rarefaction: Rarefied Species Richness

In MoBiodiv/mobr: Measurement of Biodiversity

Rarefied Species Richness

Description

The expected number of species given a particular number of individuals or samples under random and spatially explicit nearest neighbor sampling

Usage

rarefaction(
  x,
  method,
  effort = NULL,
  coords = NULL,
  latlong = NULL,
  dens_ratio = 1,
  extrapolate = FALSE,
  return_NA = FALSE,
  quiet_mode = FALSE,
  spat_algo = NULL,
  sd = FALSE
)

Arguments

x	can either be a: 1) mob_in object, 2) community matrix-like object in which rows represent plots and columns represent species, or 3) a vector which contains the abundance of each species.
method	a character string that specifies the method of rarefaction curve construction it can be one of the following: 'IBR' ... individual-based rarefaction in which species are accumulated by randomly sampling individuals 'SBR' ... sample-based rarefaction in which species are accumulated by randomly sampling samples (i.e., plots). Note that within plot spatial aggregation is maintained with this approach. Although this curve is implemented here, it is not used in the current version of the MoB framework 'nsSBR' ... non-spatial, sampled-based rarefaction in which species are accumulated by randomly sampling samples that represent a spatially random sample of individuals (i.e., no with-in plot spatial aggregation). The argument dens_ratio must also be set otherwise this sampling results in a curve identical to the IBR (see Details). 'sSBR' ... spatial sample-based rarefaction in which species are accumulated by including spatially proximate samples first. 'spexSBR' ... spatially-explicit sample-based rarefaction in which species are accumulated as in 'sSBR' but sampling effort is not measured by no. of samples, but by cumulative distance or cumulative area as specified by 'spat_algo' (see details)
effort	optional argument to specify what number of individuals, number of samples, or spatial sampling effort (i.e., cumulative distance or area) depending on 'method' to compute rarefied richness as. If not specified all possible values from 1 to the maximum sampling effort are used
coords	an optional matrix of geographic coordinates of the samples. Only required when using the spatial rarefaction method and this information is not already supplied by x. The first column should specify the x-coordinate (e.g., longitude) and the second coordinate should specify the y-coordinate (e.g., latitude)
latlong	Boolean if coordinates are latitude-longitude decimal degrees
dens_ratio	the ratio of individual density between a reference group and the community data (i.e., x) under consideration. This argument is used to rescale the rarefaction curve when estimating the effect of individual density on group differences in richness.
extrapolate	Boolean which specifies if richness should be extrapolated when effort is larger than the number of individuals using the chao1 method. Defaults to FALSE in which case it returns observed richness. Extrapolation is only implemented for individual-based rarefaction (i.e., method = 'indiv')
return_NA	Boolean defaults to FALSE in which the function returns the observed S when effort is larger than the number of individuals or number of samples (depending on the method of rarefaction). If set to TRUE then NA is returned. Note that this argument is only relevant when extrapolate = FALSE.
quiet_mode	Boolean defaults to FALSE, if TRUE then warnings and other non-error messages are suppressed.
spat_algo	character string that can be either: 'kNN', 'kNCN', or 'convexhull' for k-nearest neighbor, k-nearest centroid neighbor sampling, or convex-hull polygon calculation respectively. It defaults to k-nearest neighbor which is a more computationally efficient algorithm that closely approximates the potentially more correct k-NCN algo (see Details). Currently, 'kNN' and 'k-NCN' are available for method 'ssBR', while 'kNN' 'convexhull' are available for method 'spexSBR'.
sd	Boolean defaults to FALSE, if TRUE then standard deviation of richness is also returned using the formulation of Heck 1975 Eq. 2.

Details

The analytical formulas of Cayuela et al. (2015) are used to compute the random sampling expectation for the individual and sampled based rarefaction methods. The spatially constrained rarefaction curve (Chiarucci et al. 2009) also known as the sample-based accumulation curve (Gotelli and Colwell 2001) can be computed in one of two ways which is determined by the argument spat_algo. In the kNN approach each plot is accumulated by the order of their spatial proximity to the original focal cell. If plots have the same distance from the focal plot then one is chosen randomly to be sampled first. In the kNCN approach, a new centroid is computed after each plot is accumulated, then distances are recomputed from that new centroid to all other plots and the next nearest is sampled. The kNN is faster because the distance matrix only needs to be computed once, but the sampling of kNCN which simultaneously minimizes spatial distance and extent is more similar to an actual person searching a field for species. For both kNN and kNCN, each plot in the community matrix is treated as a starting point and then the mean of these n possible accumulation curves is computed.

For individual-based rarefaction if effort is greater than the number of individuals and extrapolate = TRUE then the Chao1 method is used (Chao 1984, 1987). The code used to perform the extrapolation was ported from iNext::D0.hat found at https://github.com/JohnsonHsieh/iNEXT. T. C. Hsieh, K. H. Ma and Anne Chao are the original authors of the iNEXT package.

If effort is greater than sample size and extrapolate = FALSE then the observed number of species is returned.

Standard deviation of richness can only be computed for individual based rarefaction and it is assigned as an attribute (see examples). The code for this computation was ported from vegan::rarefy (Oksansen et al. 2022)

Value

A vector of rarefied species richness values

Author(s)

Dan McGlinn and Xiao Xiao

References

Cayuela, L., N.J. Gotelli, & R.K. Colwell (2015) Ecological and biogeographic null hypotheses for comparing rarefaction curves. Ecological Monographs, 85, 437-454. Appendix A: http://esapubs.org/archive/mono/M085/017/appendix-A.php

Chao, A. (1984) Nonparametric estimation of the number of classes in a population. Scandinavian Journal of Statistics, 11, 265-270.

Chao, A. (1987) Estimating the population size for capture-recapture data with unequal catchability. Biometrics, 43, 783-791.

Chiarucci, A., G. Bacaro, D. Rocchini, C. Ricotta, M. Palmer, & S. Scheiner (2009) Spatially constrained rarefaction: incorporating the autocorrelated structure of biological communities into sample-based rarefaction. Community Ecology, 10, 209-214.

Gotelli, N.J. & Colwell, R.K. (2001) Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness. Ecology Letters, 4, 379-391.

Heck, K.L., van Belle, G. & Simberloff, D. (1975). Explicit calculation of the rarefaction diversity measurement and the determination of sufficient sample size. Ecology 56, 1459–1461.

Oksanen, J. et al. 2022. Vegan: community ecology package. R package version 2.6-4. https://CRAN.R-project.org/package=vegan

Examples

data(inv_comm)
data(inv_plot_attr)
sad = colSums(inv_comm)
inv_mob_in = make_mob_in(inv_comm, inv_plot_attr, coord_names = c('x', 'y'))
# rarefaction can be performed on different data inputs
# all three give same answer
# 1) the raw community site-by-species matrix
rarefaction(inv_comm, method='IBR', effort=1:10)
# 2) the SAD of the community
rarefaction(inv_comm, method='IBR', effort=1:10)
# 3) a mob_in class object
# the standard deviation of the richness estimates for IBR may be returned
# which is helpful for computing confidence intervals
S_n <- rarefaction(inv_comm, method='IBR', effort=1:10, sd=TRUE)
attr(S_n, 'sd')
plot(1:10, S_n, ylim=c(0,8), type = 'n')
z <- qnorm(1 - 0.05 / 2)
hi <- S_n + z * attr(S_n, 'sd')
lo <- S_n - z * attr(S_n, 'sd')
attributes(hi) <- NULL
attributes(lo) <- NULL
polygon(c(1:10, 10:1),  c(hi, rev(lo)), col='grey', border = NA)
lines(1:10, S_n, type = 'o')
# rescaling of individual based rarefaction 
# when the density ratio is 1 the richness values are 
# identical to the unscaled rarefaction
rarefaction(inv_comm, method='IBR', effort=1:10, dens_ratio=1)
# however the curve is either shrunk when density is higher than 
# the reference value (i.e., dens_ratio < 1)
rarefaction(inv_comm, method='IBR', effort=1:10, dens_ratio=0.5)
# the curve is stretched when density is lower than the 
# reference value (i.e., dens_ratio > 1)
rarefaction(inv_comm, method='IBR', effort=1:10, dens_ratio=1.5)
# sample based rarefaction under random sampling
rarefaction(inv_comm, method='SBR')
 
# sampled based rarefaction under spatially explicit nearest neighbor sampling
rarefaction(inv_comm, method='sSBR', coords=inv_plot_attr[ , c('x','y')],
            latlong=FALSE)
# the syntax is simpler if supplying a mob_in object
rarefaction(inv_mob_in, method='sSBR', spat_algo = 'kNCN')
rarefaction(inv_mob_in, method='sSBR', spat_algo = 'kNN')
rarefaction(inv_mob_in, method='spexSBR', spat_algo = 'kNN')

MoBiodiv/mobr documentation built on Nov. 5, 2024, 12:02 p.m.