AlexanderLabWHOI/2024-Krinos-Ghux-Darwin

Code for Krinos et al. G. huxleyi vital rates paper with Darwin model analysis

Intraspecific diversity in thermal performance determines phytoplankton ecological niche

Code and data repository

Code for Krinos et al. G. huxleyi vital rates paper with Darwin model analysis.

Directory: code

Jupyter notebooks used to generate final figures for the paper.

1. 01-map-generation.ipynb - contains code for creating the map of the isolation locations of the strains of G huxleyi included in the study
2. 02-ehux-save.ipynb - contains code for creating side scatter plots for supplemental figures and for performing thermal performance curve fitting
3. 02-ehux-vital-rates.ipynb - contains code for thermal performance curve fitting and for all parts of Figure 2
4. 02-anderson_compare.ipynb - code for comparing generated data to Anderson et al. (2021) and van Dassow et al. (2021) and generating supplementary figures
5. 03-new-darwin_maps-main-fig.ipynb - code for creating main text figure 3 & supplementary figures that show generalist-specialist vs. specialist-only scenarios
6. 04-strain-habitat-prediction.ipynb - code for predicting strain habitat based on Darwin model output
7. XX-new-darwin_maps-mostconserv-static-generalist.ipynb - code for assorted supplementary figures related to Darwin model simulations, especially generalist-only vs. specialist-only
8. XX-darwin-no-v-large-penalty.ipynb - code to compare the 3 penalty levels for the generalist-specialist simulation as shown in supplementary figure 4

darwin-processing-scripts

Code for processing Darwin model simulation results outside of Jupyter notebooks. Referenced in Darwin simulation Jupyter notebooks above.

Directory: data

Data tables useful for running code, including supplementary data tables included with submitted paper.

1. 00-ehux-all-strains.csv - metadata associated with G huxleyi strains
2. 01-concentration-table.csv - daily cell (cells/mL) concentration of G huxleyi cells