High-level functions for plotting trophic link properties.
PlotTLPS(community,
X,
Y,
xlab,
ylab,
axes.limits.equal = FALSE,
xlim = NULL,
ylim = NULL,
main = CPS(community)$title,
highlight.links = NULL,
lowlight.links = NULL,
colour.by,
colour.spec,
col = NULL,
symbol.by,
symbol.spec,
pch = NULL,
bg.by,
bg.spec,
bg = NULL,
cex.by = NULL,
cex.spec = NULL,
cex = NULL,
are.values = FALSE,
…)PlotPredationMatrix(community,
xlab='Consumer',
ylab='Resource',
resource.order,
consumer.order,
…)
PlotMRvMC(community,
xlab=Log10MLabel(community, name='italic(M)[consumer]'),
ylab=Log10MLabel(community, name='italic(M)[resource]'),
axes.limits.equal = TRUE,
…)
PlotMCvMR(community,
xlab=Log10MLabel(community, name='italic(M)[resource]'),
ylab=Log10MLabel(community, name='italic(M)[consumer]'),
axes.limits.equal = TRUE,
…)
PlotNRvNC(community,
xlab=Log10NLabel(community, name='italic(N)[consumer]'),
ylab=Log10NLabel(community, name='italic(N)[resource]'),
axes.limits.equal = TRUE,
…)
PlotNCvNR(community,
xlab=Log10NLabel(community, name='italic(N)[resource]'),
ylab=Log10NLabel(community, name='italic(N)[consumer]'),
axes.limits.equal = TRUE,
…)
PlotBRvBC(community,
xlab=Log10BLabel(community, name='italic(B)[consumer]'),
ylab=Log10BLabel(community, name='italic(B)[resource]'),
axes.limits.equal = TRUE,
…)
PlotBCvBR(community,
xlab=Log10BLabel(community, name='italic(B)[resource]'),
ylab=Log10BLabel(community, name='italic(B)[consumer]'),
axes.limits.equal = TRUE,
…)
an object of class Community.
the name of a node or link property to plot on the x axis.
If the name begins with 'resource.' or 'consumer.', the remainder of the
name is assumed to be a node property and should meet the criteria of the
node.properties parameter of TLPS, otherwise the name
is assumed to be a link property and should meet the criteria of the
link.properties parameter of TLPS.
If are.values is TRUE then X and Y should be
vectors of length NumberOfTrophicLinks.
plotted on the y axis; see X.
title of the x axis.
title of the y axis.
logical - if TRUE and xlim and
ylim are NULL then the limits of the x and y axes will be
the same.
limits of the x axis
limits of the y axis
title of the plot
trophic links to be highlighted; either NULL,
a vector of trophic link indices or a function that takes a
Community as its only parameter and returns a data.frame
containing the columns `resource' and `consumer', which should
contain node names.
trophic links to be lowlighted; should meet criteria
of lowlight.links.
trophic link colours property. Either NULL, a vector
of length NumberOfTrophicLinks or a name. If the name begins with
'resource.' or 'consumer.', the remainder of the name is assumed to be a
node property and should meet the criteria of the node.properties
parameter of TLPS, otherwise the name is assumed to be a link
property and should meet the criteria of the link.properties
parameter of TLPS.
trophic links colours specification. either NULL
or a named vector that maps values of colour.by to plotting values.
trophic links colours.
trophic links symbols property; must meet the criteria of
colour.by.
trophic links symbols specification specification; must
meet the criteria of colour.spec.
trophic links symbols.
trophic links background colours property; must meet the
criteria of colour.by
trophic links background colours specification; must meet the
criteria of colour.spec.
trophic links background colours.
trophic links cex property; must meet the criteria of
colour.by
cex values specification; must meet the criteria of
colour.spec.
cex values.
logical - if TRUE X and Y must be
vectors of values of length NumberOfTrophicLinks.
the order in which to show resources. Either missing,
which implies the native node order, a vector of length
NumberOfTrophicLinks containing the integer order of resources,
or the name of a property that meets the criteria of the properties
parameter of NPS.
the order in which to show consumer; requirements
are the same as resource.order.
other values to plot functions.
The general-purpose function PlotTLPS plots one trophic-link
property against another.
If colour.by/bg.by/symbol.by is NULL and
community has a node property named `category' then trophic-link
colours/background colours/symbols are given by `resource.category' using
colour.spec/bg.spec/symbol.spec given by
DefaultCategoryColours/DefaultCategorySymbols.
PlotPredationMatrix shows trophic links as a binary matrix with species
shown in node order, starting at the top-left. If row.node and
col.order are both missing (the default) or are the same, then a
dashed diagonal line is drawn. Points on the dashed line indicate
cannibalistic trophic links.
The convenience functions PlotMRvMC, PlotMCvMR, PlotNRvNC,
PlotNCvNR, PlotBRvBC, PlotBCvBR are `wrappers' around
PlotRankNPS that plot a log10-transformed body mass, M, numerical
abundance, N, or biomass abundance, B.
Community,
TLPS,
PlotBSpectrum,
PlotCircularWeb,
PlotNPS,
PlotNPSDistribution,
PlotNSpectrum,
PlotRankNPS,
PlotWebByLevel
# NOT RUN {
data(TL84)
# The predation matrix
PlotPredationMatrix(TL84)
# The predation matrix with rows ordered by body mass
PlotPredationMatrix(TL84, resource.order='M')
# Colours and symbols by resource.category
PlotMCvMR(TL84)
# Colours and symbols by consumer.category
PlotMCvMR(TL84, bg.by='consumer.category', symbol.by='consumer.category',
colour.by='consumer.category')
# Consumer trophic height against resource log10(M)
PlotTLPS(TL84, 'resource.Log10M', 'consumer.TrophicHeight')
# Log10(M of resource / M of consumer) against consumer log10(M)
PlotTLPS(TL84, 'consumer.Log10M', 'Log10RCMRatio')
# }
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