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.

AuthorLawrence Hudson with contributions from Dan Reuman and Rob Emerson
Date of publication2016-10-10 13:51:44
MaintainerLawrence Hudson <quicklizard@googlemail.com>
LicenseBSD_2_clause + file LICENSE
Version0.1-631
https://github.com/quicklizard99/cheddar/

View on CRAN

Man pages

AggregateCommunities: Aggregate communities

ApplyByClass: Apply by class

Benguela: Benguela

BodyMassB: Body-mass bins

BroadstoneStream: Broadstone Stream

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

CommunityHas: Community has property?

CommunityPropertyNames: Names of community properties

CP: Single community properties

CPS: Community properties

Degree: Node degree

DegreeDistribution: Node degree distribution

Intervality: Food web Intervality

IsCannibal: Cannibalistic nodes

LinearRegressionByClass: Linear regression by class

LoadCollection: Loading and saving CommunityCollection objects

LoadCommunity: Loading and saving Community objects

LumpNodes: Lump nodes

LumpTrophicSpecies: Lump trophic species

Millstream: Millstream

NodeConnectivity: Node connectivity

NodeMNUtilities: Body mass, numerical abundance and biomass abundance

NodeNameIndices: Node name indices

NodePropertyNames: A vector of names of node properties

NP: Single node properties

NPS: Node properties

NumberOfNodes: Number of nodes

NumberOfTrophicLinks: Number of trophic links

NvMConvexHull: NvMConvexHull

NvMLinearRegressions: NvMLinearRegressions

NvMTriTrophicStatistics: N-versus-M tri-trophic statistics

NvMTriTrophicTable: N-versus-M tri-trophic statistics

Omnivory: Omnivory

OrderCollection: Order a collection of communities

OrderCommunity: Order a community

pHWebs: pHWebs

PlotAuppervAlower: Plot upper-versus-lower link angles

PlotCircularWeb: Plot circular web

PlotHelpers: Plot helpers

PlotNPS: Plot node properties

PlotNPSDistribution: Plot distributions of node properties

PlotPyramid: Pyramid plots

PlotRankNPS: Plot rank of node properties

PlotSpectrum: Spectrum plots

PlotTLPS: Plot trophic-link properties

PlotWagonWheel: Plot wagon wheel

PlotWebByLevel: Plot web by level

PredationMatrix: Predation matrix

PredationMatrixToLinks: Predation matrix to trophic links

QuantitativeDescriptors: Quantitative descriptors

RemoveCannibalisticLinks: Remove cannibalistic trophic links

RemoveIsolatedNodes: Remove isolated nodes

RemoveNodes: Remove nodes

ResourceLargerThanConsumer: Resource larger than consumer

ResourcesByNode: Resources and consumers of nodes

ShortestPaths: Path lengths

SiteBySpeciesMatrix: Community collection site by species matrix

SkipwithPond: SkipwithPond

subset.CommunityCollection: A subset of a collection of communities

ThreeNodeChains: Three-node chains

TL84: Tuesday Lake datasets

TLP: A single trophic-link property

TLPS: Trophic-link properties

TrophicChains: Trophic chains

TrophicChainsStats: Trophic chains statistics

TrophicLevels: Trophic levels

TrophicLinkPropertyNames: Trophic link property names

TrophicSimilarity: Trophic similarity

TrophicSpecies: Trophic species

YthanEstuary: Ythan Estuary

Files in this package

cheddar
cheddar/inst
cheddar/inst/CITATION
cheddar/inst/doc
cheddar/inst/doc/CheddarQuickstart.Rnw
cheddar/inst/doc/ImportExport.pdf
cheddar/inst/doc/CheddarQuickstart.pdf
cheddar/inst/doc/CheddarQuickstart.R
cheddar/inst/doc/Community.pdf
cheddar/inst/doc/Community.R
cheddar/inst/doc/Collections.pdf
cheddar/inst/doc/PlotsAndStats.Rnw
cheddar/inst/doc/PlotsAndStats.R
cheddar/inst/doc/ImportExport.Rnw
cheddar/inst/doc/Community.Rnw
cheddar/inst/doc/Collections.R
cheddar/inst/doc/PlotsAndStats.pdf
cheddar/inst/doc/ImportExport.R
cheddar/inst/doc/Collections.Rnw
cheddar/tests
cheddar/tests/community_collection_test.R
cheddar/tests/graph_tests.R
cheddar/tests/community_trophic_links_test.R
cheddar/tests/run.R
cheddar/tests/community_test.R
cheddar/tests/community_MN_test.R
cheddar/tests/util_test.R
cheddar/src
cheddar/src/shortest_paths.cpp
cheddar/src/trophic_chains.cpp
cheddar/src/anneal.cpp
cheddar/src/cheddar_exception.h
cheddar/NAMESPACE
cheddar/data
cheddar/data/TL86.RData
cheddar/data/YthanEstuary.RData
cheddar/data/Benguela.RData
cheddar/data/Millstream.RData
cheddar/data/ChesapeakeBay.RData
cheddar/data/SkipwithPond.RData
cheddar/data/TL84.RData
cheddar/data/pHWebs.RData
cheddar/data/BroadstoneStream.RData
cheddar/R
cheddar/R/aggregate.R cheddar/R/chains.R cheddar/R/graph_nodes.R cheddar/R/community_MN.R cheddar/R/graph.R cheddar/R/graph_trophic_links.R cheddar/R/config.R cheddar/R/community.R cheddar/R/util.R cheddar/R/community_collection.R cheddar/R/community_trophic_links.R cheddar/R/graph_util.R
cheddar/vignettes
cheddar/vignettes/CheddarQuickstart.Rnw
cheddar/vignettes/cheddar.bib
cheddar/vignettes/PlotsAndStats.Rnw
cheddar/vignettes/ImportExport.Rnw
cheddar/vignettes/Community.Rnw
cheddar/vignettes/Stream12
cheddar/vignettes/Stream12/properties.csv
cheddar/vignettes/Stream12/nodes.csv
cheddar/vignettes/Stream12/trophic.links.csv
cheddar/vignettes/Grassland1994
cheddar/vignettes/Grassland1994/communities
cheddar/vignettes/Grassland1994/communities/Plot3
cheddar/vignettes/Grassland1994/communities/Plot3/properties.csv
cheddar/vignettes/Grassland1994/communities/Plot3/nodes.csv
cheddar/vignettes/Grassland1994/communities/Plot3/trophic.links.csv
cheddar/vignettes/Grassland1994/communities/Plot2
cheddar/vignettes/Grassland1994/communities/Plot2/properties.csv
cheddar/vignettes/Grassland1994/communities/Plot2/nodes.csv
cheddar/vignettes/Grassland1994/communities/Plot2/trophic.links.csv
cheddar/vignettes/Grassland1994/communities/Plot1
cheddar/vignettes/Grassland1994/communities/Plot1/properties.csv
cheddar/vignettes/Grassland1994/communities/Plot1/nodes.csv
cheddar/vignettes/Grassland1994/communities/Plot1/trophic.links.csv
cheddar/vignettes/Collections.Rnw
cheddar/MD5
cheddar/DESCRIPTION
cheddar/man
cheddar/man/CollectionTLPS.Rd cheddar/man/CommunityCollection.Rd cheddar/man/PlotCircularWeb.Rd cheddar/man/BodyMassB.Rd cheddar/man/ResourcesByNode.Rd cheddar/man/LoadCollection.Rd cheddar/man/TLP.Rd cheddar/man/RemoveNodes.Rd cheddar/man/PlotTLPS.Rd cheddar/man/PlotAuppervAlower.Rd cheddar/man/DegreeDistribution.Rd cheddar/man/ThreeNodeChains.Rd cheddar/man/LinearRegressionByClass.Rd cheddar/man/BroadstoneStream.Rd cheddar/man/Millstream.Rd cheddar/man/CollectionNPS.Rd cheddar/man/TLPS.Rd cheddar/man/ShortestPaths.Rd cheddar/man/CollectionCPS.Rd cheddar/man/TrophicSimilarity.Rd cheddar/man/PlotRankNPS.Rd cheddar/man/TL84.Rd cheddar/man/NP.Rd cheddar/man/AggregateCommunities.Rd cheddar/man/NodeMNUtilities.Rd cheddar/man/PlotPyramid.Rd cheddar/man/NPS.Rd cheddar/man/NvMTriTrophicTable.Rd cheddar/man/RemoveCannibalisticLinks.Rd cheddar/man/NodeConnectivity.Rd cheddar/man/cheddar.Rd cheddar/man/Omnivory.Rd cheddar/man/NodeNameIndices.Rd cheddar/man/OrderCommunity.Rd cheddar/man/ResourceLargerThanConsumer.Rd cheddar/man/ChesapeakeBay.Rd cheddar/man/pHWebs.Rd cheddar/man/PredationMatrixToLinks.Rd cheddar/man/subset.CommunityCollection.Rd cheddar/man/TrophicChains.Rd cheddar/man/OrderCollection.Rd cheddar/man/CollectionApply.Rd cheddar/man/NvMTriTrophicStatistics.Rd cheddar/man/LoadCommunity.Rd cheddar/man/NvMConvexHull.Rd cheddar/man/TrophicLevels.Rd cheddar/man/NvMLinearRegressions.Rd cheddar/man/NodePropertyNames.Rd cheddar/man/RemoveIsolatedNodes.Rd cheddar/man/NumberOfNodes.Rd cheddar/man/PredationMatrix.Rd cheddar/man/Benguela.Rd cheddar/man/TrophicSpecies.Rd cheddar/man/ApplyByClass.Rd cheddar/man/CP.Rd cheddar/man/PlotWagonWheel.Rd cheddar/man/TrophicLinkPropertyNames.Rd cheddar/man/Intervality.Rd cheddar/man/CommunityHas.Rd cheddar/man/LumpTrophicSpecies.Rd cheddar/man/NumberOfTrophicLinks.Rd cheddar/man/PlotWebByLevel.Rd cheddar/man/LumpNodes.Rd cheddar/man/PlotNPS.Rd cheddar/man/YthanEstuary.Rd cheddar/man/QuantitativeDescriptors.Rd cheddar/man/PlotNPSDistribution.Rd cheddar/man/Community.Rd cheddar/man/CommunityPropertyNames.Rd cheddar/man/TrophicChainsStats.Rd cheddar/man/SkipwithPond.Rd cheddar/man/SiteBySpeciesMatrix.Rd cheddar/man/CPS.Rd cheddar/man/IsCannibal.Rd cheddar/man/PlotSpectrum.Rd cheddar/man/PlotHelpers.Rd cheddar/man/Degree.Rd
cheddar/.Rinstignore
cheddar/LICENSE

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.