untb v1.6-5
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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.
Functions in untb
| Name | Description | |
| bci | Barro Colorado Island (BCI) dataset | |
| extractor | Extract rows of a database in count form | |
| ghats | Tree counts in 1-ha plots from the Western Ghats mountains (South India) | |
| isolate | Randomly select a subset of an ecosystem | |
| logkda | Etienne's K(D,A) | |
| optimal.params.gst | Estimation of local immigration using GST(k) statistics | |
| preston | Preston diagram of an ecosystem | |
| simpson | Simpson's diversity index | |
| saunders | Dataset due to Saunders | |
| summary.count | Summary methods for count and census objects | |
| rand.neutral | Random neutral ecosystem | |
| vallade | Various functions from Vallade and Houchmandzadeh | |
| alonso | Various functions from Alonso and McKane 2004 | |
| untb-package | Unified neutral theory of biodiversity | |
| butterflies | abundance data for butterflies | |
| copepod | Copepod data supplied by Phil Pugh | |
| caruso | Dataset due to Caruso | |
| count | Construct, coerce, and test for a count object | |
| phi | Hubbell's phi | |
| census | Construct, coerce, and test for a census object | |
| etienne | Etienne's sampling formula | |
| untb | Ecological drift simulation under the Unified Neutral Theory of Biodiversity | |
| species.count | Ecosystem diagnostics for output of untb() | |
| expected.abundance | Expected abundances under the neutral model | |
| display.untb | Animation of neutral ecological drift | |
| fisher | Various functionality to implement Fisher's logseries | |
| sahfos | Biodiversity dataset provided by SAHFOS | |
| zsm | Zero sum multinomial distribution as derived by McKane | |
| print.summary.count | Print method for summary objects | |
| logS1 | logarithms of Stirling numbers of the first kind | |
| no.of.ind | Ecosystem diagnostics | |
| print.preston | Print and plot objects of class Preston | |
| theta.prob | Posterior probabilities for theta | |
| optimal.prob | Returns an estimate of the fundamental biodiversity number | |
| optimal.params.sloss | Estimation of neutral community parameters using a two-stage maximum-likelihood procedure | |
| volkov | Expected frequency of species | |
| plot.count | Abundance curves | |
| +.count | Add two count objects | |
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Details
| Type | Package |
| Date | 2009-26-02 |
| SystemRequirements | PARI/GP >= 2.3.0 [strongly recommended for logkda()] |
| License | GPL |
| URL | http://www.r-project.org |
| Packaged | 2011-03-17 07:50:30 UTC; rksh |
| Repository | CRAN |
| Date/Publication | 2011-03-18 07:32:49 |
| depends | Brobdingnag , partitions , polynom , vegan |
| Contributors | Robin S. Hankin |
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