Remove NA when using "order"

The na.last argument to order only removes NA from the objects passed to order via .... Your NA are in aa$precipitation, not aa$year, aa$month, or aa$day, so you need:

dat <- na.omit(aa[order(aa$year, aa$month, aa$day),])

You may want to consider using a time-series class like zoo or xts for time-series data.

Because na.last is to see if NA should be last of first when ordering not to remove the NA. Use na.omit(dat) to remove the NA.

Hope that helps.