bioturbation
Simple model of bioturbation in a layered soil profile.
Science Score: 54.0%
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Repository
Simple model of bioturbation in a layered soil profile.
Basic Info
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- Stars: 0
- Watchers: 1
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- Open Issues: 0
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Metadata Files
README.md
Bioturbation Model
A simple model of earthworm bioturbation, using a layered soil profile. The model predicts the mixing of mass pools (e.g. of contaminants) over time as a function of earthworm density.
Quickstart
The model can be installed using pip:
bash
$ pip install bioturbation
Alternatively, you can download the source code and use the provided Conda environment file to install the relevant dependencies:
bash
$ git clone https://github.com/samharrison7/bioturbation-model.git
$ cd bioturbation-model
$ conda env create -f environment.yml
Usage
Check out the examples directory for examples of how to use the model.
Conceptualisation
See the conceptualisation notebook for a mathematical description of how the model works.
Limitations
No guarantee is given as the to scientific validity of this model for your data. The onus is on the user to verify this validity. Indeed, there are a number of limitations to the model as it stands which might limit its applicability: * Transport is only between adjacent soil layers, therefore neglecting preferential flow pathways, e.g. representing deep burrowing earthworms transporting tracers directly from upper to lower layers. * No change in soil properties due to bioturbation is modelled. That is, there is an implicit assumption that the amount of soil mixed between layers is negligible. This assumption might not always be valid.
We welcome requests for collaboration if you are interested in exploring the validity of the model for your own research. Please get in touch.
Owner
- Name: Sam Harrison
- Login: samharrison7
- Kind: user
- Location: Lancaster, UK
- Company: @NERC-CEH
- Website: samharrison.science
- Repositories: 33
- Profile: https://github.com/samharrison7
Research scientist with a passion for programming, design and web development.
Citation (CITATION.cff)
cff-version: 1.2.0
title: Bioturbation Model
message: 'If you use this model, please cite it.'
type: software
abstract: >-
Simple model that predicts bioturbation due to earthworm
activity in a layered soil profile.
authors:
- given-names: Sam
family-names: Harrison
email: sharrison@ceh.ac.uk
affiliation: UK Centre for Ecology & Hydrology
orcid: 'https://orcid.org/0000-0001-8491-4720'
- family-names: Keller
given-names: Virginie D
affiliation: UK Centre for Ecology & Hydrology
orcid: https://orcid.org/0000-0003-4489-5363
- family-names: Williams
given-names: Richard J
affiliation: UK Centre for Ecology & Hydrology
orcid: https://orcid.org/0000-0002-9876-0491
- family-names: Hutchins
given-names: Michael
affiliation: UK Centre for Ecology & Hydrology
orcid: https://orcid.org/0000-0003-3764-5331
- family-names: Lofts
given-names: Stephen
affiliation: UK Centre for Ecology & Hydrology
orcid: https://orcid.org/0000-0002-3627-851X
license: BSD-3-Clause
url: https://github.com/samharrison7/bioturbation-model.git
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Top Committers
| Name | Commits | |
|---|---|---|
| Sam Harrison | s****g@g****m | 22 |
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Last synced: 6 months ago
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- samharrison7 (2)
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Packages
- Total packages: 1
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Total downloads:
- pypi 29 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 2
- Total maintainers: 1
pypi.org: bioturbation
Model of earthworm bioturbation in a layered soil profile
- Homepage: https://github.com/samharrison7/bioturbation-model
- Documentation: https://bioturbation.readthedocs.io/
- License: BSD License
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Latest release: 1.0.1
published almost 4 years ago
Rankings
Maintainers (1)
Dependencies
- build
- ipykernel
- matplotlib
- nbformat
- numpy
- pandas
- plotly
- python 3.10.*
- scipy