Providing setup function for feeding kernel with variable PPMR #41
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gustavdelius
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This merges latest development version to the master branch. Here is the list of changes since the last released version implemented by this pull request (which contains the changes from the dev branch): ## Modelling unstructured resources Besides the size-structured planktonic resource, mizer can now also model any number of unstructured resource components. Such unstructured components are appropriate whenever the predation on these componente is not size based. Possible applications include the modelling of detritus as a resource for detritovores, carrion as a resource for scavengers, or macroflora on which fish can graze. (#46) * Each unstructured resource component can have its own dynamics, with its own parameters. These are set up with `changeResourceDynamics()`. * Each species can be set to consume resources. The rates are set up with `changeResourceEncounter()`. * Example dynamics are provided in `carrion_dynamics()` and `detritus_dynamics()`. ## Setting model parameters After setting up a mizer model, it is possible to change specific model parameters with the new functions * `changePredKernel()` * `changeSearchVolume()` * `changeInteraction()` * `changeIntakeMax()` * `changeMetab()` * `changeBMort()` * `changeReproduction()` * `changeFishing()` * `changePlankton()` * `changeResourceDynamics()` * `changeResourceEncounter()` The new function `changeParams()` is a wrapper for all of the above functions and is also used when setting up a new model with `set_multispecies_model()`. (#51) ## Plotting * 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. * New `plotGrowthCurves()` plots growth curves and compares them to the von Bertalanffy growth curve. * New `highlight` argument 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. * New `plot()` method for MizerParams object to plot the initial state. * Avoiding duplicate graphs in rmarkdown documents by setting the default for the `print_it` argument in plot functions to `FALSE`. * New `wlim` argument to `plotSpectra()` in analogy to the existing `ylim` argument to limit the w range in the plot. * New arguments `xlab` and `ylab` for `displayFrames()`. * Use colour and linetype for plots irrespective of the number of species. * Plot background species in the colour specified in the `linecolour` slot. ## General feeding kernel * 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. * New `box_pred_kernel()` implements a box-shaped kernel as an alternative to the default `lognormal_pred_kernel()`. * Users can sets a predation kernel that has a predator-size-dependent predator/prey mass ration (via `changePredKernel()`). Mizer automatically falls back on the old non-FFT code to handle this. (#41) * New `getPredKernel()` returns the full 3-dimensional predation kernel array, even when this is not stored in MizerParams object. ## Other new features * `project()` now shows a progress bar while a simulation is running. Can be turned off with `progress_bar = FALSE` argument. * New `getDiet()` calculates the diet of predators. (#43) * Satiation can be switched off by setting the maximum intake rate to `Inf`. * Users can now set their own plankton dynamics instead of the default `plankton_semichemostat()`. * Different species can interact with plankton with different strengths, or not feed on plankton at all, controlled by an `interaction_p` column in the species parameter data frame. * The steepness of the maturity ogive can now be controlled via a `w_mat25` column 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 resources into reproduction can now be set via the `m` column 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 `append` argument then controls whether the new results are appended to the old. * New `getGrowthCurves()` calculates the growth curves (size at age). * Values for minimum plankton size, and minimum and maximum consumer sizes are set automatically if not provided in `set_multispecies_model()`. * 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. * New `getRates()` calculates all the rates needed in the model and collects them in a list. * Can set initial state with `changeInitial()`. * Rate functions take defaults for their `initial_n`, `initial_n_pp` and `initial_B` arguments from the corresponding slot in the `params` argument. * Can remove a species from a model with `removeSpecies()`. * New `perfect` argument allows `set_scaling_model()` to produce a perfectly scale-invariant model. * In `retuneAbundance()`, Singular Value Decomposition is used to retune background species to keep the community close to power law. Background species with very low abundances are automatically removed. * Renamed some functions for consistency and to make them easier to understand, but kept old names as aliases for backwards compatibility: + `getmM2()` -> `getPredMort()` + `plotM2` -> `plotPredMort()` + `getM2background()` -> `getPlanktonMort()` + `getZ()` -> `getMort()` + `getESpawning()` -> `getERepro()` + `MizerParams()` -> `emptyParams()` or `set_multispecies_model()` ## Documentation * Mizer now has a documentation website at <https://sizespectrum.github.io/mizer> for the latest released version and at <https://sizespectrum.github.io/mizer/dev> for the development version. (#48) * The help pages of mizer functions has been extended massively, see for example the help for `set_multispecies_model()`. * The vingnette 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) ## Bug fixes * In `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) * `getEncounter()` and `getPredRate()` now set names on the returned arrays. * Plankton 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. * The `ylim` argument is not handled correctly in plots. * `display_frame()` is now exported. ## Under the hood * Increased regression test coverage from 67% to 86%. * Converted all S4 methods to functions to decrease the learning curve for new developers. * The calculation of defaults is now handled by new `get_gamma_default()`, `get_h_default()` and `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. * Using `@inherit` functionality 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 unstructured resources. Even in the absence of unstructured resources, `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 `params` to refer to an argument of class MizerParams, `sim` to refer to an argument of class MizerSim, and `object` to an argument that can be either. * Updated the calls to `setClass()` to follow the new guidelines, replacing `representation` by `class` and removing `prototype` and `validity`. * Added numerical tests. * Using assert_that to check arguments to functions more often. * Argument `shiny_progress` renamed to `progress_bar` because they control any type of progress bar. * In documentation renamed "background" to "plankton". * Using `outer()` instead of `tapply()` where possible to improve readability. * Avoiding use of `hasArg()` and `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. * Changes to MizerParams class: + Merged `std_metab` and `activity` slots into a single `metab` slot. + Moved `w_min_idx` out of `species_params` into its own slot. + Added slot `maturity` to hold the maturity ogive. + Added slot `rho` to hold the resource encounter rates. + Added slot `pred_kernel` to hold predation kernel if it has variable predator/prey ratio. + Added slot `plankton_dynamics` to allow user to specify alternative plankton dynamics. + Addes slots `resource_dynamics` and `resource_params`. + Added slot `initial_B` for the initial biomasses of the resources. * Changes to MizerSim class: + Added slot `B` to hold resource biomasses over time
SamikDatta
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Sep 6, 2019
Added set_scaling_model() to set up a scale-invariant trait-based model. Closing sizespectrum#19
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There are important cases where species are expected to have variable PPMR with size. This applies to planktivorous fish, that feed on small prey even when they grow large. Same is true for many coastal benthivorous fish, which are dominant species in e.g. Tasmanian coastal model. This point was made by @astaaudzi in a comment in issue #40
A particular choice for a feeding kernel with variable PPMR is published in Heneghan et al. 2016 (http://journal.frontiersin.org/article/10.3389/fmars.2016.00201/abstract) and only requires one extra parameter m. The code is more or less implemented in https://github.com/astaaudzi/mizer-rewiring (although the final version has not been pushed yet). We are just waiting for the resolution on the differences between different integration method for the feeding kernel (issue #39)
The way this should be added to mizer is to provide a new setup function that populates the feeding kernel slot in a MizerParams object with this new feeding kernel. No other changes to the mizer code are needed for this.
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