Code working in RStudio but not quarto

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

  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

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

Thanks... I get this:

Warning: Unknown or uninitialised column: `mean_treatment_time_hours`.
[1] "NULL"

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

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.

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

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