Null model algorithms
Neander M. Heming, Flávio Mota, and Gabriela Alves-Ferreira
2023-08-10
Source:vignettes/null-models.Rmd
null-models.Rmd
Introduction
Null models have been widely used to analyze the patterns observed in
nature in the attempt to understand the ecological and evolutionary
mechanisms structuring the biological communities. A null model is a
simplified representation of how species would be distributed or
biological communities be assembled if specific ecological processes
were not operating. Until now, algorithms were designed to create null
models using matrix data. The package SESraster
covers a current gap by implementing randomization algorithms to build
null models using presence/absence raster data.
Algorithms
The data for null model analyses usually consists of a binary
presence-absence matrix, in which the entries represent the presence (1)
or absence (0) of a particular species in a particular site, rows
represent species or taxa, columns represent sites or samples (Ulrich
and Gotelli 2012). There are nine major types of null model
algorithms for species co-occurrence analysis based on how sums of
species (originally rows) and sites (originally columns) are treated
(i.e. fixed, equiprobable, or proportional sums; see Table 1; Table 2 of
(Gotelli 2000)). When using raster data,
layers represent species or taxa and cells represent sites or samples.
SESraster
currently implements six (green cells in Table 1)
of the nine algorithms for co-occurrence analysis summarized by Gotelli
(2000).
Equiprobable | Proportional | Fixed | ||
---|---|---|---|---|
Species (Row, Layer) |
Equiprobable |
SIM1: EE occurrence frequency: E site richness: E |
SIM6: EP occurrence frequency: E site richness: P |
SIM3: EF occurrence frequency: E site richness: F |
Proportional |
SIM7: PE occurrence frequency: P site richness: E |
SIM8: PP occurrence frequency: P site richness: P |
SIM5: PF occurrence frequency: P site richness: F |
|
Fixed |
SIM2: FE occurrence frequency: F site richness: E |
SIM4: FP occurrence frequency: F site richness: P |
SIM9: FF occurrence frequency: F site richness: F |
Spatial null model algorithms in SESraster
Time to get started with SESraster
:
vignette("spatial-null-models")
. See installation
instructions and how the implemented null model algorithms work with
spatial data.