SpeciesPool: Species pool based on Beal's smoothing

In idiv-biodiversity/SpeciesPool: Plot-specific species pools based on Beal's smoothing

Description

For each relevé, this function selects all neighbouring relevés having a similar potential species composition, and fits empirical non-linear functions to rarefaction curves.

Usage

SpeciesPool(
  input.data,
  coords,
  Mij = NULL,
  ncores = 1,
  rows = NULL,
  t.radius = 20000,
  t.bray = 0.2,
  t.plot.number = 10L,
  cutoff = c("iChao2", "Gompertz", "Michaelis"),
  verbose = T,
  species.list = F,
  mycrs = NULL,
  lonlat = NULL
)

Arguments

input.data	data.frame of species abundances across relevés. It should have three columns: one with Relevé IDs, one with Species ID, and one with species abundance/cover values
coords	Either a SpatialPointsDataFrame or a DataFrame with the geographic coordinates of all plots. If SpatialPointsDataframe, it should have Relevé IDs and areas defined in the data. If DataFrame, columns 1:2 should be coordinates (Long, Lat), columns 3:4 should be RelevèIDs and plot area, respectively.
Mij	matrix of pairwise likelihood of species co-occurrence (sparse matrices accepted). If not provided, it will be calculated from the data
ncores	integer indicating the number of cores to use. If ncores>1 the calculation will be done in parallel
rows	a vector of integers indicating on which plots of the input.data the function should run
t.radius	threshold of geographic buffer around target relevé
t.bray	threshold of Bray-Curtis dissimilarity for selecting relevés compositionally similar to target relevé
t.plot.number	minimum number of neighbouring relevés for calculating rarefaction curves
cutoff	method used to estimate the size of the species pool. Default is 'iChao2', other possible are 'Gompertz' or 'Michaelis'
verbose	logical
species.list	logical: Should the list of species composing the species pool be returned?
mycrs	a CRS object defining the coordinate reference of coords, if coords is a data.frame
lonlat	Specify whether the CRS is projected (lonlat=T) or unprojected (lonlat=F)

Value

Returns a dataframe containing for each relevé: - Species - the number of species observed across all relevés neighouring the target relevé
- Chao, iChao2, jack1, jack2 - various species richness estimates and standard errors, as derived from the function SpadeR::ChaoSpecies
- nplots - number of relevés within a t.radius distance from the target relevé having a bray-curtis dissimilarity lower than t.bray
- beals.at.chao - cut-off of Beals' occurrence likelihood, selected as the ith species corresponding to chao
- n.plots.area - number of relevés within a t.radius distance, and t.bray dissimilarity from target relevés for which area data is available
- arr, gomp, mm, Asymp - parameter estimates for different empirical non-linear functions fitted to rarefaction curves, with relative AIC
- sp.pool.list - list of species compatible with target relevé, i.e. having a Beals' likelihood lower than beals.at.chao

Author(s)

Francesco Maria Sabatini

Helge Bruelheide

idiv-biodiversity/SpeciesPool documentation built on June 17, 2020, 12:32 a.m.