Comparison to well-corroborated trees

library("neotrans")
models7 <- c("by_kv", "ns_kv", "by_n_kv", "ns_n_kv", "by_nt_kv", "ns_nt_kv",
             "hg_kv", "hg_b_kv", "hg2_kv")
projects <- Config()$syab
marginals7 <- GetMarginals(projects, models7)

# uuids for PhyloPic silhouettes
sil <- c(
  "07200" = "6affa688-6da7-400b-8a28-ea2b4e5a02ba",
  "07202" = "eedde61f-3402-4f7c-9350-49b74f5e1dba",
  "07203" = "a89e224a-e374-4be0-a9bb-3481b16f87fb",
  "07204" = "822c549b-b29b-47eb-9fe3-dc5bbb0abccb",
  "07205" = "822c549b-b29b-47eb-9fe3-dc5bbb0abccb",
  "07206" = "e191c6d0-184c-4bb5-9e49-8b354f4e0014"
)

OutputPlot("tr_similar", 7.3, 7, function() {
  layout(rbind(1:5, 6:10, 11:15), widths = c(1, 0.6, 0.14, 1, 0.6))
  gap <- TRUE
  panel <- 1
  for (pID in projects[c(1:3, 6:4)]) {
    TreeSimSpindleRow(pID, marginals7, models7, sil[[pID]],
                      Annotate1 = function() Panel(panel, -1.8, 0))
    panel <- panel + 1
    if (gap) {
      oPar <- par(mar = rep(0, 4))
      plot.new()
      par(oPar)
    }
    gap <- !gap
  }
})

statV <- c("by_kv", "by_n_kv", "by_nt_kv")
nsV <- c("ns_kv", "ns_n_kv", "ns_nt_kv")
freeNTV <- c("by_nt_kv", "ns_nt_kv")
freeNV <- c("by_n_kv", "ns_n_kv")
fixedNV <- c("by_kv", "ns_kv")
homoV <- c(statV, nsV)
hetV <- setdiff(models7, homoV)

# Field et al. 2020
mean0 <- sapply(TreeSimilarities("07200", models7, "MCI"), mean)
range(mean0[homoV])

## [1] 0.7368110 0.7488201

mean0[hetV]

##     hg_kv   hg_b_kv    hg2_kv 
## 0.7205811 0.6773149 0.6779279

# Pattinson et al. 2015
mean2 <- sapply(TreeSimilarities("07202", models7, "MCI"), mean)
mean2[nsV] - mean2[statV]

##        ns_kv      ns_n_kv     ns_nt_kv 
## 0.0006937904 0.0016658996 0.0003990498

range(mean2)

## [1] 0.7163546 0.7350071

mean2[freeNV] - mean2[fixedNV]

##     by_n_kv     ns_n_kv 
## 0.001353044 0.002325153

mean2[freeNTV] - mean2[freeNV]

##     by_nt_kv     ns_nt_kv 
## -0.003940173 -0.005207023

# Asher 2007
mean3 <- sapply(TreeSimilarities("07203", models7, "MCI"), mean)
signif(mean3, 3)

##    by_kv    ns_kv  by_n_kv  ns_n_kv by_nt_kv ns_nt_kv    hg_kv  hg_b_kv 
##    0.480    0.484    0.485    0.479    0.486    0.479    0.477    0.468 
##   hg2_kv 
##    0.474

mean3[nsV] - mean3[statV]

##        ns_kv      ns_n_kv     ns_nt_kv 
##  0.003905407 -0.006267524 -0.006859651

range(mean3)

## [1] 0.4684008 0.4855875

mean3[freeNV] - mean2[fixedNV]

##    by_n_kv    ns_n_kv 
## -0.2469655 -0.2539268

mean3[freeNTV] - mean2[freeNV]

##   by_nt_kv   ns_nt_kv 
## -0.2477537 -0.2562793

# Huttenlocker et al. 2018
mean6 <- sapply(TreeSimilarities("07206", models7, "MCI"), mean)
range(mean6[-(1:2)])

## [1] 0.7207539 0.7233216

marginals7[, "07206"] - marginals7["ns_kv", "07206"]

##    by_kv    ns_kv  by_n_kv  ns_n_kv by_nt_kv ns_nt_kv    hg_kv  hg_b_kv 
##    -4.37     0.00    50.65    55.04    71.17    74.64   108.07       NA 
##   hg2_kv 
##   100.68

# Halliday All 
mean5 <- sapply(TreeSimilarities("07205", models7, "MCI"), mean)
signif(mean5, 2)

##    by_kv    ns_kv  by_n_kv  ns_n_kv by_nt_kv ns_nt_kv    hg_kv  hg_b_kv 
##     0.54     0.54     0.55     0.56     0.55     0.56     0.58     0.59 
##   hg2_kv 
##     0.60

signif(mean5[nsV], 2)

##    ns_kv  ns_n_kv ns_nt_kv 
##     0.54     0.56     0.56

signif(mean5[statV], 2)

##    by_kv  by_n_kv by_nt_kv 
##     0.54     0.55     0.55

signif(mean5[hetV], 2)

##   hg_kv hg_b_kv  hg2_kv 
##    0.58    0.59    0.60

# Halliday Reduced 
mean4 <- sapply(TreeSimilarities("07204", models7, "MCI"), mean)
signif(mean4, 3)

##    by_kv    ns_kv  by_n_kv  ns_n_kv by_nt_kv ns_nt_kv    hg_kv  hg_b_kv 
##    0.541    0.557    0.541    0.550    0.542    0.560    0.538    0.556 
##   hg2_kv 
##    0.564

stat4 <- mean4[statV]
ns4 <- mean4[nsV]
signif(ns4 - stat4, 2)

##    ns_kv  ns_n_kv ns_nt_kv 
##   0.0160   0.0087   0.0170

signif(range(mean4[hetV]), 3)

## [1] 0.538 0.564

Martin R. Smith martin.smith@durham.ac.uk

2026-03-06