res.pa.dist <- res$p.a.dist
res.pa.dist[res.pa.dist > sigth] <- 1
How many (unadjusted) values are equal to or smaller than sigth?
length(which(res.p.vec <= sigth))
The dissimilarity matrix made of the p-values can be displayed as a heat map (see
Chap. 3):
# Heat map of significant p-values
coldiss ( res.pa.dist,
nc = 10,
byrank = TRUE,
diag = TRUE)
4.10.4 Species Co-occurrence Network
Co-occurrence network analysis becomes more and more popular in community
ecology, especially to investigate ecological interactions among species or among
communities. The principle is to analyse associations among species based on
their co-occurrence in ecological meta-communities or multitrophic species
assemblages. Based on the topology of the co-occurrence network, sociological
groups of species are defined, called “modules”. Network structure is characterized by two main properties, namely “modularity” (the extent to which species
co-occurrences are organized into modules, i.e. densely connected,
non-overlapping subsets of species) and “nestedness” (the tendency of the network to show a nested pattern wherein the species composition of small assemblages is a nested subset of larger assemblages; see Sect. 8.4.3). The role of a
species is defined by its position compared with other species in its own module
(its “standardized within-module degree”, i.e., the number of links that a node has
with other nodes in the same module, standardized by the mean and standard
deviation of the number of links per node in the module) and how well it connects
to species in other modules (its among-module “connectivity”). For more details,
see e.g. Olesen et al. (2007) and Borthagaray et al. (2014).
Basically, the network is built from an adjacency matrix, which may be binary
(species significantly co-occur or not) or numeric (links among species are
weighted). Various metrics of positive, neutral or negative association among
4.10 Species Assemblages
117
res.pa.dist[res.pa.dist > sigth] <- 1
How many (unadjusted) values are equal to or smaller than sigth?
length(which(res.p.vec <= sigth))
The dissimilarity matrix made of the p-values can be displayed as a heat map (see
Chap. 3):
# Heat map of significant p-values
coldiss ( res.pa.dist,
nc = 10,
byrank = TRUE,
diag = TRUE)
4.10.4 Species Co-occurrence Network
Co-occurrence network analysis becomes more and more popular in community
ecology, especially to investigate ecological interactions among species or among
communities. The principle is to analyse associations among species based on
their co-occurrence in ecological meta-communities or multitrophic species
assemblages. Based on the topology of the co-occurrence network, sociological
groups of species are defined, called “modules”. Network structure is characterized by two main properties, namely “modularity” (the extent to which species
co-occurrences are organized into modules, i.e. densely connected,
non-overlapping subsets of species) and “nestedness” (the tendency of the network to show a nested pattern wherein the species composition of small assemblages is a nested subset of larger assemblages; see Sect. 8.4.3). The role of a
species is defined by its position compared with other species in its own module
(its “standardized within-module degree”, i.e., the number of links that a node has
with other nodes in the same module, standardized by the mean and standard
deviation of the number of links per node in the module) and how well it connects
to species in other modules (its among-module “connectivity”). For more details,
see e.g. Olesen et al. (2007) and Borthagaray et al. (2014).
Basically, the network is built from an adjacency matrix, which may be binary
(species significantly co-occur or not) or numeric (links among species are
weighted). Various metrics of positive, neutral or negative association among
4.10 Species Assemblages
117