cheddar (version 0.1-639)

SiteBySpeciesMatrix: Community collection site by species matrix

Description

Returns a matrix with a column per community and a row per unique node within communities in the collection.

Usage

SiteBySpeciesMatrix(collection, abundance=NULL, na.missing=FALSE)

Value

A matrix.

Arguments

collection

an object of class CommunityCollection.

abundance

the name of a node property that provides abundance values. This can be the name of a first-class propery or the name of a function. The name must meet the criteria of the properties parameter of NPS.

na.missing

if TRUE nodes that are absent from the community will be represented by NA; if FALSE, these nodes are represented by 0.

Author

Lawrence Hudson

Details

If abundance is NULL, the returned matrix indicates presence (1) or absence (0 or NA - see na.missing) of nodes. If abundance is given, values are the abundances of nodes, or 0 or NA where nodes are absent.

See Also

CommunityCollection, NPS, CollectionCPS, Biomass, Log10Biomass, matrix

Examples

data(pHWebs)

# If abundance is NULL, you get a presence/absence matrix:
SiteBySpeciesMatrix(pHWebs)

# Numerical abundance
SiteBySpeciesMatrix(pHWebs, 'N')

# Biomass abundance
SiteBySpeciesMatrix(pHWebs, 'Biomass')

# Log10 biomass abundance
SiteBySpeciesMatrix(pHWebs, 'Log10Biomass')

# Example showing how to model biomass in term of pH using vegan's rda function
m <- SiteBySpeciesMatrix(pHWebs, 'Biomass')

# Some nodes (e.g. CPOM) do not have a biomass. The rows in m for these nodes 
# will contain all NA. Rows containing all NA will upset vegan's rda function 
# so these rows must be removed.
m <- m[apply(m, 1, function(row) all(!is.na(row))),]

# Tranpose to get row per site - the format required by vegan's rda function
m <- t(m)

# Matrix (with a row per site) of variables on the right hand side of the 
# model equation
variables <- CollectionCPS(pHWebs)

if (FALSE) library(vegan)
if (FALSE) res <- rda(m~pH,variables)