At the SWFSC and Scripps Institution of Oceanography (SIO) under the umbrella of the 60-year CalCOFI program we conduct seasonal ship-based surveys of hydrography, plankton and ichthyoplankton using nets and fish egg counters, trawling for adult fish, multifrequency acoustics for fish and micronekton, and transect counts of birds and mammals. We also use satellite remote sensing data to provide fine resolution regional snapshots of temperature and phytoplankton production. We develop statistical models to link the results of ship surveys to 4-dimensional hydrographic models run at the SIO Climate, Atmospheric Science, and Physical Oceanography (CASPO) Division. The models predict hydrographic properties (temperature, salinity and sea surface height), and provide estimates of the flow field.

Re-assessment of the Scripps Pier Temperature Index (Request Reprint) 

A temperature-based index used as an environmental decision rule for Pacific sardine stock assessment no longer appears to be useful in part due to divergence of temperature trends between inshore and offshore areas of the Southern California Bight (McClatchie et al 2010). Inshore water at the Scripps Institution of Oceanography Pier used for the environmental index is warming more rapidly than the offshore water where sardine spawn. The increasing difference between these two areas means that the  Scripps Pier index is no longer representative of the sardine spawning habitat.

Modeling Spawning Habitat of Pacific Sardine and Northern Anchovy  (pdf)

The development of predictive models of spawning habitat as a function of oceanographic conditions may allow for better understanding of the fishes’ population dynamics, better allocation of sampling effort, and more precise estimates of stock size. We developed models to relate presence and abundance of sardine and anchovy eggs, as a proxy for spawning habitat, to physical oceanographic conditions in the California Current during spring. We used environmental variables related to water-mass properties, primary productivity, and rates of nutrient cycling that have been measured as part of the CalCOFI sampling program but also can be measured using remote-sensing technologies such as gliders or satellites.

Oxygen trends in the Southern California Bight (Request Reprint)

The secular trend in hypoxia over the last 57 years was not monotonic, but showed a trend reversal in the mid-1980s. Recent declines in oxygen on the order of 20% over the last two decades are the largest and longest sustained negative trend in the time series and have brought oxygen concentrations back to levels measured in the late 1950s to early 1960s.

rcalcofi — An R package for CalCOFI data (pdf)

We developed a package in the R statistical language to facilitate convenient formatting, visualization, and analysis of CalCOFI- and oceanographic data. Major features are: 1) The CalCOFI line/station coordinate system is integrated into standard R spatial classes, 2) functions for enhanced plotting of spatial data in the lattice graphics system, including re-projected grids and images; and 3) functions to download and regrid remotely sensed satellite data that is freely available from NOAA. The rcalcofi package source or binaries are available at: ftp://swfscftp.noaa.gov/users/eweber/rcalcofi