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.

AuthorRobin K. S. Hankin
Date of publication2013-12-12 20:26:25
MaintainerRobin K. S. Hankin <hankin.robin@gmail.com>
LicenseGPL
Version1.7-2
http://www.r-project.org

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

Functions

alonso.eqn11 Man page
alonso.eqn12 Man page
alonso.eqn6 Man page
as.census Man page
as.count Man page
bci Man page
BCI Man page
butterflies Man page
butterfly Man page
caruso Man page
Caruso Man page
census Man page
+.census Man page
copepod Man page
count Man page
+.count Man page
display.untb Man page
etienne Man page
Etienne Man page
expected.abundance Man page
extant Man page
extinct Man page
extractor Man page
fisher Man page
fisher.ecosystem Man page
fishers.alpha Man page
ghats Man page
GST.k Man page
I.k Man page
is.census Man page
is.count Man page
isolate Man page
logkda Man page
logkda.a11 Man page
logkda.pari Man page
logkda_pari_unix Man page
logkda_pari_windows Man page
logkda.polyn Man page
logkda.R Man page
logS1 Man page
logS1vect Man page
maximal.abundance Man page
no.of.extinct Man page
no.of.ind Man page
no.of.singletons Man page
no.of.spp Man page
optimal.params Man page
optimal.params.gst Man page
optimal.params.sloss Man page
optimal.prob Man page
optimal.theta Man page
oribatid Man page
Oribatid Man page
ostracod Man page
phi Man page
plot.census Man page
plot.count Man page
plot.preston Man page
preston Man page
Preston Man page
print.preston Man page
print.summary.census Man page
print.summary.count Man page
rand.neutral Man page
sahfos Man page
saunders Man page
saunders.exposed Man page
saunders.exposed.tot Man page
saunders.sheltered Man page
saunders.sheltered.tot Man page
saunders.tot Man page
select Man page
select.immigrate Man page
select.mutate Man page
simpson Man page
singletons Man page
species.count Man page
species.table Man page
spitale Man page
summary.census Man page
summary.count Man page
theta.likelihood Man page
theta.prob Man page
unphi Man page
untb Man page
untb-package Man page
vallade Man page
Vallade Man page
vallade.eqn12 Man page
vallade.eqn14 Man page
vallade.eqn16 Man page
vallade.eqn17 Man page
vallade.eqn5 Man page
vallade.eqn7 Man page
volkov Man page
zsm Man page

Files

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

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.