R: Analysis and Visualisation of Ecological Communities

# Analysis and Visualisation of Ecological Communities

## Documentation for package ‘cheddar’ version 0.1-639

- DESCRIPTION file
- User guides, package vignettes and other documentation

## Help Pages

A B C D F H I L M N O P Q R S T Y misc

cheddar-package | Analysis and visualisation of ecological communities

## -- A --

AggregateCommunities | Aggregate communities
AggregateCommunitiesBy | Aggregate communities
ApplyByClass | Apply by class

## -- B --

BasalNodes | Node connectivity
Benguela | Benguela
Biomass | Body mass, numerical abundance and biomass abundance
BodyMassBins | Body-mass bins
BroadstoneStream | Broadstone Stream

## -- C --

Cannibals | Cannibalistic nodes
ChainAveragedTrophicLevel | Trophic levels
CharacteristicPathLength | Path lengths
cheddar | Analysis and visualisation of ecological communities
ChesapeakeBay | ChesapeakeBay
CollectionApply | Collection apply
CollectionCPS | Collection community properties
CollectionNPS | Collection node properties
CollectionTLPS | Collection trophic-link properties
Community | Community
CommunityCollection | Collections of communities
CommunityPropertyNames | Names of community properties
ConnectedNodes | Node connectivity
ConsumersByNode | Resources and consumers of nodes
ConsumersOfNodes | Resources and consumers of nodes
CP | Single community properties
CPS | Community properties
CRMRatio | Body mass, numerical abundance and biomass abundance

## -- D --

DefaultCategoryColours | Plot helpers
DefaultCategoryLabelColours | Plot helpers
DefaultCategorySymbols | Plot helpers
DefaultLinkColour | Plot helpers
Degree | Node degree
DegreeDistribution | Node degree distribution
dim<-.Community | Community
dim<-.CommunityCollection | Collections of communities
DirectedConnectance | Number of trophic links

## -- F --

FlowBasedTrophicLevel | Trophic levels
FormatLM | Plot helpers
FractionBasalNodes | Node connectivity
FractionCannibalistic | Cannibalistic nodes
FractionConnectedNodes | Node connectivity
FractionIntermediateNodes | Node connectivity
FractionIsolatedNodes | Node connectivity
FractionNonBasalNodes | Node connectivity
FractionNonConnectedNodes | Node connectivity
FractionNonTopLevelNodes | Node connectivity
FractionOfNodesByClass | Number of nodes
FractionOmnivorous | Omnivory
FractionTopLevelNodes | Node connectivity

## -- H --

HasM | Community has property?
HasN | Community has property?
HasTrophicLinks | Community has property?

## -- I --

InDegree | Node degree
IntermediateNodes | Node connectivity
Intervality | Food web Intervality
is.Community | Community
is.CommunityCollection | Collections of communities
IsBasalNode | Node connectivity
IsCannibal | Cannibalistic nodes
IsConnectedNode | Node connectivity
IsIntermediateNode | Node connectivity
IsIsolatedNode | Node connectivity
IsNonBasalNode | Node connectivity
IsNonTopLevelNode | Node connectivity
IsolatedNodes | Node connectivity
IsOmnivore | Omnivory
IsTopLevelNode | Node connectivity

## -- L --

length<-.Community | Community
length<-.CommunityCollection | Collections of communities
levels<-.Community | Community
levels<-.CommunityCollection | Collections of communities
LinearRegressionByClass | Linear regression by class
LinkageDensity | Number of trophic links
LMabline | Plot helpers
LoadCollection | Loading and saving CommunityCollection objects
LoadCommunity | Loading and saving Community objects
Log10Biomass | Body mass, numerical abundance and biomass abundance
Log10BLabel | Plot helpers
Log10CRMRatio | Body mass, numerical abundance and biomass abundance
Log10M | Body mass, numerical abundance and biomass abundance
Log10MLabel | Plot helpers
Log10MNBiomass | Body mass, numerical abundance and biomass abundance
Log10N | Body mass, numerical abundance and biomass abundance
Log10NLabel | Plot helpers
Log10RCMRatio | Body mass, numerical abundance and biomass abundance
LongestTrophicLevel | Trophic levels
LongWeightedTrophicLevel | Trophic levels
LumpNodes | Lump nodes
LumpTrophicSpecies | Lump trophic species

## -- M --

MeanMaximumTrophicSimilarity | Trophic similarity
Millstream | Millstream
MinimiseSumConsumerGaps | Food web Intervality
MinimiseSumDietGaps | Food web Intervality

## -- N --

names<-.Community | Community
names<-.CommunityCollection | Collections of communities
NodeNameIndices | Node name indices
NodePropertyNames | A vector of names of node properties
NodeQuantitativeDescriptors | Quantitative descriptors
NonBasalNodes | Node connectivity
NonTopLevelNodes | Node connectivity
NormalisedTrophicGenerality | Node degree
NormalisedTrophicVulnerability | Node degree
NP | Single node properties
NPS | Node properties
NumberOfConsumers | Node degree
NumberOfNodes | Number of nodes
NumberOfNodesByClass | Number of nodes
NumberOfResources | Node degree
NumberOfTrophicLinks | Number of trophic links
NvMConvexHull | NvMConvexHull
NvMIntercept | NvMLinearRegressions
NvMInterceptByClass | NvMLinearRegressions
NvMLinearRegressions | NvMLinearRegressions
NvMSlope | NvMLinearRegressions
NvMSlopeAndIntercept | NvMLinearRegressions
NvMSlopeAndInterceptByClass | NvMLinearRegressions
NvMSlopeByClass | NvMLinearRegressions
NvMTriTrophicStatistics | N-versus-M tri-trophic statistics
NvMTriTrophicTable | N-versus-M tri-trophic statistics

## -- O --

Omnivores | Omnivory
Omnivory | Omnivory
OrderCollection | Order a collection of communities
OrderCommunity | Order a community
OutDegree | Node degree

## -- P --

pHWebs | pHWebs
PlaceMissingPoints | Plot helpers
plot.Community | Community
plot.CommunityCollection | Collections of communities
PlotAuppervAlower | Plot upper-versus-lower link angles
PlotBCvBR | Plot trophic-link properties
PlotBDistribution | Plot distributions of node properties
PlotBPyramid | Pyramid plots
PlotBRvBC | Plot trophic-link properties
PlotBSpectrum | Spectrum plots
PlotBvM | Plot node properties
PlotBvRankB | Plot rank of node properties
PlotCircularWeb | Plot circular web
PlotDegreeDistribution | Plot distributions of node properties
PlotLinearModels | Plot helpers
PlotMCvMR | Plot trophic-link properties
PlotMDistribution | Plot distributions of node properties
PlotMRvMC | Plot trophic-link properties
PlotMvB | Plot node properties
PlotMvN | Plot node properties
PlotMvRankM | Plot rank of node properties
PlotNCvNR | Plot trophic-link properties
PlotNDistribution | Plot distributions of node properties
PlotNPS | Plot node properties
PlotNPSDistribution | Plot distributions of node properties
PlotNPyramid | Pyramid plots
PlotNRvNC | Plot trophic-link properties
PlotNSpectrum | Spectrum plots
PlotNvM | Plot node properties
PlotNvRankN | Plot rank of node properties
PlotPredationMatrix | Plot trophic-link properties
PlotRankNPS | Plot rank of node properties
PlotTLPS | Plot trophic-link properties
PlotWagonWheel | Plot wagon wheel
PlotWebByLevel | Plot web by level
PredationMatrix | Predation matrix
PredationMatrixToLinks | Predation matrix to trophic links
PreyAveragedTrophicLevel | Trophic levels
print.Community | Community
print.CommunityCollection | Collections of communities

## -- Q --

QuantitativeDescriptors | Quantitative descriptors

## -- R --

RCMRatio | Body mass, numerical abundance and biomass abundance
RemoveCannibalisticLinks | Remove cannibalistic trophic links
RemoveIsolatedNodes | Remove isolated nodes
RemoveNodes | Remove nodes
ResourceLargerThanConsumer | Resource larger than consumer
ResourcesAndConsumersByNode | Resources and consumers of nodes
ResourcesByNode | Resources and consumers of nodes
ResourcesOfNodes | Resources and consumers of nodes

## -- S --

SaveCollection | Loading and saving CommunityCollection objects
SaveCommunity | Loading and saving Community objects
ShortestPaths | Path lengths
ShortestTrophicLevel | Trophic levels
ShortWeightedTrophicLevel | Trophic levels
SiteBySpeciesMatrix | Community collection site by species matrix
SkipwithPond | SkipwithPond
subset.CommunityCollection | A subset of a collection of communities
SumBiomassByClass | Apply by class
SumConsumerGaps | Food web Intervality
SumDietGaps | Food web Intervality
summary.Community | Community
summary.CommunityCollection | Collections of communities
SumMByClass | Apply by class
SumNByClass | Apply by class

## -- T --

ThreeNodeChains | Three-node chains
TL84 | Tuesday Lake datasets
TL86 | Tuesday Lake datasets
TLP | A single trophic-link property
TLPS | Trophic-link properties
TopLevelNodes | Node connectivity
TrophicChains | Trophic chains
TrophicChainsStats | Trophic chains statistics
TrophicGenerality | Node degree
TrophicHeight | Trophic levels
TrophicLevels | Trophic levels
TrophicLinkPropertyNames | Trophic link property names
TrophicLinksForNodes | Resources and consumers of nodes
TrophicSimilarity | Trophic similarity
TrophicSpecies | Trophic species
TrophicVulnerability | Node degree

## -- Y --

YthanEstuary | Ythan Estuary

## -- misc --

$<-.Community | Community
$<-.CommunityCollection | Collections of communities
[.CommunityCollection | Collections of communities
[<-.Community | Community
[<-.CommunityCollection | Collections of communities
[[<-.Community | Community
[[<-.CommunityCollection | Collections of communities