← Back

lmm_trait_site(df, trait, sp_col, site_col)

Linear mixed model partitioning trait variation between species identity, site effects and their interaction. Uses lme4::lmer.

mixed modelsITVstatistics

Args:df — individual datatrait — response traitsp_colsite_col

lmm_trait_site <- function(df, trait, sp_col, site_col) {
  if (!requireNamespace("lme4",    quietly = TRUE)) install.packages("lme4")
  if (!requireNamespace("MuMIn",   quietly = TRUE)) install.packages("MuMIn")
  library(lme4); library(MuMIn)
  
  df$y  <- df[[trait]]
  df$sp <- df[[sp_col]]
  df$st <- df[[site_col]]
  df    <- df[!is.na(df$y), ]
  
  # Full model: species + site + species:site as random
  m_full <- lmer(y ~ 1 + (1 | sp) + (1 | st) + (1 | sp:st),
                 data = df, REML = TRUE)
  
  vc <- as.data.frame(VarCorr(m_full))
  total_var <- sum(vc$vcov)
  
  data.frame(
    component  = c("species (BTV)", "site", "species:site (ITV)", "residual"),
    variance   = vc$vcov,
    pct_total  = round(vc$vcov / total_var * 100, 1)
  )
}