CommunityCollection: Collections of communities

In quicklizard99/cheddar: Analysis and Visualisation of Ecological Communities

Collections of communities

Description

Collections of communities

Usage

CommunityCollection(communities)
## S3 method for class 'CommunityCollection'
print(x, ...) 
## S3 method for class 'CommunityCollection'
plot(x, ncol=min(length(x),5), by.col=TRUE, 
     plot.fn=plot, ...)
## S3 method for class 'CommunityCollection'
summary(object, ...) 

Arguments

communities	a list of Community objects.
x	an object of class CommunityCollection.
object	an object of class CommunityCollection.
ncol	the number of columns in the plot.
by.col	logical - if TRUE communities are plotted along columns.
plot.fn	a plot function that accepts a Community obejct .
...	further arguments passed to other methods.

Details

Constructs a new CommunityCollection from a list of existing Community objects. CommunityCollection is a subclass of list. CommunityCollection objects can not be modified directly.

An error is raised if any Community objects in communities share the same ‘title’ community property. An error is also raised if the Community objects in communities do not all have the same value of the community properties ‘M.units’ and ‘N.units’. CommunityCollection places no restrictions on other properties. For example, all of the ten communities with the pHWebs collection has a valid pH property but this is not enforced by CommunityCollection - it would be possible for a Community within a collection to not have a pH property, to have a pH of NA or even to have an invalid pH, for example a negative value.

CommunityCollection supports standard generic functions plot, print, subset and summary.

Value

A new object of class CommunityCollection.

Author(s)

Lawrence Hudson

See Also

Community, CollectionCPS CollectionNPS CollectionTLPS, OrderCollection, subset.CommunityCollection, AggregateCommunitiesBy, AggregateCommunities, pHWebs

Examples

# 10 stream webs sampled over a wide pH gradient
data(pHWebs)
pHWebs


# Eyeball the webs
plot(pHWebs)

# Consistent axis limits
plot(pHWebs, xlim=c(-14,6), ylim=c(-3,13))

# Different plot function
plot(pHWebs, plot.fn=PlotWebByLevel, ylim=c(1,4.5))


# list-like operations
length(pHWebs)
sapply(pHWebs, 'NumberOfTrophicLinks')
pHWebs[['Broadstone']]  # Access the Community

# A new CommunityCollection containing every other ph web
pHWebs[seq(1, 10, by=2)]

# A new CommunityCollection containing two webs
pHWebs[c('Old Lodge','Bere Stream')]


# CollectionCPS gets community properties
CollectionCPS(pHWebs)   # Webs are sorted by increasing pH

# Order by decreasing pH
pHWebs.decreasing.pH <- OrderCollection(pHWebs, 'pH', decreasing=TRUE)
CollectionCPS(pHWebs.decreasing.pH)

# Order by name
pHWebs.name <- OrderCollection(pHWebs, 'title')
CollectionCPS(pHWebs.name, c('pH', 'NumberOfNodes'))

# The following will always be TRUE.
all(FALSE==duplicated(names(pHWebs)))


# A new collection of the two Tuesday Lake communities
data(TL84, TL86)
BothTL <- CommunityCollection(list(TL84, TL86))
CollectionCPS(BothTL)


# You can't modify CommunityCollections
## Not run: pHWebs[1] <- 'silly'

quicklizard99/cheddar documentation built on Aug. 25, 2022, 5:01 a.m.