Reference

Building and handling metanetworks

Set of functions to build a ‘metanetwork’ object and handle it

build_metanet()

Build metanetwork object

print()

print metanetwork

append_agg_nets()

append aggregated networks

extract_networks()

extract networks from a metanetwork object

is.metanetwork()

Test of belonging to class metanetwork

metanet_build_pipe()

Build and execute 'metanetwork' pipeline

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Pipe

Computing trophic levels and TL-tsne layout

Set of functions and objects to compute trophic levels and attach ‘TL-tsne’ layout

compute_TL()

compute trophic levels

attach_layout()

compute and attach metanetwork layouts

metanet_pipe()

Execute 'metanetwork' pipeline

TL_tsne.default

Default configuration for the diffusion kernel based t-sne

group_layout.default

Default configuration for group-TL-tsne layout

Visualising metanetworks

Set of functions and objects to visualise metanetworks, using computed layout

ggmetanet()

ggmetanet

ggnet.default

Default configuration for ggnet

vismetaNetwork()

vismetaNetwork

visNetwork.default

Default configuration for visNetwork

diff_plot()

plot difference network

plot_trophicTable()

Plot trophic groups hierarchy

Computing network indices

Set of functions to compute network diversities, dissimilarities and metrics

compute_metrics()

compute network metrics

compute_div()

compute network diversity indices

compute_dis()

compute pairwise network dissimilarity indices

Data sets

meta_angola

Angola fishery metanetwork metanetwork built from: Angelini & Velho 2011, Data from: Angelini, R., Velho, VF. (2011) Ecosystem structure and trophic analysis of Angolan fishery landings. Scientia Marina 75(2)

meta_norway

Norway soil metanetwork metanetwork built from: Calderon-Sanou et al. 2021, Data from: Calderon-Sanou, I., Munkemuller, T., Zinger, L., Schimann, H., Yoccoz, N. G., Gielly, L., ... & Thuiller, W. (2021). Cascading effects of moth outbreaks on subarctic soil food webs. Scientific reports, 11(1), 1-12.

meta_vrtb

European vertebrates metanetwork metanetwork built using data from: O'Connor, L. M., Pollock, L. J., Braga, J., Ficetola, G. F., Maiorano, L., Martinez-Almoyna, C., ... & Thuiller, W. (2020). Unveiling the food webs of tetrapods across Europe through the prism of the Eltonian niche. Journal of Biogeography, 47(1), 181-192. and Maiorano, L., Montemaggiori, A., Ficetola, G. F., O'connor, L., & Thuiller, W. (2020). TETRA-EU 1.0: a species-level trophic metaweb of European tetrapods. Global Ecology and Biogeography, 29(9), 1452-1457.