From 98d092f29dcb46fbc9c02ae1a2561bbd5c03d9c1 Mon Sep 17 00:00:00 2001 From: Daniel Vedder <daniel.vedder@idiv.de> Date: Thu, 31 Aug 2023 11:53:34 +0200 Subject: [PATCH] Updated tagline --- README.md | 9 +++++---- docs/src/index.md | 12 ++++++++---- src/Persefone.jl | 4 +++- src/analysis/analyse_nature.R | 2 +- src/core/input.jl | 2 +- src/core/output.jl | 2 +- src/core/simulation.jl | 2 +- src/crop/crops.jl | 2 +- src/crop/farmplot.jl | 2 +- src/farm/farm.jl | 2 +- src/nature/ecologicaldata.jl | 2 +- src/nature/energy.jl | 2 +- src/nature/insects.jl | 2 +- src/nature/nature.jl | 2 +- src/nature/populations.jl | 2 +- src/nature/species/skylark.jl | 2 +- src/nature/species/wolpertinger.jl | 2 +- src/nature/species/wyvern.jl | 2 +- src/parameters.toml | 2 +- src/world/landscape.jl | 2 +- src/world/weather.jl | 2 +- test/crop_tests.jl | 2 +- test/farm_tests.jl | 2 +- test/io_tests.jl | 2 +- test/landscape_tests.jl | 2 +- test/nature_tests.jl | 2 +- test/paramscan.toml | 2 +- test/runtests.jl | 2 +- test/simulation_tests.jl | 2 +- test/test_parameters.toml | 2 +- 30 files changed, 43 insertions(+), 36 deletions(-) diff --git a/README.md b/README.md index d99b0ed..fe1f114 100644 --- a/README.md +++ b/README.md @@ -4,10 +4,11 @@ ## Description -Persefone.jl models agricultural practice and how it impacts animal species at a landscape -scale. It includes a farm submodel, a crop growth submodel, and individual-based models -of multiple indicator species. Its aim is to investigate how changes in farm operations -(e.g. through policy changes in the CAP) influence biodiversity. +[Persefone.jl](https://git.idiv.de/xo30xoqa/persefone) models agricultural practice and +how it impacts animal species at a landscape scale. It includes a farm submodel, a crop +growth submodel, and individual-based models of multiple indicator species. Its aim is to +investigate how changes in farm operations (e.g. through policy changes in the CAP) +influence biodiversity. The model is based on the [Agents.jl](https://juliadynamics.github.io/Agents.jl/stable/) framework. It is currently in the early stages of development. diff --git a/docs/src/index.md b/docs/src/index.md index 0e3af50..6b632b5 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -47,7 +47,7 @@ defines parameter values and looks like this (see `src/parameters.toml` for a co of parameters): ```TOML -### Persefone - a socio-economic-ecological model of European agricultural landscapes. +### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe. ### ### This is the default configuration file for Persefone, containing all model parameters. ### The syntax is described here: https://toml.io/en/ @@ -66,7 +66,8 @@ enddate = 2022-12-31 [world] landcovermap = "data/landcover_jena.tif" # location of the landcover map farmfieldsmap = "data/fields_jena.tif" # location of the field geometry map - +weatherfile = "data/weather_jena.csv" # location of the weather data file + [farm] farmmodel = "FieldManager" # which version of the farm model to use (not yet implemented) @@ -74,9 +75,12 @@ farmmodel = "FieldManager" # which version of the farm model to use (not yet imp targetspecies = ["Wolpertinger", "Wyvern"] # list of target species to simulate popoutfreq = "daily" # output frequency population-level data, daily/monthly/yearly/end/never indoutfreq = "end" # output frequency individual-level data, daily/monthly/yearly/end/never +insectmodel = ["season", "habitat", "pesticides", "weather"] # factors affecting insect growth [crop] -cropmodel = "linear" # crop growth model to use, "linear" or "aquacrop" (not yet implemented) +cropmodel = "almass" # crop growth model to use, "almass" or "aquacrop" +cropfile = "data/crop_data_general.csv" # file with general crop parameters +growthfile = "data/almass_crop_growth_curves.csv" # file with crop growth parameters ``` !!! info "Parameter scanning" @@ -85,4 +89,4 @@ cropmodel = "linear" # crop growth model to use, "linear" or "aquacrop" (not yet combination of parameters that you entered (i.e. do a full-factorial simulation experiment). -*Last updated: 2023-08-31 (commit 38abd8d)* +*Last updated: 2023-08-31 (commit daba57f)* diff --git a/src/Persefone.jl b/src/Persefone.jl index a9912f6..7b666ad 100644 --- a/src/Persefone.jl +++ b/src/Persefone.jl @@ -1,6 +1,8 @@ -### Persefone - a socio-economic-ecological model of European agricultural landscapes. +### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe. ### ### Daniel Vedder <daniel.vedder@idiv.de> +### Guy Pe'er <guy.peer@idiv.de> +### https://git.idiv.de/xo30xoqa/persefone ### (c) 2022-2023, licensed under the terms of the MIT license ### ### This file defines the module/package for the Persefone model. diff --git a/src/analysis/analyse_nature.R b/src/analysis/analyse_nature.R index 979d6af..bebe052 100755 --- a/src/analysis/analyse_nature.R +++ b/src/analysis/analyse_nature.R @@ -1,5 +1,5 @@ #!/usr/bin/Rscript -### Persefone - a socio-economic-ecological model of European agricultural landscapes. +### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe. ### ### This file visualises the output of the nature model. ### diff --git a/src/core/input.jl b/src/core/input.jl index f09117c..7869c0e 100644 --- a/src/core/input.jl +++ b/src/core/input.jl @@ -1,4 +1,4 @@ -### Persefone - a socio-economic-ecological model of European agricultural landscapes. +### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe. ### ### This file includes functions for configuring the model and reading in map files. ### diff --git a/src/core/output.jl b/src/core/output.jl index 9dea302..18aab3a 100644 --- a/src/core/output.jl +++ b/src/core/output.jl @@ -1,4 +1,4 @@ -### Persefone - a socio-economic-ecological model of European agricultural landscapes. +### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe. ### ### This file includes functions for saving the model output. ### diff --git a/src/core/simulation.jl b/src/core/simulation.jl index c21578e..34eec0a 100644 --- a/src/core/simulation.jl +++ b/src/core/simulation.jl @@ -1,4 +1,4 @@ -### Persefone - a socio-economic-ecological model of European agricultural landscapes. +### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe. ### ### This file includes the core functions for initialising and running simulations. ### diff --git a/src/crop/crops.jl b/src/crop/crops.jl index f716c9e..d0495d7 100644 --- a/src/crop/crops.jl +++ b/src/crop/crops.jl @@ -1,4 +1,4 @@ -### Persefone - a socio-economic-ecological model of European agricultural landscapes. +### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe. ### ### This file is responsible for managing the crop growth modules. ### diff --git a/src/crop/farmplot.jl b/src/crop/farmplot.jl index 8b7b24b..0178506 100644 --- a/src/crop/farmplot.jl +++ b/src/crop/farmplot.jl @@ -1,4 +1,4 @@ -### Persefone - a socio-economic-ecological model of European agricultural landscapes. +### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe. ### ### This file contains code for the fields that farmers manage. ### diff --git a/src/farm/farm.jl b/src/farm/farm.jl index c42b18d..0362efe 100644 --- a/src/farm/farm.jl +++ b/src/farm/farm.jl @@ -1,4 +1,4 @@ -### Persefone - a socio-economic-ecological model of European agricultural landscapes. +### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe. ### ### This file is responsible for managing the farm module(s). ### diff --git a/src/nature/ecologicaldata.jl b/src/nature/ecologicaldata.jl index 1bc11a3..f1721a7 100644 --- a/src/nature/ecologicaldata.jl +++ b/src/nature/ecologicaldata.jl @@ -1,4 +1,4 @@ -### Persefone - a socio-economic-ecological model of European agricultural landscapes. +### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe. ### ### This file includes the functions for collecting and saving ecological output data. ### diff --git a/src/nature/energy.jl b/src/nature/energy.jl index 6aa1814..feb3a94 100644 --- a/src/nature/energy.jl +++ b/src/nature/energy.jl @@ -1,4 +1,4 @@ -### Persefone - a socio-economic-ecological model of European agricultural landscapes. +### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe. ### ### This file contains structs and functions for implementing Dynamic Energy Budgets. ### diff --git a/src/nature/insects.jl b/src/nature/insects.jl index fed9ad2..c2b81b7 100644 --- a/src/nature/insects.jl +++ b/src/nature/insects.jl @@ -1,4 +1,4 @@ -### Persefone - a socio-economic-ecological model of European agricultural landscapes. +### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe. ### ### This file contains the submodel that calculates insect biomass ### diff --git a/src/nature/nature.jl b/src/nature/nature.jl index ae58eb1..e63c993 100644 --- a/src/nature/nature.jl +++ b/src/nature/nature.jl @@ -1,4 +1,4 @@ -### Persefone - a socio-economic-ecological model of European agricultural landscapes. +### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe. ### ### This file is responsible for managing the animal modules. ### diff --git a/src/nature/populations.jl b/src/nature/populations.jl index ceb31bb..f2e80c0 100644 --- a/src/nature/populations.jl +++ b/src/nature/populations.jl @@ -1,4 +1,4 @@ -### Persefone - a socio-economic-ecological model of European agricultural landscapes. +### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe. ### ### This file contains a set of utility functions for species, including initialisation, ### reproduction, and mortality. diff --git a/src/nature/species/skylark.jl b/src/nature/species/skylark.jl index 0f5cc86..c5ecc0c 100644 --- a/src/nature/species/skylark.jl +++ b/src/nature/species/skylark.jl @@ -1,4 +1,4 @@ -### Persefone - a socio-economic-ecological model of European agricultural landscapes. +### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe. ### ### This file holds the code for the Eurasian Skylark (Alauda arvensis). ### diff --git a/src/nature/species/wolpertinger.jl b/src/nature/species/wolpertinger.jl index c389afd..4820763 100644 --- a/src/nature/species/wolpertinger.jl +++ b/src/nature/species/wolpertinger.jl @@ -1,4 +1,4 @@ -### Persefone - a socio-economic-ecological model of European agricultural landscapes. +### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe. ### ### This file holds the code for the Wolpertinger (https://en.wikipedia.org/wiki/Wolpertinger). ### NOT FOR ACTUAL USE! This is of course only a test species ;-) diff --git a/src/nature/species/wyvern.jl b/src/nature/species/wyvern.jl index e645105..eb1d988 100644 --- a/src/nature/species/wyvern.jl +++ b/src/nature/species/wyvern.jl @@ -1,4 +1,4 @@ -### Persefone - a socio-economic-ecological model of European agricultural landscapes. +### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe. ### ### This file holds the code for the Wyvern (https://en.wikipedia.org/wiki/Wyvern). ### NOT FOR ACTUAL USE! This is of course only a test species ;-) diff --git a/src/parameters.toml b/src/parameters.toml index 46d1902..90bd53b 100644 --- a/src/parameters.toml +++ b/src/parameters.toml @@ -1,4 +1,4 @@ -### Persefone - a socio-economic-ecological model of European agricultural landscapes. +### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe. ### ### This is the default configuration file for Persefone, containing all model parameters. ### The syntax is described here: https://toml.io/en/ diff --git a/src/world/landscape.jl b/src/world/landscape.jl index d8127d4..1cacf09 100644 --- a/src/world/landscape.jl +++ b/src/world/landscape.jl @@ -1,4 +1,4 @@ -### Persefone - a socio-economic-ecological model of European agricultural landscapes. +### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe. ### ### This file manages the landscape maps that underlie the model. ### diff --git a/src/world/weather.jl b/src/world/weather.jl index 6e83a9c..694586f 100644 --- a/src/world/weather.jl +++ b/src/world/weather.jl @@ -1,4 +1,4 @@ -### Persefone - a socio-economic-ecological model of European agricultural landscapes. +### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe. ### ### This file reads in weather data for the selected location and makes it available ### to the rest of the model. diff --git a/test/crop_tests.jl b/test/crop_tests.jl index e7452ee..2ab0aff 100644 --- a/test/crop_tests.jl +++ b/test/crop_tests.jl @@ -1,4 +1,4 @@ -### Persefone - a socio-economic-ecological model of European agricultural landscapes. +### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe. ### ### These are the tests for the crop growth model. ### diff --git a/test/farm_tests.jl b/test/farm_tests.jl index 33ed336..1962845 100644 --- a/test/farm_tests.jl +++ b/test/farm_tests.jl @@ -1,4 +1,4 @@ -### Persefone - a socio-economic-ecological model of European agricultural landscapes. +### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe. ### ### These are the tests for the farm model. ### diff --git a/test/io_tests.jl b/test/io_tests.jl index 38cd1d2..d9073c3 100644 --- a/test/io_tests.jl +++ b/test/io_tests.jl @@ -1,4 +1,4 @@ -### Persefone - a socio-economic-ecological model of European agricultural landscapes. +### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe. ### ### This tests the core input and output functions. ### diff --git a/test/landscape_tests.jl b/test/landscape_tests.jl index a6924f2..32f9f65 100644 --- a/test/landscape_tests.jl +++ b/test/landscape_tests.jl @@ -1,4 +1,4 @@ -### Persefone - a socio-economic-ecological model of European agricultural landscapes. +### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe. ### ### These are the tests for the landscape and weather functions. ### diff --git a/test/nature_tests.jl b/test/nature_tests.jl index 593539d..d862f58 100644 --- a/test/nature_tests.jl +++ b/test/nature_tests.jl @@ -1,4 +1,4 @@ -### Persefone - a socio-economic-ecological model of European agricultural landscapes. +### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe. ### ### These are the tests for the nature model (excluding individual species). ### diff --git a/test/paramscan.toml b/test/paramscan.toml index a5c08c4..d2db42f 100644 --- a/test/paramscan.toml +++ b/test/paramscan.toml @@ -1,4 +1,4 @@ -### Persefone - a socio-economic-ecological model of European agricultural landscapes. +### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe. ### ### This configuration file is intended to test the parameter scanning feature. ### diff --git a/test/runtests.jl b/test/runtests.jl index 9340460..9023b6b 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -1,4 +1,4 @@ -### Persefone - a socio-economic-ecological model of European agricultural landscapes. +### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe. ### ### This is the top-level file of the Persefone test suite. Execute this to run all tests. ### diff --git a/test/simulation_tests.jl b/test/simulation_tests.jl index 07c4d1d..013c382 100644 --- a/test/simulation_tests.jl +++ b/test/simulation_tests.jl @@ -1,4 +1,4 @@ -### Persefone - a socio-economic-ecological model of European agricultural landscapes. +### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe. ### ### These are the tests for the core simulation functions. ### diff --git a/test/test_parameters.toml b/test/test_parameters.toml index eac86aa..ba7d5d0 100644 --- a/test/test_parameters.toml +++ b/test/test_parameters.toml @@ -1,4 +1,4 @@ -### Persefone - a socio-economic-ecological model of European agricultural landscapes. +### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe. ### ### This configuration file is used for the test suite. ### -- GitLab