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.

Author
Lawrence Hudson with contributions from Dan Reuman and Rob Emerson
Date of publication
2016-10-10 13:51:44
Maintainer
Lawrence Hudson <quicklizard@googlemail.com>
License
BSD_2_clause + file LICENSE
Version
0.1-631
URLs

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