diff --git a/README.md b/README.md index d99b0edf6bee916027427b48588e5e5427039ec2..fe1f11462a4b404f715184c3ad2430c125b01cae 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 0e3af50abd3cdc36bb9110ff5cde8162ac341c20..6b632b53980ddfdbb8cfd17ff77bd01b70c2dbc7 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 a9912f60c23bce23c9fd4fc922f295e5e8740ee7..7b666ad3a14cea2c26396bcdd72531cdcfbe0c24 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 979d6af0a6979379e51c0b3bbf7a112913e7f0e8..bebe052b1cef996f8c421870ee93258281c1d9db 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 f09117c30f5481b72e936904be63f14381810d6d..7869c0e21e9bc5b1b32086b4606f612a5295dcf1 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 9dea302eb32bc9ec8532f118c86fd24b6aef01b4..18aab3a0b805963280d7bd34923e6c85a510ab8d 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 c21578eba35d31e9cede5e3f6324d8b0c29f4799..34eec0a5b53c65c7092f22be6a876b9a2b567bbc 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 f716c9e3b32c08e53e1083b973cfd2f9fde77c1e..d0495d7812ec9d19c0a7560e2244b27ab5e24dcc 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 8b7b24b96887a4b26d69b9d7b96014f223912988..017850651cfd07c363fecfe1e86b6fcc11244d2c 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 c42b18d1ac8119407ac1b09186e518170c5f01be..0362efe0d5fb268b3a269da6a7698f1b663a4145 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 1bc11a37f9d00978bf7143718d0c0b785144e846..f1721a73d631332587c9792f6ac3c8f874764e0e 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 6aa18147a3f2f2b4c54e69409f6fbbc56ae29bcb..feb3a9430645d03fb5fc5b3ebde758a22f57a429 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 fed9ad29c11ff331c997dd8dac64c4fe5d422d0c..c2b81b7a8d74bc1d43a34305add6184282a281b0 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 ae58eb1ba5caf39e2fc8c8008cf797a781ef5b67..e63c9931eb2080ae88c2792f5b5b6baf51dd8329 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 ceb31bb78cc74e88b1bf30183d60d14bb0829dfa..f2e80c0dc7e735a0e532b20b4905c55b1ba03a8d 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 0f5cc86d3ec44700b0fa4fd10064be3c62b98253..c5ecc0c708fcb38752147643a61ca03aa84ea982 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 c389afdb5ae4584211c39b586f08a79f1f42bec3..482076348d87664e92bbc9f565fa205b014e5d5a 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 e6451058451fe8c096eac8d498890addee26e2cc..eb1d9889fbe0abe7de221734bbf4d2b785301da7 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 46d1902be2934ccae68a731a4c4f1c3f0a15daf4..90bd53b5000958020dd84cf3fd66e0fd9a0ffae5 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 d8127d4589de3387508c861c4679fdba886f30b0..1cacf092762467096bddead5430d539c42aa52ad 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 6e83a9c88eb22950869cdb6cb5c5d70691afa584..694586f5c40c10fe92cddcc7f8d3f53e059c2fac 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 e7452eee69ecd5dab9f6f18d6e40d98eb58b89b2..2ab0affb0eaad04c1a71e141c06c49e497d21185 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 33ed3365dec2dfae4fea5bbc7627c0050b776bd0..1962845d2938aa900c08387a2026e156a12379ba 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 38cd1d25b6e61f697a89f360a7c9ed112bb16024..d9073c3d061ac4ebf66cb05402adfe297691b5ec 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 a6924f25a48498942e10ea9bc7ee510177b689ec..32f9f65e1ae0f09fd962fbb55d8876fbd10986cc 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 593539d38d48accaf010572d470d265442538ecd..d862f58b12975af4face0b8df3f21d32f213ec0b 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 a5c08c4fd9e45e56a08fb7a0e5ac6346f585039f..d2db42fb9add8f360c2247adb5cc3e65f8223054 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 93404600629800a627d81cee59241186c2a8e417..9023b6b8df21457e03af13fe946f641b750897fd 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 07c4d1d969317610fb2847396275841778295c2c..013c38268bdab64476c2afd99862c2e03b921111 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 eac86aaf4a99d094c6f46148bc7fe21913b83da6..ba7d5d000bdaaf4f1a908845af940427cbb730a0 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. ###