Null-model algorithms

Neander Heming, Flávio Mota and Gabriela Alves-Ferreira

2023-07-04

Contents

Algorithms

Gotelli (2000) summarizes nine 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 @ref(tab:table1), (Gotelli 2000)). The data for null model analyses usually consists of a binary presence-absence matrix, in which rows represent species or taxa, columns represent sites or samples, and the entries represent the presence (1) or absence (0) of a particular species in a particular site (Ulrich and Gotelli 2012).

#> Loading required package: kableExtra
Nine null model algorithms for species co-occurrence analysis listed in Gotelli (2000). Algorithms marked in green are already implemented in SESraster
Cols (Cell)
Equiprobable Proportional Fixed
Rows (Layer) Equiprobable Spp occur.: E
Site rich.: E
SIM1: EE
Spp occur.: E
Site rich.: P
SIM6: EP
Spp occur.: E
Site rich.: F
SIM3: EF
Proportional Spp occur.: P
Site rich.: E
SIM7: PE
Spp occur.: P
Site rich.: P
SIM8: PP
Spp occur.: P
Site rich.: F
SIM5: PF
Fixed Spp occur.: F
Site rich.: E
SIM2: FE
Spp occur.: F
Site rich.: P
SIM4: FP
Spp occur.: F
Site rich.: F
SIM9: FF

References

Gotelli, Nicholas J. 2000. “Null Model Analysis of Species Co-Occurrence Patterns.” Ecology 81 (9): 2606–21. https://doi.org/10.2307/177478.
Ulrich, Werner, and Nicholas J. Gotelli. 2012. “A Null Model Algorithm for Presenceabsence Matrices Based on Proportional Resampling.” Ecological Modelling 244 (October): 20–27. https://doi.org/10.1016/j.ecolmodel.2012.06.030.