DesignBasedEstBiomass.EWC.fn: Calculate yearly biomass estimates
In nwfscSurveyCode: What the package does (short line)

Description Usage Arguments Details Value Author(s) See Also Examples

Calculates yearly estimates of biomass using design-based expansion.

1	DesignBasedEstBiomass.EWC.fn(dat, strat.vars, strat.df)

`dat`	A dataframe of survey catch data with a column called catchPerArea
`strat.vars`	A character vector of the names of the strata variables. They must be associated with column names in `strat.df`. See details for more information.
`strat.df`	A dataframe describing the strata name, area, and boundaries. Boundaries are determined by latitude and bottom depth. See Details.

The dataframe of survey catch data is usually downloaded from the AFSC servers. See example below how to calculate catchPerArea.

strat.df is a dataframe with a column called “name” and two columns for each stratum variable (START_LATITUDE and BOTTOM_DEPTH) indicating the low and high bounds. The columns for each stratum variable should be named with the stratum variable name followed by .1 for the low bound and .2 for the high bound. For example, this is what a strat.df would look like (as called in the example below).

name area START_LATITUDE.2 START_LATITUDE.1 BOTTOM_DEPTH.1 BOTTOM_DEPTH.2 A 5829 49.0 45.0 183 549 B 4024 49.0 45.0 549 900 C 9259 49.0 40.5 900 1280 D 6211 45.0 40.5 183 549 E 5264 45.0 40.5 549 900 F 6952 40.5 34.5 183 549 G 7801 40.5 34.5 549 900 H 8059 40.5 34.5 900 1280

You can use StratAreas.fn to calculate the area of the strata using the SA3 data. You will need to supply boundaries available in the SA3 file.

Strata=yearlyStrataEsts,Total=ests,LNtons=ln

`Strata`	Strata specific estimates
`Total`	Estimates summed over all strata
`LNtons`	Natural log of the total for input into SS3

Allan Hicks

StratAreas.fn, ReadInBiomass.EWC.fn, SA3,

## Not run: 
 ### AFSC slope
 #datB is read in using ReadInBiomass.EWC.fn
 xB <- datB[datB$SURVEY=="AFSC.Slope" & datB$YEAR
 xB$year <- xB$YEAR
 #calculate the density (kg/km^2) using net width and distance fished
 xB$areaFished <- xB$DISTANCE_FISHED*(xB$NET_WIDTH/1000)
 tmp <- sum(is.na(xB$areaFished))
 cat("There are",tmp,"instances where area swept could not be calculated due to missing values.\n")
 xB$catchPerArea <- xB$WEIGHT/xB$areaFished
 xB$catchPerArea[is.na(xB$catchPerArea)&!is.na(xB$areaFished)] <- 0                                  #the tows with no observation of the species
 xB <- xB[!is.na(xB$catchPerArea),]
 #call the function for the Design based estimates
 #use biomass$LNtons for SS3 (with medianBhat)
 biomass <- DesignBasedEstBiomass.EWC.fn(xB,strat.vars=c("BOTTOM_DEPTH","START_LATITUDE"),strat.df=strata.AKslope)

## End(Not run)