On 1/19/21 7:50 AM, Steven Rigatti 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),
This throws an error when copy-pasted, since you posted in html and
there was no line separator.
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))####
#Added:
library(tidyverse) # since many people on rhelp are not particularly
"tidy".
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)`.
I think I got useful results with this although you might need to
extract the "new" column from the dataframe result.
test1 %>% mutate(varb = translate_seer_numeric( . , 90, lup))
#----------
old
1 99
2 95
3 93
4 8
old new
1 99 NA
2 95 5
3 93 3
4 8 8
When you want to refer to the prior result in a piped chain you use a
dot ("."). I'm guessing you know this. But what I saw was that your
successful test case was using a dataframe as the input to the first
parameter of translate_seer_numeric, but you were apparently passing a
column name when it was being used in a pipe.
The error message wasn't particularly helpful to me, but maybe that's
because I don't have enough experience in that non-standard universe. It
did tell us that the there was a problem with "varb" and that was
probably because that was the wrong parameter name. However even
changing the call to just `var=old` would probably have failed as well
because you didn't write the function to accept a variable name as the
first parameter.
Best;
David.
Thoughts??
[[alternative HTML version deleted]]
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