Dear friends, I am trying to assign node ages to a phylogenetic tree of subtropical trees in southern Brazil without using Phylocom and its popular function bladj. This is because for some reason Phylocom will not open my Phylomatic-generated tree. I managed to open it with the rncl package as indicated by François Michonneau.
I am now trying to use the AdjBrLens() function found at ( https://gist.github.com/sckott/938313#file-bladjing_twomethods-r) that uses Gene Hunt's method (see code below). I disabled the part of the code referring to Phylocom's bladj function because it won't read my tree, and also changed line 90 from tree <- read.tree(trees) to tree <- read_newick_phylo(trees) in order to use the rncl read_newick_phylo function. Yet, I am receiving an error message Error in names(node.mins) <- ii : 'names' attribute [80] must be the same length as the vector [54] Do anyone has any idea on how to circunvent this problem? Thank you very much in advance, Sincerely, Alexandre # Run these functions first (scalePhylo, assign.ages, and assign.brlen) # scalePhylo, assign.ages, and assign.brlen written by Gene Hunt ( http://paleobiology.si.edu/staff/individuals/hunt.cfm) # AdjBrLens written by Scott Chamberlain (myrmecocys...@gmail.com) scalePhylo<- function(tr, tip.ages, node.mins=NULL, min.diff=0.1) ## tr is a 'phylo' object ## tip.ages is a vector of the ages of terminal taxa (best if this vector has names that match the taxa labels) ## tip.ages MUST BE A NAMED VECTOR, that is, e.g., names(tipages) <- tree$tip.label [where tipages is a numeric vector of ## the tip ages] ## node.mins is a vector of optional constraints on nodes ## min.diff is the minimum branch length that will be imposed { aa<- assign.ages(tr, tip.ages, node.mins, min.diff) trs<- assign.brlen(tr, aa) return(trs) } assign.ages<- function(tr, tip.ages, node.mins, min.diff) # Function to assign ages to internal nodes, given tree and # ages of terminal modes # --tr is phylo (from package ape) # --tip.ages is strat ages of terminal taxa # --node.mins are (optional) minimum ages for nodes (or a subset of nodes) { ## do some error checking # makes sure tips have labels # check node labels? if(is.null(node.mins)) {node.mins<- rep(NA, times=tr$Nnode)} node.mins[is.na(node.mins)]<- -Inf # so nodes with no information have no effect #print(node.mins) # change order of ages to match tip labels of tr oo<- charmatch(tr$tip.label, names(tip.ages)) tip.ages<- tip.ages[oo] tn<- tr$edge max.term<- length(tr$tip.label) min.anc<- max.term+1 max.anc<- min.anc + tr$Nnode -1 aa<- array(dim=max(tn)) names(aa)<- as.character(1:max(tn)) aa[1:max.term]<- tip.ages ii<- min.anc:max.anc names(node.mins)<- ii # note: this assumes tree nodes not originally labelled!! # go through internal nodes, assign ages to them while (sum(is.na(aa))>=1) # loop through as long as ages for some inodes not yet known { #print(aa) for (i in ii) { ci<- as.character(i) yy<- tn[,1]==i dec<- tn[,2][yy] # direct descendants of i aad<- aa[as.character(dec)] # ages of these direct descendants #cat(ci, aad, '\n') if (sum(is.na(aad))==0) # if all ages are known. { aa[ci]<- max(aad) + min.diff # assign age as max() of nodes within if(aa[ci] < node.mins[ci]) aa[ci]<- node.mins[ci] } } } return (aa) } assign.brlen<- function (t1, all.ages) # Function to assign branch lengths to all edges of tree # --t1 is phylo # --all.ages is vector of ages of terminal and internal nodes (as given by assign.ages() ) { ne<- nrow(t1$edge) bl<- array(dim=ne) for (i in 1:ne) { anc<- t1$edge[i,1] dec<- t1$edge[i,2] bl[i]<- all.ages[anc] - all.ages[dec] } t2<- t1 t2$edge.length<- bl return(t2) } #### AdjBrLens <- function(trees, ages) { require(ape) # read, then write files to where phylocom executable is tree <- read.tree(trees) age <- read.table(ages) write.tree(tree, "phylo") write.table(age, file = "ages", sep = "\t", col.names = F, row.names = F, quote = F) # bladj method #system("./phylocom bladj > phyloout.txt") # for windows users replace #with: shell("phylocom bladj > phyloout.txt") #bladjmethod <- read.tree("phyloout.txt") # Gene Hunt method age_ <- age[,2] names(age_) <- age[,1] # set node ages diff_ <- rep(NA, length(setdiff(tree$node.label, names(age_)))) names(diff_) <- setdiff(tree$node.label, names(age_)) nodeages <- c(age_, diff_) # tipages are set to zero as all species are extant tipages <- rep(0, length(tree$tip.label)) names(tipages) <- tree$tip.label # you can set min.diff to get different results huntmethod <- scalePhylo(tree, tipages, nodeages, min.diff=0) # plot trees and write to file pdf(paste("",trees,"TheOG",".pdf","",sep="")) plot(tree) dev.off() # phynodes <- data.frame(bladjmethod$node.label, #1:length(bladjmethod$ node.label)) #names(phynodes) <- c("V1", "order") #newnodes <- merge(phynodes, age, by="V1", all=T) #newnodes_sort <- newnodes[order(newnodes[,2]), ] #bladjmethod$node.label <- newnodes_sort[, 3] pdf(paste("",trees,"bladjmethod",".pdf","",sep="")) plot(bladjmethod) nodelabels(bladjmethod$node.label, cex = 0.6) dev.off() pdf(paste("",trees,"genehuntmethod",".pdf","",sep="")) plot(huntmethod) dev.off() # write bladj tree to file # bladjmethod$node.label <- NULL # write.tree(bladjmethod, paste("",trees,"bladjtree",".txt","",sep="")) # combine trees in list trees_out <- list(tree, bladjmethod, huntmethod) trees_out } My tree ((((((((((acacia_bonariensis,inga_vera),((dalbergia_frutescens,(machaerium_glabrum,machaerium_paraguariense,machaerium_stipitatum)machaerium),(lonchocarpus_campestris,lonchocarpus_nitidus)lonchocarpus)),((celtis_iguanaea,scutia_buxifolia),prunus_myrtifolia)rosales),(((((banara_parviflora,banara_tomentosa)banara,(casearia_decandra,casearia_obliqua,casearia_sylvestris)casearia,(xylosma_pseudosalzmannii,xylosma_tweedianum)xylosma)salicaceae,(sapium_glandulatum,(sebastiania_brasiliensis,sebastiania_commersoniana)sebastiania,stillingia_oppositifolia)euphorbiaceae)malpighiales,(lamanonia_ternata,weinmania_paulliniifolia)cunoniaceae),(maytenus_aquifolia,maytenus_evonymoides)maytenus)celastrales_to_malpighiales),(((((allophylus_edulis,cupania_vernalis,matayba_elaeagnoides)sapindaceae,(cedrela_fissilis,(helietta_apiculata,pilocarpus_pennatifolius,zanthoxylum_fagara)rutaceae,picramnia_parvifolia)),lithraea_brasiliensis),luehea_divaricata),((blepharocalyx_salicifolius,(((calyptranthes_concinna,((myrciaria_delicatula,myrciaria_floribunda,myrciaria_tenella)myrciaria,siphoneugena_reitzii)pliniagroup),(myrceugenia_cucullata,myrceugenia_miersiana,myrceugenia_myrcioides,myrceugenia_oxysepala)myrceugenia),((acca_sellowiana,myrrhinium_atropurpureum,(campomanesia_rhombea,campomanesia_xanthocarpa)campomanesia),((eugenia_involucrata,eugenia_pluriflora,eugenia_psidiiflora,eugenia_uruguayensis)eugenia,(myrcianthes_gigantea,myrcianthes_pungens)myrcianthes)eugeniagroup))),(myrcia_arborescens,myrcia_bombycina,myrcia_lajeana,myrcia_oligantha)myrcia)myrtaceae)malvids),((((((((cestrum_sp,(solanum_pabstii,solanum_pseudoquina,solanum_sanctae-catharinae,solanum_sp)solanum),(((citharexylum_myrianthum,duranta_vestita)verbenaceae,tabebuia_umbellata),cunila_incisa)),(coussarea_contracta,strychnos_brasiliensis)gentianales),(citronella_gongonha,citronella_paniculata)citronella)lamiids,((((dasyphyllum_spinescens,dasyphyllum_tomentosum)dasyphyllum,vernonia_discolor)asteraceae,oreopanax_fulvus),(ilex_brevicuspis,ilex_dumosa,ilex_microdonta,ilex_paraguariensis,ilex_sp)ilex)campanulids),(gordonia_acutifolia,(styrax_leprosus,(symplocos_pentandra,symplocos_tetrandra,symplocos_uniflora)symplocos)))ericales_to_asterales,griselinia_ruscifolia)asterids,seguieria_aculeata)),roupala_brasiliensis)sabiales_to_asterales,(((aiouea_saligna,(cinnamomum_amoenum,cinnamomum_glaziovii)cinnamomum,(cryptocarya_aschersoniana,cryptocarya_moschata)cryptocarya,nectandra_megapotamica,(ocotea_indecora,ocotea_lancifolia,ocotea_puberula,ocotea_pulchella)ocotea)lauraceae,(hennecartia_omphalandra,mollinedia_elegans)monimiaceae),(rollinia_rugulosa,rollinia_salicifolia,rollinia_sylvatica)rollinia))magnoliales_to_asterales,(araucaria_angustifolia,podocarpus_lambertii))seedplants,alsophila_sp)euphyllophyte; -- Dr. Alexandre F. Souza Professor Ajunto II Universidade Federal do Rio Grande do Norte CB, Departamento de Ecologia Campus Universitário - Lagoa Nova 59072-970 - Natal, RN - Brasil lattes: lattes.cnpq.br/7844758818522706 http://www.docente.ufrn.br/alexsouza [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
