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NEWS
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mizerRewire 1.1
-----------
* Added function to get diet of predators
* Removed discrepancies between FFT method and old method for calculating integrals
* Values for minimum plankton size, and minimum and maximum consumer sizes set
automatically
* Allowing feeding kernel to be kept even when using FFT methods
* Function change_pred_kernel() for changing predation kernel
* Set names on arrays returned by getAvailEnergy and getPredRate
* Correctly deal with NAs in species parameters
* Consistently cutting off predation kernel at 0 and beta + 3 sigma
* Changed way cc_pp is calculated to reduce rounding errors
* Allowing set_scaling_model() to produce perfectly scale-invariant model when
perfect = TRUE
* Using Singular Value Decomposition to retune background species to keep
community close to power law
* Background species with very low abundances are automatically removed
* Converted all S4 methods to functions to decrease the learning curve for
new developers.
* Changed naming convention: function names are now in camelCase
* Renamed some functions for consistency and to make them easier to understand,
but kept old names as aliases for backwards compatibility:
-- getPhiPrey -> getAvailEnergy
-- getmM2 -> getPredMort
-- getM2background -> getPlanktonMort
-- getZ -> getMort
-- getESpawning -> getERepro
-- MizerParams -> emptyParams or multispeciesParams
* Improvement 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
* Started work on two new vignettes:
-- developer_vignette.Rmd
-- mathematical_details.Rmd
* Code improvements:
-- Starting to use assert_that to check arguments to functions
-- Added more unit tests
mizerRewire 1.0
-----------
* 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.
* project() now shows a progress bar while simulation is running.
* Improvements to plots:
-- Added units to axes
-- Added method for plotting growth curves
-- PlotYield no longer fails when species names are numbers or when a
species abundance is zero
-- Added a "total" parameter to several plot methods to add the curve for the
total community (sum over all species and plankton)
-- Added a "species" parameter to all plot methods 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.
* Add initial_n and initial_n_pp slots to mizer params.
* Now checking that effort times are increasing.
* Corrections in the documentation.
* Improvements to the vignette.
* Fix potential problems with negative numbers due to numerical errors.
* Fix a bug in the divisibility checks.
* Add a test of the numeric solution against an analytic solution.
mizerRewire 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.
mizerRewire 0.3
-----------
* Improvements made to the speed of the simulations. Remaining bottle necks are the sweep statements in getPhiPrey() and getPredRate().
* Moved tests to new suggested folder.
* Minor changes to documentation to pass new check requirements.
mizerRewire 0.2
-----------
* Release to coincide with the submission of the MEE paper. No major changes. Just minor bug fixes.
mizerRewire 0.1
-----------
* Beta release - just about works but still some gremlins to sort out.
There are a number of features I'd like to add in the coming relases.