Data and analyses associated with "Dermal mycobacteriosis and warming sea surface temperatures are associated with elevated mortality of striped bass in Chesapeake Bay"

Abstract

<div>The following data and analyses (R-code) are associated with the manuscript:</div><div><br></div><div>Groner ML, Hoenig JM, Pradel R, Choquet R, Vogelbein, WK, Gauthier, DT, Friedrichs MAM. Dermal mycobacteriosis and warming sea surface temperatures are associated with elevated mortality of striped bass in Chesapeake Bay. 2018 Ecology and Evolution</div><div><br></div><div><br></div><div><b>Data</b></div><div>1) SB recap data for esurge.txt: Dataset on striped bass mark-recapture from 2005-2013 as described in the manuscript. Formatted for analysis in ESURGE<br></div><div> $COV:tag- tag number of unique fish</div><div> H:year- year of study 1-2005, 2-2006, etc.</div><div> COV:rel_fl- fork length at the time of tagging</div><div>$COV:realage- age of fish at the time of tagging</div><div> RC: indicates of data is right-censored (i.e., fish was removed at capture)</div><div><br></div><div> *Note that this data was modified from the dataset available on dryad (https://datadryad.org/resource/doi:10.5061/dryad.f56v8/3), in order to fit the E-SURGE format.</div><div><br></div><div>2) SB Survival best-fit MMSMR.csv: Estimated survival of striped bass by year and disease state from the best-fit MMSMR model</div><div><br></div><div>3) SB state Transitions best-fit MMSMR.csv: Estimated transitions betwee disease states from the best-fit MMSMR model</div><div><br></div><div>4) SB Encounter rates best-fit MMSMR.csv: Estimated catchability of striped bass by year and disease state from the best-fit MMSMR model</div><div><br></div><div>5) SB Survival temp-dependent.csv: Survival rates of striped bass as a function of disease state and average summer SST</div><div><br></div><div>6) Environmental covariates.csv: yearly averages for average summer SST, #days > 25 C, #days < 5.1 mg/L Dissolved oxygen, average water flow</div><div><b><br></b></div><div><b>R-code:</b></div><div><div>1) Graph SB best-fit MMSMR output.R: graphs results from best fit MMSMR (not including environmental covariates) uses datasets 2,3,4 listed above</div><div><br></div><div>2) MMSMR results with environmental covariates.R: </div><div>graphs results from best model in table 3 (include environmental covariates of survival) uses datasets 5, 6 listed above</div><div><br></div><div>3) Temperature-dependent population projection.R: </div><div>projects and graphs a cohort of 10,000 3+ year old striped bass given different average summer SSTs</div></div><div><br></div><div><br></div