Dear all I got stuck using mvrs in ape3.4, running into the following error message:
> ph <- mvrs(ds, vs, fs = 15) *Error in mvrs(ds, vs, fs = 15) : * * distance information insufficient to construct a tree, leaves 805 and 806 isolated from tree* I would be prepared to drop a few taxa if this means that mvrs runs to completion. But I am not sure which taxa to delete, the problem persists if rows 805, 806 are deleted from my distance matrix. Does someone know of a workaround? Alternatively, is there another tree reconstruction algorithm that can also make use of the information provided through a variance matrix? I may not be aware of all options. I should add that the following works fine > njs(ds, fs = 15) but I would really want to use the variance matrix too because some of the distances are estimated from short regions where the corresponding two sequences overlap, and are therefore much less reliable than others. Thank you in advance Oliver To reproduce: The ds and vs matrix can be collected here within the next 3 weeks, size is 33MB: https://fileexchange.imperial.ac.uk/ Claim ID: aHyXuXHmf8tVXyEa Claim Passcode: GefSka7PbmyeoE2c load("mvrs_inputs.rda") na.rm.p <- 0.1 diag(d) <- NA_real_ diag(v) <- NA_real_ # remove cols/rows that contain nothing else than NAs tmp <- apply(d, 1, function(x) !all(is.na(x))) cat('\nIn D: found',length(which(!tmp)),'columns / rows with NA only: remove in D and V. ', rownames(d)[!tmp]) ds <- d[tmp,tmp] vs <- v[tmp,tmp] tmp <- apply(vs, 1, function(x) !all(is.na(x))) cat('\nIn V: found additional',length(which(!tmp)),'columns / rows with NA only: remove in D and V too. ', rownames(d)[!tmp]) ds <- ds[tmp,tmp] vs <- vs[tmp,tmp] # remove cols/rows that contain more than 10% NAs tmp <- apply(ds, 1, function(x) length(which(is.na(x))) ) / ncol(ds) tmp <- which(tmp>na.rm.p) cat('\nIn D: found',length(tmp),'columns / rows with more than',na.rm.p*100,'% NAs: remove in D and V. ', rownames(ds)[tmp]) ds <- ds[-tmp,-tmp] vs <- vs[-tmp,-tmp] ph<- mvrs(ds, vs, fs = 15) -- Oliver Ratmann Research fellow Dep Infectious Disease Epidemiology Imperial College London, St Mary's Campus Norfolk Place, London W2 1PG UK [[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/
