This repo houses code for the following paper
Bigman, J. S., B. J. Laurel, K. Kearney, A. J. Hermann, W. Cheng, K. K. Holsman, and L. A. Rogers. "Predicting Pacific cod thermal spawning habitat in a changing climate." ICES Journal of Marine Science (2023): fsad096.
Open access link is here: https://academic.oup.com/icesjms/advance-article/doi/10.1093/icesjms/fsad096/7204287
Jennifer Bigman - NOAA Alaska Fisheries Science Center (AFSC), [email protected]; Ben Laurel - AFSC, [email protected]; Kelly Kearney - AFSC, [email protected]; Al Hermann - Pacific Marine Environmental Laboratory (NOAA/PMEL), [email protected]; Wei Cheng - PMEL & Cooperative Institute for Climate, Ocean, & Ecosystem Studies (CICOES), University of Washington, [email protected]; Kirstin Holsman - AFSC, [email protected]; Lauren Rogers - AFSC, [email protected];
Bering 10k ROMS: ongoing, see https://github.com/kholsman/ACLIM2; Code creation: 2021 - 2023
Eastern Bering Sea
North Pacific Research Board (see https://projects.nprb.org/)
Licensing information: This article is a work of the United States government. Such works are not entitled to domestic copyright protection under U.S. law and are therefore in the public domain. The findings and conclusions in the paper are those of the author(s) and do not necessarily represent the views of the National Marine Fisheries Service.
00a - download and transform level 2 bottom temp data: code to download and concatenate Bering 10k ROMS model (Bering 10k) bottom temperature hindcast
00b - accessing ROMS grid cell area, depth, and domain: code to download grid cell metadata (depth, area, domain) for Bering 10k
00c - merge are, depth, domain with bottom temps & trim to grid: code to trim Bering 10k domain to area of interest for spawning
00d - calculate hatch success for hindcasts: code to combine thermal response curve from Laurel & Rogers 2020 (see citation in paper above) with Bering 10k bottom temperature hindcast timeseries
00e - read projected temp data into R: code to import Bering 10k ROMS projections timeseries into R (projections can be found downloaded here: https://github.com/kholsman/ACLIM2)
00f - bias correct projected temps (at domain level): code to bias-correct output from Bering 10k (see https://github.com/kholsman/ACLIM2 for more information on bias correction)
00g - calculate hatch success for projected temps: code to combine thermal response curve from Laurel & Rogers 2020 (see citation in paper above) with Bering 10k bottom temperature timeseries projections
01 - load each time: code to load libraries, helpful functions, data (hatch success and habitat suitability)
02 - calculating spawning habitat suitability indices: code to calculate the basis for three metrics of spawning habitat suitability (see paper above)
03 - calculating mean latitude metrics: code to calculate the first of three metrics of spawning habitat suitability (see paper above)
04 - calculating area metrics: code to calculate the second of three metrics of spawning habitat suitability (see paper above)
05 - calculating consistency of spawning habitat suitability: code to calculate the third of three metrics of spawning habitat suitability (see paper above)
06 - examining correlations of recruitment & spawning habitat suitability metrics: code to examine whether any relationship exists between spawning habitat suitability and recruitment of Pacific cod
07 - mapping newly-hatched larval distribution: code to map the distribution of Pacific cod larvae from EcoFOCI surveys (see https://www.ecofoci.noaa.gov/field-operations for more information)
08 - trends of habitat suitability metrics: code to example whether trends in habitat suitability metrics exist over time
09 - sensitivity analyses: code to examine whether variability in thermal response curve would affect estimates of spawning habitat suitability
The folder "manuscript figure scripts" has all of the code for the figures in the main paper*
R version used for project: 4.1.3, 4.2.1, 4.3 libraries used for project: here; naturalearth; tidyverse; data.table; sd; forcats; lubridate; patchwork; marmap; zoo; RcolorBrewer; beepr; mapdata; runner; tidync; cowplot; scales; glue; MuMin
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