Package: cheddar 0.1-639
cheddar: Analysis and Visualisation of Ecological Communities
Provides a flexible, extendable representation of an ecological community and a range of functions for analysis and visualisation, focusing on food web, body mass and numerical abundance data. Allows inter-web comparisons such as examining changes in community structure over environmental, temporal or spatial gradients.
Authors:
cheddar_0.1-639.tar.gz
cheddar_0.1-639.tar.gz(r-4.5-noble)cheddar_0.1-639.tar.gz(r-4.4-noble)
cheddar_0.1-639.tgz(r-4.4-emscripten)cheddar_0.1-639.tgz(r-4.3-emscripten)
cheddar.pdf |cheddar.html✨
cheddar/json (API)
# Install 'cheddar' in R: |
install.packages('cheddar', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/quicklizard99/cheddar/issues
- Benguela - Benguela
- BroadstoneStream - Broadstone Stream
- ChesapeakeBay - ChesapeakeBay
- Millstream - Millstream
- SkipwithPond - SkipwithPond
- TL84 - Tuesday Lake datasets
- TL86 - Tuesday Lake datasets
- YthanEstuary - Ythan Estuary
- pHWebs - PHWebs
Last updated 2 months agofrom:16aea56eeb. Checks:OK: 2. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Aug 24 2024 |
R-4.5-linux-x86_64 | OK | Aug 24 2024 |
Exports:[.CommunityCollection[[<-.Community[[<-.CommunityCollection[<-.Community[<-.CommunityCollection$<-.Community$<-.CommunityCollectionAggregateCommunitiesAggregateCommunitiesByApplyByClassBasalNodesBiomassBodyMassBinsCannibalsChainAveragedTrophicLevelCharacteristicPathLengthCollectionApplyCollectionCPSCollectionNPSCollectionTLPSCommunityCommunityCollectionCommunityPropertyNamesConnectedNodesConsumersByNodeConsumersOfNodesCPCPSCRMRatioDefaultCategoryColoursDefaultCategoryLabelColoursDefaultCategorySymbolsDefaultLinkColourDegreeDegreeDistributiondim<-.Communitydim<-.CommunityCollectionDirectedConnectanceFlowBasedTrophicLevelFormatLMFractionBasalNodesFractionCannibalisticFractionConnectedNodesFractionIntermediateNodesFractionIsolatedNodesFractionNonBasalNodesFractionNonTopLevelNodesFractionOfNodesByClassFractionOmnivorousFractionTopLevelNodesHasMHasNHasTrophicLinksInDegreeIntermediateNodesis.Communityis.CommunityCollectionIsBasalNodeIsCannibalIsConnectedNodeIsIntermediateNodeIsIsolatedNodeIsNonBasalNodeIsNonTopLevelNodeIsolatedNodesIsOmnivoreIsTopLevelNodelength<-.Communitylength<-.CommunityCollectionlevels<-.Communitylevels<-.CommunityCollectionLinearRegressionByClassLinkageDensityLMablineLoadCollectionLoadCommunityLog10BiomassLog10BLabelLog10CRMRatioLog10MLog10MLabelLog10MNBiomassLog10NLog10NLabelLog10RCMRatioLongestTrophicLevelLongWeightedTrophicLevelLumpNodesLumpTrophicSpeciesMeanMaximumTrophicSimilarityMinimiseSumConsumerGapsMinimiseSumDietGapsnames<-.Communitynames<-.CommunityCollectionNodeNameIndicesNodePropertyNamesNodeQuantitativeDescriptorsNonBasalNodesNonTopLevelNodesNormalisedTrophicGeneralityNormalisedTrophicVulnerabilityNPNPSNumberOfConsumersNumberOfNodesNumberOfNodesByClassNumberOfResourcesNumberOfTrophicLinksNvMConvexHullNvMInterceptNvMInterceptByClassNvMLinearRegressionsNvMSlopeNvMSlopeAndInterceptNvMSlopeAndInterceptByClassNvMSlopeByClassNvMTriTrophicStatisticsNvMTriTrophicTableOmnivoresOmnivoryOrderCollectionOrderCommunityOutDegreePlaceMissingPointsplot.Communityplot.CommunityCollectionPlotAuppervAlowerPlotBCvBRPlotBDistributionPlotBPyramidPlotBRvBCPlotBSpectrumPlotBvMPlotBvRankBPlotCircularWebPlotDegreeDistributionPlotLinearModelsPlotMCvMRPlotMDistributionPlotMRvMCPlotMvBPlotMvNPlotMvRankMPlotNCvNRPlotNDistributionPlotNPSPlotNPSDistributionPlotNPyramidPlotNRvNCPlotNSpectrumPlotNvMPlotNvRankNPlotPredationMatrixPlotRankNPSPlotTLPSPlotWagonWheelPlotWebByLevelPredationMatrixPredationMatrixToLinksPreyAveragedTrophicLevelprint.Communityprint.CommunityCollectionQuantitativeDescriptorsRCMRatioRemoveCannibalisticLinksRemoveIsolatedNodesRemoveNodesResourceLargerThanConsumerResourcesAndConsumersByNodeResourcesByNodeResourcesOfNodesSaveCollectionSaveCommunityShortestPathsShortestTrophicLevelShortWeightedTrophicLevelSiteBySpeciesMatrixsubset.CommunityCollectionSumBiomassByClassSumConsumerGapsSumDietGapssummary.Communitysummary.CommunityCollectionSumMByClassSumNByClassThreeNodeChainsTLPTLPSTopLevelNodesTrophicChainsTrophicChainsStatsTrophicGeneralityTrophicHeightTrophicLevelsTrophicLinkPropertyNamesTrophicLinksForNodesTrophicSimilarityTrophicSpeciesTrophicVulnerability
Dependencies:
A quick introduction to Cheddar
Rendered fromCheddarQuickstart.Rnw
usingutils::Sweave
on Aug 24 2024.Last update: 2020-02-13
Started: 2013-12-02
Cheddar plots and statistics
Rendered fromPlotsAndStats.Rnw
usingutils::Sweave
on Aug 24 2024.Last update: 2020-02-13
Started: 2013-12-02
Collections of communities
Rendered fromCollections.Rnw
usingutils::Sweave
on Aug 24 2024.Last update: 2020-02-13
Started: 2013-12-02
Importing and exporting data in-to and out-of Cheddar
Rendered fromImportExport.Rnw
usingutils::Sweave
on Aug 24 2024.Last update: 2020-02-13
Started: 2013-12-02
Working with Cheddar communities
Rendered fromCommunity.Rnw
usingutils::Sweave
on Aug 24 2024.Last update: 2020-02-13
Started: 2013-12-02
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Aggregate communities | AggregateCommunities AggregateCommunitiesBy |
Apply by class | ApplyByClass SumBiomassByClass SumMByClass SumNByClass |
Benguela | Benguela |
Body mass, numerical abundance and biomass abundance | Biomass CRMRatio Log10Biomass Log10CRMRatio Log10M Log10MNBiomass Log10N Log10RCMRatio RCMRatio |
Body-mass bins | BodyMassBins |
Broadstone Stream | BroadstoneStream |
Analysis and visualisation of ecological communities | cheddar-package cheddar |
ChesapeakeBay | ChesapeakeBay |
Collection apply | CollectionApply |
Collection community properties | CollectionCPS |
Collection node properties | CollectionNPS |
Collection trophic-link properties | CollectionTLPS |
Community | $<-.Community Community dim<-.Community is.Community length<-.Community levels<-.Community names<-.Community plot.Community print.Community summary.Community [<-.Community [[<-.Community |
Community has property? | HasM HasN HasTrophicLinks |
Collections of communities | $<-.CommunityCollection CommunityCollection dim<-.CommunityCollection is.CommunityCollection length<-.CommunityCollection levels<-.CommunityCollection names<-.CommunityCollection plot.CommunityCollection print.CommunityCollection summary.CommunityCollection [.CommunityCollection [<-.CommunityCollection [[<-.CommunityCollection |
Names of community properties | CommunityPropertyNames |
Single community properties | CP |
Community properties | CPS |
Node degree | Degree InDegree NormalisedTrophicGenerality NormalisedTrophicVulnerability NumberOfConsumers NumberOfResources OutDegree TrophicGenerality TrophicVulnerability |
Node degree distribution | DegreeDistribution |
Food web Intervality | Intervality MinimiseSumConsumerGaps MinimiseSumDietGaps SumConsumerGaps SumDietGaps |
Cannibalistic nodes | Cannibals FractionCannibalistic IsCannibal |
Linear regression by class | LinearRegressionByClass |
Loading and saving CommunityCollection objects | LoadCollection SaveCollection |
Loading and saving Community objects | LoadCommunity SaveCommunity |
Lump nodes | LumpNodes |
Lump trophic species | LumpTrophicSpecies |
Millstream | Millstream |
Node connectivity | BasalNodes ConnectedNodes FractionBasalNodes FractionConnectedNodes FractionIntermediateNodes FractionIsolatedNodes FractionNonBasalNodes FractionNonConnectedNodes FractionNonTopLevelNodes FractionTopLevelNodes IntermediateNodes IsBasalNode IsConnectedNode IsIntermediateNode IsIsolatedNode IsNonBasalNode IsNonTopLevelNode IsolatedNodes IsTopLevelNode NonBasalNodes NonTopLevelNodes TopLevelNodes |
Node name indices | NodeNameIndices |
A vector of names of node properties | NodePropertyNames |
Single node properties | NP |
Node properties | NPS |
Number of nodes | FractionOfNodesByClass NumberOfNodes NumberOfNodesByClass |
Number of trophic links | DirectedConnectance LinkageDensity NumberOfTrophicLinks |
NvMConvexHull | NvMConvexHull |
NvMLinearRegressions | NvMIntercept NvMInterceptByClass NvMLinearRegressions NvMSlope NvMSlopeAndIntercept NvMSlopeAndInterceptByClass NvMSlopeByClass |
N-versus-M tri-trophic statistics | NvMTriTrophicStatistics |
N-versus-M tri-trophic statistics | NvMTriTrophicTable |
Omnivory | FractionOmnivorous IsOmnivore Omnivores Omnivory |
Order a collection of communities | OrderCollection |
Order a community | OrderCommunity |
pHWebs | pHWebs |
Plot upper-versus-lower link angles | PlotAuppervAlower |
Plot circular web | PlotCircularWeb |
Plot helpers | DefaultCategoryColours DefaultCategoryLabelColours DefaultCategorySymbols DefaultLinkColour FormatLM LMabline Log10BLabel Log10MLabel Log10NLabel PlaceMissingPoints PlotLinearModels |
Plot node properties | PlotBvM PlotMvB PlotMvN PlotNPS PlotNvM |
Plot distributions of node properties | PlotBDistribution PlotDegreeDistribution PlotMDistribution PlotNDistribution PlotNPSDistribution |
Plot rank of node properties | PlotBvRankB PlotMvRankM PlotNvRankN PlotRankNPS |
Plot trophic-link properties | PlotBCvBR PlotBRvBC PlotMCvMR PlotMRvMC PlotNCvNR PlotNRvNC PlotPredationMatrix PlotTLPS |
Plot wagon wheel | PlotWagonWheel |
Plot web by level | PlotWebByLevel |
Predation matrix | PredationMatrix |
Predation matrix to trophic links | PredationMatrixToLinks |
Pyramid plots | PlotBPyramid PlotNPyramid |
Quantitative descriptors | NodeQuantitativeDescriptors QuantitativeDescriptors |
Remove cannibalistic trophic links | RemoveCannibalisticLinks |
Remove isolated nodes | RemoveIsolatedNodes |
Remove nodes | RemoveNodes |
Resource larger than consumer | ResourceLargerThanConsumer |
Resources and consumers of nodes | ConsumersByNode ConsumersOfNodes ResourcesAndConsumersByNode ResourcesByNode ResourcesOfNodes TrophicLinksForNodes |
Path lengths | CharacteristicPathLength ShortestPaths |
Community collection site by species matrix | SiteBySpeciesMatrix |
SkipwithPond | SkipwithPond |
Spectrum plots | PlotBSpectrum PlotNSpectrum |
A subset of a collection of communities | subset.CommunityCollection |
Three-node chains | ThreeNodeChains |
Tuesday Lake datasets | TL84 TL86 |
A single trophic-link property | TLP |
Trophic-link properties | TLPS |
Trophic chains | TrophicChains |
Trophic chains statistics | TrophicChainsStats |
Trophic levels | ChainAveragedTrophicLevel FlowBasedTrophicLevel LongestTrophicLevel LongWeightedTrophicLevel PreyAveragedTrophicLevel ShortestTrophicLevel ShortWeightedTrophicLevel TrophicHeight TrophicLevels |
Trophic link property names | TrophicLinkPropertyNames |
Trophic similarity | MeanMaximumTrophicSimilarity TrophicSimilarity |
Trophic species | TrophicSpecies |
Ythan Estuary | YthanEstuary |