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>
>
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