plotweb2: Visualize a tripartite interaction matrix (e.g. a tritrophic...

In bipartite: Visualising Bipartite Networks and Calculating Some (Ecological) Indices

Visualize a tripartite interaction matrix (e.g. a tritrophic foodweb)

Description

Two two dimensional matrix are plotted as a tripartite graph.

Usage

plotweb2(web, web2, method = "cca", empty = FALSE, labsize = 1, ybig = 1,
    y_width = 0.1, spacing = 0.05, arrow="no", col.interaction="grey80",
    col.pred = "grey10", col.prey="grey10", lab.space=1, lablength = NULL, 
    sequence=NULL, low.abun=NULL,low.abun.col="green", high.abun=NULL, 
    high.abun.col="red", method2 = "cca", empty2 = TRUE, spacing2 = 0.05,  
    arrow2="no", col.interaction2="grey80", col.pred2 = "grey30", 
    col.prey2="grey20", lablength2 = NULL, sequence.pred2=NULL,low.abun2=NULL,
    low.abun.col2="green", high.abun2=NULL, high.abun.col2="red")

Arguments

web	Web is a matrix representing the interactions observed between higher trophic level species (columns) and lower trophic level species (rows). Usually this will be number of pollinators on each species of plants or number of parasitoids on each species of prey.
web2	The other web to be included.
method	Default method is cca, which leads to as few crossings of interactions as possible. The other option is normal, which leaves order as given by the matrix.
empty	logical; should empty columns or empty rows be omitted from plotting; defaults to true
labsize	factor for size of labels, default is 1
ybig	vertical distance between upper and lower boxes, default is 1
y_width	width of upper and lower boxes, default is 0.1
spacing	horizonatal distance between boxes within a level, default is 0.05
arrow	display type of connection between upper and lower boxes, options are up, down, both and no, default is no, which is a polygonal connection between boxes.
col.interaction	color of interaction, default is grey80.
col.pred	color of upper boxes, default is grey10.
col.prey	color of lower boxes, default is grey10.
lab.space	sometimes it is neccessary to add additional space for labels below and above of the boxes, so all labels are shown, default is 1.
lablength	number of characters of labels that should be plotted. If zero no labels are shown, default is NULL which plots the complete labels.
sequence	list of two with two names vectors: seq.pred and seq.prey, which specify the order in which species are plotted. Cannot be set for method="cca". Defaults to NULL, where the sequence remains as given or is determined by the CCA internally.
low.abun	Vector with independent abundance estimates for the lower trophic level, NULL if none exists.
low.abun.col	Colour for depicting the abundance estimates for the lower trophic level; defaults to green.
high.abun	Vector with independent abundance estimates for the higher trophic level, NULL if none exists.
high.abun.col	Colour for depicting the abundance estimates for the lower trophic level; defaults to red.
method2	Default method is cca, which leads to as few crossings of interactions as possible. The other option is normal, which leaves order as given by the matrix.
empty2	logical; should empty columns or empty rows be omitted from plotting; defaults to true
spacing2	horizontal distance between boxes within one level, default is 0.05
arrow2	display type of connection between upper and lower boxes, options are up, down, both and no, default is no, which is a polygonal connection between boxes.
col.interaction2	color of interaction, default is grey80.
col.pred2	color of upper boxes, default is grey10.
col.prey2	color of lower boxes, default is grey10.
lablength2	number of characters of labels that should be plotted. If zero no labels are shown, default is NULL which plots the complete labels.
sequence.pred2	list of two with two names vectors: seq.pred and seq.prey, which specify the order in which species are plotted. Cannot be set for method="cca". Defaults to NULL, where the sequence remains as given or is determined by the CCA internally.
low.abun2	Vector with independent abundance estimates for the lower trophic level, NULL if none exists.
low.abun.col2	Colour for depicting the abundance estimates for the lower trophic level; defaults to green.
high.abun2	Vector with independent abundance estimates for the higher trophic level, NULL if none exists.
high.abun.col2	Colour for depicting the abundance estimates for the lower trophic level; defaults to red.

Value

Returns a window with a tripartite graph of a food web.

Author(s)

Bernd Gruber [e-mail]

See Also

For a different plot of food webs see visweb and plotweb

bipartite documentation built on May 29, 2024, 2:23 a.m.