Package: cassandRa 0.2.0

cassandRa: Finds Missing Links and Metric Confidence Intervals in Ecological Bipartite Networks

Provides methods to deal with under sampling in ecological bipartite networks from Terry and Lewis (2020) Ecology <doi:10.1002/ecy.3047> Includes tools to fit a variety of statistical network models and sample coverage estimators to highlight most likely missing links. Also includes simple functions to resample from observed networks to generate confidence intervals for common ecological network metrics.

Authors:Chris Terry [aut, cre, cph]

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cassandRa/json (API)
NEWS

# Install 'cassandRa' in R:

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

Bug tracker:https://github.com/jcdterry/cassandra/issues

On CRAN:

4.48 score 3 stars 4 scripts 520 downloads 20 exports 53 dependencies

Last updated 6 months agofrom:9b1196235b. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 04 2024
R-4.5-win	OK	Nov 04 2024
R-4.5-linux	OK	Nov 04 2024
R-4.4-win	OK	Nov 04 2024
R-4.4-mac	OK	Nov 04 2024
R-4.3-win	OK	Nov 04 2024
R-4.3-mac	OK	Nov 04 2024

Exports:%>%CalcHostLevelCoverage ComputeCI CoverageEstimator CreateListObject FitAllModels FitBothMandC FitCentrality FitMatching FitSBM make_true_and_sample_web Optimise_SBM Optimiser PlotFit PlotRarefaction PredictLinks RarefyNetwork SortResponseCategory TestAllModels TestAUC

Dependencies:bipartite boot cli cluster coda colorspace cpp11 dotCall64 dplyr fansi farver fields generics ggplot2 glue gtable igraph isoband labeling lattice lifecycle magrittr maps MASS Matrix mgcv munsell network nlme permute pillar pkgconfig plyr purrr R6 RColorBrewer Rcpp reshape2 rlang scales sna spam statnet.common stringi stringr tibble tidyr tidyselect utf8 vctrs vegan viridisLite withr

cassandRa Vignette

Chris Terry

Rendered fromintroduction.Rmdusingknitr::rmarkdownon Nov 04 2024.

Last update: 2019-06-26
Started: 2019-06-04

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Estimated probabilities of missing links based on the host Level Coverage Deficit	CalcHostLevelCoverage
Compute Basic Confidence Intervals	ComputeCI
Coverage Estimator, using Chao1 Index, Turing-Good or Binomial depending on what is possible	CoverageEstimator
Generates a network list from a food web	CreateListObject
Fit all the models	FitAllModels
Fit Matching-Centrality Model	FitBothMandC
Fit Centrality Model	FitCentrality
Fit Latent Trait (Matching Model)	FitMatching
Fit SBM Model	FitSBM
Make an artificial bipartite networks with some properties of ecological networks, then sample from it	make_true_and_sample_web
Custom optimiser function for SBM models	Optimise_SBM
Optimiser wrapper for network models	Optimiser
Plot the fitted network models	PlotFit
Plot Metric Response To Network Rarefaction	PlotRarefaction
Generates a network list from a food web and fits all network models	PredictLinks
Recalculate Network Metrics With Rarefied Webs	RarefyNetwork
Adds a dataframe that defines each interaction as true positive, false negative or true negative	SortResponseCategory
Test the models by AUC	TestAllModels
Test via AUC the predictive capacity of each model or combination of models	TestAUC