NEWS.md

In sizespectrum/mizerExperimental: Extends the mizer package with experimental features

mizerExperimental 2.4.0

New plotting functions

• plotBiomassRelative()
• plotYieldRelative()
• plotSpectraRelative()
• plotSpectra2()

mizerExperimental 2.3.1

New plotting functions

• plotDeath()
• plotEnergyBudget()
• plotResourceLevel()
• plotResourcePred()
• plotYieldVsSize()
• Also plotYieldVsF() has been improved.

Other new functions

• singleSpeciesSteady()
• alignResource()

Changes in tuneParams()

• Allow tabs to set their title, see issue #37
• resourceControl() now works also when the resource dynamics are constant.
• Reproduction plot now calculates the reproduction success correctly also for non-zero reproduction level.
• Clean-up of spectraTab code. Now button does not trigger already when it is displayed but only when it is pressed.
• Call setBevertonHolt() only for the focus species.
• The feature whereby one can call tuneParams() without a parameter to recover it from log files after a crash is now working again.
• The catch tab now has the same functionality for calibration and matching as the biomass tab.
• When changing predation kernel parameters, the search volume is also rescaled to keep the same encounter rate for larvae.
• Now one can also match abundances to observed numbers instead of observed biomasses.
• Extracted more of the plotting code into plot functions.
• Corrected the plotting of observed catch.
• Corrected the y-axis scale in density plots.
• New abundanceTab() showing both biomasses and numbers.
• Double-clicking on a species on the biomass graph now changes its biomass to the clicked value rather than the observed value.
• Separated spectra and biomass tabs.
• An observed biomass of 0 (not possible) is now converted to NA
• Using the same theme as the mizer website
• Beginnings of an example tab that can be used as a well-documented base for new custom tabs. Needs to be expanded to get better documentation.

Other changes

• Allow mizer extensions to overwrite the steady() function.

mizerExperimental 2.3.0

• New tuneGrowth() shiny gadget to help tune growth curves.

Changes in tuneParams()

• Important change: The updated species abundance is now always calculated in the unchanged background.
• Using params instead of p as argument name.
• Many more help popups.
• Main panel utilises all available space.
• Add buttons and keyboard shortcuts for cycling through species.
• Move tabs and controls into individual files and add roxygen comments.
• New match argument that determines whether biomasses or yields or neither should be matched at each press of the steady button.
• Remove the ability to upload params objects.
• New growthControl controls.
• New biomassTab tab.
• Controls can now also update species sliders.
• By default preserves erepro.
• Scaling of background now happens by clicking on the slider without need for a 'Go' button.
• Double-clicking on a growth curve plot now toggles between the panel view and the individual species view.
• Do not overrride ggplot2 theme, just adjust font size.
• Rename cutoff_size to biomass_cutoff everywhere.
• Many more changes.

Other changes

• New plotBiomassVsSpecies() and plotYieldVsSpecies().
• Egg density slider is now updated by run to steady.
• Improved handling of missing values in plotBiomassVsSpecies().
• New scaleDownBackground() and removeBackgroundspecies().

Developments moved to core mizer

• New mizer::plotBiomassObservedVsModel()
• New mizer::calibrateBiomass(), mizer::matchBiomasses(), mizer::calibrateYield(), mizer::matchYields(), mizer::scaleModel().

mizerExperimental 2.2.1

• Much polishing of tuneParams() and some added documentation.
• First stab at a validSim() function that will be useful when simulations produce non-finite values.
• Graduated the updated setBevertonHolt() and the new getReproductionLevel() to mizer package.
• Removed dislayFrames(), getBiomassFrame() and getSSBFrame() because these are superseeded by the new plotDataFrame() in mizer.
• Removed the vignette explaining size-spectrum dynamics in single-species example because this has graduated to mizer.
• Improvements to argument checks in getYieldVsF()

mizerExperimental 2.2.0

The version number will now always be that of the latest mizer package that this version of mizerExperimental requires.

• Graduated animateSpectra(), addSpecies(), removeSpecies() and renameSpecies() to mizer package.
• newSheldonParams() has graduated to mizer package under the new name newSingleSpeciesParams().
• Improvements to tuneParams(), but still work in progress.

mizerExperimental 0.1.2

• Graduated projectToSteady(), constantEggRDI(), customFunction() and compareParams() to mizer package.
• Added a NEWS.md file to track changes to the package.
• Vignette explaining size-spectrum dynamics in single-species example.
• removeSpecies() work also with 3d pred kernel.
• removeSpecies() to handles gear_params correctly

sizespectrum/mizerExperimental documentation built on April 16, 2024, 8:39 a.m.