Nothing
## ----setup, include = FALSE----------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
require(bipartite)
require(cassandRa)
require(purrr)
require(dplyr)
require(tidyr)
require(ggplot2)
## ------------------------------------------------------------------------
data(Safariland, package= 'bipartite')
Safariland[1:5, 1:2]
## ------------------------------------------------------------------------
PredictFit <- PredictLinks(Safariland , RepeatModels = 1) # Set to 1 here for speed in the vignette
knitr::kable(head(PredictFit$Predictions), digits = 4 )
## ----fig.height=4, fig.width=8, warning=FALSE----------------------------
PlotFit(PredictFit, Matrix_to_plot = 'SBM')
PlotFit(PredictFit,
Matrix_to_plot = c('SBM', 'C_def'),
Combine = '+',
OrderBy = 'Degree',
title = 'Combined SBM and Coverage Deficit Model') + guides(fill= FALSE, col=FALSE)
## ----fig.height=4, fig.width=8-------------------------------------------
MetricsAfterReSampling<- RarefyNetwork(Safariland,
n_per_level = 50, # v. small for the vignette
metrics = c('H2', 'nestedness', 'links per species'))
PlotRarefaction(MetricsAfterReSampling)
ComputeCI(MetricsAfterReSampling)
## ----fig.height=8, fig.width=8, message=FALSE----------------------------
RarefyNetwork(Safariland,
n_per_level = 50,
abs_sample_levels = c(500, 1000, 5000),
metrics = 'info',
output = 'plot')
## ------------------------------------------------------------------------
sessionInfo()
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