ovaskain
commented
3 years ago Hi Bermhard,
I recommend that you download from the Hmsc pages (https://www2.helsinki.fi/en/researchgroups/statistical-ecology/hmsc) the template we used for the past Hmsc course for submitting data for Hmsc analyses: https://www2.helsinki.fi/sites/default/files/atoms/files/hmsc_course_sign_up_material.zip
This includes a script that makes several consistency checks that point out the most usual problems. I would guess that in your case the species names do not match between the phylogeny & the Y-matrix. The script should help to identity if this is the case or if the problem is in something else.
Best,
O2
From: bwegsche @.> Sent: torstai 1. heinäkuuta 2021 13:26 To: hmsc-r/HMSC @.> Cc: Subscribed @.***> Subject: [hmsc-r/HMSC] Birdtree.org phylogenetic trees (#107)
Hello,
I'm working on a joint species distribution model for birds in a Canadian watershed. We have defined a model including YData, XData and TrData following the workflow outlined in the Statistical Ecology website. When I try to include phylogenetic infromation, however, I run into problems.
m = Hmsc(Y=YData, XData = XData, XFormula=XFormula,
· TrData = TrData, TrFormula = TrFormula,phyloTree = phyloTree,
*
· distr="probit", studyDesign=studyDesign,
*
· ranLevels=list(site_id=rL))
*
Error in corM[hM$spNames, hM$spNames] : subscript out of bounds
I assume the species names of the tree and the YData are not matching.
I'm using phylogenetic trees downloaded from the birdtree.org website similar as in the Tikhonov et al (2019) paper. When I compare the format of the phylogenetic tree in the example Rscript from your website to our tree there are some differences. Ours is in the nexus format and includes a list of 100 trees, whereas in the template script there is a single tree in the parenthic format (.tree ending). I tried running our script using a arbitrarily chosen tree (1 out of the 100 tree list) but I only get the error stated above. What was your strategy when you used birdtree.org as a data source and how do I have to format the data to use it in Hmsc? Unfortunately I'm not very familiar working with phylogenetic trees, so any guidance is highly appreciated. Is there an obvious mistake that you can already identify in my description.
Please let me know if you need further information.
Best regards, Bernhard
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bwegsche
andburch
Hello,
I'm working on a joint species distribution model for birds in a Canadian watershed. We have defined a model including YData, XData and TrData following the workflow outlined in the Statistical Ecology website. When I try to include phylogenetic infromation, however, I run into problems.
m = Hmsc(Y=YData, XData = XData, XFormula=XFormula,
I assume the species names of the tree and the YData are not matching.
I'm using phylogenetic trees downloaded from the birdtree.org website similar as in the Tikhonov et al (2019) paper. When I compare the format of the phylogenetic tree in the example Rscript from your website to our tree there are some differences. Ours is in the nexus format and includes a list of 100 trees, whereas in the template script there is a single tree in the parenthic format (.tree ending). I tried running our script using a arbitrarily chosen tree (1 out of the 100 tree list) but I only get the error stated above. What was your strategy when you used birdtree.org as a data source and how do I have to format the data to use it in Hmsc? Unfortunately I'm not very familiar working with phylogenetic trees, so any guidance is highly appreciated. Is there an obvious mistake that you can already identify in my description.
Please let me know if you need further information.
Best regards, Bernhard