Selecting covariates for Grampians

knitr::opts_chunk$set(cache = TRUE, dev = c("png", "pdf"))
library(ClustOfVar)
library(vegan)
library(eucs)
library(lme4)

Clustering Grampians Plots

Distance matrix of Grampians plots

dist_grampians <- vegdist(wide_grampians[-1:-5], "raup", TRUE)

Cluster analysis of Grampians commmunites

hclust_grampians <- hclust(dist_grampians)

Split plots into 20 clusters

clusters_grampians <- cutree(hclust_grampians, ncol(wide_grampians) - 5)

Calculate F-statisic (analog) for each environment variable

Extract environmental data for the Grampians

covariates <- covariates_grampians[-1:-5]

For each env variable calculate the ratio of between and within cluster variance

fratios <- sapply(
  covariates,
  function(x) {
    out <- VarCorr(
      lmer(y ~ 1 + 1 | clusters_grampians, data = data.frame(y = x))
    )
    out$clusters_grampians[[1]] / attr(out, "sc")^2
  }
)
colnames(covariates) <- paste(colnames(covariates), round(fratios, 1))

Clustering environmental variables

Cluster the environmental variables based on their correlations (groups will be more correlated).

clusters_covariates <- hclustvar(covariates)

Plot dendrogram

par(mar = c(4, 0, 0, 19), ps = 8)
plot(as.dendrogram(clusters_covariates), horiz = TRUE)