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Calculate tree summary statistics

Source: R/calc_tr_stats.R
calc_tr_stats.Rd

See vignette('analyze_output') for more details.

Usage

calc_tr_stats(tr, timepoints, bl_thresh = 1e-08)

Arguments

tr

Rooted phylogeny

timepoints

Factor vector of time points named by tree tip label. The levels should be ordered correctly (most often by sampling time). All tip lables must be included in this vector. If you want to exclude certain tips, you must drop them from the tree prior to using this function.

bl_thresh

Branch length threshold under which branches are collapsed to prior to calculations (default: 1e-08). This is the tol argument in ape::di2multi().

Value

Tibble including tree summary statistics:

  • Mean leaf depth (normalized Sackin index)

  • Mean branch length

  • Mean internal branch length

  • Mean external branch length

  • Mean divergence (mean per-generation root-to-tip distance)

  • Mean diversity (mean per-generation tip-to-tip distance)

  • Divergence slope across timepoints

  • Diversity slope across timepoints

  • Mean number of lineages through time

Examples

tr <- ape::rtree(100)
times <- factor(sample(3, 100, replace = TRUE), levels = 1:3)
names(times) <- tr$tip.label
calc_tr_stats(tr, times)
#> # A tibble: 9 × 2
#>   stat_name        stat_value
#>   <chr>                 <dbl>
#> 1 mean_leaf_depth       8.37 
#> 2 mean_bl               0.527
#> 3 mean_int_bl           0.548
#> 4 mean_ext_bl           0.506
#> 5 mean_divergence       4.74 
#> 6 mean_diversity        7.65 
#> 7 divergence_slope      0.288
#> 8 diversity_slope       0.429
#> 9 mean_ltt             22.5