Mya arenaria population and disease survey

R code and data sets support/recreate all analysis in the following manuscript:

Glaspie, CN, RD Seitz, MB Ogburn, CF Dungan, and AH Hines. Impacts of predators, habitat, recruitment, and disease on soft-shell clams Mya arenaria and stout razor clams Tagelus plebeius in Chesapeake Bay. Submitted to Marine Ecology Progress Series.

A bivalve survey was conducted in Chesapeake Bay to examine influential factors on bivalve populations, focusing on predation (crab, fish, and cownose rays), habitat type (mud, sand, gravel, shell, or seagrass), environment (temperature, salinity, and dissolved oxygen), recruitment, and disease. M. arenaria and T. plebeius were found more often in more-complex habitats such as seagrass or shell than any other habitat. Clams were collected from three river systems of lower Chesapeake Bay (Lynnhaven River, York River, Mobjack Bay), and three river systems of upper Chesapeake Bay (Western Shore, Eastern Bay, Chester River) in fall 2011; spring/summer/fall 2012; and either spring/summer 2013 (for lower Bay) or summer/fall 2013. Each sampling season, four to nine sites within each subestuary were sampled, with three to four replicate samples from each site. The long-term trend of M. arenaria recruitment in Maryland was evaluated using data from surveys conducted by SERC in the Rhode River, Maryland. Benthic core samples were collected approximately quarterly (typically March/April, June, October, December) at two sandy subtidal sites from 1981-2016. Spring/summer temperature (April-August) obtained from the Chesapeake Bay Program Water Quality Database (http://www.chesapeakebay.net/data) for all tidal mainstem Chesapeake Bay stations, and annually averaged Susquehanna River discharge obtained from the USGS water quality monitoring station at Harrisburg, PA (National Water Information System at https://waterdata.usgs.gov/usa/nwis).