Initial commit with planning documents and project skeleton

LICENSE

+MIT LICENSE
+
+Copyright (c) 2022 Daniel Vedder, Lea Kolb
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
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+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
+

README.md

+# Persephone
+
+**An agent-based, socio-economic-ecological model of agricultural landscapes
+in Europe under the CAP.**
+
+
+---
+
+© 2022 Daniel Vedder, Lea Kolb
+MIT license

docs/planning/model_components.md

+# Model components & justifications
+
+**Aim: We want to be able to model how key eco-schemes and AECM affect
+	crop yields, biodiversity, and ESS at a mechanistic level.**
+
+## Farm model
+
+*Lea's model*
+
+- ...
+
+- **Management actions:** Influence habitat availability and mortality of
+  plants and animals in the landscape (e.g. through tillage, pesticide or
+  fertiliser application). Timing is important as it interacts with species'
+  phenologies.
+
+## Nature model
+
+*Daniel's model*
+
+- **Weather:** Temperature and precipitation in the course of a year are two 
+  of the most important predictors of crop yield, as well as influencing the
+  timing of management actions such as sowing or harvest.
+
+- **Soil:** Water and nutrient content of soil determines rates of plant growth.
+  Soil organic matter is important for overall soil health, as well as providing
+  regulatory ESS via carbon sequestration. All three soil properties are modified
+  by management actions, especially tillage.
+	  -> *I would like to leave this out as it seems rather complicated, but
+		I do think fertiliser application is important and I don't know how to
+		include that without also including soil nutrients?*
+
+- **Plants:** Wild plants provide habitat for insects and animals. Crop plants
+  provide income for farmers. Modelling plant growth allows us to implement
+  realistic rules for when and why farm actors carry out management actions (e.g.
+  fertiliser application, grass cutting). Also, plant phenology influences habitat
+  and food availability for insects and vertebrates.
+
+- **Insects:** Insects provide important ecosystem services and disservices, as
+  pollinators, pests, and pest control. The abundance of crop-specific pests in
+  a field is used by farmers to gauge the necessity of pesticide application,
+  thus their population dynamics influence management actions. Additionally,
+  insects are important food sources for many vertebrates and therefore relevant
+  to the animal components.
+
+- **Animals:**
+  - *Alauda arvensis*: ground-nesting, insectivorous & granivorous
+  - *Emberiza citrinella*: hedge-nesting, insectivorous & granivorous
+  - *Milvus milvus*: raptor (?)
+  - *Cricetus cricetus*: ground-dwelling, herbivorous & insectivorous
+  - *Maniola jurtina*: low-intensive grassland
+  - ...
+
+

docs/planning/target_species.md

+# Target species
+
+Criteria:
+	- data availability
+	- indicator for other species
+	- habitat requirements (niche complementarity)
+	- charismatic
+	- not studied too little or too much
+	- provide ecosystem services
+	
+Exclusion criteria:
+	- migratory species
+	- unusual behaviour/population dynamics
+	- stakeholder conflicts
+	- too large home range
+	
+
+- Judith could create contacts to bird experts
+
+- Carla is still working on identifying grassland/agricultural specialists
+
+## Birds
+
+**Selected: Feldlerche, Goldammer, Rotmilan** (plus Kiebitz, Neuntöter?)
+(5 out of 10 national indicator species for agrarian landscapes)
+
+1. Neuntöter *Lanius collurio*
+  - 8% decline 2004-2016
+  - insectivorous, migratory
+  - open areas with grassland, hedges, forest edges
+  - national indicator species
+  - Judith: not mentioned often as an umbrella species
+
+2. Goldammer *Emberiza citrinella*
+  - very common, but declining
+  - pretty bird, easy to spot
+  - 14% decline 2004-2016
+  - open areas, hedges, forest edges
+  - national indicator species
+  - insectivorous juveniles, seed-eating adults
+  - non-migratory, ground-nesting
+  - Judith: not mentioned often as an umbrella species
+
+- Feldlerche *Alauda arvensis*
+  - still common, but conservation concern
+  - 11% decline 2004-2016
+  - well-known flagship species
+  - but also frequently modelled
+  - ground-nesting
+
+- Braunkehlchen *Saxicola rubetra*
+  - 41% decline 2004-2016
+  - quite rare & hard to spot
+  - meadows, fallows, heathland
+  - national indicator species
+
+- Grauammer *Emberiza calandra*
+  - 34% decline 2004-2016
+  - open areas with perches, field borders, fallows, meadows
+  - insectivorous juveniles, seed-eating adults
+  - partly migratory
+  
+- Kiebitz *Vanellus vanellus*
+  - used for Birds@Farmlands conservation schemes
+  - but rare in TH & BW?
+
+- Rebhuhn *Perdix perdix*
+  - used for Birds@Farmlands conservation schemes
+
+- Rotmilan (or other raptors, e.g. Wiesenweihe)
+  - pest control
+
+- Steinkauz
+
+Decline numbers from Deutsche Ornithologen-Gesellschaft, Fachgruppe Agrarvögel 
+(2019): DO-G Positionspapier: Weiterentwicklung der Gemeinsamen Agrarpolitik 
+ab 2021. Vogelwarte, 57(4), 345–357. 
+http://www.do-g.de/fileadmin/DO-G_Positionspapier_Agrarvoegel_21.10.2019_n.pdf
+
+See also Busch et al. (2020): Drivers of population change in common farmland 
+birds in Germany. Bird Conservation International, 30(3), 335–354. 
+https://doi.org/10.1017/S0959270919000480
+
+
+## Butterflies
+
+**Selected: Maniola jurtina, ...**
+  
+1. Großes Ochsenauge *Maniola jurtina*
+  - offene Graslandbiotope
+  - abhängig von lückigem/kurzem Bewuchs, z.B. durch Mahd/Beweidung
+  - verschwindet bei intensiver Düngung/mehr als dreimal jährlicher Mahd
+  - nicht gefährdet
+
+- Kleines Wiesenvögelchen *Coenonympha pamphilus*
+  - offene Graslandbiotope
+  - abhängig von lückigem/kurzem Bewuchs, z.B. durch Mahd/Beweidung
+  - besonders geschützt, nicht gefährdet
+
+- Hauhechelbläuling *Polyommatus icarus*
+
+- *Limenitis reducta*
+
+- Carla: Butterflies of the EU Grassland Butterfly Indicator: 
+Generalists: Ochlodes sylvanus, Anthocharis cardamines, Lycaena phlaes, 
+Polyommatus icarus, Lasiommata megera, Coenonympha pamphilus, Maniola jurtina; 
+Specialists: Erynnis tages, Thymelicus acteon, Spialia sertorius, Cupido minimus, 
+Phengaris arion, Phengaris nausithous, Lysandra bellargus, Cyaniris semiargus, 
+Lysandra coridon, Euphydryas aurinia 
+
+For modelling butterflies in agricultural landscapes, see:
+Sybertz, J., Matthies, S., Schaarschmidt, F., Reich, M., & von Haaren, C. (2017). 
+Assessing the value of field margins for butterflies and plants: How to document 
+and enhance biodiversity at the farm scale. Agriculture, Ecosystems & Environment, 
+249, 165–176. https://doi.org/10.1016/j.agee.2017.08.018
+
+## Mammals
+
+**Selected: ...**
+  
+1. Feldhase *Lepus europaeus*
+  - Äcker und Wiesen
+  - bekannte, beliebte Art
+  - wird auch in ALMaSS modelliert
+  - gefährdet
+  
+2. Feldhamster *Cricetus cricetus*
+  - frisst Pflanzen und Wirbellose
+  - Ernteschädling, aber stark eingebrochener Bestand
+  - geschützte Art
+
+- Reh *Capreolus capreolus*
+  - kleinstrukturierte Landschaften
+  - Nahrungssuche auf Feldern
+  - verursacht Ernteschäden
+  
+- Feldmaus *Microtus arvalis*
+  - Äcker, Wiesen, Brachen
+  - primär vegetarische Ernährung, z.T. Insekten
+  - häufiger Ernteschädling
+  - starke Populationszyklen
+
+- Wildkatze *Felis sylvestris*
+
+- Lynx
+
+## Other taxa
+
+- bumble bees
+
+- amphibians?