From 8e47306a92d3dc00c3fae2355fa762e2a3b9d3b4 Mon Sep 17 00:00:00 2001
From: Daniel Vedder <daniel.vedder@idiv.de>
Date: Tue, 30 Jul 2024 11:47:05 +0200
Subject: [PATCH] Updated CHANGELOG, bumped to v0.5.2
---
CHANGELOG.md | 56 +++++++++++++++++++++++++----------
Project.toml | 2 +-
src/nature/populations.jl | 2 +-
src/nature/species/skylark.jl | 17 +++++++++--
4 files changed, 56 insertions(+), 21 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2f9f15e..3710dc6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,14 +12,34 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
## [0.6.0] - in planning
-*Plan: integrate multiple crop growth models, set up first experiments*
+*Plan: integrate AquaCrop (#79), set up first experiments*
-## [0.5.3] - in planning
+---
-*Plan: basic farm model (#16), decouple CairoMakie (#81)*
+## [0.5.4] - in planning
+*Plan: basic farm model (#16), decouple CairoMakie (#81), test Skylark model (#96, #97)*
-## [0.5.2] - unreleased
+
+## [0.5.3] - unreleased
+
+*Plan: code restructuring to allow multiple crop models (#70)*
+
+### Added
+
+### Changed
+
+### Deprecated
+
+### Removed
+
+### Fixed
+
+
+
+## [0.5.2] - 30-07-2024
+
+**Rewrote the skylark model**
### Added
@@ -29,7 +49,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- `@cropcover` macro and function
-- scientific documentation for Skylark (will become ODD)
+- ODD documentation for Skylark
### Changed
@@ -37,8 +57,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- `EventType` renamed to `Management` for clarity
-
-### Deprecated
+- documentation website now has a "Scientific Documentation" section
### Removed
@@ -50,7 +69,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- `insectbiomass()` uses units
-## [v0.5.1] - 13-06-2024
+
+## [0.5.1] - 13-06-2024
+
+**Added Unitful.jl**
### Added
@@ -68,11 +90,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- all species definitions and tests updated to use units
-## [v0.5.0] - 07-06-2024
+---
-This release doesn't add much new functionality, but represents a major restructuring
+## [0.5.0] - 07-06-2024
+
+**This release doesn't add much new functionality, but represents a major restructuring
of the code base. Specifically, it removes the Agents.jl dependency and changes the
-way the species definition macros work and are used.
+way the species definition macros work and are used.**
### Added
@@ -113,10 +137,11 @@ way the species definition macros work and are used.
- Agents.jl dependency (including `AgentBasedModel` and functions for adding/moving/removing agents)
+---
-## [v0.4.1] - 2023-11-14
+## [0.4.1] - 2023-11-14
-*Wrote tests for skylark migration -> made graphics output format configurable*
+**Initial version of the skylark model**
### Added
@@ -135,10 +160,9 @@ way the species definition macros work and are used.
- graphics output is more configurable
-## [v0.4.0] - 2023-10-28
-
-*Refactored makieplots.jl -> Wrote tests for skylark migration*
+## [0.4.0] - 2023-10-28
+**Functions for animal populations**
### Added
diff --git a/Project.toml b/Project.toml
index 12bc3cd..6b2af59 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,7 +1,7 @@
name = "Persefone"
uuid = "039acd1d-2a07-4b33-b082-83a1ff0fd136"
authors = ["Daniel Vedder <daniel.vedder@idiv.de>"]
-version = "0.5.1"
+version = "0.5.2"
[deps]
ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
diff --git a/src/nature/populations.jl b/src/nature/populations.jl
index d48d759..f3c7bed 100644
--- a/src/nature/populations.jl
+++ b/src/nature/populations.jl
@@ -7,7 +7,7 @@
"""
PopInitParams
-A set of parameters used by [`initpopulation`](@ref) to initialise the population
+A set of parameters used by [`initpopulation!`](@ref) to initialise the population
of a species at the start of a simulation. Define these parameters for each species
using [`@populate`](@ref).
diff --git a/src/nature/species/skylark.jl b/src/nature/species/skylark.jl
index 6ec6835..5a75f7e 100644
--- a/src/nature/species/skylark.jl
+++ b/src/nature/species/skylark.jl
@@ -3,11 +3,18 @@
### This file holds the code for the Eurasian Skylark (Alauda arvensis).
###
+##TODO
+## - habitat-dependent juvenile predation mortality
+## - habitat-dependent dispersal movement
+## - mid-season territory adjustment
+## - temperature-dependent migration, breeding begin, and mortality
+## - first-year mortality
+
+
"""
Skylark
*Alauda arvensis* is a common and charismatic species of agricultural landscapes.
-At the moment, this implementation is still in development.
**Sources:**
- Bauer, H.-G., Bezzel, E., & Fiedler, W. (Eds.). (2012). Das Kompendium
@@ -118,7 +125,7 @@ Once a male has found a territory, he remains in it until the breeding season is
adjusting it to new conditions when and as necessary.
"""
@phase Skylark occupation begin
- #move to a random location in the territory
+ # move to a random location in the territory
@move(@rand(self.territory))
if month(model.date) > self.nestingend
# once the breeding season is over and all the young have left the nest, stop breeding
@@ -223,7 +230,7 @@ chicks are independent or in case of brood loss.
@chance(self.fledglingpredationmortality) && destroynest!(self, "predation")
else
# create new young, reset timer and clutch counter
- #TODO first year mortality
+ #FIXME first year mortality
@reproduce(self.clutch, self.mate)
self.clutch = 0
end
@@ -374,6 +381,10 @@ should currently be on migration. Also sets other individual-specific variables.
end
end
+"""
+Initialise the skylark population. Creates pairs of skylarks on grassland and agricultural
+land, keeping a distance of 60m to vertical structures and giving each pair an area of 3ha.
+"""
@populate Skylark begin
# initialise on open land, at least 60m from vertical structures
habitat = @habitat((@landcover() == grass || @landcover() == agriculture) &&
--
GitLab