demo/dune_dcCA_fitted.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

mod <- dc_CA(formulaEnv = ~ A1 + Moist + Mag + Use + Condition(Manure),
             formulaTraits = ~ SLA + Height + LDMC + Condition(Seedmass) + Lifespan,
             response = dune_trait_env$comm[, -1],  # must delete "Sites"
             dataEnv = dune_trait_env$envir,
             dataTraits = dune_trait_env$traits, 
             verbose = FALSE)
# fit the mean traits at each site (20x6),
# that is CWM at each site
CWM.traits <- fitted(mod, type = "CWM")
head(CWM.traits)

# fit the mean environment for each species (28x8)
# that is SNC of each species
SNC.env <- fitted(mod, type = "SNC")
head(SNC.env)

fit.resp <- fitted(mod, type = "response")
# fitted often gives negative values and dc_CA cannot have negatives in the 
# response so, modify fit.resp,
# which gives about similar eigenvalues as the original data
fit.resp[fit.resp < 0] <- 0
mod3 <- dc_CA(formulaEnv = mod$formulaEnv,
              formulaTraits = mod$formulaTraits,
              response = fit.resp, 
              dataEnv = dune_trait_env$envir,
              dataTraits = dune_trait_env$traits, 
              verbose = FALSE)
mod3$eigenvalues / mod$eigenvalues