model_linear_locality_variance_components.R

knitr::opts_chunk$set(cache = TRUE, dev = c("png", "pdf"))
library(here)
source(here("src", "model_linear_locality_grampians.R"))

residual_variance <- VarCorr(model_grampians)$taxon

trait_values <- unique(mdg[c("taxon", "sla", "sm", "mh")])

full_sd <- sqrt(diag(cov(apply(coef_sims(model_grampians), 1:2, mean))))

resid_sd <- attr(residual_variance, "stddev")

par(mar = c(4, 5, 1, 1), lend = 1)
barplot(
  full_sd[-1], las = 1, col = "lightgrey", border = NA,
  ylim = c(0, 1.2), ylab = "Standard Deviations",
  panel.last = for(i in seq(.2, .8, .2)) {
    abline(h=i, lty = 3, xpd = FALSE, col = "grey")
  }
)
barplot(
  resid_sd[-1], col = "darkgrey", add = TRUE, axes = FALSE, names.arg = NA,
  border = NA
)
legend(
  "topright",
  legend = c("Variation\nexplained\nby traits", "Variation\nUnexplained"),
  col = c("lightgrey", "darkgrey"), ncol = 2, bty = "n",
  border = NA, lty = 1, lwd = 30
)
box()