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.

Install the latest version of this package by entering the following in R:
install.packages("cheddar")
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

Functions

AggregateCommunities Man page
AggregateCommunitiesBy Man page
ApplyByClass Man page
BasalNodes Man page
Benguela Man page
Biomass Man page
BodyMassBins Man page
BroadstoneStream Man page
Cannibals Man page
ChainAveragedTrophicLevel Man page
CharacteristicPathLength Man page
cheddar Man page
cheddar-package Man page
ChesapeakeBay Man page
CollectionApply Man page
CollectionCPS Man page
CollectionNPS Man page
CollectionTLPS Man page
Community Man page
[<-.Community Man page
[[<-.Community Man page
$<-.Community Man page
CommunityCollection Man page
[<-.CommunityCollection Man page
[.CommunityCollection Man page
[[<-.CommunityCollection Man page
$<-.CommunityCollection Man page
CommunityPropertyNames Man page
ConnectedNodes Man page
ConsumersByNode Man page
ConsumersOfNodes Man page
CP Man page
CPS Man page
CRMRatio Man page
DefaultCategoryColours Man page
DefaultCategoryLabelColours Man page
DefaultCategorySymbols Man page
DefaultLinkColour Man page
Degree Man page
DegreeDistribution Man page
dim<-.Community Man page
dim<-.CommunityCollection Man page
DirectedConnectance Man page
FlowBasedTrophicLevel Man page
FormatLM Man page
FractionBasalNodes Man page
FractionCannibalistic Man page
FractionConnectedNodes Man page
FractionIntermediateNodes Man page
FractionIsolatedNodes Man page
FractionNonBasalNodes Man page
FractionNonConnectedNodes Man page
FractionNonTopLevelNodes Man page
FractionOfNodesByClass Man page
FractionOmnivorous Man page
FractionTopLevelNodes Man page
HasM Man page
HasN Man page
HasTrophicLinks Man page
InDegree Man page
IntermediateNodes Man page
Intervality Man page
IsBasalNode Man page
IsCannibal Man page
is.Community Man page
is.CommunityCollection Man page
IsConnectedNode Man page
IsIntermediateNode Man page
IsIsolatedNode Man page
IsNonBasalNode Man page
IsNonTopLevelNode Man page
IsolatedNodes Man page
IsOmnivore Man page
IsTopLevelNode Man page
length<-.Community Man page
length<-.CommunityCollection Man page
levels<-.Community Man page
levels<-.CommunityCollection Man page
LinearRegressionByClass Man page
LinkageDensity Man page
LMabline Man page
LoadCollection Man page
LoadCommunity Man page
Log10Biomass Man page
Log10BLabel Man page
Log10CRMRatio Man page
Log10M Man page
Log10MLabel Man page
Log10MNBiomass Man page
Log10N Man page
Log10NLabel Man page
Log10RCMRatio Man page
LongestTrophicLevel Man page
LongWeightedTrophicLevel Man page
LumpNodes Man page
LumpTrophicSpecies Man page
MeanMaximumTrophicSimilarity Man page
Millstream Man page
MinimiseSumConsumerGaps Man page
MinimiseSumDietGaps Man page
names<-.Community Man page
names<-.CommunityCollection Man page
NodeNameIndices Man page
NodePropertyNames Man page
NodeQuantitativeDescriptors Man page
NonBasalNodes Man page
NonTopLevelNodes Man page
NormalisedTrophicGenerality Man page
NormalisedTrophicVulnerability Man page
NP Man page
NPS Man page
NumberOfConsumers Man page
NumberOfNodes Man page
NumberOfNodesByClass Man page
NumberOfResources Man page
NumberOfTrophicLinks Man page
NvMConvexHull Man page
NvMIntercept Man page
NvMInterceptByClass Man page
NvMLinearRegressions Man page
NvMSlope Man page
NvMSlopeAndIntercept Man page
NvMSlopeAndInterceptByClass Man page
NvMSlopeByClass Man page
NvMTriTrophicStatistics Man page
NvMTriTrophicTable Man page
Omnivores Man page
Omnivory Man page
OrderCollection Man page
OrderCommunity Man page
OutDegree Man page
pHWebs Man page
PlaceMissingPoints Man page
PlotAuppervAlower Man page
PlotBCvBR Man page
PlotBDistribution Man page
PlotBPyramid Man page
PlotBRvBC Man page
PlotBSpectrum Man page
PlotBvM Man page
PlotBvRankB Man page
PlotCircularWeb Man page
plot.Community Man page
plot.CommunityCollection Man page
PlotDegreeDistribution Man page
PlotLinearModels Man page
PlotMCvMR Man page
PlotMDistribution Man page
PlotMRvMC Man page
PlotMvB Man page
PlotMvN Man page
PlotMvRankM Man page
PlotNCvNR Man page
PlotNDistribution Man page
PlotNPS Man page
PlotNPSDistribution Man page
PlotNPyramid Man page
PlotNRvNC Man page
PlotNSpectrum Man page
PlotNvM Man page
PlotNvRankN Man page
PlotPredationMatrix Man page
PlotRankNPS Man page
PlotTLPS Man page
PlotWagonWheel Man page
PlotWebByLevel Man page
PredationMatrix Man page
PredationMatrixToLinks Man page
PreyAveragedTrophicLevel Man page
print.Community Man page
print.CommunityCollection Man page
QuantitativeDescriptors Man page
RCMRatio Man page
RemoveCannibalisticLinks Man page
RemoveIsolatedNodes Man page
RemoveNodes Man page
ResourceLargerThanConsumer Man page
ResourcesAndConsumersByNode Man page
ResourcesByNode Man page
ResourcesOfNodes Man page
SaveCollection Man page
SaveCommunity Man page
ShortestPaths Man page
ShortestTrophicLevel Man page
ShortWeightedTrophicLevel Man page
SiteBySpeciesMatrix Man page
SkipwithPond Man page
subset.CommunityCollection Man page
SumBiomassByClass Man page
SumConsumerGaps Man page
SumDietGaps Man page
summary.Community Man page
summary.CommunityCollection Man page
SumMByClass Man page
SumNByClass Man page
ThreeNodeChains Man page
TL84 Man page
TL86 Man page
TLP Man page
TLPS Man page
TopLevelNodes Man page
TrophicChains Man page
TrophicChainsStats Man page
TrophicGenerality Man page
TrophicHeight Man page
TrophicLevels Man page
TrophicLinkPropertyNames Man page
TrophicLinksForNodes Man page
TrophicSimilarity Man page
TrophicSpecies Man page
TrophicVulnerability Man page
YthanEstuary Man page

Files

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

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

Please suggest features or report bugs with the GitHub issue tracker.

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