Package: metanetwork 0.8.0

metanetwork: Handling and Representing Trophic Networks in Space and Time

A toolbox to handle and represent trophic networks in space or time across aggregation levels. This package contains a layout algorithm specifically designed for trophic networks, using dimension reduction on a diffusion graph kernel and trophic levels. Importantly, this package provides a layout method applicable for large trophic networks. The package also implements network diversity indices at different aggregation levels and connectance computation.

Authors:Marc Ohlmann [aut, cre], Jimmy Garnier [aut, ctb], Laurent Vuillon [aut, ctb]

metanetwork_0.8.0.tar.gz
metanetwork_0.8.0.zip(r-4.5)metanetwork_0.8.0.zip(r-4.4)metanetwork_0.8.0.zip(r-4.3)
metanetwork_0.8.0.tgz(r-4.4-any)metanetwork_0.8.0.tgz(r-4.3-any)
metanetwork_0.8.0.tar.gz(r-4.5-noble)metanetwork_0.8.0.tar.gz(r-4.4-noble)
metanetwork_0.8.0.tgz(r-4.4-emscripten)metanetwork_0.8.0.tgz(r-4.3-emscripten)
metanetwork.pdf |metanetwork.html✨
metanetwork/json (API)

# Install 'metanetwork' in R:

install.packages('metanetwork', repos = c('https://marcohlmann.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/marcohlmann/metanetwork/issues

Datasets:

meta_angola - Angola fishery metanetwork metanetwork built from: Angelini & Velho 2011, Data from: Angelini, R., Velho, VF.
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.

On CRAN:

3.88 score 2 stars 75 scripts 161 downloads 21 exports 82 dependencies

Last updated 1 years agofrom:1d3a7b6659. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 27 2024
R-4.5-win	OK	Oct 27 2024
R-4.5-linux	OK	Oct 27 2024
R-4.4-win	OK	Oct 27 2024
R-4.4-mac	OK	Oct 27 2024
R-4.3-win	OK	Oct 27 2024
R-4.3-mac	OK	Oct 27 2024

Exports:%>%append_agg_nets attach_layout build_metanet compute_dis compute_div compute_metrics compute_TL diff_plot extract_networks ggmetanet ggnet.default group_layout.default is.metanetwork metanet_build_pipe metanet_pipe plot_trophicTable print TL_tsne.default vismetaNetwork visNetwork.default

Dependencies:base64enc bslib cachem cli coda colorspace cpp11 crayon curl digest dplyr evaluate fansi farver fastmap fontawesome forcats fs generics GGally ggfun ggimage ggplot2 ggplotify ggstats glue gridGraphics gtable highr hms htmltools htmlwidgets igraph intergraph isoband jquerylib jsonlite knitr labeling lattice lifecycle magick magrittr MASS Matrix memoise mgcv mime munsell network nlme patchwork pillar pkgconfig plyr prettyunits progress purrr R6 rappdirs RColorBrewer Rcpp rlang rmarkdown sass scales sna statnet.common stringi stringr tibble tidyr tidyselect tinytex utf8 vctrs viridisLite visNetwork withr xfun yaml yulab.utils

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Pipe	%>%
append aggregated networks	append_agg_nets append_agg_nets.metanetwork
compute and attach metanetwork layouts	attach_layout attach_layout.metanetwork
Build metanetwork object	build_metanet
compute pairwise network dissimilarity indices	compute_dis
compute network diversity indices	compute_div
compute network metrics	compute_metrics
compute trophic levels	compute_TL compute_TL.metanetwork
plot difference network	diff_plot
extract networks from a metanetwork object	extract_networks
ggmetanet	ggmetanet
Default configuration for ggnet	ggnet.default
Default configuration for group-TL-tsne layout	group_layout.default
Test of belonging to class metanetwork	is.metanetwork is.metanetwork.metanetwork
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_angola
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_norway
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.	meta_vrtb
Build and execute 'metanetwork' pipeline	metanet_build_pipe
Execute 'metanetwork' pipeline	metanet_pipe metanet_pipe.metanetwork
Plot trophic groups hierarchy	plot_trophicTable
print metanetwork	print print.metanetwork
Default configuration for the diffusion kernel based t-sne	TL_tsne.default
vismetaNetwork	vismetaNetwork
Default configuration for visNetwork	visNetwork.default