Merge main branch and fix workflow failures

[Copilot]

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Changes

Merged latest main branch into decay-curve-2 feature branch to incorporate upstream changes and fixed all resulting workflow failures.

Conflicts Resolved

• DESCRIPTION: Combined imports from both branches, removed duplicate mixtools (kept only in Suggests), removed unused pkgload, added missing config dependency
• NAMESPACE: Combined exports from both branches (analyze_sims, antibody_decay_curve, compare_seroincidence, count_strata, curve_app, t1f, y1f) and imports (theme_bw, vars)
• R/serocalculator-package.R: Retained both theme_bw and vars importFrom statements

Note: Used merge instead of rebase due to force-push restrictions.

Workflow Fixes

After merging, addressed all CI/CD workflow failures:

• Linting Issues: Replaced stop() with cli::cli_abort() in R/autoplot.seroincidence.by.R and R/autoplot.seroincidence.R to comply with package style guidelines
• Missing Shiny Imports: Added missing shiny function imports (h2, renderPlot, renderTable, sliderInput) for curve_app functionality
• Data Masking Variables: Used .data pronoun in R/curve_app_server.R for proper data masking of variables (mu_y, mu_b, y0, b0, t1) within tibble construction, following tidyverse guidelines instead of utils::globalVariables() to eliminate R CMD check NOTEs
• Partial Argument Matching: Fixed all sliderInput() calls in R/curve_app_ui.R by replacing abbreviated parameter val with the full parameter name value to eliminate R CMD check warnings

All tests pass and package loads successfully.

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[codecov]

Codecov Report

❌ Patch coverage is 79.66574% with 146 lines in your changes missing coverage. Please review.
✅ All tests successful. No failed tests found.

Files with missing lines	Patch %	Lines
R/sim_pop_data_multi.R	0.00%	29 Missing ⚠️
R/utils.R	23.52%	26 Missing ⚠️
R/graph_seroresponse_model_1.R	0.00%	21 Missing ⚠️
R/as_sr_params.R	20.00%	16 Missing ⚠️
R/strat_ests_scatterplot.R	70.00%	15 Missing ⚠️
R/curve_app_ui.R	0.00%	9 Missing ⚠️
R/curve_app_server.R	0.00%	8 Missing ⚠️
R/density_plot.R	90.74%	5 Missing ⚠️
R/load_sr_params.R	54.54%	5 Missing ⚠️
R/autoplot.seroincidence.R	25.00%	3 Missing ⚠️
... and 4 more

Files with missing lines	Coverage Δ
R/ab1.R	100.00% <100.00%> (ø)
R/age_scatter.R	100.00% <100.00%> (ø)
R/analyze_sims.R	100.00% <100.00%> (ø)
R/autoplot.curve_params.R	100.00% <100.00%> (+100.00%)	⬆️
R/autoplot.pop_data.R	100.00% <ø> (+28.31%)	⬆️
R/autoplot.sim_results.R	100.00% <100.00%> (ø)
R/autoplot.summary.seroincidence.by.R	100.00% <100.00%> (ø)
R/check_parallel_cores.R	100.00% <100.00%> (ø)
R/check_pop_data.R	100.00% <100.00%> (ø)
R/check_strata.R	100.00% <100.00%> (ø)
... and 28 more

... and 6 files with indirect coverage changes

[d-morrison]

fix the code issues found by the failing workflows

[Copilot]

fix the code issues found by the failing workflows

Fixed all workflow failures:

Linting issues: Replaced stop() with cli::cli_abort() in R/autoplot.seroincidence.by.R and R/autoplot.seroincidence.R

R CMD check issues:

• Removed duplicate mixtools from Imports (kept in Suggests)
• Removed unused pkgload from Imports
• Added config to Imports (used in R/app_config.R)
• Added missing shiny function imports (h2, renderPlot, renderTable, sliderInput)
• Added utils::globalVariables declarations for curve_app variables (mu_y, mu_b, y0, b0, t1)

Package loads successfully and all tests pass. (commit 4e6b489)

[d-morrison]

fix issues identified in latest workflow run (21191111690)

[Copilot]

fix issues identified in latest workflow run (21191111690)

Fixed partial argument matching issues in R/curve_app_ui.R - replaced all instances of val parameter with the correct value parameter in sliderInput() calls. This eliminates the R CMD check NOTEs about partial argument matching. (commit 0e30f17)