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