Description Usage Arguments Details References See Also Examples
Acts as a wrapper for the bipartite
package's
plotweb
function (Dormann et al., 2008),
colour coding the links in the familiar bipartite plots according to
whether they are stronger, weaker or consistent with the null model.
1 2 | plot_bipartite(nullnet, signif.level = 0.95, edge.cols = c("#67A9CF",
"#F7F7F7", "#EF8A62"), ...)
|
nullnet |
An object of class "nullnet" from |
signif.level |
An optional value specifying the threshold used for testing for 'significant' deviations from the null model. Defaults to 0.95 |
edge.cols |
An optional character vector of length three specifying the colours for links in the bipartite plot: they should represent interactions that are weaker than expected, consistent with the null model and stronger than expected in that order. The default is a colourblind friendly blue, white and red scheme, using colorbrewer's Red-Blue colour scheme (Brewer 2017). |
... |
Other arguments to be supplied to |
Extensive options can be passed to plotweb
to customise the network plot beyond the colour coding of the links. See
the appropriate help file in the bipartite package for details.
Brewer, C.A. (2017) http://www.ColorBrewer.org
Dormann, C.F., Gruber B. & Frund, J. (2008). Introducing the bipartite package: analysing ecological networks. R news, 8, 8-11.
Vaughan, I.P., Gotelli, N.J., Memmott, J., Pearson, C.E., Woodward, G. and Symondson, W.O.C. (2017) nullnetr: an R package using null models to analyse the structure of ecological networks and identify resource selection (submitted)
generate_null_net
, bipartite_stats
,
plotweb
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | # Run the null model
set.seed(1234)
sil.null <- generate_null_net(Silene[, 2:7], Silene.plants[, 2:6], sims = 10,
c.samples = Silene[, 1],
r.samples = Silene.plants[, 1])
# Basic plot
plot_bipartite(sil.null)
# With alternative colour scheme and nodes width in the lower level proportional
# to mean floral abundance
mean.abunds <- colMeans(Silene.plants[, 2:6])
plot_bipartite(sil.null, signif.level = 0.95, edge.cols = c("#67a9cf",
"#F7F7F7", "#ef8a62"), low.abun = mean.abunds,
abuns.type = "independent", low.abun.col = "black",
high.abun.col = "black", high.lablength = 0, low.lablength = 0)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.