R: Ecological Drift under the UNTB

# Ecological Drift under the UNTB

## Documentation for package ‘untb’ version 1.7-7-1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Code demos. Use demo() to run them.
- Package README

## Help Pages

untb-package | Unified neutral theory of biodiversity
+.census | Add two count objects
+.count | Add two count objects
alonso.eqn11 | Various functions from Alonso and McKane 2004
alonso.eqn12 | Various functions from Alonso and McKane 2004
alonso.eqn6 | Various functions from Alonso and McKane 2004
as.census | Construct, coerce, and test for a census object
as.count | Construct, coerce, and test for a count object
BCI | Barro Colorado Island (BCI) dataset
bci | Barro Colorado Island (BCI) dataset
butterflies | abundance data for butterflies
butterfly | abundance data for butterflies
Caruso | Dataset due to Caruso
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
etienne | Etienne's sampling formula
expected.abundance | Expected abundances under the neutral model
extant | Ecosystem diagnostics
extinct | Ecosystem diagnostics
extractor | Extract rows of a database in count form
fisher | Various functionality to implement Fisher's logseries
fisher.ecosystem | Various functionality to implement Fisher's logseries
fishers.alpha | Various functionality to implement Fisher's logseries
ghats | Tree counts in 1-ha plots from the Western Ghats mountains (South India)
GST.k | Estimation of local immigration using GST(k) statistics
I.k | Estimation of local immigration using GST(k) statistics
is.census | Construct, coerce, and test for a census object
is.count | Construct, coerce, and test for a count object
isolate | Randomly select a subset of an ecosystem
logkda | Etienne's K(D,A)
logkda.a11 | Etienne's K(D,A)
logkda.pari | Etienne's K(D,A)
logkda.polyn | Etienne's K(D,A)
logkda.R | Etienne's K(D,A)
logkda_pari_unix | Etienne's K(D,A)
logkda_pari_windows | Etienne's K(D,A)
logS1 | logarithms of Stirling numbers of the first kind
logS1vect | logarithms of Stirling numbers of the first kind
maximal.abundance | Ecosystem diagnostics
no.of.extinct | Ecosystem diagnostics
no.of.ind | Ecosystem diagnostics
no.of.singletons | Ecosystem diagnostics
no.of.spp | Ecosystem diagnostics
optimal.params | Etienne's sampling formula
optimal.params.gst | Estimation of local immigration using GST(k) statistics
optimal.params.sloss | Estimation of neutral community parameters using a two-stage maximum-likelihood procedure
optimal.prob | Returns an estimate of the fundamental biodiversity number
optimal.theta | Returns an estimate of the fundamental biodiversity number
Oribatid | Dataset due to Caruso
oribatid | Dataset due to Caruso
ostracod | Copepod data supplied by Phil Pugh
phi | Hubbell's phi
plot.census | Abundance curves
plot.count | Abundance curves
plot.preston | Print and plot objects of class Preston
Preston | Preston diagram of an ecosystem
preston | Preston diagram of an ecosystem
print.preston | Print and plot objects of class Preston
print.summary.census | Print method for summary objects
print.summary.count | Print method for summary objects
rand.neutral | Random neutral ecosystem
sahfos | Biodiversity dataset provided by SAHFOS
saunders | Dataset due to Saunders
saunders.exposed | Dataset due to Saunders
saunders.exposed.tot | Dataset due to Saunders
saunders.sheltered | Dataset due to Saunders
saunders.sheltered.tot | Dataset due to Saunders
saunders.tot | Dataset due to Saunders
select | Ecological drift simulation under the Unified Neutral Theory of Biodiversity
select.immigrate | Ecological drift simulation under the Unified Neutral Theory of Biodiversity
select.mutate | Ecological drift simulation under the Unified Neutral Theory of Biodiversity
simpson | Simpson's diversity index
singletons | Ecosystem diagnostics
species.count | Ecosystem diagnostics for output of untb()
species.table | Ecosystem diagnostics for output of untb()
spitale | Counts of diatom species in springs of the Adamello-Brenta Nature Park
summary.census | Summary methods for count and census objects
summary.count | Summary methods for count and census objects
theta.likelihood | Posterior probabilities for theta
theta.prob | Posterior probabilities for theta
unphi | Hubbell's phi
untb | Ecological drift simulation under the Unified Neutral Theory of Biodiversity
Vallade | Various functions from Vallade and Houchmandzadeh
vallade | Various functions from Vallade and Houchmandzadeh
vallade.eqn12 | Various functions from Vallade and Houchmandzadeh
vallade.eqn14 | Various functions from Vallade and Houchmandzadeh
vallade.eqn16 | Various functions from Vallade and Houchmandzadeh
vallade.eqn17 | Various functions from Vallade and Houchmandzadeh
vallade.eqn5 | Various functions from Vallade and Houchmandzadeh
vallade.eqn7 | Various functions from Vallade and Houchmandzadeh
volkov | Expected frequency of species
zsm | Zero sum multinomial distribution as derived by McKane