OrderCommunity {cheddar}R Documentation

Order a community

Description

Order a Community.

Usage

OrderCommunity(community, ..., decreasing=FALSE, na.last = TRUE, 
               new.order=NULL, title=NULL)

Arguments

community

an object of class Community.

...

the names of properties by which to order the communities.

decreasing

logical.

na.last

logical.

new.order

a vector of either node integer indices or node names giving the order.

title

the title of the new Community.

Details

Returns a new Community object. dots can contain any name that meets the criteria of the properties parameter of NPS. If new.order is NULL then ... and optionally decreasing are used to compute the new node ordering.

Different node orders will yield different SumDietGaps and SumConsumerGaps (e.g. Stouffer et al 2006, Zook et al 2011).

Value

A Community.

Author(s)

Lawrence Hudson

References

Stouffer, D.B. and Camacho, J. and Amaral, L.A.N. (2006) Proceedings of the National Academy of Sciences of the United States of America 103, 50, 19015–19020.

Zook, A.E. and Eklof, A. and Jacob, U. and Allesina, S. (2011) Journal of Theoretical Biology 271, 1 106–113.

See Also

Community, order, Intervality, CollectionNPS, PreyAveragedTrophicLevel, PlotPredationMatrix

Examples

data(TL84)
NPS(TL84)

# Order by increasing M
TL84.increasing.M <- OrderCommunity(TL84, 'M', title='Increasing M')
NPS(TL84.increasing.M)

# Order by decreasing M
TL84.decreasing.M <- OrderCommunity(TL84, 'M', decreasing=TRUE)
NPS(TL84.decreasing.M)

# Order by increasing M and N
TL84.increasing.MN <- OrderCommunity(TL84, 'M', 'N')
NPS(TL84.increasing.MN)

# Reverse existing order
TL84.reversed <- OrderCommunity(TL84, new.order=56:1)
NPS(TL84.reversed)

# Sort alphabetically by category and by increasing M within each category
TL84.category <- OrderCommunity(TL84, 'category', 'M')

# Increasing trophic level, then randomly sorted within trophic level
new.order <- order(PreyAveragedTrophicLevel(TL84), sample(1:56))
TL84.increasing.TL <- OrderCommunity(TL84, new.order=new.order, 
                                     title='Increasing TL')
NPS(TL84.increasing.TL)

# Graphically show the effect of different orders
par(mfrow=c(1,2))
PlotPredationMatrix(TL84.increasing.M)
PlotPredationMatrix(TL84.increasing.TL)

[Package cheddar version 0.1-636 Index]