Add chain_color option to graph.curve.params() for customizing MCMC line color#455
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Merge branch 'main' into update_graph_curve2 # Conflicts: # R/graph.curve.params.R # man/graph.curve.params.Rd # tests/testthat/_snaps/graph.curve.params/curve-samples.svg # tests/testthat/test-graph.curve.params.R
Codecov ReportAll modified and coverable lines are covered by tests ✅ ✅ All tests successful. No failed tests found.
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# Conditionally sets the legend title in `graph.curve.params()` to accurately reflect the plot contents. - Displays "MCMC chain" when colored chains and quantiles are shown. - Hides the title when black chains and quantiles are shown to avoid confusion. - Displays "Quantile" when only quantile lines are plotted.
d-morrison
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Jul 17, 2025
Co-authored-by: Douglas Ezra Morrison <demorrison@ucdavis.edu>
This commit refactors the graph.curve.params function for clarity and improved output. The if/else block for adding geom_line layers has been streamlined by dynamically building a parameter list. This makes the code more concise and easier to maintain. Additionally, the legend title 'Quantile' has been removed when only quantile lines are plotted, resulting in a cleaner visualization.
This commit adds more descriptive comments to the tests for graph.curve.params to clarify the purpose of each test case. This makes it clear why certain parameters are used, for example, to specifically test the disabling of quantile lines.
This reverts commit bccf311.
This commit refactors the plotting logic for MCMC samples by consolidating the if/else block into a single geom_line call. A conditional is now used inside the aes() mapping to dynamically handle the color aesthetic, making the code more concise and removing duplication.
This reverts commit 760a6c5.
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almost there! two more comments
This commit refactors the nested if-else block for setting the legend label. The logic is now consolidated into a single conditional expression to determine the label text, which is then applied in one step. This improves readability and maintainability by removing duplicated code.
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Thanks! This PR looks great to me - short and sweet!
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This PR introduces a new
chain_colorargument to thegraph.curve.params()function, allowing users to control whether MCMC sample lines are colored by chain (default) or plotted in black (chain_color = FALSE).Summary of changes:
chain_colorargument added tograph.curve.params().chain_color = FALSEmakes all MCMC lines black.inst/examples/exm-graph.curve.params.Rto demonstrate:chain_color = FALSEtests/testthat/test-graph.curve.params.R:vdiffr::expect_doppelganger()log_x = TRUEoption for coverageThis update enhances visual flexibility and clarity for plotting antibody decay models, especially in publication-quality figures with many MCMC samples.