plotGMPhyloMorphoSpace-> Error in svd(x, nu = 0, nv = k) : infinite or missing values in 'x'

[cshobbs]

Hiya,

I've been trying to resolve this issue for a couple of days now, and I have absolutely no idea what I'm doing wrong and would really appreciate your assistance if possible!

I'm trying to use the function plotGMPhyloMorphoSpace with a landmark dataset of 42 individuals with 13 landmarks from two species, with a tree with the same 42 individuals.

When I first ran the analysis I got the error:
Error in plotGMPhyloMorphoSpace(phy = crassula_uniplicata_tree, A = crassula_uniplicata_gpa) :
tree is not fully bifurcating (consider 'multi2di' in ape.

Ran multi2di in ape, and now the phy file is binary. However when I run the analysis it now comes up with the error "Error in svd(x, nu = 0, nv = k) : infinite or missing values in 'x". I used the original tree and the bifurcating tree both in the physignal function and it works.

My tree is:

crassula_uniplicata_bifurcating_tree

Phylogenetic tree with 42 tips and 41 internal nodes.

Tip labels:
HLS21122_crassula, HLS21125_crassula, HLS21133_crassula, HLS20698_uniplicata, HLS20692_uniplicata, HLS20704_uniplicata, ...

Rooted; includes branch lengths

I've checked through some of the normal issues, such as names not matching up, and used the match function to check this

match(crassula_uniplicata_bifurcating_tree$tip.label,tpsnames)
[1] 32 34 38 20 16 23 19 3 4 28 17 22 25 24 35 33 18 21 41 42 1 2 15 26 5 8 36 37 9 6 7 10 14 12 11 13 29 27 30
[40] 39 31 40

Any help you can give me on this would be greatly appreciated.

Best wishes,

Chris

[antkal]

Chris, this is difficult to diagnose without looking at the data, but is crassula_uniplicata_gpa the matrix of coordinates, or the full gpa result? If the second, try $coords there. Antigoni

…

On 22/05/2020 01:15, cshobbs wrote: Hiya, I've been trying to resolve this issue for a couple of days now, and I have absolutely no idea what I'm doing wrong and would really appreciate your assistance if possible! I'm trying to use the function plotGMPhyloMorphoSpace with a landmark dataset of 42 individuals with 13 landmarks from two species, with a tree with the same 42 individuals. When I first ran the analysis I got the error: Error in plotGMPhyloMorphoSpace(phy = crassula_uniplicata_tree, A = crassula_uniplicata_gpa) : tree is not fully bifurcating (consider 'multi2di' in ape. Ran multi2di in ape, and now the phy file is binary. However when I run the analysis it now comes up with the error "object 'x' not found". I used the original tree and the bifurcating tree both in the physignal function and it works. My tree is: crassula_uniplicata_bifurcating_tree Phylogenetic tree with 42 tips and 41 internal nodes. Tip labels: HLS21122_crassula, HLS21125_crassula, HLS21133_crassula, HLS20698_uniplicata, HLS20692_uniplicata, HLS20704_uniplicata, ... Rooted; includes branch lengths I've checked through some of the normal issues, such as names not matching up, and used the match function to check this match(crassula_uniplicata_bifurcating_tree$tip.label,tpsnames) [1] 32 34 38 20 16 23 19 3 4 28 17 22 25 24 35 33 18 21 41 42 1 2 15 26 5 8 36 37 9 6 7 10 14 12 11 13 29 27 30 [40] 39 31 40 Any help you can give me on this would be greatly appreciated. Best wishes, Chris — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#28>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEVLB7MBP2U6NQBQANBDUJ3RSW7ZNANCNFSM4NHKLL4Q>.Web Bug from https://github.com/notifications/beacon/AEVLB7PHKQRXXHOP7HQLDM3RSW7ZNA5CNFSM4NHKLL42YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4JJAFPIA.gif [ { ***@***.***": "http://schema.org", ***@***.***": "EmailMessage", "potentialAction": { ***@***.***": "ViewAction", "target": "#28", "url": "#28", "name": "View Issue" }, "description": "View this Issue on GitHub", "publisher": { ***@***.***": "Organization", "name": "GitHub", "url": "https://github.com" } } ]

-- Antigoni Kaliontzopoulou Auxiliary Researcher CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos University of Porto Campus Agrário de Vairão, 4485-661 Vairão PORTUGAL https://sites.google.com/view/akaliontzopoulou/home https://cibio.up.pt/research-groups-1/details/phenevol http://cibio.up.pt/people/details/akaliont http://www.seh-herpetology.org/

[cshobbs]

Hi Antigoni,

Thank you so much for your quick reply!
Unfortunately I am using $coords and it's still not working.
Please find attached my data and script, if you have a chance to see if there are any glaring errors I've made that could be stopping this from working I'd greatly appreciate it!

Troubleshooting Data.zip

[antkal]

The issue here is the tree, and the fact that while it is not rooted and bifurcating, you are resolving it, which results in some branches having zero length. For illustration try making a random tree as such: tr <- rtree(42, tip.label = crassula_uniplicata_bifurcating_tree$tip.label) plotGMPhyloMorphoSpace(phy=tr, A=crassula_uniplicata_gpa$coords) Works fine. So the issue is the tree, which means I can´t be of much help there. You need to obtain a fully resolved tree, or somehow (arbitrarily) give (maybe very small) values to all branch lengths. Antigoni

…

On 22/05/2020 17:15, cshobbs wrote: Hi Antigoni, Thank you so much for your quick reply! Unfortunately I am using $coords and it's still not working. Please find attached my data and script, if you have a chance to see if there are any glaring errors I've made that could be stopping this from working I'd greatly appreciate it! Troubleshooting Data.zip <https://github.com/geomorphR/geomorph/files/4669199/Troubleshooting.Data.zip> — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#28 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEVLB7LPNLDDIGM4Q6SUCADRS2QI3ANCNFSM4NHKLL4Q>.Web Bug from https://github.com/notifications/beacon/AEVLB7PKNNV6ZD4QVDSBRXTRS2QI3A5CNFSM4NHKLL42YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEW3WBRY.gif [ { ***@***.***": "http://schema.org", ***@***.***": "EmailMessage", "potentialAction": { ***@***.***": "ViewAction", "target": "#28 (comment)","url": "#28 (comment)", "name": "View Issue" }, "description": "View this Issue on GitHub", "publisher": { ***@***.***": "Organization", "name": "GitHub", "url": "https://github.com" } } ]

-- Antigoni Kaliontzopoulou Auxiliary Researcher CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos University of Porto Campus Agrário de Vairão, 4485-661 Vairão PORTUGAL https://sites.google.com/view/akaliontzopoulou/home https://cibio.up.pt/research-groups-1/details/phenevol http://cibio.up.pt/people/details/akaliont http://www.seh-herpetology.org/

[cshobbs]

Hi Antigoni,

Thank you so much for looking at the data and working out what was wrong, I really appreciate it!