getPlotdata {douconca} | R Documentation |
dc_CA
object for
plotting a single axis by your own code or plot.dcca
.getPlotdata
extracts data from a dc_CA
object for
plotting the CWMs and SNCs of a single axis.
getPlotdata(
x,
axis = 1,
envfactor = NULL,
traitfactor = NULL,
newnames = NULL,
facet = TRUE,
remove_centroids = FALSE
)
x |
results from |
axis |
the axis number to get (default 1). |
envfactor |
name of row factor to display as color and lines in the CWM
plot (default |
traitfactor |
name of column factor to display as color and lines in
the SNC plot (default |
newnames |
a list with two elements: names for traits and for
environmental variables, default |
facet |
logical. Default |
remove_centroids |
logical to remove any centroids from the plot data
(default |
The current implementation sets the traitfactor
to
NA
if the trait model contains more than a single trait factor
and the envfactor
to NA
if the environmental model
contains more than a single environmental factor.
A list with three components
a data.frame containing plot data
a vector of scores per trait/environment
a vector of new names to be used in the plot
data("dune_trait_env")
# rownames are carried forward in results
rownames(dune_trait_env$comm) <- dune_trait_env$comm$Sites
# must delete "Sites" from response matrix or data frame
Y <- dune_trait_env$comm[, -1] # must delete "Sites"
out <- dc_CA(formulaEnv = ~ A1 + Moist + Use + Manure + Mag,
formulaTraits = ~ SLA + Height + LDMC + Seedmass + Lifespan,
response = Y,
dataEnv = dune_trait_env$envir,
dataTraits = dune_trait_env$traits,
verbose = FALSE)
dat <- getPlotdata(out)
names(dat)
names(dat$CWM_SNC)
levels(dat$CWM_SNC$groups)
plot(out)