PlotTLPS: Plot trophic-link properties
In quicklizard99/cheddar: Analysis and Visualisation of Ecological Communities

PlotTLPS

R Documentation

Plot trophic-link properties

Description

High-level functions for plotting trophic link properties.

Usage

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,
          ...)

Arguments

`community`	an object of class `Community`.
`X`	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`.
`Y`	plotted on the y axis; see `X`.
`xlab`	title of the x axis.
`ylab`	title of the y axis.
`axes.limits.equal`	logical - if `TRUE` and `xlim` and `ylim` are `NULL` then the limits of the x and y axes will be the same.
`xlim`	limits of the x axis
`ylim`	limits of the y axis
`main`	title of the plot
`highlight.links`	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.
`lowlight.links`	trophic links to be lowlighted; should meet criteria of `lowlight.links`.
`colour.by`	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`.
`colour.spec`	trophic links colours specification. either `NULL` or a named vector that maps values of `colour.by` to plotting values.
`col`	trophic links colours.
`symbol.by`	trophic links symbols property; must meet the criteria of `colour.by`.
`symbol.spec`	trophic links symbols specification specification; must meet the criteria of `colour.spec`.
`pch`	trophic links symbols.
`bg.by`	trophic links background colours property; must meet the criteria of `colour.by`
`bg.spec`	trophic links background colours specification; must meet the criteria of `colour.spec`.
`bg`	trophic links background colours.
`cex.by`	trophic links cex property; must meet the criteria of `colour.by`
`cex.spec`	cex values specification; must meet the criteria of `colour.spec`.
`cex`	cex values.
`are.values`	logical - if `TRUE` `X` and `Y` must be vectors of values of length `NumberOfTrophicLinks`.
`resource.order`	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`.
`consumer.order`	the order in which to show consumer; requirements are the same as `resource.order`.
`...`	other values to plot functions.

Details

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.

Author(s)

Lawrence Hudson

Examples

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')

quicklizard99/cheddar documentation built on Aug. 25, 2022, 5:01 a.m.