0

我正在使用使用该函数的picante包测试植物性状中的系统发育信号。multiPhylosignal我根据手册设置了数据和树,但每次运行代码时都会弹出“R Session Aborted R 遇到致命错误。会话已终止。” 唯一的选择是开始一个新的会话。我没有让它运行而不会崩溃一次,我不确定错误是什么。

这是下载我的系统发育的链接,其中包含我测量特征的物种。系统发育是一个过时的.new 文件,在没有系统发育包的情况下无法在 excel 或 R 中打开(例如picante

我现在还上传了带有特征数据的 CSV,位于此处

这是我的代码:

YLRtreetraits <-read.tree(file.choose())  #use this to open the newick tree
YLRtreetraits$tip.label <- capitalize(YLRtreetraits$tip.label)  
plot(YLRtreetraits); axisPhylo() 

STraits <- read.csv("YLRSpeciesTraitPhylo.csv")
rownames(STraits) <- STraits[,1]
STraits[1:1] <- list(NULL)    #Trait Data


dput(STraits)

STraits <- df2vec(as.matrix.data.frame(STraits), colID=1:13)
STraits <- STraits[1:23,]

#this is where the code always crashses
multikphylo <- multiPhylosignal(STraits, YLRtreetraits)

这是特征矩阵

> STraits
                         Thickness       SLA        VLA      PtoA  Lobedness      d13C      d15N
Achillea_millefolium     0.2460014 313.37277  3.9266603 27.883472 324.192137 -31.72317  6.866000
Artemisia_californica    0.2457496 147.26442 12.4538144 21.405490 145.468053 -28.76412  7.184118
Avena_barbata            0.1806000 266.22604  2.0010967  4.258448  43.671745 -31.00733  7.724667
Baccharis.glutinosa      0.2921833 188.55328  2.0902859  2.197490   8.126878 -29.00889  4.723333
Baccharis_pilularis      0.4607274  94.83021  0.9670566  3.374101   6.844047 -28.01133  4.700667
Bromus_carinatus         0.1753837 253.13750  1.8565264  4.053892  50.287960 -29.97682  7.592727
Bromus_hordeaceus        0.1366190 242.76840  3.8998693  8.868943  67.526653 -31.44143  7.357143
Carduus_pycnocephalus    0.4474833 188.19508  3.5401087  5.345907  81.591838 -31.29000  8.280000
Erigeron_canadensis      0.1235545 354.77298  0.9662612  2.741911   5.658662 -31.41667  7.683333
Ericameria_ericoides     0.2088789 198.12134 22.6190345 56.108810  64.019041 -31.89667  4.216667
Eschscholzia_californica 0.1208374 390.00074  5.5741182 13.358293 167.892846 -29.77000  9.060333
Festuca_bromoides        0.1177983 203.64997 12.8318043 27.118006 128.823768 -32.42333  7.225000
Festuca_perennis         0.1898500 279.29192  1.9362350  4.169356  70.740632 -32.04333  8.923333
Geranium_dissectum       0.1178849 269.83951  7.3046587 12.376485 115.190032 -31.08545  6.132727
Lupinus_nanus            0.1255962 268.69517  5.2903927 11.972935  56.477617 -32.25429  1.635714
Lupinus_variicolor       0.1610315 170.60479  5.5774146 14.817408  60.068747 -32.22429  1.937143
Medicago_polymorpha      0.1138167 304.04214  9.2125266  3.831219  18.404729 -30.29400  0.454000
Mimulus_aurantiacus      0.1688437 190.93752  2.5959366  2.434252   8.486408 -29.89455  5.967273
Raphanus_sativus         0.2499250 253.25415  2.9799423  2.611690  13.187371 -32.29800 10.564667
Sisyrinchium_bellum      0.1691389 199.43090  3.1102748  5.974129  90.706224 -29.67333  6.218333
Sidalcea_malviflora      0.1917777 171.95936  1.6222312  5.696670  98.516985 -29.32925  9.943000
Sonchus_asper            0.0983500 279.67666  2.1107129  4.459474  28.220847 -31.69133  7.418000
Nasella_pulchra          0.1771103 169.22917  7.0029006 14.378510 198.470881 -30.96810  7.439483
                              Carbon    Nitrogen       CN     PD.0    PD.10    PD.50
Achillea_millefolium     0.000866350 0.000051300 18.04167 7.081424 48.22289 280.7975
Artemisia_californica    0.000756765 0.000037200 21.05556 6.980966 46.40463 286.1870
Avena_barbata            0.001227267 0.000062100 23.38667 8.706421 71.72344 268.6173
Baccharis.glutinosa      0.001388333 0.000069200 23.78889 8.235222 71.48248 266.3621
Baccharis_pilularis      0.001386733 0.000062800 26.03333 8.706421 71.72344 268.6173
Bromus_carinatus         0.001240318 0.000057600 22.02727 8.731711 71.32551 271.3872
Bromus_hordeaceus        0.001143786 0.000054000 25.44286 8.877748 71.80232 266.8042
Carduus_pycnocephalus    0.001116000 0.000060000 18.60000 8.706421 71.72344 268.6173
Erigeron_canadensis      0.001135000 0.000061300 20.93333 7.884788 72.81775 261.0000
Ericameria_ericoides     0.001291667 0.000058000 22.93333 8.706421 71.72344 268.6173
Eschscholzia_californica 0.000770033 0.000056100 14.10000 7.187413 45.37536 293.4173
Festuca_bromoides        0.000965667 0.000045500 25.00000 8.706421 71.72344 268.6173
Festuca_perennis         0.001129400 0.000050000 26.68000 8.706421 71.72344 268.6173
Geranium_dissectum       0.001210091 0.000057100 26.43636 8.706421 71.72344 268.6173
Lupinus_nanus            0.001171857 0.000105714 11.15714 8.785906 71.11917 277.3228
Lupinus_variicolor       0.001153429 0.000061700 20.22857 8.662868 71.17415 269.9471
Medicago_polymorpha      0.001256933 0.000115867 13.21333 8.706421 71.72344 268.6173
Mimulus_aurantiacus      0.001411091 0.000050400 28.50909 8.529721 71.26665 265.9383
Raphanus_sativus         0.001146867 0.000080900 17.61333 8.706421 71.72344 268.6173
Sisyrinchium_bellum      0.000526667 0.000020500 25.25000 5.561880 31.85195 297.3334
Sidalcea_malviflora      0.000692364 0.000037000 19.46250 6.815302 49.24619 280.0572
Sonchus_asper            0.001153933 0.000049900 27.28667 8.706421 71.72344 268.6173
Nasella_pulchra          0.000795431 0.000042000 19.22931 6.911401 47.45061 280.3423

如果需要,我可以以不同的格式粘贴数据

4

0 回答 0