cc.manip: Manipulating and examining comparative.comm objects

In pez: Phylogenetics for the Environmental Sciences

Manipulating and examining comparative.comm objects

Description

As described in the vignette, we recommend using these wrappers to manipulate species and site data, as it guarantees that everything will be kept consistent across all parts of the comparative.comm object. With them, you can drop species, sites, and work directly with each part of your data. You can also manipulate your comparative.comm object's phy, data, env, and comm slots directly if you wish, but altering the object directly yourself runs the risk of things getting unsynchronised.

Usage

## S3 method for class 'comparative.comm'
x[sites, spp, warn = FALSE]

trait.names(object)

env.names(object)

species(x)

species(x) <- value

sites(x)

sites(x) <- value

traits(x) <- value

traits(x)

env(x) <- value

env(x)

comm(x) <- value

comm(x)

tree(x)

phy(x)

tree(x) <- value

phy(x) <- value

assemblage.phylogenies(data)

## S3 method for class 'comparative.comm'
as.data.frame(
  x,
  row.names = NULL,
  optional = FALSE,
  abundance.weighted = FALSE,
  ...
)

## S3 method for class 'comparative.comm'
within(data, expr, ...)

Arguments

x	comparative.comm object
sites	numbers of sites to be kept or dropped from x; must be given as numbers. For example, x[1:5,], or x[-1:-5,], but not x[c("site a", "site b"),].
spp	numbers of species to be kept or dropped from x; must be given as numbers. For example, x[,1:5], or x[,-1:-5], but not x[c("sp a", "sp b"),].
warn	whether to warn if species/sites are dropped when creating object (default: TRUE)
object	A comparative.comm object
value	when altering a comparative.comm object's internal structure, the thing that you're inserting into it!
data	A comparative.comm object
row.names	ignored
optional	ignored presence-absence dataset (default: FALSE)
abundance.weighted	whether to create to create a
...	ignored
expr	expression to be evaluated within the scope of data

Value

Names of the traits or environmental variables

Note

As described in comparative.comm, each comparative.comm object contains a phylogeny ($phy) and a site-by-species community matrix (as used in vegan). Optionally, it may contain a data.frame of trait data (each row a species, each column a trait ) *called data* for compatibility with comparative.data.

See Also

comparative.comm plot.comaparative.comm

Examples

data(laja)
data <- comparative.comm(invert.tree, river.sites, invert.traits, river.env)
#Subset on species, then sites
data <- data[1:5,]
data <- data[,1:5]
#Site and species can be manipulated
species(data)
sites(data)[1:3] <- c("lovely", "invert", "sites")
#Other data can be viewed
trait.names(data)
env.names(data)
#Get assemblage phylogenies of all sites
assemblage.phylogenies(data)
#Add some trait/env data in
traits(data)$new.trait <- sample(letters, nrow(comm(data)), replace=TRUE)
env(data)$new.env <- sample(letters, ncol(comm(data)), replace=TRUE)
#Manipulate/check phylogeny and community matrix
phy(data) #...tree(data) works too...
comm(data)[1,3] <- 3
comm(data) <- comm(data)[-3,]

pez documentation built on Sept. 1, 2022, 1:09 a.m.