LumpNodes {cheddar} | R Documentation |

A function that lumps together nodes in a `Community`

.

LumpNodes(community, lump, title = NULL, weight.by = 'N')

`community` |
an object of class |

`lump` |
a vector of of length |

`title` |
the title of the new |

`weight.by` |
the name of a column by which to compute weighted mean of numeric values. |

If `weight.by`

is not `NULL`

and it is the name of
a node property, it is used to compute weighted means of all the other
numeric node properties. The arithmetic mean of `weight.by`

is
computed.
If `weight.by`

is `NULL`

or is not the name of a node property,
the arithmetic mean is computed for each numeric node property.
Node properties that are characters or logicals are aggregated by joining
unique values with a ‘,’. Empty character strings are ignored.

A new object of class `Community`

.

Lawrence Hudson

`LumpTrophicSpecies`

,
`IsIsolatedNode`

, `IsolatedNodes`

,
`NPS`

, `weighted.mean`

data(TL84) # Lump together isolated nodes in TL84 length(which(IsIsolatedNode(TL84))) # 6 isolated species IsolatedNodes(TL84) # Names of isolated nodes lump <- NP(TL84, 'node') # Existing node names # Give isolated nodes the same lump value lump[IsolatedNodes(TL84)] <- 'Isolated nodes lumped together' TL84.lumped <- LumpNodes(TL84, lump) NumberOfNodes(TL84) # 56 nodes in unlumped web NumberOfNodes(TL84.lumped) # 51 nodes in lumped web IsolatedNodes(TL84.lumped) # A single node # This trivial example shows that no nodes are lumped if values in lump are # unique to each node lump <- NP(TL84, 'node') identical(TL84, LumpNodes(TL84, lump, title=CP(TL84, 'title'))) # Ythan Estuary contains two species that are split in to adult and # juvenile forms. The example below lumps these in to single species. data(YthanEstuary) # The names of nodes in YthanEstuary lump <- NP(YthanEstuary, 'node') # European flounder: # "Platichthys flesus" and "Platichthys flesus (juvenile)" # Lump these in to one node lump["Platichthys flesus (juvenile)"==lump] <- "Platichthys flesus" # Common eider: # "Somateria mollissima" and "Somateria mollissima (juvenile)" # Lump these in to one node lump["Somateria mollissima (juvenile)"==lump] <- "Somateria mollissima" YthanEstuary.lumped <- LumpNodes(YthanEstuary, lump) # Examine the computed means for Somateria mollissima # Arithmetic mean of N is 2592 NP(YthanEstuary.lumped, 'N')['Somateria mollissima'] mean(NP(YthanEstuary, 'N')[c("Somateria mollissima (juvenile)", "Somateria mollissima")]) # N-weighted mean of M is 1637.018 NP(YthanEstuary.lumped, 'M')['Somateria mollissima'] weighted.mean(NP(YthanEstuary, 'M')[c("Somateria mollissima (juvenile)", "Somateria mollissima")], NP(YthanEstuary, 'N')[c("Somateria mollissima (juvenile)", "Somateria mollissima")], ) # Plot the original community and the community with lumped nodes par(mfrow=c(1,2)) plot(YthanEstuary, highlight.nodes=c("Platichthys flesus", "Platichthys flesus (juvenile)", "Somateria mollissima", "Somateria mollissima (juvenile)")) plot(YthanEstuary.lumped, highlight.nodes=c("Platichthys flesus", "Somateria mollissima"))

[Package *cheddar* version 0.1-636 Index]