运行 一个 for 循环，其中模拟数据然后在其中取平均值
Run a for loop where data is simulated then averaged within
我想运行下面的代码100次：
require(phytools)
require(RRphylo)
linbm <- rowMeans(fastBM(lattree, a = spreadlind[1,1], bounds=c(min(spreadlind),max(spreadlind)), nsim = 100))
RRlinbm <- RRphylo(lattree,linbm)
trendlinbm <- search.trend(RRlinbm,linbm,foldername=tempdir())
spreadlindbm <- trendlinbm$pbt[,1:2]
spreadlindbm1 <- spreadlindbm[order(spreadlindbm$age),]
spreadlindbm2 <- (max(spreadlindbm1$phenotype)-min(spreadlindbm1$phenotype))
spreadlindbm3 <- spreadlindbm1[which(spreadlind1$age < ((max(spreadlindbm1$age)-min(spreadlindbm1$age))/2+min(spreadlindbm1))),]
spreadlindbm4 <- (max(spreadlindbm3$phenotype)-min(spreadlindbm3$phenotype))
spreadlindbm5 <- spreadlindbm2/spreadlindbm4
spreads <- spreadlind5/spreadlindbm5
这工作正常（尽管有一些警告）并且做了我想要它做的事情。但是，当我这样做时：
linbm <- list()
RRlinbm <- list()
trendlinbm <- list()
spreadlindbm <- list()
spreadlindbm1 <- list()
spreadlindbm2 <- list()
spreadlindbm3 <- list()
spreadlindbm4 <- list()
spreadlindbm5 <- list()
spreads <- list()
for (i in 1:100) {
linbm[[i]] <- rowMeans(fastBM(lattree, a = spreadlind[1,1][[i]], bounds=c(min(spreadlind[[i]]),max(spreadlind[[i]])), nsim = 100))
RRlinbm[[i]] <- RRphylo(lattree,linbm[[i]])
trendlinbm[[i]] <- search.trend(RRlinbm[[i]],linbm[[i]],foldername=tempdir())
spreadlindbm[[i]] <- trendlinbm$pbt[,1:2][[i]]
spreadlindbm1[[i]] <- spreadlindbm[[i]][order(spreadlindbm$age[[i]]),]
spreadlindbm2[[i]] <- (max(spreadlindbm1$phenotype[[i]])-min(spreadlindbm1$phenotype[[i]]))
spreadlindbm3[[i]] <- spreadlindbm1[[i]][which(spreadlind1$age[[i]] < ((max(spreadlindbm1$age[[i]])-min(spreadlindbm1$age[[i]]))/2+min(spreadlindbm1[[i]]))),]
spreadlindbm4[[i]] <- (max(spreadlindbm3$phenotype[[i]])-min(spreadlindbm3$phenotype[[i]]))
spreadlindbm5[[i]] <- spreadlindbm2[[i]]/spreadlindbm4[[i]]
spreads[[i]] <- spreadlind5[[i]]/spreadlindbm5[[i]]
}
我收到这个错误：
Error in spreadlindbm[[i]] : subscript out of bounds
似乎只有 1 个 linbm 模拟而不是 100 个，这就是我出错的原因。
我认为这与我似乎无法做到这一点有关 lattree[[i]] 因为如果我这样做，出于某种原因它会调用一个数据集来显示哪些节点连接到哪些节点而不是树本身，因此我最终得到一个错误，指出该对象不再是 class phylo.
因此我不确定如何解决这个问题。
循环中的警告与原始脚本中的警告相同。
如有任何帮助，我们将不胜感激！
谢谢，
卡罗莱纳州
这是数据：
> dput(spreadlind)
structure(list(y.multi = c(0.00155347055674816, 0.161613111788121,
0.782198041620036, 1.53091468559125, 1.5374150126118, 1.95106361585544,
2.84877753353601, 3.30856549415935, 3.66347992385696, 3.61603383156884,
4.14173027008837, 4.81866865201557, 5.96045394613843, 3.62927975265028,
3.63693964926282, 6.36794280876027, 6.31025739368824, 3.68593745526834,
3.97891742720543, 6.93648438239245, 0.494718563277189, 0.582320520627804,
1.80998664230687, 2.07126271026748, 2.09882261692225, 2.04819403524499,
2.67566519385064, 2.72232617371275, 0.494718563277189, 0.51140775510139,
3.54745844047975, 0.51140775510139, 1.25074485672904, 1.55010916708204,
1.2871994431796, 1.32085767556071, 1.37033008644747, 0.515214782210954,
0.885611593749094, 0.927624990707522, 1.2353386216543, 1.20393998975362,
1.05078386017598, 1.53796097273876, 1.43610602382877, 0.571743119736813,
3.59952827678168, 0.571885350269405, 1.2853590224863, 0.579301896064088,
2.86926984203778, 0.587708152457224, 1.82659625228065, 3.60766146697518,
0.494882679677509, 0.506429821730035, 0.522518109651434, 1.90891540289338,
2.3451011743209, 2.33727446999219, 0.523615252037944, 2.36609248926363,
2.59202193074751, 2.66474569109868, 1.72333855229808, 2.4163690782667,
1.73287568525806, 2.49842570272719, 1.80664555049829, 2.38385429265236,
2.73704621987446, 0.506784376709435, 0.507707989713869, 2.2820288381412,
1.92420878906418, 1.94303773985105, 2.55650284133446, 2.23982669071852,
2.62370104646633, 2.74849048160226, 2.7516366913285, 0.540677960556539,
0.565447800474045, 2.97105772656143, 1.26383072332201, 0.543457139827625,
3.58939916599798, 1.11500285637845, 1.14441613040443, 1.19209724885874,
0.783385958851092, 1.91325256635718, 3.04797028869207, 1.92396908318128,
4.08905782084652, 1.97222419679872, 3.67244745727709, 2.07774303591261,
3.90466176531347, 2.91480361864387, 0.798118906868094, 1.45926213747926,
3.52510770252059, 1.58839858730842, 1.79707280379355, 2.47505145152866,
2.42499608715655, 1.59253486654689, 2.590738827913, 1.64370161579295,
3.81646886358259, 3.82520657528986, 1.33563102388181, 1.43009331011062,
2.56134735686846, 1.49433262087347, 3.27754161801841, 1.50755033198619,
2.45008826727309, 2.43835482679194, 1.33914528685374, 2.67199581109489,
1.68819329149765, 2.06661520323385, 1.69782065598436, 2.37622959857406,
2.3078393520338, 2.64428969434044, 2.31132541432424, 2.79957533334395,
2.68374060836952), age = c(1.0001, 22.8060363126218, 54.5976175658671,
69.753316771761, 69.7533167717499, 80.414170921278, 88.2586282621069,
93.7004406841295, 93.7004406841094, 90.9184836136638, 95.0615012270222,
101.543733610294, 101.543733610292, 91.4587431450015, 92.8185903007135,
99.6528647376402, 99.6528647376378, 92.5908102945527, 101.011824568968,
101.011824568975, 18.259071508084, 25.993913616012, 59.8238331049015,
68.743553809163, 68.7435538091594, 86.2934244425716, 102.57347329813,
102.573473298177, 18.259071508084, 21.1774077435026, 96.7763651286279,
21.1774077435026, 80.3066760159123, 98.0397518161518, 86.9698144837543,
98.0397518161568, 98.0397518161501, 22.741886784047, 42.9286275525969,
52.0750257961256, 66.3690315373348, 66.3690315373326, 56.6487478575139,
75.5154297808487, 75.5154297807598, 28.0487885610707, 95.7021705494929,
28.3608373184629, 95.3901217920203, 30.6460556878806, 95.3901217919969,
33.5941512838692, 92.4420261960504, 92.4420261960636, 18.6204905115437,
20.3679013654434, 22.560804157767, 88.2577872001976, 101.080471597327,
101.080471597338, 23.1614011949379, 84.3358417514739, 100.479874560188,
100.479874560183, 43.8197893493495, 79.8214864058532, 45.7871594004954,
77.8541163546938, 51.6615048191536, 71.979770936008, 71.9797709360253,
21.0176870990147, 22.0184256013505, 99.4647314842312, 67.2132181179478,
71.8437889797186, 94.8341606223199, 94.83416062225, 97.4250876440769,
99.4647314840716, 99.4647314840717, 29.1448747815453, 35.5461381027468,
94.05802155308, 94.0580215530736, 31.2193215751653, 100.459284874452,
84.0675074329436, 100.459284874353, 100.45928487436, 27.2065400456165,
44.9626265916094, 92.3960105252684, 46.5900338274134, 90.8408601707908,
50.2586889363923, 87.2788979028246, 56.4058856487657, 81.1317011904194,
81.1317011904359, 30.8212285638619, 48.4056327901052, 88.8880148481789,
55.1125261701695, 62.7514247521627, 81.0334816994758, 81.033481699512,
55.9884815439191, 88.8293630359064, 58.930241329349, 86.066774970786,
86.0667749707636, 49.3396177771712, 54.4444816307805, 70.3696256347752,
60.2061611560702, 70.2835027623113, 61.0861700776571, 70.4929740447419,
70.4208129948606, 50.5926362075624, 69.1166072043804, 62.7279938432217,
69.116607204367, 63.6382587409568, 68.2063423066373, 67.4018609248549,
68.1881923860238, 67.4823724506412, 68.1491655977022, 68.1463399182352
)), class = "data.frame", row.names = c("67", "68", "69", "Meleagris_gallopavo",
"Lagopus_lagopus", "70", "71", "Branta_canadensis", "Branta_bernicla",
"72", "73", "Anas_crecca", "Anas_clypeata", "74", "75", "Mergus_merganser",
"Bucephala_islandica", "76", "Aix_sponsa", "Tadorna_tadorna",
"77", "78", "79", "Caprimulgus_climacurus", "Caprimulgus_europaeus",
"80", "Apus_apus", "Tachymarptis_melba", "81", "82", "Podiceps_cristatus",
"83", "84", "Streptopelia_decaocto", "85", "Columba_livia", "Columba_palumbus",
"86", "87", "88", "Fulica_atra", "Gallinula_chloropus", "89",
"Rallus_aquaticus", "Crex_crex", "90", "Gavia_stellata", "91",
"Fulmarus_glacialis", "92", "Platalea_leucorodia", "93", "Fregata_aquila",
"Phalacrocorax_carbo", "94", "95", "96", "97", "Falco_peregrinus",
"Falco_columbarius", "98", "99", "Hirundo_rustica", "Delichon_urbicum",
"100", "Amazona_aestiva", "101", "Psittacula_krameri", "102",
"Trichoglossus_haematodus", "Melopsittacus_undulatus", "103",
"104", "Sarcoramphus_papa", "105", "106", "Accipiter_nisus",
"Accipiter_gentilis", "107", "Aquila_pomarina", "Aquila_clanga",
"108", "109", "Anthracoceros_coronatus", "Upupa_epops", "110",
"Alcedo_atthis", "111", "Picus_viridis", "Dendrocopos_major",
"112", "113", "Pluvialis_apricaria", "114", "Haematopus_ostralegus",
"115", "Vanellus_vanellus", "116", "Charadrius_dubius", "Charadrius_hiaticula",
"117", "118", "Numenius_arquata", "119", "120", "Philomachus_pugnax",
"Calidris_alpina", "121", "Actitis_hypoleucos", "122", "Scolopax_rusticola",
"Gallinago_gallinago", "123", "124", "Fratercula_arctica", "125",
"Uria_aalge", "126", "Alca_torda", "Alle_alle", "127", "Chlidonias_leucopterus",
"128", "Rissa_tridactyla", "129", "Larus_ridibundus", "130",
"Larus_glaucoides", "131", "Larus_marinus", "Larus_argentatus"
))
还有我的树：
> dput(lattree)
structure(list(edge = structure(c(67L, 68L, 69L, 69L, 68L, 70L,
71L, 71L, 70L, 72L, 73L, 73L, 72L, 74L, 75L, 75L, 74L, 76L, 76L,
67L, 77L, 78L, 79L, 79L, 78L, 80L, 80L, 77L, 81L, 81L, 82L, 82L,
83L, 83L, 81L, 84L, 85L, 86L, 86L, 85L, 87L, 87L, 84L, 88L, 88L,
89L, 89L, 90L, 90L, 91L, 91L, 77L, 92L, 93L, 94L, 95L, 95L, 94L,
96L, 97L, 97L, 96L, 98L, 98L, 99L, 99L, 100L, 100L, 93L, 101L,
102L, 102L, 103L, 104L, 104L, 103L, 105L, 105L, 101L, 106L, 107L,
107L, 106L, 108L, 108L, 109L, 109L, 92L, 110L, 111L, 111L, 112L,
112L, 113L, 113L, 114L, 114L, 110L, 115L, 116L, 116L, 117L, 118L,
118L, 117L, 119L, 119L, 120L, 120L, 115L, 121L, 122L, 122L, 123L,
123L, 124L, 124L, 121L, 125L, 125L, 126L, 126L, 127L, 127L, 128L,
128L, 129L, 129L, 68L, 69L, 1L, 2L, 70L, 71L, 3L, 4L, 72L, 73L,
9L, 10L, 74L, 75L, 5L, 6L, 76L, 7L, 8L, 77L, 78L, 79L, 63L, 64L,
80L, 65L, 66L, 81L, 20L, 82L, 21L, 83L, 22L, 23L, 84L, 85L, 86L,
11L, 12L, 87L, 13L, 14L, 88L, 19L, 89L, 15L, 90L, 18L, 91L, 16L,
17L, 92L, 93L, 94L, 95L, 61L, 62L, 96L, 97L, 59L, 60L, 98L, 58L,
99L, 57L, 100L, 55L, 56L, 101L, 102L, 45L, 103L, 104L, 46L, 47L,
105L, 48L, 49L, 106L, 107L, 50L, 51L, 108L, 52L, 109L, 53L, 54L,
110L, 111L, 44L, 112L, 43L, 113L, 42L, 114L, 40L, 41L, 115L,
116L, 34L, 117L, 118L, 35L, 36L, 119L, 39L, 120L, 37L, 38L, 121L,
122L, 30L, 123L, 33L, 124L, 31L, 32L, 125L, 24L, 126L, 29L, 127L,
25L, 128L, 28L, 129L, 26L, 27L), .Dim = c(128L, 2L)), edge.length = c(21.8060363126218,
31.7915812532453, 15.155699205894, 15.1556992058829, 57.6081346086562,
7.84445734082895, 5.44181242202259, 5.44181242200252, 10.5043126923859,
4.14301761335842, 6.48223238327186, 6.48223238327021, 0.540259531337661,
1.35984715571197, 6.8342744369267, 6.83427443692435, 1.13206714955123,
8.42101427441535, 8.42101427442253, 17.259071508084, 7.73484210792803,
33.8299194888895, 8.91972070426153, 8.91972070425791, 60.2995108265596,
16.2800488555586, 16.2800488556051, 2.91833623541861, 75.5989573851252,
59.1292682724097, 17.7330758002395, 6.66313846784204, 11.0699373324024,
11.0699373323958, 1.56447904054438, 20.1867407685499, 9.14639824352872,
14.2940057412092, 14.294005741207, 13.720120304917, 18.8666819233348,
18.8666819232459, 5.30690177702373, 67.6533819884221, 0.312048757392168,
67.0292844735574, 2.28521836941774, 64.7440661041163, 2.94809559598857,
58.8478749121812, 58.8478749121944, 0.361419003459647, 1.74741085389973,
2.19290279232366, 65.6969830424305, 12.8226843971294, 12.8226843971402,
0.600597037170883, 61.174440556536, 16.1440328087146, 16.1440328087093,
20.6583881544116, 36.0016970565037, 1.96737005114587, 32.0669569541984,
5.87434541865818, 20.3182661168544, 20.3182661168717, 0.649785733571314,
1.00073850233577, 77.4463058828807, 45.1947925165973, 4.63057086177076,
22.9903716426013, 22.9903716425314, 30.2118695261291, 2.03964383999477,
2.03964383999479, 8.12718768253063, 6.40126332120143, 58.5118834503332,
58.5118834503268, 2.07444679362001, 69.2399632992864, 52.8481858577782,
16.3917774414099, 16.3917774414166, 8.58604953407289, 17.7560865459928,
47.4333839336591, 1.627407235804, 44.2508263433775, 3.6686551089789,
37.0202089664324, 6.14719671237347, 24.7258155416537, 24.7258155416702,
3.61468851824533, 17.5844042262434, 40.4823820580737, 6.70689338006431,
7.6388985819932, 18.2820569473131, 18.2820569473492, 0.875955373749606,
32.8408814919872, 2.94175978542986, 27.136533641437, 27.1365336414146,
18.5183892133093, 5.10486385360935, 15.9251440039946, 5.76167952528963,
10.0773416062411, 0.880008921586962, 9.40680396708479, 9.33464291720349,
1.25301843039117, 18.523970996818, 12.1353576356593, 6.38861336114526,
0.910264897735043, 4.56808356568051, 3.76360218389816, 0.786331461168885,
0.0805115257862825, 0.666793147061034, 0.663967467593978), Nnode = 63L,
root.edge = 0, tip.label = c("Meleagris_gallopavo", "Lagopus_lagopus",
"Branta_canadensis", "Branta_bernicla", "Mergus_merganser",
"Bucephala_islandica", "Aix_sponsa", "Tadorna_tadorna", "Anas_crecca",
"Anas_clypeata", "Fulica_atra", "Gallinula_chloropus", "Rallus_aquaticus",
"Crex_crex", "Fulmarus_glacialis", "Fregata_aquila", "Phalacrocorax_carbo",
"Platalea_leucorodia", "Gavia_stellata", "Podiceps_cristatus",
"Streptopelia_decaocto", "Columba_livia", "Columba_palumbus",
"Chlidonias_leucopterus", "Larus_ridibundus", "Larus_marinus",
"Larus_argentatus", "Larus_glaucoides", "Rissa_tridactyla",
"Fratercula_arctica", "Alca_torda", "Alle_alle", "Uria_aalge",
"Numenius_arquata", "Philomachus_pugnax", "Calidris_alpina",
"Scolopax_rusticola", "Gallinago_gallinago", "Actitis_hypoleucos",
"Charadrius_dubius", "Charadrius_hiaticula", "Vanellus_vanellus",
"Haematopus_ostralegus", "Pluvialis_apricaria", "Sarcoramphus_papa",
"Accipiter_nisus", "Accipiter_gentilis", "Aquila_pomarina",
"Aquila_clanga", "Anthracoceros_coronatus", "Upupa_epops",
"Alcedo_atthis", "Picus_viridis", "Dendrocopos_major", "Trichoglossus_haematodus",
"Melopsittacus_undulatus", "Psittacula_krameri", "Amazona_aestiva",
"Hirundo_rustica", "Delichon_urbicum", "Falco_peregrinus",
"Falco_columbarius", "Caprimulgus_climacurus", "Caprimulgus_europaeus",
"Apus_apus", "Tachymarptis_melba")), class = "phylo", order = "cladewise")
所以经过几次尝试，这个解决方案似乎有效：
linbm <- list()
linbm2 <- list()
RRlinbm <- list()
trendlinbm <- list()
spreadlindbm <- list()
spreadlindbm1 <- list()
spreadlindbm2 <- list()
spreadlindbm3 <- list()
spreadlindbm4 <- list()
spreadlindbm5 <- list()
spreads <- list()
lintrees <- rep.multiPhylo(lattree,100)
alin <- rep(spreadlind[1,1],100)
minlin <- rep(min(spreadlind),100)
maxlin <- rep(max(spreadlind),100)
for (i in 1:100) {
linbm[[i]] <- fastBM(lintrees[[i]], a = alin[[i]], bounds = c(minlin[[i]], maxlin[[i]]), nsim = 100)
}
for (i in 1:100){
linbm2[[i]] <- rowMeans(linbm[[i]])
}
for (i in 1:100){
RRlinbm[[i]] <- RRphylo(lintrees[[i]], linbm2[[i]])
}
for (i in 1:100){
trendlinbm[[i]] <- search.trend(RRlinbm[[i]],linbm2[[i]],foldername=tempdir())
}
for (i in 1:100){
spreadlindbm[[i]] <- trendlinbm[[i]]$pbt
}
for (i in 1:100){
spreadlindbm1[[i]] <- spreadlindbm[[i]][order(spreadlindbm[[i]]$age),]
}
for (i in 1:100){
spreadlindbm2[[i]] <- (max(spreadlindbm1[[i]]$phenotype)-min(spreadlindbm1[[i]]$phenotype))
}
for (i in 1:100){
spreadlindbm3[[i]] <- spreadlindbm1[[i]][which(spreadlind1$age < ((max(spreadlindbm1[[i]]$age)-min(spreadlindbm1[[i]]$age))/2+min(spreadlindbm1[[i]]))),]
}
for (i in 1:100){
spreadlindbm4[[i]] <- (max(spreadlindbm3[[i]]$phenotype)-min(spreadlindbm3[[i]]$phenotype))
}
for (i in 1:100){
spreadlindbm5[[i]] <- spreadlindbm2[[i]]/spreadlindbm4[[i]]
}
for (i in 1:100){
spreads[[i]] <- spreadlind5/spreadlindbm5[[i]]
}
虽然它绝对不优雅，但如果有人有更好的解决方案，请post它，我会接受它作为解决方案:)
我想运行下面的代码100次：
require(phytools)
require(RRphylo)
linbm <- rowMeans(fastBM(lattree, a = spreadlind[1,1], bounds=c(min(spreadlind),max(spreadlind)), nsim = 100))
RRlinbm <- RRphylo(lattree,linbm)
trendlinbm <- search.trend(RRlinbm,linbm,foldername=tempdir())
spreadlindbm <- trendlinbm$pbt[,1:2]
spreadlindbm1 <- spreadlindbm[order(spreadlindbm$age),]
spreadlindbm2 <- (max(spreadlindbm1$phenotype)-min(spreadlindbm1$phenotype))
spreadlindbm3 <- spreadlindbm1[which(spreadlind1$age < ((max(spreadlindbm1$age)-min(spreadlindbm1$age))/2+min(spreadlindbm1))),]
spreadlindbm4 <- (max(spreadlindbm3$phenotype)-min(spreadlindbm3$phenotype))
spreadlindbm5 <- spreadlindbm2/spreadlindbm4
spreads <- spreadlind5/spreadlindbm5
这工作正常（尽管有一些警告）并且做了我想要它做的事情。但是，当我这样做时：
linbm <- list()
RRlinbm <- list()
trendlinbm <- list()
spreadlindbm <- list()
spreadlindbm1 <- list()
spreadlindbm2 <- list()
spreadlindbm3 <- list()
spreadlindbm4 <- list()
spreadlindbm5 <- list()
spreads <- list()
for (i in 1:100) {
linbm[[i]] <- rowMeans(fastBM(lattree, a = spreadlind[1,1][[i]], bounds=c(min(spreadlind[[i]]),max(spreadlind[[i]])), nsim = 100))
RRlinbm[[i]] <- RRphylo(lattree,linbm[[i]])
trendlinbm[[i]] <- search.trend(RRlinbm[[i]],linbm[[i]],foldername=tempdir())
spreadlindbm[[i]] <- trendlinbm$pbt[,1:2][[i]]
spreadlindbm1[[i]] <- spreadlindbm[[i]][order(spreadlindbm$age[[i]]),]
spreadlindbm2[[i]] <- (max(spreadlindbm1$phenotype[[i]])-min(spreadlindbm1$phenotype[[i]]))
spreadlindbm3[[i]] <- spreadlindbm1[[i]][which(spreadlind1$age[[i]] < ((max(spreadlindbm1$age[[i]])-min(spreadlindbm1$age[[i]]))/2+min(spreadlindbm1[[i]]))),]
spreadlindbm4[[i]] <- (max(spreadlindbm3$phenotype[[i]])-min(spreadlindbm3$phenotype[[i]]))
spreadlindbm5[[i]] <- spreadlindbm2[[i]]/spreadlindbm4[[i]]
spreads[[i]] <- spreadlind5[[i]]/spreadlindbm5[[i]]
}
我收到这个错误：
Error in spreadlindbm[[i]] : subscript out of bounds
似乎只有 1 个 linbm 模拟而不是 100 个，这就是我出错的原因。
我认为这与我似乎无法做到这一点有关 lattree[[i]] 因为如果我这样做，出于某种原因它会调用一个数据集来显示哪些节点连接到哪些节点而不是树本身，因此我最终得到一个错误，指出该对象不再是 class phylo.
因此我不确定如何解决这个问题。
循环中的警告与原始脚本中的警告相同。
如有任何帮助，我们将不胜感激！
谢谢，
卡罗莱纳州
这是数据：
> dput(spreadlind)
structure(list(y.multi = c(0.00155347055674816, 0.161613111788121,
0.782198041620036, 1.53091468559125, 1.5374150126118, 1.95106361585544,
2.84877753353601, 3.30856549415935, 3.66347992385696, 3.61603383156884,
4.14173027008837, 4.81866865201557, 5.96045394613843, 3.62927975265028,
3.63693964926282, 6.36794280876027, 6.31025739368824, 3.68593745526834,
3.97891742720543, 6.93648438239245, 0.494718563277189, 0.582320520627804,
1.80998664230687, 2.07126271026748, 2.09882261692225, 2.04819403524499,
2.67566519385064, 2.72232617371275, 0.494718563277189, 0.51140775510139,
3.54745844047975, 0.51140775510139, 1.25074485672904, 1.55010916708204,
1.2871994431796, 1.32085767556071, 1.37033008644747, 0.515214782210954,
0.885611593749094, 0.927624990707522, 1.2353386216543, 1.20393998975362,
1.05078386017598, 1.53796097273876, 1.43610602382877, 0.571743119736813,
3.59952827678168, 0.571885350269405, 1.2853590224863, 0.579301896064088,
2.86926984203778, 0.587708152457224, 1.82659625228065, 3.60766146697518,
0.494882679677509, 0.506429821730035, 0.522518109651434, 1.90891540289338,
2.3451011743209, 2.33727446999219, 0.523615252037944, 2.36609248926363,
2.59202193074751, 2.66474569109868, 1.72333855229808, 2.4163690782667,
1.73287568525806, 2.49842570272719, 1.80664555049829, 2.38385429265236,
2.73704621987446, 0.506784376709435, 0.507707989713869, 2.2820288381412,
1.92420878906418, 1.94303773985105, 2.55650284133446, 2.23982669071852,
2.62370104646633, 2.74849048160226, 2.7516366913285, 0.540677960556539,
0.565447800474045, 2.97105772656143, 1.26383072332201, 0.543457139827625,
3.58939916599798, 1.11500285637845, 1.14441613040443, 1.19209724885874,
0.783385958851092, 1.91325256635718, 3.04797028869207, 1.92396908318128,
4.08905782084652, 1.97222419679872, 3.67244745727709, 2.07774303591261,
3.90466176531347, 2.91480361864387, 0.798118906868094, 1.45926213747926,
3.52510770252059, 1.58839858730842, 1.79707280379355, 2.47505145152866,
2.42499608715655, 1.59253486654689, 2.590738827913, 1.64370161579295,
3.81646886358259, 3.82520657528986, 1.33563102388181, 1.43009331011062,
2.56134735686846, 1.49433262087347, 3.27754161801841, 1.50755033198619,
2.45008826727309, 2.43835482679194, 1.33914528685374, 2.67199581109489,
1.68819329149765, 2.06661520323385, 1.69782065598436, 2.37622959857406,
2.3078393520338, 2.64428969434044, 2.31132541432424, 2.79957533334395,
2.68374060836952), age = c(1.0001, 22.8060363126218, 54.5976175658671,
69.753316771761, 69.7533167717499, 80.414170921278, 88.2586282621069,
93.7004406841295, 93.7004406841094, 90.9184836136638, 95.0615012270222,
101.543733610294, 101.543733610292, 91.4587431450015, 92.8185903007135,
99.6528647376402, 99.6528647376378, 92.5908102945527, 101.011824568968,
101.011824568975, 18.259071508084, 25.993913616012, 59.8238331049015,
68.743553809163, 68.7435538091594, 86.2934244425716, 102.57347329813,
102.573473298177, 18.259071508084, 21.1774077435026, 96.7763651286279,
21.1774077435026, 80.3066760159123, 98.0397518161518, 86.9698144837543,
98.0397518161568, 98.0397518161501, 22.741886784047, 42.9286275525969,
52.0750257961256, 66.3690315373348, 66.3690315373326, 56.6487478575139,
75.5154297808487, 75.5154297807598, 28.0487885610707, 95.7021705494929,
28.3608373184629, 95.3901217920203, 30.6460556878806, 95.3901217919969,
33.5941512838692, 92.4420261960504, 92.4420261960636, 18.6204905115437,
20.3679013654434, 22.560804157767, 88.2577872001976, 101.080471597327,
101.080471597338, 23.1614011949379, 84.3358417514739, 100.479874560188,
100.479874560183, 43.8197893493495, 79.8214864058532, 45.7871594004954,
77.8541163546938, 51.6615048191536, 71.979770936008, 71.9797709360253,
21.0176870990147, 22.0184256013505, 99.4647314842312, 67.2132181179478,
71.8437889797186, 94.8341606223199, 94.83416062225, 97.4250876440769,
99.4647314840716, 99.4647314840717, 29.1448747815453, 35.5461381027468,
94.05802155308, 94.0580215530736, 31.2193215751653, 100.459284874452,
84.0675074329436, 100.459284874353, 100.45928487436, 27.2065400456165,
44.9626265916094, 92.3960105252684, 46.5900338274134, 90.8408601707908,
50.2586889363923, 87.2788979028246, 56.4058856487657, 81.1317011904194,
81.1317011904359, 30.8212285638619, 48.4056327901052, 88.8880148481789,
55.1125261701695, 62.7514247521627, 81.0334816994758, 81.033481699512,
55.9884815439191, 88.8293630359064, 58.930241329349, 86.066774970786,
86.0667749707636, 49.3396177771712, 54.4444816307805, 70.3696256347752,
60.2061611560702, 70.2835027623113, 61.0861700776571, 70.4929740447419,
70.4208129948606, 50.5926362075624, 69.1166072043804, 62.7279938432217,
69.116607204367, 63.6382587409568, 68.2063423066373, 67.4018609248549,
68.1881923860238, 67.4823724506412, 68.1491655977022, 68.1463399182352
)), class = "data.frame", row.names = c("67", "68", "69", "Meleagris_gallopavo",
"Lagopus_lagopus", "70", "71", "Branta_canadensis", "Branta_bernicla",
"72", "73", "Anas_crecca", "Anas_clypeata", "74", "75", "Mergus_merganser",
"Bucephala_islandica", "76", "Aix_sponsa", "Tadorna_tadorna",
"77", "78", "79", "Caprimulgus_climacurus", "Caprimulgus_europaeus",
"80", "Apus_apus", "Tachymarptis_melba", "81", "82", "Podiceps_cristatus",
"83", "84", "Streptopelia_decaocto", "85", "Columba_livia", "Columba_palumbus",
"86", "87", "88", "Fulica_atra", "Gallinula_chloropus", "89",
"Rallus_aquaticus", "Crex_crex", "90", "Gavia_stellata", "91",
"Fulmarus_glacialis", "92", "Platalea_leucorodia", "93", "Fregata_aquila",
"Phalacrocorax_carbo", "94", "95", "96", "97", "Falco_peregrinus",
"Falco_columbarius", "98", "99", "Hirundo_rustica", "Delichon_urbicum",
"100", "Amazona_aestiva", "101", "Psittacula_krameri", "102",
"Trichoglossus_haematodus", "Melopsittacus_undulatus", "103",
"104", "Sarcoramphus_papa", "105", "106", "Accipiter_nisus",
"Accipiter_gentilis", "107", "Aquila_pomarina", "Aquila_clanga",
"108", "109", "Anthracoceros_coronatus", "Upupa_epops", "110",
"Alcedo_atthis", "111", "Picus_viridis", "Dendrocopos_major",
"112", "113", "Pluvialis_apricaria", "114", "Haematopus_ostralegus",
"115", "Vanellus_vanellus", "116", "Charadrius_dubius", "Charadrius_hiaticula",
"117", "118", "Numenius_arquata", "119", "120", "Philomachus_pugnax",
"Calidris_alpina", "121", "Actitis_hypoleucos", "122", "Scolopax_rusticola",
"Gallinago_gallinago", "123", "124", "Fratercula_arctica", "125",
"Uria_aalge", "126", "Alca_torda", "Alle_alle", "127", "Chlidonias_leucopterus",
"128", "Rissa_tridactyla", "129", "Larus_ridibundus", "130",
"Larus_glaucoides", "131", "Larus_marinus", "Larus_argentatus"
))
还有我的树：
> dput(lattree)
structure(list(edge = structure(c(67L, 68L, 69L, 69L, 68L, 70L,
71L, 71L, 70L, 72L, 73L, 73L, 72L, 74L, 75L, 75L, 74L, 76L, 76L,
67L, 77L, 78L, 79L, 79L, 78L, 80L, 80L, 77L, 81L, 81L, 82L, 82L,
83L, 83L, 81L, 84L, 85L, 86L, 86L, 85L, 87L, 87L, 84L, 88L, 88L,
89L, 89L, 90L, 90L, 91L, 91L, 77L, 92L, 93L, 94L, 95L, 95L, 94L,
96L, 97L, 97L, 96L, 98L, 98L, 99L, 99L, 100L, 100L, 93L, 101L,
102L, 102L, 103L, 104L, 104L, 103L, 105L, 105L, 101L, 106L, 107L,
107L, 106L, 108L, 108L, 109L, 109L, 92L, 110L, 111L, 111L, 112L,
112L, 113L, 113L, 114L, 114L, 110L, 115L, 116L, 116L, 117L, 118L,
118L, 117L, 119L, 119L, 120L, 120L, 115L, 121L, 122L, 122L, 123L,
123L, 124L, 124L, 121L, 125L, 125L, 126L, 126L, 127L, 127L, 128L,
128L, 129L, 129L, 68L, 69L, 1L, 2L, 70L, 71L, 3L, 4L, 72L, 73L,
9L, 10L, 74L, 75L, 5L, 6L, 76L, 7L, 8L, 77L, 78L, 79L, 63L, 64L,
80L, 65L, 66L, 81L, 20L, 82L, 21L, 83L, 22L, 23L, 84L, 85L, 86L,
11L, 12L, 87L, 13L, 14L, 88L, 19L, 89L, 15L, 90L, 18L, 91L, 16L,
17L, 92L, 93L, 94L, 95L, 61L, 62L, 96L, 97L, 59L, 60L, 98L, 58L,
99L, 57L, 100L, 55L, 56L, 101L, 102L, 45L, 103L, 104L, 46L, 47L,
105L, 48L, 49L, 106L, 107L, 50L, 51L, 108L, 52L, 109L, 53L, 54L,
110L, 111L, 44L, 112L, 43L, 113L, 42L, 114L, 40L, 41L, 115L,
116L, 34L, 117L, 118L, 35L, 36L, 119L, 39L, 120L, 37L, 38L, 121L,
122L, 30L, 123L, 33L, 124L, 31L, 32L, 125L, 24L, 126L, 29L, 127L,
25L, 128L, 28L, 129L, 26L, 27L), .Dim = c(128L, 2L)), edge.length = c(21.8060363126218,
31.7915812532453, 15.155699205894, 15.1556992058829, 57.6081346086562,
7.84445734082895, 5.44181242202259, 5.44181242200252, 10.5043126923859,
4.14301761335842, 6.48223238327186, 6.48223238327021, 0.540259531337661,
1.35984715571197, 6.8342744369267, 6.83427443692435, 1.13206714955123,
8.42101427441535, 8.42101427442253, 17.259071508084, 7.73484210792803,
33.8299194888895, 8.91972070426153, 8.91972070425791, 60.2995108265596,
16.2800488555586, 16.2800488556051, 2.91833623541861, 75.5989573851252,
59.1292682724097, 17.7330758002395, 6.66313846784204, 11.0699373324024,
11.0699373323958, 1.56447904054438, 20.1867407685499, 9.14639824352872,
14.2940057412092, 14.294005741207, 13.720120304917, 18.8666819233348,
18.8666819232459, 5.30690177702373, 67.6533819884221, 0.312048757392168,
67.0292844735574, 2.28521836941774, 64.7440661041163, 2.94809559598857,
58.8478749121812, 58.8478749121944, 0.361419003459647, 1.74741085389973,
2.19290279232366, 65.6969830424305, 12.8226843971294, 12.8226843971402,
0.600597037170883, 61.174440556536, 16.1440328087146, 16.1440328087093,
20.6583881544116, 36.0016970565037, 1.96737005114587, 32.0669569541984,
5.87434541865818, 20.3182661168544, 20.3182661168717, 0.649785733571314,
1.00073850233577, 77.4463058828807, 45.1947925165973, 4.63057086177076,
22.9903716426013, 22.9903716425314, 30.2118695261291, 2.03964383999477,
2.03964383999479, 8.12718768253063, 6.40126332120143, 58.5118834503332,
58.5118834503268, 2.07444679362001, 69.2399632992864, 52.8481858577782,
16.3917774414099, 16.3917774414166, 8.58604953407289, 17.7560865459928,
47.4333839336591, 1.627407235804, 44.2508263433775, 3.6686551089789,
37.0202089664324, 6.14719671237347, 24.7258155416537, 24.7258155416702,
3.61468851824533, 17.5844042262434, 40.4823820580737, 6.70689338006431,
7.6388985819932, 18.2820569473131, 18.2820569473492, 0.875955373749606,
32.8408814919872, 2.94175978542986, 27.136533641437, 27.1365336414146,
18.5183892133093, 5.10486385360935, 15.9251440039946, 5.76167952528963,
10.0773416062411, 0.880008921586962, 9.40680396708479, 9.33464291720349,
1.25301843039117, 18.523970996818, 12.1353576356593, 6.38861336114526,
0.910264897735043, 4.56808356568051, 3.76360218389816, 0.786331461168885,
0.0805115257862825, 0.666793147061034, 0.663967467593978), Nnode = 63L,
root.edge = 0, tip.label = c("Meleagris_gallopavo", "Lagopus_lagopus",
"Branta_canadensis", "Branta_bernicla", "Mergus_merganser",
"Bucephala_islandica", "Aix_sponsa", "Tadorna_tadorna", "Anas_crecca",
"Anas_clypeata", "Fulica_atra", "Gallinula_chloropus", "Rallus_aquaticus",
"Crex_crex", "Fulmarus_glacialis", "Fregata_aquila", "Phalacrocorax_carbo",
"Platalea_leucorodia", "Gavia_stellata", "Podiceps_cristatus",
"Streptopelia_decaocto", "Columba_livia", "Columba_palumbus",
"Chlidonias_leucopterus", "Larus_ridibundus", "Larus_marinus",
"Larus_argentatus", "Larus_glaucoides", "Rissa_tridactyla",
"Fratercula_arctica", "Alca_torda", "Alle_alle", "Uria_aalge",
"Numenius_arquata", "Philomachus_pugnax", "Calidris_alpina",
"Scolopax_rusticola", "Gallinago_gallinago", "Actitis_hypoleucos",
"Charadrius_dubius", "Charadrius_hiaticula", "Vanellus_vanellus",
"Haematopus_ostralegus", "Pluvialis_apricaria", "Sarcoramphus_papa",
"Accipiter_nisus", "Accipiter_gentilis", "Aquila_pomarina",
"Aquila_clanga", "Anthracoceros_coronatus", "Upupa_epops",
"Alcedo_atthis", "Picus_viridis", "Dendrocopos_major", "Trichoglossus_haematodus",
"Melopsittacus_undulatus", "Psittacula_krameri", "Amazona_aestiva",
"Hirundo_rustica", "Delichon_urbicum", "Falco_peregrinus",
"Falco_columbarius", "Caprimulgus_climacurus", "Caprimulgus_europaeus",
"Apus_apus", "Tachymarptis_melba")), class = "phylo", order = "cladewise")
所以经过几次尝试，这个解决方案似乎有效：
linbm <- list()
linbm2 <- list()
RRlinbm <- list()
trendlinbm <- list()
spreadlindbm <- list()
spreadlindbm1 <- list()
spreadlindbm2 <- list()
spreadlindbm3 <- list()
spreadlindbm4 <- list()
spreadlindbm5 <- list()
spreads <- list()
lintrees <- rep.multiPhylo(lattree,100)
alin <- rep(spreadlind[1,1],100)
minlin <- rep(min(spreadlind),100)
maxlin <- rep(max(spreadlind),100)
for (i in 1:100) {
linbm[[i]] <- fastBM(lintrees[[i]], a = alin[[i]], bounds = c(minlin[[i]], maxlin[[i]]), nsim = 100)
}
for (i in 1:100){
linbm2[[i]] <- rowMeans(linbm[[i]])
}
for (i in 1:100){
RRlinbm[[i]] <- RRphylo(lintrees[[i]], linbm2[[i]])
}
for (i in 1:100){
trendlinbm[[i]] <- search.trend(RRlinbm[[i]],linbm2[[i]],foldername=tempdir())
}
for (i in 1:100){
spreadlindbm[[i]] <- trendlinbm[[i]]$pbt
}
for (i in 1:100){
spreadlindbm1[[i]] <- spreadlindbm[[i]][order(spreadlindbm[[i]]$age),]
}
for (i in 1:100){
spreadlindbm2[[i]] <- (max(spreadlindbm1[[i]]$phenotype)-min(spreadlindbm1[[i]]$phenotype))
}
for (i in 1:100){
spreadlindbm3[[i]] <- spreadlindbm1[[i]][which(spreadlind1$age < ((max(spreadlindbm1[[i]]$age)-min(spreadlindbm1[[i]]$age))/2+min(spreadlindbm1[[i]]))),]
}
for (i in 1:100){
spreadlindbm4[[i]] <- (max(spreadlindbm3[[i]]$phenotype)-min(spreadlindbm3[[i]]$phenotype))
}
for (i in 1:100){
spreadlindbm5[[i]] <- spreadlindbm2[[i]]/spreadlindbm4[[i]]
}
for (i in 1:100){
spreads[[i]] <- spreadlind5/spreadlindbm5[[i]]
}
虽然它绝对不优雅，但如果有人有更好的解决方案，请post它，我会接受它作为解决方案:)