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James-Thorson-NOAA / VAST

Spatio-temporal analysis of univariate or multivariate data, e.g., standardizing data for multiple species or stages
http://www.FishStats.org
GNU General Public License v3.0
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California_current region for the extrapolation grid contains the CCA #21

Closed John-R-Wallace-NOAA closed 7 years ago

John-R-Wallace-NOAA commented 7 years ago

The California_current region for the extrapolation grid contains the CCA (Cowcod Conservation Area) where previously it did not. The CCA is not trawled by the WCGBTS nor commercial fishers.

James-Thorson commented 7 years ago

Investigation shows that VAST is plotting densities for WCGBTS in all areas that were previously included in the design-based estimator, which seems like a reasonable default behavior.

James-Thorson commented 7 years ago

For WCGBTS plots, an alternative is to exclude plotting density in the Cowcod conservation area. To do so, replace the line calling function SpatialDeltaGLMM::MapDetails_Fn with the following:

MapDetails_List = SpatialDeltaGLMM::MapDetails_Fn( "Region"=Region, "NN_Extrap"=Spatial_List$PolygonList$NN_Extrap, "Extrapolation_List"=Extrapolation_List, "Include"=(Extrapolation_List[["Area_km2_x"]]>0 & ifelse(is.na(Extrapolation_List$Data_Extrap[,'Cowcod']),0,Extrapolation_List$Data_Extrap[,'Cowcod'])==0) )