Skip to content

Matlab program reproducing results and figures from the paper "Coastal upwelling drives ecosystem temporal variability from the surface to the abyssal seafloor".

License

Notifications You must be signed in to change notification settings

messiem/sourcecode_ITS

Folders and files

NameName
Last commit message
Last commit date

Latest commit

4c82a52 · Nov 7, 2024

History

3 Commits
Feb 17, 2023
Feb 17, 2023
Feb 17, 2023
Nov 7, 2024
Feb 17, 2023
Feb 17, 2023
Nov 7, 2024
Feb 17, 2023
Feb 17, 2023
Feb 17, 2023
Feb 17, 2023

Repository files navigation

Source code for paper "Coastal upwelling drives ecosystem temporal variability from the surface to the abyssal seafloor"

This toolbox contains the programs used to reproduce results and figures from Messié et al. (2023).
The programs are written for Matlab.


Get started

See script:

start_sourcecode_ITS

(ITS stands for Integrated Time Series). Set the community variable to either surface, midwater, or benthos to reproduce results for each time series.
The code generates figures, saved in outputs/, reproducing results from Fig. 1, 2, 3, and 5 from the paper with 2 main differences. First, the code runs for a given community so figures are broken down by community instead of being combined as in the paper. Second, the figures are simplified versions of the paper figures, with Matlab native colorbars and functions. Please contact me if you want to be able to reproduce the exact same figures as in the paper.

Description of functions

its_load_taxa: reads the csv file in data/ for the requested community, and displays the time series
its_load_upw: reads the upwelling time series provided in data/
its_compute_PCA: computes Principal Component Analysis of the taxonomic time series
its_compute_integration: computes wind integration following Di Lorenzo and Ohman (2013, https://doi.org/10.1073/pnas.1218022110 )
its_compute_adjusted_correlation: compute Pearson correlations, and adjusted p-values following Pyper and Peterman (1998, https://doi.org/10.1139/f98-104 )
its_agestructured_model: returns the modeled density over time of a population characterized by a given natural mortality rate and forced by an input forcing function

Description of data

Taxonomic time series:
surface.csv, midwater.csv, benthos.csv
Time series for each community on original time steps, except monthly for benthos (lines = time, columns = taxonomic groups).

Upwelling time series:
upwelling_MontereyBay.csv, upwelling_PtConception.csv
Daily time series of upwelling computed for the Monterey Bay and Point Conception regions, as explained in the paper. Primary sources of data are NDBC buoys 46042 for Monterey Bay and PTGC1 for Point Conception.


Reference

Please refer this paper when using these scripts (PDF available upon request):

Messié, M., R.E. Sherlock, C.L. Huffard, J.T. Pennington, C.A. Choy, R.P. Michisaki, K. Gomes, F.P. Chavez, B.H. Robison, and K.L. Smith Jr (2023). Coastal upwelling drives ecosystem temporal variability from the surface to the abyssal seafloor. Proceedings of the National Academy of Sciences, 120(13), e2214567120, https://doi.org/10.1073/pnas.221456712.


Contact

[email protected]

Do not hesitate to contact me if you cannot run the code in start_sourcecode_ITS, if you notice bugs, or if you need help implementing the code for a custom application.

About

Matlab program reproducing results and figures from the paper "Coastal upwelling drives ecosystem temporal variability from the surface to the abyssal seafloor".

Resources

License

Stars

Watchers

Forks

Packages

No packages published

Languages