plotweb2 {bipartite}R Documentation

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 bernd.gruber@canberra.edu.au

See Also

For a different plot of food webs see visweb and plotweb


[Package bipartite version 2.19 Index]