Re: [R-sig-phylo] phyl.RMA error

2020-06-12 Thread Ted Stankowich
Thank you Simone, 
I think we're going to first try the model in Rphylopars that accounts for 
measurement error and intraspecific variation. But we'll check out your JAGS 
program if that doesn't turn out to be appropriate for our dataset. 
Best,
Ted

-Original Message-
From: Simone Blomberg [mailto:s.blombe...@uq.edu.au] 
Sent: Friday, June 12, 2020 1:21 AM
To: Theodore Garland ; Ted Stankowich 

Cc: r-sig-phylo@r-project.org; Nicole Lopez 
Subject: Re: [R-sig-phylo] phyl.RMA error

CAUTION: This email was sent from an external source. Use caution when 
replying, opening links or attachments.


Hi all,

If you want to go Bayesian, we provide a program in JAGS or BUGS that will do 
measurement error models incorporating phylogenetic uncertainty.
(de Villemereuil et al. BMC Evolutionary Biology 2012, 12:102 
http://www.biomedcentral.com/1471-2148/12/102, attached). We took our approach 
from the book by Carrol et al. which I highly recommend (Carroll RJ, Ruppert D, 
Stefanski LA: Measurement Error in Nonlinear
Models: A Modern Perspective. Boca Raton, FL, USA, London, New York: CRC Press; 
2006.). They condemn RMA (or "orthogonal" regression) because although the 
slope parameters of an ordinary regression are negatively biased in the 
presence of measurement error, the slopes are even more positively biased if 
you use orthogonal regression. A properly constructed measurement error model 
will give unbiased estimates (so long as the assumptions are met.) I think I 
might have been involved in the discussion on this list about the futility of 
RMA regression. I still stand by my views.

Best,

Simone.

On 10/6/20 6:49 am, Theodore Garland wrote:
> A slope from RMA will always be > than the corresponding OLS slope 
> because RMA = OLS/r, where r is the correlation coefficient.
> And note that the RMA slope calculated this way is undefined if r = 0.
>
> This is why you want to use measurement-error models.
>
> Cheers,
> Ted
>
>
>
>
> On Tue, Jun 9, 2020 at 1:34 PM Ted Stankowich 
> 
> wrote:
>
>> Thank you Liam and Ted!
>> That worked. I've never named my data columns this way and when I 
>> call names(Data), it does give me the column names "Binomial", 
>> "Skull", and "Tusk". This method appears to pull out the vectors and 
>> use them outside of the original dataframe, is this a particular 
>> requirement/feature of phyl.RMA?
>>
>> Regarding RMA vs. other methods, this is a study of allometry of 
>> tusks and antlers. In our first submission of this project we got 
>> raked over the coals for only using OLS methods so we're doing both 
>> OLS and RMA this time around, but are struggling to interpret the 
>> slope discrepancies between the two methods (RMA always returns 
>> larger slopes). There is measurement error in our independent factor 
>> (Skull) since some of those data come from PCA estimates based on 
>> landmark measures in skulls that were broken/partial (full skull 
>> length wasn't possible). We'll definitely look at the paper Ted 
>> posted though. There appears to be some strong divergent 
>> methodological opinions among the allometry community though, so it's hard 
>> to know the best way to proceed!
>>
>> Thanks!
>> -Ted
>>
>>
>>
>> -Original Message-
>> From: Liam J. Revell [mailto:liam.rev...@umb.edu]
>> Sent: Tuesday, June 9, 2020 1:07 PM
>> To: Ted Stankowich ; 
>> r-sig-phylo@r-project.org
>> Subject: Re: [R-sig-phylo] phyl.RMA error
>>
>> CAUTION: This email was sent from an external source. Use caution 
>> when replying, opening links or attachments.
>>
>>
>> Hi Ted.
>>
>> It's a good bet that your input vectors, log(Skull) and log(Tusk), 
>> don't have names.
>>
>> In your case, if your data frame is called Data, you might first compute:
>>
>> ln.Skull<-setNames(log(Data$Skull),Data$Binomial)
>> ln.Tusk<-setNames(log(Data$Tusk),Data$Binomial)
>>
>> and then run:
>>
>> Model<-phyl.RMA(ln.Skull,ln.Tusk,tree,h0=1.0)
>> Model
>> plot(Model) ## this is kind of cool.
>>
>> Note, that as pointed out in the documentation of the function: "some 
>> statistician think there is never a condition in which a 
>> reduced-major-axis regression should be used" (I believe this has 
>> even been discussed on this list); and "The statistical hypothesis 
>> testing is based on Clarke (1980; reviewed in McArdle 1988), which 
>> differs from some other implementations of non-phylogenetic major axis 
>> regression in R."
>>
>> All the best, Liam
>>
>> Liam J. Revell
>> Associate Professor,

Re: [R-sig-phylo] phyl.RMA error

2020-06-09 Thread Ted Stankowich
Right – I was saying it’s more of an issue with interpretation and comparing 
with past studies, many of which don’t even incorporate phylogenetic methods 
(traditional regression).
I found the Rphylopars package in R, which appears to consider both 
intraspecific variation and measurement error (or at least multiple 
measurements of the same species).
https://cran.r-project.org/web/packages/Rphylopars/Rphylopars.pdf

Best,
Ted

From: Theodore Garland [mailto:theodore.garl...@ucr.edu]
Sent: Tuesday, June 9, 2020 1:49 PM
To: Ted Stankowich 
Cc: Liam J. Revell ; r-sig-phylo@r-project.org; Nicole 
Lopez 
Subject: Re: [R-sig-phylo] phyl.RMA error

CAUTION: This email was sent from an external source. Use caution when 
replying, opening links or attachments.

A slope from RMA will always be > than the corresponding OLS slope because RMA 
= OLS/r, where r is the correlation coefficient.
And note that the RMA slope calculated this way is undefined if r = 0.

This is why you want to use measurement-error models.

Cheers,
Ted





On Tue, Jun 9, 2020 at 1:34 PM Ted Stankowich 
mailto:theodore.stankow...@csulb.edu>> wrote:
Thank you Liam and Ted!
That worked. I've never named my data columns this way and when I call 
names(Data), it does give me the column names "Binomial", "Skull", and "Tusk". 
This method appears to pull out the vectors and use them outside of the 
original dataframe, is this a particular requirement/feature of phyl.RMA?

Regarding RMA vs. other methods, this is a study of allometry of tusks and 
antlers. In our first submission of this project we got raked over the coals 
for only using OLS methods so we're doing both OLS and RMA this time around, 
but are struggling to interpret the slope discrepancies between the two methods 
(RMA always returns larger slopes). There is measurement error in our 
independent factor (Skull) since some of those data come from PCA estimates 
based on landmark measures in skulls that were broken/partial (full skull 
length wasn't possible). We'll definitely look at the paper Ted posted though. 
There appears to be some strong divergent methodological opinions among the 
allometry community though, so it's hard to know the best way to proceed!

Thanks!
-Ted



-Original Message-
From: Liam J. Revell [mailto:liam.rev...@umb.edu<mailto:liam.rev...@umb.edu>]
Sent: Tuesday, June 9, 2020 1:07 PM
To: Ted Stankowich 
mailto:theodore.stankow...@csulb.edu>>; 
r-sig-phylo@r-project.org<mailto:r-sig-phylo@r-project.org>
Subject: Re: [R-sig-phylo] phyl.RMA error

CAUTION: This email was sent from an external source. Use caution when 
replying, opening links or attachments.


Hi Ted.

It's a good bet that your input vectors, log(Skull) and log(Tusk), don't have 
names.

In your case, if your data frame is called Data, you might first compute:

ln.Skull<-setNames(log(Data$Skull),Data$Binomial)
ln.Tusk<-setNames(log(Data$Tusk),Data$Binomial)

and then run:

Model<-phyl.RMA(ln.Skull,ln.Tusk,tree,h0=1.0)
Model
plot(Model) ## this is kind of cool.

Note, that as pointed out in the documentation of the function: "some 
statistician think there is never a condition in which a reduced-major-axis 
regression should be used" (I believe this has even been discussed on this 
list); and "The statistical hypothesis testing is based on Clarke (1980; 
reviewed in McArdle 1988), which differs from some other implementations of 
non-phylogenetic major axis regression in R."

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 6/8/2020 4:18 PM, Ted Stankowich wrote:
> [EXTERNAL SENDER]
>
> Hello,
>
> We're trying to run phylogenetically corrected reduced major axes regression 
> analyses and have encountered an error we can't debug. We're using the 
> function phyl.RMA in the package 'phytools'. Here is the code we are using 
> and the error it returns.
>
>
>
>> Model <- phyl.RMA(log(Skull), log(Tusk), tree, h0=1.0)
>
> Error in if (sign(beta1) != sign(h0)) { :
>
>missing value where TRUE/FALSE needed
>
> We can't seem to figure out which argument is missing, and we've tried 
> including all of the T/F based arguments we think are possible. Our species 
> dataset and nexus file are printed below.  Any advice would be greatly 
> appreciated.
>
> We have the following dataset:
> Binomial Skull  Tusk
>  
> 1 Tragulus_javanicus93.7  14.6
> 2 Tragulus_kanchil  99.7  13.9
> 3 Tragulus_napu 98.1  11.1
> 4 Tragulus_nigricans99.8  13.2
> 5 Moschiola_meminna  

Re: [R-sig-phylo] phyl.RMA error

2020-06-09 Thread Theodore Garland
A slope from RMA will always be > than the corresponding OLS slope because
RMA = OLS/r, where r is the correlation coefficient.
And note that the RMA slope calculated this way is undefined if r = 0.

This is why you want to use measurement-error models.

Cheers,
Ted




On Tue, Jun 9, 2020 at 1:34 PM Ted Stankowich 
wrote:

> Thank you Liam and Ted!
> That worked. I've never named my data columns this way and when I call
> names(Data), it does give me the column names "Binomial", "Skull", and
> "Tusk". This method appears to pull out the vectors and use them outside of
> the original dataframe, is this a particular requirement/feature of
> phyl.RMA?
>
> Regarding RMA vs. other methods, this is a study of allometry of tusks and
> antlers. In our first submission of this project we got raked over the
> coals for only using OLS methods so we're doing both OLS and RMA this time
> around, but are struggling to interpret the slope discrepancies between the
> two methods (RMA always returns larger slopes). There is measurement error
> in our independent factor (Skull) since some of those data come from PCA
> estimates based on landmark measures in skulls that were broken/partial
> (full skull length wasn't possible). We'll definitely look at the paper Ted
> posted though. There appears to be some strong divergent methodological
> opinions among the allometry community though, so it's hard to know the
> best way to proceed!
>
> Thanks!
> -Ted
>
>
>
> -Original Message-
> From: Liam J. Revell [mailto:liam.rev...@umb.edu]
> Sent: Tuesday, June 9, 2020 1:07 PM
> To: Ted Stankowich ;
> r-sig-phylo@r-project.org
> Subject: Re: [R-sig-phylo] phyl.RMA error
>
> CAUTION: This email was sent from an external source. Use caution when
> replying, opening links or attachments.
>
>
> Hi Ted.
>
> It's a good bet that your input vectors, log(Skull) and log(Tusk), don't
> have names.
>
> In your case, if your data frame is called Data, you might first compute:
>
> ln.Skull<-setNames(log(Data$Skull),Data$Binomial)
> ln.Tusk<-setNames(log(Data$Tusk),Data$Binomial)
>
> and then run:
>
> Model<-phyl.RMA(ln.Skull,ln.Tusk,tree,h0=1.0)
> Model
> plot(Model) ## this is kind of cool.
>
> Note, that as pointed out in the documentation of the function: "some
> statistician think there is never a condition in which a reduced-major-axis
> regression should be used" (I believe this has even been discussed on this
> list); and "The statistical hypothesis testing is based on Clarke (1980;
> reviewed in McArdle 1988), which differs from some other implementations of
> non-phylogenetic major axis regression in R."
>
> 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 6/8/2020 4:18 PM, Ted Stankowich wrote:
> > [EXTERNAL SENDER]
> >
> > Hello,
> >
> > We're trying to run phylogenetically corrected reduced major axes
> regression analyses and have encountered an error we can't debug. We're
> using the function phyl.RMA in the package 'phytools'. Here is the code we
> are using and the error it returns.
> >
> >
> >
> >> Model <- phyl.RMA(log(Skull), log(Tusk), tree, h0=1.0)
> >
> > Error in if (sign(beta1) != sign(h0)) { :
> >
> >missing value where TRUE/FALSE needed
> >
> > We can't seem to figure out which argument is missing, and we've tried
> including all of the T/F based arguments we think are possible. Our species
> dataset and nexus file are printed below.  Any advice would be greatly
> appreciated.
> >
> > We have the following dataset:
> > Binomial Skull  Tusk
> >  
> > 1 Tragulus_javanicus93.7  14.6
> > 2 Tragulus_kanchil  99.7  13.9
> > 3 Tragulus_napu 98.1  11.1
> > 4 Tragulus_nigricans99.8  13.2
> > 5 Moschiola_meminna101.   14.6
> > 6 Moschus_berezovskii  134.   55.0
> > 7 Moschus_moschiferus  152.   52.9
> > 8 Muntiacus_muntjak193.   26.4
> > 9 Muntiacus_reevesi159.   23.4
> > 10 Muntiacus_truongsonensis 184.   27.7
> > 11 Muntiacus_vaginalis  203.   28.6
> > 12 Hydropotes_inermis   162.   48.5
> > 13 Hyemoschus_aquaticus 122.   20.1
> > 14 Elaphodus_cephalophus186.   17.3
> >

Re: [R-sig-phylo] phyl.RMA error

2020-06-09 Thread Ted Stankowich
Thank you Liam and Ted! 
That worked. I've never named my data columns this way and when I call 
names(Data), it does give me the column names "Binomial", "Skull", and "Tusk". 
This method appears to pull out the vectors and use them outside of the 
original dataframe, is this a particular requirement/feature of phyl.RMA?

Regarding RMA vs. other methods, this is a study of allometry of tusks and 
antlers. In our first submission of this project we got raked over the coals 
for only using OLS methods so we're doing both OLS and RMA this time around, 
but are struggling to interpret the slope discrepancies between the two methods 
(RMA always returns larger slopes). There is measurement error in our 
independent factor (Skull) since some of those data come from PCA estimates 
based on landmark measures in skulls that were broken/partial (full skull 
length wasn't possible). We'll definitely look at the paper Ted posted though. 
There appears to be some strong divergent methodological opinions among the 
allometry community though, so it's hard to know the best way to proceed!

Thanks!
-Ted



-Original Message-
From: Liam J. Revell [mailto:liam.rev...@umb.edu] 
Sent: Tuesday, June 9, 2020 1:07 PM
To: Ted Stankowich ; r-sig-phylo@r-project.org
Subject: Re: [R-sig-phylo] phyl.RMA error

CAUTION: This email was sent from an external source. Use caution when 
replying, opening links or attachments.


Hi Ted.

It's a good bet that your input vectors, log(Skull) and log(Tusk), don't have 
names.

In your case, if your data frame is called Data, you might first compute:

ln.Skull<-setNames(log(Data$Skull),Data$Binomial)
ln.Tusk<-setNames(log(Data$Tusk),Data$Binomial)

and then run:

Model<-phyl.RMA(ln.Skull,ln.Tusk,tree,h0=1.0)
Model
plot(Model) ## this is kind of cool.

Note, that as pointed out in the documentation of the function: "some 
statistician think there is never a condition in which a reduced-major-axis 
regression should be used" (I believe this has even been discussed on this 
list); and "The statistical hypothesis testing is based on Clarke (1980; 
reviewed in McArdle 1988), which differs from some other implementations of 
non-phylogenetic major axis regression in R."

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 6/8/2020 4:18 PM, Ted Stankowich wrote:
> [EXTERNAL SENDER]
>
> Hello,
>
> We're trying to run phylogenetically corrected reduced major axes regression 
> analyses and have encountered an error we can't debug. We're using the 
> function phyl.RMA in the package 'phytools'. Here is the code we are using 
> and the error it returns.
>
>
>
>> Model <- phyl.RMA(log(Skull), log(Tusk), tree, h0=1.0)
>
> Error in if (sign(beta1) != sign(h0)) { :
>
>missing value where TRUE/FALSE needed
>
> We can't seem to figure out which argument is missing, and we've tried 
> including all of the T/F based arguments we think are possible. Our species 
> dataset and nexus file are printed below.  Any advice would be greatly 
> appreciated.
>
> We have the following dataset:
> Binomial Skull  Tusk
>  
> 1 Tragulus_javanicus93.7  14.6
> 2 Tragulus_kanchil  99.7  13.9
> 3 Tragulus_napu 98.1  11.1
> 4 Tragulus_nigricans99.8  13.2
> 5 Moschiola_meminna101.   14.6
> 6 Moschus_berezovskii  134.   55.0
> 7 Moschus_moschiferus  152.   52.9
> 8 Muntiacus_muntjak193.   26.4
> 9 Muntiacus_reevesi159.   23.4
> 10 Muntiacus_truongsonensis 184.   27.7
> 11 Muntiacus_vaginalis  203.   28.6
> 12 Hydropotes_inermis   162.   48.5
> 13 Hyemoschus_aquaticus 122.   20.1
> 14 Elaphodus_cephalophus186.   17.3
>
> And the following nexus tree:
>
> #NEXUS
> [R-package APE, Mon Jun 08 12:20:01 2020]
>
> BEGIN TAXA;
>DIMENSIONS NTAX = 12;
>TAXLABELS
>   Tragulus_napu
>   Tragulus_kanchil
>   Tragulus_javanicus
>   Hyemoschus_aquaticus
>   Moschiola_meminna
>   Muntiacus_reevesi
>   Muntiacus_muntjak
>   Muntiacus_truongsonensis
>   Elaphodus_cephalophus
>   Hydropotes_inermis
>   Moschus_moschiferus
>  

Re: [R-sig-phylo] phyl.RMA error

2020-06-09 Thread Liam J. Revell

Hi Ted.

It's a good bet that your input vectors, log(Skull) and log(Tusk), don't 
have names.


In your case, if your data frame is called Data, you might first compute:

ln.Skull<-setNames(log(Data$Skull),Data$Binomial)
ln.Tusk<-setNames(log(Data$Tusk),Data$Binomial)

and then run:

Model<-phyl.RMA(ln.Skull,ln.Tusk,tree,h0=1.0)
Model
plot(Model) ## this is kind of cool.

Note, that as pointed out in the documentation of the function: "some 
statistician think there is never a condition in which a 
reduced-major-axis regression should be used" (I believe this has even 
been discussed on this list); and "The statistical hypothesis testing is 
based on Clarke (1980; reviewed in McArdle 1988), which differs from 
some other implementations of non-phylogenetic major axis regression in R."


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 6/8/2020 4:18 PM, Ted Stankowich wrote:

[EXTERNAL SENDER]

Hello,

We're trying to run phylogenetically corrected reduced major axes regression 
analyses and have encountered an error we can't debug. We're using the function 
phyl.RMA in the package 'phytools'. Here is the code we are using and the error 
it returns.




Model <- phyl.RMA(log(Skull), log(Tusk), tree, h0=1.0)


Error in if (sign(beta1) != sign(h0)) { :

   missing value where TRUE/FALSE needed

We can't seem to figure out which argument is missing, and we've tried 
including all of the T/F based arguments we think are possible. Our species 
dataset and nexus file are printed below.  Any advice would be greatly 
appreciated.

We have the following dataset:
Binomial Skull  Tusk
 
1 Tragulus_javanicus93.7  14.6
2 Tragulus_kanchil  99.7  13.9
3 Tragulus_napu 98.1  11.1
4 Tragulus_nigricans99.8  13.2
5 Moschiola_meminna101.   14.6
6 Moschus_berezovskii  134.   55.0
7 Moschus_moschiferus  152.   52.9
8 Muntiacus_muntjak193.   26.4
9 Muntiacus_reevesi159.   23.4
10 Muntiacus_truongsonensis 184.   27.7
11 Muntiacus_vaginalis  203.   28.6
12 Hydropotes_inermis   162.   48.5
13 Hyemoschus_aquaticus 122.   20.1
14 Elaphodus_cephalophus186.   17.3

And the following nexus tree:

#NEXUS
[R-package APE, Mon Jun 08 12:20:01 2020]

BEGIN TAXA;
   DIMENSIONS NTAX = 12;
   TAXLABELS
  Tragulus_napu
  Tragulus_kanchil
  Tragulus_javanicus
  Hyemoschus_aquaticus
  Moschiola_meminna
  Muntiacus_reevesi
  Muntiacus_muntjak
  Muntiacus_truongsonensis
  Elaphodus_cephalophus
  Hydropotes_inermis
  Moschus_moschiferus
  Moschus_berezovskii
   ;
END;
BEGIN TREES;
   TRANSLATE
  1Tragulus_napu,
  2Tragulus_kanchil,
  3Tragulus_javanicus,
  4Hyemoschus_aquaticus,
  5Moschiola_meminna,
  6Muntiacus_reevesi,
  7Muntiacus_muntjak,
  8Muntiacus_truongsonensis,
  9Elaphodus_cephalophus,
  10  Hydropotes_inermis,
  11  Moschus_moschiferus,
  12  Moschus_berezovskii
   ;
   TREE * UNTITLED = [] 
1:5.540957781,(2:2.978817423,3:2.978817423):2.562139698):10.78911152,4:16.33006601):6.360692368,5:22.69076035):5.725388419,(6:1.611149584,7:1.611149848):1.556474893,8:3.167624477):4.130280196,9:7.297904013):1.497063399,10:8.794967413):7.19682079,(11:2.539095678,12:2.539096008):13.45269085):12.42436025);



Dr. Ted Stankowich
Associate Professor
Department of Biological Sciences
California State University Long Beach
Long Beach, CA 90840
theodore.stankow...@csulb.edu
562-985-4826
https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.csulb.edu%2Fmammal-lab%2Fdata=02%7C01%7Cliam.revell%40umb.edu%7C5a74928c910446b96b1508d80caf5765%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637273294515730787sdata=7FUGnuFJCdRHmPiVrWPPAu%2BLEyK6O%2B4VyAKHz1n63qw%3Dreserved=0
@CSULBMammalLab



Dr. Ted Stankowich
Associate Professor
Department of 

[R-sig-phylo] phyl.RMA error

2020-06-09 Thread Ted Stankowich
Hello,

We're trying to run phylogenetically corrected reduced major axes regression 
analyses and have encountered an error we can't debug. We're using the function 
phyl.RMA in the package 'phytools'. Here is the code we are using and the error 
it returns.



>Model <- phyl.RMA(log(Skull), log(Tusk), tree, h0=1.0)

Error in if (sign(beta1) != sign(h0)) { :

  missing value where TRUE/FALSE needed

We can't seem to figure out which argument is missing, and we've tried 
including all of the T/F based arguments we think are possible. Our species 
dataset and nexus file are printed below.  Any advice would be greatly 
appreciated.

We have the following dataset:
Binomial Skull  Tusk

1 Tragulus_javanicus93.7  14.6
2 Tragulus_kanchil  99.7  13.9
3 Tragulus_napu 98.1  11.1
4 Tragulus_nigricans99.8  13.2
5 Moschiola_meminna101.   14.6
6 Moschus_berezovskii  134.   55.0
7 Moschus_moschiferus  152.   52.9
8 Muntiacus_muntjak193.   26.4
9 Muntiacus_reevesi159.   23.4
10 Muntiacus_truongsonensis 184.   27.7
11 Muntiacus_vaginalis  203.   28.6
12 Hydropotes_inermis   162.   48.5
13 Hyemoschus_aquaticus 122.   20.1
14 Elaphodus_cephalophus186.   17.3

And the following nexus tree:

#NEXUS
[R-package APE, Mon Jun 08 12:20:01 2020]

BEGIN TAXA;
  DIMENSIONS NTAX = 12;
  TAXLABELS
 Tragulus_napu
 Tragulus_kanchil
 Tragulus_javanicus
 Hyemoschus_aquaticus
 Moschiola_meminna
 Muntiacus_reevesi
 Muntiacus_muntjak
 Muntiacus_truongsonensis
 Elaphodus_cephalophus
 Hydropotes_inermis
 Moschus_moschiferus
 Moschus_berezovskii
  ;
END;
BEGIN TREES;
  TRANSLATE
 1Tragulus_napu,
 2Tragulus_kanchil,
 3Tragulus_javanicus,
 4Hyemoschus_aquaticus,
 5Moschiola_meminna,
 6Muntiacus_reevesi,
 7Muntiacus_muntjak,
 8Muntiacus_truongsonensis,
 9Elaphodus_cephalophus,
 10  Hydropotes_inermis,
 11  Moschus_moschiferus,
 12  Moschus_berezovskii
  ;
  TREE * UNTITLED = [] 
1:5.540957781,(2:2.978817423,3:2.978817423):2.562139698):10.78911152,4:16.33006601):6.360692368,5:22.69076035):5.725388419,(6:1.611149584,7:1.611149848):1.556474893,8:3.167624477):4.130280196,9:7.297904013):1.497063399,10:8.794967413):7.19682079,(11:2.539095678,12:2.539096008):13.45269085):12.42436025);



Dr. Ted Stankowich
Associate Professor
Department of Biological Sciences
California State University Long Beach
Long Beach, CA 90840
theodore.stankow...@csulb.edu
562-985-4826
http://www.csulb.edu/mammal-lab/
@CSULBMammalLab



Dr. Ted Stankowich
Associate Professor
Department of Biological Sciences
California State University Long Beach
Long Beach, CA 90840
theodore.stankow...@csulb.edu
562-985-4826
http://www.csulb.edu/mammal-lab/
@CSULBMammalLab




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