Creating default print methods for class sr_model by sschildhauer · Pull Request #114 · ucdavis/serodynamics

sschildhauer · 2025-07-09T23:08:52Z

I am creating a default print methods for sr_model using the S3 object system. The default print provides the mean value of the posterior distribution for each parameter and all stratification iso_type combinations.

Merge commit '4ee4b99f9f601b2f95fab79fb25a7d781b37e1a7' #Conflicts: # R/Run_Mod.R

…ifications

codecov · 2025-07-09T23:12:05Z

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 · 2025-07-09T23:25:41Z

📖 https://ucd-serg.github.io/serodynamics/preview/pr114
Preview documentation for this PR (at commit dee362d)

sschildhauer · 2025-07-14T03:41:30Z

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!

sschildhauer · 2025-10-01T23:54:30Z

Hi Ezra and Kwan. I checked the snaps and having a hard time finding a solution. It looks like the test for print.sr_model in the github review is producing different median values than when I run the function locally. There also seems to be something going on with autoplot.case_data documention -- this is a new issue and has me stumped as well. Thank you so much for review. These should almost be there!

d-morrison

@sschildhauer re: the document error: ggplot2 recently updated to v4.0 and changed a lot of stuff, including documentation, which the documentation for autoplot.case_data() depends on.

Please update ggplot2 and its dependencies on your local machine and re-run document(); once you do that, the changes you introduced in autoplot.case_data.Rd will hopefully go away.

d-morrison · 2025-10-02T00:11:06Z

@sschildhauer PS - I bet updating ggplot2 will also resolve the snapshot discrepancies; feel free to re-ping me if you're still stuck after that.

Merge commit '783e92bef4e57e1fa0a000041fe2906346d81e1b'

sschildhauer · 2025-10-09T03:22:54Z

@Kwan-Jenny , can you also take a quick look at this when you get a chance? I recently created an option in the print to make the output similar to that of print.tbl_df.

R/print.sr_model.R

Co-authored-by: Kwan-Jenny <68584166+Kwan-Jenny@users.noreply.github.com>

Merge commit 'fcdeafb1bf63c03cdeb86504ad1235ecf179ffb7' #Conflicts: # DESCRIPTION # NEWS.md # R/expect_snapshot_data.R # inst/WORDLIST

Copilot

Pull request overview

Adds an S3 print() method for sr_model objects (the primary output type of run_mod()), with snapshot tests and documentation, and surfaces the method in pkgdown.

Changes:

Introduces print.sr_model() with an option to print either a median-summary table or the underlying tibble.
Adds snapshot tests + snapshot outputs for the new print behavior.
Updates documentation/indexing (NAMESPACE, Rd, pkgdown reference) and project metadata (NEWS, WORDLIST).

Reviewed changes

Copilot reviewed 10 out of 10 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
`R/print.sr_model.R`	New S3 print method for `sr_model` including a summary view and a “print as tibble” option.
`tests/testthat/test-print.sr_model.R`	Adds snapshot tests covering printed output for `sr_model`.
`tests/testthat/_snaps/print.sr_model.md`	Snapshot expectations for the new print outputs.
`man/print.sr_model.Rd`	Roxygen-generated documentation for `print.sr_model`.
`NAMESPACE`	Registers `print.sr_model` as an S3 method.
`pkgdown/_pkgdown.yml`	Adds `print.sr_model` to the reference index.
`NEWS.md`	Changelog entry for the new print method.
`inst/WORDLIST`	Adds new spelling whitelist terms.
`R/Run_Mod.R`	Minor formatting-only change at end of file.

Copilot · 2026-03-30T03:23:43Z

tests/testthat/test-print.sr_model.R

+test_that(
+  desc = "results are consistent with printed output for sr_model class",
+  code = {
+    testthat::expect_snapshot(nepal_sees_jags_output) 
+  }
+)
+
+test_that(
+  desc = "results are consistent with printed output for sr_model class as tbl",
+  code = {
+    testthat::expect_snapshot(print(nepal_sees_jags_output, print_tbl = TRUE)) 
+  }
+)


The print method has logic to drop the Stratification column when it’s missing or all "None", but the added snapshot tests only cover stratified data (typhi/paratyphi). Add a test case for an sr_model with Stratification == "None" to exercise this branch and prevent regressions.

Copilot · 2026-03-30T03:23:44Z

R/print.sr_model.R

+    x <- x |>
+      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) |>


The printed summary is currently computed across all Subject values. Since sr_model contains subject-specific parameter draws, aggregating without filtering (e.g., to Subject == "newperson") produces a mixture that depends on how many subjects are in the object and is inconsistent with post_summ() / diagnostic helpers that summarise only newperson draws.

Copilot · 2026-03-30T03:23:44Z

R/print.sr_model.R

+    cat("An sr_model with the following median values:")
+    cat("\n")
+    cat("\n")
+    x <- x |>
+      dplyr::summarise(.by = c(.data$Stratification, .data$Iso_type, 
+                               .data$Parameter), 
+                       median_val = stats::median(.data$value)) |>


The PR description says the default print shows the mean of the posterior distribution, but the implementation/message and docs use the median (stats::median() and "median values"). Please align the implementation, printed wording, and documentation with the intended statistic.

Copilot · 2026-03-30T03:23:44Z

R/print.sr_model.R

+#' @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.


... is documented as affecting the summary produced by run_mod(), but this is a print method and ... is not used/forwarded. Consider documenting ... as additional arguments passed to print() (and actually pass ... through), or remove it if intentionally unused.

Copilot · 2026-03-30T03:23:44Z

R/print.sr_model.R

+  if (print_tbl) {
+    x <- dplyr::as_tibble(x)
+    print(x)
+  } else {


In the print_tbl = TRUE branch, the method converts x to a tibble and returns the result of print(x) (visible) without invisible(). For S3 print() methods, it’s conventional to return the original object invisibly; also consider not overwriting/dropping the sr_model class just for printing.

sschildhauer added 20 commits June 24, 2025 22:48

Adding class sero_mod_output to run_mod output

aea299a

Specifying class in run_mod

a13db94

creating default print function method for sero_mod_output objects

eef3d8e

Adding S3 method to NameSpace

147ae9e

Documentation for default print method

ea74517

Merging with main

4af5d36

Merge commit '4ee4b99f9f601b2f95fab79fb25a7d781b37e1a7' #Conflicts: # R/Run_Mod.R

Creating default print for run_mod objects

102cb80

Creating a test for default run_mod object print

7323fda

Updating example for print default

88b96af

Updating documentation for default print

91a887f

Arranging data by Iso_type to allow for easy comparison between strat…

a7afd63

…ifications

Adding test snap for run_mod object default print

f5be2b3

Updating default sr_model print documentation

ba5973f

Updating example for print.sr_model

4ed27e6

Increment version number to 0.0.0.9035

8e5eba7

Updating news

f377d5c

Adding print.sr_model to pkgdown

9711df6

Deleting a previous default print method that was being created

ff9ee85

Updating function for pivot_wider

8eed4a7

Updating documentation to take out old print function

7a5ec62

sschildhauer added 7 commits July 9, 2025 17:34

Updating wordlist

eb4e282

Updating lint

141ba3c

Fixing no lint.

f95a88a

Updating test lint

4dcd890

Changing review recommended test code

ee0a73c

Updating test code based on review recommendations

0dbc9a2

Adding .data$ back in to code

a22ed27

Changing the median function to try and fix the snap issue

2cad837

sschildhauer requested a review from d-morrison October 1, 2025 23:54

d-morrison requested changes Oct 2, 2025

View reviewed changes

sschildhauer added 11 commits October 2, 2025 15:30

Updating plot_predicted curve snaps after ggplot update

97f2931

Updating autoplot documentation

f9a3f53

Merged origin/main into default_print

597d613

Updating print snap

3fc100c

Merge commit '783e92bef4e57e1fa0a000041fe2906346d81e1b'

Increment version number to 0.0.0.9044

64d7ea4

Adding option to print output as tibble

2985fc6

Updating lint and structure of logical indicator

46d53a3

Updating tests for print

f0bf068

Updadting snaps for default print to test a tbl output

c25630c

Fixing lint

4a14365

Updating stats::median call

89e5bf5

Merged origin/main into default_print

a2be022

Kwan-Jenny reviewed Oct 22, 2025

View reviewed changes

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Kwan-Jenny reviewed Oct 22, 2025

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sschildhauer and others added 6 commits October 26, 2025 17:31

Updating print documentation

c9847dc

Update R/print.sr_model.R

e160b39

Co-authored-by: Kwan-Jenny <68584166+Kwan-Jenny@users.noreply.github.com>

Updating lint for print

7fdb0d4

Merge branch 'main' into default_print

c6de84f

Merged origin/main into default_print

2eb9a29

Merging with main

91de966

Merge commit 'fcdeafb1bf63c03cdeb86504ad1235ecf179ffb7' #Conflicts: # DESCRIPTION # NEWS.md # R/expect_snapshot_data.R # inst/WORDLIST

Copilot AI review requested due to automatic review settings March 30, 2026 03:18

Copilot started reviewing on behalf of sschildhauer March 30, 2026 03:19 View session

Increment version number to 0.0.0.9048

dee362d

Copilot AI reviewed Mar 30, 2026

View reviewed changes

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