demo/plot_CWM_SNC.R

In douconca: Double Constrained Correspondence Analysis for Trait-Environment Analysis in Ecology

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 + Condition(Mag),
             formulaTraits = ~ SLA + Height + LDMC + Seedmass + Lifespan,
             response = Y,
             dataEnv = dune_trait_env$envir,
             dataTraits = dune_trait_env$traits,
             verbose = FALSE)

plot_dcCA_CWM_SNC(out, facet = FALSE)

newnames_without_covariates <-
  list(traits = c("SLA", "Height", "LDMC", "Seedmass", "annual", "perennial"),
       env = c("A1 horizon", "Moisture", "Type of use",  "Manure"))

plot_dcCA_CWM_SNC(out, newnames = newnames_without_covariates)

CWM_SNC_env_trait_scores <- getPlotdata(out)