untb: ecological drift under the UNTB

A collection of utilities for biodiversity data. Includes the simulation of ecological drift under Hubbell's Unified Neutral Theory of Biodiversity, and the calculation of various diagnostics such as Preston curves. Now includes functionality provided by Francois Munoz and Andrea Manica.

Author
Robin K. S. Hankin
Date of publication
2013-12-12 20:26:25
Maintainer
Robin K. S. Hankin <hankin.robin@gmail.com>
License
GPL
Version
1.7-2
URLs

View on CRAN

Man pages

alonso
Various functions from Alonso and McKane 2004
bci
Barro Colorado Island (BCI) dataset
butterflies
abundance data for butterflies
caruso
Dataset due to Caruso
census
Construct, coerce, and test for a census object
copepod
Copepod data supplied by Phil Pugh
count
Construct, coerce, and test for a count object
display.untb
Animation of neutral ecological drift
etienne
Etienne's sampling formula
expected.abundance
Expected abundances under the neutral model
extractor
Extract rows of a database in count form
fisher
Various functionality to implement Fisher's logseries
ghats
Tree counts in 1-ha plots from the Western Ghats mountains...
isolate
Randomly select a subset of an ecosystem
logkda
Etienne's K(D,A)
logS1
logarithms of Stirling numbers of the first kind
no.of.ind
Ecosystem diagnostics
optimal.params.gst
Estimation of local immigration using GST(k) statistics
optimal.params.sloss
Estimation of neutral community parameters using a two-stage...
optimal.prob
Returns an estimate of the fundamental biodiversity number
phi
Hubbell's phi
plot.count
Abundance curves
plus
Add two count objects
preston
Preston diagram of an ecosystem
print.preston
Print and plot objects of class Preston
print.summary.count
Print method for summary objects
rand.neutral
Random neutral ecosystem
sahfos
Biodiversity dataset provided by SAHFOS
saunders
Dataset due to Saunders
simpson
Simpson's diversity index
species.count
Ecosystem diagnostics for output of untb()
spitale
Counts of diatom species in springs of the Adamello-Brenta...
summary
Summary methods for count and census objects
theta.prob
Posterior probabilities for theta
untb
Ecological drift simulation under the Unified Neutral Theory...
untb.package
Unified neutral theory of biodiversity
vallade
Various functions from Vallade and Houchmandzadeh
volkov
Expected frequency of species
zsm
Zero sum multinomial distribution as derived by McKane

Files in this package

untb
untb/inst
untb/inst/CITATION
untb/inst/doc
untb/inst/doc/untbpaper.pdf
untb/inst/doc/untbpaper.R
untb/inst/doc/untbpaper.Rnw
untb/NAMESPACE
untb/demo
untb/demo/untb.R
untb/demo/00Index
untb/data
untb/data/ostracod.rda
untb/data/sahfos.rda
untb/data/butterflies.rda
untb/data/ghats.rda
untb/data/copepod.rda
untb/data/saunders.rda
untb/data/spitale.rda
untb/data/caruso.rda
untb/R
untb/R/untb.R
untb/R/sysdata.rda
untb/R/munoz.R
untb/vignettes
untb/vignettes/dat.Rdata
untb/vignettes/rn.Rdata
untb/vignettes/synthetic_spp.Rdata
untb/vignettes/a_logkda.Rdata
untb/vignettes/untb.bib
untb/vignettes/untbpaper.Rnw
untb/MD5
untb/build
untb/build/vignette.rds
untb/DESCRIPTION
untb/man
untb/man/logS1.Rd
untb/man/ghats.Rd
untb/man/plot.count.Rd
untb/man/rand.neutral.Rd
untb/man/butterflies.Rd
untb/man/untb.package.Rd
untb/man/simpson.Rd
untb/man/optimal.params.sloss.Rd
untb/man/print.preston.Rd
untb/man/alonso.Rd
untb/man/bci.Rd
untb/man/isolate.Rd
untb/man/optimal.prob.Rd
untb/man/vallade.Rd
untb/man/zsm.Rd
untb/man/etienne.Rd
untb/man/untb.Rd
untb/man/fisher.Rd
untb/man/spitale.Rd
untb/man/display.untb.Rd
untb/man/volkov.Rd
untb/man/plus.Rd
untb/man/census.Rd
untb/man/sahfos.Rd
untb/man/extractor.Rd
untb/man/species.count.Rd
untb/man/preston.Rd
untb/man/phi.Rd
untb/man/print.summary.count.Rd
untb/man/no.of.ind.Rd
untb/man/count.Rd
untb/man/theta.prob.Rd
untb/man/saunders.Rd
untb/man/expected.abundance.Rd
untb/man/copepod.Rd
untb/man/caruso.Rd
untb/man/summary.Rd
untb/man/optimal.params.gst.Rd
untb/man/logkda.Rd