make.node.age.df - Extract node age information from an annotated phylogeny

The code for the function can be downloaded here. This function takes an annotated phylogeny as an argument.

library(OutbreakTools)
## Loading required package: ggplot2
## Loading required package: network
## network: Classes for Relational Data
## Version 1.13.0 created on 2015-08-31.
## copyright (c) 2005, Carter T. Butts, University of California-Irvine
##                     Mark S. Handcock, University of California -- Los Angeles
##                     David R. Hunter, Penn State University
##                     Martina Morris, University of Washington
##                     Skye Bender-deMoll, University of Washington
##  For citation information, type citation("network").
##  Type help("network-package") to get started.
## Loading required package: knitr
##  OutbreakTools 0.1-14 has been loaded
library(ape)

source("make.node.age.df.R")

phy <- read.annotated.nexus("beast_ophidiiform_v04_02_phyloch_test.tre")

node.ages <- make.node.age.df(phy)

node.ages
##        Lower95%  Upper95% node
## 1   112.4742163 166.60677   54
## 12   71.8664074 123.74435   55
## 2    57.4122325  98.98174   56
## 3    47.4202788  83.33303   57
## 4    38.2002140  71.99557   58
## 7    21.7264045  48.56044   59
## 9    13.7674038  32.54472   60
## 10    9.9346375  22.96849   61
## 11    7.7180653  19.20702   62
## 13    5.2454633  15.32933   63
## 20   99.8554470 123.63707   64
## 21   93.4354424 115.48929   65
## 22   83.6843196 106.64131   66
## 23   76.0340142  92.13732   67
## 24   65.8898127  84.51596   68
## 25   55.9881565  62.18035   69
## 28   13.8066090  39.41201   70
## 31   56.9634262  75.16239   71
## 34   47.7156748  84.44428   72
## 37   83.5989293 104.08200   73
## 38   72.9441462  97.42948   74
## 40   60.1869392  86.94662   75
## 41   33.4628348  57.99894   76
## 44   39.4667208  69.33560   77
## 45   37.0099611  62.57525   78
## 46   31.7100237  56.39871   79
## 48   23.6888411  48.86645   80
## 51   26.2927603  50.78223   81
## 52   20.0471351  41.74582   82
## 54   15.0599999  39.91034   83
## 56    9.2249791  32.63858   84
## 59   16.6543009  42.46940   85
## 63   70.7313968  79.52990   86
## 64   27.0386482  48.49548   87
## 65   16.0024699  34.80740   88
## 66   12.2560475  30.33529   89
## 67    0.6470549   4.50941   90
## 72   15.6843546  34.45678   91
## 74   10.7669988  27.17710   92
## 76    5.0522886  18.30044   93
## 79   42.9548718  64.93858   94
## 81   38.5763716  59.59446   95
## 82   34.4823517  54.47268   96
## 83   31.5852950  52.38201   97
## 84   25.9559434  47.17883   98
## 85    8.8695740  26.35220   99
## 90   28.5898849  49.02411  100
## 91   24.7619804  47.18065  101
## 96   94.4211272 110.06939  102
## 98   41.8981341  87.47148  103
## 99   24.0384515  64.96807  104
## 102   2.8108064  12.31919  105