Hey Liam, Thanks alot! I really appreciate it! I installed the new version and I saw your edits to the locate.fossil function on github.
I just have one more question, I am new to the tol argument and I am not sure what the default should be set to. I've set it to a couple numbers (ex, 0.5, 0.1 0.01) and my fossil now places correctly but could you possibly tell me what this argument means and what I should be setting it to? Best, Lindsey On Tue, Jan 10, 2023 at 6:07 PM Liam J. Revell <liam.rev...@umb.edu> wrote: > Dear Lindsey. > > Thanks for sharing the code & data. It made the problem pretty easy to > resolve. > > Turns out it is a simple numerical precision issue. > > I have resolved it by adding an optional argument tol with a sensible > default value which most users can probably ignore (but can set to tol=0 > if they want to guarantee the current behavior of locate.fossil). I > pushed this update to *GitHub*: > https://github.com/liamrevell/phytools/commit/f1dcddbf56a7ae6bf9bece223cd6a949a57eac5f > . > > To obtain this updated version of *phytools* I recommend installing the > package *remotes* and then running (from a fresh R session): > > remotes::install_github("liamrevell/phytools") > > Let us know if this fixes everything! > > All the best, Liam > Liam J. Revell > Professor of Biology, University of Massachusetts Boston > Web: http://faculty.umb.edu/liam.revell/ > > > On 1/10/2023 4:42 PM, Lindsey Dehaan wrote: > > CAUTION: EXTERNAL SENDER > Hey Liam, > > Thanks for the fast response. > > Attached is a simple script with the fossil I am having problems with. All > the files should be attached. Let me know if I missed a file or you need > anything else. > > I greatly appreciate your help on this. I have been stuck on this for a > while now. > > Best, > Lindsey > > > On Tue, Jan 10, 2023 at 4:23 PM Liam J. Revell <liam.rev...@umb.edu> > wrote: > >> Dear Lindsey. >> >> Thanks for posting your code, but would you mind sending me (it can be >> off-list) an example in which I can also pull your data & tree and re-run >> it with the real data that is generating the error? This might be helpful >> in getting to the bottom of your issue. Thanks! >> >> All the best, Liam >> Liam J. Revell >> Professor of Biology, University of Massachusetts Boston >> Web: http://faculty.umb.edu/liam.revell/ >> <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Ffaculty.umb.edu%2Fliam.revell%2F&data=05%7C01%7Cliam.revell%40umb.edu%7C9a241369fe2542ce1c0408daf3538a5b%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C638089837406791068%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Wb5zlO%2B26s185WebtNT7rh0o1w1yy0KAJg%2BzTBsycNQ%3D&reserved=0> >> >> >> On 1/10/2023 4:20 PM, Lindsey Dehaan wrote: >> >> CAUTION: EXTERNAL SENDER >> >> Hi all, >> >> I have a question regarding the phytools function locate.fossil(). >> >> I have had a lot of success with this function but there are two fossils of >> mine that the function does not like. I give the function my phylogeny, a >> max and min age for the fossil, and the edge for the fossil to be placed >> on. So I basically just want the function to estimate the branch length >> subtending the fossil and the position of where the node subtending the >> fossil attaches in the phylogeny. >> >> For two of my fossils I get the following error. >> >> >> >> *Error in bind.tree(tree, tip, where = where, position = pp) : 'position' >> is larger than the branch length* >> >> The function does not seem to like my edge constraint with these two >> fossils. When I remove my edge constraint it works and the fossil is placed >> in the correct time interval but just on a different edge estimated using >> ML. For one of my fossils, the edge I place my fossil on ranges from 42 mya >> to 4 mya and the age range for the fossil is between 33 and 28 mya. I am >> confused why the function does not like the edge constraints I am giving >> it. The error that I receive makes me believe that the position the >> function is estimating for my fossil may be older than the edge constraint >> I am giving it or I could just be missing something, most likely the >> latter... >> >> Below is my code. This code works for almost all my fossils except for two >> of them. >> >> >> >> >> >> >> >> >> >> >> >> *fossil_to_add<-fossil_trait_data[13,] locate_fossil_data<-rbind(extant_data, >> fossil_to_add) # used this data in >> locate.fossil()extant_sister_clade<-rownames(extant_data)[c(grep(fossil_info[13,7], >> rownames(extant_data)), grep(fossil_info[13,8], >> rownames(extant_data)))]mrca<-getMRCA(tree, >> extant_sister_clade)edge<-mrcamin_time<- depth - fossil_info[13,4] # depth >> is the root age of the phylogeny max_time<-depth - fossil_info[13,3] # the >> max and min ages are positive numbers time_constraints<-c(max_time, >> min_time)locate_fossil_tree<-locate.fossil(tree, locate_fossil_data, >> time.constraint=time_constraints,edge.constraint=edge, plot=TRUE)* >> >> Any help or advice, would be greatly appreciated! >> >> Best, >> Lindsey >> -- >> Lindsey DeHaan >> Ph.D. Candidate >> Department of Earth and Environmental Sciences >> University of Michigan >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> R-sig-phylo mailing list - >> R-sig-phylo@r-project.orghttps://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylo&data=05%7C01%7Cliam.revell%40umb.edu%7C27cb8a8eb3dc4651433008daf35090b6%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C638089824617167715%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=tYwyCJW%2BdLBEpy4Tn290%2BXqmQNkV6%2FdGGsJmgnBXUcU%3D&reserved=0 >> >> <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylo&data=05%7C01%7Cliam.revell%40umb.edu%7C9a241369fe2542ce1c0408daf3538a5b%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C638089837406791068%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=OQZ4%2BfVRV4djYAuL2ykJRNHnZybQt6b827hgLycCu%2BQ%3D&reserved=0> >> Searchable archive at >> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2F&data=05%7C01%7Cliam.revell%40umb.edu%7C27cb8a8eb3dc4651433008daf35090b6%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C638089824617167715%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=AGbpdEbfZDhgeTNHnQsgzRkj2%2FngM5Ud%2FCDVEFDCvnw%3D&reserved=0 >> >> <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2F&data=05%7C01%7Cliam.revell%40umb.edu%7C9a241369fe2542ce1c0408daf3538a5b%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C638089837406791068%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=gJDnbSmyuBEJy5cohhnDHP62kyrbpM1Yag6GjzzrPn4%3D&reserved=0> >> >> > > -- > Lindsey DeHaan > Ph.D. Candidate > Department of Earth and Environmental Sciences > University of Michigan > > -- Lindsey DeHaan Ph.D. Candidate Department of Earth and Environmental Sciences University of Michigan [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
