R/qBiomass.R
In dempseydanielle/SSdata: Extracts Fishery Independent and Commercial Landings Data for the Scotian Shelf from DFO-Maritimes Databases
Defines functions
qBiomass
Documented in
qBiomass
#'@title Applies q-adjustment to biomass and abundance data at the set level
#'@description Applies q-adjustments to biomass and abundance data at the set
#' level and returns to the results to \code{biomassData()}. Length-based
#' adjustments are applied for several functional groups; not length-based
#' adjustments are applied for some species; no adjustment is applied for
#' remaining species.
#'
#'@details \code{qBiomass()} is called by the \code{biomassData()} function.
#' Arguments are supplied to \code{qBiomass()} from the \code{catch_coefs}
#' table (SQL call to gomezc.indiseas_catchability_coeffs), which includes
#' columns \code{FUNGROUP}, \code{Q}, and \code{LENCORR} for 88 \code{SPECIES}.
#' \code{qBiomass()} loops over each row of this table for each year supplied
#' to \code{biomassData()}.
#'
#' \code{qBiomass()} obtains numbers (\code{ABUNDANCE}) at length for the given
#' \code{species} for 1 cm intervals from the groundfish database.
#'
#' Biomass estimates are based on the length-weight relationship:
#' \deqn{ln(Weight) = a + ln(Length) * b} The function obtains length and
#' weight data for \code{species} in \code{year} from the groundfish database
#' and estimates \eqn{a} and \eqn{b}. The average weight of fish at each length
#' is then estimated using: \deqn{Weight_{Avg} = exp(a + ln(Length)*b)} and the
#' biomass estimate is: \deqn{\code{BIOMASS} = \code{ABUNDANCE} *
#' Weight_{Avg}}
#'
#' If there are less than 100 length-weight observations in the database for
#' the given \code{species} in \code{year}, the function will include
#' observations from the 5 years before and after \code{year}. If there are
#' still less than 100 observations, data from all years will be included. This
#' can result is some discrepancies when biomass data is extracted in different
#' years.
#'
#' \bold{q-correction}
#'
#' q is calculated based on the arguments \code{fun_group} and \code{q}.
#'
#' If \code{q} > \code{0} and \code{fun_group} = \code{NA}, then a single q is applied for
#' all length classes. Otherwise, \code{q} is calculated using the equation:
#' \deqn{q =
#' g1*(exp(a1+b1*(\code{LENGTH}*\code{lencorr})))/(1+exp(a1+b1*(\code{LENGTH}*\code{lencorr})))}
#' where \eqn{g1}, \eqn{a1}, and \eqn{b1} are hard-coded for each
#' \code{fun_group}, \code{len_corr} is an argument provided by
#' \code{biomassData()}, and \code{LENGTH} is the length interval (cm).
#'
#' q-corrected abundance: \eqn{\code{QABUNDANCE} = \code{ABUNDANCE}/q}.
#'
#' q-corrected biomass: \eqn{\code{QBIOMASS} = \code{QABUNDANCE} *
#' Weight_{Avg}}
#'
#'@param species Species code from the \code{catch_coeffs} table. This argument
#' is supplied by \code{biomassData()}.
#'@param year Year to calculate the data, supplied by \code{biomasData()}
#'@param fun_group Functional group from the \code{catch_coeffs} table. This
#' argument is supplied by \code{biomassData()}. If \code{fun_group} = \code{NA}, then
#' this \code{q} values is applied to all length classes.
#'@param q Initial q-correction from the \code{catch_coeffs} table. This
#' argument is supplied by \code{biomassData()}. If \code{q} > \code{0} and
#' \code{fun_group} = \code{NA}, then this \code{q} value is applied to all length
#' classes.
#'@param len_corr Initial length correction from the \code{catch_coeffs} table.
#' This argument is supplied by \code{biomassData()}.
#'@return Returns the not q-adjusted and q-adjusted length-based biomass and
#' abundance to \code{biomassData()} for species that have q-adjustments.
#'@references Modified code from AC's ExtractIndicators/R/qBiomass (function
#' \code{biomass_q_adj()})
#'@importFrom stats coef
#'@importFrom graphics curve
#'@importFrom graphics title
#'@importFrom RODBC sqlQuery
#'@family RV functions
#'@export
qBiomass <- function(species, year, fun_group = NA, q = 0, len_corr = 1) {
area = "4VWX"
# make a dummy table of lengths (this is to deal with the herring switch from cm to mm)
# it makes the code WAY slower. Leaving for now, but there may be a way to speed up!
suppressWarnings(sqlQuery(channel,paste("DROP table gs_len;")))
flens = data.frame(CLASS=1, FLEN=1:500)
sqlSave(channel,dat=flens, tablename='GS_LEN',rownames=F)
# Check to see if there is enough data to bother with this species
initial <- sqlQuery(channel,paste("select count(distinct c.mission||','||c.setno||','||",species,"||','||fshno) from groundfish.gsdet c, groundfish.gsinf i where i.mission=c.mission and i.setno=c.setno and to_char(sdate,'mm') in ('06','07','08') and strat in (select distinct strat from mflib.gsmgt where unit in ('",area,"')) and spec=",species,";",sep=""))
go <- ifelse(initial>30,TRUE,FALSE)
if(go==TRUE) {
# Obtain the numbers at length for 1 cm length interval
aa<-sqlQuery(channel, paste("select distinct year,strat,mission,YDDMMSS,XDDMMSS,setno,flen,SUM(clen * DECODE(NVL(totwgt,0),0,1,DECODE(NVL(sampwgt,0),0,1,totwgt/sampwgt))) catch
from
(SELECT distinct year, icl.strat, icl.mission, icl.setno, icl.flen FLEN,sampwgt,totwgt,nvl(clen,0)*1.75/dist clen, YDDMMSS,XDDMMSS
FROM
(SELECT mission,setno, flen, SUM(clen) clen, AVG(fwt) avg_fwt
FROM groundfish.gsdet
WHERE flen IS NOT NULL AND spec=",species,"
GROUP BY mission,setno, FLEN) d,
(SELECT year, mission, setno, strat, dist, totwgt, sampwgt, flen,YDDMMSS,XDDMMSS
FROM
(SELECT flen
FROM GS_LEN
WHERE class=1
AND flen <=(SELECT max(flen) + 1
fROM groundfish.gsdet
WHERE spec=",species," AND flen IS NOT NULL
AND (mission, setno) IN
(SELECT DISTINCT i.mission, i.setno
FROM groundfish.gsinf i
WHERE to_char(sdate,'mm') in ('06','07','08')
AND to_char(sdate,'yyyy') in (",year,") AND i.type=1))) l,
(SELECT year, i.mission, i.setno, strat, dist, totwgt,YDDMMSS,XDDMMSS, sampwgt
FROM
(SELECT mission, setno, totwgt, sampwgt
FROM groundfish.gscat WHERE spec=",species,") c,
(SELECT to_char(sdate,'yyyy') year, i.mission, i.setno,slat YDDMMSS,slong*-1 XDDMMSS, i.strat, dist
FROM groundfish.gsinf i
WHERE to_char(sdate,'mm') in ('06','07','08')
AND to_char(sdate,'yyyy') in (",year,") AND i.type=1) i
WHERE i.mission=c.mission(+)
AND i.setno=c.setno(+)) ic) icl
WHERE icl.mission=d.mission(+) AND icl.setno=d.setno(+) AND icl.flen=d.flen(+) and icl.strat in (select distinct strat from mflib.gsmgt where unit in ('",area,"')))
group by year,strat,mission,setno,flen, XDDMMSS,YDDMMSS;",sep="" ))
run <- ifelse(nrow(aa) < 1, FALSE, TRUE)
if(run==TRUE) {
#order the data by fork length
aa <- aa[order(aa$FLEN),]
# Not length-based q for some species (e.g., herring,)
if(is.na(fun_group) && q > 0) {
aa$q <- q
aa$corCatch <- aa$CATCH/aa$q
aa$model<-paste('single_q-', q)
}
# adjust the catch at lengths by appropriate q and length correction
# cod length-based q
if(fun_group == 'cod' && q == 0) {
a1 = -5.14
b1 = 0.141
g1 = 0.870
aa$q <- g1*(exp(a1+b1*(aa$FLEN*len_corr)))/(1+exp(a1+b1*(aa$FLEN*len_corr)))
aa$corCatch <- aa$CATCH/aa$q
aa$model <- 'cod'
}
# haddock length-based q
if(fun_group == 'haddock'&& q == 0) {
a1=-2.80
b1 = 0.0661
g1 = 1.5
aa$q <- g1*(exp(a1+b1*(aa$FLEN*len_corr)))/(1+exp(a1+b1*(aa$FLEN*len_corr)))
aa$corCatch <- aa$CATCH/aa$q
aa$model <- 'haddock'
}
# pelagic gadoids length-based q
if(fun_group == 'pg'&& q == 0 ) {
a1 = -4.61
b1 = 0.0789
g1 = 0.58
aa$q <-g1*(exp(a1+b1*(aa$FLEN*len_corr)))/(1+exp(a1+b1*(aa$FLEN*len_corr)))
aa$corCatch<-aa$CATCH/aa$q
aa$model<-'pg'
}
# demersal gadoids length-based q
if(fun_group == 'dg'&& q == 0) {
a1=-3.50
b1=0.0925
g1=0.968
aa$q<-g1*(exp(a1+b1*(aa$FLEN*len_corr)))/(1+exp(a1+b1*(aa$FLEN*len_corr)))
aa$corCatch<-aa$CATCH/aa$q
aa$model<-'dg'
}
# flatfish length-based q
if(fun_group == 'ff'&& q == 0) {
a1=-4.35
b1=0.111
g1=0.831
aa$q<-g1*(exp(a1+b1*(aa$FLEN*len_corr)))/(1+exp(a1+b1*(aa$FLEN*len_corr)))
aa$corCatch<-aa$CATCH/aa$q
aa$model<-'ff'
}
# ling length-based q
if(fun_group == 'ling' && q == 0) {
a1=-13.9
b1=0.193
g1=1.66
aa$q<-g1*(exp(a1+b1*(aa$FLEN*len_corr)))/(1+exp(a1+b1*(aa$FLEN*len_corr)))
aa$corCatch<-aa$CATCH/aa$q
aa$model<-'ling'
}
# small pelagics length-based q from H.Benoit
if(fun_group == 'sp' && q == 0) {
a1=-17.7165
b1=0.175
g1=37710.7
aa$q<-g1*(exp(a1+b1*(aa$FLEN*len_corr)))/(1+exp(a1+b1*(aa$FLEN*len_corr)))
aa$corCatch<-aa$CATCH/aa$q
aa$model<-'sp'
}
# calculate appropriate length weight parameters (a's and b's)
bb<-sqlQuery(channel,paste("select ",species,",flen,fwt from groundfish.gsdet d, groundfish.gsinf i where i.mission=d.mission and i.setno=d.setno and i.strat in (select strat from
mflib.gsmgt where unit in '",area,"') and to_char(sdate,'mm') in ('06','07','08') AND to_char(sdate,'yyyy') in ('",year,"') and spec in (",species,") and fwt is not null;",sep=""))
if(nrow(bb)<100) {bb<-sqlQuery(channel,paste("select ",species,",flen,fwt from groundfish.gsdet d, groundfish.gsinf i where i.mission=d.mission and i.setno=d.setno and i.strat in (select strat from
mflib.gsmgt where unit in '",area,"') and to_char(sdate,'mm') in ('06','07','08') AND to_char(sdate,'yyyy') between ('",year,"'-5) and ('",year,"'+5) and spec in (",species,") and fwt is not null;",sep=""))
}
if(nrow(bb)<100){bb<-sqlQuery(channel,paste("select ",species,",flen,fwt from groundfish.gsdet d, groundfish.gsinf i where i.mission=d.mission and i.setno=d.setno and i.strat in (select strat from
mflib.gsmgt where unit in '",area,"') and to_char(sdate,'mm') in ('06','07','08') and spec in (",species,") and fwt is not null;",sep=""))
}
out <- with(bb, lm(log(FWT)~log(FLEN), bb))
a.est <- coef(out)[1]
b.est <- coef(out)[2]
#q-adj biomass estimate
aa$est.wt <- exp(a.est+log(aa$FLEN)*b.est)
aa$qBiomass <- aa$corCatch*aa$est.wt
aa$rvBiomass <- aa$CATCH*aa$est.wt
names(aa)[8:14] <- c('ABUNDANCE','Q','QABUNDANCE','MODEL','ESTWT','QBIOMASS','BIOMASS')
aa <- aa[,c(1:8,10,13,14)]
aa$SPECIES <- species
aa$QBIOMASS <- aa$QBIOMASS/1000 #for kg
aa$BIOMASS <- aa$BIOMASS/1000 #for kg
return(aa)
}
}
}
dempseydanielle/SSdata documentation built on May 3, 2020, 5:09 p.m.
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Defines functions qBiomass
Documented in qBiomass
#'@title Applies q-adjustment to biomass and abundance data at the set level
#'@description Applies q-adjustments to biomass and abundance data at the set
#' level and returns to the results to \code{biomassData()}. Length-based
#' adjustments are applied for several functional groups; not length-based
#' adjustments are applied for some species; no adjustment is applied for
#' remaining species.
#'
#'@details \code{qBiomass()} is called by the \code{biomassData()} function.
#' Arguments are supplied to \code{qBiomass()} from the \code{catch_coefs}
#' table (SQL call to gomezc.indiseas_catchability_coeffs), which includes
#' columns \code{FUNGROUP}, \code{Q}, and \code{LENCORR} for 88 \code{SPECIES}.
#' \code{qBiomass()} loops over each row of this table for each year supplied
#' to \code{biomassData()}.
#'
#' \code{qBiomass()} obtains numbers (\code{ABUNDANCE}) at length for the given
#' \code{species} for 1 cm intervals from the groundfish database.
#'
#' Biomass estimates are based on the length-weight relationship:
#' \deqn{ln(Weight) = a + ln(Length) * b} The function obtains length and
#' weight data for \code{species} in \code{year} from the groundfish database
#' and estimates \eqn{a} and \eqn{b}. The average weight of fish at each length
#' is then estimated using: \deqn{Weight_{Avg} = exp(a + ln(Length)*b)} and the
#' biomass estimate is: \deqn{\code{BIOMASS} = \code{ABUNDANCE} *
#' Weight_{Avg}}
#'
#' If there are less than 100 length-weight observations in the database for
#' the given \code{species} in \code{year}, the function will include
#' observations from the 5 years before and after \code{year}. If there are
#' still less than 100 observations, data from all years will be included. This
#' can result is some discrepancies when biomass data is extracted in different
#' years.
#'
#' \bold{q-correction}
#'
#' q is calculated based on the arguments \code{fun_group} and \code{q}.
#'
#' If \code{q} > \code{0} and \code{fun_group} = \code{NA}, then a single q is applied for
#' all length classes. Otherwise, \code{q} is calculated using the equation:
#' \deqn{q =
#' g1*(exp(a1+b1*(\code{LENGTH}*\code{lencorr})))/(1+exp(a1+b1*(\code{LENGTH}*\code{lencorr})))}
#' where \eqn{g1}, \eqn{a1}, and \eqn{b1} are hard-coded for each
#' \code{fun_group}, \code{len_corr} is an argument provided by
#' \code{biomassData()}, and \code{LENGTH} is the length interval (cm).
#'
#' q-corrected abundance: \eqn{\code{QABUNDANCE} = \code{ABUNDANCE}/q}.
#'
#' q-corrected biomass: \eqn{\code{QBIOMASS} = \code{QABUNDANCE} *
#' Weight_{Avg}}
#'
#'@param species Species code from the \code{catch_coeffs} table. This argument
#' is supplied by \code{biomassData()}.
#'@param year Year to calculate the data, supplied by \code{biomasData()}
#'@param fun_group Functional group from the \code{catch_coeffs} table. This
#' argument is supplied by \code{biomassData()}. If \code{fun_group} = \code{NA}, then
#' this \code{q} values is applied to all length classes.
#'@param q Initial q-correction from the \code{catch_coeffs} table. This
#' argument is supplied by \code{biomassData()}. If \code{q} > \code{0} and
#' \code{fun_group} = \code{NA}, then this \code{q} value is applied to all length
#' classes.
#'@param len_corr Initial length correction from the \code{catch_coeffs} table.
#' This argument is supplied by \code{biomassData()}.
#'@return Returns the not q-adjusted and q-adjusted length-based biomass and
#' abundance to \code{biomassData()} for species that have q-adjustments.
#'@references Modified code from AC's ExtractIndicators/R/qBiomass (function
#' \code{biomass_q_adj()})
#'@importFrom stats coef
#'@importFrom graphics curve
#'@importFrom graphics title
#'@importFrom RODBC sqlQuery
#'@family RV functions
#'@export
qBiomass <- function(species, year, fun_group = NA, q = 0, len_corr = 1) {
area = "4VWX"
# make a dummy table of lengths (this is to deal with the herring switch from cm to mm)
# it makes the code WAY slower. Leaving for now, but there may be a way to speed up!
suppressWarnings(sqlQuery(channel,paste("DROP table gs_len;")))
flens = data.frame(CLASS=1, FLEN=1:500)
sqlSave(channel,dat=flens, tablename='GS_LEN',rownames=F)
# Check to see if there is enough data to bother with this species
initial <- sqlQuery(channel,paste("select count(distinct c.mission||','||c.setno||','||",species,"||','||fshno) from groundfish.gsdet c, groundfish.gsinf i where i.mission=c.mission and i.setno=c.setno and to_char(sdate,'mm') in ('06','07','08') and strat in (select distinct strat from mflib.gsmgt where unit in ('",area,"')) and spec=",species,";",sep=""))
go <- ifelse(initial>30,TRUE,FALSE)
if(go==TRUE) {
# Obtain the numbers at length for 1 cm length interval
aa<-sqlQuery(channel, paste("select distinct year,strat,mission,YDDMMSS,XDDMMSS,setno,flen,SUM(clen * DECODE(NVL(totwgt,0),0,1,DECODE(NVL(sampwgt,0),0,1,totwgt/sampwgt))) catch
from
(SELECT distinct year, icl.strat, icl.mission, icl.setno, icl.flen FLEN,sampwgt,totwgt,nvl(clen,0)*1.75/dist clen, YDDMMSS,XDDMMSS
FROM
(SELECT mission,setno, flen, SUM(clen) clen, AVG(fwt) avg_fwt
FROM groundfish.gsdet
WHERE flen IS NOT NULL AND spec=",species,"
GROUP BY mission,setno, FLEN) d,
(SELECT year, mission, setno, strat, dist, totwgt, sampwgt, flen,YDDMMSS,XDDMMSS
FROM
(SELECT flen
FROM GS_LEN
WHERE class=1
AND flen <=(SELECT max(flen) + 1
fROM groundfish.gsdet
WHERE spec=",species," AND flen IS NOT NULL
AND (mission, setno) IN
(SELECT DISTINCT i.mission, i.setno
FROM groundfish.gsinf i
WHERE to_char(sdate,'mm') in ('06','07','08')
AND to_char(sdate,'yyyy') in (",year,") AND i.type=1))) l,
(SELECT year, i.mission, i.setno, strat, dist, totwgt,YDDMMSS,XDDMMSS, sampwgt
FROM
(SELECT mission, setno, totwgt, sampwgt
FROM groundfish.gscat WHERE spec=",species,") c,
(SELECT to_char(sdate,'yyyy') year, i.mission, i.setno,slat YDDMMSS,slong*-1 XDDMMSS, i.strat, dist
FROM groundfish.gsinf i
WHERE to_char(sdate,'mm') in ('06','07','08')
AND to_char(sdate,'yyyy') in (",year,") AND i.type=1) i
WHERE i.mission=c.mission(+)
AND i.setno=c.setno(+)) ic) icl
WHERE icl.mission=d.mission(+) AND icl.setno=d.setno(+) AND icl.flen=d.flen(+) and icl.strat in (select distinct strat from mflib.gsmgt where unit in ('",area,"')))
group by year,strat,mission,setno,flen, XDDMMSS,YDDMMSS;",sep="" ))
run <- ifelse(nrow(aa) < 1, FALSE, TRUE)
if(run==TRUE) {
#order the data by fork length
aa <- aa[order(aa$FLEN),]
# Not length-based q for some species (e.g., herring,)
if(is.na(fun_group) && q > 0) {
aa$q <- q
aa$corCatch <- aa$CATCH/aa$q
aa$model<-paste('single_q-', q)
}
# adjust the catch at lengths by appropriate q and length correction
# cod length-based q
if(fun_group == 'cod' && q == 0) {
a1 = -5.14
b1 = 0.141
g1 = 0.870
aa$q <- g1*(exp(a1+b1*(aa$FLEN*len_corr)))/(1+exp(a1+b1*(aa$FLEN*len_corr)))
aa$corCatch <- aa$CATCH/aa$q
aa$model <- 'cod'
}
# haddock length-based q
if(fun_group == 'haddock'&& q == 0) {
a1=-2.80
b1 = 0.0661
g1 = 1.5
aa$q <- g1*(exp(a1+b1*(aa$FLEN*len_corr)))/(1+exp(a1+b1*(aa$FLEN*len_corr)))
aa$corCatch <- aa$CATCH/aa$q
aa$model <- 'haddock'
}
# pelagic gadoids length-based q
if(fun_group == 'pg'&& q == 0 ) {
a1 = -4.61
b1 = 0.0789
g1 = 0.58
aa$q <-g1*(exp(a1+b1*(aa$FLEN*len_corr)))/(1+exp(a1+b1*(aa$FLEN*len_corr)))
aa$corCatch<-aa$CATCH/aa$q
aa$model<-'pg'
}
# demersal gadoids length-based q
if(fun_group == 'dg'&& q == 0) {
a1=-3.50
b1=0.0925
g1=0.968
aa$q<-g1*(exp(a1+b1*(aa$FLEN*len_corr)))/(1+exp(a1+b1*(aa$FLEN*len_corr)))
aa$corCatch<-aa$CATCH/aa$q
aa$model<-'dg'
}
# flatfish length-based q
if(fun_group == 'ff'&& q == 0) {
a1=-4.35
b1=0.111
g1=0.831
aa$q<-g1*(exp(a1+b1*(aa$FLEN*len_corr)))/(1+exp(a1+b1*(aa$FLEN*len_corr)))
aa$corCatch<-aa$CATCH/aa$q
aa$model<-'ff'
}
# ling length-based q
if(fun_group == 'ling' && q == 0) {
a1=-13.9
b1=0.193
g1=1.66
aa$q<-g1*(exp(a1+b1*(aa$FLEN*len_corr)))/(1+exp(a1+b1*(aa$FLEN*len_corr)))
aa$corCatch<-aa$CATCH/aa$q
aa$model<-'ling'
}
# small pelagics length-based q from H.Benoit
if(fun_group == 'sp' && q == 0) {
a1=-17.7165
b1=0.175
g1=37710.7
aa$q<-g1*(exp(a1+b1*(aa$FLEN*len_corr)))/(1+exp(a1+b1*(aa$FLEN*len_corr)))
aa$corCatch<-aa$CATCH/aa$q
aa$model<-'sp'
}
# calculate appropriate length weight parameters (a's and b's)
bb<-sqlQuery(channel,paste("select ",species,",flen,fwt from groundfish.gsdet d, groundfish.gsinf i where i.mission=d.mission and i.setno=d.setno and i.strat in (select strat from
mflib.gsmgt where unit in '",area,"') and to_char(sdate,'mm') in ('06','07','08') AND to_char(sdate,'yyyy') in ('",year,"') and spec in (",species,") and fwt is not null;",sep=""))
if(nrow(bb)<100) {bb<-sqlQuery(channel,paste("select ",species,",flen,fwt from groundfish.gsdet d, groundfish.gsinf i where i.mission=d.mission and i.setno=d.setno and i.strat in (select strat from
mflib.gsmgt where unit in '",area,"') and to_char(sdate,'mm') in ('06','07','08') AND to_char(sdate,'yyyy') between ('",year,"'-5) and ('",year,"'+5) and spec in (",species,") and fwt is not null;",sep=""))
}
if(nrow(bb)<100){bb<-sqlQuery(channel,paste("select ",species,",flen,fwt from groundfish.gsdet d, groundfish.gsinf i where i.mission=d.mission and i.setno=d.setno and i.strat in (select strat from
mflib.gsmgt where unit in '",area,"') and to_char(sdate,'mm') in ('06','07','08') and spec in (",species,") and fwt is not null;",sep=""))
}
out <- with(bb, lm(log(FWT)~log(FLEN), bb))
a.est <- coef(out)[1]
b.est <- coef(out)[2]
#q-adj biomass estimate
aa$est.wt <- exp(a.est+log(aa$FLEN)*b.est)
aa$qBiomass <- aa$corCatch*aa$est.wt
aa$rvBiomass <- aa$CATCH*aa$est.wt
names(aa)[8:14] <- c('ABUNDANCE','Q','QABUNDANCE','MODEL','ESTWT','QBIOMASS','BIOMASS')
aa <- aa[,c(1:8,10,13,14)]
aa$SPECIES <- species
aa$QBIOMASS <- aa$QBIOMASS/1000 #for kg
aa$BIOMASS <- aa$BIOMASS/1000 #for kg
return(aa)
}
}
}
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