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