Package: tapnet 0.5

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_0.5.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_0.5.tar.gz(r-4.4-noble)
tapnet_0.5.tgz(r-4.4-emscripten)tapnet_0.5.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'))

Peer review:

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

Datasets:

On CRAN:

7 exports 1 stars 0.92 score 52 dependencies 2 scripts 149 downloads

Last updated 10 months agofrom:318440909e. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 12 2024
R-4.5-winOKSep 12 2024
R-4.5-linuxOKSep 12 2024
R-4.4-winOKSep 12 2024
R-4.4-macOKSep 12 2024
R-4.3-winOKSep 12 2024
R-4.3-macOKSep 12 2024

Exports:fit_tapnetgof_tapnetmake_tapnetpredict_tapnetsimnetfromtapsimulate_tapnettapnet2df

Dependencies:apebipartitecliclusterclusterGenerationcodacodetoolscombinatcpp11DEoptimdigestdoParalleldotCall64expmfansifastmatchfieldsforeachgenericsglueigraphiteratorslatticelifecyclemagrittrmapsMASSMatrixmgcvmnormtMPSEMnetworknlmenumDerivoptimParallelpermutephangornphytoolspillarpkgconfigquadprogRcpprlangscatterplot3dsnaspamstatnet.commontibbleutf8vctrsveganviridisLite

Case Study

Rendered fromCaseStudy.Rnwusingutils::Sweaveon Sep 12 2024.

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

Readme and manuals

Help Manual

Help pageTopics
tapnet: A package for fitting, and predicting from, bipartite interaction networks.tapnet-package
Fit the tapnet model to a networkfit_tapnet
Goodness-of-fit of a tapnet fitgof_tapnet
Helper functions for tapnetbjornloglik 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 datapredict_tapnet
Simulates a network from parameters, abundances, traits and phylogeny providedsimnetfromtap
Creates a simulated along with all parameters, abundances, traits and phylogeny usedsimulate_tapnet
Convert tapnet object into data.frametapnet2df
Hummingbird-flower networkshumm_abun humm_traits humm_tree networks plant_abun plant_traits plant_tree Tinoco