Package: untb 1.7-7-2

untb: Ecological Drift under the UNTB

Hubbell's Unified Neutral Theory of Biodiversity.

Authors:Robin K. S. Hankin [aut, cre]

untb_1.7-7-2.tar.gz
untb_1.7-7-2.zip(r-4.7)untb_1.7-7-2.zip(r-4.6)untb_1.7-7-2.zip(r-4.5)
untb_1.7-7-2.tgz(r-4.6-any)untb_1.7-7-2.tgz(r-4.5-any)
untb_1.7-7-2.tar.gz(r-4.7-any)untb_1.7-7-2.tar.gz(r-4.6-any)
untb_1.7-7-2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
untb/json (API)

# Install 'untb' in R:

install.packages('untb', repos = c('https://robinhankin.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/robinhankin/untb/issues

Pkgdown/docs site:https://robinhankin.github.io

Datasets:

butterflies - Abundance data for butterflies
caruso - Dataset due to Caruso
copepod - Copepod data supplied by Phil Pugh
ghats - Tree counts in 1-ha plots from the Western Ghats mountains
ostracod - Copepod data supplied by Phil Pugh
sahfos - Biodiversity dataset provided by SAHFOS
saunders - Dataset due to Saunders
saunders.tot - Dataset due to Saunders
spitale - Counts of diatom species in springs of the Adamello-Brenta Nature Park

On CRAN:

6.56 score 4 stars 87 scripts 337 downloads 7 mentions 70 exports 9 dependencies

Last updated from:7ab3402804. Checks:7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	NOTE	230
source / vignettes	OK	249
linux-release-x86_64	NOTE	178
macos-release-arm64	NOTE	117
macos-oldrel-arm64	NOTE	87
windows-devel	NOTE	117
windows-release	NOTE	121
windows-oldrel	NOTE	96
wasm-release	OK	112

Exports:+.census +.count alonso.eqn11 alonso.eqn12 alonso.eqn6 as.census as.count census count display.untb etienne expected.abundance extant extinct extractor fisher.ecosystem fishers.alpha GST.k I.k is.census is.count isolate logkda logkda_pari_unix logkda_pari_windows logkda.a11 logkda.pari logkda.polyn logkda.R logS1 logS1vect maximal.abundance no.of.extinct no.of.ind no.of.singletons no.of.spp optimal.params optimal.params.gst optimal.params.sloss optimal.prob optimal.theta phi plot.census plot.count plot.preston preston print.preston print.summary.count rand.neutral select select.immigrate select.mutate simpson singletons species.count species.table summary.census summary.count theta.likelihood theta.prob unphi untb vallade.eqn12 vallade.eqn14 vallade.eqn16 vallade.eqn17 vallade.eqn5 vallade.eqn7 volkov zsm

Dependencies:Brobdingnag gmp lattice Matrix partitions polynom rbibutils Rdpack sets

A vignette for the untb package

Island biogeography and biodiversity | Package untb in use | Conclusions

Rendered fromuntb.Rnwusingutils::Sweave

Last update: 2024-12-04
Started: 2022-06-06

Citation

Development and contributors

Readme and manuals

Help Manual

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