Closed cecileane closed 7 years ago
This is to fix an error, which can be reproduced on this example:
library(l1ou) library(geiger) set.seed(120) ntaxa = 10 tr = rcoal(ntaxa) x = c(rnorm(5, 15, 1), rnorm(5, 15, 1)) # no shift: so shift.configuration=NULL below names(x) = tr$tip.label ll = adjust_data(tr, x, normalize=FALSE) myzero = 0.0 # same error with 1e-16 or smaller. # force alpha=0 below, which does not fit the data, hence numerical instability fo = fit_OU(ll$tree, ll$Y, shift.configuration=NULL, criterion="pBIC", alpha.starting.value=myzero, alpha.upper=myzero, alpha.lower=myzero)
It returns this error with this traceback:
Error in !silent : invalid argument type 8. value[[3L]](cond) 7. tryCatchOne(expr, names, parentenv, handlers[[1L]]) 6. tryCatchList(expr, classes, parentenv, handlers) 5. tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) ... 4. try(phylolm(Y ~ preds - 1, phy = tree, model = opt$root.model, starting.value = s, lower.bound = l, upper.bound = u), silent = opt$quietly) 3. my_phylolm_interface(tr, y, s.c, opt) 2. fit_OU_model(tree, Y, shift.configuration, opt) 1. fit_OU(ll$tree, ll$Y, shift.configuration = NULL, criterion = "pBIC", alpha.starting.value = myzero, alpha.upper = myzero, alpha.lower = myzero)
This is to fix an error, which can be reproduced on this example:
It returns this error with this traceback: