Finds Missing Links and Metric Confidence Intervals in Ecological Bipartite Networks

[Up] [Top]

Documentation for package ‘cassandRa’ version 0.1.0

Help Pages

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