Definition of data objects contained in this archive.

2020-11-05_sturgeon_clim.cat_flyer.png – Example flyer of the Atlantic Sturgeon Risk of Occurrence forecast produce using this code. 

Depth_boundaries.Rdata – A set of six objects to be read into program R to facilitate forecast building and mapping. colr- color palate with varying shades of green. d_depth – a matrix of water depths in the Delaware Bay in meters on a uniform grid to match satellite data. d_land – the portion of d_depth above water to ease plotting of the land mask. Depthr – a raster of water depth in the Delaware Bay in meters. lat – latitude grid array. lon – longitude grid array. 

EA_shiny_sturgeon_app.R – The program R code to build the Atlantic Sturgeon Risk of Occurrence Application. 

Stur_forecast_and_messaging.R - The program R code to create the forecast and distribute the images and messages for the Atlantic Sturgeon Risk of Occurrence forecast 

aqua.grid.nc4 – The latitude and longitude grid in which the satellite and gapfilled data sets are arranged. 

debay.climatology.nc3 – The daily climatologies of the ocean color and sea surface temperature compiled from the available MODIS-Aqua satellite record for the Delaware Bay. 

clim_text.Rdata – The premade text alert for the daily Atlantic Sturgeon Risk of Occurrence climatology to be read into the shiny app. 

debay.a443.viirs.init, debay.chl.viirs.init, debay.rrs_555.viirs.init, debay.sst.viirs.init – initialization parameters for the DINEOF gapfilling for Delaware Bay Satellite data. 

grid.Rdata – Larger footprint matrix of lat-lon grid to align satellite data prior to subsetting in for the study area. 

lon_lat.Rdata – Longitude (sub_lon) and Latitude (sub_lat) for x and y values of grid.Rdata. 

model_predictions_climatology.nc4 – The daily climatologies of the Atlantic Sturgeon Risk of Occurrence compiled from the available MODIS-Aqua satellite record. Produce from Breece, M. W., D. A. Fox, D. E. Haulsee, I. Wirgin, and M. J. Oliver. 2017. Satellite Driven Distribution Models of Endangered Atlantic Sturgeon Occurrence in the Mid-Atlantic. ICES Journal of Marine Science fsx187.

product_template.png – Blank template with project information to produce the Atlantic Sturgeon Risk of Occurrence flyers 

raster_masks.Rdata – raster layers that delineate the regions of the Delaware Bay for forecast distribution. 

sturgeon_model_predictions.R – Code to produce the pixel by pixel predictions of Atlantic Sturgeon Risk of Occurrence from the satellite data. The details of model development can be found in Breece, M. W., D. A. Fox, D. E. Haulsee, I. Wirgin, and M. J. Oliver. 2017. Satellite Driven Distribution Models of Endangered Atlantic Sturgeon Occurrence in the Mid-Atlantic. ICES Journal of Marine Science fsx187. 

v2_ts_dxdoy_temp_443.Rdata – An R object containing the Generalized Additive Mixed Model to estimate Atlantic Sturgeon presence given the input conditions. This model was developed in Breece, M. W., D. A. Fox, D. E. Haulsee, I. Wirgin, and M. J. Oliver. 2017. Satellite Driven Distribution Models of Endangered Atlantic Sturgeon Occurrence in the Mid-Atlantic. ICES Journal of Marine Science fsx187.