Package: untb 1.7-7-1

untb: Ecological Drift under the UNTB

Hubbell's Unified Neutral Theory of Biodiversity.

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

untb_1.7-7-1.tar.gz
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untb.pdf |untb.html✨
untb/json (API)

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

Peer review:

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

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:

70 exports 4 stars 2.32 score 10 dependencies 7 mentions 77 scripts 425 downloads

Last updated 7 days agofrom:720236afd0. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 11 2024
R-4.5-winNOTESep 11 2024
R-4.5-linuxNOTESep 11 2024
R-4.4-winNOTESep 11 2024
R-4.4-macNOTESep 11 2024
R-4.3-winNOTESep 11 2024
R-4.3-macNOTESep 11 2024

Exports:+.census+.countalonso.eqn11alonso.eqn12alonso.eqn6as.censusas.countcensuscountdisplay.untbetienneexpected.abundanceextantextinctextractorfisher.ecosystemfishers.alphaGST.kI.kis.censusis.countisolatelogkdalogkda_pari_unixlogkda_pari_windowslogkda.a11logkda.parilogkda.polynlogkda.RlogS1logS1vectmaximal.abundanceno.of.extinctno.of.indno.of.singletonsno.of.sppoptimal.paramsoptimal.params.gstoptimal.params.slossoptimal.proboptimal.thetaphiplot.censusplot.countplot.prestonprestonprint.prestonprint.summary.countrand.neutralselectselect.immigrateselect.mutatesimpsonsingletonsspecies.countspecies.tablesummary.censussummary.counttheta.likelihoodtheta.probunphiuntbvallade.eqn12vallade.eqn14vallade.eqn16vallade.eqn17vallade.eqn5vallade.eqn7volkovzsm

Dependencies:BrobdingnaggmplatticemathjaxrMatrixpartitionspolynomrbibutilsRdpacksets

A vignette for the untb package

Rendered fromuntb.Rnwusingutils::Sweaveon Sep 11 2024.

Last update: 2022-06-06
Started: 2022-06-06

Readme and manuals

Help Manual

Help pageTopics
Unified neutral theory of biodiversityuntb-package
Add two count objects+.census +.count
Various functions from Alonso and McKane 2004alonso.eqn11 alonso.eqn12 alonso.eqn6
Barro Colorado Island (BCI) datasetBCI bci
abundance data for butterfliesbutterflies butterfly
Dataset due to CarusoCaruso caruso Oribatid oribatid
Construct, coerce, and test for a census objectas.census census is.census
Copepod data supplied by Phil Pughcopepod ostracod
Construct, coerce, and test for a count objectas.count count is.count
Animation of neutral ecological driftdisplay.untb
Etienne's sampling formulaEtienne etienne optimal.params
Expected abundances under the neutral modelexpected.abundance
Extract rows of a database in count formextractor
Various functionality to implement Fisher's logseriesfisher fisher.ecosystem fishers.alpha
Tree counts in 1-ha plots from the Western Ghats mountains (South India)ghats
Randomly select a subset of an ecosystemisolate
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 kindlogS1 logS1vect
Ecosystem diagnosticsextant extinct maximal.abundance no.of.extinct no.of.ind no.of.singletons no.of.spp singletons
Estimation of local immigration using GST(k) statisticsGST.k I.k optimal.params.gst
Estimation of neutral community parameters using a two-stage maximum-likelihood procedureoptimal.params.sloss
Returns an estimate of the fundamental biodiversity numberoptimal.prob optimal.theta
Hubbell's phiphi unphi
Abundance curvesplot.census plot.count
Preston diagram of an ecosystemPreston preston
Print and plot objects of class Prestonplot.preston print.preston
Print method for summary objectsprint.summary.census print.summary.count
Random neutral ecosystemrand.neutral
Biodiversity dataset provided by SAHFOSsahfos
Dataset due to Saunderssaunders saunders.exposed saunders.exposed.tot saunders.sheltered saunders.sheltered.tot saunders.tot
Simpson's diversity indexsimpson
Ecosystem diagnostics for output of untb()species.count species.table
Counts of diatom species in springs of the Adamello-Brenta Nature Parkspitale
Summary methods for count and census objectssummary.census summary.count
Posterior probabilities for thetatheta.likelihood theta.prob
Ecological drift simulation under the Unified Neutral Theory of Biodiversityselect select.immigrate select.mutate untb
Various functions from Vallade and HouchmandzadehVallade vallade vallade.eqn12 vallade.eqn14 vallade.eqn16 vallade.eqn17 vallade.eqn5 vallade.eqn7
Expected frequency of speciesvolkov
Zero sum multinomial distribution as derived by McKanezsm