Project repository for data and Python code associated with the preprint
Shoemaker WR, Locey KJ, Lennon JT. (2016) A unifying ecological theory of microbial biodiversity. PeerJ Preprints 4:e1450v3 https://doi.org/10.7287/peerj.preprints.1450v3
and the accepted manuscript
Shoemaker WR, Locey KJ, Lennon JT. (2017) A macroecological theory of microbial biodiversity. Nature Ecology & Evolution 1:0107 doi:10.1038/s41559-017-0107
The following files and folders need to be uncompressed before you run the analsis:
~/MicrobialBiodiversityTheory/data/EMPclosed-Data/EMPclosed-SADs.txt.zip
~/MicrobialBiodiversityTheory/data/EMPopen-Data/EMPopen-SADs.txt.zip
~/MicrobialBiodiversityTheory/data/HMP-Data/hmp1.v35.hq.otu.counts.bz2
~/MicrobialBiodiversityTheory/data/ObsPred.zip
To Figure2 and supplementary figures 1 and 2 you will need to request data, as the files are too large to store on GitHub.
The code accepts the following arguments from the user.
Flags
-a or --analysis: Runs the analysis required for the figure.
-f: The figure or table you want to generate. Indicate what figure/ table you want to generate after the flag using the table below.
| Argument | Figure/ Table |
|---|---|
| F1 | Figure 1 |
| F2 | Figure 2 |
| F3 | Figure 3 |
| F4 | Figure 4 |
| FS1 | Supplementary figure 1 |
| FS2 | Supplementary figure 2 |
| FS3 | Supplementary figure 3 |
| FS4 | Supplementary figure 4 |
| FS5 | Supplementary figure 5 |
| FS6 | Supplementary figure 6 |
| T1 | Table 1 |
| T2 | Table 2 |
| TS1 | Supplementary table 1 |
| TS2 | Supplementary table 2 |
| TS3 | Supplementary table 3 |
| TS4 | Supplementary table 4 |
| TS5 | Supplementary table 5 |
| TS6 | Supplementary table 6 |
If you want to regenerate the data (warning, this is very computationally intensive and will take several days to complete) start with step 1, otherwise run step 2 for the figures.
-
Run the following command.
python runAnalysis.py -a -
Run this command
python runAnalysis.py -f
and indicate what figure you want after "-f"
Python 2.7.10-2 is used.
The following Python modules/versions are used in this analysis.
-
numpy 1.10.1 -
matplotlib 1.4.2 -
Pandas 0.16.2 -
scipy 0.16.0 -
setuptools 18.4 -
statsmodels 0.6.1
Since we wrote the code for this analysis (~2015) the Weecology group has updated macroecotools. Newer versions of macroecotools are incompatible with this code. In addition, as described in the manuscript, we ran into issues with fitting the lognormal using maximum likelihood estimation on microbial communities with a large number of individuals. If you want to just reproduce our results, then using macroecotools 0.2 is fine. However, if you want to fit the lognormal to your data, we strongly recommend that you work with the most recent version of macroecotools.
Copyright (c) 2015 William R. Shoemaker, Kenneth J. Locey, Jay T. Lennon
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.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
To write the code in this repository we used MIT liscensed code from the GitHub repositories mete 0.1 and macroecotools 0.2 on 9/20/2015.