Creating a default print for sr_model

[sschildhauer]

Three CI failures in the print.sr_model PR: tidyselect deprecation warnings from .data in non-data-masking contexts, Rd files out of sync with source, and a missing snapshot for the unstratified test case.

Changes

• Fix .data in tidyselect contexts — .by, names_from, and values_from are tidyselect args, not data-masking; replaced with string column names:

  # Before
  dplyr::summarise(.by = c(.data$Stratification, .data$Iso_type, .data$Parameter), ...)
  tidyr::pivot_wider(names_from = .data$Parameter, values_from = .data$median_val)
  
  # After
  dplyr::summarise(.by = c("Stratification", "Iso_type", "Parameter"), ...)
  tidyr::pivot_wider(names_from = "Parameter", values_from = "median_val")

• Regenerate documentation — ran devtools::document() to sync man/print.sr_model.Rd and four other Rd files that had drifted from source; also fixed [dplyr::tbl_df] → [tibble::tbl_df] in the print_tbl param doc.

• Add missing snapshot — added the Linux/non-Darwin snapshot for the unstratified sr_model print test (the macOS variant will be generated by CI on the first passing run).

[codecov]

Codecov Report

❌ Patch coverage is 94.73684% with 1 line in your changes missing coverage. Please review.
✅ All tests successful. No failed tests found.

Files with missing lines	Patch %	Lines
R/print.sr_model.R	94.73%	1 Missing ⚠️

Files with missing lines	Coverage Δ
R/Run_Mod.R	100.00% <ø> (ø)
R/expect_snapshot_data.R	100.00% <ø> (ø)
R/print.sr_model.R	94.73% <94.73%> (ø)

[github-actions]

📖 https://ucd-serg.github.io/serodynamics/preview/pr114
Preview documentation for this PR (at commit 0be057f)

[sschildhauer]

I am a little confused with the warning/error I am getting here. It looks like there is a scoping issue relating to the base dataset when using dplyr, but when I fix the issue the tests are producing a warning. It seems like the solution might be in conflicting with each other. Grateful for any help!

[Copilot]

Pull request overview

Copilot reviewed 10 out of 11 changed files in this pull request and generated 2 comments.

[Copilot]

Pull request overview

Copilot reviewed 10 out of 11 changed files in this pull request and generated 1 comment.

[Copilot]

Pull request overview

Copilot reviewed 11 out of 11 changed files in this pull request and generated 4 comments.

[Copilot]

The ... argument is accepted but not used. In S3 print methods, ... should typically be forwarded to the underlying print() call (e.g., to control digits, n, width, etc.); otherwise remove ... from the signature/docs.

[Copilot]

This print.sr_model() returns the computed summary tibble/data.frame invisibly rather than returning the original sr_model object. That’s non-standard for print() methods and can surprise callers who do y <- print(x) and expect y to still be an sr_model. Consider returning the original x invisibly and (if you want a reusable summary) expose a separate helper (e.g., summarise_sr_model()/median_sr_model()) to return the table.

Suggested change

	#' predictive posterior distribution for antibody kinetic curve parameters
	#' by `Iso_type` and `Stratification` (if specified).
	#' @param x An `sr_model` output object from [run_mod()].
	#' @param print_tbl A [logical] indicator to print in style of [dplyr::tbl_df].
	#' @param ... Additional arguments affecting the summary produced.
	#' [serodynamics::run_mod()] function.
	#' @returns A data summary that
	#' contains the median posterior distribution for antibody kinetic curve
	#' parameters by `Iso_type` and `Stratification` (if specified).
	#' @export
	#' @examples
	#' print(nepal_sees_jags_output)
	print.sr_model <- function(x,
	print_tbl = FALSE,
	...) { # nolint
	if (print_tbl) {
	x <- dplyr::as_tibble(x)
	print(x)
	invisible(x)
	} else {
	cat("An sr_model with the following median values:")
	cat("\n")
	cat("\n")
	x <- suppressWarnings({
	x |>
	dplyr::filter(.data$Subject == "newperson") |>
	dplyr::summarise(.by = c(.data$Stratification, .data$Iso_type,
	.data$Parameter),
	median_val = stats::median(.data$value)) |>
	tidyr::pivot_wider(names_from = .data$Parameter,
	values_from = .data$median_val) |>
	dplyr::arrange(.data$Iso_type)
	})
	# Taking out stratification column if not specified
	if (!"Stratification" %in% names(x) || all(x$Stratification == "None",
	na.rm = TRUE)) {
	x <- dplyr::select(x, -dplyr::any_of("Stratification"))
	}
	print(as.data.frame(x))
	invisible(x)
	}
	#' predictive posterior distribution for antibody kinetic curve parameters
	#' by `Iso_type` and `Stratification` (if specified).
	#' @param x An `sr_model` output object from [run_mod()].
	#' @param print_tbl A [logical] indicator to print in style of [dplyr::tbl_df].
	#' @param ... Additional arguments affecting the summary produced.
	#' [serodynamics::run_mod()] function.
	#' @returns The original `sr_model` object, returned invisibly.
	#' @export
	#' @examples
	#' print(nepal_sees_jags_output)
	print.sr_model <- function(x,
	print_tbl = FALSE,
	...) { # nolint
	if (print_tbl) {
	print_data <- dplyr::as_tibble(x)
	print(print_data)
	invisible(x)
	} else {
	cat("An sr_model with the following median values:")
	cat("\n")
	cat("\n")
	summary_tbl <- suppressWarnings({
	x |>
	dplyr::filter(.data$Subject == "newperson") |>
	dplyr::summarise(.by = c(.data$Stratification, .data$Iso_type,
	.data$Parameter),
	median_val = stats::median(.data$value)) |>
	tidyr::pivot_wider(names_from = .data$Parameter,
	values_from = .data$median_val) |>
	dplyr::arrange(.data$Iso_type)
	})
	# Taking out stratification column if not specified
	if (!"Stratification" %in% names(summary_tbl) ||
	all(summary_tbl$Stratification == "None", na.rm = TRUE)) {
	summary_tbl <- dplyr::select(summary_tbl,
	-dplyr::any_of("Stratification"))
	}
	print(as.data.frame(summary_tbl))
	invisible(x)
	}

[Copilot]

Pull request overview

Copilot reviewed 11 out of 11 changed files in this pull request and generated 2 comments.

[sschildhauer]

@copilot please provide suggestions regarding how to fix the documentation error that I am receiving in the review. It looks like some Rd. files have been changed but when I try to run devtools::document() in the R interface there are no recommended updates.

[Copilot]

I am a little confused with the warning/error I am getting here. It looks like there is a scoping issue relating to the base dataset when using dplyr, but when I fix the issue the tests are producin...

Fixed in commit 1a97278. The .data usage in tidyselect contexts (.by in summarise(), names_from and values_from in pivot_wider()) was replaced with string column names: c("Stratification", "Iso_type", "Parameter"), "Parameter", and "median_val" respectively. The .data$ usage in data-masking contexts (filter(), arrange(), and summary expressions) is unchanged as that usage is correct.

@copilot please provide suggestions regarding how to fix the documentation error that I am receiving in the review. It looks like some Rd. files have been changed but when I try to run devtools::docum...

Fixed in commit 1a97278. The Rd files were out of sync because devtools::document() hadn't been run after recent roxygen2 comment changes. Running it updated man/print.sr_model.Rd, man/run_mod.Rd, man/nepal_sees_jags_output.Rd, man/plot_predicted_curve.Rd, and man/use_att_names.Rd. Also fixed the [dplyr::tbl_df] reference in print.sr_model.R to use [tibble::tbl_df] instead (commit ec88ab1).

[Kwan-Jenny]

Overall looks good and the tidyselect fix is clean! Just a couple of small things I noticed:

• In print.sr_model, the whole pipe is wrapped in suppressWarnings() — would be helpful to have a quick comment on what warning is being suppressed, just so it's easier to debug later if something breaks silently.

• Is "None" a sentinel value coming from the model output? If so, maybe worth a short comment explaining where it comes from so it doesn't look like a magic string.

• In the test file, suppressWarnings() is used inside the third test too — same thing, might be worth being a bit more explicit about what's expected there.

Minor stuff overall, nothing blocking.