Release new version and update website

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: mizerExperimental
 Type: Package
 Title: Extends the mizer package with experimental features
-Version: 2.4.0.9008
+Version: 2.5.3
 Author: Various contributors
 Maintainer: Gustav Delius <gustav.delius@gmail.com>
 Description: This mizer extension package collects contributions from the mizer
@@ -10,7 +10,7 @@ Description: This mizer extension package collects contributions from the mizer
     core mizer package.
 License: GPL-3
 Depends:
-    mizer (>= 2.4.0),
+    mizer (>= 2.5.3),
     R (>= 3.1)
 Imports:
     assertthat,
@@ -73,7 +73,6 @@ Collate:
     test-helpers.R
     tuneParams_helpers.R
     getYieldVsFcurve.R
-    validSim.R
     plots.R
 Encoding: UTF-8
 RoxygenNote: 7.3.2

NAMESPACE

@@ -36,7 +36,6 @@ export(singleSpeciesSteady)
 export(tuneGrowth)
 export(tuneParams)
 export(updateInitialValues)
-export(validSim)
 import(assertthat)
 import(dplyr)
 import(ggplot2)

NEWS.md

@@ -1,3 +1,53 @@
+# mizerExperimental 2.5.3
+
+Now works with and expects mizer 2.5.3
+
+## Bug fixes in tuneParams gadget
+
+* Fixed bug that caused `tuneParams()` to crash when some species had no 
+  associated gear.
+* Fixed sliders for control of `double_sigmoid_length` gears
+* Slider for `n` and `m` exponents now update as intended.
+* Gear selectivity sliders are now always active as expected.
+* Avoid crash when double-clicking on catch tab.
+* Update `intake_max` when changing `h`.
+* Make sure that species sliders get updated when values change during "steady".
+
+## Other bug fixes
+
+* Fixed bug in `plotYieldVsF()` that caused it to crash when no `F_max` was 
+  specified (#61) thanks to @SamikDatta
+* `plotSpectra2()` now shows models in the expected order (#63) thanks to 
+  @cmbeese
+* `plotYieldVsSize()` now works with single species and single gear.
+
+## New functionality in tuneParams gadget
+
+* `tuneParams()` is not longer restricted to a single gear per species.
+* `tuneParams()` can now keep the yield matched to observations.
+* Allow smaller effort values in `fishingControl` and shallower maturity curves 
+  in `reproductionControl`
+* Allow `otherControl()` to change external mortality even if it is protected.
+* Allow `m` parameter to be decreased as well as increased
+* Changed mortality slider to control external mortality at maturity size.
+
+## New functionality
+
+* New plotting function `plotBiomassFlux()`, which plots the rate at which
+  growth transports biomass up the size axis.
+* `getYieldVsF()` now also works for species targeted by multiple gears.
+* Introduced `F_min` argument to `getYieldVsF()` and `plotYieldVsF()` to allow
+  the user to set a minimum fishing mortality rate for the plot.
+* In `plotYieldVsF()` set sensible default for `F_max`.
+* `tuneYield()` can now keep biomass or numbers constant.
+
+
+## Functions moved to mizer
+
+* `plotDiet()`
+* `validSim()`
+* `singleSpeciesSteady()` has become `steadySingleSpecies()`
+
 # mizerExperimental 2.4.0
 
 ## New plotting functions

_pkgdown.yml

@@ -51,6 +51,7 @@ reference:
   - ends_with("Control")
 - title: Helper functions for model tuning
 - contents:
+  - matchYield
   - markBackground
   - adjustBackgroundSpecies
   - removeBackgroundSpecies
@@ -59,16 +60,12 @@ reference:
   - updateInitialValues
   - pruneSpecies
   - getYieldVsF
-  - singleSpeciesSteady
   - alignResource
-- title: New plotting functions
+- title: Plotting functions
 - contents:
   - starts_with("plot")
 - title: Helper functions for `plotYieldVsF()`
 - contents:
   - distanceSSLogYield
   - yieldCalculator
-- title: Others
-- contents:
-  - validSim