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cheddar (version 0.1-626)

Analysis and visualisation of ecological communities

Description

Cheddar 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. It also allows inter-web comparisons such as examining changes in community structure over environmental, temporal or spatial gradients.

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Version

Install

install.packages('cheddar')

Monthly Downloads

448

Version

0.1-626

License

BSD_2_clause + file LICENSE

Issues

Pull Requests

Stars

Forks

Maintainer

Lawrence Hudson

Last Published

August 28th, 2014

Functions in cheddar (0.1-626)

CollectionTLPS

Collection trophic-link properties
BodyMassBins

Body-mass bins
NodePropertyNames

A vector of names of node properties
NvMTriTrophicTable

N-versus-M tri-trophic statistics
CommunityPropertyNames

Names of community properties
NP

Single node properties
NumberOfTrophicLinks

Number of trophic links
pHWebs

pHWebs
YthanEstuary

Ythan Estuary
LinearRegressionByClass

Linear regression by class
LumpNodes

Lump nodes
PlotCircularWeb

Plot circular web
Spectrum plots

Spectrum plots
PlotTLPS

Plot trophic-link properties
TrophicSpecies

Trophic species
RemoveNodes

Remove nodes
subset.CommunityCollection

A subset of a collection of communities
CommunityCollection

Collections of communities
Community has property?

Community has property?
LoadCommunity

Loading and saving Community objects
Intervality

Food web Intervality
Millstream

Millstream
LumpTrophicSpecies

Lump trophic species
QuantitativeDescriptors

Quantitative descriptors
OrderCommunity

Order a community
RemoveCannibalisticLinks

Remove cannibalistic trophic links
PredationMatrixToLinks

Predation matrix to trophic links
SkipwithPond

SkipwithPond
Community

Community
Degree

Node degree
Body mass, numerical abundance and biomass abundance

Body mass, numerical abundance and biomass abundance
Node connectivity

Node connectivity
PlotNPSDistribution

Plot distributions of node properties
PlotWebByLevel

Plot web by level
ShortestPaths

Path lengths
RemoveIsolatedNodes

Remove isolated nodes
TL84

Tuesday Lake datasets
TrophicLevels

Trophic levels
TLP

A single trophic-link property
cheddar

Analysis and visualisation of ecological communities
ApplyByClass

Apply by class
CP

Single community properties
BroadstoneStream

Broadstone Stream
Omnivory

Omnivory
PlotAuppervAlower

Plot upper-versus-lower link angles
PlotHelpers

Plot helpers
CollectionCPS

Collection community properties
AggregateCommunities

Aggregate communities
CollectionNPS

Collection node properties
NodeNameIndices

Node name indices
ThreeNodeChains

Three-node chains
ResourcesByNode

Resources and consumers of nodes
CPS

Community properties
PlotNPS

Plot node properties
PlotRankNPS

Plot rank of node properties
NvMLinearRegressions

NvMLinearRegressions
NumberOfNodes

Number of nodes
NvMTriTrophicStatistics

N-versus-M tri-trophic statistics
OrderCollection

Order a collection of communities
ChesapeakeBay

ChesapeakeBay
ResourceLargerThanConsumer

Resource larger than consumer
IsCannibal

Cannibalistic nodes
TrophicSimilarity

Trophic similarity
TrophicLinkPropertyNames

Trophic link property names
Benguela

Benguela
NPS

Node properties
TrophicChains

Trophic chains
PredationMatrix

Predation matrix
CollectionApply

Collection apply
TLPS

Trophic-link properties
DegreeDistribution

Node degree distribution
NvMConvexHull

NvMConvexHull
LoadCollection

Loading and saving CommunityCollection objects
TrophicChainsStats

Trophic chains statistics
Pyramid plots

Pyramid plots
SiteBySpeciesMatrix

Community collection site by species matrix