Package: tapnet 0.6

Carsten Dormann

tapnet: Trait Matching and Abundance for Predicting Bipartite Networks

Functions to produce, fit and predict from bipartite networks with abundance, trait and phylogenetic information. Its methods are described in detail in Benadi, G., Dormann, C.F., Fruend, J., Stephan, R. & Vazquez, D.P. (2021) Quantitative prediction of interactions in bipartite networks based on traits, abundances, and phylogeny. The American Naturalist, in press.

Authors:Carsten Dormann [aut, cre], Gita Benadi [aut], Boris Tinoco [dtc], Ruth Stephan [ctb], Jochen Fruend [ctb]

tapnet_0.6.tar.gz
tapnet_0.5.zip(r-4.5)tapnet_0.5.zip(r-4.4)tapnet_0.5.zip(r-4.3)
tapnet_0.5.tgz(r-4.4-any)tapnet_0.5.tgz(r-4.3-any)
tapnet_0.5.tar.gz(r-4.5-noble)tapnet_0.6.tar.gz(r-4.4-noble)
tapnet_0.6.tgz(r-4.4-emscripten)tapnet_0.6.tgz(r-4.3-emscripten)
tapnet.pdf |tapnet.html✨
tapnet/json (API)

# Install 'tapnet' in R:

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

Bug tracker:https://github.com/biometry/tapnet/issues

Datasets:

humm_abun - Hummingbird-flower networks
humm_traits - Hummingbird-flower networks
humm_tree - Hummingbird-flower networks
networks - Hummingbird-flower networks
plant_abun - Hummingbird-flower networks
plant_traits - Hummingbird-flower networks
plant_tree - Hummingbird-flower networks

On CRAN:

4.18 score 1 stars 2 scripts 119 downloads 8 exports 52 dependencies

Last updated 2 months agofrom:07819a2665. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 25 2024
R-4.5-win	OK	Sep 12 2024
R-4.5-linux	OK	Sep 12 2024
R-4.4-win	OK	Sep 12 2024
R-4.4-mac	OK	Sep 12 2024
R-4.3-win	OK	Sep 12 2024
R-4.3-mac	OK	Sep 12 2024

Exports:fit_tapnet fit_tapnetDE gof_tapnet make_tapnet predict_tapnet simnetfromtap simulate_tapnet tapnet2df

Dependencies:ape bipartite cli cluster clusterGeneration coda codetools combinat cpp11 DEoptim digest doParallel dotCall64 expm fansi fastmatch fields foreach generics glue igraph iterators lattice lifecycle magrittr maps MASS Matrix mgcv mnormt MPSEM network nlme numDeriv optimParallel permute phangorn phytools pillar pkgconfig quadprog Rcpp rlang scatterplot3d sna spam statnet.common tibble utf8 vctrs vegan viridisLite

Case Study

Rendered fromCaseStudy.Rnwusingutils::Sweaveon Oct 25 2024.

Last update: 2021-01-19
Started: 2021-01-18

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
tapnet: A package for fitting, and predicting from, bipartite interaction networks.	tapnet-package
Fit the tapnet model to a network	fit_tapnet
Fit the tapnet model to a network	fit_tapnetDE
Goodness-of-fit of a tapnet fit	gof_tapnet
Helper functions for tapnet	bjornloglik fit_abund functions helper internalFunctions latent_cor loglik_tapnet param_vec2list pems_from_tree refit_params select_relevant_pems tmatch web_indices
Constructs an object of type "tapnet"	make_tapnet
Predict from fitted tapnet to new data	predict_tapnet
Simulates a network from parameters, abundances, traits and phylogeny provided	simnetfromtap
Creates a simulated along with all parameters, abundances, traits and phylogeny used	simulate_tapnet
Convert tapnet object into data.frame	tapnet2df
Hummingbird-flower networks	humm_abun humm_traits humm_tree networks plant_abun plant_traits plant_tree Tinoco