sizespectrum/mizer issues and pull requests

#304 - Adjust plotDiet() to Restrict Plots to Relevant Size Ranges

Issue - State: open - Opened by JamesRimmerEco 16 days ago - 1 comment

#303 - Confusing documentation of `kappa`

Issue - State: closed - Opened by gustavdelius 24 days ago
Labels: documentation

#302 - Rename `params` argument to `w2l()` and `l2w()` to `species_params`

Issue - State: open - Opened by gustavdelius about 2 months ago
Labels: minor effort

#301 - Round down `w_repro_max` to next-lower point on w grid

Issue - State: open - Opened by gustavdelius about 2 months ago

#300 - What to do if not all fish are mature at maximum size?

Issue - State: open - Opened by gustavdelius 2 months ago
Labels: discussion

#299 - `getReproductiveProportion()` can return values > 1

Issue - State: closed - Opened by gustavdelius 2 months ago
Labels: bug

#298 - Issue warning when a species abundance is not negligible above its w_max

Issue - State: open - Opened by gustavdelius 4 months ago
Labels: enhancement, core, minor effort

#297 - Mistake in numerical differentiation

Issue - State: open - Opened by gustavdelius 4 months ago
Labels: discussion, core, major effort

#296 - Changing `w_max` should also change `ft_mask`

Issue - State: closed - Opened by gustavdelius 4 months ago
Labels: bug

#295 - `steadySingleSpecies()` does not update `time_modified`

Issue - State: closed - Opened by gustavdelius 4 months ago
Labels: bug, minor effort

#294 - `summary()` should also show metadata

Issue - State: open - Opened by gustavdelius 5 months ago
Labels: enhancement, minor effort

#293 - The output of `newCommunityParams()` changed in version 2.4.0

Issue - State: closed - Opened by gustavdelius 6 months ago - 1 comment
Labels: bug

#291 - Make `matchGrowth()` work when `n != p`

Issue - State: open - Opened by gustavdelius 10 months ago

#290 - `addSpecies()` should get `info_level` argument

Issue - State: open - Opened by gustavdelius 10 months ago
Labels: enhancement, minor effort

#289 - External encounter rate

Issue - State: closed - Opened by gustavdelius 11 months ago - 1 comment
Labels: enhancement, core, minor effort

#288 - Using ratio by default for plotBiomassObservedVsModel...

Pull Request - State: closed - Opened by SamikDatta 11 months ago - 14 comments

#287 - Append argument in project function appears non-functional

Issue - State: closed - Opened by JamesRimmerEco 12 months ago - 1 comment

#287 - Append argument in project function appears non-functional

Issue - State: closed - Opened by JamesRimmerEco 12 months ago - 1 comment

#286 - Adapt `plotYieldObservedVsModel()` and `matchYield()` to work with multiple gears

Issue - State: open - Opened by gustavdelius almost 2 years ago

#285 - Other components at all time steps are always equal to final time step

Issue - State: closed - Opened by gustavdelius about 1 year ago
Labels: bug, core

#284 - Getting ready for version 2.5.0

Pull Request - State: closed - Opened by gustavdelius about 1 year ago

#283 - `get_phi()` should check that it returns valid positive values

Issue - State: closed - Opened by gustavdelius over 1 year ago
Labels: setting parameters, minor effort

#282 - `get_h_default()` should provide default even when no growth info is available

Issue - State: closed - Opened by gustavdelius over 1 year ago
Labels: bug, setting parameters, minor effort

#281 - Different resource's default values between newTraitParams() and newMultispeciesParams()

Issue - State: open - Opened by baldrech almost 2 years ago - 1 comment

#280 - In `addSpecies()` only issue warning if feeding level drops below critical level

Issue - State: open - Opened by gustavdelius about 2 years ago
Labels: enhancement, setting parameters, minor effort, low priority

#279 - `matchGrowth()` gives error when there is no `w_inf` column

Issue - State: closed - Opened by gustavdelius about 2 years ago - 1 comment
Labels: bug, setting parameters, minor effort

#278 - Speed up inner loop

Issue - State: open - Opened by gustavdelius about 2 years ago
Labels: enhancement, core, minor effort

#277 - Don't warn repeatedly when l_mat and w_mat are inconsistent

Issue - State: closed - Opened by gustavdelius about 2 years ago - 2 comments
Labels: setting parameters, minor effort

#276 - Release mizer 2.4.0

Issue - State: closed - Opened by gustavdelius about 2 years ago

#275 - Iterative method for finding steady state

Issue - State: closed - Opened by gustavdelius about 2 years ago - 1 comment
Labels: enhancement

#274 - Extra parameters to model discards

Issue - State: closed - Opened by gustavdelius about 2 years ago - 2 comments
Labels: enhancement

#273 - Better error message when `getParams()` is not called with MizerSim object

Issue - State: closed - Opened by gustavdelius about 2 years ago

#272 - Avoid using $ notation for species parameters with short names

Issue - State: closed - Opened by gustavdelius about 2 years ago
Labels: minor effort, code improvement, low priority

#271 - Set and document default for exponents in `set...()` functions

Issue - State: open - Opened by gustavdelius about 2 years ago
Labels: setting parameters, documentation, minor effort, code improvement, low priority

#270 - Fix colours for species in NS_params

Issue - State: closed - Opened by gustavdelius about 2 years ago
Labels: bug, plots, minor effort

#269 - Comment on `w_inf` leads to error in `plyr::aaply()`

Issue - State: closed - Opened by gustavdelius about 2 years ago
Labels: bug, setting parameters, minor effort

#268 - Comment field not preserved by `set_species_param_default()`

Issue - State: closed - Opened by gustavdelius about 2 years ago
Labels: bug, setting parameters, minor effort

#267 - Allow `plotDiet()` to display diets of several species

Issue - State: closed - Opened by gustavdelius about 2 years ago
Labels: enhancement, plots, minor effort

#266 - Wrong species listed in the legend of `plotYieldObservedVsModel()`

Issue - State: closed - Opened by gustavdelius about 2 years ago - 1 comment
Labels: bug, plots

#265 - ggplot2.3.4 has changed the ordering of legends in `plotDiet()`

Issue - State: closed - Opened by gustavdelius about 2 years ago
Labels: bug, plots, minor effort

#264 - Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.

Issue - State: closed - Opened by gustavdelius about 2 years ago
Labels: plots, minor effort

#263 - Deal better with column names when interaction matrix is read from .csv

Issue - State: closed - Opened by gustavdelius about 2 years ago
Labels: enhancement, setting parameters, minor effort

#262 - The indicator functions should also work with a MizerParams object

Issue - State: open - Opened by gustavdelius over 2 years ago
Labels: enhancement, minor effort, low priority

#261 - Function for automatically adjusting `h` and `gamma` to match observed growth and feeding level

Issue - State: closed - Opened by gustavdelius over 2 years ago - 2 comments
Labels: enhancement

#260 - New species parameter `age_mat` for age at maturity

Issue - State: closed - Opened by gustavdelius over 2 years ago
Labels: enhancement, setting parameters, minor effort

#259 - Distinguish between maximum size and asymptotic size

Issue - State: closed - Opened by gustavdelius over 2 years ago - 6 comments
Labels: enhancement, setting parameters, minor effort

#258 - Add functions for conversion between weight and length

Issue - State: closed - Opened by gustavdelius over 2 years ago
Labels: enhancement, minor effort

#257 - Allow users to specify length-based species parameters

Issue - State: closed - Opened by gustavdelius over 2 years ago - 1 comment
Labels: enhancement, setting parameters, minor effort, low priority

#256 - S4 class-based extension mechanism

Issue - State: open - Opened by gustavdelius over 2 years ago - 2 comments
Labels: enhancement, core

#255 - Better error message when `time_range` is empty

Issue - State: closed - Opened by gustavdelius over 2 years ago
Labels: minor effort, code improvement, low priority

#254 - Warn if step size is too big

Issue - State: open - Opened by gustavdelius over 2 years ago
Labels: enhancement, core

#253 - Incorporate modifications from mizerExperimental

Issue - State: closed - Opened by gustavdelius over 2 years ago

#252 - `getReproductionLevel()` should make sense as long as `R_max` exists

Issue - State: closed - Opened by gustavdelius over 2 years ago

#251 - Give useful error if `valid_species_arg()` is called only with invalid names

Issue - State: closed - Opened by gustavdelius over 2 years ago - 1 comment

#250 - Allow user to specify range on axes in plots

Issue - State: open - Opened by gustavdelius over 2 years ago
Labels: plots

#249 - `newTraitParams()` can produce unrealistic `erepro` values.

Issue - State: open - Opened by gustavdelius over 2 years ago
Labels: setting parameters

#248 - Use `age_max` and `age_mat` in `plotGrowthCurves()`

Issue - State: closed - Opened by gustavdelius over 2 years ago - 2 comments
Labels: enhancement, plots, minor effort

#247 - Accept column names in interaction matrix

Issue - State: closed - Opened by gustavdelius over 2 years ago

#246 - Release mizer 2.3.1

Issue - State: closed - Opened by gustavdelius over 2 years ago

#245 - Let users set steady-state resource abundance and resource level

Issue - State: closed - Opened by gustavdelius over 2 years ago - 1 comment
Labels: enhancement

#244 - `setBevertonHolt()` does not respect `erepro` input

Issue - State: closed - Opened by patricksykes over 2 years ago - 8 comments

#243 - Set initial effort to 1

Issue - State: closed - Opened by gustavdelius about 3 years ago - 3 comments
Labels: enhancement, setting parameters, core, minor effort

#242 - Be careful when decreasing `w_min` or increasing `w_inf`

Issue - State: open - Opened by gustavdelius about 3 years ago

#241 - Allow for non-feeding larval stage

Issue - State: open - Opened by gustavdelius over 3 years ago
Labels: enhancement, minor effort

#240 - adding plot functions from tuneParams

Pull Request - State: closed - Opened by baldrech over 3 years ago - 2 comments

#239 - renameGear()

Issue - State: open - Opened by gustavdelius over 3 years ago
Labels: enhancement, minor effort

#238 - In default for `gamma` take `interaction_resource` into account

Issue - State: closed - Opened by gustavdelius over 3 years ago

#237 - Allow time-dependent rates

Issue - State: open - Opened by gustavdelius over 3 years ago
Labels: enhancement, discussion, extension

#236 - Add a callback function to `project()`

Issue - State: open - Opened by gustavdelius over 3 years ago - 1 comment

#235 - Use resource parameter names `w_min` and `w_max`

Issue - State: open - Opened by gustavdelius over 3 years ago
Labels: enhancement, minor effort

#234 - New function `registerExtension()`

Issue - State: open - Opened by gustavdelius over 3 years ago

#233 - Comparing quantities between mizer and stock-assessment models

Issue - State: open - Opened by michaelspence over 3 years ago - 9 comments
Labels: documentation

#232 - Drop the requirement that interaction matrix entries are between 0 and 1

Issue - State: closed - Opened by gustavdelius over 3 years ago - 3 comments

#231 - Use `t_max` and `t_save` even when effort array is supplied to `project()`

Issue - State: open - Opened by gustavdelius over 3 years ago
Labels: enhancement, low priority

#230 - `validEffortVector()` and `validEffortArray()` should not accept NAs

Issue - State: closed - Opened by gustavdelius over 3 years ago - 1 comment

#229 - `show()` method for MizerParams and MizerSim objects

Issue - State: open - Opened by gustavdelius almost 5 years ago
Labels: enhancement

#228 - Add `background` argument to `animateSpectra()`

Issue - State: open - Opened by gustavdelius over 4 years ago
Labels: enhancement, plots

#227 - `compare()` method for MizerParams class

Issue - State: closed - Opened by gustavdelius almost 5 years ago - 3 comments

#226 - Allow user to call `project()` with a stopping condition

Issue - State: closed - Opened by gustavdelius almost 5 years ago - 9 comments

#225 - addSpecies module not working correctly...

Issue - State: closed - Opened by SamikDatta almost 5 years ago - 1 comment

#224 - Extend `removeSpecies()` to handle `gear_params` correctly

Issue - State: closed - Opened by gustavdelius over 4 years ago - 1 comment

#223 - Add ability to add species with greater asymptotic weight to existing params object using addSpecies

Issue - State: closed - Opened by SamikDatta over 4 years ago - 5 comments

#222 - Document all the arguments to 'addSpecies()'

Issue - State: closed - Opened by gustavdelius almost 4 years ago

#221 - Adding plots for comparing model and observed biomasses...

Issue - State: closed - Opened by SamikDatta over 3 years ago - 8 comments

#220 - Include unobserved species in `plotBiomassObservedVsModel()`

Issue - State: closed - Opened by gustavdelius over 3 years ago - 4 comments

#219 - Metadata for MizerParams

Pull Request - State: closed - Opened by gustavdelius over 3 years ago

#218 - Allow initial_effort to be specified via gear_params data frame

Issue - State: closed - Opened by gustavdelius over 3 years ago - 1 comment

#217 - Clean up use of `@A` and `@sc` slots

Issue - State: open - Opened by gustavdelius over 3 years ago

#216 - Improvements to `addSpecies()`

Pull Request - State: closed - Opened by gustavdelius over 3 years ago

#215 - Check for all functions that documentation and tests agree

Issue - State: open - Opened by gustavdelius over 3 years ago
Labels: documentation, help wanted, code improvement

#214 - Change behaviour of `comment` argument of setter functions

Issue - State: closed - Opened by gustavdelius over 3 years ago - 1 comment

#213 - Alternative syntax for accessing and changing MizerParams slots

Issue - State: closed - Opened by gustavdelius over 3 years ago - 1 comment
Labels: enhancement, setting parameters

#212 - Make accessing and changing individual species and gear parameters easier

Issue - State: closed - Opened by gustavdelius over 3 years ago - 1 comment
Labels: enhancement, setting parameters

#211 - Better tests for extension mechanism

Issue - State: open - Opened by gustavdelius over 3 years ago

#210 - Preserve reproduction parameters during tuning

Pull Request - State: closed - Opened by gustavdelius over 3 years ago

#209 - Framework for informing users about defaults

Pull Request - State: closed - Opened by gustavdelius over 3 years ago

#208 - Preserve reproduction parameters during tuning.

Issue - State: closed - Opened by gustavdelius over 3 years ago - 2 comments
Labels: enhancement, setting parameters, discussion

#207 - Better initial state for multispecies model

Issue - State: open - Opened by gustavdelius over 3 years ago
Labels: enhancement, setting parameters, discussion

#206 - Dependence on `t_per` in `steady()`

Issue - State: open - Opened by gustavdelius over 3 years ago

#205 - Improvements to `compareParams()`

Issue - State: open - Opened by gustavdelius over 3 years ago

GitHub / sizespectrum/mizer issues and pull requests