r - 为什么我的系统发育树与我的数据不匹配？

Question

试图将我的数据与系统发育树相匹配。

这是我加载的内容：

library(phytools)
library(adephylo)
library(geiger)
library(nlme)
library(evomap)
library(caper)
library(scales)
library(coda)
library(ggplot2); theme_set(theme_light())
library(HDInterval)

> FrogTree<- read.nexus("C:/Users/Zach/Desktop/frog_contree")
> Call.duration. <- read.csv("C:/Users/Zach/Desktop/Call duration .csv")
> cd <- Call.duration
> Data2<- comparative.data(data = cd , phy=FrogTree, names.col="Species")

然后，即使它们与树完全匹配，也会删除大量名称。

   Data2[["dropped"]][["tips"]]
  [1] "Adelastes_hylonomos"           
  [2] "Adelophryne_patamona"          
  [3] "Adenomera_andreae"             
  [4] "Allobates_trilineatus"         
  [5] "Alytes_muletensis"             
  [6] "Alytes_obstetricans"           
  [7] "Ameerega_andina"               
  [8] "Ameerega_braccata"             
  [9] "Ameerega_erythromos"           
  [10] "Ameerega_yoshina"              
  [11] "Anaxyrus_compactilis"          
  [12] "Anaxyrus_terrestris"           
  [13] "Anaxyrus_woodhousii"           
  [14] "Andinobates_fulguritus".....

等等

unmatched.rows 的结果相同

 Data2[["dropped"]][["unmatched.rows"]]
 [1] "Adelastes_hylonomos "           
 [2] "Adelophryne_patamona "          
 [3] "Adenomera_andreae "             
 [4] "Allobates_trilineatus "         
 [5] "Alytes_muletensis "             
 [6] "Alytes_obstetricans "           
 [7] "Ameerega_andina "               
 [8] "Ameerega_braccata ".. continuing on into the 100's

树数据看起来像这样

Begin taxa;
Dimensions ntax=1074;
    Taxlabels
        Acris_crepitans
        Adelastes_hylonomos
        Adelophryne_gutturosa
        Adelophryne_mucronatus
        Adelophryne_patamona
        Adenomera_andreae
        Adenomera_hylaedactyla
        Adenomus_kandianus
        Adenomus_kelaartii
        Afrixalus_aureus
        Afrixalus_delicatus...

; 结尾;

   Begin trees;
   Translate
       1 Acris_crepitans,
       2 Adelastes_hylonomos,
       3 Adelophryne_gutturosa,
       4 Adelophryne_mucronatus,
       5 Adelophryne_patamona,
       6 Adenomera_andreae,
       7 Adenomera_hylaedactyla,
       8 Adenomus_kandianus,
       9 Adenomus_kelaartii,
      10 Afrixalus_aureus,
      11 Afrixalus_delicatus,
      12 Afrixalus_dorsalis,
      13 Afrixalus_osorioi,
      14 Afrixalus_paradorsalis,
      15 Afrixalus_quadrivittatus,
      16 Afrixalus_spinifrons,
      17 Afrixalus_stuhlmanni,
      18 Afrixalus_sylvaticus,
      19 Agalychnis_moreletii,
      20 Allobates_alessandroi,
      21 Allobates_brunneus,
      22 Allobates_femoralis,
      23 Allobates_goianus,
      24 Allobates_melanolaemus,
      25 Allobates_subfolionidificans,
      26 Allobates_talamancae,
      27 Allobates_trilineatus,
      28 Allophryne_relicta,
      29 Allophryne_ruthveni,...


  ;
  tree TREE1 = (((((((((((((((1[&CAheight_95%_HPD={5.9510000198770285E-6,6.320199997844611E- 
  5},CAheight_mean=3.541627306594819E-5,CAheight_median=3.5342499955959283E-5,CAheight_range= 
  {6.000391294946894E-10,8.610099996531062E-5},height=3.541627306594819E-5,height_95%_HPD= 
  {5.9510000198770285E-6,6.320199997844611E-5},height_median=3.5342499955959283E- 
  5,height_range={6.000391294946894E-10,8.610099996531062E- 
  5},length=43.98949405441469,length_95%_HPD= 
  {28.716825863999986,61.41630823900002},length_median=43.57504501599999,length_range= 
  {19.35619276060001,76.597113834}]:43.98949405441467,(((((880[&CAheight_95%_HPD= 
  {9.705000024951005E-6,6.113400004892355E-5},CAheight_mean=3.559584041556718E- 
  5,CAheight_median=3.5046500030944117E-5,CAheight_range={2.6263999757247802E- 
  6,7.813699994585477E-5},height=.....

  Data to match the tree:  
  Species ,CD 
  Acris_crepitans,29.421
  Adelastes_hylonomos ,2900
  Adelophryne_gutturosa,1270
  Adelophryne_mucronatus,29.5
  Adelophryne_patamona ,630
  Adenomera_andreae ,66.5
  Adenomera_hylaedactyla,56.8
  Adenomus_kandianus,47
  Adenomus_kelaartii,34
  Afrixalus_aureus,470
  Afrixalus_delicatus,146.25
  Afrixalus_dorsalis,749
  Afrixalus_osorioi,937.7
  Afrixalus_paradorsalis,386.4
  Afrixalus_quadrivittatus,2855
  Afrixalus_spinifrons,3300
  Afrixalus_stuhlmanni,500
  Afrixalus_sylvaticus,75.25
  Agalychnis_moreletii,39.3
  Allobates_alessandroi,219.71
  Allobates_brunneus,3842
  Allobates_femoralis,559
  Allobates_goianus,154.4 
 Allobates_melanolaemus,748
  Allobates_subfolionidificans,34
 Allobates_talamancae,446.61
 Allobates_trilineatus ,1260
 Allophryne_relicta,509
 Allophryne_ruthveni,364
 Alytes_cisternasii,177
 Alytes_dickhilleni,166
 Alytes_muletensis ,102
 Alytes_obstetricans ,155.4
 Amazophrynella_bokermanni,146
 Amazophrynella_manaos,1445
 Amazophrynella_vote,127
 Ameerega_altamazonica,70
 Ameerega_andina ,118
 Ameerega_bassleri,4420
 Ameerega_berohoka,82.5
 Ameerega_boliviana,70.2
 Ameerega_braccata ,145
 Ameerega_erythromos ,135
 Ameerega_flavopicta,1300
 Ameerega_hahneli,90
 Ameerega_ignipedis,97
 Ameerega_macero,38
 Ameerega_pepperi,800
 Ameerega_picta,200
 Ameerega_simulans,105
 Ameerega_trivittata,44
 Ameerega_yoshina ,130
 Amietia_angolensis,282
 Amietophrynus_maculatus,463
 Amietophrynus_regularis,719
 Amolops_chunganensis,30000
 Amolops_larutensis,490
 Amolops_vitreus,14282
 Amolops_wuyiensis,2198.2
 Anaxyrus_americanus,9636
 Anaxyrus_cognatus,20548.2
 Anaxyrus _compactilis ,23875
 Anaxyrus_hemiophrys,3035.2
 Anaxyrus_houstonensis,14591.1
 Anaxyrus_microscaphus,4581.1
 Anaxyrus_speciosus,690.8
 Anaxyrus_terrestris ,9944.8
 Anaxyrus_woodhousii ,1962.9
 Andinobates_cassidyhornae,1940
 Andinobates_claudiae,265
 Andinobates_fulguritus ,940
 Andinobates_minutus,650...
 etc. 

出了什么问题？为什么我要放弃应该匹配的提示？

谢谢！

标签： r