Code working in RStudio but not quarto

[jimmy_squids]

Hi all.. I am doing an survival analysis, and the code works fine in RStudio, but when copying it into Quarto, I get the following error message:

"Quitting from lines 480-491 [quartiles] (report.qmd)
Error in cut.default():
! 'x' must be numeric
Backtrace:

1. base::cut(...)
2. base::cut.default(...)
   Execution halted

The code is as follows:

data$quartiles <- cut(data$mean_treatment_time_hours,
breaks = quantile(data$mean_treatment_time_hours,
probs = c(0, 1/4, 2/4, 3/4, 1), na.rm = TRUE),
labels = c("Quartile 1", "Quartile 2", "Quartile 3", "Quartile 4"),
include.lowest = TRUE)

quartilenames <- c("Quartile 1", "Quartile 2", "Quartile 3", "Quartile 4")
data$quartiles.fac <- factor(x = data$quartiles, levels = quartilenames, ordered = TRUE)

When I check class(data$mean_treatment_time_hours) - the console returns numeric....

Any ideas? Thanks in advance, Jim

[FJCC]

Did you run class(data$mean_treatment_time_hours) in your Quarto document or in your local RStudio environment? Try it in the document.

[jimmy_squids]

Thanks... I get this:

Warning: Unknown or uninitialised column: `mean_treatment_time_hours`.

[1] "NULL"

[jimmy_squids]

Which is odd as I've been using the same variable previously for tables, plots etc!

[FJCC]

You should be able to use the same class() call in earlier parts of your code to find where you lose the mean_treatment_hours column.

[cderv]

@jimmy_squids if you still have issue, can you share more about your document and formatted correctly ? FAQ: How to Format R Markdown Source