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NEWS.md

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mizerExperimental 2.5.3.9000

  • plotEnergyBudget() now calculates ERepro correctly and uses line plot instead of area plot.

mizerExperimental 2.5.3

Now works with and expects mizer 2.5.3

Bug fixes in tuneParams gadget

  • Fixed bug that caused tuneParams() to crash when some species had no associated gear.
  • Fixed sliders for control of double_sigmoid_length gears
  • Slider for n and m exponents now update as intended.
  • Gear selectivity sliders are now always active as expected.
  • Avoid crash when double-clicking on catch tab.
  • Update intake_max when changing h.
  • Make sure that species sliders get updated when values change during "steady".

Other bug fixes

  • Fixed bug in plotYieldVsF() that caused it to crash when no F_max was specified (#61) thanks to @SamikDatta
  • plotSpectra2() now shows models in the expected order (#63) thanks to @cmbeese
  • plotYieldVsSize() now works with single species and single gear.

New functionality in tuneParams gadget

  • tuneParams() is not longer restricted to a single gear per species.
  • tuneParams() can now keep the yield matched to observations.
  • Allow smaller effort values in fishingControl and shallower maturity curves in reproductionControl
  • Allow otherControl() to change external mortality even if it is protected.
  • Allow m parameter to be decreased as well as increased
  • Changed mortality slider to control external mortality at maturity size.

New functionality

  • New plotting function plotBiomassFlux(), which plots the rate at which growth transports biomass up the size axis.
  • getYieldVsF() now also works for species targeted by multiple gears.
  • Introduced F_min argument to getYieldVsF() and plotYieldVsF() to allow the user to set a minimum fishing mortality rate for the plot.
  • In plotYieldVsF() set sensible default for F_max.
  • tuneYield() can now keep biomass or numbers constant.

Functions moved to mizer

  • plotDiet()
  • validSim()
  • singleSpeciesSteady() has become steadySingleSpecies()

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