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cheddar (version 0.1-636)

Analysis and Visualisation of Ecological Communities

Description

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.

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Version

Install

install.packages('cheddar')

Monthly Downloads

475

Version

0.1-636

License

BSD_2_clause + file LICENSE

Issues

Pull Requests

Stars

Forks

Maintainer

Lawrence Hudson

Last Published

February 13th, 2020

Functions in cheddar (0.1-636)

Degree

Node degree
Intervality

Food web Intervality
CollectionNPS

Collection node properties
NP

Single node properties
NPS

Node properties
IsCannibal

Cannibalistic nodes
Millstream

Millstream
LumpTrophicSpecies

Lump trophic species
NodeNameIndices

Node name indices
CollectionTLPS

Collection trophic-link properties
Community has property?

Community has property?
NvMTriTrophicTable

N-versus-M tri-trophic statistics
ChesapeakeBay

ChesapeakeBay
PlotNPS

Plot node properties
NvMTriTrophicStatistics

N-versus-M tri-trophic statistics
CommunityPropertyNames

Names of community properties
Node connectivity

Node connectivity
DegreeDistribution

Node degree distribution
LumpNodes

Lump nodes
LoadCommunity

Loading and saving Community objects
NodePropertyNames

A vector of names of node properties
NumberOfNodes

Number of nodes
NvMConvexHull

NvMConvexHull
PlotWagonWheel

Plot wagon wheel
NvMLinearRegressions

NvMLinearRegressions
Spectrum plots

Spectrum plots
QuantitativeDescriptors

Quantitative descriptors
Body mass, numerical abundance and biomass abundance

Body mass, numerical abundance and biomass abundance
PlotNPSDistribution

Plot distributions of node properties
NumberOfTrophicLinks

Number of trophic links
OrderCommunity

Order a community
Pyramid plots

Pyramid plots
PlotAuppervAlower

Plot upper-versus-lower link angles
PlotRankNPS

Plot rank of node properties
Community

Community
PlotTLPS

Plot trophic-link properties
PlotHelpers

Plot helpers
PlotCircularWeb

Plot circular web
Omnivory

Omnivory
LoadCollection

Loading and saving CommunityCollection objects
CommunityCollection

Collections of communities
LinearRegressionByClass

Linear regression by class
ShortestPaths

Path lengths
TL84

Tuesday Lake datasets
SkipwithPond

SkipwithPond
PlotWebByLevel

Plot web by level
SiteBySpeciesMatrix

Community collection site by species matrix
OrderCollection

Order a collection of communities
PredationMatrix

Predation matrix
RemoveCannibalisticLinks

Remove cannibalistic trophic links
ResourceLargerThanConsumer

Resource larger than consumer
TrophicLevels

Trophic levels
TrophicChainsStats

Trophic chains statistics
RemoveIsolatedNodes

Remove isolated nodes
ResourcesByNode

Resources and consumers of nodes
cheddar

Analysis and visualisation of ecological communities
PredationMatrixToLinks

Predation matrix to trophic links
TrophicSimilarity

Trophic similarity
pHWebs

pHWebs
TLPS

Trophic-link properties
ThreeNodeChains

Three-node chains
TrophicChains

Trophic chains
TrophicLinkPropertyNames

Trophic link property names
TrophicSpecies

Trophic species
subset.CommunityCollection

A subset of a collection of communities
TLP

A single trophic-link property
YthanEstuary

Ythan Estuary
RemoveNodes

Remove nodes
BodyMassBins

Body-mass bins
ApplyByClass

Apply by class
CollectionApply

Collection apply
BroadstoneStream

Broadstone Stream
Benguela

Benguela
CPS

Community properties
AggregateCommunities

Aggregate communities
CollectionCPS

Collection community properties
CP

Single community properties