We corresponded with Carolina offline, but here I'm including a generalized solution of the quick solution we just sent her in case it's useful for others (avoiding the issue lampooned in https://xkcd.com/979/).
The data was a delimited file with a species column and columns for each character, with column labels "species" and then the character numbers. So, loaded into R after calling the relevant libraries: library(ape) library(corHMM) library(geiger) phy <- read.nexus("cladeb_tree.nex") data <- read.delim("cladeb_sexch.txt", stringsAsFactors = FALSE) corHMM can handle polymorphic data, but it needs to be in format 0&3, not 0+3, which was how it was coded initially. So change that: for (i in 2:ncol(data)) { data[,i] <- gsub('\\+', '&', data[,i]) } Then reconstruct ancestral states and show the output in a pdf. Loop over each character, deleting taxa from the matrix that have an NA and deleting taxa from the matrix and from the tree that aren't on both: trait_indices <- c(2:ncol(data)) pdf(file="CarolinaPlots.pdf") for (i in seq_along(trait_indices)) { col_num <- trait_indices[i] data_local <- data[,c(1,col_num)] data_local <- data_local[!is.na(data_local[,2]),] data_local <- data_local[data_local$species%in%phy$tip.label,] bad_tips <- phy$tip.label[!phy$tip.label%in%data_local$species] phy_local <- phy if(length(bad_tips)>0) { phy_local <- ape::drop.tip(phy, bad_tips) } recon <- rayDISC(phy_local, data_local, model="ARD") plotRECON(recon$phy,recon$states,title=paste0(colnames(data)[col_num], ": ", paste(names(table(data_local[,2])), "=", table(data_local[,2]), collapse=", "))) } dev.off() Hopefully a few general tips there. Slightly better style would be to preface most functions with the package name: use corHMM::rayDISC() rather than rayDISC -- this is becoming more expected in packages. Best, Brian _______________________________________________________________________ Brian O'Meara Professor, Dept. of Ecology & Evolutionary Biology, UT Knoxville Associate Head, Dept. of Ecology & Evolutionary Biology, UT Knoxville He/Him/His On Mon, Apr 13, 2020 at 4:18 PM Carolina Santos Vieira < carolsantosvie...@gmail.com> wrote: > Hi Liam and everyone > > The numbers from this message "1000 trees with a mapped discrete character > with states: 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, > 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55" are the same numbers from > the nodes on my tree. As I replied to Brian, I assumed that this was a list > of which states were mapped during make.simmap simulation. This warning > message only returns when applying the ARD model. > This character in particular is binary, and has no missing data or > non-applicable coding. > > As I mentioned previously, a big part of my dataset contains polymorphic > and non-applicable coding, and characters with 3 states (0,1,2). For those, > when the script runs, the likelihoods are very high, and plots don't agree > with coding. > > Thank you so much for your replies. > Best, > Carolina Vieira > Bióloga - Mestre em Ecologia e Conservação > Doutoranda em Biologia Animal (PPGBAN - UFRGS) > > > > <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> > Livre > de vírus. www.avast.com > <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail>. > > <#m_2399085183096779712_m_1993609250326834374_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > > Em seg., 13 de abr. de 2020 às 16:57, Liam J. Revell <liam.rev...@umb.edu> > escreveu: > >> Hi Carolina. >> >> I agree with Brian that a Q matrix in which the elements of a row are >> all zeros is not likely to be you problem. It just means that the ML >> estimated transition rate from 1->0, in your case, is zero. >> >> I agree with Brian that the message "1000 trees with a mapped discrete >> character with states: 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, >> 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55" is >> surprising. Does your discrete character really have 27 states? >> >> All the best, Liam >> >> Liam J. Revell >> Associate Professor, University of Massachusetts Boston >> Profesor Asistente, Universidad Católica de la Ssma Concepción >> web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org >> >> Academic Director UMass Boston Chile Abroad: >> https://www.umb.edu/academics/caps/international/biology_chile >> >> On 4/13/2020 3:23 PM, Brian O'Meara wrote: >> > **[EXTERNAL SENDER] >> > >> > With raydisc, you need one column with the species name and a column >> > with the data; so something like data[,c(1,2)] might be needed. If you >> > want, you could email the files (tree, data, script to run) to Jeremy >> > (jmbea...@uark.edu <mailto:jmbea...@uark.edu>) and me to check out. >> > >> > For the simmap results, a rate of zero can be the estimate if it seems >> > that there are no transitions from state 0 to 1. But the number of >> > discrete states at the end ("1000 trees with a mapped discrete >> character >> > with states: 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, >> 43, >> > 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55") seems unexpected to me. >> > >> > Best, >> > Brian >> > >> > >> > _______________________________________________________________________ >> > Brian O'Meara >> > >> > Professor, Dept. of Ecology & Evolutionary Biology, UT Knoxville >> > Associate Head, Dept. of Ecology & Evolutionary Biology, UT Knoxville >> > He/Him/His >> > >> > >> > >> > On Mon, Apr 13, 2020 at 2:32 PM Carolina Santos Vieira >> > <carolsantosvie...@gmail.com <mailto:carolsantosvie...@gmail.com>> >> wrote: >> > >> > Hi Liam and all users >> > >> > My morphological data varies from binary and multisate characters, >> > including polymorphism and non-applicable coding for many of those >> > characters. I've made a lot of progress after Liam's advices, but >> > lately I >> > have been getting an error from make.simmap. >> > >> > By trying to run a simulation with make.simmap under ARD model on >> > characters with states that the probability is zero on occuring in a >> > given >> > terminal, after calling summary(), this error is displayed: >> > >> > Error in colMeans(x$count) : 'x' must be an array of at least two >> > dimensions >> > >> > When changing the input of the same data in a two column array, the >> > error >> > still persists. The same data was analyzed with make.simmap under >> > "ER" and >> > "SYM" models, and they run just fine. I am also comparing the >> > results using >> > fitDiscrete (geiger) and ace (ape) functions and they display >> > results for >> > "ARD" model without a glitch. According to output from fitDiscrete >> > function, ARD model is indicated as the "best" model comparing AIC >> > likelihoods. >> > I've noticed that in this particular character, the "Q" matrix >> extracted >> > from make.simmap simmulation under "ARD" is the following: >> > >> > Q = >> > 0 1 >> > 0 -1.916782 1.916782 >> > 1 0.000000 0.000000 >> > >> > Are those "zero" probabilities the cause of the error? And by that I >> > mean, >> > should I take from this evidence that "ARD" is not an appropriate >> > model to >> > this character? >> > >> > Also, results from characters with "non-applicable" coding (NA in >> > matrix) >> > for some terminal are coming out very different from what I would >> > expect. >> > Is this coding allowed for ancestral reconstruction? >> > I am sorry for the many questions, and I would be very glad if any >> > suggestions come to mind. >> > >> > Best wishes, >> > Carolina Vieira. >> > >> > --------------------------------------------- >> > This is the error rundown: >> > >> > > anc.tree_ard<-make.simmap(tree,ch434,model="ARD") >> > make.simmap is sampling character histories conditioned on the >> > transition >> > matrix >> > >> > Q = >> > 0 1 >> > 0 -1.916782 1.916782 >> > 1 0.000000 0.000000 >> > (estimated using likelihood); >> > and (mean) root node prior probabilities >> > pi = >> > 0 1 >> > 0.5 0.5 >> > Done. >> > > plot(anc.tree_ard,node.numbers=T,cores,fsize=0.5,ftype="i") >> > > add.simmap.legend(colors=cores,prompt=FALSE,x=0.5*par()$usr[1], >> > + y=-30*par()$usr[3],fsize=0.8) >> > > title(main="ACSR \"ARD\" model (make.simmap)") >> > > anc.tree_ard<-make.simmap(tree,ch434,model="ARD",nsim=1000) >> > make.simmap is sampling character histories conditioned on the >> > transition >> > matrix >> > >> > Q = >> > 0 1 >> > 0 -1.916782 1.916782 >> > 1 0.000000 0.000000 >> > (estimated using likelihood); >> > and (mean) root node prior probabilities >> > pi = >> > 0 1 >> > 0.5 0.5 >> > Done. >> > > anc.tree_ard >> > 1000 phylogenetic trees with mapped discrete characters >> > > simmap_ard<-summary(anc.tree_ard) >> > > simmap_ard >> > 1000 trees with a mapped discrete character with states: >> > 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, >> > 45, 46, >> > 47, 48, 49, 50, 51, 52, 53, 54, 55 >> > >> > Error in colMeans(x$count) : 'x' must be an array of at least two >> > dimensions >> > >> > >> > >> > Carolina Vieira >> > Bióloga - Mestre em Ecologia e Conservação >> > Doutoranda em Biologia Animal (PPGBAN - UFRGS) >> > >> > >> > < >> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail >> > < >> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail&data=02%7C01%7Cliam.revell%40umb.edu%7C73d132c831904839eafd08d7dfe04b3b%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637224026744352824&sdata=8aMhSQUh6A3MqSeMrDAHh9c745UmPUvGds5K%2Br63ajI%3D&reserved=0 >> >> >> > Livre >> > de vírus. www.avast.com >> > < >> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.avast.com%2F&data=02%7C01%7Cliam.revell%40umb.edu%7C73d132c831904839eafd08d7dfe04b3b%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637224026744362820&sdata=cg2Up9JlFgNsiiwIZiQL8hQC71GLJTc451DcjkCCzuQ%3D&reserved=0 >> > >> > < >> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail >> > < >> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail&data=02%7C01%7Cliam.revell%40umb.edu%7C73d132c831904839eafd08d7dfe04b3b%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637224026744372816&sdata=t1T5s0t5Ja2b44KXhYWZlruL583hgKc1Wn0XJymJVVg%3D&reserved=0 >> >>. >> > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> >> > >> > Em qua., 26 de fev. de 2020 às 23:54, Liam J. Revell >> > <liam.rev...@umb.edu <mailto:liam.rev...@umb.edu>> >> > escreveu: >> > >> > > Dear Carolina. >> > > >> > > After running make.simmap with nsim=100 or more, just run >> > summary( ) on >> > > your "multiSimmap" object and then plot the result. For instance: >> > > >> > > map.trees<-make.simmap(tree,x,model="SYM",nsim=200) >> > > map.summary<-summary(map.trees) >> > > print(map.summary) >> > > plot(map.summary,ftype="off",lwd=1,cex=c(0.7,0.4)) >> > > map.summary$ace ## probabilities at nodes >> > > >> > > All the best, Liam >> > > >> > > Liam J. Revell >> > > Associate Professor, University of Massachusetts Boston >> > > Profesor Asistente, Universidad Católica de la Ssma Concepción >> > > web: http://faculty.umb.edu/liam.revell/, >> http://www.phytools.org >> > < >> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.phytools.org%2F&data=02%7C01%7Cliam.revell%40umb.edu%7C73d132c831904839eafd08d7dfe04b3b%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637224026744372816&sdata=EqrmVIJ9PLPHYORoyMVoKxUAWtPhjbEZNZMowogNAf4%3D&reserved=0 >> > >> > > >> > > Academic Director UMass Boston Chile Abroad: >> > > https://www.umb.edu/academics/caps/international/biology_chile >> > > >> > > On 2/24/2020 2:33 PM, Carolina Santos Vieira wrote: >> > > > **[EXTERNAL SENDER] >> > > > >> > > > Hi Liam, >> > > > >> > > > Thank you very much for clearing that up! >> > > > I was able to run the make.simmap script, but in the first plot >> > instead >> > > > of getting one symbol of the corresponding state at the tips, >> > they are >> > > > displayed in proportional sizes (I've attached the plot). >> > > > >> > > > I have also looked into how to get the likelihoods from each >> > ancestral >> > > > state from this analysis (like we get from "lik.anc" in ace >> > function), >> > > > but didn't find it. Is it possible to get it? >> > > > >> > > > Thank you again for the help! >> > > > Best regards, >> > > > Carolina Vieira >> > > > Bióloga - Mestre em Ecologia e Conservação >> > > > Doutoranda em Biologia Animal (PPGBAN - UFRGS) >> > > > >> > > > >> > > > Em sex., 21 de fev. de 2020 às 22:53, Liam J. Revell >> > > > <liam.rev...@umb.edu <mailto:liam.rev...@umb.edu> >> > <mailto:liam.rev...@umb.edu <mailto:liam.rev...@umb.edu>>> >> escreveu: >> > > > >> > > > Dear Carolina. >> > > > >> > > > I don't know how rayDISC works (but the authors of corHMM >> > are on this >> > > > list, so they will probably respond); however, for >> > > > phytools::make.simmap >> > > > & phytools::rerootingMethod, which can also handle missing >> > data, >> > > > missingness is coded by supplying the input data in the >> > form of an N >> > > > x k >> > > > matrix for N species & k character states. In this case, we >> > would >> > > > put 0s >> > > > and 1s in any row in which the character state was known; >> and a >> > > series >> > > > of values of 1/k for any completely unknown state. >> > > > >> > > > For instance: >> > > > 0 1 2 >> > > > sp A 0 0 1 >> > > > sp B 1 0 0 >> > > > sp C 1/3 1/3 1/3 >> > > > sp D 0 1/2 1/2 >> > > > >> > > > corresponds to species A in state '2', species B in state >> > '0', and >> > > > species C unknown or missing. Species D is in either state >> > '1' or >> > > '2', >> > > > but not in state '0'. (Instead of 1/k you can also set them >> > all to >> > > > be 1. >> > > > The likelihood changes, but ancestral states are the same.) >> > > > >> > > > I hope this is helpful. All the best, Liam >> > > > >> > > > Liam J. Revell >> > > > Associate Professor, University of Massachusetts Boston >> > > > Profesor Asistente, Universidad Católica de la Ssma >> Concepción >> > > > web: http://faculty.umb.edu/liam.revell/, >> > http://www.phytools.org >> > < >> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.phytools.org%2F&data=02%7C01%7Cliam.revell%40umb.edu%7C73d132c831904839eafd08d7dfe04b3b%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637224026744382812&sdata=MiSJfz5HhNxh3mABi1aS3DOTfjtX%2BCecnB1wRdh9MIs%3D&reserved=0 >> > >> > > > < >> > > >> > >> https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.phytools.org%2F&data=02%7C01%7Cliam.revell%40umb.edu%7Cbeaccbb894534e0785d708d7b9607ccd%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637181696380978269&sdata=%2Fialzss4jrVm8Rpt6jDUXwkdGqQZMMFA4N84HgVhWps%3D&reserved=0 >> > < >> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.phytools.org%2F&data=02%7C01%7Cliam.revell%40umb.edu%7C73d132c831904839eafd08d7dfe04b3b%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637224026744392807&sdata=5bqkzQzEOS4eR%2FtVBD0sbHLXRXCfxQealNo1xCjCk30%3D&reserved=0 >> > >> > > > >> > > > >> > > > Academic Director UMass Boston Chile Abroad: >> > > > https://www.umb.edu/academics/caps/international/biology_chile >> > > > >> > > > On 2/21/2020 8:22 PM, Carolina Santos Vieira wrote: >> > > > > [EXTERNAL SENDER] >> > > > > >> > > > > Dear all, >> > > > > >> > > > > I am working with a morphological matrix which contains >> > multistate >> > > > > characters (including polymorphism) and some missing >> > data entries >> > > > (coded as >> > > > > NA in data file for input). There are no unvariable >> > characters in >> > > > coding. >> > > > > For the reconstruction of ancestral characters, I came >> > across >> > > > with rayDISC >> > > > > function from corHMM package (since fitDiscrete doesn't >> > seem to >> > > > account for >> > > > > it). >> > > > > >> > > > > However, when running the script two kinds of errors are >> > > displayed: >> > > > > >> > > > > - Calling the full data file with the rayDISC function, >> > no matter >> > > > which >> > > > > character is selected for the analysis, it returns with >> this >> > > error: >> > > > > >> > > > > rayDISC(phy,data, ntraits=1, charnum=1, rate.mat=NULL, >> > > model=c("ER"), >> > > > > node.states=c("marginal"), >> state.recon=c("subsequently"), >> > > > > lewis.asc.bias=FALSE, p=NULL, root.p=NULL, ip=NULL, >> > lb=0, ub=100, >> > > > verbose=TRUE, >> > > > > diagn=FALSE) >> > > > > >> > > > > $diagnostic >> > > > > [1] "Character 1 is invariant. Analysis stopped." >> > > > > >> > > > > >> > > > > - I have tried clipping the data creating a new object >> > with just >> > > one >> > > > > of the characters, but a new error appears: >> > > > > >> > > > > Error in data[, 1] : incorrect number of dimensions >> > > > > >> > > > > I also looked into running make.simmap in parallel >> > > > > >> > > > ( >> > > >> > >> https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fblog.phytools.org%2F2017%2F11%2Frunning-makesimmap-in-parallel.html&data=02%7C01%7Cliam.revell%40umb.edu%7Ce210401fdd8c483d2bde08d7b735d3f4%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637179314141242835&sdata=%2FHwtbpjRxREIS7T2PPIQZ%2B5iyRpVbGaHMKWX6e8%2Fb5U%3D&reserved=0 >> > < >> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fblog.phytools.org%2F2017%2F11%2Frunning-makesimmap-in-parallel.html&data=02%7C01%7Cliam.revell%40umb.edu%7C73d132c831904839eafd08d7dfe04b3b%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637224026744392807&sdata=hoPlDeB6asUHdZlW9aq0sv8uBQUvGpQUlaKmXg33RHs%3D&reserved=0 >> > >> > > > < >> > > >> > >> https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fblog.phytools.org%2F2017%2F11%2Frunning-makesimmap-in-parallel.html&data=02%7C01%7Cliam.revell%40umb.edu%7Cbeaccbb894534e0785d708d7b9607ccd%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637181696380988260&sdata=Xbyv%2F2R6lsf7ArCi%2F5SmiV2r2nE57ZMsAsYrsL5uhhI%3D&reserved=0 >> > < >> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fblog.phytools.org%2F2017%2F11%2Frunning-makesimmap-in-parallel.html&data=02%7C01%7Cliam.revell%40umb.edu%7C73d132c831904839eafd08d7dfe04b3b%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637224026744402801&sdata=jiFlXe7r3xXkH6NIu4aO1%2BiKtOTQZ7R1JUiRhAGo8%2Fk%3D&reserved=0 >> > >> > > >), >> > > > > and this happens: " Error in if (any(x < 0)) x <- x - >> > min(x) : >> > > > > missing Value when TRUE/FALSE needed ". Trying to >> > replace NA as >> > > > > 'unknown' to be considered in the analysis by changing >> its >> > > > "status" to >> > > > > FALSE, it returns in the matrix coded as "0", which is >> not >> > > properly >> > > > > valid since this implies coding it as a known state >> (and not >> > > missing >> > > > > data, as it truly is). >> > > > > >> > > > > >> > > > > I appreciate if anyone could shine a light on this >> matter. >> > > > > With regards, >> > > > > Carolina Vieira >> > > > > Bióloga - Mestre em Ecologia e Conservação >> > > > > Doutoranda em Biologia Animal (PPGBAN - UFRGS) >> > > > > >> > > > > [[alternative HTML version deleted]] >> > > > > >> > > > > _______________________________________________ >> > > > > R-sig-phylo mailing list - R-sig-phylo@r-project.org >> > <mailto:R-sig-phylo@r-project.org> >> > > > <mailto:R-sig-phylo@r-project.org >> > <mailto:R-sig-phylo@r-project.org>> >> > > > > >> > > > >> > > >> > >> https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylo&data=02%7C01%7Cliam.revell%40umb.edu%7Ce210401fdd8c483d2bde08d7b735d3f4%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637179314141252833&sdata=feVEKUpekTBV5FVzfZDdDU7sJGi6x%2FGtumn3TpmhRuk%3D&reserved=0 >> > < >> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylo&data=02%7C01%7Cliam.revell%40umb.edu%7C73d132c831904839eafd08d7dfe04b3b%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637224026744412798&sdata=68Q5FHefFQqCWjv2JjnZSUM0%2FlpXg7YgSsgBY69EFHI%3D&reserved=0 >> > >> > > > < >> > > >> > >> https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylo&data=02%7C01%7Cliam.revell%40umb.edu%7Cbeaccbb894534e0785d708d7b9607ccd%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637181696380988260&sdata=3OcfvhEJpXJEhCeN8M4LnvU1Kn385TZUY7mewlTtnB0%3D&reserved=0 >> > < >> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylo&data=02%7C01%7Cliam.revell%40umb.edu%7C73d132c831904839eafd08d7dfe04b3b%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637224026744412798&sdata=68Q5FHefFQqCWjv2JjnZSUM0%2FlpXg7YgSsgBY69EFHI%3D&reserved=0 >> > >> > > > >> > > > > Searchable archive at >> > > > >> > > >> > >> https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2F&data=02%7C01%7Cliam.revell%40umb.edu%7Ce210401fdd8c483d2bde08d7b735d3f4%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637179314141252833&sdata=8otz0Vyk02Uo2uGw4fWbOqfuA4EKp8GQ71cZufu3XFg%3D&reserved=0 >> > < >> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2F&data=02%7C01%7Cliam.revell%40umb.edu%7C73d132c831904839eafd08d7dfe04b3b%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637224026744422791&sdata=y1nhLo0SIMuEWLkUKiQbBaLVU2577gANk4bYgeAmDPQ%3D&reserved=0 >> > >> > > > < >> > > >> > >> https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2F&data=02%7C01%7Cliam.revell%40umb.edu%7Cbeaccbb894534e0785d708d7b9607ccd%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637181696380998258&sdata=RhuYW6qY%2ByiZBEBZT6J0buhER4Ks9s74JFKr%2BV%2Bnsfw%3D&reserved=0 >> > < >> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2F&data=02%7C01%7Cliam.revell%40umb.edu%7C73d132c831904839eafd08d7dfe04b3b%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637224026744432780&sdata=E0rlCxU4PsCuQ1C3QHg38Xd5iVdFeF%2FtlSn0asuUeyg%3D&reserved=0 >> > >> > > > >> > > > > >> > > > >> > > >> > >> > < >> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail >> > < >> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail&data=02%7C01%7Cliam.revell%40umb.edu%7C73d132c831904839eafd08d7dfe04b3b%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637224026744432780&sdata=1kpzUpEjiwCiuH5FMxln6vtoGwmmEGM51f8H7Hj23wk%3D&reserved=0 >> >> >> > Livre >> > de vírus. www.avast.com >> > < >> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.avast.com%2F&data=02%7C01%7Cliam.revell%40umb.edu%7C73d132c831904839eafd08d7dfe04b3b%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637224026744442780&sdata=tEhF3wOAyvknUahvjJ5%2BRKwxOgOgXABEOrbqeFsnLEU%3D&reserved=0 >> > >> > < >> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail >> > < >> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail&data=02%7C01%7Cliam.revell%40umb.edu%7C73d132c831904839eafd08d7dfe04b3b%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637224026744452779&sdata=KPi8M98OAXHfxgrnm%2BabKEbj7qcw1%2FTwwdvDDhEyj4o%3D&reserved=0 >> >>. >> > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> >> > >> > [[alternative HTML version deleted]] >> > >> > _______________________________________________ >> > R-sig-phylo mailing list - R-sig-phylo@r-project.org >> > <mailto:R-sig-phylo@r-project.org> >> > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> > < >> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylo&data=02%7C01%7Cliam.revell%40umb.edu%7C73d132c831904839eafd08d7dfe04b3b%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637224026744452779&sdata=0gvMUwExo61wRgytWW4HAsJe%2BD%2F8a%2BKUQnOy2WHO%2FBo%3D&reserved=0 >> > >> > Searchable archive at >> > http://www.mail-archive.com/r-sig-phylo@r-project.org/ >> > < >> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2F&data=02%7C01%7Cliam.revell%40umb.edu%7C73d132c831904839eafd08d7dfe04b3b%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637224026744462768&sdata=AkvOfbizLeji8%2FIZfwQSVTIMvQ5Bwtg2BbL42zRzRLM%3D&reserved=0 >> > >> > >> > > > <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> > Livre > de vírus. www.avast.com > <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail>. > > <#m_2399085183096779712_m_1993609250326834374_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > [[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/