mizer -

This is a patch release with many small fixes and improvements since the v2.5.0 release.

• validSpeciesParams() has extra checks on consistency of species parameters.
• validParams() checks that rate arrays contain finite numeric values.
• validSim() checks that simulation results are finite and truncates the simulation if they are not.
• Fixed bug that had led newCommunityParams() to set up resource parameters differently since version 2.4.0 (#293).
• addSpecies() now correctly preserves all species_params of the existing model.
• addSpecies() no longer requires new species to grow to maximum size, only maturity size is required.
• Now validGivenSpeciesParams() validates the given species parameters without adding defaults and validSpeciesParams() validates and returns a completed species parameter dataframe.
• New species parameter w_repro_max giving the size at which a species invests 100% of its energy into reproduction. Set to w_max by default.
• removeSpecies() now also removes species parameters that are NA for all of the remaining species.
• Changing w_max now also correctly updates ft_mask (#296).
• compareParams() now also spells out differences in given species parameters.
• getDiet() now also includes the contribution of the external encounter rate to the diet.
• setPredKernel() now throws an error if some of the required predation kernel parameters are NA.
• In plotYieldGear() one can select a subset of gears with a new gears argument.
• New helper function valid_gears_arg() to check the gears argument in functions that take a gears argument.
• Improved scaling of the y-axis in plotGrowthCurves().
• steadySingleSpecies() no longer requires species to grow to w_max.
• matchGrowth() now also rescales the external encounter rate.
• setExtEncounter() no longer resets the external encounter rate to zero when called without the ext_encounter argument.
• The function plotBiomassObservedVsModel() now plots the ratio of modelled to observed biomass as default (ratio = TRUE).
• The time_modified field is now updated correctly by steadySingleSpecies(), setColours() and setLinetypes().
• Deprecated matchYields() and calibrateYield().
• project() and projectToSteady(..., return_sim = TRUE) now correctly returns also the other components of the MizerSim object stored in n_other. #285
• Improved some unit tests.
• Some improvements to documentation.

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Published by gustavdelius over 1 year ago

mizer - mizer 2.5.0

This release introduces a change that requires you to upgrade your old MizerParams and MizerSim objects with upgradeParams() or upgradeSim().

External encounter rate

Now the model can include an external encounter rate that represents the rate at which a predator encounters food that is not explicitly modelled. This encounter rate is set with setExtEncounter() or ext_encounter<-() and can be read with getExtEncounter() or ext_encounter(). So this is similar to how external mortality is handled.

Given versus calculated species parameters

You can now use given_species_params() to see the species parameter values that you have explicitly specified and calculated_species_params() to see the species parameter values that mizer has calculated automatically or set to defaults. You can continue to use species_params() to get all species parameters, irrespective of whether they were given or calculated.

You can still set parameter values with species_params<-(), but you can also use the stronger given_species_params<-() which not only sets the values you give but also triggers a re-calculation of the calculated species parameters. Using given_species_params<-() is therefore usually the better option.

New mizer course

There is now a three-part mizer course at https://mizer.course.sizespectrum.org with each part consisting of several tutorials, including code and exercises:

• Part 1: Understand\ You will gain an understanding of size spectra and their dynamics by exploring simple example systems hands-on with mizer.

• Part 2: Build\ You will build your own multi-species mizer model for the Celtic sea, following our example. You can also create a model for your own area of interest.

• Part 3: Use\ You will explore the effects of changes in fishing and changes in resource dynamics on the fish community and the fisheries yield. You will run your own model scenarios.

Other improvements

• Warnings are given if user gives irrelevant species parameter values.
• Some messages have been converted to warnings and some to signals that are not shown as frequently.
• Frequent warnings are avoided when length-based and weight-based parameters are both given and are inconsistent. #277
• Documentation of effort argument in project() is improved.
• An error message is given if a predation kernel returns negative values or is everywhere zero. #283

Bug fixes

• When the coefficient h of the maximum intake rate is not given, it is now again given a default value. #282
• matchGrowth() no longer gives an error when there is no w_inf column. #279

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Published by gustavdelius over 2 years ago

mizer - mizer 2.4.0

This release introduces a change that requires you to upgrade your old MizerParams and MizerSim objects with upgradeParams() or upgradeSim():

Avoid confusion between maximum size and von Bertalanffy asymptotic size

For an explanation see blog post at https://blog.mizer.sizespectrum.org/posts/2022-11-30-dont-use-von-bertalanffy-growth-parameters/

The species parameter that specifies the size at which also the largest fish stop growing is renamed from w_inf to w_max. The parameter w_inf is now reserved for the von Bertalanffy asymptotic size parameter. If you upgrade your existing MizerParams object with upgradeParams() the w_inf column is copied over to the w_max column automatically, but you may want to change the values yourself if they do not currently reflect the maximum size of the species. Otherwise the size distributions predicted by mizer will not match observations.

Set resource abundance rather than carrying capacity

The resource parameters kappa and lambda are now used to set the abundance of the resource in the steady state rather than the carrying capacity, because the latter is not observable.

While tuning the steady state using the steady() function the resource abundance is now being kept fixed at the chosen value. Then the resource dynamics can be switched on later with setResource() without changing the steady state. At that stage you only choose either the resource intrinsic growth rate or the resource carrying capacity and the other is determined by setResource() in such a way that the resource replenishes at the same rate at which it is consumed. If you want to keep the old behaviour and switch off this automatic balancing you have to add the balance = FALSE argument when calling setResource().

You can also choose between semichemostat dynamics resource_semichemostat() or logistic dynamics resource_logistic() or you can write your own function implementing more sophisticated resource dynamics.

The setParams() function no longer includes the arguments for setting the resource parameters. Instead you set these separately with setResource().

Automatically match growth rates

As explained in the blog post at https://blog.mizer.sizespectrum.org/posts/2022-11-30-dont-use-von-bertalanffy-growth-parameters/, the von Bertalanffy curves fitted to size-at-age data are not suitable for estimating the size-dependent growth rates in mizer. It is therefore now recommended that instead of von Bertalanffy parameters you supply the age at maturity in the age_mat column of the species parameter data frame. This is then used by mizer to calculate a default for the maximum intake rate parameter h if you do not supply this.

In the past, whenever you changed any model parameters, you needed to re-tune other parameters to keep the growth rates in line with observations. There is now a new function matchGrowth() that automatically scales the search volume, the maximum consumption rate and the metabolic rate all by the same factor in order to achieve a growth rate that allows individuals to reach their maturity size by their maturity age while keeping the feeding level and the critical feeding level unchanged. This function does not however preserve the steady state, so you will need to also call steady() after matching the growth rates.

Other improvements

• New function steadySingleSpecies() that only balances the size-spectrum dynamics while ignoring multi-species effects. In other words, it calculates the steady-state size spectrum of each species as it would be if the abundance of prey and predators could be kept constant at their current values.
• plotGrowthCurves() can now superimpose a scatterplot of size-at-age data if you supply this via the new size_at_age argument.
• New functions calibrateNumber() and matchNumbers() that are like calibrateBiomass() and matchBiomasses() but work with observed numbers instead of observed biomasses.
• New function age_mat() to calculate the age at maturity from the growth rate and the size at maturity.
• If an effort vector or effort array contains NA's, these are now replaced by the default effort value. #230
• The entries of the interaction matrix and of interaction_resource are no longer restricted to be less or equal to 1. #232
• If user supplies no row names in the interaction matrix but gives column names then the column names are also used as row names. #247
• project() now also works when called with a MizerSim object with additional components.
• steady() now preserves the RDD function in the MizerParams object rather than always setting it to "BevertonHoltRDD".
• When averaging abundances over time in plotSpectra() or setInitialValues() the user can now choose geometric averaging with geometric_mean = TRUE.
• The w_mat25 species parameter is no longer filled in automatically if it is not supplied. This makes it easier to change w_mat without having to change w_mat25 at the same time.
• compareParams() now also checks the validity of its second argument.
• Hide the printing of messages about chosen defaults in newTraitParams().
• Higher values for the info_level argument in newMultispeciesParams() now leads to more messages.
• Giving more helpful messages in validSpeciesParams(). #136
• New helper functions l2w() and w2l() for converting between length-based and weight-based species parameters. #258
• Check that assessor functions for MizerSim slots are called with a MizerSim object.
• Add style argument to plotDataFrame() to facilitate producing area plots.
• Add wrap_scale argument to plotDataFrame() to control scaling of axes in faceted plots.
• plotDiet() can now show diets of several predator species in a faceted plot. #267
• Change from size to linewidth aesthetic to avoid warnings in new version of ggplot2.
• Better error message when functions are called with no valid species selected. #251
• If there are no differences then compareParams() says so clearly.
• getReproductionLevel() works as long as R_max is set. #252
• Converted several unit tests to edition 3 of testthat package.
• Improved documentation for gear_params().
• Improved defaults can now be implemented while keeping backwards compatibility via defaults_edition(). #186
• New defaults edition 2: catchability = 0.3 instead of 1, initial effort = 1 instead of 0. #243
• In defaults edition 2, get_gamma_default() ensures a feeding level of f0 for larvae also if interaction_resource is not equal to 1. #238
• Set default linecolour and linetype for external mortality.

Bug fixes

• Restored the line colours to NS_params
• Comment field now preserved by set_species_default(). #268
• Comment on w_inf no longer leads to error in plyr::aaply(). #269
• Can now again set url field in metadata.
• Correct species now listed in the legend of plotYieldObservedVsModel() and plotBiomassObservedVsModel(). #266
• Standard order for legend in plotDiet() restored after change to ggplot2 package. #265
• Fix handling of column names when interaction matrix is read from .csv file. #263

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Published by gustavdelius about 3 years ago

mizer - mizer 2.3.1

• Resolved conflict in mizerPredRate() between the argument t and the function base::t().
• Assert that upgradeParams() must be called with a MizerParams object and upgradeSim() with a MizerSim object.
• Errors changed to warnings in getRequiredRDD()
• renameSpecies() no longer fails when linecolour and linetype are of different lengths.
• matchYields() now also works for a model with only a single species.
• setInitialValues() can now average over a time_range.
• getSSB(), getBiomass(), getN(), getYieldGear() and getYield() can now be called with a MizerParams object as well as with a MizerSim object. (#200)
• Updated the shiny app in inst/shiny/selectivity_effects to current mizer version.

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Published by gustavdelius over 3 years ago

mizer - v2.3.0

New features

• New plots plotBiomassObservedVsModel() and plotYieldObservedVsModel() contributed by @SamikDatta., together with their plotly counterparts.
• New calibrateBiomass(), calibrateYield() to set the model scale to agree with total observed biomass or total observed yield. Uses the new scaleModel().
• New matchBiomasses() and matchYields() will try to adjust the abundances of the species to produce the observed biomasses or yields. See blog post at https://bit.ly/2YqXESV .
• There are now accessor and replacement functions for rates. So for example instead of params <- setReproduction(params, maturity = my_maturity) one can simply use maturity(params) <- my_maturity. These are documented together with the setter functions. #213
• New setMetadata() to add information to a MizerParams object describing the model, for example a title, a description, the author or list of authors, a url and a doi. This will be particularly useful for sharing your models with others
• New saveParams() for saving a MizerParams object to a file and readParams() for reading it back in. The resulting files can be shared with others who want to run your model.
• A MizerParams object now registers the mizer version under which the model was last saved. Should the model not be working as expected in the current version of mizer, you can go back to the older version under which presumably it was working. This helps with the reproducibility of your research.
• A MizerParams object registers the time when it was created and the time it was last modified. See getMetadata(). This helps you keep track of different versions of your model.
• steady() now has a preserve argument with possible values erepro, R_max or reproduction_level to specify which quantity to preserve. This means that one can continue to use steady() also once one has started to tune the density dependence in reproduction. #208
• Our website is now using the nice new mizer logo designed by Kira Askaroff (www.kiraaskaroff.com)
• There is a new mizer extension package mizerMR allowing you to include multiple resource spectra in your model.

Small improvements

• The rownames of gear_params are now set to "species, gear", so that one can access individual entries with for example gear_params(NS_params)["Cod, Otter", "catchability"]. #212
• The z0 argument of setExtMort() has been deprecated in favour of ext_mort in order to avoid confusion with the species parameter z0.
• setColours() and setLinetypes() now issue warnings when invalid values are given and ignores NAs.
• The experimental comment arguments to the setter functions have been removed. #214
• The setter functions have a new reset argument which, when set to TRUE will recalculate the rates from the species, gear and resource_params even when custom values had been set. #214
• The species argument to various functions, which is checked with valid_species_arg(), now does not throw an error even when there is no valid species included. Only a warning is issued. That means that for example plotSpectra(NS_params, species = list(), total = TRUE) is now allowed.
• getComponent() from the mizer extension mechanism now returns NULL when asked for a non-existent component instead of giving an error. This gives an easy way to check for the existence of a component.
• The example interaction matrix inter for the North Sea model now has the alternative name NS_interaction, with the old name deprecated.
• Species added with addSpecies() are now by default given a reproduction level of 1/4 instead of 0, because at the low densities at which they are introduced there would otherwise not be enough density dependence to stabilise them.
• The size range arguments min_w, max_w, min_l and max_l used in some summary functions and processed by get_size_range_array() accept vector values setting different limits for different species.
• The resource dynamics function is now also passed the resource_rate and the resource_capacity as arguments, which makes it easier to use them in extension packages.
• Species names are now always coerced to strings, even if the user gives them as numbers. #202
• There is a new system for informing the user about how defaults were set by newMultispeciesParams(), #199
• Many improvements in the documentation.
• Many small improvements to code quality and testing.
• Better social media cards, especially for twitter.
• mizer can be run on binder, https://mybinder.org/v2/gh/sizespectrum/mizer/HEAD?urlpath=rstudio

Bug fixes

• Changing linecolour or linetype in the species parameters now actually changes the linecolours and linetypes as intended.
• Growth curves calculated with getGrowthCurves() and plotted with plotGrowthCurves() are now correct, and no longer extend above the asymptotic size.
• plotGrowthCurves() with species_panel = TRUE now respects the species argument to only show growth curves for selected species, it works with a MizerParams object as well as a MizerSim object, and it shows the panels in the correct order. #201
• Reinstated the example .csv files that were missing from the package because the vignettes are no longer included.

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Published by gustavdelius over 4 years ago

mizer - v2.2.1

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Published by gustavdelius over 4 years ago

mizer - v2.1.0

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Published by gustavdelius almost 5 years ago

mizer - v2.0.4

A maintenance release

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Published by gustavdelius over 5 years ago

mizer - v2.0.3

A maintenance release.

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Published by gustavdelius over 5 years ago

mizer - v2.0.2

A maintenance release.

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Published by gustavdelius almost 6 years ago

mizer - v2.0.1

A maintenance release.

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Published by gustavdelius almost 6 years ago

mizer - v2.0.0

This is a major new release with many new features, an internal refactoring of the code and a new extension mechanism.

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Published by gustavdelius almost 6 years ago

mizer -

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Published by gustavdelius almost 7 years ago

mizer -

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Published by gustavdelius almost 7 years ago

mizer - Performance Improvements

mizer 0.4

• Improvements made to the speed by evaluating convolution sums via fft, removing the bottlenecks in getPhiPrey() and getPredRate().
• Using C++ for the inner loop in the project method for extra speed.
• Minor corrections to vignette and documentation to bring them into alignment and to document the new home on github and new maintainers.

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Published by gustavdelius about 8 years ago