Buenas! Estoy intentando hacer un script que me permita integrar la información filogenetica, funcional, ambiental y espacial para saber si hay filtrado ambiental en mis comunidades. Aunque el script creo que esta bien hecho, me sale un error que no puedo solucionar y no se porque me aparece. Alguien podrÃa darme alguna idea? Gracias!!!!
library("picante")
library("stringr")
library("ecodist")
library("ade4")
library("ape")
my.xys <- read.table("C:/Filogenia/IN_my.xys.txt",sep="\t",header=T,row.names=1)
my.env <- read.table("C:/Filogenia/IN_my.env.txt",sep="\t",header=T,row.names=1)
my.sample <- read.delim(file="C:/Filogenia/IN_my.sample.txt", sep="\t",
header=T,row.names=1)
my.traits <-
read.delim("C:/Filogenia/IN_traits_norm.txt",sep="\t",header=T,row.names=1)
stand.value <-apply(my.env, MARGIN=2, max)-apply(my.env, MARGIN=2, min)
stand.envs <-sweep(my.env,2,stand.value,"/")
my.phylo <- read.tree("BCTree_Ports.nwk")
######################################### RLQ
#######################################################
# Convertimos el arbol en un arbol de la clase "phylog" gracias a la funcion
"newick2phylog()"
# la cual ya incluye la matriz de distancias filogeneticas.
my.phylog <-newick2phylog(write.tree(my.phylo))
# L matrix: COA para my.sample:
COA.sample <- dudi.coa(my.sample,scan=FALSE,nf=dim(my.sample)[2]-1)
# Hacemos un PCA con la matriz de datos geograficos. Esto constituira la mitad
de la matriz R.
PCA.xy <- dudi.pca(my.xys,COA.sample$lw,scan=FALSE, nf=dim(my.xys)[1]-1)
# Hacemos un PCA que sera la otra mitad de la matriz R.
PCA.env<- dudi.pca(stand.envs,COA.sample$lw,scale=FALSE, scan=FALSE,
nf=dim(stand.envs)[2])
# Hacemos un PCO para los traits:
dist.traits <- dist(my.traits,method="euclidean")
dist.traits<-as.matrix(dist.traits)
# Primera mitad de la matriz Q:
PCO.traits <-dudi.pco(d=dist.traits, row.w=COA.sample$cw,full=TRUE)
Error in dudi.pco(d = dist.traits, row.w = COA.sample$cw, full = TRUE) :
Distance matrix expected
# Segunda mitad de la matriz Q:
PCO.phylo
<-dudi.pco(as.dist(as.matrix(my.phylog$Wdist)[names(my.sample),names(my.sample)]),COA.sample$cw,full=TRUE)
# Modificamos las matrices:
source("RLQ.R")
rlq.output <-
rlqESLTP(PCA.env,PCA.xy,COA.sample,PCO.traits,PCO.phylo,scan=FALSE,nf=2)
LOC DIAM TMEAN PPT NEIGHBOURS Preste 207.4583333 7 999 173.0952703 Ports 181.625 11 717 220.7983265 Toran 236.0416667 10 911 235.6761387
LOC Amblystegium_serpens Porella_platyphylla Amblystegium_subtile Anomodon_attenuatus Anomodon_viticulosus Apometzgeria_pubescens Brachythecium_populeum Brachythecium_velutinum Bryum_moravicum Cf_Hypnum Cryphaea_heteromalla Scleropodium_cespitans Eurhynchium_sp Kindbergia praelonga Frullania_tamarisci Frullania_dilatata Homalothecium_sericeum Hypnum_cupressiforme HypCupCup HypCupFil Hypnum_recurvatum Hypnum_revolutum Isothecium_alopecuroides Jungermannia_sp Leptodon_smithii Leucodon_sciuroides Lejeunea_cavifolia Lophocolea_bidentata Metzgeria_furcata Mnium_stellare Neckera_besseri Neckera_complanata Neckera_crispa Orthotrichum_affine Orthotrichum_lyelli Orthotrichum_speciosum Orthotrichum_rupestre Orthotrichum_sp Orthotrichum_pallens Orthotrichum_stramineum Orthotrichum_striatum Orthotrichum_schimperi Orthotrichum_tenellum Plagiochila_porelloides Plagiothecium_nemorale Porella_arboris_vitae Pseudoleskeella_nervosa Pterigynandrum_filiforme Radula_complanata Rhynchostegiella_curviseta Thuidium_delicatum Ulota_crispa Tortella_flavovirens Tortella_tortuosa Els Ports 0 58 60 0 0 0 0 10 0 20 8 0 0 0 12 465.5 127 65 0 65 45 6 0 2 181 0 31 3 540 0 38.5 2434.5 84 44.5 3 0 0 46.5 6 5 45 0 0 21.5 0 100 0 82 180 0 0 0 0 0 La Preste 1 159 0 0 0 12 0 0 2 0 0 8 15.5 2 0 377 0 23.5 0 23.5 19 0 1 0 0 6 0 0 13 0 0 0 0 65 0 76 52 109 41 0 139.5 21 0 5 0 0 250 159.5 35.5 0 18 0 2 2.5 Toran 30 701 46 305 148 0 8 6 1.5 0 0 0 8 0 49 451 491 55 28 27 102 0 669 0 0 163 1 0 171 1 0 1052.5 0 5 0 0 13 58.5 0 25 24 0 3.5 5 30 0 6 504.5 332 24 0 41.5 0 0
LOC X Y Preste 0448098 4690857 Ports 71135 15801 Toran 20253 43068
Cap Hid LonFil AmpFil Lfil.Afil GroLam GroNer GroPar LonCel AmpCel Lcel.Acel LonSet LonUrn AncUrn Lurn.Aurn DiamEsp EspCap AmbSer 0 0 -0.40346711 -1.62964062 1.2261735 2.730029 3.164068 0 3.350781 2.115251 1.2355299 2.8622009 0.55961579 -0.030459207 0.590075 -4.465408 6.139295 AmbSub 2.897061 2.1563267 -0.70117935 -1.820158944 1.1189796 2.351375 0 0 3.086487 1.856298 1.23018865 2.1065702 -0.02020271 -0.653926467 0.63372376 0 0 AnoAtt 3.720296 0.6562426 0.40546511 -0.430782916 0.836248 2.74084 3.725693 1.0986123 1.94591 1.969431 -0.0235212 2.5257286 0.78845736 0 0 -4.465408 0 AnoVit 4.402896 1.8578755 0.69314718 -0.051293294 0.7444405 5.31812 6.081077 1.686399 4.718499 4.351567 0.36693144 2.6390573 0.89608802 1.029619417 -0.13353139 -3.963316 7.033754 ApoPub 4.272178 2.6634819 0 0 0 0 0 0 3.583519 3.295837 0.28768207 2.1972246 0 0 0 -3.863233 0 BraPop 3.535268 1.5935488 0.18232156 -0.980829253 1.1631508 2.268684 3.149883 0 3.94739 2.00148 1.94591015 2.5649494 0.30010459 0 0 -4.342806 0 BraVel 3.054573 2.5389739 0.09531018 -0.980829253 1.0761394 2.140066 3.032546 0 4.146304 1.824549 2.32175501 2.6390573 0.47000363 -0.010050336 0.48005396 -4.268698 5.873381 BryMor 0 0 0.73620667 -0.271808723 1.0080154 3.320228 4.077537 0.4054651 4.051785 3.068053 0.98373201 2.6026897 0.74193734 0 0 -4.53285 0 CryHet 0 0 -0.07796154 -0.693147181 0.6151856 2.525729 3.48124 0.9162907 2.545531 1.909543 0.63598877 -1.6873995 0.50077529 -0.278832457 0.77960775 -3.963316 5.329989 EurStr 3.60081 1.9057978 -0.24079849 -1.757358043 1.5165596 0 0 0 3.916015 1.818726 2.09728911 0 1.01038806 0.267734435 0.74265362 -4.074542 6.497394 FruDil 4.277247 0 -0.31197477 -0.544727175 0.2327524 3.044522 0 0 3.135494 2.75684 0.37865385 0 -0.32850407 -0.328504067 0 -3.101093 1.468551 FruTam 3.857519 0.7422926 0.40546511 0 0.4054651 3.48124 0 0.9162907 3.032546 2.70805 0.32449605 0 0 0 0 -3.036554 0 HomSer 2.96441 2.107062 0.40546511 -1.049822124 1.4552872 2.079442 2.926739 0 4.174387 1.704748 2.46963918 2.7080502 0.91629073 0.113328685 0.80296205 -4.104395 6.278744 HypCupCup 4.285268 1.778071 0.40546511 -0.916290732 1.3217558 2.251292 0 0 4.248495 1.252763 2.99573227 2.8622009 0.76546784 -0.061875404 0.82734325 -3.963316 5.811639 HypCupFil 3.998841 2.5956504 0.18232156 -1.203972804 1.3862944 2.302585 3.218876 0 4.053957 1.609438 2.44451859 2.8622009 0.76546784 -0.061875404 0.82734325 -3.963316 5.811639 HypRec 4.028995 2.9721224 0.43178242 -0.798507696 1.2302901 2.351375 0 0 3.806662 1.098612 2.7080502 2.390596 0.67294447 -0.030459207 0.70340368 -4.50986 6.297075 HypRev 0 0 0.13976194 -0.693147181 0.8329091 0 0 0 3.465736 1.7492 1.71653605 0.4054651 0.91629073 -0.061875404 0.97816614 -3.963316 5.962462 IsoAlo 3.557478 2.2494753 0.72658196 -0.053400777 0.7799827 2.484907 3.465736 0.2231436 3.458522 1.967112 1.49141009 2.6468838 0.57097955 -0.755022584 1.32600213 -4.268698 5.229385 KinPra 4.028065 2.585921 0.28668157 -1.164752091 1.4514337 1.94591 3.091042 0.4054651 3.844547 1.62186 2.22268641 2.9957323 0.61518564 -0.133531393 0.74871703 -4.422849 6.049233 LejCav 0 0 -0.28768207 -1.049822124 0.7621401 2.662588 0 0 3.540959 3.540959 0 0 0 0 0 0 0 LepSmi 3.658932 1.7789879 -0.597837 -0.916290732 0.3184537 2.397895 0 0 2.772589 1.609438 1.16315081 0.4054651 0.81093022 -0.105360516 0.91629073 -4.045554 5.895854 LeuSci 4.466415 2.357978 0.13976194 -0.798507696 0.9382696 2.140066 0 0 3.86073 2.047693 1.81303687 2.1972246 1.09861229 -0.356674944 1.45528723 -3.688879 5.575547 LopBid 0 0 0.30010459 0.182321557 0.117783 3.120895 0 0 3.394508 3.135494 0.25901418 0 0 0 0 -4.045554 0 MetFur 3.906232 1.900518 0 0 0 0 0 0 3.650658 3.511545 0.1391128 1.6094379 0 0 0 -3.457768 0 MniSte 0 0 0.81093022 0.336472237 0.474458 3.075775 4.267364 0.6931472 3.349904 3.277145 0.07275935 2.5257286 0.55961579 0.3074847 0.25213109 -3.649659 5.661489 NecBes 3.715617 1.7631646 -0.7985077 -1.203972804 0.4054651 2.525729 0 0.9162907 2.80336 2.047693 0.75566754 1.8718022 0.26236426 0 0 -4.045554 0 NecCom 3.610457 2.2061932 0.55961579 -0.798507696 1.3581235 2.233592 0 0 3.663562 1.832581 1.83098018 2.3025851 0.37156356 0.009950331 0.36161323 -3.79424 5.320484 NecCri 3.271841 1.9703652 1.14740245 0.09531018 1.0520923 1.94591 0 0 4.007333 1.470176 2.53715734 2.7080502 1.01160091 0.182321557 0.82927936 -3.688879 6.027532 OrtAff 4.270598 0 1.09861229 -0.223143551 1.3217558 2.772589 3.64632 0.8472979 2.564949 2.525729 0.03922071 -0.2876821 0.74193734 -0.076881044 0.81881839 -3.912023 5.721809 OrtLye 3.944458 2.3168764 1.42310833 -0.162518929 1.5856273 3.113515 3.749504 1.4663371 2.674149 2.484907 0.189242 0.1823216 0.85441533 -0.634878272 1.4892936 -3.611918 4.976185 OrtPal 3.74284 0 0.93609336 -0.510825624 1.446919 3.191847 3.912023 1.3862944 2.639057 2.442347 0.19671029 -0.4307829 0.69314718 -0.133531393 0.82667857 -4.268698 5.973044 OrtRup 4.052565 0 1.16315081 -0.162518929 1.3256697 2.662588 3.776585 0.8472979 2.525729 2.140066 0.38566248 -0.2231436 0.58778666 0.231111721 0.35667494 -4.074542 6.03817 OrtSpe 0 0 1.23837423 -0.162518929 1.4008932 2.793208 3.84303 1.2039728 2.772589 2.525729 0.24686008 0.5596158 0.71783979 -0.235722334 0.95356213 -4.074542 5.701389 OrtStra 3.944813 2.1249422 0.85441533 -0.510825624 1.365241 2.961831 3.526361 1.299283 2.397895 2.251292 0.14660347 -0.1625189 0.61518564 -0.051293294 0.66647893 -4.342806 6.051428 OrtStri 4.374029 1.5804326 1.14740245 -0.430782916 1.5781854 3.245193 3.850148 1.2039728 2.639057 2.302585 0.33647224 -0.5108256 0.55961579 -0.0965109 0.65612669 -3.611918 5.219753 OrtTen 3.980491 2.0392373 0.87546874 -0.287682072 1.1631508 0 0 0 2.525729 2.442347 0.08338161 -0.5108256 0.61518564 -0.223143551 0.83832919 -4.233607 5.770379 PlaNem 0 0 0.97644465 -0.005012542 0.9814572 3.918668 3.164068 0 4.78096 2.949361 1.83159898 0 1.10955223 0.101653654 1.00789857 -4.422849 6.778784 PlaPor 4.248758 0 0.61518564 0.500775288 0.1144104 3.258097 0 0.4054651 3.442019 3.526361 -0.08434115 0.5596158 0 0 0 -4.074542 0 PorArbVit 0 0.7303954 0.66782937 0.405465108 0.2623643 3.091042 0 0 3.456317 3.258097 0.19822014 -0.8556661 0 0 0 -2.956512 0 PorPla 4.026981 2.0049721 0.69314718 0.371563556 0.3215836 3.283414 0 0.4054651 3.422837 3.147648 0.27518824 -0.8556661 0 0 0 -2.956512 0 PseNer 3.851398 1.835751 -0.20456717 -1.216551587 1.0119844 2.61496 3.564827 0 2.374906 1.974515 0.40039079 3.2188758 0.69314718 -0.324346057 1.01749324 -4.135167 5.648698 PteFil -1.065371 0.6051899 -0.43386458 -1.276543497 0.8426789 2.159484 0 0 3.269569 1.609438 1.66013103 2.3025851 0.55961579 -0.371063681 0.93067947 -4.422849 5.756131 RadCom 4.039162 1.5935775 0.30010459 0.113328685 0.1867759 3.113515 0 0.9162907 3.637586 2.904165 0.73342108 0 -0.28768207 -0.356674944 0.06899287 -3.506558 1.789503 RhyCur 4.01937 2.1648167 0.04305949 -1.027222293 1.0702818 2.302585 2.995732 0.9162907 3.532226 1.734601 1.79762459 0 0.30010459 -0.186329578 0.48643417 -4.233607 5.492112 SclCes 0 0 0.18232156 -0.597837001 0.7801586 2.302585 0 0 3.871201 1.791759 2.07944154 2.4849066 0 0 0 -4.017384 0 ThuDel 3.782073 1.8466119 -1.2039728 -1.673976434 0.4700036 2.944439 2.224624 1.0986123 2.270836 1.983154 0.28768207 3.4011974 1.06471074 -0.223143551 1.28785429 -4.017384 6.003681 TorFlaFla 0 0 0.91629073 -0.597837001 1.5141277 2.862201 4.007333 1.3217558 2.374906 2.251292 0.12361396 2.6026897 0.69314718 -0.549913012 1.24306019 -4.382027 5.669991 TorTor 0 0 1.5040774 -0.597837001 2.1019144 3.314186 4.007333 2.1690537 2.224624 2.140066 0.08455739 2.944439 0.81093022 -0.119346758 0.93027697 -4.50986 6.346173 UloCri 3.632599 1.3500452 0.99325177 -0.510825624 1.5040774 2.302585 3.533687 0.6931472 2.525729 2.351375 0.17435339 0.7884574
BCTree_Ports.nwk
Description: Binary data
_______________________________________________ R-help-es mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-help-es
