`to_integer()` removes column `spending_time` from the bound table
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Description
While reviewing #673, I noticed that to_integer() removes the column spending_time from the bound table. Is this a bug? Below is a reprex using the latest commit on main, https://github.com/Merck/gsDesign2/commit/732921e6db24b1fe84b0681d5c4753c679bb91b9:
library("gsDesign2")
x <- gs_design_ahr()
colnames(x$bound)
## [1] "analysis" "bound" "probability" "probability0" "z" "~hr at bound"
## [7] "nominal p" "spending_time"
xint <- to_integer(x)
colnames(xint$bound)
## [1] "analysis" "bound" "probability" "probability0" "z" "~hr at bound"
## [7] "nominal p"
summary(x, display_spending_time = TRUE)
## # A tibble: 1 × 8
## # Groups: Analysis [1]
## Analysis Bound Z `Spending time` `~HR at bound` `Nominal p` `Alternate hypothesis` `Null hypothesis`
## <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 Analysi… Effi… 1.96 1 0.795 0.025 0.9 0.025
summary(xint, display_spending_time = TRUE)
## Error in `select()` at gsDesign2/R/summary.R:349:3:
## ℹ In argument: `all_of(col_vars)`.
## Caused by error in `all_of()`:
## ! Can't subset elements that don't exist.
## ✖ Element `Spending time` doesn't exist.
## Run `rlang::last_trace()` to see where the error occurred.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by running the provided R reprex, then inspect to_integer() and the select() call at gsDesign2/R/summary.R:349. Trace how the bound table's spending_time column is transformed; done means to_integer(x) retains it and summary(xint, display_spending_time = TRUE) completes without the missing-column error.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- data
- Issue type
- Bug
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Active
- Clarity
- Clearly specified
- Newbie friendliness
- 82/100