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Commit 24785cf6 authored by Adam Reichold's avatar Adam Reichold
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Update README w.r.t. nightly Rust and Git LFS

Fixes #31
Fixes #32
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......@@ -17,6 +17,20 @@
abstract = {Multiple global change pressures, and their interplay, cause plant–pollinator extinctions and modify species assemblages and interactions. This may alter the risks of pathogen host shifts, intra- or interspecific pathogen spread, and emergence of novel population or community epidemics. Flowers are hubs for pathogen transmission. Consequently, the structure of plant–pollinator interaction networks may be pivotal in pathogen host shifts and modulating disease dynamics. Traits of plants, pollinators, and pathogens may also govern the interspecific spread of pathogens. Pathogen spillover–spillback between managed and wild pollinators risks driving the evolution of virulence and community epidemics. Understanding this interplay between host–pathogen dynamics and global change will be crucial to predicting impacts on pollinators and pollination underpinning ecosystems and human wellbeing.}
}
@article{threats_to_an_ecosystem_service,
author = {Vanbergen, Adam J and Initiative, the Insect Pollinators},
title = {Threats to an ecosystem service: pressures on pollinators},
journal = {Frontiers in Ecology and the Environment},
volume = {11},
number = {5},
pages = {251-259},
doi = {https://doi.org/10.1890/120126},
url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/120126},
eprint = {https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1890/120126},
abstract = {Insect pollinators of crops and wild plants are under threat globally and their decline or loss could have profound economic and environmental consequences. Here, we argue that multiple anthropogenic pressures – including land-use intensification, climate change, and the spread of alien species and diseases – are primarily responsible for insect-pollinator declines. We show that a complex interplay between pressures (eg lack of food sources, diseases, and pesticides) and biological processes (eg species dispersal and interactions) at a range of scales (from genes to ecosystems) underpins the general decline in insect-pollinator populations. Interdisciplinary research on the nature and impacts of these interactions will be needed if human food security and ecosystem function are to be preserved. We highlight key areas that require research focus and outline some practical steps to alleviate the pressures on pollinators and the pollination services they deliver to wild and crop plants.},
year = {2013}
}
@misc{experimental_protocol_2020,
author = {VOODOO collaboration},
title = {Protocol for field site selection and sampling for season 2020}
......@@ -482,6 +496,21 @@
year = {1999}
}
@article{the_city_as_a_refuge_for_insect_pollinators,
author = {Hall, Damon M. and Camilo, Gerardo R. and Tonietto, Rebecca K. and Ollerton, Jeff and Ahrné, Karin and Arduser, Mike and Ascher, John S. and Baldock, Katherine C. R. and Fowler, Robert and Frankie, Gordon and Goulson, Dave and Gunnarsson, Bengt and Hanley, Mick E. and Jackson, Janet I. and Langellotto, Gail and Lowenstein, David and Minor, Emily S. and Philpott, Stacy M. and Potts, Simon G. and Sirohi, Muzafar H. and Spevak, Edward M. and Stone, Graham N. and Threlfall, Caragh G.},
title = {The city as a refuge for insect pollinators},
journal = {Conservation Biology},
volume = {31},
number = {1},
pages = {24-29},
keywords = {communication, conservation planning, ecosystem services, funding and philanthropy, governance, politics and policy, sustainability science, urban ecology, ciencia de la sustentabilidad, comunicación, ecología urbana, financiamiento y filantropía, gobernanza, planeación de la conservación, políticas y leyes, servicios ambientales},
doi = {https://doi.org/10.1111/cobi.12840},
url = {https://conbio.onlinelibrary.wiley.com/doi/abs/10.1111/cobi.12840},
eprint = {https://conbio.onlinelibrary.wiley.com/doi/pdf/10.1111/cobi.12840},
abstract = {Abstract Research on urban insect pollinators is changing views on the biological value and ecological importance of cities. The abundance and diversity of native bee species in urban landscapes that are absent in nearby rural lands evidence the biological value and ecological importance of cities and have implications for biodiversity conservation. Lagging behind this revised image of the city are urban conservation programs that historically have invested in education and outreach rather than programs designed to achieve high-priority species conservation results. We synthesized research on urban bee species diversity and abundance to determine how urban conservation could be repositioned to better align with new views on the ecological importance of urban landscapes. Due to insect pollinators’ relatively small functional requirements—habitat range, life cycle, and nesting behavior—relative to larger mammals, we argue that pollinators put high-priority and high-impact urban conservation within reach. In a rapidly urbanizing world, transforming how environmental managers view the city can improve citizen engagement and contribute to the development of more sustainable urbanization.},
year = {2017}
}
@article{monitor_ecological_communities_cost_efficiently,
title = {How to monitor ecological communities cost-efficiently: The example of plant–pollinator networks},
journal = {Biological Conservation},
......
# sick-bees
This repository collects information regarding the epidemiological models developed for the [VOODOO project][VOODOO].
This repository collects information regarding the epidemiological models developed for the [VOODOO project][VOODOO]. It uses [Git LFS][git-lfs] which should be installed before cloning.
## Building and running
......@@ -16,26 +16,36 @@ To compile the LaTeX files into PDF documents, run
cargo documents compile
```
The Rust code requires a nightly toolchain. It is recommended to install this using [rustup][rustup].
### Documents
| file | description |
|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|--------------------------------------------------------------------|
| [references.bib](documents/references.bib) | BibTeX-based reference collection for all LaTeX documents |
| [odd.tex](documents/odd.tex) ([PDF][odd.pdf]) | Overview, design concepts and details |
| [diet_breadth_and_pathogen_prevalence.tex](documents/diet_breadth_and_pathogen_prevalence/diet_breadth_and_pathogen_prevalence.tex) ([PDF][diet_breadth_and_pathogen_prevalence.pdf]) | Paper on the relation between diet breadth and pathogen prevalence |
| file | description |
|----------------------------------------------------------------------------------------------------------------------------------------|--------------------------------------------------------------------|
| [references.bib](documents/references.bib) | BibTeX-based reference collection for all LaTeX documents |
| [odd.tex][odd.tex] ([PDF][odd.pdf]) | Overview, design concepts and details |
| [diet_breadth_and_pathogen_prevalence.tex][diet_breadth_and_pathogen_prevalence.tex] ([PDF][diet_breadth_and_pathogen_prevalence.pdf]) | Paper on the relation between diet breadth and pathogen prevalence |
| [dach21.tex][dach21.tex] ([PDF][dach21.pdf]) | Slides for a talk given at DACH-Tagung 2021 |
### Programs
The main Cargo project is the model code. Additional Cargo projects provide support programs and libraries.
| folder | description |
|----------------|-----------------------------------------------------------------|
| `documents` | Literate programming toolchain and main LaTeX files |
| `experiments` | Programs that execute the model and periodically dump its state |
| `measurements` | Programs which read the dumps and extract CSV files |
| `plots` | Python scripts which load the CSV files and generate plots |
| `libraries` | Support libraries for e.g. message passing and spatial indexing |
| folder | description |
|-----------------|-----------------------------------------------------------------|
| `documents` | Literate programming toolchain and main LaTeX files |
| `experiments` | Programs that execute the model and periodically dump its state |
| `measurements` | Programs which read the dumps and extract CSV files |
| `plots` | Python scripts which load the CSV files and generate plots |
| `visualisation` | Real-time 3D visualisation of the model state |
| `libraries` | Support libraries for e.g. message passing and spatial indexing |
[VOODOO]: https://voodoo-project.eu/
[git-lfs]: https://git-lfs.github.com/
[rustup]: https://rustup.rs/
[odd.tex]: documents/odd.tex
[odd.pdf]: https://git.ufz.de/ecoepi/sick-bees/-/jobs/artifacts/main/raw/documents/odd.pdf?job=document
[diet_breadth_and_pathogen_prevalence.tex]: documents/diet_breadth_and_pathogen_prevalence/diet_breadth_and_pathogen_prevalence.tex
[diet_breadth_and_pathogen_prevalence.pdf]: https://git.ufz.de/ecoepi/sick-bees/-/jobs/artifacts/main/raw/documents/diet_breadth_and_pathogen_prevalence/diet_breadth_and_pathogen_prevalence.pdf?job=document
[dach21.tex]: documents/dach21/dach21.tex
[dach21.pdf]: https://git.ufz.de/ecoepi/sick-bees/-/jobs/artifacts/main/raw/documents/dach21/dach21.pdf?job=document
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