[R] writing a function to work with dplyr::mutate()

[Bert Gunter]

If you are willing to entertain another approach, have a look at ?cut. By
defining the 'breaks' argument appropriately, you can easily create a
factor that tells you which values should be looked up and which accepted
as is. If I understand correctly, this seems to be what you want. If I have
not, just ignore and wait for a more useful reply.

Cheers,
Bert

Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Tue, Jan 19, 2021 at 10:24 AM Steven Rigatti <sjrigatti using gmail.com> wrote:

> I am having some problems with what seems like a pretty simple issue. I
> have some data where I want to convert numbers. Specifically, this is
> cancer data and the size of tumors is encoded using millimeter
> measurements. However, if the actual measurement is not available the
> coding may imply a less specific range of sizes. For instance numbers 0-89
> may indicate size in mm, but 90 indicates "greater than 90 mm" , 91
> indicates "1 to 2 cm", etc. So, I want to translate 91 to 90, 92 to 15,
> etc.
>
> I have many such tables so I would like to be able to write a function
> which takes as input a threshold over which new values need to be looked
> up, and the new lookup table, returning the new values.
>
> I successfully wrote the function:
>
> translate_seer_numeric <- function(var, upper, lookup) {
>     names(lookup) <- c('old','new')
>     names(var) <- 'old'
>     var <- as.data.frame(var)
>     lookup2 <- data.frame(old = c(1:upper),
>                           new = c(1:upper))
>     lookup3 <- rbind(lookup, lookup2)
>  print(var)
>     res <- left_join(var, lookup3, by = 'old') %>%
>          select(new)
>
>     res
>
> }
>
> test1 <- data.frame(old = c(99,95,93, 8))lup <- data.frame(bif = c(93, 95,
> 99),
>                   new = c(3, 5, NA))
> translate_seer_numeric(test1, 90, lup)
>
> The above test generates the desired output:
>
>   old1  992  953  934   8
>   new1  NA2   53   34   8
>
> My problem comes when I try to put this in line with pipes and the mutate
> function:
>
> test1 %>%
>      mutate(varb = translate_seer_numeric(var = old, 90, lup))####
>  Error: Problem with `mutate()` input `varb`.
> x Join columns must be present in data.
> x Problem with `old`.
> i Input `varb` is `translate_seer_numeric(var = test1$old, 90, lup)`.
>
> Thoughts??
>
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>
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