rtt function no longer handles NAs in dates
brj1 opened this issue · comments
The rrt function performs root-to-tip regression on trees. In previous versions, you could put NA in the dates parameter to censor tips from the regression. However, this does not seem to be possible anymore. I can make a PR to fix this, if you want.
Would a line like this:
if (anyNA(tip.dates)) stop("missing values not allowed in 'tip.dates'")at the start of rtt() be enough?
I can add a note in rtt.Rd too.
Could you add the ability to censor tip dates with NAs back? I need this functionality for some of the software that I maintain.
You mean change nothing with respect to the current version?
The problem is an update in R. Consider the following code:
library(ape)
set.seed(0)
tree <- rtree(5)
dates <- c(1, 2, 3, NA, NA)
rtt(tree, dates)In R version 4.2.2 it gives an error:
Error in cor(y, x) : incompatible dimensions
In addition: There were 50 or more warnings (use warnings() to see the first 50)
In R version 4.0.5 it roots the tree.
The issue is that the cor() function changed in the latest version of R so that by default NA are included in he correlation calculation where previously they would be censored.
The fix is fairly simple. Just change line 31 of rtt.R to:
cor(y, x, use = "complete.obs")Fixed and pushed.