cheddar (version 0.1-639)

CommunityCollection: Collections of communities

Description

Collections of communities

Usage

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

Value

A new object of class CommunityCollection.

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.

Author

Lawrence Hudson

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.

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
if (FALSE) pHWebs[1] <- 'silly'