library(phytools)
## Loading required package: ape
## Loading required package: maps
library(kableExtra)
library(phangorn)
library(ape)
# if (!require("BiocManager", quietly = TRUE))
# install.packages("BiocManager")
# BiocManager::install("ggtree")
#library(ggtree)
tree<- read.tree("~/Dropbox/FCU/Teaching/Mentoring/2016Spring-2021Fall_AssociateProfessor/2020Fall/ChiYuWu/rcodeCYW/mammal2.nwk")
plot(tree)
df<-read.csv("~/Dropbox/FCU/Teaching/Mentoring/2016Spring-2021Fall_AssociateProfessor/2020Fall/ChiYuWu/dataset/capellini2015role.csv")
head(df,30)
## Binomial Intro Est Spread NoLocs LG BM GT WA
## 1 Tachyglossus_aculeatus 1 1 NA 3 50.0 4499.97 17.72 170.08
## 2 Ornithorhynchus_anatinus 1 1 NA 2 22.6 1484.25 12.48 120.97
## 3 Didelphis_marsupialis 1 1 1 6 4.2 1134.75 14.00 92.47
## 4 Parantechinus_apicalis 1 NA NA 1 5.5 71.31 48.50 112.70
## 5 Perameles_bougainville 0 NA NA NA 5.8 230.80 12.00 61.00
## 6 Perameles_gunnii 0 NA NA NA 6.1 903.46 12.50 59.99
## 7 Isoodon_auratus 1 NA NA 1 6.7 425.00 12.00 NA
## 8 Isoodon_obesulus 1 0 NA 1 6.5 824.76 15.00 59.99
## 9 Macrotis_lagotis 1 NA NA 1 10.0 1229.58 14.60 93.73
## 10 Phascolarctos_cinereus 1 1 NA 20 22.1 6528.74 34.29 347.53
## 11 Lasiorhinus_latifrons 1 1 NA 2 29.9 26163.80 20.74 326.07
## 12 Vombatus_ursinus 1 NA NA 1 30.0 26000.00 30.00 447.45
## 13 Trichosurus_vulpecula 1 1 1 36 15.9 2685.39 17.50 191.59
## 14 Spilocuscus_maculatus 1 1 0 2 17.0 4060.46 12.99 240.75
## 15 Phalanger_orientalis 1 1 NA 14 4.0 2487.50 NA NA
## 16 Petaurus_breviceps 1 1 1 1 17.8 120.76 16.68 118.65
## 17 Pseudocheirus_peregrinus 1 1 NA 3 10.1 895.22 NA 197.14
## 18 Potorous_tridactylus 1 0 NA 2 14.5 1054.67 33.55 167.33
## 19 Bettongia_gaimardi 1 1 NA 1 11.8 1667.55 21.14 121.32
## 20 Bettongia_lesueur 1 1 0 1 10.0 1447.27 21.28 164.53
## 21 Bettongia_penicillata 1 1 NA 1 18.8 1184.35 20.35 150.00
## 22 Lagorchestes_hirsutus 1 NA NA 1 13.2 1407.14 30.00 150.00
## 23 Thylogale_billardierii 0 NA NA NA 10.0 5865.86 30.73 289.17
## 24 Thylogale_browni 1 1 NA 6 NA 5478.00 NA NA
## 25 Petrogale_lateralis 1 1 NA 5 12.0 4567.88 NA NA
## 26 Petrogale_penicillata 1 1 0 4 14.4 6931.60 30.99 290.00
## 27 Macropus_agilis 1 0 NA 2 16.9 11815.75 30.51 321.74
## 28 Macropus_dorsalis 0 NA NA NA 15.0 11249.96 34.98 335.00
## 29 Macropus_eugenii 1 1 0 6 15.1 5278.48 29.89 315.00
## 30 Macropus_fuliginosus 1 1 NA 2 23.2 25564.70 30.80 518.67
## NBM LS LY AFB RL OV
## 1 0.37 1.00 0.5000 2799.5500 15450.450 0.047247815
## 2 NA 2.00 1.0000 730.0000 7519.000 0.048543689
## 3 0.16 7.09 2.0000 182.5000 1350.500 0.135135135
## 4 NA 7.50 1.0000 NA NA <NA>
## 5 NA 2.00 2.0000 NA NA <NA>
## 6 0.22 2.31 3.8000 121.7472 2104.753 0.045636063
## 7 NA 2.60 NA NA NA <NA>
## 8 0.34 2.33 2.2000 NA NA <NA>
## 9 NA 1.50 4.0000 182.6208 3467.379 0.026316706
## 10 0.36 1.01 1.0000 730.0000 7336.500 0.049751244
## 11 0.49 1.00 1.0000 2737.5000 8176.000 0.044642857
## 12 0.49 1.00 0.5000 NA NA <NA>
## 13 0.20 1.02 1.5000 547.5000 5256.000 0.046296296
## 14 NA 1.26 1.0000 NA NA <NA>
## 15 NA 1.71 NA NA NA <NA>
## 16 0.18 1.82 1.3000 403.0200 6093.980 0.046073212
## 17 0.29 1.89 1.5000 365.0000 3321.500 0.073260073
## 18 0.31 1.00 2.0000 399.2100 4893.290 0.037295971
## 19 0.30 1.00 3.2500 272.0000 4035.000 0.027833381
## 20 0.31 1.00 3.0000 206.4500 3443.550 0.035331756
## 21 0.28 1.00 3.0000 288.9500 6573.050 0.018509926
## 22 NA 1.00 2.9200 NA NA <NA>
## 23 0.40 1.00 1.0000 441.0400 3208.960 0.113744017
## 24 NA 1.02 NA NA NA <NA>
## 25 NA 1.00 NA NA NA <NA>
## 26 103.00 1.00 1.8250 NA NA <NA>
## 27 0.63 1.01 1.8000 410.6200 5757.880 0.035217437
## 28 0.75 1.00 1.7299 NA NA <NA>
## 29 0.44 1.01 1.0000 319.3700 5192.130 0.070298702
## 30 0.86 1.00 1.0000 608.3300 7859.670 0.046439609