Analysis and Visualisation of Ecological Communities


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Documentation for package ‘cheddar’ version 0.1-636

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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