Add course to website and get ready for version 2.5.0

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: mizer
 Title: Dynamic Multi-Species Size Spectrum Modelling
-Date: 2023-04-25
+Date: 2023-12-07
 Type: Package
 Description: A set of classes and methods to set up and run multi-species, trait
     based and community size spectrum ecological models, focused on the marine
@@ -19,7 +19,7 @@ Authors@R: c(person("Gustav", "Delius", email="[email protected]",
                     comment = c(ORCID = "0000-0002-8478-3430")),
              person("Richard", "Southwell", email="[email protected]",
                     role=c("ctb", "cph")))
-Version: 2.4.1.9002
+Version: 2.5.0
 License: GPL-3
 Imports:
     assertthat,

NEWS.md

@@ -1,9 +1,61 @@
-# mizer 2.4.2 (in preparation)
+# mizer 2.5.0
+
+This release introduces a change that requires you to upgrade your old 
+MizerParams and MizerSim objects with `upgradeParams()` or `upgradeSim()`.
+
+## External encounter rate
 
 Now the model can include an external encounter rate that represents the
 rate at which a predator encounters food that is not explicitly modelled.
 This encounter rate is set with `setExtEncounter()` or `ext_encounter<-()`
-and can be read with `getExtEncounter()` or `ext_encounter()`.
+and can be read with `getExtEncounter()` or `ext_encounter()`. So this is
+similar to how mortality from unmodelled sources is handled via `ext_mort()`.
+
+## Given versus calculated species parameters
+
+You can now use `given_species_params()` to see the species parameter
+values that you have explicitly specified and `calculated_species_params()`
+to see the species parameter values that mizer has calculated automatically or
+set to defaults. You can continue to use `species_params()` to get all
+species parameters, irrespective of whether they were given or calculated.
+
+You can still set parameter values with `species_params<-()`, but you can also
+use the stronger `given_species_params<-()` which not only sets the values you
+give but also triggers a re-calculation of the calculated species parameters.
+Using `given_species_params<-()` is therefore usually the better option.
+
+## New mizer course
+
+There is now a three-part mizer course at https://mizer.course.sizespectrum.org
+with each part consisting of several tutorials, including code and exercises:
+
+-   **Part 1: Understand**\
+    You will gain an understanding of size spectra and their dynamics by exploring simple example systems hands-on with mizer.
+
+-   **Part 2: Build**\
+    You will build your own multi-species mizer model for the Celtic sea, following our example. You can also create a model for your own area of interest.
+
+-   **Part 3: Use**\
+    You will explore the effects of changes in fishing and changes in resource dynamics on the fish community and the fisheries yield. You will run your own model scenarios.
+
+
+## Other improvements
+
+- Warnings are given if user gives irrelevant species parameter values.
+- Some messages have been converted to warnings and some to signals that are not
+  shown as frequently.
+- Frequent warnings are avoided when length-based and weight-based parameters 
+  are both given and are inconsistent. #277
+- Documentation of `effort` argument in `project()` is improved.
+- An error message is given if a predation kernel returns negative values or
+  is everywhere zero. #283
+
+## Bug fixes
+
+- When the coefficient `h` of the maximum intake rate is not given, it is now
+  again given a default value. #282
+- `matchGrowth()` no longer gives an error when there is no `w_inf` column. #279
+
 
 # mizer 2.4.1
 

pkgdown/_pkgdown.yml

@@ -36,10 +36,13 @@ toc:
 
 navbar:
   structure:
-    left: [intro, articles, reference, news]
+    left: [intro, course, articles, reference, news]
     right: [blog, twitter, github]
   components:
     home: ~
+    course:
+      text: Course
+      href: https://mizer.course.sizespectrum.org
     blog:
       text: Blog
       href: https://blog.mizer.sizespectrum.org

vignettes/mizer.Rmd

@@ -35,6 +35,19 @@ know about it by posting about it on our [issue tracker](https://github.com/size
 to @[mizer_model](https://twitter.com/mizer_model). We love to hear from
 you.
 
+A good way to get into mizer is to follow the online [mizer course](mizer.course.sizespectrum.org).
+This course has three parts, each consisting of several tutorials with example code and exercises:
+
+-   **[Part 1: Understand](https://mizer.course.sizespectrum.org/understand)**\
+    You will gain an understanding of size spectra and their dynamics by exploring simple example systems hands-on with mizer.
+
+-   **[Part 2: Build](https://mizer.course.sizespectrum.org/build)**\
+    You will build your own multi-species mizer model for the Celtic sea, following our example. You can also create a model for your own area of interest.
+
+-   **[Part 3: Use]((https://mizer.course.sizespectrum.org/use)**\
+    You will explore the effects of changes in fishing and changes in resource dynamics on the fish community and the fisheries yield. You will run your own model scenarios.
+
+
 Click on this preview to open a mizer cheat sheet.
 [![Cheat Sheet](images/cheat_sheet_preview.png)](https://sizespectrum.org/mizer/articles/images/cheat_sheet.pdf)