Author: Thijs Janzen
Date: 2025-11-11

# Example: data

#### Thijs Janzen

#### 2025-11-11

## Data

The treestats package can rapidly calculate summary statistics on phylogenetic trees, and in this vignette, we demonstrate this on empirical trees. We will make use of family-level pruned trees stemming from the clootl supertree of birds. These were created for the original publication accompanying the treestats paper.

    focal_trees <- ape::read.tree(file = "https://raw.githubusercontent.com/thijsjanzen/treestats-scripts/main/datasets/phylogenies/fracced/birds.trees")  # nolint

We can now calculate all summary statistics for all trees:

    all_stats <- c()
    for (i in seq_along(focal_trees)) {
      if (!ape::is.ultrametric(focal_trees[[i]])) {
        testthat::expect_output(
        focal_trees[[i]] <- phytools::force.ultrametric(focal_trees[[i]])
        )
      }
      focal_stats <- treestats::calc_all_stats(focal_trees[[i]])
      all_stats <- rbind(all_stats, focal_stats)
    }

    ## Loading required namespace: RSpectra

    all_stats <- as.data.frame(all_stats)

We can now, for instance, plot the distribution of family sizes in birds:

    hist(all_stats$number_of_lineages)

Furthermore, we can make a heatmap of all correlations:

    cor.dist <- cor(all_stats)
    diag(cor.dist) <- NA
    heatmap(cor.dist)

This will generate a distorted image: correlations are not corrected for tree size. We can study this a bit more in detail:

    opar <- par()
    par(mfrow = c(3, 3))
    for (stat in c("area_per_pair", "colless", "eigen_centrality",
                   "four_prong", "max_betweenness", "max_width",
                   "mntd", "sackin", "wiener")) {
      if (stat != "number_of_lineages") {
        x <- all_stats[, colnames(all_stats) == "number_of_lineages"]
        y <- all_stats[, colnames(all_stats) == stat]
        plot(y ~ x, xlab = "Tree size", ylab = stat, pch = 16)
      }
    }

    par(opar)

    ## Warning in par(opar): graphical parameter "cin" cannot be set

    ## Warning in par(opar): graphical parameter "cra" cannot be set

    ## Warning in par(opar): graphical parameter "csi" cannot be set

    ## Warning in par(opar): graphical parameter "cxy" cannot be set

    ## Warning in par(opar): graphical parameter "din" cannot be set

    ## Warning in par(opar): graphical parameter "page" cannot be set

To correct for this, we will have to go over the entire correlation matrix.

    tree_size <- all_stats[, colnames(all_stats) == "number_of_lineages"]

    for (i in seq_len(nrow(cor.dist))) {
      for (j in seq_len(ncol(cor.dist))) {
        stat1 <- rownames(cor.dist)[i]
        stat2 <- colnames(cor.dist)[j]
        x <- all_stats[, colnames(all_stats) == stat1]
        y <- all_stats[, colnames(all_stats) == stat2]

        a1 <- lm(x ~ tree_size)
        a2 <- lm(y ~ tree_size)
        new_cor <- cor(a1$residuals, a2$residuals)
        cor.dist[i, j] <- new_cor
      }
    }
    diag(cor.dist) <- NA
    heatmap(cor.dist)

A nicer way to visualize this is given by the package ppheatmap:

    if (requireNamespace("pheatmap")) pheatmap::pheatmap(cor.dist)