gg_survival with 'by' handles factors with NA incorrectly when occurring before other levels

[daniellemccool]

I don't have a good minimal working example or anything, but I'm going to try my best to describe what's going on.

After calling gg_survival with either type "kaplan" or type "nelson" and supplying a factor for 'by', survfit with strata on 'by' is called. The default is na.group = FALSE, so it stratifies only on the other levels of the factor.

A little further down in the code, we have this bit:

  if(!is.null(by)){
    tm_splits <- which(c(FALSE,sapply(2:nrow(tbl), function(ind){tbl$time[ind] < tbl$time[ind - 1]})))

    lbls <- unique(data[,by])
    tbl$groups <- lbls[1]

    for(ind in 2:(length(tm_splits) + 1)){
      tbl$groups[tm_splits[ind - 1]:nrow(tbl)] <- lbls[ind]
    }
  }

Unique also returns 'NA' as an option, but NA was not included as a stratum level, so if you have a situation where NA occurs before at least one of your levels, it will take its place and you'll drop a factor level you potentially cared about.

I solved it myself by editing in na.group = TRUE to the call to strata in the kaplan and nelson functions because I wanted that information anyway, but I guess this might be something encountered by others as well!

[ehrlinger]

If I understand this correctly, I'll need to:

add a na.group argument to the gg_survival.
Set na.group correctly in the strata call
adjust the unique call to include or not NA

I'll take a look at this more soon.