Analysis and Visualisation of Ecological Communities
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Documentation for package ‘cheddar’ version 0.1-638
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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 |