Streamline plotting code and unify array comparison methods - #541
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- Add size_axis, llim, per_log_size, and proportion scaling support to ArrayResourceBySize and ArrayTimeByResourceBySize plotting methods (plot2, plotRelative, addPlot), achieving full symmetry with species arrays. - Add array_log_y() and array_ylim() to plot2.ArraySpeciesBySize, plot2.ArrayTimeBySpecies, and animate.ArrayTimeBySpeciesBySize so proportion arrays default to linear [0, 1] y-axes uniformly. - Streamline plotYield.MizerSim to delegate single-simulation plotting directly to plot(getYield(sim)) and deprecate the two-simulation sim2 argument in favour of plot2(getYield(sim1), getYield(sim2)). - Remove redundant internal parseTimePlotLog in favour of parsePlotLog. - Refactor plotFeedingLevel to delegate to plot() and addPlot() on ArraySpeciesBySize, with non-clipping cartesian coordinates for proportion ranges, and simplify plotlyFeedingLevel to plotHover(plotFeedingLevel(...)). - Ensure length-axis Total calculation in plot_cdf(), plotSpectra2(), plotSpectraRelative(), and plotCDF2() properly evaluates species-specific conversions before total aggregation. - Add tests covering resource array methods on length/log-size axes, comparison totals, and feeding level delegation.
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Summary of Changes
This pull request streamlines the plotting codebase and makes method behaviours more uniform, logical, and maintainable on top of PRs #538, #539, and #540:
1. Resource Array Method Symmetry
size_axis,llim,per_log_size,array_log_y(),array_ylim(), and unit-aware axis labelling helpers (plot_size_xlab(),plot_size_xlim()) acrossplot2(),plotRelative(), andaddPlot()for bothArrayResourceBySizeandArrayTimeByResourceBySize.2. Uniform Proportion Array Scaling
array_log_y()andarray_ylim()toplot2.ArraySpeciesBySize,plot2.ArrayTimeBySpecies, andanimate.ArrayTimeBySpeciesBySize.[0, 1]y-axes (widening to accommodate data when needed) across both single and comparison plots.3.
plotYieldStreamlining & Redundant Parser RemovalparseTimePlotLogwithparsePlotLogacrossplotBiomassandplotYieldGear.plotYield.MizerSimso that a single simulation delegates directly toplot(getYield(object))(settingvalue_name = "Yield"for proper labelling).sim2argument ofplotYield()withlifecycle::deprecate_warn("2.6.0", "plotYield(sim2)", "plot2()", details = "Use plot2(getYield(sim1), getYield(sim2)) instead.").4. Length-axis Total Calculation
plot_cdf()withvalidParams(params)so that missing length–weight coefficientsaandbare resolved before conversion.plot_cdf(),plotSpectra2(),plotSpectraRelative(), andplotCDF2()to properly evaluate species-specific length conversions before computing total curves and normalisations.5.
plotFeedingLevel&plotlyFeedingLevelRefactoringplotFeedingLevel()to delegate directly toplot()andaddPlot()onArraySpeciesBySize, using non-clipping cartesian coordinate limits for proportion ranges.plotlyFeedingLevel()toplotHover(plotFeedingLevel(...)).6. Testing & Documentation
tests/testthat/test-ArrayResourceBySize-class.Randtests/testthat/test-plots.R.NEWS.mdand package documentation.Testing
test-plots.R, 91 in array classes, and full test suite passing cleanly).