species Occurrence Dataset at Fine Scale over South-East Australia

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

27 exports 3 stars 1.38 score 66 dependencies 4 mentions 60 scripts 331 downloads

Last updated 2 years agofrom:68130abd19. Checks:OK: 1 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 25 2024
R-4.5-linuxNOTEAug 25 2024

Exports:glm.consglm.fit.consIsplinepie.negPlot.isplinePlot.zeta.ddecayPlot.zeta.ddecaysPlot.zeta.declinePlot.zeta.scale.min.distPlot.zeta.scale.regularPredict.msgdmReg.isplinerescale.min.distrescale.regularReturn.isplineZeta.ddecayZeta.ddecaysZeta.decline.exZeta.decline.mcZeta.msgdmZeta.order.exZeta.order.mcZeta.order.mc.multZeta.sam.sensitivityZeta.scale.min.distZeta.scale.regularZeta.varpart

Dependencies:abindbackportsbootbroomcarcarDatacliclustercolorspacecowplotcpp11DerivdoBydplyrfansifarvergenericsgeodistggplot2glm2gluegtableisobandlabelinglatticelifecyclelme4magrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkminqamodelrmunsellnlmenloptrnnetnnlsnumDerivpbkrtestpermutepillarpkgconfigpurrrquantregR6RColorBrewerRcppRcppEigenrlangscalesscamSparseMstringistringrsurvivaltibbletidyrtidyselectutf8vctrsveganviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
South-East Australia Environmental Dataset at Coarse Scalebird.env.coarse
South-East Australia Environmental Dataset at Fine Scalebird.env.fine
Australia Bird Atlas Species Occurrence Dataset at Coarse Scale over South-East Australiabird.spec.coarse
Australia Bird Atlas Species Occurrence Dataset at Fine Scale over South-East Australiabird.spec.fine
Fitting Generalized Linear Models with constraint on the coefficients signsglm.cons
Generalized Linear Models fitting method with negative coefficients constraintglm.fit.cons
Transform data using I-splinesIspline
Marion Island Environmental DatasetMarion.env
Marion Island Species Presence-Absence DatasetMarion.species
Pie Chart, considering negative values as zerospie.neg
Plots I-splines for Multi-Site Generalised Dissimilarity ModellingPlot.ispline
Zeta distance-decay plottingPlot.zeta.ddecay
Zeta distance-decay plotting for multiple ordersPlot.zeta.ddecays
Zeta diversity decline plottingPlot.zeta.decline
Plotting of zeta diversity scaling with sample grain dependency based on the minimum distance between sitesPlot.zeta.scale.min.dist
Plotting of zeta diversity scaling with sample grain using hierarchical increases in grain sizePlot.zeta.scale.regular
Predict zeta values for new environmental and distance dataPredict.msgdm
Perform an I-spline regressionReg.ispline
Rescaling of data based on the minimum distance between sitesrescale.min.dist
Rescaling of data following a hierarchical increase in grain sizerescale.regular
Computing splines coordinates from I-spline-based multi-site generalised dissimilarity modellingReturn.ispline
Zeta distance decay for a specific number of assemblages or sitesZeta.ddecay
Zeta distance decay for a range of numbers of assemblages or sitesZeta.ddecays
Expectation of zeta diversity declineZeta.decline.ex
Zeta diversity decline using Monte Carlo samplingZeta.decline.mc
Multi-site generalised dissimilarity modelling for a set of environmental variables and distancesZeta.msgdm
Expectation of zeta diversity for a specific number of assemblages or sitesZeta.order.ex
Zeta diversity for a specific number of assemblages or sites using Monte Carlo samplingZeta.order.mc
Number of species in common between a specific number of assemblages or sites using Monte Carlo sampling, for multiple combinations and several groups of taxaZeta.order.mc.mult
Sensitivity analysis for the sample size of zetaZeta.sam.sensitivity
Zeta diversity scaling with sample grain dependency based on the minimum distance between sitesZeta.scale.min.dist
Zeta diversity scaling with sample grain using hierarchical increases in grain sizeZeta.scale.regular
Variation partitioning for zeta diversityZeta.varpart