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
<chr> <dbl> <dbl>
1 Tragulus_javanicus 93.7 14.6
2 Tragulus_kanchil 99.7 13.9
3 Tragulus_napu 98.1 11.1
4 Tragulus_nigricans 99.8 13.2
5 Moschiola_meminna 101. 14.6
6 Moschus_berezovskii 134. 55.0
7 Moschus_moschiferus 152. 52.9
8 Muntiacus_muntjak 193. 26.4
9 Muntiacus_reevesi 159. 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_cephalophus 186. 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
1 Tragulus_napu,
2 Tragulus_kanchil,
3 Tragulus_javanicus,
4 Hyemoschus_aquaticus,
5 Moschiola_meminna,
6 Muntiacus_reevesi,
7 Muntiacus_muntjak,
8 Muntiacus_truongsonensis,
9 Elaphodus_cephalophus,
10 Hydropotes_inermis,
11 Moschus_moschiferus,
12 Moschus_berezovskii
;
TREE * UNTITLED = [&R]
((((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<mailto:theodore.stankow...@csulb.edu>
562-985-4826
https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.csulb.edu%2Fmammal-lab%2F&data=02%7C01%7Cliam.revell%40umb.edu%7C5a74928c910446b96b1508d80caf5765%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637273294515730787&sdata=7FUGnuFJCdRHmPiVrWPPAu%2BLEyK6O%2B4VyAKHz1n63qw%3D&reserved=0
@CSULBMammalLab
Dr. Ted Stankowich
Associate Professor
Department of Biological Sciences
California State University Long Beach
Long Beach, CA 90840
theodore.stankow...@csulb.edu<mailto:theodore.stankow...@csulb.edu>
562-985-4826
https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.csulb.edu%2Fmammal-lab%2F&data=02%7C01%7Cliam.revell%40umb.edu%7C5a74928c910446b96b1508d80caf5765%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637273294515730787&sdata=7FUGnuFJCdRHmPiVrWPPAu%2BLEyK6O%2B4VyAKHz1n63qw%3D&reserved=0
@CSULBMammalLab
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