survdat is a collection of tools that:
These data are available to qualified researchers upon request.
The Northeast Fisheries Science Center (NEFSC) has been conducting standardized bottom trawl surveys in the fall since 1963 and spring since 1968. The surveys follow a stratified random design. Fish species and several invertebrate species are enumerated on a tow by tow basis (Azarovitz 1981). The data are housed in the NEFSC’s survey database (SVDBS) maintained by the Ecosystem Survey Branch.
Direct pulls from the database are not advisable as there have been
several gear modifications and vessel changes over the course of the
time series (Miller et al. 2010).
survdat was developed as a database query that applies the
appropriate calibration factors for a seamless time series since the
1960s.
The survdat package can be broken down into two
sections. The first pulls the raw data from SVDBS. survdat
identifies those research cruises associated with the seasonal bottom
trawl surveys and pulls the station and biological data. Station data
includes tow identification (cruise, station, and stratum), tow location
and date, as well as several environmental variables (depth,
surface/bottom salinity, and surface/bottom temperature). Stations are
filtered for representativness using a station, haul, gear (SHG) code
for tows prior to 2009 and a tow, operations, gear, and aquisition
(TOGA) code from 2009 onward. The codes that correspond to a
representative tow (SHG <= 136 or TOGA <= 1324) are the same used
by assessment biologists at the NEFSC. Biological data includes the
total biomass and abundance by species, as well as lengths and number at
length.
The second section of the Survdat script applies the calibration factors. There are four calibrartion factors applied (Table @ref(tab:calibration)). Calibration factors are pulled directly from SVDBS. Vessel conversions were made from either the NOAA Ship Delaware II or NOAA Ship Henry Bigelow to the NOAA Ship Albatross IV which was the primary vessel for most of the time series. The Albatross was decommisioned in 2009 and the Bigelow is now the primary vessel for the bottom trawl survey.
| Name | Code | Applied |
|---|---|---|
| Door Conversion | DCF | <1985 |
| Net Conversion | GCF | 1973 - 1981 (Spring) |
| Vessel Conversion I | VCF | Delaware II records |
| Vessel Conversion II | BCF | Henry Bigelow records |
The output from survdat is a data.table that contains
all the station and biological data, corrected as noted above, from the
NEFSC Spring Bottom Trawl Survey and NEFSC Fall Bottom Trawl Survey.
For the purposes of the aggregate biomass indicators, fall and spring survey data are treated separately. Additionally, all length data is dropped and species seperated by sex at the catch level are merged back together.
The data pulled from SVDBS is first post stratified into geographical
regions (any user supplied geospatial shapefile) by labeling sampling
stations by the geographical region they fell within
(post_strat.r) Next, the total number of stations within
each geographical region per year is counted using unique station
records (strat_prep.r). Biomass is summed by species per
year per region and divided by the appropriate station count to get the
regional mean (strat_mean.r). Finally, the mean biomasses
are summed over the defined regions (swept_area.r).