- Resolved conflict in
mizerPredRate()between the argument
tand the function
- Assert that upgradeParams() must be called with a MizerParams object and
upgradeSim()with a MizerSim object.
- Errors changed to warnings in
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.
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.
CRAN release: 2021-09-11
- New plots
plotYieldObservedVsModel()contributed by @SamikDatta., together with their plotly counterparts.
calibrateYield()to set the model scale to agree with total observed biomass or total observed yield. Uses the new
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
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
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
preserveargument with possible values
reproduction_levelto 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.
- The rownames of
gear_paramsare now set to “species, gear”, so that one can access individual entries with for example
gear_params(NS_params)["Cod, Otter", "catchability"]. #212
setExtMort()has been deprecated in favour of
ext_mortin order to avoid confusion with the species parameter
setLinetypes()now issue warnings when invalid values are given and ignores NAs.
- The experimental
commentarguments to the setter functions have been removed. #214
- The setter functions have a new
resetargument which, when set to
TRUEwill recalculate the rates from the species_, gear_ and resource_params even when custom values had been set. #214
speciesargument 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
interfor 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
max_lused 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_capacityas 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
- 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
linetypein 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.
species_panel = TRUEnow respects the
speciesargument 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.
CRAN release: 2021-08-03
setBevertonHolt()function has been expanded with more arguments. It allows you to change the density dependence in reproduction without changing the steady state of your model.
- The new
getReproductionLevel()function tells you at what proportion of their maximum reproduction rate the species are operating in your model.
- The package now comes with an example MizerSim object
NS_simwhich holds a simulation of the North Sea model.
- New function
plotDataFrame()allows easier creation of plots.
setInitialValues()correctly preserves the gear names on the initial effort. Thanks to Axel Rossberg.
getFMort()correctly passes the
targument on to any custom fishing mortality function you may have written.
- The legends in the plots now only show the species that are actually included in the plot.
- Speed improvement in
mizerPredMort()suggested by Axel Rossberg.
plotSpectra()now only shows those species in the legend that are actually contained in the plot.
- Updated tests of plots to use new version of vdiffr package.
- Some improvements to the examples on the help pages.
- Some functions do more thorough tests of their arguments to give more useful error messages.
initialNOther()also works with MizerSim object.
projectToSteady()is called with
effort, this effort is now also stored in the
- Improvement to
summary()which is now using
sprintf()for better formatting and also gives the initial_effort.
- Improved documentation of size grid and bins.
- The arguments to
project_simple()have been given convenient defaults.
- The tooltips in the plotly plots have been cleaned up a bit.
- Species names are now always coerced to strings, even if the user supplies numeric names.
- Update to the “A Multi-Species Model of the North Sea” tutorial to use
CRAN release: 2021-06-24
- New function
newSingleSpeciesParams()for creating a single species in a power-law background.
- New function
animateSpectra()creating an animated plot of a simulation.
- New functions
- The parameters for an ecosystem component added with
setComponent()can now take any form, they no longer have to be a named list.
- New argument
return_datain the plot’s functions allows to return the data frame used for the ggplot instead of the plot.
getYield()now also works with density-dependent fishing mortality. Thanks to James Roger for discovering the problem.
gammaargument now is no longer ignored in
newTraitParams()but correctly overrides the
getFMort()again works correctly when called with a MizerSim object.
resource_semichemostat()no longer fail when at some sizes both the resource growth rate and the resource mortality rate are both zero.
- The default for
newTraitParams()is now always an integer.
- Problems with different machine precision no longer prompts the error “The
w_min_idxshould point to the start of the size bin containing the egg size
- `addSpecies() no longer extends grid due to rounding errors.
valid_species_arg()is called with
species = NULLand there are no background species then it returns
CRAN release: 2021-03-21
- New function
projectToSteady()to run the full dynamics to steady state.
- New functions
distanceMaxRelRDI()to measure distance between two states.
- New function
compareParams()to compare two MizerParams objects.
constantEggRDI()to allow keeping egg densities fixed.
- When setting custom parameter arrays with the setter functions, it is now easy for the user to document that via “comment” arguments. #177
- New function
customFunction()to allow users to overwrite mizer functions.
- Now if the effort is specified as a named vector giving values only for some gears, the effort for the remaining gears is assumed to be zero.
- Added the possibility to see the output of
plotGrowthCurvesas a panel of species with their respective Von Bertalanffy curves
- By default, the functions
plotFMortwill stop displaying mortality values past the species’ asymptotic size. The argument
all.sizesallows you to continue to show these values.
lifecyclepackage to indicate status of some functions and arguments as ‘experimental’ or ‘deprecated’.
- Improved error handling in
- Made use of vdiffr conditional, as required by §184.108.40.206 of ‘Writing R Extensions’.
- Consistent handling of
speciesargument in mizer functions, via the new
- More tests. Test coverage now at 94.71%
- Improved argument checking in
- Throwing error if
min_w_ppis larger than
- Improved documentation of functions for getting fishing mortality.
CRAN release: 2020-08-30
- The value of
tpassed to dynamics functions has been corrected.
setReproduction()now correctly sets the the total proportion psi when the maturity proportion is changed.
- The way times are set in
project()has been simplified. They are now either set by the arguments
t_saveor by the dimension names of the
setBevertonHolt()and allow it to work on an arbitrary MizerParams object. The old name
setRmax()is still available as alias.
mizerFMort()now can also use the abundances and the rates
pred_mort. This is useful for example for implementing balanced harvesting.
- A calculation in the numeric scheme has been simplified.
gear_paramsis allowed to have zero rows.
validGearParams()the species name is used as gear name in case
validGearParams()ensures that all required arguments of the selectivity function are supplied and checks validity of species names.
steady()fails because RDI is zero it gives a meaningful error message.
newCommunityParams()now protects its zero investment in reproduction with a comment.
- The default maturity ogive is truncated at proportions smaller than 1e-8.
- A new helper function
valid_species_arg()checks validity of species selection arguments.
upgradeParams()can now also upgrade old MizerParams objects that do not have a consistent
- A new helper function
validParams()validates a MizerParams object and automatically upgrades it with
- Old MizerParams objects are updated automatically when used in plot functions, rate functions, summary functions or in
- New function
getRates()to calculates all rates and collects them in a list.
return_sim = TRUEnow creates the MizerSim object the same way as
project(), namely with the original values in the first time slot.
- Added documentation for
- Numerous small improvements to documentation.
CRAN release: 2020-07-28
- Correct handling of shiny progress bar in
- Consistently passing the time argument to the rate functions. This will allow extensions to implement time-dependent rates.
- Passing growth and mortality rate to RDI function.
- Simplified the
getRates()functions by removing the arguments that passed in other rates. Instead the required rates are now always calculated within these functions.
- Improved documentation of rate functions and of how to register your own rate functions.
validGearParams()handle NAs more gracefully and check that there are no duplicates.
- Updated hake-mullet selectivity demonstration shiny app.
- Improved user documentation in several places.
CRAN release: 2020-06-08
- Time passed to rate functions is now the actual simulation time, not the time elapsed since start of simulation.
upgradeParams()works also on params objects that were created with a development version of mizer.
- When upgrading an older params object,
upgradeParams()does a better job at guessing the value for
steady()now work also when model has extra components.
- The critical feeding level lines are now mentioned in the legend of
plotFeedinglevel()when called with
include_critical = TRUE, see #162.
- Avoid annoying warnings from dplyr package when
species_paramsis a tibble.
- Some improvements to documentation.
- More unit tests.
- Uses less memory when time step is very small by not creating array with effort values at each time step.
getDiet()also takes into account possible contributions by user-defined other components.
- In extension mechanism, now the name of a component is also passed to the functions implementing dynamics, encounter and mortality.
project()is called with
t_max < t_savethen
t_saveis automatically reduced so that the result at
t_maxwill get saved.
- Start showing progress bar earlier during
- New helper function
project_simple()that projects a given number of time steps. This might be useful to extension writers.
project()is passed on to the dynamics and rate functions.
steady()runs faster by using
- Documentation on mizer website now has a search bar.
CRAN release: 2020-05-05
Some inconsistencies in the choice of names for parameters was removed by renaming
CRAN release: 2020-04-04
This is a major new release with many new features, an internal refactoring of the code and a new extension mechanism.
Nevertheless this version of mizer is almost fully backwards compatible with version 1.0 with the exception of bug fixes and the following breaking changes:
- The previous version of mizer inconsistently truncated the lognormal predation kernel when calculating predation but not when calculating encounter. The new version never truncates. That leads to very small differences in simulation results.
- Removed the
print_itargument from plot functions.
plotFeedingLevel()now only plots the values within the size range of each species. If for some reason you want the old plots that show a feeding level also for sizes that the fish can never have, you need to supply an argument
all.sizes = TRUE.
- The way the density-dependence in the reproduction rate is set has changed, see
sex_ratioargument has been removed from
set_scaling_model()function has been removed because such models can now be set up with
newTraitParams()with the options
perfect_scaling = TRUEand
egg_size_scaling = TRUE.
- The functions
retuneAbundance()have been removed to the “mizerExperimental” package (https://sizespectrum.org/mizerExperimental/)
- During runs of
project()a progress bar is displayed by default. You can turn this off with the option `progress_bar = FALSE.
- Throughout mizer the term “plankton” has been replaced by “resource”, which affects the labelling of the resource spectrum in plots.
The new functions
replace the old functions
MizerParams(), which are now deprecated. The new functions choose better default values, in particular for metabolic rate and maximum intake rate.
After setting up a mizer model, it is possible to change specific model parameters with the new functions
The documentation for these functions serves to explain the details of the mizer model.
Along with these setter functions there are accessor functions for getting the parameter arrays:
- Setting of the maximum reproduction rate has been separated out into new function
The MizerParams object now also contains the initial values for the size spectra. This is particularly useful if the model has been tuned to produce the observed steady state. The new function
steady() finds a steady state for a model and sets it as the initial value. The initial values can be accessed and changed via functions
initialNResource(). The initial values can be set to the final values of a previous simulation with
The MizerParams object now has a slot
initial_effort that specifies the initial fishing effort to which the steady state has been calibrated.
Mizer now has an extension mechanism that allows other R packages to be written to generalise the mizer model. See
setComponent(). This mechanism is still experimental and may change as we gain experience in writing extensions for mizer.
- Every plot function now has a plotly version that makes the plot interactive using the plotly package. So for example there is
plotlyBiomass()as the plotly version of
plotBiomass(), and so on.
plotGrowthCurves()plots growth curves and compares them to the von Bertalanffy growth curve.
plotDiet()plots the diet composition as a function of predator size.
highlightargument to all plot functions that display curves for multiple species. Displays highlighted species with wider lines.
- In the legends of all plots the species are now consistently ordered in the same way as in the species parameter data frame.
- All plot functions that are not time-resolved now accept also a MizerParams object as an alternative to the MizerSim object to plot the initial state.
plot()method for MizerParams object to plot the initial state.
- Avoiding duplicate graphs in R Markdown documents.
- New argument
plotFeedingLevel()allows to show also the critical feeding level.
plotSpectra()in analogy to the existing
ylimargument to limit the
wrange in the plot.
- The colours used in plot functions can be set with
- The default line type is
solidbut this can be changed via the
- Use colour and linetype for plots irrespective of the number of species.
- Users can now replace the lognormal function in the predation kernel by a function of their choice, allowing a differently shaped kernel for each species.
box_pred_kernel()implements a box-shaped kernel as an alternative to the default
power_law_pred_kernel()implements a power-law kernel with sigmoidal cutoffs at both ends. This is suitable for filter feeders.
- Users can sets a predation kernel that has a predator-size-dependent predator/prey mass ration (via
setPredKernel()). Mizer automatically falls back on the old non-FFT code to handle this. (#41)
getPredKernel()returns the full 3-dimensional predation kernel array, even when this is not stored in MizerParams object.
- There are now accessor functions for all slots in the MizerParams and MizerSim objects. For example to get at the size grid and its spacing you would now use
upgradeSim()can upgrade objects from previous versions of mizer so they work with the new version.
getDiet()calculates the diet of predators. (#43)
- Alternative functions
SheperdRDD()for density-dependence in reproduction, as well as
- New gear selectivity function
double_sigmoid_length()allows modelling of escape of large individuals.
- New gear selectivity function
sigmoidal_weight()is weight-based trawl selectivity function. (Ken H Andersen)
getGrowthCurves()calculates the growth curves (size at age).
mizerRates()calculates all the rates needed in the model and collects them in a list.
- A convenience function
times()to extract the times at which simulation results are saved in a MizerSim object.
- Convenience functions
finalNOther()as well as
idxFinalT()to access the values at the final time of a simulation.
- New function
getCriticalFeedingLevel()returns the critical feeding level for each species at each size.
- Mizer reexports the
melt()function from the reshape2 package which allows users to convert the arrays returned by mizer functions into data frames that can be used for example in ggplot2 and plotly.
validSpeciesParams()checks validity of species parameter data frame and sets defaults for missing but required parameters.
- The allometric exponents
qas well as the feeding level
f0can now be set at the species level via columns in
- The critical feeding level
fccan now be specified as a species parameter and will be used to calculate the metabolic rate parameter
ksif it is not supplied.
project()now shows a progress bar while a simulation is running. Can be turned off with
progress_bar = FALSEargument.
- Satiation can be switched off by setting the maximum intake rate to
- Users can now set their own resource dynamics instead of the default
- Different species can interact with resource with different strengths, or not feed on resource at all, controlled by an
interaction_resourcecolumn in the species parameter data frame.
- The steepness of the maturity ogive can now be controlled via a
w_mat25column in the species parameter dataframe, which gives the size at which 25% of the individuals of a species are mature.
- The scaling exponent for the allocation of energy into reproduction can now be set via the
mcolumn in the species parameter data frame.
project()can now continue projection from last time step of a previous simulation if the first argument is a MizerSim object. The new
appendargument then controls whether the new results are appended to the old.
- Values for minimum resource size, and minimum and maximum consumer sizes are set automatically if not provided in
- Default values for species parameters are used for missing values within a column in the species parameter data frame, not only if the column is missing entirely.
- Rate functions take defaults for their
n_otherarguments from the initial values in the
newTraitParams()to produce a perfectly scale-invariant model.
- A new
newTraitParams()allows the inclusion of external mortality.
- Added a data file
NS_paramswith the North Sea model MizerParams object.
- Comments can be added to MizerParams objects and any of their slots. Slots that have comments are protected from being overwritten with allometric defaults.
- Gear selectivity functions now can use the species parameters.
- Mizer now has a documentation website at https://sizespectrum.org/mizer/ for the latest released version and at https://sizespectrum.org/mizer/dev/ for the development version. (#48)
- The help pages of mizer functions has been extended massively, see for example the help for
- The vignette chapters are shown as pages on the website.
- The html help pages for plotting functions now show example plots.
- Clarified that mizer uses grams and years as size and time units and is agnostic about whether abundances are per area, per volume or per study area. (#42)
- Added a tutorial on using ggplot2 and plotly with mizer.
- Added a tutorial on working with git and GitHub for mizer development.
- Added a FAQ page for developers.
- Added a unit test to automatically run a spell check on documentation.
- Renamed some functions for consistency and to make them easier to understand, but kept old names as aliases for backwards compatibility:
- Renamed maximum reproductive rate from
- Updated list of publications (@Kenhasteandersen)
- Using R Markdown in all roxygen comments.
getSSB(), the calculation of the spawning stock biomass is done correctly using the maturity ogive instead of the proportion of energy allocated to reproduction. (#47)
- The fast FFT method and the old method for calculating integrals now give the same numerical results. (#39)
getPredRate()now set names on the returned arrays.
- Resource carrying capacity for scale-invariant model is calculated in a way that reduces rounding errors.
- Avoids potential problems with negative numbers due to numerical errors.
- Consistently cutting off predation kernel at 0 and beta + 3 sigma.
ylimargument is not handled correctly in plots.
display_frame()is now exported.
getGrowthCurves()also works when there is only a single species
project()is used correctly
- times are not truncated at 3 significant figures, because that would not allow something like 2019.
get_initial_n()gets values for
qfrom params object
summary()of MizerParams object reflects the number of non-empty resource bins. (@patricksykes)
- Now using vdiffr package to test plots.
- Converted all S4 methods to functions to decrease the learning curve for new developers.
- The calculation of defaults is now handled by new
get_ks_default(), making it easier to change or extend these in the future.
- Helper function
set_species_param_default()makes it easier to set default values for species parameters.
- Simplified FFT calculations are more readable.
@inheritfunctionality of roxygen2 to reduce duplication in roxygen documentation.
- Using `@family’ to group function documentation pages.
- The helper functions are now documented and exported.
getPhiPrey()is replaced by
getEncounter()which now returns the full encounter rate, including the contribution from other components. Even in the absence of other components,
getEncounter()differs from the old
getPhiPrey()because it includes the search volume factor.
- Changed naming convention: user-facing function names are now in camelCase.
- Consistently use
paramsto refer to an argument of class MizerParams,
simto refer to an argument of class MizerSim, and
objectto an argument that can be either.
- Updated the calls to
setClass()to follow the new guidelines, replacing
- Added numerical tests.
- Using assert_that to check arguments to functions more often.
progress_barbecause they control any type of progress bar.
- In documentation renamed “background” and “plankton” consistently to “resource”.
tapply()where possible to improve readability.
- Avoiding use of
anyNA()because they were not available in R 3.1
- A more robust code for setting up the size grids.
- Improved consistency of when to issue warnings and when to issue messages.
- Split large code files into smaller files.
- Changes to MizerParams class:
@activityslots into a single
@species_paramsinto its own slot.
- Added slot
@maturityto hold the maturity ogive.
- Added slot
@pred_kernelto hold predation kernel if it has variable predator/prey ratio.
- Added slot
@resource_dynamicsto allow user to specify alternative resource dynamics.
- Added slot
@gear_dynamicsto species to be targeted by multiple gears.
- Added slot
@ft_maskthat is used when calculating predation rates using the Fourier transform method.
- Added slot
@rates_funcsto allow mizer extensions to replace mizer rate functions with their own rate functions.
- Instead of the function in the slot
@srrwe now have the name of the function in
@rate_funcs$RDD, see #91.
- Added slots
@initial_n_otherto allow mizer extensions to add more ecosystem components.
CRAN release: 2019-01-27
- Now compatible with older versions of R > 3.1.0.
- Skipping a test on CRAN that fails on some machines with different precision.
- Fixing minor typos in documentation.
CRAN release: 2018-05-01
- Fixed bugs in how the start time of a simulation was handled. This leads to small corrections, so that the output of this version is slightly different from previous versions.
- Introduced a scale-invariant trait-based model, set up with
set_scaling_model(), see section 12 in the vignette.
- Added a function that adds news species to a scale-invariant background, and computes an approximately steady state close to the power law, see section 13 in the vignette.
- Created an example shiny app to allow people to use mizer through a web browser without having to install mizer. The app explores the effect of more selective fishing gear in a case study.
- Improvements to plots:
- Added units to axes
- Added function for plotting growth curves
PlotYield()no longer fails when species names are numbers or when a species abundance is zero
- Added a
totalparameter to several plot functions to add the curve for the total community (sum over all species and resource)
- Added a
speciesparameter to all plot functions to allow for only a selection of species to be plotted
- Allow the number of ticks on y-axis in biomass plot to be controlled
- Allow for size- and species-dependent background death.
@initial_n_ppslots to MizerParams class.
- Now checking that effort times are increasing.
- Corrections in the documentation.
- Improvements to the vignette.
- Add a test of the numeric solution against an analytic solution.
CRAN release: 2017-12-14
- Improvements made to the speed by evaluating convolution sums via fft, removing the bottlenecks in
- 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.
CRAN release: 2014-04-16
- Release to coincide with the submission of the MEE paper. No major changes. Just minor bug fixes.