Monitor population parameters #141

sschildhauer · 2025-12-09T19:13:28Z

Creating a pull request for monitoring population parameters. This PR adds a dataframe of pop_params to the output of run_mod that includes mu.par and prec.par.

codecov · 2025-12-09T19:18:35Z

❌ 5 Tests Failed:

Tests completed	Failed	Passed	Skipped
29	5	24	0

View the top 3 failed test(s) by shortest run time

run_mod::results_are_consistent_with_unstratified_SEES_data_with_jags.post_included

Stack Traces | 0.022s run time

Error in `tibble(Iteration = NULL, Chain = NULL, value = NULL, Subject = NULL, Parameter = NULL, Iso_type = NULL, Stratification = NULL)`: could not find function "tibble"
Backtrace:
    x
 1. +-base::suppressWarnings(...) at test-run_mod.R:135:5
 2. | \-base::withCallingHandlers(...)
 3. \-serodynamics::run_mod(...)

run_mod::results_are_consistent_with_unstratified_SEES_data_with_modified_priors

Stack Traces | 0.023s run time

Error in `tibble(Iteration = NULL, Chain = NULL, value = NULL, Subject = NULL, Parameter = NULL, Iso_type = NULL, Stratification = NULL)`: could not find function "tibble"
Backtrace:
    x
 1. +-base::suppressWarnings(...) at test-run_mod.R:169:5
 2. | \-base::withCallingHandlers(...)
 3. \-serodynamics::run_mod(...)

run_mod::results_are_consistent_with_unstratified_SEES_data

Stack Traces | 0.035s run time

Error in `tibble(Iteration = NULL, Chain = NULL, value = NULL, Subject = NULL, Parameter = NULL, Iso_type = NULL, Stratification = NULL)`: could not find function "tibble"
Backtrace:
    x
 1. +-base::suppressWarnings(...) at test-run_mod.R:96:5
 2. | \-base::withCallingHandlers(...)
 3. \-serodynamics::run_mod(...)

run_mod::results_are_consistent_with_SEES_data

Stack Traces | 0.053s run time

Error in `tibble(Iteration = NULL, Chain = NULL, value = NULL, Subject = NULL, Parameter = NULL, Iso_type = NULL, Stratification = NULL)`: could not find function "tibble"
Backtrace:
    x
 1. +-base::suppressWarnings(...) at test-run_mod.R:57:5
 2. | \-base::withCallingHandlers(...)
 3. \-serodynamics::run_mod(...)

run_mod::results_are_consistent_with_simulated_data

Stack Traces | 0.286s run time

Error in `tibble(Iteration = NULL, Chain = NULL, value = NULL, Subject = NULL, Parameter = NULL, Iso_type = NULL, Stratification = NULL)`: could not find function "tibble"
Backtrace:
    x
 1. +-base::suppressWarnings(...) at test-run_mod.R:16:5
 2. | \-base::withCallingHandlers(...)
 3. \-serodynamics::run_mod(...)

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github-actions · 2025-12-09T19:39:53Z

📖 https://ucd-serg.github.io/serodynamics/preview/pr141
Preview documentation for this PR (at commit bd6981a)

sschildhauer · 2025-12-10T05:16:28Z

I am unsure why these final tests aren't passing. @Kwan-Jenny Any thoughts?

…fferent population parameters

NEWS.md

pkgdown/_pkgdown.yml

Kwan-Jenny · 2025-12-16T15:58:28Z

I am unsure why these final tests aren't passing. @Kwan-Jenny Any thoughts?

I am not sure what’s causing these final test failures. It may be helpful to ask @d-morrison for his thoughts.

into mon_popparams

sschildhauer · 2025-12-20T19:30:12Z

Hi @d-morrison , I have not seen this review fail message. I am a but confused how this came up as I made very few changes from the last review. It looks like it might have something to do with package dependencies, but unsure. Once this is done I can send up the posterior predictive check for review.

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Copilot

Pull request overview

Copilot reviewed 16 out of 22 changed files in this pull request and generated 1 comment.

R/unpack_jags.R

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Copilot

Pull request overview

Copilot reviewed 16 out of 22 changed files in this pull request and generated 6 comments.

Comments suppressed due to low confidence (1)

tests/testthat/_snaps/run_mod/strat-fitted_residuals.csv:1

The snapshot CSV files for fitted_residuals appear to have been completely deleted from the main snapshot directory (tests/testthat/_snaps/run_mod/) but they still exist in the darwin variant directory (tests/testthat/_snaps/darwin/run_mod/). This appears to be unintentional - the diff shows the entire file contents being removed with "-" prefixes for all lines.

The test file (test-run_mod.R) still references these snapshots in lines 40-44, 80-84, and 119-123, using expect_snapshot_data() calls. This will cause test failures because the snapshot files are missing.

Either the snapshots need to be restored to the main directory, or the test code needs to be updated to only use the darwin variant if that's the intended behavior. Given that the PR description doesn't mention intentionally removing these snapshots, this appears to be an accidental deletion.

R/unpack_jags.R

R/Run_Mod.R

man/run_mod.Rd

man/expect_snapshot_data.Rd

DESCRIPTION

sschildhauer · 2026-01-24T22:16:48Z

@copilot please implement your suggestions and troubleshoot areas where there are errors, specifically in the unpack_jags functions which does not seem to be working. Please keep all edits within this pull request.

Copilot · 2026-01-24T22:16:58Z

@sschildhauer I've opened a new pull request, #183, to work on those changes. Once the pull request is ready, I'll request review from you.

- Add default case and error handling to param_recode() - Fix unpack_jags() to handle factor Parameter column from ggmcmc::ggs() - Improve pattern matching in unpack_jags using startsWith() for precision - Add column validation before reordering in run_mod() - Update documentation for prec.logy to clarify it's a vector of precisions - Accept updated test snapshots with population_params now properly populated Co-authored-by: sschildhauer <165851188+sschildhauer@users.noreply.github.com>

- Add 33 unit tests for param_recode(), unpack_jags(), prep_popparams(), and ex_popparams() - Test valid and invalid parameter indices with error handling - Test factor Parameter column handling from ggmcmc::ggs() - Test mu.par, prec.par, and prec.logy parameter unpacking - Test individual-level parameter unpacking - Test population parameter filtering and exclusion - Verify prep_popparams and ex_popparams are complementary Co-authored-by: sschildhauer <165851188+sschildhauer@users.noreply.github.com>

- Replace .data$Subject with "Subject" in dplyr::rename() - Resolves tidyselect 1.2.0 deprecation warning Co-authored-by: sschildhauer <165851188+sschildhauer@users.noreply.github.com>

Co-authored-by: sschildhauer <165851188+sschildhauer@users.noreply.github.com>

- Remove error handling from param_recode() for invalid parameter indices - Remove column validation from run_mod() before reordering - Remove tests for invalid parameter handling - Keep only essential functionality since JAGS outputs are always consistent Co-authored-by: sschildhauer <165851188+sschildhauer@users.noreply.github.com>

Fix unpack_jags() factor handling and add test coverage for population parameters. Copilot made requested changes and will not merge into base branch for mon_popparams.

Copilot

Pull request overview

Copilot reviewed 14 out of 15 changed files in this pull request and generated 4 comments.

R/unpack_jags.R

Copilot · 2026-01-28T03:53:00Z

tests/testthat/test-internal-popparams.R

+test_that("param_recode correctly recodes parameter indices", {
+  # Test valid parameter indices
+  expect_equal(serodynamics:::param_recode("1"), "y0")
+  expect_equal(serodynamics:::param_recode("2"), "y1")
+  expect_equal(serodynamics:::param_recode("3"), "t1")
+  expect_equal(serodynamics:::param_recode("4"), "alpha")
+  expect_equal(serodynamics:::param_recode("5"), "shape")
+
+  # Test vector of valid indices
+  expect_equal(
+    serodynamics:::param_recode(c("1", "2", "3", "4", "5")),
+    c("y0", "y1", "t1", "alpha", "shape")
+  )
+})
+
+test_that("unpack_jags handles factor Parameter column", {
+  # Create a simple ggs-like object with factor Parameter column
+  test_data <- tibble::tibble(
+    Iteration = rep(1:5, 3),
+    Chain = rep(1, 15),
+    Parameter = factor(
+      rep(c("mu.par[1,1]", "prec.par[1,1,2]", "y0[1,1]"), each = 5)
+    ),
+    value = rnorm(15)
+  )
+
+  # Should not error with factor column
+  result <- serodynamics:::unpack_jags(test_data)
+
+  expect_true(is.data.frame(result))
+  expect_true("Subject" %in% names(result))
+  expect_true("Param" %in% names(result))
+})
+
+test_that("unpack_jags correctly unpacks mu.par parameters", {
+  test_data <- tibble::tibble(
+    Iteration = rep(1:3, 2),
+    Chain = rep(1, 6),
+    Parameter = rep(c("mu.par[1,1]", "mu.par[1,2]"), each = 3),
+    value = rnorm(6)
+  )
+
+  result <- serodynamics:::unpack_jags(test_data)
+
+  # Check that mu.par rows are present
+  mu_rows <- result[result$Subject == "mu.par", ]
+  expect_gt(nrow(mu_rows), 0)
+
+  # Check Subject is correctly set
+  expect_true("mu.par" %in% result$Subject)
+
+  # Check Param is correctly decoded
+  expect_true(all(mu_rows$Param %in% c("y0", "y1", "t1", "alpha", "shape")))
+})
+
+test_that("unpack_jags correctly unpacks prec.par parameters", {
+  test_data <- tibble::tibble(
+    Iteration = rep(1:3, 2),
+    Chain = rep(1, 6),
+    Parameter = rep(c("prec.par[1,1,2]", "prec.par[1,2,3]"), each = 3),
+    value = rnorm(6)
+  )
+
+  result <- serodynamics:::unpack_jags(test_data)
+
+  # Check that prec.par rows are present
+  prec_rows <- result[result$Subject == "prec.par", ]
+  expect_gt(nrow(prec_rows), 0)
+
+  # Check Subject is correctly set
+  expect_true("prec.par" %in% result$Subject)
+
+  # Check Param contains pairs (e.g., "y0, y1")
+  expect_true(any(grepl(",", prec_rows$Param)))
+})
+
+test_that("unpack_jags correctly unpacks prec.logy parameters", {
+  test_data <- tibble::tibble(
+    Iteration = rep(1:3, 2),
+    Chain = rep(1, 6),
+    Parameter = rep(c("prec.logy[1]", "prec.logy[2]"), each = 3),
+    value = rnorm(6)
+  )
+
+  result <- serodynamics:::unpack_jags(test_data)
+
+  # Check that prec.logy rows are present
+  logy_rows <- result[result$Subject == "prec.logy", ]
+  expect_gt(nrow(logy_rows), 0)
+
+  # Check Subject is correctly set
+  expect_true("prec.logy" %in% result$Subject)
+})
+
+test_that("unpack_jags correctly unpacks individual-level parameters", {
+  test_data <- tibble::tibble(
+    Iteration = rep(1:3, 2),
+    Chain = rep(1, 6),
+    Parameter = rep(c("y0[1,1]", "alpha[2,1]"), each = 3),
+    value = rnorm(6)
+  )
+
+  result <- serodynamics:::unpack_jags(test_data)
+
+  # Check individual-level parameters are unpacked
+  expect_true("1" %in% result$Subject | "2" %in% result$Subject)
+  expect_true("y0" %in% result$Param | "alpha" %in% result$Param)
+})
+
+test_that("prep_popparams filters to population parameters only", {
+  test_data <- tibble::tibble(
+    Iteration = 1:10,
+    Chain = rep(1, 10),
+    Parameter = rep(c("y0", "mu.par"), each = 5),
+    Subject = rep(c("1", "mu.par"), each = 5),
+    value = rnorm(10)
+  )
+
+  result <- serodynamics:::prep_popparams(test_data)
+
+  # Should only have population parameters
+  expect_true(all(result$Population_Parameter %in% 
+                    c("mu.par", "prec.par", "prec.logy")))
+
+  # Should rename Subject to Population_Parameter
+  expect_true("Population_Parameter" %in% names(result))
+  expect_false("Subject" %in% names(result))
+
+  # Should have 5 rows (only mu.par rows)
+  expect_equal(nrow(result), 5)
+})
+
+test_that("ex_popparams excludes population parameters", {
+  test_data <- tibble::tibble(
+    Iteration = 1:10,
+    Chain = rep(1, 10),
+    Parameter = rep(c("y0", "mu.par"), each = 5),
+    Subject = rep(c("1", "mu.par"), each = 5),
+    value = rnorm(10)
+  )
+
+  result <- serodynamics:::ex_popparams(test_data)
+
+  # Should not have any population parameters
+  expect_false(any(result$Subject %in% c("mu.par", "prec.par", "prec.logy")))
+
+  # Should have 5 rows (only y0 rows)
+  expect_equal(nrow(result), 5)
+
+  # Should keep original structure
+  expect_equal(names(result), names(test_data))
+})
+
+test_that("prep_popparams and ex_popparams are complementary", {
+  test_data <- tibble::tibble(
+    Iteration = rep(1:5, 4),
+    Chain = rep(1, 20),
+    Parameter = rep(c("y0", "mu.par", "prec.par", "prec.logy"), each = 5),
+    Subject = rep(c("1", "mu.par", "prec.par", "prec.logy"), each = 5),
+    value = rnorm(20)
+  )
+
+  pop_params <- serodynamics:::prep_popparams(test_data)
+  individual_params <- serodynamics:::ex_popparams(test_data)
+
+  # Together they should account for all rows
+  expect_equal(nrow(pop_params) + nrow(individual_params), nrow(test_data))
+
+  # No overlap in subjects
+  # Note: pop_params has Population_Parameter column, not Subject
+  expect_false(any(individual_params$Subject %in% 
+                     c("mu.par", "prec.par", "prec.logy")))
+})


The tests use rnorm() to generate random data but do not seed the random number generator. According to the coding guidelines and patterns in the codebase (see tests/testthat/test-run_mod.R), tests that involve random number generation should use withr::local_seed() for reproducibility. Add withr::local_seed(123) (or another seed value) at the beginning of each test that uses rnorm().

R/Run_Mod.R

Copilot · 2026-01-28T03:53:01Z

R/Run_Mod.R

+#'   - `population_params`: Modeled population parameters, indexed by 
+#'   `Iteration`, 
+#'   `Chain`, `Parameter`, `Iso_type`, and `Stratification`. Includes the 
+#'   following modeled population parameters:
+#'     - `mu.par` = The population means of the host-specific model parameters 
+#'     (on logarithmic scales).
+#'     - `prec.par` = The population precision matrix of the hyperparameters
+#'     (with diagonal elements equal to inverse variances).  
+#'     - `prec.logy` = A vector of population precisions (inverse variances), 
+#'     one per antigen/isotype combination.  


The documentation for population_params is incomplete. It lists the columns as "Iteration, Chain, Parameter, Iso_type, and Stratification" but doesn't mention the Population_Parameter column (which identifies which population parameter it is: mu.par, prec.par, or prec.logy) or the value column (which contains the MCMC sample values). These columns should be documented to match the actual data structure.

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

sschildhauer · 2026-01-28T04:15:32Z

@copilot open a new pull request to apply changes based on the comments in this thread

Copilot · 2026-01-28T04:15:44Z

@sschildhauer I've opened a new pull request, #185, to work on those changes. Once the pull request is ready, I'll request review from you.

Copilot

Pull request overview

Copilot reviewed 14 out of 15 changed files in this pull request and generated no new comments.

sschildhauer added 5 commits December 9, 2025 10:55

Updating run_mod to monitor pop_params

1194641

Updating News

216de96

Updating run_mod for pop_params

3b44be0

Increment version number to 0.0.0.9044

d167acf

Updating run_mod tests to include population parameters

806389c

Adding visisble binding

12fd909

Updating lint for run_mod

9e5b61f

sschildhauer requested a review from Kwan-Jenny December 10, 2025 05:16

sschildhauer requested a review from d-morrison December 10, 2025 17:49

sschildhauer added 5 commits December 10, 2025 11:00

Comitting unpack_jags for unpacking an MCMC object with all of the di…

c1956ce

…fferent population parameters

jags_unpack documentation

c1ccc63

Updating run_mod and documentation to include prec.logy

23cb959

Adding unpack_jags to yaml

ab0876b

documentation and lint

9c6255d

d-morrison reviewed Dec 16, 2025

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d-morrison reviewed Dec 16, 2025

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d-morrison added 2 commits December 16, 2025 01:13

Merge branch 'main' into mon_popparams

e819741

Merge branch 'main' into mon_popparams

808eb60

sschildhauer added 6 commits December 18, 2025 12:45

Increment version number to 0.0.0.9045

6f7b224

Updating tests for monitor popupation parameters

1ea38a0

Merge branch 'mon_popparams' of https://github.com/UCD-SERG/serodynamics

920ae66

into mon_popparams

Taking unpack_jags out of pkgdown

b78a454

Updating news

2d5a841

Updating the documentation.

6b63587

sschildhauer requested a review from d-morrison December 20, 2025 19:26

sschildhauer and others added 2 commits January 24, 2026 13:42

Update R/unpack_jags.R

3f1cf90

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Update R/Run_Mod.R

5568f37

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Copilot AI reviewed Jan 24, 2026

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Update R/Run_Mod.R

5f62438

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Copilot AI review requested due to automatic review settings January 24, 2026 21:46

Copilot started reviewing on behalf of sschildhauer January 24, 2026 21:47 View session

Update man/run_mod.Rd

92e54f0

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Copilot AI reviewed Jan 24, 2026

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sschildhauer added 2 commits January 24, 2026 13:54

Changing final data frame to tibble

3ea9aca

Fixing param recode

516c3e7

Initial plan

05bf272

Copilot AI mentioned this pull request Jan 24, 2026

Fix unpack_jags() factor handling and add test coverage for population parameters #183

Merged

Copilot AI and others added 6 commits January 24, 2026 22:33

Fix deprecated tidyselect syntax in prep_popparams

5974909

- Replace .data$Subject with "Subject" in dplyr::rename() - Resolves tidyselect 1.2.0 deprecation warning Co-authored-by: sschildhauer <165851188+sschildhauer@users.noreply.github.com>

Add 'precisions' to spelling wordlist

c3ea272

Co-authored-by: sschildhauer <165851188+sschildhauer@users.noreply.github.com>

Merge pull request #183 from ucdavis/copilot/sub-pr-141-again

42cf453

Fix unpack_jags() factor handling and add test coverage for population parameters. Copilot made requested changes and will not merge into base branch for mon_popparams.

Copilot AI review requested due to automatic review settings January 28, 2026 03:48

Copilot started reviewing on behalf of sschildhauer January 28, 2026 03:48 View session

Copilot AI reviewed Jan 28, 2026

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Update R/Run_Mod.R

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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Copilot AI review requested due to automatic review settings January 28, 2026 04:12

Copilot started reviewing on behalf of sschildhauer January 28, 2026 04:12 View session

Copilot AI mentioned this pull request Jan 28, 2026

Clarify capabilities regarding new PR creation #185

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Copilot AI reviewed Jan 28, 2026

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Monitor population parameters #141

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