View source: R/comparative.comm.R
| comparative.comm | R Documentation |
Basic checking of whether the input data match up is performed; you
need only supply comm and phy, nothing else is
mandatory. You can manipulate the internals of
comparative.comm, or use the wrappers inside pez to
keep everything in order. Examples of these features are given
below; they are described in detailed at cc.manip.
comparative.comm(
phy,
comm,
traits = NULL,
env = NULL,
warn = TRUE,
force.root = -1
)
## S3 method for class 'comparative.comm'
print(x, ...)
phy |
phylogeny (in |
comm |
community |
traits |
|
env |
|
warn |
whether to warn if species/sites are dropped when creating object (default: TRUE) |
force.root |
if |
x |
|
... |
ignored |
comparative.comm object
comparative.comm is compatible with
comparative.data; this means
that the slot for species' trait data is called data. I
appreciate this is somewhat unwieldy, but hopefully you agree it is
helpful in the long-term.
Will Pearse
plot.comparative.comm cc.manip link[caper:comparative.data]{comparative.data}
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)
#Do some manual manipulation of your objects (NOTE: $data for traits)
data$data$new.trait <- sample(letters, nrow(data$comm), replace=TRUE)
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