phyl.RMA error

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phyl.RMA error

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
   <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
[hidden email]<mailto:[hidden email]>
562-985-4826
http://www.csulb.edu/mammal-lab/
@CSULBMammalLab




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Re: phyl.RMA error

Bert Gunter-2
Do you have NA's or Infs in your beta1 due to the use of log(Skull) and
log(Tusk) in your modeling or did you misspell something?.

If it's not something "obvious" like that, you should probably post on the
r-sig-ecology list instead, where you are more likely to find both the
interest and expertise in this specialized topic. This list is for general
R language questions primarily.

Cheers,
Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Mon, Jun 8, 2020 at 12:28 PM Ted Stankowich <
[hidden email]> wrote:

> 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
> [hidden email]<mailto:[hidden email]>
> 562-985-4826
> http://www.csulb.edu/mammal-lab/
> @CSULBMammalLab
>
>
>
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.