Errors when using infer_multittree_share_param

[lingxuan85511]

Dear author,

I am usig infer_multittree_share_param (TransPhylo v1.4.10) to infer the parameters of transmission chain with my data. I found this function performed well when the dataset is not big. However, error occurred when I used a big dataset(>3000 tips). I have no idea how to solve this problem. Do you have any suggestions? The script and error information was as follow:

library(ape) library(TransPhylo) library(coda) packageVersion("TransPhylo") [1] ‘1.4.10’ tree1<-multi2di(read.nexus("timetree_21.nexus")) tree1$edge.length[tree1$edge.length<=0]<-0.1/365 tree1$edge.length<-tree1$edge.length*365 ptree1<-ptreeFromPhylo(tree1,dateLastSample=60)

tree2<-multi2di(read.nexus("timetree_36.nexus")) tree2$edge.length[tree2$edge.length<=0]<-0.1/365 tree2$edge.length<-tree2$edge.length*365 ptree2<-ptreeFromPhylo(tree2,dateLastSample=60)

ptrees<-list(ptree1,ptree2) w.shape<-2.892313 w.scale<-2.938824 dateT<-61 record<-infer_multittree_share_param(ptrees,mcmcIterations=1000000,thinning=100,w.shape=w.shape,w.scale=w.scale,updateNeg=T,updateOff.p=T,dateT=dateT,share=c("off.r","off.p","pi"),delta_t=1)

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| | 0%Error in if (log(runif(1)) < sum(pTTree2) - sum(pTTree)) { : missing value where TRUE/FALSE needed Calls: infer_multittree_share_param ... with -> with.default -> eval -> eval -> one_update_share Execution halted

[xavierdidelot]

Does it work if you use only ptree1 or ptree2?

[lingxuan85511]

Yese, when using inferTTree function with each tree, the program is running correctly.

[xavierdidelot]

Ok, in that case the problem is specific to the infer_multitree_share_param that was written by Yuanwei Xu. I don't think he monitors the issues on this repository though, so you should probably try to contact him directly using his email address provided in the DESCRIPTION file.

[lingxuan85511]

Thank you for your kindly help. I will directly contact him via email.