GitHub - BCGardner/logistic_models: Code for results of "Microbial communities experimental time series captured by stochastic logistic models"

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Code for results of "Microbial communities experimental time series captured by stochastic logistic models"

BSD-3-Clause license

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Name		Name	Last commit message	Last commit date
Latest commit History 11 Commits
Data		Data
results		results
Experimental.ipynb		Experimental.ipynb
Figures eLife.ipynb		Figures eLife.ipynb
Fisher Mehta neutral model annotated.ipynb		Fisher Mehta neutral model annotated.ipynb
Influence interactions SOI and sgLV.ipynb		Influence interactions SOI and sgLV.ipynb
LICENSE		LICENSE
Noise color fit comparison (linear vs spline).ipynb		Noise color fit comparison (linear vs spline).ipynb
README		README
Study noise no interaction.ipynb		Study noise no interaction.ipynb
Study noise with interaction.ipynb		Study noise with interaction.ipynb
Understand noise color.ipynb		Understand noise color.ipynb
Understanding Fisher Mehta Figure 2B.ipynb		Understanding Fisher Mehta Figure 2B.ipynb
Width distribution dx.ipynb		Width distribution dx.ipynb
brownian.py		brownian.py
elife_settings.py		elife_settings.py
make_colormap.py		make_colormap.py
neutral_covariance_test.py		neutral_covariance_test.py
neutrality_analysis.py		neutrality_analysis.py
noise_analysis.py		noise_analysis.py
noise_color_analysis.py		noise_color_analysis.py
noise_parameters.py		noise_parameters.py
noise_properties_plotting.py		noise_properties_plotting.py
smooth_spline.py		smooth_spline.py
timeseries_plotting.py		timeseries_plotting.py

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Logistic models

This code produces the results of "Stochastic logistic models reproduce experimental time series of microbial communities".

elife_settings.py
generate_timeseries.py
make_colormap.py
neutral_covariance_test.py
neutrality_analysis.py
noise_analysis.py
noise_color_analysis.py
noise_parameters.py
noise_properties_plotting.py

Figures of main text in 'Figures eLife'

Figures of supplemental:
Fig 1 : Fisher Mehta neutral model
Fig 2 : Experimental
Fig 3 : Supplemental
Fig 4 : Understand noise color
Fig 5 : Study noise no interaction
Fig 6 : Experimental
Fig 7 : Experimental
Fig 8 : Experimental
Fig 9 : Experimental
Fig 10 : Experimental
Fig 11 : Experimental
Fig 12 : Study noise with interaction
Fig 13 : Study noise no interaction
Fig 14 : Study noise no interaction
Fig 15 : Figures eLife
Fig 16 : Study noise with interaction
Fig 17 : Width distribution dx
Fig 18 : Width distribution dx
Fig 19 : Understanding Fisher Mehta Figure 2B
Fig 20 : Influence interactions SOI and sgLV
Fig 21 : Influence interactions SOI and sgLV
Fig 22 : Influence interactions SOI and sgLV
Fig 23 : Influence interactions SOI and sgLV