siberia1987_matrix: Siberia 1987 host-parasite temporal matrix

In Ecological-Complexity-Lab/infomap_ecology_package: Community Detection using Infomap, Inspired by Ecological Networks

Siberia 1987 host-parasite temporal matrix

Description

Host-parasite temporal multilayer network. This data set contains the matrices of a temporal multilayer network representing the infection of 22 small mammalian host species by 56 ectoparasite species during 6 consecutive summers in Siberia (1982–1987).

Usage

data(siberia1987_matrix)

Format

A numeric matrix with rows representing host species and columns representing parasite species.

Details

The data set is in an matrix format.Each layer is a host-parasite bipartite network. Intralayer edges between a parasite species and a host species are the number of parasite individuals divided by the number of host individuals. Interlayer coupling edges connect each physical node to itself in the next layer (e.g., host A in layer 1 to host A in layer 2), and are calculated as the number of individuals in layer l+1 divided by the number of individuals in layer l. They therefore represent population dynamics. Interlayer edges only go one way (_l–>l+1_) because time flow one way.

See siberia_nodes for information about the nodes.

See siberia_interlayer for information about the interlayer edges.

Source

Simulated data for illustration purposes.

References

Krasnov BR, Matthee S, Lareschi M, Korallo-Vinarskaya NP, Vinarski MV. Co-occurrence of ectoparasites on rodent hosts: null model analyses of data from three continents. Oikos. 2010;119: 120–128.

Pilosof S, Fortuna MA, Vinarski MV, Korallo-Vinarskaya NP, Krasnov BR. Temporal dynamics of direct reciprocal and indirect effects in a host-parasite network. J Anim Ecol. 2013;82: 987–996.

Pilosof S, Porter MA, Pascual M, Kéfi S. The multilayer nature of ecological networks. Nature Ecology & Evolution. 2017;1: 0101.

Examples

data(siberia1982_matrix)
data(siberia1983_matrix)
data(siberia1984_matrix)
data(siberia1985_matrix)
data(siberia1986_matrix)
data(siberia1987_matrix)
data(siberia_nodes)
data(siberia_interlayer)

# Create a multilayer object
layer_attrib <- tibble(layer_id=1:6, layer_name=c('1982','1983','1984','1985','1986','1987'))                                     

multilayer_siberia <- create_multilayer_network(list_of_layers = list(siberia1982_matrix,
                                                                      siberia1983_matrix,
                                                                      siberia1984_matrix,
                                                                      siberia1985_matrix,
                                                                      siberia1986_matrix,
                                                                      siberia1987_matrix),
                                                layer_attributes = layer_attrib,
                                                bipartite = T,
                                                directed = F, physical_node_attributes = siberia_nodes )

Ecological-Complexity-Lab/infomap_ecology_package documentation built on June 6, 2024, 5:28 a.m.