Code from analyses for Key sensitivities for long-distance dispersal models in the North Central Pacific Ocean by Taylor D. Ely¶, Gabriella N. M. Mukai¶, Donald R. Kobayashi, Peter B. Marko, Amy L. Moran, Johanna L. K. Wren.¶ = co-first authots. Datasets are too large for github. Please contact us if interested.
LAPS_Sensitivity_stopRelease_Distance_Settle_withFreeSlip_3Oct2022.ipynb contains a jupyter notebook python file to simulate larval dispersal using OceanParcels
LAPS_release_sites_noHI.csv contains the coordinates of where particles are released in the simulation in LAPS_Sensitivity_stopRelease_Distance_Settle_withFreeSlip_3Oct2022.ipynb
None of the HYCOM input values and none of the ouput netcdf files were included in this folder because they are too large
LAPS_FUV_final.Rmd contains an example set of code used to go from the netcdf files to then calculate a particle density distribution (PDD) and then calculated the fraction of unexplained variance (FUV) between 2 PDDs.
divide_by_days.py contains python script using xarray. For the number of particles released sensitivity test, the netcdf files were extremely large and therefore a step before using this R markdown file was used which extracted only the day of interest from the entire netcdf file.
Nearest_Neighbor_Scrpit.ipynb contains a jupyter notebook python file to calculate settlement and larval connections into the Hawaiian Archipelago with varying PLDs. We defined a connection as any successful larval exchange between an island in the study domain and the Hawaiian Archipelago. Successful larval exchange occurred if a particle’s closest distance to an island in the Hawaiian archipelago was ≤10km during the settlement window. The settlement window had a constant pre-competency period of 15 days and a maximum PLD of either 30, 60, 90, or 180 days. However, the code allows for you to change the PLD, pre-competency window, and settlement distance to whatever you want.
HIreefsNew.csv contains coordinates of habitat for the nearest_neighbor.ipynb script to use
Connectivity_Significance.R contains the R code to pull differences in larval connections from the files created by nearest_neighbor.ipynb for the different parameters used for each sensitivity test at the chosen PLD
Heatmap.R contains the R code to create a heatmap from the heatmap files created by the Connectivity_Significance.R file