inst/Projects/FSRS/FSRS.DatacheckVH.r
In LobsterScience/bio.lobster: Lobster Stock Assessment Tools for DFO Maritimes
require (chron)
require (lattice)
require (MASS)
require (doBy)
require (RODBC)
##Checks overwritten for 2017 data - uploaded in Jan 2018##
lobster.db("fsrs.redo")
lobster.db("fsrs")
str(fsrs) #1365712 Records for 2017
FSRS<-fsrs
##COLUMN ADDITIONS TO DATA FRAME ALLOWING DIFFERENT DATE FORMATS
fsrs$julian = as.integer(julian(fsrs$HAUL_DATE))
summary(fsrs)
##TIDY UP THE LFA SPECIFICATIONS
sort(unique(fsrs$LFA))
#CHECK SOAK DAYS BY COMPARING SAME VESSEL, SAME DAY THAT HAS DIFFERENT DEPTHS:
fsrs$Unique<-paste(fsrs$VESSEL_CD,as.character(fsrs$HAUL_DATE),sep = " ")
Depth.dif<-sapply(split(fsrs$DEPTH,fsrs$Unique),function(x){length(unique(x))}) #Should only be one record: LFA 34 - 1230 2001-11-30 (0.5 SD)
table(Depth.dif)
a<-names(Depth.dif)[which(Depth.dif==2)] #Should only be one record: LFA 34 - 1230 2001-11-30 (0.5 SD)
dups<-fsrs[which(fsrs$Unique %in% a),]
unique(dups$Unique)
library(xlsx)
write.xlsx(dups, file=paste("Duplicates",Sys.Date(),".xlsx"))
fsrs<-fsrs[,-29]
#----------------------------------------------------------------------------------------------------------------------------------------------------------------
## CREATION OF DATA FILES FOR EACH LFA:
#---------------------------------------------------------------------------LFA27--------------------------------------------------------------------------------
LFA27.9917=which(fsrs$LFA==27 & fsrs$HAUL_YEAR)
length(LFA27.9917) # 238,973 RECORDS 2016 259,917 for 2017
LFA27.9917=fsrs[LFA27.9917,]
unique(LFA27.9917$HAUL_YEAR)
summary(LFA27.9917)
##EMPTY TRAPS
e=which(LFA27.9917$LOBSTER_NO == 0)
length(e) #7917 records for 2016 and 8029 records for 2017
##VALIDATE SOAK DAYS:
table(LFA27.9917$SOAK_DAYS,LFA27.9917$HAUL_YEAR)
# 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017
#1 5878 5205 5353 4834 6369 7641 7661 10960 8494 9878 8010 8288 8421 7206 8230 8900 9732 9790 12952
#2 2844 2539 2944 2547 4066 3591 3689 5108 4577 5384 4854 5372 4336 3569 5009 5476 6917 6906 5844
#3 285 375 370 430 1004 734 843 687 483 789 1082 1082 635 475 863 1185 1936 1441 1615
#4 33 101 129 103 179 59 155 53 18 413 196 143 97 34 160 180 246 233 332
#5 84 9 32 68 27 29 0 82 0 0 92 0 112 89 106 75 31 90 116
#6 0 21 0 0 0 0 0 8 0 55 30 0 12 46 0 0 0 0 0
#7 0 30 0 0 0 0 4 0 0 0 0 0 0 15 0 0 0 0 85
#9 0 0 0 0 0 6 0 0 0 0 11 0 0 0 0 0 0 0 0
write.table(LFA27.9917, file=paste('rec.LFA27 9917.Noremovals.from.datacheck.9917.',Sys.Date(),'.txt'), row.names=FALSE, col.names=TRUE, sep=" ")
#SOAK DAY REMOVALS (FOR MODELING):
#LFA 27 SOAK DAYS ARE MOSTLY WITHN 1 TO 5 DAYS
sd=which(LFA27.9917$SOAK_DAYS > 5)
length(sd) #289 RECORDS ( I'm getting 238 records for 2016 and 323 for 2017)
LFA27.9917.sd=LFA27.9917[-sd,]
##CALCULATE TRAP # PER DAY
LFA27.9917.traps<-aggregate(TRAP_NO~HAUL_YEAR+VESSEL_CD+HAUL_DATE, data=LFA27.9917.sd, FUN=function(x) length(unique(x)))
#LFA27.9917.traps<-ddply(LFA27.9917.sd,c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE"),summarize,TOT_TRAPS=length(unique(TRAP_NO)))
str(LFA27.9917.traps) # 19446 for 2017
##SIZE ADJUSTMENTS for MLS CHANGE IN 1999-2002
table(LFA27.9917$SIZE_CD,LFA27.9917$SHORT)
a1= which (LFA27.9917$SIZE_CD==8 & LFA27.9917$SHORT==1)
LFA27.9917[a1,"SIZE_CD"]=8.1
summary(LFA27.9917[a1,])
a2= which (LFA27.9917$SIZE_CD==8 & LFA27.9917$SHORT==0)
LFA27.9917[a2,"SIZE_CD"]=8.2
summary(LFA27.9917[a2,])
summary(LFA27.9917)
str(LFA27.9917)
a3= which (LFA27.9917$SIZE_CD==9 & LFA27.9917$SHORT==1)
LFA27.9917[a3,"SIZE_CD"]=9.1
summary(LFA27.9917[a3,])
a4= which (LFA27.9917$SIZE_CD==9 & LFA27.9917$SHORT==0)
LFA27.9917[a4,"SIZE_CD"]=9.2
summary(LFA27.9917[a4,])
summary(LFA27.9917)
str(LFA27.9917)
a5= which (LFA27.9917$SIZE_CD==10 & LFA27.9917$SHORT==1)
LFA27.9917[a5,"SIZE_CD"]=10.1
summary(LFA27.9917[a5,])
a6= which (LFA27.9917$SIZE_CD==10 & LFA27.9917$SHORT==0)
LFA27.9917[a6,"SIZE_CD"]=10.2
summary(LFA27.9917[a6,])
summary(LFA27.9917)
str(LFA27.9917)
table(LFA27.9917$SIZE_CD,LFA27.9917$SHORT)
##CALCULATE TOTAL COUNT OF BERRIED PER DAY PER SIZE
b= which (LFA27.9917$SEX==3)
length (b) #24,765 RECORDS JAN.2016 SQL EXPORT
rec.LFA27.ber.fem <- LFA27.9917[b,]
rec.LFA27.ber.fem =aggregate(rec.LFA27.ber.fem[,1], by=as.list(rec.LFA27.ber.fem[c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE","SOAK_DAYS", "SIZE_CD")]), length, simplify = TRUE)
rec.LFA27.ber.fem = na.omit (rec.LFA27.ber.fem)
library(gdata)
rec.LFA27.ber.fem <- rename.vars(rec.LFA27.ber.fem, from="x", to="Freq")
summary(rec.LFA27.ber.fem)
str(rec.LFA27.ber.fem) #17,790 RECORDS
##MERGE TOTAL TRAPS INFO WITH BERRIED FEMALE SIZE COUNTS PER DAY
rec.LFA27.berfem.cpue.size = merge(LFA27.9917.traps,rec.LFA27.ber.fem, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE"),all.x=T,all.y=F, sort=F)
rec.LFA27.berfem.cpue.size = na.omit (rec.LFA27.berfem.cpue.size)
str(rec.LFA27.berfem.cpue.size) #17,770 RECORDS JAN_2016
summary(rec.LFA27.berfem.cpue.size)
write.table(rec.LFA27.berfem.cpue.size, file="rec.LFA27.berfem.9916.JAN.2016_1to5_1.txt", row.names=FALSE, col.names=TRUE, sep=" ")
##REMOVE RECORDS FOR BERRIED BY INCLUDING IN SEX COLUMN - FOR CPUE ANALYSIS
LFA27.9917=LFA27.9917[-b,]
str(LFA27.9917)
##CALCULATE TOTAL COUNT PER SIZE CLASS
LFA27.9917.counts.at.size =aggregate(LFA27.9917[,1], by=as.list(LFA27.9917[c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "SIZE_CD")]), length, simplify = TRUE)
LFA27.9917.counts.at.size = na.omit (LFA27.9917.counts.at.size)
library(gdata)
LFA27.9917.counts.at.size <- rename.vars(LFA27.9917.counts.at.size, from="x", to="Freq")
summary(LFA27.9917.counts.at.size)
str(LFA27.9917.counts.at.size) #76,121 RECORDS
unique(LFA27.9917.counts.at.size$SIZE_CD) #SIZE 0-16; NO NA VALUES
##SIZE CLASS FREQUENCY TABLE
LFA27.cpue.size = merge(LFA27.9917.traps,LFA27.9917.counts.at.size, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE"),all.x=T,all.y=F, sort=F)
LFA27.0=which(LFA27.cpue.size$SIZE_CD=='0')
LFA27.size0=LFA27.cpue.size[LFA27.0,]
LFA27.size0 = rename.df(LFA27.size0,"Freq", "size0")
LFA27.size0$SIZE_CD=NULL
LFA27.2=which(LFA27.cpue.size$SIZE_CD=='2')
LFA27.size2=LFA27.cpue.size[LFA27.2,]
LFA27.size2 = rename.df(LFA27.size2, "Freq", "size2")
LFA27.size2$SIZE_CD=NULL
LFA27.0.2 = merge(LFA27.size0,LFA27.size2, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.3=which(LFA27.cpue.size$SIZE_CD=='3')
LFA27.size3=LFA27.cpue.size[LFA27.3,]
LFA27.size3 = rename.df(LFA27.size3, "Freq", "size3")
LFA27.size3$SIZE_CD=NULL
LFA27.0.3 = merge(LFA27.0.2,LFA27.size3, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.4=which(LFA27.cpue.size$SIZE_CD=='4')
LFA27.size4=LFA27.cpue.size[LFA27.4,]
LFA27.size4 = rename.df(LFA27.size4, "Freq", "size4")
LFA27.size4$SIZE_CD=NULL
LFA27.0.4 = merge(LFA27.0.3,LFA27.size4, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.5=which(LFA27.cpue.size$SIZE_CD=='5')
LFA27.size5=LFA27.cpue.size[LFA27.5,]
LFA27.size5 = rename.df(LFA27.size5, "Freq", "size5")
LFA27.size5$SIZE_CD=NULL
LFA27.0.5 = merge(LFA27.0.4,LFA27.size5, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.6=which(LFA27.cpue.size$SIZE_CD=='6')
LFA27.size6=LFA27.cpue.size[LFA27.6,]
LFA27.size6 = rename.df(LFA27.size6, "Freq", "size6")
LFA27.size6$SIZE_CD=NULL
LFA27.0.6 = merge(LFA27.0.5,LFA27.size6, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.7=which(LFA27.cpue.size$SIZE_CD=='7')
LFA27.size7=LFA27.cpue.size[LFA27.7,]
LFA27.size7 = rename.df(LFA27.size7, "Freq", "size7")
LFA27.size7$SIZE_CD=NULL
LFA27.0.7 = merge(LFA27.0.6,LFA27.size7, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.8.1=which(LFA27.cpue.size$SIZE_CD=='8.1')
LFA27.size8.1=LFA27.cpue.size[LFA27.8.1,]
LFA27.size8.1 = rename.df(LFA27.size8.1, "Freq", "size8.1")
LFA27.size8.1$SIZE_CD=NULL
LFA27.0.8.1 = merge(LFA27.0.7,LFA27.size8.1, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.8.2=which(LFA27.cpue.size$SIZE_CD=='8.2')
LFA27.size8.2=LFA27.cpue.size[LFA27.8.2,]
LFA27.size8.2 = rename.df(LFA27.size8.2, "Freq", "size8.2")
LFA27.size8.2$SIZE_CD=NULL
LFA27.0.8.2 = merge(LFA27.0.8.1,LFA27.size8.2, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.9.1=which(LFA27.cpue.size$SIZE_CD=='9.1')
LFA27.size9.1=LFA27.cpue.size[LFA27.9.1,]
LFA27.size9.1 = rename.df(LFA27.size9.1, "Freq", "size9.1")
LFA27.size9.1$SIZE_CD=NULL
LFA27.0.9.1 = merge(LFA27.0.8.2,LFA27.size9.1, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.9.2=which(LFA27.cpue.size$SIZE_CD=='9.2')
LFA27.size9.2=LFA27.cpue.size[LFA27.9.2,]
LFA27.size9.2 = rename.df(LFA27.size9.2, "Freq", "size9.2")
LFA27.size9.2$SIZE_CD=NULL
LFA27.0.9.2 = merge(LFA27.0.9.1,LFA27.size9.2, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.10.1=which(LFA27.cpue.size$SIZE_CD=='10.1')
LFA27.size10.1=LFA27.cpue.size[LFA27.10.1,]
LFA27.size10.1 = rename.df(LFA27.size10.1, "Freq", "size10.1")
LFA27.size10.1$SIZE_CD=NULL
LFA27.0.10.1 = merge(LFA27.0.9.2,LFA27.size10.1, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.10.2=which(LFA27.cpue.size$SIZE_CD=='10.2')
LFA27.size10.2=LFA27.cpue.size[LFA27.10.2,]
LFA27.size10.2 = rename.df(LFA27.size10.2, "Freq", "size10.2")
LFA27.size10.2$SIZE_CD=NULL
LFA27.0.10.2 = merge(LFA27.0.10.1,LFA27.size10.2, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.11=which(LFA27.cpue.size$SIZE_CD=='11')
LFA27.size11=LFA27.cpue.size[LFA27.11,]
LFA27.size11 = rename.df(LFA27.size11, "Freq", "size11")
LFA27.size11$SIZE_CD=NULL
LFA27.0.11 = merge(LFA27.0.10.2,LFA27.size11, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.12=which(LFA27.cpue.size$SIZE_CD=='12')
LFA27.size12=LFA27.cpue.size[LFA27.12,]
LFA27.size12 = rename.df(LFA27.size12, "Freq", "size12")
LFA27.size12$SIZE_CD=NULL
LFA27.0.12 = merge(LFA27.0.11,LFA27.size12, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.13=which(LFA27.cpue.size$SIZE_CD=='13')
LFA27.size13=LFA27.cpue.size[LFA27.13,]
LFA27.size13 = rename.df(LFA27.size13, "Freq", "size13")
LFA27.size13$SIZE_CD=NULL
LFA27.0.13 = merge(LFA27.0.12,LFA27.size13, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.14=which(LFA27.cpue.size$SIZE_CD=='14')
LFA27.size14=LFA27.cpue.size[LFA27.14,]
LFA27.size14 = rename.df(LFA27.size14, "Freq", "size14")
LFA27.size14$SIZE_CD=NULL
LFA27.0.14 = merge(LFA27.0.13,LFA27.size14, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.15=which(LFA27.cpue.size$SIZE_CD=='15')
LFA27.size15=LFA27.cpue.size[LFA27.15,]
LFA27.size15 = rename.df(LFA27.size15, "Freq", "size15")
LFA27.size15$SIZE_CD=NULL
LFA27.0.15 = merge(LFA27.0.14,LFA27.size15, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.16=which(LFA27.cpue.size$SIZE_CD=='16')
LFA27.size16=LFA27.cpue.size[LFA27.16,]
LFA27.size16 = rename.df(LFA27.size16, "Freq", "size16")
LFA27.size16$SIZE_CD=NULL
LFA27.0.16 = merge(LFA27.0.15,LFA27.size16, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.0.16[is.na(LFA27.0.16)]=0
summary(LFA27.0.16)
##SIZE CLASS SPECS FOR all LOBSTERS FROM 1999-2014
LFA27.0.16$shorts=NA
LFA27.0.16$shorts=LFA27.0.16$size0+LFA27.0.16$size2+LFA27.0.16$size3+LFA27.0.16$size4+LFA27.0.16$size5+LFA27.0.16$size6+
LFA27.0.16$size7+LFA27.0.16$size8.1+LFA27.0.16$size9.1 + LFA27.0.16$size10.1
LFA27.0.16$legals=NA
LFA27.0.16$legals=LFA27.0.16$size8.2+LFA27.0.16$size9.2+LFA27.0.16$size10.2+LFA27.0.16$size11+LFA27.0.16$size12+LFA27.0.16$size13+
LFA27.0.16$size14+LFA27.0.16$size15+LFA27.0.16$size16
summary(LFA27.0.16)
#Max shorts = 78; Max legals = 29
write.table(LFA27.0.16, file=paste("rec.LFA27.9917.SD1to5.nober.",Sys.Date(),".txt"), row.names=TRUE, col.names=TRUE, sep=" ")
#--------------------------------LFA28---------------------------------------
##LFA 28 - NO PARTICIPATION SINCE 2013
LFA28.9913=which(fsrs$LFA==28)
length(LFA28.9913) #7198 JAN_2018
LFA28.9913=fsrs[LFA28.9913,]
unique(LFA28.9913$HAUL_YEAR)
summary(LFA28.9913)
##EMPTY TRAPS
e=which(LFA28.9913$LOBSTER_NO==0)
length(e) #558 Jan 2018
##VALIDATE SOAK DAYS:
table(LFA28.9913$SOAK_DAYS, LFA28.9913$HAUL_YEAR)
# 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013
#1 64 208 22 209 125 73 0 30 499 65 433 379 47
#2 298 503 459 289 413 492 127 202 299 153 70 136 279
#3 115 108 96 93 96 181 117 96 0 123 71 0 5
#4 60 0 46 13 15 0 0 26 0 0 20 0 0
#5 5 0 0 0 0 0 18 0 0 20 0 0 0
>
write.table(LFA28.9913, file=paste("rec.LFA28 9913.Noremovals.from.datacheck.9913",Sys.Date(),".txt"), row.names=FALSE, col.names=TRUE, sep=" ")
#CPUE PREP FILE:
##DAILY AGGREGATE FOR CPUE ANALYSIS:
#SOAK DAY CONSTRAINT:
#FOR THIS LFA SOAK DAYS ARE ALL BETWEEN 1 AND 5
##CALCULATE TRAP # PER DAY
LFA28.9913.traps = compute.unique.lengths(x=LFA28.9913, var="TRAP_NO", index=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE"))
LFA28.9913.traps = na.omit (LFA28.9913.traps)
LFA28.9913.traps = rename.df(LFA28.9913.traps,"Freq", "TOT_TRAPS")
summary(LFA28.9913.traps)
str(LFA28.9913.traps) #573 MAY_2014
#SHOWS NUMBER OF RECORDS WITH TRAP NUMBER DISTRIBUTION PER VESSEL
table(LFA28.9913.traps$TOT_TRAPS,LFA28.9913.traps$VESSEL_CD)
##SIZE CLASS ADJUSTMENT TO SPLIT THE SHORTS AND LEGAL SIZES IN CLASS 10
table(LFA28.9917$SIZE_CD, LFA28.9916$SHORT)
b1= which (LFA28.9913$SIZE_CD==10 & LFA28.9913$SHORT==1)
LFA28.9913[b1,"SIZE_CD"]=10.1
summary(LFA28.9913[b1,])
b2= which (LFA28.9913$SIZE_CD==10 & LFA28.9913$SHORT==0)
LFA28.9913[b2,"SIZE_CD"]=10.2
summary(LFA28.9913[b2,])
table(LFA28.9916$SIZE_CD, LFA28.9916$SHORT)
##REMOVE RECORDS FOR BERRIED BY INCLUDING IN SEX COLUMN - FOR CPUE ANALYSIS
b= which (LFA28.9913$SEX==3)
length (b) #2319 MAY_2014
LFA28.9913.sd.noberried=LFA28.9913[-b,]
str(LFA28.9913.sd.noberried)
##CALCULATE TOTAL COUNT PER SIZE CLASS
LFA28.9913.sd.noberried$VESSEL_CD <- as.factor(LFA28.9913.sd.noberried$VESSEL_CD)
LFA28.9913.sd.noberried$SIZE_CD <- as.factor(LFA28.9913.sd.noberried$SIZE_CD)
LFA28.9913.counts.at.size =aggregate(LFA28.9913.sd.noberried[,1], by=as.list(LFA28.9913.sd.noberried[c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "SIZE_CD")]), length, simplify = TRUE)
LFA28.9913.counts.at.size = na.omit (LFA28.9913.counts.at.size)
library(gdata)
LFA28.9913.counts.at.size <- rename.vars(LFA28.9913.counts.at.size, from="x", to="Freq")
summary(LFA28.9913.counts.at.size)
str(LFA28.9913.counts.at.size) #MAY_2014 2403 RECORDS
unique(LFA28.9913.counts.at.size$SIZE_CD) #SIZE 0-16; NO NA VALUES
##SIZE CLASS FREQUENCY TABLE
LFA28.cpue.size = merge(LFA28.9913.traps,LFA28.9913.counts.at.size, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE"),all.x=T,all.y=F, sort=F)
LFA28.0=which(LFA28.cpue.size$SIZE_CD=='0')
LFA28.size0=LFA28.cpue.size[LFA28.0,]
LFA28.size0 = rename.df(LFA28.size0,"Freq", "size0")
LFA28.size0$SIZE_CD=NULL
LFA28.3=which(LFA28.cpue.size$SIZE_CD=='3')
LFA28.size3=LFA28.cpue.size[LFA28.3,]
LFA28.size3 = rename.df(LFA28.size3, "Freq", "size3")
LFA28.size3$SIZE_CD=NULL
LFA28.0.3 = merge(LFA28.size0,LFA28.size3, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA28.4=which(LFA28.cpue.size$SIZE_CD=='4')
LFA28.size4=LFA28.cpue.size[LFA28.4,]
LFA28.size4 = rename.df(LFA28.size4, "Freq", "size4")
LFA28.size4$SIZE_CD=NULL
LFA28.0.4 = merge(LFA28.0.3,LFA28.size4, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA28.5=which(LFA28.cpue.size$SIZE_CD=='5')
LFA28.size5=LFA28.cpue.size[LFA28.5,]
LFA28.size5 = rename.df(LFA28.size5, "Freq", "size5")
LFA28.size5$SIZE_CD=NULL
LFA28.0.5 = merge(LFA28.0.4,LFA28.size5, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA28.6=which(LFA28.cpue.size$SIZE_CD=='6')
LFA28.size6=LFA28.cpue.size[LFA28.6,]
LFA28.size6 = rename.df(LFA28.size6, "Freq", "size6")
LFA28.size6$SIZE_CD=NULL
LFA28.0.6 = merge(LFA28.0.5,LFA28.size6, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA28.7=which(LFA28.cpue.size$SIZE_CD=='7')
LFA28.size7=LFA28.cpue.size[LFA28.7,]
LFA28.size7 = rename.df(LFA28.size7, "Freq", "size7")
LFA28.size7$SIZE_CD=NULL
LFA28.0.7 = merge(LFA28.0.6,LFA28.size7, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA28.8=which(LFA28.cpue.size$SIZE_CD=='8')
LFA28.size8=LFA28.cpue.size[LFA28.8,]
LFA28.size8 = rename.df(LFA28.size8, "Freq", "size8")
LFA28.size8$SIZE_CD=NULL
LFA28.0.8 = merge(LFA28.0.7,LFA28.size8, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA28.9=which(LFA28.cpue.size$SIZE_CD=='9')
LFA28.size9=LFA28.cpue.size[LFA28.9,]
LFA28.size9 = rename.df(LFA28.size9, "Freq", "size9")
LFA28.size9$SIZE_CD=NULL
LFA28.0.9 = merge(LFA28.0.8,LFA28.size9, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA28.10.1=which(LFA28.cpue.size$SIZE_CD=='10.1')
LFA28.size10.1=LFA28.cpue.size[LFA28.10.1,]
LFA28.size10.1 = rename.df(LFA28.size10.1, "Freq", "size10.1")
LFA28.size10.1$SIZE_CD=NULL
LFA28.0.10.1 = merge(LFA28.0.9,LFA28.size10.1, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA28.10.2=which(LFA28.cpue.size$SIZE_CD=='10.2')
LFA28.size10.2=LFA28.cpue.size[LFA28.10.2,]
LFA28.size10.2 = rename.df(LFA28.size10.2, "Freq", "size10.2")
LFA28.size10.2$SIZE_CD=NULL
LFA28.0.10.2 = merge(LFA28.0.10.1,LFA28.size10.2, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA28.11=which(LFA28.cpue.size$SIZE_CD=='11')
LFA28.size11=LFA28.cpue.size[LFA28.11,]
LFA28.size11 = rename.df(LFA28.size11, "Freq", "size11")
LFA28.size11$SIZE_CD=NULL
LFA28.0.11 = merge(LFA28.0.10.2,LFA28.size11, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA28.12=which(LFA28.cpue.size$SIZE_CD=='12')
LFA28.size12=LFA28.cpue.size[LFA28.12,]
LFA28.size12 = rename.df(LFA28.size12, "Freq", "size12")
LFA28.size12$SIZE_CD=NULL
LFA28.0.12 = merge(LFA28.0.11,LFA28.size12, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA28.13=which(LFA28.cpue.size$SIZE_CD=='13')
LFA28.size13=LFA28.cpue.size[LFA28.13,]
LFA28.size13 = rename.df(LFA28.size13, "Freq", "size13")
LFA28.size13$SIZE_CD=NULL
LFA28.0.13 = merge(LFA28.0.12,LFA28.size13, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA28.14=which(LFA28.cpue.size$SIZE_CD=='14')
LFA28.size14=LFA28.cpue.size[LFA28.14,]
LFA28.size14 = rename.df(LFA28.size14, "Freq", "size14")
LFA28.size14$SIZE_CD=NULL
LFA28.0.14 = merge(LFA28.0.13,LFA28.size14, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA28.15=which(LFA28.cpue.size$SIZE_CD=='15')
LFA28.size15=LFA28.cpue.size[LFA28.15,]
LFA28.size15 = rename.df(LFA28.size15, "Freq", "size15")
LFA28.size15$SIZE_CD=NULL
LFA28.0.15 = merge(LFA28.0.14,LFA28.size15, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA28.16=which(LFA28.cpue.size$SIZE_CD=='16')
LFA28.size16=LFA28.cpue.size[LFA28.16,]
LFA28.size16 = rename.df(LFA28.size16, "Freq", "size16")
LFA28.size16$SIZE_CD=NULL
LFA28.0.16 = merge(LFA28.0.15,LFA28.size16, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA28.0.16[is.na(LFA28.0.16)]=0
summary(LFA28.0.16)
##SIZE CLASS SPECS FOR UNDERSIZED LOBSTERS FROM 1999-2013
LFA28.0.16$shorts=NA
LFA28.0.16$shorts=LFA28.0.16$size0+LFA28.0.16$size3+LFA28.0.16$size4+LFA28.0.16$size5+LFA28.0.16$size6+
LFA28.0.16$size7+LFA28.0.16$size8+LFA28.0.16$size9+LFA28.0.16$size10.1
##SIZE CLASS SPECS FOR LEGAL LOBSTERS FROM 2004-2011
LFA28.0.16$legals=NA
LFA28.0.16$legals=LFA28.0.16$size10.2+LFA28.0.16$size11+LFA28.0.16$size12+LFA28.0.16$size13+
LFA28.0.16$size14+LFA28.0.16$size15+LFA28.0.16$size16
summary(LFA28.0.16)
#Max shorts = 28; Max legals = 14
write.table(LFA28.0.16, file=paste("rec.LFA28.9913.SD1to5.nober.",Sys.Date(),".txt"), row.names=TRUE, col.names=TRUE, sep=" ")
#--------------------------------LFA29---------------------------------------
LFA29.9917=which(fsrs$LFA==29)
length(LFA29.9917) # 110608 RECORDS FOR 2017
LFA29.9917=fsrs[LFA29.9917,]
unique(LFA29.9917$HAUL_YEAR)
summary(LFA29.9917)
##EMPTY TRAPS
e=which(LFA29.9917$LOBSTER_NO==0)
length(e) #2178 RECORDS FOR 2017
##VALIDATE SOAK DAYS:
table(LFA29.9917$SOAK_DAYS,LFA29.9917$HAUL_YEAR)
# 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017
#1 88 414 483 461 902 1770 2911 7665 7851 8892 8232 6566 5892 6233 5838 6041 8342 8121 8956
#2 111 246 371 388 378 784 475 721 933 589 547 894 851 531 927 889 1146 924 1090
#3 12 50 20 50 158 81 91 8 76 148 195 125 60 0 94 105 44 36 260
#4 0 16 5 0 12 0 13 17 40 98 30 0 0 0 0 98 21 0 17
#5 0 0 0 0 0 0 0 0 76 15 0 0 0 0 0 0 0 0 60
#6 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#7 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
write.table(LFA29.9917, file=paste("rec.LFA29 9917.Noremovals.from.datacheck.9917",Sys.Date(),".txt"), row.names=FALSE, col.names=TRUE, sep=" ")
#CPUE PREP FILE:
#SOAK DAY CONSTRAINT:
sd=which(LFA29.9917$SOAK_DAYS > 5)
length(sd) #24 RECORDS
LFA29.9917.sd=LFA29.9917[-sd,]
##CALCULATE TRAP # PER DAY
#LFA29.9917.traps = compute.unique.lengths( x=LFA29.9917.sd, var="TRAP_NO", index=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE") )
#LFA29.9917.traps = na.omit (LFA29.9917.traps)
#LFA29.9917.traps = rename.df(LFA29.9917.traps,"Freq", "TOT_TRAPS")
LFA29.9917.traps<-aggregate(TRAP_NO~HAUL_YEAR+VESSEL_CD+HAUL_DATE, data=LFA29.9917.sd, FUN=function(x) length(unique(x)))
str(LFA29.9917.traps) # 5436 Records for 2017
summary(LFA29.9917.traps)
#SHOWS NUMBER OF RECORDS WITH TRAP NUMBER DISTRIBUTION PER VESSEL
table(LFA29.9917.traps$TOT_TRAPS,LFA29.9917.traps$VESSEL_CD)
##SIZE ADJUSTMENTS for MLS to 84 mm IN 1999-2013
table(LFA29.9916.sd$SIZE_CD,LFA29.9916.sd$SHORT)
c1= which (LFA29.9916.sd$SIZE_CD==10 & LFA29.9916.sd$SHORT==1)
LFA29.9916.sd[c1,"SIZE_CD"]=10.1
c2= which (LFA29.9916.sd$SIZE_CD==10 & LFA29.9916.sd$SHORT==0)
LFA29.9916.sd[c2,"SIZE_CD"]=10.2
summary(LFA29.9916.sd[c1,])
summary(LFA29.9916.sd[c2,])
##REMOVE RECORDS FOR BERRIED BY INCLUDING IN SEX COLUMN - FOR CPUE ANALYSIS
b= which (LFA29.9916.sd$SEX==3)
length (b) #12,563 RECORDS
LFA29.9916.sd.noberried=LFA29.9916.sd[-b,]
str(LFA29.9916.sd.noberried)
##FILE EDITS BEFORE FURTHER COMPUTING
LFA29.9913.sd.noberried$VESSEL_CD <- as.factor(LFA29.9913.sd.noberried$VESSEL_CD)
LFA29.9913.sd.noberried$SIZE_CD <- as.factor(LFA29.9913.sd.noberried$SIZE_CD)
##CALCULATE TOTAL COUNT PER SIZE CLASS
LFA29.9913.counts.at.size =aggregate(LFA29.9913.sd.noberried[,1], by=as.list(LFA29.9913.sd.noberried[c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "SIZE_CD")]), length, simplify = TRUE)
LFA29.9913.counts.at.size = na.omit (LFA29.9913.counts.at.size)
library(gdata)
LFA29.9913.counts.at.size <- rename.vars(LFA29.9913.counts.at.size, from="x", to="Freq")
summary(LFA29.9913.counts.at.size)
str(LFA29.9913.counts.at.size) #21,435 RECORDS MAY_2014
unique(LFA29.9913.counts.at.size$SIZE_CD) #SIZE 0-16; NO NA VALUES
##SIZE CLASS FREQUENCY TABLE
LFA29.cpue.size = merge(LFA29.9913.traps,LFA29.9913.counts.at.size, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE"),all.x=T,all.y=F, sort=F)
LFA29.0=which(LFA29.cpue.size$SIZE_CD=='0')
LFA29.size0=LFA29.cpue.size[LFA29.0,]
LFA29.size0 = rename.df(LFA29.size0,"Freq", "size0")
LFA29.size0$SIZE_CD=NULL
LFA29.2=which(LFA29.cpue.size$SIZE_CD=='2')
LFA29.size2=LFA29.cpue.size[LFA29.2,]
LFA29.size2 = rename.df(LFA29.size2, "Freq", "size2")
LFA29.size2$SIZE_CD=NULL
LFA29.0.2 = merge(LFA29.size0,LFA29.size2, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA29.3=which(LFA29.cpue.size$SIZE_CD=='3')
LFA29.size3=LFA29.cpue.size[LFA29.3,]
LFA29.size3 = rename.df(LFA29.size3, "Freq", "size3")
LFA29.size3$SIZE_CD=NULL
LFA29.0.3 = merge(LFA29.0.2,LFA29.size3, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA29.4=which(LFA29.cpue.size$SIZE_CD=='4')
LFA29.size4=LFA29.cpue.size[LFA29.4,]
LFA29.size4 = rename.df(LFA29.size4, "Freq", "size4")
LFA29.size4$SIZE_CD=NULL
LFA29.0.4 = merge(LFA29.0.3,LFA29.size4, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA29.5=which(LFA29.cpue.size$SIZE_CD=='5')
LFA29.size5=LFA29.cpue.size[LFA29.5,]
LFA29.size5 = rename.df(LFA29.size5, "Freq", "size5")
LFA29.size5$SIZE_CD=NULL
LFA29.0.5 = merge(LFA29.0.4,LFA29.size5, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA29.6=which(LFA29.cpue.size$SIZE_CD=='6')
LFA29.size6=LFA29.cpue.size[LFA29.6,]
LFA29.size6 = rename.df(LFA29.size6, "Freq", "size6")
LFA29.size6$SIZE_CD=NULL
LFA29.0.6 = merge(LFA29.0.5,LFA29.size6, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA29.7=which(LFA29.cpue.size$SIZE_CD=='7')
LFA29.size7=LFA29.cpue.size[LFA29.7,]
LFA29.size7 = rename.df(LFA29.size7, "Freq", "size7")
LFA29.size7$SIZE_CD=NULL
LFA29.0.7 = merge(LFA29.0.6,LFA29.size7, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA29.8=which(LFA29.cpue.size$SIZE_CD=='8')
LFA29.size8=LFA29.cpue.size[LFA29.8,]
LFA29.size8 = rename.df(LFA29.size8, "Freq", "size8")
LFA29.size8$SIZE_CD=NULL
LFA29.0.8 = merge(LFA29.0.7,LFA29.size8, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA29.9=which(LFA29.cpue.size$SIZE_CD=='9')
LFA29.size9=LFA29.cpue.size[LFA29.9,]
LFA29.size9 = rename.df(LFA29.size9, "Freq", "size9")
LFA29.size9$SIZE_CD=NULL
LFA29.0.9 = merge(LFA29.0.8,LFA29.size9, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA29.10.1=which(LFA29.cpue.size$SIZE_CD=='10.1')
LFA29.size10.1=LFA29.cpue.size[LFA29.10.1,]
LFA29.size10.1 = rename.df(LFA29.size10.1, "Freq", "size10.1")
LFA29.size10.1$SIZE_CD=NULL
LFA29.0.10.1 = merge(LFA29.0.9,LFA29.size10.1, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA29.10.2=which(LFA29.cpue.size$SIZE_CD=='10.2')
LFA29.size10.2=LFA29.cpue.size[LFA29.10.2,]
LFA29.size10.2 = rename.df(LFA29.size10.2, "Freq", "size10.2")
LFA29.size10.2$SIZE_CD=NULL
LFA29.0.10.2 = merge(LFA29.0.10.1,LFA29.size10.2, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA29.11=which(LFA29.cpue.size$SIZE_CD=='11')
LFA29.size11=LFA29.cpue.size[LFA29.11,]
LFA29.size11 = rename.df(LFA29.size11, "Freq", "size11")
LFA29.size11$SIZE_CD=NULL
LFA29.0.11 = merge(LFA29.0.10.2,LFA29.size11, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA29.12=which(LFA29.cpue.size$SIZE_CD=='12')
LFA29.size12=LFA29.cpue.size[LFA29.12,]
LFA29.size12 = rename.df(LFA29.size12, "Freq", "size12")
LFA29.size12$SIZE_CD=NULL
LFA29.0.12 = merge(LFA29.0.11,LFA29.size12, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA29.13=which(LFA29.cpue.size$SIZE_CD=='13')
LFA29.size13=LFA29.cpue.size[LFA29.13,]
LFA29.size13 = rename.df(LFA29.size13, "Freq", "size13")
LFA29.size13$SIZE_CD=NULL
LFA29.0.13 = merge(LFA29.0.12,LFA29.size13, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA29.14=which(LFA29.cpue.size$SIZE_CD=='14')
LFA29.size14=LFA29.cpue.size[LFA29.14,]
LFA29.size14 = rename.df(LFA29.size14, "Freq", "size14")
LFA29.size14$SIZE_CD=NULL
LFA29.0.14 = merge(LFA29.0.13,LFA29.size14, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA29.15=which(LFA29.cpue.size$SIZE_CD=='15')
LFA29.size15=LFA29.cpue.size[LFA29.15,]
LFA29.size15 = rename.df(LFA29.size15, "Freq", "size15")
LFA29.size15$SIZE_CD=NULL
LFA29.0.15 = merge(LFA29.0.14,LFA29.size15, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA29.16=which(LFA29.cpue.size$SIZE_CD=='16')
LFA29.size16=LFA29.cpue.size[LFA29.16,]
LFA29.size16 = rename.df(LFA29.size16, "Freq", "size16")
LFA29.size16$SIZE_CD=NULL
LFA29.0.16 = merge(LFA29.0.15,LFA29.size16, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA29.0.16[is.na(LFA29.0.16)]=0
summary(LFA29.0.16)
##SIZE CLASS SPECS FOR UNDERSIZED LOBSTERS FROM 1999-2013
LFA29.0.16$shorts=NA
LFA29.0.16$shorts=LFA29.0.16$size0+LFA29.0.16$size2+LFA29.0.16$size3+LFA29.0.16$size4+LFA29.0.16$size5+LFA29.0.16$size6+
LFA29.0.16$size7+LFA29.0.16$size8+LFA29.0.16$size9+LFA29.0.16$size10.1
##SIZE CLASS SPECS FOR LEGAL LOBSTERS FROM 1999-2013
LFA29.0.16$legals=NA
LFA29.0.16$legals=LFA29.0.16$size10.2+LFA29.0.16$size11+LFA29.0.16$size12+LFA29.0.16$size13+
LFA29.0.16$size14+LFA29.0.16$size15+LFA29.0.16$size16
summary(LFA29.0.16)
#Max shorts = 58; Max legals = 34
write.table(LFA29.0.16, file=paste("rec.LFA29.9913.SD1to5.nober.",Sys.Date(),".txt"), row.names=TRUE, col.names=TRUE, sep=" ")
#----------------------------------LFA30------------------------------------
#LFA 30
LFA30.9916=which(fsrs$LFA==30)
length(LFA30.9916) #70,574 JAN_2016
LFA30.9916=fsrs[LFA30.9916,]
unique(LFA30.9916$HAUL_YEAR)
summary(LFA30.9916)
##EMPTY TRAPS
e=which(LFA30.9916$LOBSTER_NO==0)
length(e) #1,310 RECORDS
##VALIDATE SOAK DAYS:
> table(LFA30.9916$SOAK_DAYS, LFA30.9916$HAUL_YEAR)
2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015
1 352 374 364 354 1030 1320 4538 5080 4444 5191 4839 4423 5029 4811 4869 5425
2 88 116 113 151 335 623 1345 1469 1426 1225 1309 1585 1161 1118 1258 1627
3 0 43 40 38 22 165 278 43 234 280 322 191 196 134 188 319
4 9 19 13 16 18 17 56 0 73 12 99 71 9 58 60 0
5 0 0 0 0 0 0 0 0 81 0 0 0 0 0 46 0
6 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0
7 0 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0
>
write.table(LFA30.9916, file=paste("rec.LFA30 9916.Noremovals.from.datacheck.9916",Sys.Date(),".txt"), row.names=FALSE, col.names=TRUE, sep=" ")
#CPUE PREP FILE:
##DAILY AGGREGATE FOR CPUE ANALYSIS
#SOAK DAY CONSTRAINT:
sd=which(LFA30.9916$SOAK_DAYS > 5)
length(sd) #32 RECORDS
LFA30.9916.sd=LFA30.9916[-sd,]
##CALCULATE TRAP # PER DAY
LFA30.9916.traps = ddply(LFA30.9916.sd,c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE"),summarize,TOT_TRAPS=length(unique(TRAP_NO)))
summary(LFA30.9916.traps)
str(LFA30.9916.traps) #3,721 RECORDS
#SHOWS NUMBER OF RECORDS WITH TRAP NUMBER DISTRIBUTION PER VESSEL
table(LFA30.9916.traps$TOT_TRAPS,LFA30.9916.traps$VESSEL_CD)
table(LFA30.9916.traps$HAUL_YEAR,LFA30.9916.traps$VESSEL_CD)
##SIZE CLASS ADJUSTMENT TO SPLIT THE SHORTS AND LEGAL SIZES IN CLASS 10
table(LFA30.9916.sd$SIZE_CD, LFA30.9916.sd$SHORT)
d1= which (LFA30.9916.sd$SIZE_CD==10 & LFA30.9916.sd$SHORT==1)
LFA30.9916.sd[d1,"SIZE_CD"]=10.1
summary(LFA30.9916.sd[d1,])
d2= which (LFA30.9916.sd$SIZE_CD==10 & LFA30.9916.sd$SHORT==0)
LFA30.9916.sd[d2,"SIZE_CD"]=10.2
summary(LFA30.9916.sd[d2,])
##REMOVE RECORDS FOR BERRIED BY INCLUDING IN SEX COLUMN - FOR CPUE ANALYSIS
b= which (LFA30.9916.sd$SEX==3)
length (b) #10,446 RECORDS
LFA30.9916.sd.noberried=LFA30.9916.sd[-b,]
str(LFA30.9916.sd.noberried)
##CALCULATE TOTAL COUNT PER SIZE CLASS
LFA30.9916.counts.at.size =aggregate(LFA30.9916.sd.noberried[,1], by=as.list(LFA30.9916.sd.noberried[c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "SIZE_CD")]), length, simplify = TRUE)
LFA30.9916.counts.at.size = na.omit (LFA30.9916.counts.at.size)
library(gdata)
LFA30.9916.counts.at.size <- rename.vars(LFA30.9916.counts.at.size, from="x", to="Freq")
summary(LFA30.9916.counts.at.size)
str(LFA30.9916.counts.at.size) #17,686 RECORDS
unique(LFA30.9916.counts.at.size$SIZE_CD) #SIZE 0-16; NO NA VALUES
##SIZE CLASS FREQUENCY TABLE
LFA30.cpue.size = merge(LFA30.9916.traps,LFA30.9916.counts.at.size, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE"),all.x=T,all.y=F, sort=F)
LFA30.0=which(LFA30.cpue.size$SIZE_CD=='0')
LFA30.size0=LFA30.cpue.size[LFA30.0,]
LFA30.size0 = rename.df(LFA30.size0,"Freq", "size0")
LFA30.size0$SIZE_CD=NULL
LFA30.2=which(LFA30.cpue.size$SIZE_CD=='2')
LFA30.size2=LFA30.cpue.size[LFA30.2,]
LFA30.size2 = rename.df(LFA30.size2,"Freq", "size2")
LFA30.size2$SIZE_CD=NULL
LFA30.0.2 = merge(LFA30.size0,LFA30.size2, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA30.3=which(LFA30.cpue.size$SIZE_CD=='3')
LFA30.size3=LFA30.cpue.size[LFA30.3,]
LFA30.size3 = rename.df(LFA30.size3, "Freq", "size3")
LFA30.size3$SIZE_CD=NULL
LFA30.0.3 = merge(LFA30.0.2,LFA30.size3, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA30.4=which(LFA30.cpue.size$SIZE_CD=='4')
LFA30.size4=LFA30.cpue.size[LFA30.4,]
LFA30.size4 = rename.df(LFA30.size4, "Freq", "size4")
LFA30.size4$SIZE_CD=NULL
LFA30.0.4 = merge(LFA30.0.3,LFA30.size4, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA30.5=which(LFA30.cpue.size$SIZE_CD=='5')
LFA30.size5=LFA30.cpue.size[LFA30.5,]
LFA30.size5 = rename.df(LFA30.size5, "Freq", "size5")
LFA30.size5$SIZE_CD=NULL
LFA30.0.5 = merge(LFA30.0.4,LFA30.size5, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA30.6=which(LFA30.cpue.size$SIZE_CD=='6')
LFA30.size6=LFA30.cpue.size[LFA30.6,]
LFA30.size6 = rename.df(LFA30.size6, "Freq", "size6")
LFA30.size6$SIZE_CD=NULL
LFA30.0.6 = merge(LFA30.0.5,LFA30.size6, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA30.7=which(LFA30.cpue.size$SIZE_CD=='7')
LFA30.size7=LFA30.cpue.size[LFA30.7,]
LFA30.size7 = rename.df(LFA30.size7, "Freq", "size7")
LFA30.size7$SIZE_CD=NULL
LFA30.0.7 = merge(LFA30.0.6,LFA30.size7, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA30.8=which(LFA30.cpue.size$SIZE_CD=='8')
LFA30.size8=LFA30.cpue.size[LFA30.8,]
LFA30.size8 = rename.df(LFA30.size8, "Freq", "size8")
LFA30.size8$SIZE_CD=NULL
LFA30.0.8 = merge(LFA30.0.7,LFA30.size8, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA30.9=which(LFA30.cpue.size$SIZE_CD=='9')
LFA30.size9=LFA30.cpue.size[LFA30.9,]
LFA30.size9 = rename.df(LFA30.size9, "Freq", "size9")
LFA30.size9$SIZE_CD=NULL
LFA30.0.9 = merge(LFA30.0.8,LFA30.size9, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA30.10.1=which(LFA30.cpue.size$SIZE_CD=='10.1')
LFA30.size10.1=LFA30.cpue.size[LFA30.10.1,]
LFA30.size10.1 = rename.df(LFA30.size10.1, "Freq", "size10.1")
LFA30.size10.1$SIZE_CD=NULL
LFA30.0.10.1 = merge(LFA30.0.9,LFA30.size10.1, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA30.10.2=which(LFA30.cpue.size$SIZE_CD=='10.2')
LFA30.size10.2=LFA30.cpue.size[LFA30.10.2,]
LFA30.size10.2 = rename.df(LFA30.size10.2, "Freq", "size10.2")
LFA30.size10.2$SIZE_CD=NULL
LFA30.0.10.2 = merge(LFA30.0.10.1,LFA30.size10.2, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA30.11=which(LFA30.cpue.size$SIZE_CD=='11')
LFA30.size11=LFA30.cpue.size[LFA30.11,]
LFA30.size11 = rename.df(LFA30.size11, "Freq", "size11")
LFA30.size11$SIZE_CD=NULL
LFA30.0.11 = merge(LFA30.0.10.2,LFA30.size11, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA30.12=which(LFA30.cpue.size$SIZE_CD=='12')
LFA30.size12=LFA30.cpue.size[LFA30.12,]
LFA30.size12 = rename.df(LFA30.size12, "Freq", "size12")
LFA30.size12$SIZE_CD=NULL
LFA30.0.12 = merge(LFA30.0.11,LFA30.size12, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA30.13=which(LFA30.cpue.size$SIZE_CD=='13')
LFA30.size13=LFA30.cpue.size[LFA30.13,]
LFA30.size13 = rename.df(LFA30.size13, "Freq", "size13")
LFA30.size13$SIZE_CD=NULL
LFA30.0.13 = merge(LFA30.0.12,LFA30.size13, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA30.14=which(LFA30.cpue.size$SIZE_CD=='14')
LFA30.size14=LFA30.cpue.size[LFA30.14,]
LFA30.size14 = rename.df(LFA30.size14, "Freq", "size14")
LFA30.size14$SIZE_CD=NULL
LFA30.0.14 = merge(LFA30.0.13,LFA30.size14, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA30.15=which(LFA30.cpue.size$SIZE_CD=='15')
LFA30.size15=LFA30.cpue.size[LFA30.15,]
LFA30.size15 = rename.df(LFA30.size15, "Freq", "size15")
LFA30.size15$SIZE_CD=NULL
LFA30.0.15 = merge(LFA30.0.14,LFA30.size15, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA30.16=which(LFA30.cpue.size$SIZE_CD=='16')
LFA30.size16=LFA30.cpue.size[LFA30.16,]
LFA30.size16 = rename.df(LFA30.size16, "Freq", "size16")
LFA30.size16$SIZE_CD=NULL
LFA30.0.16 = merge(LFA30.0.15,LFA30.size16, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA30.0.16[is.na(LFA30.0.16)]=0
summary(LFA30.0.16)
##SIZE CLASS SPECS FOR UNDERSIZED LOBSTERS
LFA30.0.16$shorts=NA
LFA30.0.16$shorts=LFA30.0.16$size0+LFA30.0.16$size2+LFA30.0.16$size3+LFA30.0.16$size4+LFA30.0.16$size5+LFA30.0.16$size6+
LFA30.0.16$size7+LFA30.0.16$size8+LFA30.0.16$size9+LFA30.0.16$size10.1
##SIZE CLASS SPECS FOR LEGAL LOBSTERS
LFA30.0.16$legals=NA
LFA30.0.16$legals=LFA30.0.16$size10.2+LFA30.0.16$size11+LFA30.0.16$size12+LFA30.0.16$size13+
LFA30.0.16$size14+LFA30.0.16$size15+LFA30.0.16$size16
summary(LFA30.0.16)
#Max shorts = 44; Max legals = 62
write.table(LFA30.0.16, file=paste("rec.LFA30.9916.SD1to5.nober.",Sys.Date(),".txt"), row.names=TRUE, col.names=TRUE, sep=" ")
#----------------------------------LFA31A--------------------------------------
##LFA 31A
LFA31A.9916=which(fsrs$LFA==31.1)
length(LFA31A.9916) #34,688 RECORDS JAN_2016
LFA31A.9916=fsrs[LFA31A.9916,]
unique(LFA31A.9916$HAUL_YEAR)
summary(LFA31A.9916)
##EMPTY TRAPS
e=which(LFA31A.9916$LOBSTER_NO==0)
length(e) #1,263 RECORDS
##VALIDATE SOAK DAYS:
> table(LFA31A.9916$SOAK_DAYS, LFA31A.9916$HAUL_YEAR)
1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015
1 207 254 287 452 718 560 744 1692 1052 2318 3231 2492 2377 2364 2055 2681 2525
2 137 185 115 184 359 539 720 890 741 331 444 430 369 255 452 543 849
3 30 8 35 39 115 82 35 36 0 0 104 59 79 34 45 45 12
4 2 5 4 2 37 24 28 10 45 13 0 0 37 15 52 0 0
5 0 2 6 0 0 0 0 0 0 2 0 0 9 2 0 0 0
6 0 0 9 0 0 0 17 0 0 13 0 0 0 0 0 0 0
7 0 3 4 0 8 0 10 0 0 0 0 0 0 0 0 0 0
8 0 0 0 0 0 14 0 0 0 0 0 0 0 0 0 0 0
9 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0
>
write.table(LFA31A.9916, file=paste("rec.LFA31A 9916.Noremovals.from.datacheck.9916",Sys.Date(),".txt"), row.names=FALSE, col.names=TRUE, sep=" ")
#CPUE PREP FILE
##DAILY AGGREGATE FOR CPUE ANALYSIS
#SOAK DAY CONSTRAINT:
sd=which(LFA31A.9916$SOAK_DAYS > 5)
length(sd) #83 RECORDS
LFA31A.9916.sd=LFA31A.9916[-sd,]
##CALCULATE TRAP # PER DAY
LFA31A.9916.traps = ddply(LFA31A.9916.sd,c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE"),summarize,TOT_TRAPS=length(unique(TRAP_NO)))
summary(LFA31A.9916.traps)
str(LFA31A.9916.traps) #5,165 RECORDS
#SHOWS NUMBER OF RECORDS WITH TRAP NUMBER DISTRIBUTION PER VESSEL
table(LFA31A.9916.traps$TOT_TRAPS,LFA31A.9916.traps$VESSEL_CD)
table(LFA31A.9916.traps$HAUL_YEAR,LFA31A.9916.traps$VESSEL_CD)
##SIZE CLASS ADJUSTMENT TO SPLIT THE SHORTS AND LEGAL SIZES IN CLASS 10
table(LFA31A.9916.sd$SIZE_CD,LFA31A.9916.sd$SHORT)
e1= which (LFA31A.9916.sd$SIZE_CD==10 & LFA31A.9916.sd$SHORT==1)
LFA31A.9916.sd[e1,"SIZE_CD"]=10.1
summary(LFA31A.9916.sd[e1,])
e2= which (LFA31A.9916.sd$SIZE==10 & LFA31A.9916.sd$SHORT==0)
LFA31A.9916.sd[e2,"SIZE_CD"]=10.2
summary(LFA31A.9916.sd[e2,])
##REMOVE RECORDS FOR BERRIED BY INCLUDING IN SEX COLUMN - FOR CPUE ANALYSIS
b= which (LFA31A.9916.sd$SEX==3)
length (b) #4,305 RECORDS
LFA31A.9916.sd.noberried=LFA31A.9916.sd[-b,]
str(LFA31A.9916.sd.noberried)
##CALCULATE TOTAL COUNT PER SIZE CLASS
LFA31A.9916.sd.noberried$VESSEL_CD <- as.factor(LFA31A.9916.sd.noberried$VESSEL_CD)
LFA31A.9916.sd.noberried$SIZE_CD <- as.factor(LFA31A.9916.sd.noberried$SIZE_CD)
LFA31A.9916.counts.at.size =aggregate(LFA31A.9916.sd.noberried[,1], by=as.list(LFA31A.9916.sd.noberried[c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "SIZE_CD")]), length, simplify = TRUE)
LFA31A.9916.counts.at.size = na.omit (LFA31A.9916.counts.at.size)
library(gdata)
LFA31A.9916.counts.at.size <- rename.vars(LFA31A.9916.counts.at.size, from="x", to="Freq")
summary(LFA31A.9916.counts.at.size)
str(LFA31A.9916.counts.at.size) #15,546 RECORDS
unique(LFA31A.9916.counts.at.size$SIZE_CD) #SIZE 0-16; NO NA VALUES
##SIZE CLASS FREQUENCY TABLE
LFA31A.cpue.size = merge(LFA31A.9916.traps,LFA31A.9916.counts.at.size, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE"),all.x=T,all.y=F, sort=F)
LFA31A.0=which(LFA31A.cpue.size$SIZE_CD=='0')
LFA31A.size0=LFA31A.cpue.size[LFA31A.0,]
LFA31A.size0 = rename.df(LFA31A.size0,"Freq", "size0")
LFA31A.size0$SIZE_CD=NULL
LFA31A.2=which(LFA31A.cpue.size$SIZE_CD=='2')
LFA31A.size2=LFA31A.cpue.size[LFA31A.2,]
LFA31A.size2 = rename.df(LFA31A.size2,"Freq", "size2")
LFA31A.size2$SIZE_CD=NULL
LFA31A.0.2 = merge(LFA31A.size0,LFA31A.size2, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31A.3=which(LFA31A.cpue.size$SIZE_CD=='3')
LFA31A.size3=LFA31A.cpue.size[LFA31A.3,]
LFA31A.size3 = rename.df(LFA31A.size3, "Freq", "size3")
LFA31A.size3$SIZE_CD=NULL
LFA31A.0.3 = merge(LFA31A.0.2,LFA31A.size3, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31A.4=which(LFA31A.cpue.size$SIZE_CD=='4')
LFA31A.size4=LFA31A.cpue.size[LFA31A.4,]
LFA31A.size4 = rename.df(LFA31A.size4, "Freq", "size4")
LFA31A.size4$SIZE_CD=NULL
LFA31A.0.4 = merge(LFA31A.0.3,LFA31A.size4, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31A.5=which(LFA31A.cpue.size$SIZE_CD=='5')
LFA31A.size5=LFA31A.cpue.size[LFA31A.5,]
LFA31A.size5 = rename.df(LFA31A.size5, "Freq", "size5")
LFA31A.size5$SIZE_CD=NULL
LFA31A.0.5 = merge(LFA31A.0.4,LFA31A.size5, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31A.6=which(LFA31A.cpue.size$SIZE_CD=='6')
LFA31A.size6=LFA31A.cpue.size[LFA31A.6,]
LFA31A.size6 = rename.df(LFA31A.size6, "Freq", "size6")
LFA31A.size6$SIZE_CD=NULL
LFA31A.0.6 = merge(LFA31A.0.5,LFA31A.size6, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31A.7=which(LFA31A.cpue.size$SIZE_CD=='7')
LFA31A.size7=LFA31A.cpue.size[LFA31A.7,]
LFA31A.size7 = rename.df(LFA31A.size7, "Freq", "size7")
LFA31A.size7$SIZE_CD=NULL
LFA31A.0.7 = merge(LFA31A.0.6,LFA31A.size7, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31A.8=which(LFA31A.cpue.size$SIZE_CD=='8')
LFA31A.size8=LFA31A.cpue.size[LFA31A.8,]
LFA31A.size8 = rename.df(LFA31A.size8, "Freq", "size8")
LFA31A.size8$SIZE_CD=NULL
LFA31A.0.8 = merge(LFA31A.0.7,LFA31A.size8, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31A.9=which(LFA31A.cpue.size$SIZE_CD=='9')
LFA31A.size9=LFA31A.cpue.size[LFA31A.9,]
LFA31A.size9 = rename.df(LFA31A.size9, "Freq", "size9")
LFA31A.size9$SIZE_CD=NULL
LFA31A.0.9 = merge(LFA31A.0.8,LFA31A.size9, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31A.10.1=which(LFA31A.cpue.size$SIZE_CD=='10.1')
LFA31A.size10.1=LFA31A.cpue.size[LFA31A.10.1,]
LFA31A.size10.1 = rename.df(LFA31A.size10.1, "Freq", "size10.1")
LFA31A.size10.1$SIZE_CD=NULL
LFA31A.0.10.1 = merge(LFA31A.0.9,LFA31A.size10.1, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31A.10.2=which(LFA31A.cpue.size$SIZE_CD=='10.2')
LFA31A.size10.2=LFA31A.cpue.size[LFA31A.10.2,]
LFA31A.size10.2 = rename.df(LFA31A.size10.2, "Freq", "size10.2")
LFA31A.size10.2$SIZE_CD=NULL
LFA31A.0.10.2 = merge(LFA31A.0.10.1,LFA31A.size10.2, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31A.11=which(LFA31A.cpue.size$SIZE_CD=='11')
LFA31A.size11=LFA31A.cpue.size[LFA31A.11,]
LFA31A.size11 = rename.df(LFA31A.size11, "Freq", "size11")
LFA31A.size11$SIZE_CD=NULL
LFA31A.0.11 = merge(LFA31A.0.10.2,LFA31A.size11, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31A.12=which(LFA31A.cpue.size$SIZE_CD=='12')
LFA31A.size12=LFA31A.cpue.size[LFA31A.12,]
LFA31A.size12 = rename.df(LFA31A.size12, "Freq", "size12")
LFA31A.size12$SIZE_CD=NULL
LFA31A.0.12 = merge(LFA31A.0.11,LFA31A.size12, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31A.13=which(LFA31A.cpue.size$SIZE_CD=='13')
LFA31A.size13=LFA31A.cpue.size[LFA31A.13,]
LFA31A.size13 = rename.df(LFA31A.size13, "Freq", "size13")
LFA31A.size13$SIZE_CD=NULL
LFA31A.0.13 = merge(LFA31A.0.12,LFA31A.size13, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31A.14=which(LFA31A.cpue.size$SIZE_CD=='14')
LFA31A.size14=LFA31A.cpue.size[LFA31A.14,]
LFA31A.size14 = rename.df(LFA31A.size14, "Freq", "size14")
LFA31A.size14$SIZE_CD=NULL
LFA31A.0.14 = merge(LFA31A.0.13,LFA31A.size14, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31A.15=which(LFA31A.cpue.size$SIZE_CD=='15')
LFA31A.size15=LFA31A.cpue.size[LFA31A.15,]
LFA31A.size15 = rename.df(LFA31A.size15, "Freq", "size15")
LFA31A.size15$SIZE_CD=NULL
LFA31A.0.15 = merge(LFA31A.0.14,LFA31A.size15, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31A.16=which(LFA31A.cpue.size$SIZE_CD=='16')
LFA31A.size16=LFA31A.cpue.size[LFA31A.16,]
LFA31A.size16 = rename.df(LFA31A.size16, "Freq", "size16")
LFA31A.size16$SIZE_CD=NULL
LFA31A.0.16 = merge(LFA31A.0.15,LFA31A.size16, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31A.0.16[is.na(LFA31A.0.16)]=0
summary(LFA31A.0.16)
##SIZE CLASS SPECS FOR UNDERSIZED LOBSTERS
LFA31A.0.16$shorts=NA
LFA31A.0.16$shorts=LFA31A.0.16$size0+LFA31A.0.16$size2+LFA31A.0.16$size3+LFA31A.0.16$size4+LFA31A.0.16$size5+LFA31A.0.16$size6+
LFA31A.0.16$size7+LFA31A.0.16$size8+LFA31A.0.16$size9+LFA31A.0.16$size10.1
##SIZE CLASS SPECS FOR LEGAL LOBSTERS
LFA31A.0.16$legals=NA
LFA31A.0.16$legals=LFA31A.0.16$size10.2+LFA31A.0.16$size11+LFA31A.0.16$size12+LFA31A.0.16$size13+
LFA31A.0.16$size14+LFA31A.0.16$size15+LFA31A.0.16$size16
summary(LFA31A.0.16)
#Max shorts = 18; Max legals = 20
write.table(LFA31A.0.16, file=paste("rec.LFA31A.9916.SD1to5.nober.",Sys.Date(),".txt"), row.names=TRUE, col.names=TRUE, sep=" ")
#---------------------------------------LFA31B---------------------------------
#LFA 31B
LFA31B.9916=which(fsrs$LFA==31.2)
length(LFA31B.9916) #46,125 RECORDS JAN_2016
LFA31B.9916=fsrs[LFA31B.9916,]
unique(LFA31B.9916$HAUL_YEAR)
summary(LFA31B.9916)
##EMPTY TRAPS
e=which(LFA31B.9916$LOBSTER_NO==0)
length(e) #2,410 RECORDS
##VALIDATE SOAK DAYS:
>table(LFA31B.9916$SOAK_DAYS, LFA31B.9916$HAUL_YEAR)
1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015
1 282 889 856 1446 2590 2235 3035 4118 2700 3283 3741 2132 1925 2908 2310 2930 3709
2 106 237 188 300 392 155 290 629 174 275 193 172 116 121 302 219 222
3 32 36 37 48 40 7 108 57 24 32 44 0 69 86 81 80 15
4 0 6 5 20 0 0 0 0 0 0 0 0 6 0 0 30 0
5 0 0 0 14 0 0 13 0 0 0 0 0 8 0 0 0 0
6 0 0 0 0 3 0 0 0 0 0 0 0 12 0 0 0 0
7 0 6 0 0 0 0 6 0 0 0 0 0 0 0 0 0 6
8 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 7 0
>
write.table(LFA31B.9916, file=paste("rec.LFA31B 9916.Noremovals.from.datacheck.9916",Sys.Date(),".txt"), row.names=FALSE, col.names=TRUE, sep=" ")
#CPUE PREP FILE
##DAILY AGGREGATE FOR CPUE ANALYSIS
#SOAK DAY CONSTRAINT:
sd=which(LFA31B.9916$SOAK_DAYS > 5)
length(sd) #47 RECORDS
LFA31B.9916.sd=LFA31B.9916[-sd,]
##CALCULATE TRAP # PER DAY
LFA31B.9916.traps = compute.unique.lengths( x=LFA31B.9916.sd, var="TRAP_NO", index=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE"))
LFA31B.9916.traps = na.omit (LFA31B.9916.traps)
LFA31B.9916.traps = rename.df(LFA31B.9916.traps,"Freq", "TOT_TRAPS")
summary(LFA31B.9916.traps)
str(LFA31B.9916.traps) #8,597 RECORDS
#SHOWS NUMBER OF RECORDS WITH TRAP NUMBER DISTRIBUTION PER VESSEL
table(LFA31B.9916.traps$TOT_TRAPS,LFA31B.9916.traps$VESSEL_CD)
table(LFA31B.9916.traps$HAUL_YEAR,LFA31B.9916.traps$VESSEL_CD)
##SIZE CLASS ADJUSTMENT TO SPLIT THE SHORTS AND LEGAL SIZES IN CLASS 10
table(LFA31B.9916.sd$SIZE_CD,LFA31B.9916.sd$SHORT)
f1= which (LFA31B.9913.sd$SIZE_CD==10 & LFA31B.9913.sd$SHORT==1)
LFA31B.9913.sd[f1,"SIZE_CD"]=10.1
summary(LFA31B.9913.sd[f1,])
f2= which (LFA31B.9913.sd$SIZE_CD==10 & LFA31B.9913.sd$SHORT==0)
LFA31B.9913.sd[f2,"SIZE_CD"]=10.2
summary(LFA31B.9913.sd[f2,])
##REMOVE RECORDS FOR BERRIED BY INCLUDING IN SEX COLUMN - FOR CPUE ANALYSIS
b= which (LFA31B.9913.sd$SEX==3)
length (b) #2798 RECORDS
LFA31B.9913.sd.noberried=LFA31B.9913.sd[-b,]
str(LFA31B.9913.sd.noberried)
##CALCULATE TOTAL COUNT PER SIZE CLASS
LFA31B.9913.sd.noberried$VESSEL_CD <- as.factor(LFA31B.9913.sd.noberried$VESSEL_CD)
LFA31B.9913.sd.noberried$SIZE_CD <- as.factor(LFA31B.9913.sd.noberried$SIZE_CD)
LFA31B.9913.counts.at.size =aggregate(LFA31B.9913.sd.noberried[,1], by=as.list(LFA31B.9913.sd.noberried[c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "SIZE_CD")]), length, simplify = TRUE)
LFA31B.9913.counts.at.size = na.omit (LFA31B.9913.counts.at.size)
library(gdata)
LFA31B.9913.counts.at.size <- rename.vars(LFA31B.9913.counts.at.size, from="x", to="Freq")
summary(LFA31B.9913.counts.at.size)
str(LFA31B.9913.counts.at.size) #22,001 RECORDS
unique(LFA31B.9913.counts.at.size$SIZE_CD) #SIZE 0-16; NO NA VALUES
##SIZE CLASS FREQUENCY TABLE
LFA31B.cpue.size = merge(LFA31B.9913.traps,LFA31B.9913.counts.at.size, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE"),all.x=T,all.y=F, sort=F)
LFA31B.0=which(LFA31B.cpue.size$SIZE_CD=='0')
LFA31B.size0=LFA31B.cpue.size[LFA31B.0,]
LFA31B.size0 = rename.df(LFA31B.size0,"Freq", "size0")
LFA31B.size0$SIZE_CD=NULL
LFA31B.2=which(LFA31B.cpue.size$SIZE_CD=='2')
LFA31B.size2=LFA31B.cpue.size[LFA31B.2,]
LFA31B.size2 = rename.df(LFA31B.size2, "Freq", "size2")
LFA31B.size2$SIZE_CD=NULL
LFA31B.0.2 = merge(LFA31B.size0,LFA31B.size2, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31B.3=which(LFA31B.cpue.size$SIZE_CD=='3')
LFA31B.size3=LFA31B.cpue.size[LFA31B.3,]
LFA31B.size3 = rename.df(LFA31B.size3, "Freq", "size3")
LFA31B.size3$SIZE_CD=NULL
LFA31B.0.3 = merge(LFA31B.0.2,LFA31B.size3, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31B.4=which(LFA31B.cpue.size$SIZE_CD=='4')
LFA31B.size4=LFA31B.cpue.size[LFA31B.4,]
LFA31B.size4 = rename.df(LFA31B.size4, "Freq", "size4")
LFA31B.size4$SIZE_CD=NULL
LFA31B.0.4 = merge(LFA31B.0.3,LFA31B.size4, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31B.5=which(LFA31B.cpue.size$SIZE_CD=='5')
LFA31B.size5=LFA31B.cpue.size[LFA31B.5,]
LFA31B.size5 = rename.df(LFA31B.size5, "Freq", "size5")
LFA31B.size5$SIZE_CD=NULL
LFA31B.0.5 = merge(LFA31B.0.4,LFA31B.size5, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31B.6=which(LFA31B.cpue.size$SIZE_CD=='6')
LFA31B.size6=LFA31B.cpue.size[LFA31B.6,]
LFA31B.size6 = rename.df(LFA31B.size6, "Freq", "size6")
LFA31B.size6$SIZE_CD=NULL
LFA31B.0.6 = merge(LFA31B.0.5,LFA31B.size6, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31B.7=which(LFA31B.cpue.size$SIZE_CD=='7')
LFA31B.size7=LFA31B.cpue.size[LFA31B.7,]
LFA31B.size7 = rename.df(LFA31B.size7, "Freq", "size7")
LFA31B.size7$SIZE_CD=NULL
LFA31B.0.7 = merge(LFA31B.0.6,LFA31B.size7, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31B.8=which(LFA31B.cpue.size$SIZE_CD=='8')
LFA31B.size8=LFA31B.cpue.size[LFA31B.8,]
LFA31B.size8 = rename.df(LFA31B.size8, "Freq", "size8")
LFA31B.size8$SIZE_CD=NULL
LFA31B.0.8 = merge(LFA31B.0.7,LFA31B.size8, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31B.9=which(LFA31B.cpue.size$SIZE_CD=='9')
LFA31B.size9=LFA31B.cpue.size[LFA31B.9,]
LFA31B.size9 = rename.df(LFA31B.size9, "Freq", "size9")
LFA31B.size9$SIZE_CD=NULL
LFA31B.0.9 = merge(LFA31B.0.8,LFA31B.size9, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31B.10.1=which(LFA31B.cpue.size$SIZE_CD=='10.1')
LFA31B.size10.1=LFA31B.cpue.size[LFA31B.10.1,]
LFA31B.size10.1 = rename.df(LFA31B.size10.1, "Freq", "size10.1")
LFA31B.size10.1$SIZE_CD=NULL
LFA31B.0.10.1 = merge(LFA31B.0.9,LFA31B.size10.1, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31B.10.2=which(LFA31B.cpue.size$SIZE_CD=='10.2')
LFA31B.size10.2=LFA31B.cpue.size[LFA31B.10.2,]
LFA31B.size10.2 = rename.df(LFA31B.size10.2, "Freq", "size10.2")
LFA31B.size10.2$SIZE_CD=NULL
LFA31B.0.10.2 = merge(LFA31B.0.10.1,LFA31B.size10.2, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31B.11=which(LFA31B.cpue.size$SIZE_CD=='11')
LFA31B.size11=LFA31B.cpue.size[LFA31B.11,]
LFA31B.size11 = rename.df(LFA31B.size11, "Freq", "size11")
LFA31B.size11$SIZE_CD=NULL
LFA31B.0.11 = merge(LFA31B.0.10.2,LFA31B.size11, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31B.12=which(LFA31B.cpue.size$SIZE_CD=='12')
LFA31B.size12=LFA31B.cpue.size[LFA31B.12,]
LFA31B.size12 = rename.df(LFA31B.size12, "Freq", "size12")
LFA31B.size12$SIZE_CD=NULL
LFA31B.0.12 = merge(LFA31B.0.11,LFA31B.size12, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31B.13=which(LFA31B.cpue.size$SIZE_CD=='13')
LFA31B.size13=LFA31B.cpue.size[LFA31B.13,]
LFA31B.size13 = rename.df(LFA31B.size13, "Freq", "size13")
LFA31B.size13$SIZE_CD=NULL
LFA31B.0.13 = merge(LFA31B.0.12,LFA31B.size13, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31B.14=which(LFA31B.cpue.size$SIZE_CD=='14')
LFA31B.size14=LFA31B.cpue.size[LFA31B.14,]
LFA31B.size14 = rename.df(LFA31B.size14, "Freq", "size14")
LFA31B.size14$SIZE_CD=NULL
LFA31B.0.14 = merge(LFA31B.0.13,LFA31B.size14, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31B.15=which(LFA31B.cpue.size$SIZE_CD=='15')
LFA31B.size15=LFA31B.cpue.size[LFA31B.15,]
LFA31B.size15 = rename.df(LFA31B.size15, "Freq", "size15")
LFA31B.size15$SIZE_CD=NULL
LFA31B.0.15 = merge(LFA31B.0.14,LFA31B.size15, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31B.16=which(LFA31B.cpue.size$SIZE_CD=='16')
LFA31B.size16=LFA31B.cpue.size[LFA31B.16,]
LFA31B.size16 = rename.df(LFA31B.size16, "Freq", "size16")
LFA31B.size16$SIZE_CD=NULL
LFA31B.0.16 = merge(LFA31B.0.15,LFA31B.size16, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31B.0.16[is.na(LFA31B.0.16)]=0
summary(LFA31B.0.16)
##SIZE CLASS SPECS FOR UNDERSIZED LOBSTERS FROM 1999-2013
LFA31B.0.16$shorts=NA
LFA31B.0.16$shorts=LFA31B.0.16$size0+LFA31B.0.16$size2+LFA31B.0.16$size3+LFA31B.0.16$size4+LFA31B.0.16$size5+LFA31B.0.16$size6+
LFA31B.0.16$size7+LFA31B.0.16$size8+LFA31B.0.16$size9+LFA31B.0.16$size10.1
##SIZE CLASS SPECS FOR LEGAL LOBSTERS FROM 1999-2013
LFA31B.0.16$legals=NA
LFA31B.0.16$legals=LFA31B.0.16$size10.2+LFA31B.0.16$size11+LFA31B.0.16$size12+LFA31B.0.16$size13+
LFA31B.0.16$size14+LFA31B.0.16$size15+LFA31B.0.16$size16
summary(LFA31B.0.16)
#Max shorts = 15; Max legals = 18
write.table(LFA31B.0.16, file=paste("rec.LFA31B.9913.SD1to5.nober.",Sys.Date(),".txt"), row.names=TRUE, col.names=TRUE, sep=" ")
#-------------------------------------LFA32-------------------------------------
#LFA 32
LFA32.9916=which(fsrs$LFA==32)
length(LFA32.9916) #45,019 RECORDS JAN_2016
LFA32.9916=fsrs[LFA32.9916,]
unique(LFA32.9916$HAUL_YEAR)
summary(LFA32.9916)
##EMPTY TRAPS
e=which(LFA32.9916$LOBSTER_NO==0)
length(e) #6,253 RECORDS
##VALIDATE SOAK DAYS:
>table(LFA32.9916$SOAK_DAYS, LFA32.9916$HAUL_YEAR)
1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015
1 854 1238 1158 1276 1715 1707 1945 2950 1594 2605 2885 2432 2522 3184 1972 4051 3152
2 222 337 211 295 213 325 290 376 188 321 431 337 559 518 272 431 492
3 39 36 46 46 46 9 57 102 56 71 121 102 90 146 173 157 49
4 17 1 25 18 2 2 11 4 23 36 37 37 52 37 36 18 2
5 2 1 8 2 2 0 24 4 0 2 0 2 39 7 14 0 0
6 0 0 4 1 2 0 30 2 5 18 0 0 0 0 0 14 4
7 0 0 1 0 2 0 10 4 6 0 0 2 13 0 0 0 0
8 0 0 0 0 2 0 0 2 0 2 0 0 10 0 0 0 0
9 0 2 0 0 2 0 6 0 0 0 0 0 0 0 0 0 0
10 0 0 0 0 3 0 3 0 0 0 0 0 0 0 0 0 0
>
write.table(LFA32.9916, file=paste("rec.LFA32 9916.Noremovals.from.datacheck.9916",Sys.Date(),".txt"), row.names=FALSE, col.names=TRUE, sep=" ")
#CPUE PREP FILE
##DAILY AGGREGATE FOR CPUE ANALYSIS
#SOAK DAY CONSTRAINT:
sd=which(LFA32.9916$SOAK_DAYS> 5)
length(sd) #150 RECORDS
LFA32.9916.sd=LFA32.9916[-sd,]
##CALCULATE TRAP # PER DAY
LFA32.9916.traps = ddply(LFA32.9916.sd,c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE"),summarize,TOT_TRAPS=length(unique(TRAP_NO)))
summary(LFA32.9916.traps)
str(LFA32.9916.traps) #11,772 RECORDS
#SHOWS NUMBER OF RECORDS WITH TRAP NUMBER DISTRIBUTION PER VESSEL
table(LFA32.9916.traps$TOT_TRAPS,LFA32.9916.traps$VESSEL_CD)
table(LFA32.9916.traps$HAUL_YEAR,LFA32.9916.traps$VESSEL_CD)
##SIZE CLASS ADJUSTMENT TO SPLIT THE SHORTS AND LEGAL SIZES IN CLASS 10
table(LFA32.9916.sd$SIZE_CD,LFA32.9916.sd$SHORT)
g1= which (LFA32.9916.sd$SIZE_CD==10 & LFA32.9916.sd$SHORT==1)
LFA32.9916.sd[g1,"SIZE_CD"]=10.1
summary(LFA32.9916.sd[g1,])
g2= which (LFA32.9916.sd$SIZE_CD==10 & LFA32.9916.sd$SHORT==0)
LFA32.9916.sd[g2,"SIZE_CD"]=10.2
summary(LFA32.9916.sd[g2,])
##REMOVE RECORDS FOR BERRIED BY INCLUDING IN SEX COLUMN - FOR CPUE ANALYSIS
b= which (LFA32.9916.sd$SEX==3)
length (b) #1,783 RECORDS
LFA32.9916.sd.noberried=LFA32.9916.sd[-b,]
str(LFA32.9916.sd.noberried)
##CALCULATE TOTAL COUNT PER SIZE CLASS
LFA32.9916.counts.at.size =aggregate(LFA32.9916.sd.noberried[,1], by=as.list(LFA32.9916.sd.noberried[c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "SIZE_CD")]), length, simplify = TRUE)
LFA32.9916.counts.at.size = na.omit (LFA32.9916.counts.at.size)
library(gdata)
LFA32.9916.counts.at.size <- rename.vars(LFA32.9916.counts.at.size, from="x", to="Freq")
summary(LFA32.9916.counts.at.size)
str(LFA32.9916.counts.at.size) #24,701 RECORDS
unique(LFA32.9916.counts.at.size$SIZE_CD) #SIZE 0-16; NO NA VALUES
##SIZE CLASS FREQUENCY TABLE
LFA32.cpue.size = merge(LFA32.9916.traps,LFA32.9916.counts.at.size, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE"),all.x=T,all.y=F, sort=F)
LFA32.0=which(LFA32.cpue.size$SIZE_CD=='0')
LFA32.size0=LFA32.cpue.size[LFA32.0,]
LFA32.size0 = rename.df(LFA32.size0,"Freq", "size0")
LFA32.size0$SIZE_CD=NULL
LFA32.2=which(LFA32.cpue.size$SIZE_CD=='2')
LFA32.size2=LFA32.cpue.size[LFA32.2,]
LFA32.size2 = rename.df(LFA32.size2, "Freq", "size2")
LFA32.size2$SIZE_CD=NULL
LFA32.0.2 = merge(LFA32.size0,LFA32.size2, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA32.3=which(LFA32.cpue.size$SIZE_CD=='3')
LFA32.size3=LFA32.cpue.size[LFA32.3,]
LFA32.size3 = rename.df(LFA32.size3, "Freq", "size3")
LFA32.size3$SIZE_CD=NULL
LFA32.0.3 = merge(LFA32.0.2,LFA32.size3, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA32.4=which(LFA32.cpue.size$SIZE_CD=='4')
LFA32.size4=LFA32.cpue.size[LFA32.4,]
LFA32.size4 = rename.df(LFA32.size4, "Freq", "size4")
LFA32.size4$SIZE_CD=NULL
LFA32.0.4 = merge(LFA32.0.3,LFA32.size4, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA32.5=which(LFA32.cpue.size$SIZE_CD=='5')
LFA32.size5=LFA32.cpue.size[LFA32.5,]
LFA32.size5 = rename.df(LFA32.size5, "Freq", "size5")
LFA32.size5$SIZE_CD=NULL
LFA32.0.5 = merge(LFA32.0.4,LFA32.size5, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA32.6=which(LFA32.cpue.size$SIZE_CD=='6')
LFA32.size6=LFA32.cpue.size[LFA32.6,]
LFA32.size6 = rename.df(LFA32.size6, "Freq", "size6")
LFA32.size6$SIZE_CD=NULL
LFA32.0.6 = merge(LFA32.0.5,LFA32.size6, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA32.7=which(LFA32.cpue.size$SIZE_CD=='7')
LFA32.size7=LFA32.cpue.size[LFA32.7,]
LFA32.size7 = rename.df(LFA32.size7, "Freq", "size7")
LFA32.size7$SIZE_CD=NULL
LFA32.0.7 = merge(LFA32.0.6,LFA32.size7, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA32.8=which(LFA32.cpue.size$SIZE_CD=='8')
LFA32.size8=LFA32.cpue.size[LFA32.8,]
LFA32.size8 = rename.df(LFA32.size8, "Freq", "size8")
LFA32.size8$SIZE_CD=NULL
LFA32.0.8 = merge(LFA32.0.7,LFA32.size8, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA32.9=which(LFA32.cpue.size$SIZE_CD=='9')
LFA32.size9=LFA32.cpue.size[LFA32.9,]
LFA32.size9 = rename.df(LFA32.size9, "Freq", "size9")
LFA32.size9$SIZE_CD=NULL
LFA32.0.9 = merge(LFA32.0.8,LFA32.size9, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA32.10.1=which(LFA32.cpue.size$SIZE_CD=='10.1')
LFA32.size10.1=LFA32.cpue.size[LFA32.10.1,]
LFA32.size10.1 = rename.df(LFA32.size10.1, "Freq", "size10.1")
LFA32.size10.1$SIZE_CD=NULL
LFA32.0.10.1 = merge(LFA32.0.9,LFA32.size10.1, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA32.10.2=which(LFA32.cpue.size$SIZE_CD=='10.2')
LFA32.size10.2=LFA32.cpue.size[LFA32.10.2,]
LFA32.size10.2 = rename.df(LFA32.size10.2, "Freq", "size10.2")
LFA32.size10.2$SIZE_CD=NULL
LFA32.0.10.2 = merge(LFA32.0.10.1,LFA32.size10.2, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA32.11=which(LFA32.cpue.size$SIZE_CD=='11')
LFA32.size11=LFA32.cpue.size[LFA32.11,]
LFA32.size11 = rename.df(LFA32.size11, "Freq", "size11")
LFA32.size11$SIZE_CD=NULL
LFA32.0.11 = merge(LFA32.0.10.2,LFA32.size11, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA32.12=which(LFA32.cpue.size$SIZE_CD=='12')
LFA32.size12=LFA32.cpue.size[LFA32.12,]
LFA32.size12 = rename.df(LFA32.size12, "Freq", "size12")
LFA32.size12$SIZE_CD=NULL
LFA32.0.12 = merge(LFA32.0.11,LFA32.size12, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA32.13=which(LFA32.cpue.size$SIZE_CD=='13')
LFA32.size13=LFA32.cpue.size[LFA32.13,]
LFA32.size13 = rename.df(LFA32.size13, "Freq", "size13")
LFA32.size13$SIZE_CD=NULL
LFA32.0.13 = merge(LFA32.0.12,LFA32.size13, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA32.14=which(LFA32.cpue.size$SIZE_CD=='14')
LFA32.size14=LFA32.cpue.size[LFA32.14,]
LFA32.size14 = rename.df(LFA32.size14, "Freq", "size14")
LFA32.size14$SIZE_CD=NULL
LFA32.0.14 = merge(LFA32.0.13,LFA32.size14, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA32.15=which(LFA32.cpue.size$SIZE_CD=='15')
LFA32.size15=LFA32.cpue.size[LFA32.15,]
LFA32.size15 = rename.df(LFA32.size15, "Freq", "size15")
LFA32.size15$SIZE_CD=NULL
LFA32.0.15 = merge(LFA32.0.14,LFA32.size15, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA32.16=which(LFA32.cpue.size$SIZE_CD=='16')
LFA32.size16=LFA32.cpue.size[LFA32.16,]
LFA32.size16 = rename.df(LFA32.size16, "Freq", "size16")
LFA32.size16$SIZE_CD=NULL
LFA32.0.16 = merge(LFA32.0.15,LFA32.size16, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA32.0.16[is.na(LFA32.0.16)]=0
summary(LFA32.0.16)
##SIZE CLASS SPECS FOR UNDERSIZED LOBSTERS FROM 1999-2013
LFA32.0.16$shorts=NA
LFA32.0.16$shorts=LFA32.0.16$size0+LFA32.0.16$size2+LFA32.0.16$size3+LFA32.0.16$size4+LFA32.0.16$size5+LFA32.0.16$size6+
LFA32.0.16$size7+LFA32.0.16$size8+LFA32.0.16$size9+LFA32.0.16$size10.1
##SIZE CLASS SPECS FOR LEGAL LOBSTERS FROM 1999-2013
LFA32.0.16$legals=NA
LFA32.0.16$legals=LFA32.0.16$size10.2+LFA32.0.16$size11+LFA32.0.16$size12+LFA32.0.16$size13+
LFA32.0.16$size14+LFA32.0.16$size15+LFA32.0.16$size16
summary(LFA32.0.16)
#Max shorts = 18; Max legals = 13
write.table(LFA32.0.16, file=paste("rec.LFA32.9916.SD1to5.nober.",Sys.Date(),".txt"), row.names=TRUE, col.names=TRUE, sep=" ")
#------------------------------------------LFA33-------------------------------
##LFA 33
LFA33.9916=which(fsrs$LFA==33)
length(LFA33.9916) #279,629 RECORDS JAN_2016
LFA33.9916=fsrs[LFA33.9916,]
summary(LFA33.9916)
##EMPTY TRAPS
e=which(LFA33.9916$LOBSTER_NO==0)
length(e) #15,085 RECORDS
##VALIDATE SOAK DAYS:
> table(LFA33.9916$SOAK_DAYS,LFA33.9916$S_LABEL) # A PORTION OF RECORDS HAVE TO HAVE LABEL ADDED - THESE ARE PAST NORMAL SEASON DATES
#LFA33.9916$S_LABEL<-recode(LFA33.9916$S_LABEL,"is.na='2004-2005'")
1998-1999 1999-2000 2000-2001 2001-2002 2002-2003 2003-2004 2004-2005 2005-2006 2006-2007 2007-2008 2008-2009 2009-2010 2010-2011 2011-2012 2012-2013 2013-2014
0.5 0 0 0 38 0 0 0 27 61 0 0 0 0 0 0 0
1 2583 5257 6864 8635 8108 8509 10908 11185 11008 8631 10414 13106 12111 10008 10598 11626
2 978 2682 2376 3144 3283 3190 4023 3875 4075 3200 5275 4503 3838 5452 4663 4108
3 240 1143 961 1308 1064 1349 1407 1667 1323 1329 1767 1861 2059 2083 3004 1637
4 25 461 396 351 347 622 598 811 596 325 681 1421 995 1073 879 609
5 12 92 176 251 270 362 277 425 379 339 489 511 1079 575 420 643
6 2 117 54 176 144 120 233 405 141 180 167 295 279 291 321 206
7 6 29 54 27 50 120 212 218 75 84 68 202 293 197 179 214
8 0 38 14 41 13 43 104 120 86 6 114 104 200 43 144 154
9 0 10 16 16 19 128 64 88 56 18 68 96 84 185 149 146
10 0 10 11 25 10 28 49 21 26 35 67 24 33 41 138 55
11 0 0 12 30 0 0 8 69 4 37 40 52 78 62 51 15
12 0 8 0 0 0 8 0 113 33 20 21 18 43 9 31 16
13 0 0 3 0 0 3 0 1 15 3 7 26 7 27 65 57
14 0 6 0 0 9 9 0 10 10 0 13 36 15 0 13 11
15 0 0 3 5 21 23 7 0 7 7 0 23 44 41 25 0
16 0 0 3 0 0 0 5 12 14 12 0 4 9 18 0 11
17 0 0 0 0 2 10 0 3 0 0 6 11 14 16 55 0
18 0 0 0 0 0 9 0 0 0 0 0 17 21 5 25 12
19 0 0 3 0 22 45 0 27 0 0 0 0 7 0 7 0
20 0 0 0 0 0 0 0 1 13 5 14 0 21 0 12 22
21 0 0 3 14 0 0 0 0 0 0 0 0 0 0 0 27
22 0 0 0 0 0 4 4 0 0 0 0 5 7 5 0 31
23 0 0 0 0 0 0 13 3 0 0 0 0 0 0 20 0
24 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0
25 0 0 0 0 0 3 0 0 0 0 10 3 0 0 6 0
26 0 0 0 0 0 0 0 3 0 0 33 0 0 0 0 19
27 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0 0
28 0 0 0 0 0 0 0 0 0 0 0 0 11 9 0 0
29 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 5
30 0 3 0 0 5 4 0 0 0 0 0 0 0 0 0 0
31 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0
32 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0
33 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0
34 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0
35 0 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0
36 0 0 0 0 0 0 0 0 0 0 0 0 0 21 0 0
37 0 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0
38 0 0 0 0 0 0 0 3 0 6 0 0 0 0 0 0
40 0 0 0 0 0 0 0 4 0 0 0 0 0 0 8 12
42 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0
43 0 0 0 0 0 5 4 0 0 0 0 0 3 0 0 0
48 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0
50 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0
57 0 0 0 0 0 20 0 0 0 0 0 0 0 0 0 0
59 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0
60 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0
64 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0
>
write.table(LFA33.9916, file=paste("rec.LFA33 9916.Noremovals.from.datacheck.9916",Sys.Date(),".txt"), row.names=FALSE, col.names=TRUE, sep=" ")
#CPUE PREP FILE:
##DAILY AGGREGATE FOR CPUE ANALYSIS
#SOAK DAY CONSTRAINT:
sd=which(LFA33.9916$SOAK_DAYS > 5)
length(sd) #10,355 RECORDS
LFA33.9916.sd=LFA33.9916[-sd,]
short.soak.days=which(LFA33.9916.sd$SOAK_DAYS < 1)
length(short.soak.days) # 126 RECORDS
LFA33.9916.sd=LFA33.9916.sd[-short.soak.days,]
##CALCULATE TRAP # PER DAY
LFA33.9916.traps<-ddply(LFA33.9916.sd,c("S_LABEL", "VESSEL_CD", "HAUL_DATE"),summarize, TOT_TRAPS=length(unique(TRAP_NO))) #27,647 RECORDS
str(LFA33.9916.traps) #27,647 RECORDS (SD 1 to 5 SELECTION) DEC.2014 SQL EXPORT
#SHOWS NUMBER OF RECORDS WITH TRAP NUMBER DISTRIBUTION PER VESSEL
table(LFA33.9916.traps$S_LABEL,LFA33.9916.traps$TOT_TRAPS)
table(LFA33.9916.traps$S_LABEL,LFA33.9916.traps$VESSEL_CD)
##SIZE CLASS ADJUSTMENT TO SPLIT THE SHORTS AND LEGAL SIZES IN CLASS 10
table(LFA33.9916.sd$SIZE_CD, LFA33.9916.sd$SHORT)
h1= which (LFA33.9916.sd$SIZE_CD==10 & LFA33.9916.sd$SHORT==1)
LFA33.9916.sd[h1,"SIZE_CD"]=10.1
summary(LFA33.9916.sd[h1,])
h2= which (LFA33.9916.sd$SIZE_CD==10 & LFA33.9916.sd$SHORT==0)
LFA33.9916.sd[h2,"SIZE_CD"]=10.2
summary(LFA33.9916.sd[h2,])
str(LFA33.9916.sd)
##REMOVE RECORDS FOR BERRIED BY INCLUDING IN SEX COLUMN - FOR CPUE ANALYSIS
b= which (LFA33.9916.sd$SEX==3)
length (b) #3861 RECORDS
LFA33.9916.sd.noberried=LFA33.9916.sd[-b,]
str(LFA33.9916.sd.noberried)
##CALCULATE TOTAL COUNT PER SIZE CLASS
LFA33.9916.counts.at.size =aggregate(LFA33.9916.sd.noberried[,1], by=as.list(LFA33.9916.sd.noberried[c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "SIZE_CD")]), length, simplify = TRUE)
LFA33.9916.counts.at.size = na.omit (LFA33.9916.counts.at.size)
library(gdata)
LFA33.9916.counts.at.size <- rename.vars(LFA33.9916.counts.at.size, from="x", to="Freq")
summary(LFA33.9916.counts.at.size)
str(LFA33.9916.counts.at.size) #100,527 RECORDS
unique(LFA33.9916.counts.at.size$SIZE_CD) #SIZE 0-16; NO NA VALUES
##SIZE CLASS FREQUENCY TABLE
LFA33.cpue.size = merge(LFA33.9916.traps,LFA33.9916.counts.at.size, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE"),all.x=T,all.y=F, sort=F)
LFA33.0=which(LFA33.cpue.size$SIZE_CD=='0')
LFA33.size0=LFA33.cpue.size[LFA33.0,]
LFA33.size0 = rename.df(LFA33.size0,"Freq", "size0")
LFA33.size0$SIZE_CD=NULL
LFA33.2=which(LFA33.cpue.size$SIZE_CD=='2')
LFA33.size2=LFA33.cpue.size[LFA33.2,]
LFA33.size2 = rename.df(LFA33.size2, "Freq", "size2")
LFA33.size2$SIZE_CD=NULL
LFA33.0.2 = merge(LFA33.size0,LFA33.size2, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA33.3=which(LFA33.cpue.size$SIZE_CD=='3')
LFA33.size3=LFA33.cpue.size[LFA33.3,]
LFA33.size3 = rename.df(LFA33.size3, "Freq", "size3")
LFA33.size3$SIZE_CD=NULL
LFA33.0.3 = merge(LFA33.0.2,LFA33.size3, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA33.4=which(LFA33.cpue.size$SIZE_CD=='4')
LFA33.size4=LFA33.cpue.size[LFA33.4,]
LFA33.size4 = rename.df(LFA33.size4, "Freq", "size4")
LFA33.size4$SIZE_CD=NULL
LFA33.0.4 = merge(LFA33.0.3,LFA33.size4, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA33.5=which(LFA33.cpue.size$SIZE_CD=='5')
LFA33.size5=LFA33.cpue.size[LFA33.5,]
LFA33.size5 = rename.df(LFA33.size5, "Freq", "size5")
LFA33.size5$SIZE_CD=NULL
LFA33.0.5 = merge(LFA33.0.4,LFA33.size5, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA33.6=which(LFA33.cpue.size$SIZE_CD=='6')
LFA33.size6=LFA33.cpue.size[LFA33.6,]
LFA33.size6 = rename.df(LFA33.size6, "Freq", "size6")
LFA33.size6$SIZE_CD=NULL
LFA33.0.6 = merge(LFA33.0.5,LFA33.size6, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA33.7=which(LFA33.cpue.size$SIZE_CD=='7')
LFA33.size7=LFA33.cpue.size[LFA33.7,]
LFA33.size7 = rename.df(LFA33.size7, "Freq", "size7")
LFA33.size7$SIZE_CD=NULL
LFA33.0.7 = merge(LFA33.0.6,LFA33.size7, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA33.8=which(LFA33.cpue.size$SIZE_CD=='8')
LFA33.size8=LFA33.cpue.size[LFA33.8,]
LFA33.size8 = rename.df(LFA33.size8, "Freq", "size8")
LFA33.size8$SIZE_CD=NULL
LFA33.0.8 = merge(LFA33.0.7,LFA33.size8, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA33.9=which(LFA33.cpue.size$SIZE_CD=='9')
LFA33.size9=LFA33.cpue.size[LFA33.9,]
LFA33.size9 = rename.df(LFA33.size9, "Freq", "size9")
LFA33.size9$SIZE_CD=NULL
LFA33.0.9 = merge(LFA33.0.8,LFA33.size9, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA33.10.1=which(LFA33.cpue.size$SIZE_CD=='10.1')
LFA33.size10.1=LFA33.cpue.size[LFA33.10.1,]
LFA33.size10.1 = rename.df(LFA33.size10.1, "Freq", "size10.1")
LFA33.size10.1$SIZE_CD=NULL
LFA33.0.10.1 = merge(LFA33.0.9,LFA33.size10.1, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA33.10.2=which(LFA33.cpue.size$SIZE_CD=='10.2')
LFA33.size10.2=LFA33.cpue.size[LFA33.10.2,]
LFA33.size10.2 = rename.df(LFA33.size10.2, "Freq", "size10.2")
LFA33.size10.2$SIZE_CD=NULL
LFA33.0.10.2 = merge(LFA33.0.10.1,LFA33.size10.2, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA33.11=which(LFA33.cpue.size$SIZE_CD=='11')
LFA33.size11=LFA33.cpue.size[LFA33.11,]
LFA33.size11 = rename.df(LFA33.size11, "Freq", "size11")
LFA33.size11$SIZE_CD=NULL
LFA33.0.11 = merge(LFA33.0.10.2,LFA33.size11, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA33.12=which(LFA33.cpue.size$SIZE_CD=='12')
LFA33.size12=LFA33.cpue.size[LFA33.12,]
LFA33.size12 = rename.df(LFA33.size12, "Freq", "size12")
LFA33.size12$SIZE_CD=NULL
LFA33.0.12 = merge(LFA33.0.11,LFA33.size12, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA33.13=which(LFA33.cpue.size$SIZE_CD=='13')
LFA33.size13=LFA33.cpue.size[LFA33.13,]
LFA33.size13 = rename.df(LFA33.size13, "Freq", "size13")
LFA33.size13$SIZE_CD=NULL
LFA33.0.13 = merge(LFA33.0.12,LFA33.size13, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA33.14=which(LFA33.cpue.size$SIZE_CD=='14')
LFA33.size14=LFA33.cpue.size[LFA33.14,]
LFA33.size14 = rename.df(LFA33.size14, "Freq", "size14")
LFA33.size14$SIZE_CD=NULL
LFA33.0.14 = merge(LFA33.0.13,LFA33.size14, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA33.15=which(LFA33.cpue.size$SIZE_CD=='15')
LFA33.size15=LFA33.cpue.size[LFA33.15,]
LFA33.size15 = rename.df(LFA33.size15, "Freq", "size15")
LFA33.size15$SIZE_CD=NULL
LFA33.0.15 = merge(LFA33.0.14,LFA33.size15, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA33.16=which(LFA33.cpue.size$SIZE_CD=='16')
LFA33.size16=LFA33.cpue.size[LFA33.16,]
LFA33.size16 = rename.df(LFA33.size16, "Freq", "size16")
LFA33.size16$SIZE_CD=NULL
LFA33.0.16 = merge(LFA33.0.15,LFA33.size16, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA33.0.16[is.na(LFA33.0.16)]=0
summary(LFA33.0.16)
##SIZE CLASS SPECS FOR UNDERSIZED LOBSTERS FROM 1999-2013
LFA33.0.16$shorts=NA
LFA33.0.16$shorts=LFA33.0.16$size0+LFA33.0.16$size2+LFA33.0.16$size3+LFA33.0.16$size4+LFA33.0.16$size5+LFA33.0.16$size6+
LFA33.0.16$size7+LFA33.0.16$size8+LFA33.0.16$size9+LFA33.0.16$size10.1
##SIZE CLASS SPECS FOR LEGAL LOBSTERS FROM 1999-2013
LFA33.0.16$legals=NA
LFA33.0.16$legals=LFA33.0.16$size10.2+LFA33.0.16$size11+LFA33.0.16$size12+LFA33.0.16$size13+
LFA33.0.16$size14+LFA33.0.16$size15+LFA33.0.16$size16
summary(LFA33.0.16)
#Max shorts = 95; Max legals = 33
write.table(LFA33.0.16, file=paste("rec.LFA33.9916.SD1to5.nober.",Sys.Date(),".txt"), row.names=TRUE, col.names=TRUE, sep=" ")
#------------------------------------------LFA34-------------------------------
##LFA 34
LFA34.9916=which(fsrs$LFA==34)
length(LFA34.9916) #308,726 RECORDS DEC_2014
LFA34.9916=fsrs[LFA34.9916,]
summary(LFA34.9916)
##EMPTY TRAPS
e=which(LFA34.9916$LOBSTER_NO==0)
length(e) #5129 RECORDS
##VALIDATE SOAK DAYS:
LFA34.9916$S_LABEL<-as.character(LFA34.9916$S_LABEL)
#out.of.season<-subset(LFA34.9916,S_LABEL=="")
#LFA34.9916$S_LABEL<-recode(LFA34.9916$S_LABEL,"''='2004-2005'")
> table(LFA34.9916$SOAK_DAYS,LFA34.9916$S_LABEL)# A PORTION OF RECORDS HAVE TO HAVE LABEL ADDED - THESE ARE PAST NORMAL SEASON DATES
1998-1999 1999-2000 2000-2001 2001-2002 2002-2003 2003-2004 2004-2005 2005-2006 2006-2007 2007-2008 2008-2009 2009-2010 2010-2011 2011-2012 2012-2013 2013-2014
0.5 0 0 0 129 0 0 0 27 78 13 0 0 0 0 0 0
1 197 3697 8964 12911 11168 7130 10171 10786 10222 6303 6117 7413 6611 8077 5305 4974
2 202 3541 7537 8088 7853 5069 8490 11545 6187 6168 6020 6331 4143 4774 5177 2536
3 37 2191 2481 3856 3683 3177 2833 4807 1727 1957 2030 1953 2105 2369 3242 1630
4 7 705 1237 1776 1803 1464 1128 2431 993 1053 1134 1559 1308 1136 1010 481
5 9 227 698 809 859 559 598 1348 914 861 454 637 749 682 864 525
6 0 192 443 571 533 532 635 717 300 200 361 273 398 379 631 222
7 0 69 462 271 108 616 641 785 142 294 284 204 331 299 319 169
8 0 52 194 374 216 236 268 210 97 121 169 112 247 201 228 148
9 0 105 123 33 167 158 90 230 61 31 32 31 82 280 323 41
10 0 39 75 267 57 62 53 340 40 55 79 10 94 167 287 76
11 0 53 78 42 172 17 99 97 57 30 12 47 40 83 191 18
12 0 42 41 98 39 62 10 110 47 59 4 85 34 131 105 68
13 0 36 55 59 3 52 73 77 4 26 13 27 14 35 34 21
14 0 14 15 13 34 104 21 116 66 13 28 26 5 49 51 4
15 0 2 31 17 66 88 57 28 34 18 12 2 20 11 2 33
16 0 37 43 19 3 34 46 10 15 11 2 0 4 33 7 24
17 0 11 10 0 34 6 0 3 52 13 9 2 5 18 53 31
18 0 0 20 12 33 0 2 8 15 17 4 9 29 38 11 9
19 0 7 17 7 43 6 22 8 15 0 9 30 4 9 14 13
20 0 0 11 8 35 9 14 5 13 2 8 13 0 0 0 34
21 0 3 15 0 4 4 9 0 7 11 7 0 4 0 0 8
22 0 3 13 5 7 0 3 6 3 0 0 0 5 0 0 0
23 0 0 9 4 2 21 5 0 0 3 0 0 23 0 0 6
24 0 4 0 0 12 34 10 0 2 2 2 0 0 2 0 0
25 0 4 0 0 8 16 4 0 0 0 2 5 2 0 0 0
26 0 0 0 0 3 0 0 0 24 0 0 0 8 3 0 0
27 0 8 0 7 19 0 0 0 0 4 0 15 0 4 19 0
28 0 5 7 0 11 38 0 0 0 3 0 0 0 0 15 7
29 0 0 0 0 0 12 0 0 17 0 0 0 0 0 0 0
30 0 0 4 0 23 9 32 24 2 0 2 6 2 0 26 0
31 0 0 0 0 8 0 2 0 2 0 2 0 0 0 0 0
32 0 0 0 0 0 0 0 0 0 7 13 0 7 0 0 0
33 0 0 0 8 0 0 0 0 2 0 0 0 0 0 0 0
34 0 0 0 0 8 0 0 3 0 0 0 0 0 0 0 0
35 0 0 2 3 7 12 0 0 17 0 2 0 3 0 8 0
36 0 0 0 0 0 10 0 0 4 0 2 0 0 0 0 0
37 0 0 0 0 0 2 9 0 0 0 0 0 0 0 0 0
38 0 0 0 0 23 3 16 0 0 0 0 0 12 0 0 0
39 0 0 0 39 0 11 0 0 0 0 0 0 0 0 0 0
40 0 0 0 0 0 16 2 0 3 0 0 0 0 0 11 33
41 0 0 0 0 0 11 0 0 0 0 0 0 0 0 0 0
42 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 0
43 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0
44 0 0 8 0 7 0 0 0 0 0 2 0 0 0 0 0
45 0 0 0 0 0 0 3 0 0 0 0 3 0 0 0 0
46 0 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0
47 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0
48 0 0 5 0 0 5 0 0 0 0 0 0 0 0 0 0
50 0 4 0 0 0 0 0 0 0 0 0 12 9 0 0 0
52 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0
53 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0
54 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0
55 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 0
56 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0
57 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0
59 0 0 16 4 0 0 0 0 0 0 0 0 0 0 0 0
60 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0
61 0 0 0 0 8 0 0 0 0 0 0 0 0 0 0 0
62 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0
65 0 0 0 0 2 0 0 0 0 0 7 0 0 0 0 0
68 0 0 0 0 13 0 0 7 0 0 0 0 0 0 0 0
70 0 0 0 0 10 0 0 14 0 0 19 0 0 0 0 0
72 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0
79 0 0 0 0 0 0 0 0 21 0 0 0 0 0 0 0
80 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0
83 0 0 0 0 18 0 0 0 0 0 0 0 0 0 0 0
84 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0
90 0 0 0 0 0 9 0 0 0 0 0 0 0 0 0 0
92 0 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0
>
write.table(LFA34.9916, file=paste("rec.LFA34 9916.Noremovals.from.datacheck.9916",Sys.Date(),".txt"), row.names=FALSE, col.names=TRUE, sep=" ")
#CPUE PREP FILE
##DAILY AGGREGATE FOR CPUE ANALYSIS:
#SOAK DAY CONSTRAINT:
sd=which(LFA34.9916$SOAK_DAYS > 5)
length(sd) #22,598 RECORDS
LFA34.9916.sd=LFA34.9916[-sd,]
short.soak.days=which(LFA34.9916.sd$SOAK_DAYS < 1)
length(short.soak.days) #247 RECORDS
LFA34.9916.sd=LFA34.9916.sd[-short.soak.days,]
##CALCULATE TRAP # PER DAY
LFA34.9913.traps = compute.unique.lengths( x=LFA34.9913.sd, var="TRAP_NO", index=c("S_LABEL", "VESSEL_CD", "HAUL_DATE") )
LFA34.9913.traps = na.omit (LFA34.9913.traps)
LFA34.9913.traps = rename.df(LFA34.9913.traps,"Freq", "TOT_TRAPS")
summary(LFA34.9913.traps)
str(LFA34.9913.traps) #24,819 RECORDS
#SHOWS NUMBER OF RECORDS WITH TRAP NUMBER DISTRIBUTION PER VESSEL
table(LFA34.9913.traps$TOT_TRAPS,LFA34.9913.traps$VESSEL_CD)
##SIZE CLASS ADJUSTMENT TO SPLIT THE SHORTS AND LEGAL SIZES IN CLASS 10
table(LFA34.9916.sd$SIZE_CD,LFA34.9916.sd$SHORT)
i1= which (LFA34.9913.sd$SIZE_CD==10 & LFA34.9913.sd$SHORT==1)
LFA34.9913.sd[i1,"SIZE_CD"]=10.1
summary(LFA34.9913.sd[i1,])
i2= which (LFA34.9913.sd$SIZE_CD==10 & LFA34.9913.sd$SHORT==0)
LFA34.9913.sd[i2,"SIZE_CD"]=10.2
summary(LFA34.9913.sd[i2,])
str(LFA34.9913.sd)
##REMOVE RECORDS FOR BERRIED BY INCLUDING IN SEX COLUMN - FOR CPUE ANALYSIS
b= which (LFA34.9913.sd$SEX==3)
length (b) #1631 RECORDS
LFA34.9913.sd.noberried=LFA34.9913.sd[-b,]
str(LFA34.9913.sd.noberried)
##CALCULATE TOTAL COUNT PER SIZE CLASS
LFA34.9913.sd.noberried$VESSEL_CD <- as.factor(LFA34.9913.sd.noberried$VESSEL_CD)
LFA34.9913.sd.noberried$SIZE_CD <- as.factor(LFA34.9913.sd.noberried$SIZE_CD)
LFA34.9913.counts.at.size =aggregate(LFA34.9913.sd.noberried[,1], by=as.list(LFA34.9913.sd.noberried[c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "SIZE_CD")]), length, simplify = TRUE)
LFA34.9913.counts.at.size = na.omit (LFA34.9913.counts.at.size)
library(gdata)
LFA34.9913.counts.at.size <- rename.vars(LFA34.9913.counts.at.size, from="x", to="Freq")
summary(LFA34.9913.counts.at.size)
str(LFA34.9913.counts.at.size) #104,705 RECORDS
unique(LFA34.9913.counts.at.size$SIZE_CD) #SIZE 0-16; NO NA VALUES
##SIZE CLASS FREQUENCY TABLE
LFA34.cpue.size = merge(LFA34.9913.traps,LFA34.9913.counts.at.size, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE"),all.x=T,all.y=F, sort=F)
LFA34.0=which(LFA34.cpue.size$SIZE_CD=='0')
LFA34.size0=LFA34.cpue.size[LFA34.0,]
LFA34.size0 = rename.df(LFA34.size0,"Freq", "size0")
LFA34.size0$SIZE_CD=NULL
LFA34.2=which(LFA34.cpue.size$SIZE_CD=='2')
LFA34.size2=LFA34.cpue.size[LFA34.2,]
LFA34.size2 = rename.df(LFA34.size2, "Freq", "size2")
LFA34.size2$SIZE_CD=NULL
LFA34.0.2 = merge(LFA34.size0,LFA34.size2, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA34.3=which(LFA34.cpue.size$SIZE_CD=='3')
LFA34.size3=LFA34.cpue.size[LFA34.3,]
LFA34.size3 = rename.df(LFA34.size3, "Freq", "size3")
LFA34.size3$SIZE_CD=NULL
LFA34.0.3 = merge(LFA34.0.2,LFA34.size3, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA34.4=which(LFA34.cpue.size$SIZE_CD=='4')
LFA34.size4=LFA34.cpue.size[LFA34.4,]
LFA34.size4 = rename.df(LFA34.size4, "Freq", "size4")
LFA34.size4$SIZE_CD=NULL
LFA34.0.4 = merge(LFA34.0.3,LFA34.size4, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA34.5=which(LFA34.cpue.size$SIZE_CD=='5')
LFA34.size5=LFA34.cpue.size[LFA34.5,]
LFA34.size5 = rename.df(LFA34.size5, "Freq", "size5")
LFA34.size5$SIZE_CD=NULL
LFA34.0.5 = merge(LFA34.0.4,LFA34.size5, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA34.6=which(LFA34.cpue.size$SIZE_CD=='6')
LFA34.size6=LFA34.cpue.size[LFA34.6,]
LFA34.size6 = rename.df(LFA34.size6, "Freq", "size6")
LFA34.size6$SIZE_CD=NULL
LFA34.0.6 = merge(LFA34.0.5,LFA34.size6, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA34.7=which(LFA34.cpue.size$SIZE_CD=='7')
LFA34.size7=LFA34.cpue.size[LFA34.7,]
LFA34.size7 = rename.df(LFA34.size7, "Freq", "size7")
LFA34.size7$SIZE_CD=NULL
LFA34.0.7 = merge(LFA34.0.6,LFA34.size7, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA34.8=which(LFA34.cpue.size$SIZE_CD=='8')
LFA34.size8=LFA34.cpue.size[LFA34.8,]
LFA34.size8 = rename.df(LFA34.size8, "Freq", "size8")
LFA34.size8$SIZE_CD=NULL
LFA34.0.8 = merge(LFA34.0.7,LFA34.size8, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA34.9=which(LFA34.cpue.size$SIZE_CD=='9')
LFA34.size9=LFA34.cpue.size[LFA34.9,]
LFA34.size9 = rename.df(LFA34.size9, "Freq", "size9")
LFA34.size9$SIZE_CD=NULL
LFA34.0.9 = merge(LFA34.0.8,LFA34.size9, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA34.10.1=which(LFA34.cpue.size$SIZE_CD=='10.1')
LFA34.size10.1=LFA34.cpue.size[LFA34.10.1,]
LFA34.size10.1 = rename.df(LFA34.size10.1, "Freq", "size10.1")
LFA34.size10.1$SIZE_CD=NULL
LFA34.0.10.1 = merge(LFA34.0.9,LFA34.size10.1, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA34.10.2=which(LFA34.cpue.size$SIZE_CD=='10.2')
LFA34.size10.2=LFA34.cpue.size[LFA34.10.2,]
LFA34.size10.2 = rename.df(LFA34.size10.2, "Freq", "size10.2")
LFA34.size10.2$SIZE_CD=NULL
LFA34.0.10.2 = merge(LFA34.0.10.1,LFA34.size10.2, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA34.11=which(LFA34.cpue.size$SIZE_CD=='11')
LFA34.size11=LFA34.cpue.size[LFA34.11,]
LFA34.size11 = rename.df(LFA34.size11, "Freq", "size11")
LFA34.size11$SIZE_CD=NULL
LFA34.0.11 = merge(LFA34.0.10.2,LFA34.size11, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA34.12=which(LFA34.cpue.size$SIZE_CD=='12')
LFA34.size12=LFA34.cpue.size[LFA34.12,]
LFA34.size12 = rename.df(LFA34.size12, "Freq", "size12")
LFA34.size12$SIZE_CD=NULL
LFA34.0.12 = merge(LFA34.0.11,LFA34.size12, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA34.13=which(LFA34.cpue.size$SIZE_CD=='13')
LFA34.size13=LFA34.cpue.size[LFA34.13,]
LFA34.size13 = rename.df(LFA34.size13, "Freq", "size13")
LFA34.size13$SIZE_CD=NULL
LFA34.0.13 = merge(LFA34.0.12,LFA34.size13, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA34.14=which(LFA34.cpue.size$SIZE_CD=='14')
LFA34.size14=LFA34.cpue.size[LFA34.14,]
LFA34.size14 = rename.df(LFA34.size14, "Freq", "size14")
LFA34.size14$SIZE_CD=NULL
LFA34.0.14 = merge(LFA34.0.13,LFA34.size14, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA34.15=which(LFA34.cpue.size$SIZE_CD=='15')
LFA34.size15=LFA34.cpue.size[LFA34.15,]
LFA34.size15 = rename.df(LFA34.size15, "Freq", "size15")
LFA34.size15$SIZE_CD=NULL
LFA34.0.15 = merge(LFA34.0.14,LFA34.size15, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA34.16=which(LFA34.cpue.size$SIZE_CD=='16')
LFA34.size16=LFA34.cpue.size[LFA34.16,]
LFA34.size16 = rename.df(LFA34.size16, "Freq", "size16")
LFA34.size16$SIZE_CD=NULL
LFA34.0.16 = merge(LFA34.0.15,LFA34.size16, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA34.0.16[is.na(LFA34.0.16)]=0
summary(LFA34.0.16)
##SIZE CLASS SPECS FOR UNDERSIZED LOBSTERS FROM 1999-2013
LFA34.0.16$shorts=NA
LFA34.0.16$shorts=LFA34.0.16$size0+LFA34.0.16$size2+LFA34.0.16$size3+LFA34.0.16$size4+LFA34.0.16$size5+LFA34.0.16$size6+
LFA34.0.16$size7+LFA34.0.16$size8+LFA34.0.16$size9+LFA34.0.16$size10.1
##SIZE CLASS SPECS FOR LEGAL LOBSTERS FROM 1999-2013
LFA34.0.16$legals=NA
LFA34.0.16$legals=LFA34.0.16$size10.2+LFA34.0.16$size11+LFA34.0.16$size12+LFA34.0.16$size13+
LFA34.0.16$size14+LFA34.0.16$size15+LFA34.0.16$size16
summary(LFA34.0.16)
#Max shorts = 146; Max legals = 35
write.table(LFA34.0.16, file=paste("rec.LFA34.9913.SD1to5.nober.",Sys.Date(),".txt"), row.names=TRUE, col.names=TRUE, sep=" ")
#------------------------------------------LFA35-------------------------------
##LFA 35
LFA35.9916=which(fsrs$LFA==35)
length(LFA35.9916) #58,406 RECORDS MAY_2014
LFA35.9916=fsrs[LFA35.9916,]
summary(LFA35.9916)
##EMPTY TRAPS
e=which(LFA35.9913$LOBSTER_NO==0)
length(e) #505 RECORDS
##VALIDATE SOAK DAYS:
LFA35.9916$S_LABEL<-as.character(LFA35.9916$S_LABEL)
> table(LFA35.9916$SOAK_DAYS,LFA35.9916$S_LABEL)
2007 2008 2009 2010 2011 2012 2013
1 1262 413 1438 886 1061 1916 1974
2 1480 1021 2390 1691 3237 2749 1862
3 661 355 3117 2878 2267 2804 1527
4 420 76 1435 1874 1290 1872 853
5 250 57 1233 974 1361 789 832
6 139 71 496 509 569 467 284
7 9 0 696 444 436 416 270
8 0 0 78 132 234 189 228
9 22 0 29 160 256 124 165
10 80 6 168 49 91 119 21
11 7 0 0 51 12 18 8
12 0 0 0 36 58 25 0
13 0 0 0 0 0 29 0
14 0 23 79 0 23 0 7
15 0 0 25 22 0 0 20
16 0 0 0 0 29 38 0
17 12 0 0 0 0 0 0
18 0 0 0 0 9 0 0
19 0 0 0 36 0 0 0
30 0 0 0 0 0 0 13
36 0 0 16 0 0 0 0
>
write.table(LFA35.9913f, file=paste("rec.LFA35 9913.Noremovals.from.datacheck.9913",Sys.Date(),".txt"), row.names=FALSE, col.names=TRUE, sep=" ")
#CPUE PREP FILE
#DAILY AGGREGATE FOR CPUE ANALYSIS
#SOAK DAY CONSTRAINT:
sd=which(LFA35.9913$SOAK_DAYS > 5)
length(sd) # 7584 RECORDS
LFA35.9913.sd=LFA35.9913[-sd,]
##CALCULATE TRAP # PER DAY
LFA35.9913.traps = compute.unique.lengths( x=LFA35.9913.sd, var="TRAP_NO", index=c("S_LABEL", "VESSEL_CD", "HAUL_DATE") )
LFA35.9913.traps = na.omit (LFA35.9913.traps)
LFA35.9913.traps = rename.df(LFA35.9913.traps,"Freq", "TOT_TRAPS")
summary(LFA35.9913.traps)
str(LFA35.9913.traps) # 1960 RECORDS
#SHOWS NUMBER OF RECORDS WITH TRAP NUMBER DISTRIBUTION PER VESSEL
table(LFA35.9913.traps$TOT_TRAPS,LFA35.9913.traps$VESSEL_CD)
##SIZE CLASS ADJUSTMENT TO SPLIT THE SHORTS AND LEGAL SIZES IN CLASS 10
table(LFA35.9913.sd$SIZE_CD,LFA35.9913.sd$SHORT)
j1= which (LFA35.9913.sd$SIZE_CD==10 & LFA35.9913.sd$SHORT==1)
LFA35.9913.sd[j1,"SIZE_CD"]=10.1
summary(LFA35.9913.sd[j1,])
j2= which (LFA35.9913.sd$SIZE_CD==10 & LFA35.9913.sd$SHORT==0)
LFA35.9913.sd[j2,"SIZE_CD"]=10.2
summary(LFA35.9913.sd[j2,])
str(LFA35.9913.sd)
##REMOVE RECORDS FOR BERRIED BY INCLUDING IN SEX COLUMN - FOR CPUE ANALYSIS
b= which (LFA35.9913.sd$SEX==3)
length (b) #521 RECORDS
LFA35.9913.sd.noberried=LFA35.9913.sd[-b,]
str(LFA35.9913.sd.noberried)
##CALCULATE TOTAL COUNT PER SIZE CLASS
LFA35.9913.sd.noberried$VESSEL_CD <- as.factor(LFA35.9913.sd.noberried$VESSEL_CD)
LFA35.9913.sd.noberried$SIZE_CD <- as.factor(LFA35.9913.sd.noberried$SIZE_CD)
LFA35.9913.counts.at.size =aggregate(LFA35.9913.sd.noberried[,1], by=as.list(LFA35.9913.sd.noberried[c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "SIZE_CD")]), length, simplify = TRUE)
LFA35.9913.counts.at.size = na.omit (LFA35.9913.counts.at.size)
library(gdata)
LFA35.9913.counts.at.size <- rename.vars(LFA35.9913.counts.at.size, from="x", to="Freq")
summary(LFA35.9913.counts.at.size)
str(LFA35.9913.counts.at.size) #12,982 RECORDS
unique(LFA35.9913.counts.at.size$SIZE_CD) #SIZE 2-16; NO NA VALUES
##SIZE CLASS FREQUENCY TABLE
LFA35.cpue.size = merge(LFA35.9913.traps,LFA35.9913.counts.at.size, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE"),all.x=T,all.y=F, sort=F)
LFA35.2=which(LFA35.cpue.size$SIZE_CD=='2')
LFA35.size2=LFA35.cpue.size[LFA35.2,]
LFA35.size2 = rename.df(LFA35.size2, "Freq", "size2")
LFA35.size2$SIZE_CD=NULL
LFA35.3=which(LFA35.cpue.size$SIZE_CD=='3')
LFA35.size3=LFA35.cpue.size[LFA35.3,]
LFA35.size3 = rename.df(LFA35.size3, "Freq", "size3")
LFA35.size3$SIZE_CD=NULL
LFA35.2.3 = merge(LFA35.2,LFA35.size3, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA35.4=which(LFA35.cpue.size$SIZE_CD=='4')
LFA35.size4=LFA35.cpue.size[LFA35.4,]
LFA35.size4 = rename.df(LFA35.size4, "Freq", "size4")
LFA35.size4$SIZE_CD=NULL
LFA35.2.4 = merge(LFA35.2.3,LFA35.size4, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA35.5=which(LFA35.cpue.size$SIZE_CD=='5')
LFA35.size5=LFA35.cpue.size[LFA35.5,]
LFA35.size5 = rename.df(LFA35.size5, "Freq", "size5")
LFA35.size5$SIZE_CD=NULL
LFA35.2.5 = merge(LFA35.2.4,LFA35.size5, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA35.6=which(LFA35.cpue.size$SIZE_CD=='6')
LFA35.size6=LFA35.cpue.size[LFA35.6,]
LFA35.size6 = rename.df(LFA35.size6, "Freq", "size6")
LFA35.size6$SIZE_CD=NULL
LFA35.2.6 = merge(LFA35.2.5,LFA35.size6, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA35.7=which(LFA35.cpue.size$SIZE_CD=='7')
LFA35.size7=LFA35.cpue.size[LFA35.7,]
LFA35.size7 = rename.df(LFA35.size7, "Freq", "size7")
LFA35.size7$SIZE_CD=NULL
LFA35.2.7 = merge(LFA35.2.6,LFA35.size7, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA35.8=which(LFA35.cpue.size$SIZE_CD=='8')
LFA35.size8=LFA35.cpue.size[LFA35.8,]
LFA35.size8 = rename.df(LFA35.size8, "Freq", "size8")
LFA35.size8$SIZE_CD=NULL
LFA35.2.8 = merge(LFA35.2.7,LFA35.size8, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA35.9=which(LFA35.cpue.size$SIZE_CD=='9')
LFA35.size9=LFA35.cpue.size[LFA35.9,]
LFA35.size9 = rename.df(LFA35.size9, "Freq", "size9")
LFA35.size9$SIZE_CD=NULL
LFA35.2.9 = merge(LFA35.2.8,LFA35.size9, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA35.10.1=which(LFA35.cpue.size$SIZE_CD=='10.1')
LFA35.size10.1=LFA35.cpue.size[LFA35.10.1,]
LFA35.size10.1 = rename.df(LFA35.size10.1, "Freq", "size10.1")
LFA35.size10.1$SIZE_CD=NULL
LFA35.2.10.1 = merge(LFA35.2.9,LFA35.size10.1, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA35.10.2=which(LFA35.cpue.size$SIZE_CD=='10.2')
LFA35.size10.2=LFA35.cpue.size[LFA35.10.2,]
LFA35.size10.2 = rename.df(LFA35.size10.2, "Freq", "size10.2")
LFA35.size10.2$SIZE_CD=NULL
LFA35.2.10.2 = merge(LFA35.2.10.1,LFA35.size10.2, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA35.11=which(LFA35.cpue.size$SIZE_CD=='11')
LFA35.size11=LFA35.cpue.size[LFA35.11,]
LFA35.size11 = rename.df(LFA35.size11, "Freq", "size11")
LFA35.size11$SIZE_CD=NULL
LFA35.2.11 = merge(LFA35.2.10.2,LFA35.size11, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA35.12=which(LFA35.cpue.size$SIZE_CD=='12')
LFA35.size12=LFA35.cpue.size[LFA35.12,]
LFA35.size12 = rename.df(LFA35.size12, "Freq", "size12")
LFA35.size12$SIZE_CD=NULL
LFA35.2.12 = merge(LFA35.2.11,LFA35.size12, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA35.13=which(LFA35.cpue.size$SIZE_CD=='13')
LFA35.size13=LFA35.cpue.size[LFA35.13,]
LFA35.size13 = rename.df(LFA35.size13, "Freq", "size13")
LFA35.size13$SIZE_CD=NULL
LFA35.2.13 = merge(LFA35.2.12,LFA35.size13, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA35.14=which(LFA35.cpue.size$SIZE_CD=='14')
LFA35.size14=LFA35.cpue.size[LFA35.14,]
LFA35.size14 = rename.df(LFA35.size14, "Freq", "size14")
LFA35.size14$SIZE_CD=NULL
LFA35.2.14 = merge(LFA35.2.13,LFA35.size14, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA35.15=which(LFA35.cpue.size$SIZE_CD=='15')
LFA35.size15=LFA35.cpue.size[LFA35.15,]
LFA35.size15 = rename.df(LFA35.size15, "Freq", "size15")
LFA35.size15$SIZE_CD=NULL
LFA35.2.15 = merge(LFA35.2.14,LFA35.size15, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA35.16=which(LFA35.cpue.size$SIZE_CD=='16')
LFA35.size16=LFA35.cpue.size[LFA35.16,]
LFA35.size16 = rename.df(LFA35.size16, "Freq", "size16")
LFA35.size16$SIZE_CD=NULL
LFA35.2.16 = merge(LFA35.2.15,LFA35.size16, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA35.2.16[is.na(LFA35.2.16)]=0
summary(LFA35.2.16)
##SIZE CLASS SPECS FOR UNDERSIZED LOBSTERS FROM 1999-2013
LFA35.2.16$shorts=NA
LFA35.2.16$shorts=LFA35.2.16$size0+LFA35.2.16$size2+LFA35.2.16$size3+LFA35.2.16$size4+LFA35.2.16$size5+LFA35.2.16$size6+
LFA35.2.16$size7+LFA35.2.16$size8+LFA35.2.16$size9+LFA35.2.16$size10.1
##SIZE CLASS SPECS FOR LEGAL LOBSTERS FROM 1999-2013
LFA35.2.16$legals=NA
LFA35.2.16$legals=LFA35.2.16$size10.2+LFA35.2.16$size11+LFA35.2.16$size12+LFA35.2.16$size13+
LFA35.2.16$size14+LFA35.2.16$size15+LFA35.2.16$size16
summary(LFA35.2.16)
#Max shorts = 146; Max legals = 35
write.table(LFA35.2.16, file=paste("rec.LFA35.9913.SD1to5.nober.",Sys.Date(),".txt"), row.names=TRUE, col.names=TRUE, sep=" ")
LobsterScience/bio.lobster documentation built on Feb. 14, 2025, 3:28 p.m.
R Package Documentation
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require (chron)
require (lattice)
require (MASS)
require (doBy)
require (RODBC)
##Checks overwritten for 2017 data - uploaded in Jan 2018##
lobster.db("fsrs.redo")
lobster.db("fsrs")
str(fsrs) #1365712 Records for 2017
FSRS<-fsrs
##COLUMN ADDITIONS TO DATA FRAME ALLOWING DIFFERENT DATE FORMATS
fsrs$julian = as.integer(julian(fsrs$HAUL_DATE))
summary(fsrs)
##TIDY UP THE LFA SPECIFICATIONS
sort(unique(fsrs$LFA))
#CHECK SOAK DAYS BY COMPARING SAME VESSEL, SAME DAY THAT HAS DIFFERENT DEPTHS:
fsrs$Unique<-paste(fsrs$VESSEL_CD,as.character(fsrs$HAUL_DATE),sep = " ")
Depth.dif<-sapply(split(fsrs$DEPTH,fsrs$Unique),function(x){length(unique(x))}) #Should only be one record: LFA 34 - 1230 2001-11-30 (0.5 SD)
table(Depth.dif)
a<-names(Depth.dif)[which(Depth.dif==2)] #Should only be one record: LFA 34 - 1230 2001-11-30 (0.5 SD)
dups<-fsrs[which(fsrs$Unique %in% a),]
unique(dups$Unique)
library(xlsx)
write.xlsx(dups, file=paste("Duplicates",Sys.Date(),".xlsx"))
fsrs<-fsrs[,-29]
#----------------------------------------------------------------------------------------------------------------------------------------------------------------
## CREATION OF DATA FILES FOR EACH LFA:
#---------------------------------------------------------------------------LFA27--------------------------------------------------------------------------------
LFA27.9917=which(fsrs$LFA==27 & fsrs$HAUL_YEAR)
length(LFA27.9917) # 238,973 RECORDS 2016 259,917 for 2017
LFA27.9917=fsrs[LFA27.9917,]
unique(LFA27.9917$HAUL_YEAR)
summary(LFA27.9917)
##EMPTY TRAPS
e=which(LFA27.9917$LOBSTER_NO == 0)
length(e) #7917 records for 2016 and 8029 records for 2017
##VALIDATE SOAK DAYS:
table(LFA27.9917$SOAK_DAYS,LFA27.9917$HAUL_YEAR)
# 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017
#1 5878 5205 5353 4834 6369 7641 7661 10960 8494 9878 8010 8288 8421 7206 8230 8900 9732 9790 12952
#2 2844 2539 2944 2547 4066 3591 3689 5108 4577 5384 4854 5372 4336 3569 5009 5476 6917 6906 5844
#3 285 375 370 430 1004 734 843 687 483 789 1082 1082 635 475 863 1185 1936 1441 1615
#4 33 101 129 103 179 59 155 53 18 413 196 143 97 34 160 180 246 233 332
#5 84 9 32 68 27 29 0 82 0 0 92 0 112 89 106 75 31 90 116
#6 0 21 0 0 0 0 0 8 0 55 30 0 12 46 0 0 0 0 0
#7 0 30 0 0 0 0 4 0 0 0 0 0 0 15 0 0 0 0 85
#9 0 0 0 0 0 6 0 0 0 0 11 0 0 0 0 0 0 0 0
write.table(LFA27.9917, file=paste('rec.LFA27 9917.Noremovals.from.datacheck.9917.',Sys.Date(),'.txt'), row.names=FALSE, col.names=TRUE, sep=" ")
#SOAK DAY REMOVALS (FOR MODELING):
#LFA 27 SOAK DAYS ARE MOSTLY WITHN 1 TO 5 DAYS
sd=which(LFA27.9917$SOAK_DAYS > 5)
length(sd) #289 RECORDS ( I'm getting 238 records for 2016 and 323 for 2017)
LFA27.9917.sd=LFA27.9917[-sd,]
##CALCULATE TRAP # PER DAY
LFA27.9917.traps<-aggregate(TRAP_NO~HAUL_YEAR+VESSEL_CD+HAUL_DATE, data=LFA27.9917.sd, FUN=function(x) length(unique(x)))
#LFA27.9917.traps<-ddply(LFA27.9917.sd,c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE"),summarize,TOT_TRAPS=length(unique(TRAP_NO)))
str(LFA27.9917.traps) # 19446 for 2017
##SIZE ADJUSTMENTS for MLS CHANGE IN 1999-2002
table(LFA27.9917$SIZE_CD,LFA27.9917$SHORT)
a1= which (LFA27.9917$SIZE_CD==8 & LFA27.9917$SHORT==1)
LFA27.9917[a1,"SIZE_CD"]=8.1
summary(LFA27.9917[a1,])
a2= which (LFA27.9917$SIZE_CD==8 & LFA27.9917$SHORT==0)
LFA27.9917[a2,"SIZE_CD"]=8.2
summary(LFA27.9917[a2,])
summary(LFA27.9917)
str(LFA27.9917)
a3= which (LFA27.9917$SIZE_CD==9 & LFA27.9917$SHORT==1)
LFA27.9917[a3,"SIZE_CD"]=9.1
summary(LFA27.9917[a3,])
a4= which (LFA27.9917$SIZE_CD==9 & LFA27.9917$SHORT==0)
LFA27.9917[a4,"SIZE_CD"]=9.2
summary(LFA27.9917[a4,])
summary(LFA27.9917)
str(LFA27.9917)
a5= which (LFA27.9917$SIZE_CD==10 & LFA27.9917$SHORT==1)
LFA27.9917[a5,"SIZE_CD"]=10.1
summary(LFA27.9917[a5,])
a6= which (LFA27.9917$SIZE_CD==10 & LFA27.9917$SHORT==0)
LFA27.9917[a6,"SIZE_CD"]=10.2
summary(LFA27.9917[a6,])
summary(LFA27.9917)
str(LFA27.9917)
table(LFA27.9917$SIZE_CD,LFA27.9917$SHORT)
##CALCULATE TOTAL COUNT OF BERRIED PER DAY PER SIZE
b= which (LFA27.9917$SEX==3)
length (b) #24,765 RECORDS JAN.2016 SQL EXPORT
rec.LFA27.ber.fem <- LFA27.9917[b,]
rec.LFA27.ber.fem =aggregate(rec.LFA27.ber.fem[,1], by=as.list(rec.LFA27.ber.fem[c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE","SOAK_DAYS", "SIZE_CD")]), length, simplify = TRUE)
rec.LFA27.ber.fem = na.omit (rec.LFA27.ber.fem)
library(gdata)
rec.LFA27.ber.fem <- rename.vars(rec.LFA27.ber.fem, from="x", to="Freq")
summary(rec.LFA27.ber.fem)
str(rec.LFA27.ber.fem) #17,790 RECORDS
##MERGE TOTAL TRAPS INFO WITH BERRIED FEMALE SIZE COUNTS PER DAY
rec.LFA27.berfem.cpue.size = merge(LFA27.9917.traps,rec.LFA27.ber.fem, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE"),all.x=T,all.y=F, sort=F)
rec.LFA27.berfem.cpue.size = na.omit (rec.LFA27.berfem.cpue.size)
str(rec.LFA27.berfem.cpue.size) #17,770 RECORDS JAN_2016
summary(rec.LFA27.berfem.cpue.size)
write.table(rec.LFA27.berfem.cpue.size, file="rec.LFA27.berfem.9916.JAN.2016_1to5_1.txt", row.names=FALSE, col.names=TRUE, sep=" ")
##REMOVE RECORDS FOR BERRIED BY INCLUDING IN SEX COLUMN - FOR CPUE ANALYSIS
LFA27.9917=LFA27.9917[-b,]
str(LFA27.9917)
##CALCULATE TOTAL COUNT PER SIZE CLASS
LFA27.9917.counts.at.size =aggregate(LFA27.9917[,1], by=as.list(LFA27.9917[c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "SIZE_CD")]), length, simplify = TRUE)
LFA27.9917.counts.at.size = na.omit (LFA27.9917.counts.at.size)
library(gdata)
LFA27.9917.counts.at.size <- rename.vars(LFA27.9917.counts.at.size, from="x", to="Freq")
summary(LFA27.9917.counts.at.size)
str(LFA27.9917.counts.at.size) #76,121 RECORDS
unique(LFA27.9917.counts.at.size$SIZE_CD) #SIZE 0-16; NO NA VALUES
##SIZE CLASS FREQUENCY TABLE
LFA27.cpue.size = merge(LFA27.9917.traps,LFA27.9917.counts.at.size, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE"),all.x=T,all.y=F, sort=F)
LFA27.0=which(LFA27.cpue.size$SIZE_CD=='0')
LFA27.size0=LFA27.cpue.size[LFA27.0,]
LFA27.size0 = rename.df(LFA27.size0,"Freq", "size0")
LFA27.size0$SIZE_CD=NULL
LFA27.2=which(LFA27.cpue.size$SIZE_CD=='2')
LFA27.size2=LFA27.cpue.size[LFA27.2,]
LFA27.size2 = rename.df(LFA27.size2, "Freq", "size2")
LFA27.size2$SIZE_CD=NULL
LFA27.0.2 = merge(LFA27.size0,LFA27.size2, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.3=which(LFA27.cpue.size$SIZE_CD=='3')
LFA27.size3=LFA27.cpue.size[LFA27.3,]
LFA27.size3 = rename.df(LFA27.size3, "Freq", "size3")
LFA27.size3$SIZE_CD=NULL
LFA27.0.3 = merge(LFA27.0.2,LFA27.size3, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.4=which(LFA27.cpue.size$SIZE_CD=='4')
LFA27.size4=LFA27.cpue.size[LFA27.4,]
LFA27.size4 = rename.df(LFA27.size4, "Freq", "size4")
LFA27.size4$SIZE_CD=NULL
LFA27.0.4 = merge(LFA27.0.3,LFA27.size4, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.5=which(LFA27.cpue.size$SIZE_CD=='5')
LFA27.size5=LFA27.cpue.size[LFA27.5,]
LFA27.size5 = rename.df(LFA27.size5, "Freq", "size5")
LFA27.size5$SIZE_CD=NULL
LFA27.0.5 = merge(LFA27.0.4,LFA27.size5, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.6=which(LFA27.cpue.size$SIZE_CD=='6')
LFA27.size6=LFA27.cpue.size[LFA27.6,]
LFA27.size6 = rename.df(LFA27.size6, "Freq", "size6")
LFA27.size6$SIZE_CD=NULL
LFA27.0.6 = merge(LFA27.0.5,LFA27.size6, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.7=which(LFA27.cpue.size$SIZE_CD=='7')
LFA27.size7=LFA27.cpue.size[LFA27.7,]
LFA27.size7 = rename.df(LFA27.size7, "Freq", "size7")
LFA27.size7$SIZE_CD=NULL
LFA27.0.7 = merge(LFA27.0.6,LFA27.size7, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.8.1=which(LFA27.cpue.size$SIZE_CD=='8.1')
LFA27.size8.1=LFA27.cpue.size[LFA27.8.1,]
LFA27.size8.1 = rename.df(LFA27.size8.1, "Freq", "size8.1")
LFA27.size8.1$SIZE_CD=NULL
LFA27.0.8.1 = merge(LFA27.0.7,LFA27.size8.1, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.8.2=which(LFA27.cpue.size$SIZE_CD=='8.2')
LFA27.size8.2=LFA27.cpue.size[LFA27.8.2,]
LFA27.size8.2 = rename.df(LFA27.size8.2, "Freq", "size8.2")
LFA27.size8.2$SIZE_CD=NULL
LFA27.0.8.2 = merge(LFA27.0.8.1,LFA27.size8.2, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.9.1=which(LFA27.cpue.size$SIZE_CD=='9.1')
LFA27.size9.1=LFA27.cpue.size[LFA27.9.1,]
LFA27.size9.1 = rename.df(LFA27.size9.1, "Freq", "size9.1")
LFA27.size9.1$SIZE_CD=NULL
LFA27.0.9.1 = merge(LFA27.0.8.2,LFA27.size9.1, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.9.2=which(LFA27.cpue.size$SIZE_CD=='9.2')
LFA27.size9.2=LFA27.cpue.size[LFA27.9.2,]
LFA27.size9.2 = rename.df(LFA27.size9.2, "Freq", "size9.2")
LFA27.size9.2$SIZE_CD=NULL
LFA27.0.9.2 = merge(LFA27.0.9.1,LFA27.size9.2, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.10.1=which(LFA27.cpue.size$SIZE_CD=='10.1')
LFA27.size10.1=LFA27.cpue.size[LFA27.10.1,]
LFA27.size10.1 = rename.df(LFA27.size10.1, "Freq", "size10.1")
LFA27.size10.1$SIZE_CD=NULL
LFA27.0.10.1 = merge(LFA27.0.9.2,LFA27.size10.1, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.10.2=which(LFA27.cpue.size$SIZE_CD=='10.2')
LFA27.size10.2=LFA27.cpue.size[LFA27.10.2,]
LFA27.size10.2 = rename.df(LFA27.size10.2, "Freq", "size10.2")
LFA27.size10.2$SIZE_CD=NULL
LFA27.0.10.2 = merge(LFA27.0.10.1,LFA27.size10.2, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.11=which(LFA27.cpue.size$SIZE_CD=='11')
LFA27.size11=LFA27.cpue.size[LFA27.11,]
LFA27.size11 = rename.df(LFA27.size11, "Freq", "size11")
LFA27.size11$SIZE_CD=NULL
LFA27.0.11 = merge(LFA27.0.10.2,LFA27.size11, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.12=which(LFA27.cpue.size$SIZE_CD=='12')
LFA27.size12=LFA27.cpue.size[LFA27.12,]
LFA27.size12 = rename.df(LFA27.size12, "Freq", "size12")
LFA27.size12$SIZE_CD=NULL
LFA27.0.12 = merge(LFA27.0.11,LFA27.size12, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.13=which(LFA27.cpue.size$SIZE_CD=='13')
LFA27.size13=LFA27.cpue.size[LFA27.13,]
LFA27.size13 = rename.df(LFA27.size13, "Freq", "size13")
LFA27.size13$SIZE_CD=NULL
LFA27.0.13 = merge(LFA27.0.12,LFA27.size13, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.14=which(LFA27.cpue.size$SIZE_CD=='14')
LFA27.size14=LFA27.cpue.size[LFA27.14,]
LFA27.size14 = rename.df(LFA27.size14, "Freq", "size14")
LFA27.size14$SIZE_CD=NULL
LFA27.0.14 = merge(LFA27.0.13,LFA27.size14, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.15=which(LFA27.cpue.size$SIZE_CD=='15')
LFA27.size15=LFA27.cpue.size[LFA27.15,]
LFA27.size15 = rename.df(LFA27.size15, "Freq", "size15")
LFA27.size15$SIZE_CD=NULL
LFA27.0.15 = merge(LFA27.0.14,LFA27.size15, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.16=which(LFA27.cpue.size$SIZE_CD=='16')
LFA27.size16=LFA27.cpue.size[LFA27.16,]
LFA27.size16 = rename.df(LFA27.size16, "Freq", "size16")
LFA27.size16$SIZE_CD=NULL
LFA27.0.16 = merge(LFA27.0.15,LFA27.size16, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA27.0.16[is.na(LFA27.0.16)]=0
summary(LFA27.0.16)
##SIZE CLASS SPECS FOR all LOBSTERS FROM 1999-2014
LFA27.0.16$shorts=NA
LFA27.0.16$shorts=LFA27.0.16$size0+LFA27.0.16$size2+LFA27.0.16$size3+LFA27.0.16$size4+LFA27.0.16$size5+LFA27.0.16$size6+
LFA27.0.16$size7+LFA27.0.16$size8.1+LFA27.0.16$size9.1 + LFA27.0.16$size10.1
LFA27.0.16$legals=NA
LFA27.0.16$legals=LFA27.0.16$size8.2+LFA27.0.16$size9.2+LFA27.0.16$size10.2+LFA27.0.16$size11+LFA27.0.16$size12+LFA27.0.16$size13+
LFA27.0.16$size14+LFA27.0.16$size15+LFA27.0.16$size16
summary(LFA27.0.16)
#Max shorts = 78; Max legals = 29
write.table(LFA27.0.16, file=paste("rec.LFA27.9917.SD1to5.nober.",Sys.Date(),".txt"), row.names=TRUE, col.names=TRUE, sep=" ")
#--------------------------------LFA28---------------------------------------
##LFA 28 - NO PARTICIPATION SINCE 2013
LFA28.9913=which(fsrs$LFA==28)
length(LFA28.9913) #7198 JAN_2018
LFA28.9913=fsrs[LFA28.9913,]
unique(LFA28.9913$HAUL_YEAR)
summary(LFA28.9913)
##EMPTY TRAPS
e=which(LFA28.9913$LOBSTER_NO==0)
length(e) #558 Jan 2018
##VALIDATE SOAK DAYS:
table(LFA28.9913$SOAK_DAYS, LFA28.9913$HAUL_YEAR)
# 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013
#1 64 208 22 209 125 73 0 30 499 65 433 379 47
#2 298 503 459 289 413 492 127 202 299 153 70 136 279
#3 115 108 96 93 96 181 117 96 0 123 71 0 5
#4 60 0 46 13 15 0 0 26 0 0 20 0 0
#5 5 0 0 0 0 0 18 0 0 20 0 0 0
>
write.table(LFA28.9913, file=paste("rec.LFA28 9913.Noremovals.from.datacheck.9913",Sys.Date(),".txt"), row.names=FALSE, col.names=TRUE, sep=" ")
#CPUE PREP FILE:
##DAILY AGGREGATE FOR CPUE ANALYSIS:
#SOAK DAY CONSTRAINT:
#FOR THIS LFA SOAK DAYS ARE ALL BETWEEN 1 AND 5
##CALCULATE TRAP # PER DAY
LFA28.9913.traps = compute.unique.lengths(x=LFA28.9913, var="TRAP_NO", index=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE"))
LFA28.9913.traps = na.omit (LFA28.9913.traps)
LFA28.9913.traps = rename.df(LFA28.9913.traps,"Freq", "TOT_TRAPS")
summary(LFA28.9913.traps)
str(LFA28.9913.traps) #573 MAY_2014
#SHOWS NUMBER OF RECORDS WITH TRAP NUMBER DISTRIBUTION PER VESSEL
table(LFA28.9913.traps$TOT_TRAPS,LFA28.9913.traps$VESSEL_CD)
##SIZE CLASS ADJUSTMENT TO SPLIT THE SHORTS AND LEGAL SIZES IN CLASS 10
table(LFA28.9917$SIZE_CD, LFA28.9916$SHORT)
b1= which (LFA28.9913$SIZE_CD==10 & LFA28.9913$SHORT==1)
LFA28.9913[b1,"SIZE_CD"]=10.1
summary(LFA28.9913[b1,])
b2= which (LFA28.9913$SIZE_CD==10 & LFA28.9913$SHORT==0)
LFA28.9913[b2,"SIZE_CD"]=10.2
summary(LFA28.9913[b2,])
table(LFA28.9916$SIZE_CD, LFA28.9916$SHORT)
##REMOVE RECORDS FOR BERRIED BY INCLUDING IN SEX COLUMN - FOR CPUE ANALYSIS
b= which (LFA28.9913$SEX==3)
length (b) #2319 MAY_2014
LFA28.9913.sd.noberried=LFA28.9913[-b,]
str(LFA28.9913.sd.noberried)
##CALCULATE TOTAL COUNT PER SIZE CLASS
LFA28.9913.sd.noberried$VESSEL_CD <- as.factor(LFA28.9913.sd.noberried$VESSEL_CD)
LFA28.9913.sd.noberried$SIZE_CD <- as.factor(LFA28.9913.sd.noberried$SIZE_CD)
LFA28.9913.counts.at.size =aggregate(LFA28.9913.sd.noberried[,1], by=as.list(LFA28.9913.sd.noberried[c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "SIZE_CD")]), length, simplify = TRUE)
LFA28.9913.counts.at.size = na.omit (LFA28.9913.counts.at.size)
library(gdata)
LFA28.9913.counts.at.size <- rename.vars(LFA28.9913.counts.at.size, from="x", to="Freq")
summary(LFA28.9913.counts.at.size)
str(LFA28.9913.counts.at.size) #MAY_2014 2403 RECORDS
unique(LFA28.9913.counts.at.size$SIZE_CD) #SIZE 0-16; NO NA VALUES
##SIZE CLASS FREQUENCY TABLE
LFA28.cpue.size = merge(LFA28.9913.traps,LFA28.9913.counts.at.size, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE"),all.x=T,all.y=F, sort=F)
LFA28.0=which(LFA28.cpue.size$SIZE_CD=='0')
LFA28.size0=LFA28.cpue.size[LFA28.0,]
LFA28.size0 = rename.df(LFA28.size0,"Freq", "size0")
LFA28.size0$SIZE_CD=NULL
LFA28.3=which(LFA28.cpue.size$SIZE_CD=='3')
LFA28.size3=LFA28.cpue.size[LFA28.3,]
LFA28.size3 = rename.df(LFA28.size3, "Freq", "size3")
LFA28.size3$SIZE_CD=NULL
LFA28.0.3 = merge(LFA28.size0,LFA28.size3, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA28.4=which(LFA28.cpue.size$SIZE_CD=='4')
LFA28.size4=LFA28.cpue.size[LFA28.4,]
LFA28.size4 = rename.df(LFA28.size4, "Freq", "size4")
LFA28.size4$SIZE_CD=NULL
LFA28.0.4 = merge(LFA28.0.3,LFA28.size4, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA28.5=which(LFA28.cpue.size$SIZE_CD=='5')
LFA28.size5=LFA28.cpue.size[LFA28.5,]
LFA28.size5 = rename.df(LFA28.size5, "Freq", "size5")
LFA28.size5$SIZE_CD=NULL
LFA28.0.5 = merge(LFA28.0.4,LFA28.size5, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA28.6=which(LFA28.cpue.size$SIZE_CD=='6')
LFA28.size6=LFA28.cpue.size[LFA28.6,]
LFA28.size6 = rename.df(LFA28.size6, "Freq", "size6")
LFA28.size6$SIZE_CD=NULL
LFA28.0.6 = merge(LFA28.0.5,LFA28.size6, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA28.7=which(LFA28.cpue.size$SIZE_CD=='7')
LFA28.size7=LFA28.cpue.size[LFA28.7,]
LFA28.size7 = rename.df(LFA28.size7, "Freq", "size7")
LFA28.size7$SIZE_CD=NULL
LFA28.0.7 = merge(LFA28.0.6,LFA28.size7, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA28.8=which(LFA28.cpue.size$SIZE_CD=='8')
LFA28.size8=LFA28.cpue.size[LFA28.8,]
LFA28.size8 = rename.df(LFA28.size8, "Freq", "size8")
LFA28.size8$SIZE_CD=NULL
LFA28.0.8 = merge(LFA28.0.7,LFA28.size8, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA28.9=which(LFA28.cpue.size$SIZE_CD=='9')
LFA28.size9=LFA28.cpue.size[LFA28.9,]
LFA28.size9 = rename.df(LFA28.size9, "Freq", "size9")
LFA28.size9$SIZE_CD=NULL
LFA28.0.9 = merge(LFA28.0.8,LFA28.size9, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA28.10.1=which(LFA28.cpue.size$SIZE_CD=='10.1')
LFA28.size10.1=LFA28.cpue.size[LFA28.10.1,]
LFA28.size10.1 = rename.df(LFA28.size10.1, "Freq", "size10.1")
LFA28.size10.1$SIZE_CD=NULL
LFA28.0.10.1 = merge(LFA28.0.9,LFA28.size10.1, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA28.10.2=which(LFA28.cpue.size$SIZE_CD=='10.2')
LFA28.size10.2=LFA28.cpue.size[LFA28.10.2,]
LFA28.size10.2 = rename.df(LFA28.size10.2, "Freq", "size10.2")
LFA28.size10.2$SIZE_CD=NULL
LFA28.0.10.2 = merge(LFA28.0.10.1,LFA28.size10.2, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA28.11=which(LFA28.cpue.size$SIZE_CD=='11')
LFA28.size11=LFA28.cpue.size[LFA28.11,]
LFA28.size11 = rename.df(LFA28.size11, "Freq", "size11")
LFA28.size11$SIZE_CD=NULL
LFA28.0.11 = merge(LFA28.0.10.2,LFA28.size11, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA28.12=which(LFA28.cpue.size$SIZE_CD=='12')
LFA28.size12=LFA28.cpue.size[LFA28.12,]
LFA28.size12 = rename.df(LFA28.size12, "Freq", "size12")
LFA28.size12$SIZE_CD=NULL
LFA28.0.12 = merge(LFA28.0.11,LFA28.size12, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA28.13=which(LFA28.cpue.size$SIZE_CD=='13')
LFA28.size13=LFA28.cpue.size[LFA28.13,]
LFA28.size13 = rename.df(LFA28.size13, "Freq", "size13")
LFA28.size13$SIZE_CD=NULL
LFA28.0.13 = merge(LFA28.0.12,LFA28.size13, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA28.14=which(LFA28.cpue.size$SIZE_CD=='14')
LFA28.size14=LFA28.cpue.size[LFA28.14,]
LFA28.size14 = rename.df(LFA28.size14, "Freq", "size14")
LFA28.size14$SIZE_CD=NULL
LFA28.0.14 = merge(LFA28.0.13,LFA28.size14, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA28.15=which(LFA28.cpue.size$SIZE_CD=='15')
LFA28.size15=LFA28.cpue.size[LFA28.15,]
LFA28.size15 = rename.df(LFA28.size15, "Freq", "size15")
LFA28.size15$SIZE_CD=NULL
LFA28.0.15 = merge(LFA28.0.14,LFA28.size15, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA28.16=which(LFA28.cpue.size$SIZE_CD=='16')
LFA28.size16=LFA28.cpue.size[LFA28.16,]
LFA28.size16 = rename.df(LFA28.size16, "Freq", "size16")
LFA28.size16$SIZE_CD=NULL
LFA28.0.16 = merge(LFA28.0.15,LFA28.size16, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA28.0.16[is.na(LFA28.0.16)]=0
summary(LFA28.0.16)
##SIZE CLASS SPECS FOR UNDERSIZED LOBSTERS FROM 1999-2013
LFA28.0.16$shorts=NA
LFA28.0.16$shorts=LFA28.0.16$size0+LFA28.0.16$size3+LFA28.0.16$size4+LFA28.0.16$size5+LFA28.0.16$size6+
LFA28.0.16$size7+LFA28.0.16$size8+LFA28.0.16$size9+LFA28.0.16$size10.1
##SIZE CLASS SPECS FOR LEGAL LOBSTERS FROM 2004-2011
LFA28.0.16$legals=NA
LFA28.0.16$legals=LFA28.0.16$size10.2+LFA28.0.16$size11+LFA28.0.16$size12+LFA28.0.16$size13+
LFA28.0.16$size14+LFA28.0.16$size15+LFA28.0.16$size16
summary(LFA28.0.16)
#Max shorts = 28; Max legals = 14
write.table(LFA28.0.16, file=paste("rec.LFA28.9913.SD1to5.nober.",Sys.Date(),".txt"), row.names=TRUE, col.names=TRUE, sep=" ")
#--------------------------------LFA29---------------------------------------
LFA29.9917=which(fsrs$LFA==29)
length(LFA29.9917) # 110608 RECORDS FOR 2017
LFA29.9917=fsrs[LFA29.9917,]
unique(LFA29.9917$HAUL_YEAR)
summary(LFA29.9917)
##EMPTY TRAPS
e=which(LFA29.9917$LOBSTER_NO==0)
length(e) #2178 RECORDS FOR 2017
##VALIDATE SOAK DAYS:
table(LFA29.9917$SOAK_DAYS,LFA29.9917$HAUL_YEAR)
# 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017
#1 88 414 483 461 902 1770 2911 7665 7851 8892 8232 6566 5892 6233 5838 6041 8342 8121 8956
#2 111 246 371 388 378 784 475 721 933 589 547 894 851 531 927 889 1146 924 1090
#3 12 50 20 50 158 81 91 8 76 148 195 125 60 0 94 105 44 36 260
#4 0 16 5 0 12 0 13 17 40 98 30 0 0 0 0 98 21 0 17
#5 0 0 0 0 0 0 0 0 76 15 0 0 0 0 0 0 0 0 60
#6 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#7 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
write.table(LFA29.9917, file=paste("rec.LFA29 9917.Noremovals.from.datacheck.9917",Sys.Date(),".txt"), row.names=FALSE, col.names=TRUE, sep=" ")
#CPUE PREP FILE:
#SOAK DAY CONSTRAINT:
sd=which(LFA29.9917$SOAK_DAYS > 5)
length(sd) #24 RECORDS
LFA29.9917.sd=LFA29.9917[-sd,]
##CALCULATE TRAP # PER DAY
#LFA29.9917.traps = compute.unique.lengths( x=LFA29.9917.sd, var="TRAP_NO", index=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE") )
#LFA29.9917.traps = na.omit (LFA29.9917.traps)
#LFA29.9917.traps = rename.df(LFA29.9917.traps,"Freq", "TOT_TRAPS")
LFA29.9917.traps<-aggregate(TRAP_NO~HAUL_YEAR+VESSEL_CD+HAUL_DATE, data=LFA29.9917.sd, FUN=function(x) length(unique(x)))
str(LFA29.9917.traps) # 5436 Records for 2017
summary(LFA29.9917.traps)
#SHOWS NUMBER OF RECORDS WITH TRAP NUMBER DISTRIBUTION PER VESSEL
table(LFA29.9917.traps$TOT_TRAPS,LFA29.9917.traps$VESSEL_CD)
##SIZE ADJUSTMENTS for MLS to 84 mm IN 1999-2013
table(LFA29.9916.sd$SIZE_CD,LFA29.9916.sd$SHORT)
c1= which (LFA29.9916.sd$SIZE_CD==10 & LFA29.9916.sd$SHORT==1)
LFA29.9916.sd[c1,"SIZE_CD"]=10.1
c2= which (LFA29.9916.sd$SIZE_CD==10 & LFA29.9916.sd$SHORT==0)
LFA29.9916.sd[c2,"SIZE_CD"]=10.2
summary(LFA29.9916.sd[c1,])
summary(LFA29.9916.sd[c2,])
##REMOVE RECORDS FOR BERRIED BY INCLUDING IN SEX COLUMN - FOR CPUE ANALYSIS
b= which (LFA29.9916.sd$SEX==3)
length (b) #12,563 RECORDS
LFA29.9916.sd.noberried=LFA29.9916.sd[-b,]
str(LFA29.9916.sd.noberried)
##FILE EDITS BEFORE FURTHER COMPUTING
LFA29.9913.sd.noberried$VESSEL_CD <- as.factor(LFA29.9913.sd.noberried$VESSEL_CD)
LFA29.9913.sd.noberried$SIZE_CD <- as.factor(LFA29.9913.sd.noberried$SIZE_CD)
##CALCULATE TOTAL COUNT PER SIZE CLASS
LFA29.9913.counts.at.size =aggregate(LFA29.9913.sd.noberried[,1], by=as.list(LFA29.9913.sd.noberried[c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "SIZE_CD")]), length, simplify = TRUE)
LFA29.9913.counts.at.size = na.omit (LFA29.9913.counts.at.size)
library(gdata)
LFA29.9913.counts.at.size <- rename.vars(LFA29.9913.counts.at.size, from="x", to="Freq")
summary(LFA29.9913.counts.at.size)
str(LFA29.9913.counts.at.size) #21,435 RECORDS MAY_2014
unique(LFA29.9913.counts.at.size$SIZE_CD) #SIZE 0-16; NO NA VALUES
##SIZE CLASS FREQUENCY TABLE
LFA29.cpue.size = merge(LFA29.9913.traps,LFA29.9913.counts.at.size, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE"),all.x=T,all.y=F, sort=F)
LFA29.0=which(LFA29.cpue.size$SIZE_CD=='0')
LFA29.size0=LFA29.cpue.size[LFA29.0,]
LFA29.size0 = rename.df(LFA29.size0,"Freq", "size0")
LFA29.size0$SIZE_CD=NULL
LFA29.2=which(LFA29.cpue.size$SIZE_CD=='2')
LFA29.size2=LFA29.cpue.size[LFA29.2,]
LFA29.size2 = rename.df(LFA29.size2, "Freq", "size2")
LFA29.size2$SIZE_CD=NULL
LFA29.0.2 = merge(LFA29.size0,LFA29.size2, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA29.3=which(LFA29.cpue.size$SIZE_CD=='3')
LFA29.size3=LFA29.cpue.size[LFA29.3,]
LFA29.size3 = rename.df(LFA29.size3, "Freq", "size3")
LFA29.size3$SIZE_CD=NULL
LFA29.0.3 = merge(LFA29.0.2,LFA29.size3, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA29.4=which(LFA29.cpue.size$SIZE_CD=='4')
LFA29.size4=LFA29.cpue.size[LFA29.4,]
LFA29.size4 = rename.df(LFA29.size4, "Freq", "size4")
LFA29.size4$SIZE_CD=NULL
LFA29.0.4 = merge(LFA29.0.3,LFA29.size4, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA29.5=which(LFA29.cpue.size$SIZE_CD=='5')
LFA29.size5=LFA29.cpue.size[LFA29.5,]
LFA29.size5 = rename.df(LFA29.size5, "Freq", "size5")
LFA29.size5$SIZE_CD=NULL
LFA29.0.5 = merge(LFA29.0.4,LFA29.size5, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA29.6=which(LFA29.cpue.size$SIZE_CD=='6')
LFA29.size6=LFA29.cpue.size[LFA29.6,]
LFA29.size6 = rename.df(LFA29.size6, "Freq", "size6")
LFA29.size6$SIZE_CD=NULL
LFA29.0.6 = merge(LFA29.0.5,LFA29.size6, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA29.7=which(LFA29.cpue.size$SIZE_CD=='7')
LFA29.size7=LFA29.cpue.size[LFA29.7,]
LFA29.size7 = rename.df(LFA29.size7, "Freq", "size7")
LFA29.size7$SIZE_CD=NULL
LFA29.0.7 = merge(LFA29.0.6,LFA29.size7, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA29.8=which(LFA29.cpue.size$SIZE_CD=='8')
LFA29.size8=LFA29.cpue.size[LFA29.8,]
LFA29.size8 = rename.df(LFA29.size8, "Freq", "size8")
LFA29.size8$SIZE_CD=NULL
LFA29.0.8 = merge(LFA29.0.7,LFA29.size8, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA29.9=which(LFA29.cpue.size$SIZE_CD=='9')
LFA29.size9=LFA29.cpue.size[LFA29.9,]
LFA29.size9 = rename.df(LFA29.size9, "Freq", "size9")
LFA29.size9$SIZE_CD=NULL
LFA29.0.9 = merge(LFA29.0.8,LFA29.size9, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA29.10.1=which(LFA29.cpue.size$SIZE_CD=='10.1')
LFA29.size10.1=LFA29.cpue.size[LFA29.10.1,]
LFA29.size10.1 = rename.df(LFA29.size10.1, "Freq", "size10.1")
LFA29.size10.1$SIZE_CD=NULL
LFA29.0.10.1 = merge(LFA29.0.9,LFA29.size10.1, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA29.10.2=which(LFA29.cpue.size$SIZE_CD=='10.2')
LFA29.size10.2=LFA29.cpue.size[LFA29.10.2,]
LFA29.size10.2 = rename.df(LFA29.size10.2, "Freq", "size10.2")
LFA29.size10.2$SIZE_CD=NULL
LFA29.0.10.2 = merge(LFA29.0.10.1,LFA29.size10.2, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA29.11=which(LFA29.cpue.size$SIZE_CD=='11')
LFA29.size11=LFA29.cpue.size[LFA29.11,]
LFA29.size11 = rename.df(LFA29.size11, "Freq", "size11")
LFA29.size11$SIZE_CD=NULL
LFA29.0.11 = merge(LFA29.0.10.2,LFA29.size11, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA29.12=which(LFA29.cpue.size$SIZE_CD=='12')
LFA29.size12=LFA29.cpue.size[LFA29.12,]
LFA29.size12 = rename.df(LFA29.size12, "Freq", "size12")
LFA29.size12$SIZE_CD=NULL
LFA29.0.12 = merge(LFA29.0.11,LFA29.size12, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA29.13=which(LFA29.cpue.size$SIZE_CD=='13')
LFA29.size13=LFA29.cpue.size[LFA29.13,]
LFA29.size13 = rename.df(LFA29.size13, "Freq", "size13")
LFA29.size13$SIZE_CD=NULL
LFA29.0.13 = merge(LFA29.0.12,LFA29.size13, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA29.14=which(LFA29.cpue.size$SIZE_CD=='14')
LFA29.size14=LFA29.cpue.size[LFA29.14,]
LFA29.size14 = rename.df(LFA29.size14, "Freq", "size14")
LFA29.size14$SIZE_CD=NULL
LFA29.0.14 = merge(LFA29.0.13,LFA29.size14, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA29.15=which(LFA29.cpue.size$SIZE_CD=='15')
LFA29.size15=LFA29.cpue.size[LFA29.15,]
LFA29.size15 = rename.df(LFA29.size15, "Freq", "size15")
LFA29.size15$SIZE_CD=NULL
LFA29.0.15 = merge(LFA29.0.14,LFA29.size15, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA29.16=which(LFA29.cpue.size$SIZE_CD=='16')
LFA29.size16=LFA29.cpue.size[LFA29.16,]
LFA29.size16 = rename.df(LFA29.size16, "Freq", "size16")
LFA29.size16$SIZE_CD=NULL
LFA29.0.16 = merge(LFA29.0.15,LFA29.size16, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA29.0.16[is.na(LFA29.0.16)]=0
summary(LFA29.0.16)
##SIZE CLASS SPECS FOR UNDERSIZED LOBSTERS FROM 1999-2013
LFA29.0.16$shorts=NA
LFA29.0.16$shorts=LFA29.0.16$size0+LFA29.0.16$size2+LFA29.0.16$size3+LFA29.0.16$size4+LFA29.0.16$size5+LFA29.0.16$size6+
LFA29.0.16$size7+LFA29.0.16$size8+LFA29.0.16$size9+LFA29.0.16$size10.1
##SIZE CLASS SPECS FOR LEGAL LOBSTERS FROM 1999-2013
LFA29.0.16$legals=NA
LFA29.0.16$legals=LFA29.0.16$size10.2+LFA29.0.16$size11+LFA29.0.16$size12+LFA29.0.16$size13+
LFA29.0.16$size14+LFA29.0.16$size15+LFA29.0.16$size16
summary(LFA29.0.16)
#Max shorts = 58; Max legals = 34
write.table(LFA29.0.16, file=paste("rec.LFA29.9913.SD1to5.nober.",Sys.Date(),".txt"), row.names=TRUE, col.names=TRUE, sep=" ")
#----------------------------------LFA30------------------------------------
#LFA 30
LFA30.9916=which(fsrs$LFA==30)
length(LFA30.9916) #70,574 JAN_2016
LFA30.9916=fsrs[LFA30.9916,]
unique(LFA30.9916$HAUL_YEAR)
summary(LFA30.9916)
##EMPTY TRAPS
e=which(LFA30.9916$LOBSTER_NO==0)
length(e) #1,310 RECORDS
##VALIDATE SOAK DAYS:
> table(LFA30.9916$SOAK_DAYS, LFA30.9916$HAUL_YEAR)
2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015
1 352 374 364 354 1030 1320 4538 5080 4444 5191 4839 4423 5029 4811 4869 5425
2 88 116 113 151 335 623 1345 1469 1426 1225 1309 1585 1161 1118 1258 1627
3 0 43 40 38 22 165 278 43 234 280 322 191 196 134 188 319
4 9 19 13 16 18 17 56 0 73 12 99 71 9 58 60 0
5 0 0 0 0 0 0 0 0 81 0 0 0 0 0 46 0
6 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0
7 0 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0
>
write.table(LFA30.9916, file=paste("rec.LFA30 9916.Noremovals.from.datacheck.9916",Sys.Date(),".txt"), row.names=FALSE, col.names=TRUE, sep=" ")
#CPUE PREP FILE:
##DAILY AGGREGATE FOR CPUE ANALYSIS
#SOAK DAY CONSTRAINT:
sd=which(LFA30.9916$SOAK_DAYS > 5)
length(sd) #32 RECORDS
LFA30.9916.sd=LFA30.9916[-sd,]
##CALCULATE TRAP # PER DAY
LFA30.9916.traps = ddply(LFA30.9916.sd,c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE"),summarize,TOT_TRAPS=length(unique(TRAP_NO)))
summary(LFA30.9916.traps)
str(LFA30.9916.traps) #3,721 RECORDS
#SHOWS NUMBER OF RECORDS WITH TRAP NUMBER DISTRIBUTION PER VESSEL
table(LFA30.9916.traps$TOT_TRAPS,LFA30.9916.traps$VESSEL_CD)
table(LFA30.9916.traps$HAUL_YEAR,LFA30.9916.traps$VESSEL_CD)
##SIZE CLASS ADJUSTMENT TO SPLIT THE SHORTS AND LEGAL SIZES IN CLASS 10
table(LFA30.9916.sd$SIZE_CD, LFA30.9916.sd$SHORT)
d1= which (LFA30.9916.sd$SIZE_CD==10 & LFA30.9916.sd$SHORT==1)
LFA30.9916.sd[d1,"SIZE_CD"]=10.1
summary(LFA30.9916.sd[d1,])
d2= which (LFA30.9916.sd$SIZE_CD==10 & LFA30.9916.sd$SHORT==0)
LFA30.9916.sd[d2,"SIZE_CD"]=10.2
summary(LFA30.9916.sd[d2,])
##REMOVE RECORDS FOR BERRIED BY INCLUDING IN SEX COLUMN - FOR CPUE ANALYSIS
b= which (LFA30.9916.sd$SEX==3)
length (b) #10,446 RECORDS
LFA30.9916.sd.noberried=LFA30.9916.sd[-b,]
str(LFA30.9916.sd.noberried)
##CALCULATE TOTAL COUNT PER SIZE CLASS
LFA30.9916.counts.at.size =aggregate(LFA30.9916.sd.noberried[,1], by=as.list(LFA30.9916.sd.noberried[c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "SIZE_CD")]), length, simplify = TRUE)
LFA30.9916.counts.at.size = na.omit (LFA30.9916.counts.at.size)
library(gdata)
LFA30.9916.counts.at.size <- rename.vars(LFA30.9916.counts.at.size, from="x", to="Freq")
summary(LFA30.9916.counts.at.size)
str(LFA30.9916.counts.at.size) #17,686 RECORDS
unique(LFA30.9916.counts.at.size$SIZE_CD) #SIZE 0-16; NO NA VALUES
##SIZE CLASS FREQUENCY TABLE
LFA30.cpue.size = merge(LFA30.9916.traps,LFA30.9916.counts.at.size, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE"),all.x=T,all.y=F, sort=F)
LFA30.0=which(LFA30.cpue.size$SIZE_CD=='0')
LFA30.size0=LFA30.cpue.size[LFA30.0,]
LFA30.size0 = rename.df(LFA30.size0,"Freq", "size0")
LFA30.size0$SIZE_CD=NULL
LFA30.2=which(LFA30.cpue.size$SIZE_CD=='2')
LFA30.size2=LFA30.cpue.size[LFA30.2,]
LFA30.size2 = rename.df(LFA30.size2,"Freq", "size2")
LFA30.size2$SIZE_CD=NULL
LFA30.0.2 = merge(LFA30.size0,LFA30.size2, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA30.3=which(LFA30.cpue.size$SIZE_CD=='3')
LFA30.size3=LFA30.cpue.size[LFA30.3,]
LFA30.size3 = rename.df(LFA30.size3, "Freq", "size3")
LFA30.size3$SIZE_CD=NULL
LFA30.0.3 = merge(LFA30.0.2,LFA30.size3, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA30.4=which(LFA30.cpue.size$SIZE_CD=='4')
LFA30.size4=LFA30.cpue.size[LFA30.4,]
LFA30.size4 = rename.df(LFA30.size4, "Freq", "size4")
LFA30.size4$SIZE_CD=NULL
LFA30.0.4 = merge(LFA30.0.3,LFA30.size4, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA30.5=which(LFA30.cpue.size$SIZE_CD=='5')
LFA30.size5=LFA30.cpue.size[LFA30.5,]
LFA30.size5 = rename.df(LFA30.size5, "Freq", "size5")
LFA30.size5$SIZE_CD=NULL
LFA30.0.5 = merge(LFA30.0.4,LFA30.size5, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA30.6=which(LFA30.cpue.size$SIZE_CD=='6')
LFA30.size6=LFA30.cpue.size[LFA30.6,]
LFA30.size6 = rename.df(LFA30.size6, "Freq", "size6")
LFA30.size6$SIZE_CD=NULL
LFA30.0.6 = merge(LFA30.0.5,LFA30.size6, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA30.7=which(LFA30.cpue.size$SIZE_CD=='7')
LFA30.size7=LFA30.cpue.size[LFA30.7,]
LFA30.size7 = rename.df(LFA30.size7, "Freq", "size7")
LFA30.size7$SIZE_CD=NULL
LFA30.0.7 = merge(LFA30.0.6,LFA30.size7, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA30.8=which(LFA30.cpue.size$SIZE_CD=='8')
LFA30.size8=LFA30.cpue.size[LFA30.8,]
LFA30.size8 = rename.df(LFA30.size8, "Freq", "size8")
LFA30.size8$SIZE_CD=NULL
LFA30.0.8 = merge(LFA30.0.7,LFA30.size8, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA30.9=which(LFA30.cpue.size$SIZE_CD=='9')
LFA30.size9=LFA30.cpue.size[LFA30.9,]
LFA30.size9 = rename.df(LFA30.size9, "Freq", "size9")
LFA30.size9$SIZE_CD=NULL
LFA30.0.9 = merge(LFA30.0.8,LFA30.size9, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA30.10.1=which(LFA30.cpue.size$SIZE_CD=='10.1')
LFA30.size10.1=LFA30.cpue.size[LFA30.10.1,]
LFA30.size10.1 = rename.df(LFA30.size10.1, "Freq", "size10.1")
LFA30.size10.1$SIZE_CD=NULL
LFA30.0.10.1 = merge(LFA30.0.9,LFA30.size10.1, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA30.10.2=which(LFA30.cpue.size$SIZE_CD=='10.2')
LFA30.size10.2=LFA30.cpue.size[LFA30.10.2,]
LFA30.size10.2 = rename.df(LFA30.size10.2, "Freq", "size10.2")
LFA30.size10.2$SIZE_CD=NULL
LFA30.0.10.2 = merge(LFA30.0.10.1,LFA30.size10.2, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA30.11=which(LFA30.cpue.size$SIZE_CD=='11')
LFA30.size11=LFA30.cpue.size[LFA30.11,]
LFA30.size11 = rename.df(LFA30.size11, "Freq", "size11")
LFA30.size11$SIZE_CD=NULL
LFA30.0.11 = merge(LFA30.0.10.2,LFA30.size11, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA30.12=which(LFA30.cpue.size$SIZE_CD=='12')
LFA30.size12=LFA30.cpue.size[LFA30.12,]
LFA30.size12 = rename.df(LFA30.size12, "Freq", "size12")
LFA30.size12$SIZE_CD=NULL
LFA30.0.12 = merge(LFA30.0.11,LFA30.size12, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA30.13=which(LFA30.cpue.size$SIZE_CD=='13')
LFA30.size13=LFA30.cpue.size[LFA30.13,]
LFA30.size13 = rename.df(LFA30.size13, "Freq", "size13")
LFA30.size13$SIZE_CD=NULL
LFA30.0.13 = merge(LFA30.0.12,LFA30.size13, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA30.14=which(LFA30.cpue.size$SIZE_CD=='14')
LFA30.size14=LFA30.cpue.size[LFA30.14,]
LFA30.size14 = rename.df(LFA30.size14, "Freq", "size14")
LFA30.size14$SIZE_CD=NULL
LFA30.0.14 = merge(LFA30.0.13,LFA30.size14, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA30.15=which(LFA30.cpue.size$SIZE_CD=='15')
LFA30.size15=LFA30.cpue.size[LFA30.15,]
LFA30.size15 = rename.df(LFA30.size15, "Freq", "size15")
LFA30.size15$SIZE_CD=NULL
LFA30.0.15 = merge(LFA30.0.14,LFA30.size15, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA30.16=which(LFA30.cpue.size$SIZE_CD=='16')
LFA30.size16=LFA30.cpue.size[LFA30.16,]
LFA30.size16 = rename.df(LFA30.size16, "Freq", "size16")
LFA30.size16$SIZE_CD=NULL
LFA30.0.16 = merge(LFA30.0.15,LFA30.size16, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA30.0.16[is.na(LFA30.0.16)]=0
summary(LFA30.0.16)
##SIZE CLASS SPECS FOR UNDERSIZED LOBSTERS
LFA30.0.16$shorts=NA
LFA30.0.16$shorts=LFA30.0.16$size0+LFA30.0.16$size2+LFA30.0.16$size3+LFA30.0.16$size4+LFA30.0.16$size5+LFA30.0.16$size6+
LFA30.0.16$size7+LFA30.0.16$size8+LFA30.0.16$size9+LFA30.0.16$size10.1
##SIZE CLASS SPECS FOR LEGAL LOBSTERS
LFA30.0.16$legals=NA
LFA30.0.16$legals=LFA30.0.16$size10.2+LFA30.0.16$size11+LFA30.0.16$size12+LFA30.0.16$size13+
LFA30.0.16$size14+LFA30.0.16$size15+LFA30.0.16$size16
summary(LFA30.0.16)
#Max shorts = 44; Max legals = 62
write.table(LFA30.0.16, file=paste("rec.LFA30.9916.SD1to5.nober.",Sys.Date(),".txt"), row.names=TRUE, col.names=TRUE, sep=" ")
#----------------------------------LFA31A--------------------------------------
##LFA 31A
LFA31A.9916=which(fsrs$LFA==31.1)
length(LFA31A.9916) #34,688 RECORDS JAN_2016
LFA31A.9916=fsrs[LFA31A.9916,]
unique(LFA31A.9916$HAUL_YEAR)
summary(LFA31A.9916)
##EMPTY TRAPS
e=which(LFA31A.9916$LOBSTER_NO==0)
length(e) #1,263 RECORDS
##VALIDATE SOAK DAYS:
> table(LFA31A.9916$SOAK_DAYS, LFA31A.9916$HAUL_YEAR)
1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015
1 207 254 287 452 718 560 744 1692 1052 2318 3231 2492 2377 2364 2055 2681 2525
2 137 185 115 184 359 539 720 890 741 331 444 430 369 255 452 543 849
3 30 8 35 39 115 82 35 36 0 0 104 59 79 34 45 45 12
4 2 5 4 2 37 24 28 10 45 13 0 0 37 15 52 0 0
5 0 2 6 0 0 0 0 0 0 2 0 0 9 2 0 0 0
6 0 0 9 0 0 0 17 0 0 13 0 0 0 0 0 0 0
7 0 3 4 0 8 0 10 0 0 0 0 0 0 0 0 0 0
8 0 0 0 0 0 14 0 0 0 0 0 0 0 0 0 0 0
9 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0
>
write.table(LFA31A.9916, file=paste("rec.LFA31A 9916.Noremovals.from.datacheck.9916",Sys.Date(),".txt"), row.names=FALSE, col.names=TRUE, sep=" ")
#CPUE PREP FILE
##DAILY AGGREGATE FOR CPUE ANALYSIS
#SOAK DAY CONSTRAINT:
sd=which(LFA31A.9916$SOAK_DAYS > 5)
length(sd) #83 RECORDS
LFA31A.9916.sd=LFA31A.9916[-sd,]
##CALCULATE TRAP # PER DAY
LFA31A.9916.traps = ddply(LFA31A.9916.sd,c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE"),summarize,TOT_TRAPS=length(unique(TRAP_NO)))
summary(LFA31A.9916.traps)
str(LFA31A.9916.traps) #5,165 RECORDS
#SHOWS NUMBER OF RECORDS WITH TRAP NUMBER DISTRIBUTION PER VESSEL
table(LFA31A.9916.traps$TOT_TRAPS,LFA31A.9916.traps$VESSEL_CD)
table(LFA31A.9916.traps$HAUL_YEAR,LFA31A.9916.traps$VESSEL_CD)
##SIZE CLASS ADJUSTMENT TO SPLIT THE SHORTS AND LEGAL SIZES IN CLASS 10
table(LFA31A.9916.sd$SIZE_CD,LFA31A.9916.sd$SHORT)
e1= which (LFA31A.9916.sd$SIZE_CD==10 & LFA31A.9916.sd$SHORT==1)
LFA31A.9916.sd[e1,"SIZE_CD"]=10.1
summary(LFA31A.9916.sd[e1,])
e2= which (LFA31A.9916.sd$SIZE==10 & LFA31A.9916.sd$SHORT==0)
LFA31A.9916.sd[e2,"SIZE_CD"]=10.2
summary(LFA31A.9916.sd[e2,])
##REMOVE RECORDS FOR BERRIED BY INCLUDING IN SEX COLUMN - FOR CPUE ANALYSIS
b= which (LFA31A.9916.sd$SEX==3)
length (b) #4,305 RECORDS
LFA31A.9916.sd.noberried=LFA31A.9916.sd[-b,]
str(LFA31A.9916.sd.noberried)
##CALCULATE TOTAL COUNT PER SIZE CLASS
LFA31A.9916.sd.noberried$VESSEL_CD <- as.factor(LFA31A.9916.sd.noberried$VESSEL_CD)
LFA31A.9916.sd.noberried$SIZE_CD <- as.factor(LFA31A.9916.sd.noberried$SIZE_CD)
LFA31A.9916.counts.at.size =aggregate(LFA31A.9916.sd.noberried[,1], by=as.list(LFA31A.9916.sd.noberried[c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "SIZE_CD")]), length, simplify = TRUE)
LFA31A.9916.counts.at.size = na.omit (LFA31A.9916.counts.at.size)
library(gdata)
LFA31A.9916.counts.at.size <- rename.vars(LFA31A.9916.counts.at.size, from="x", to="Freq")
summary(LFA31A.9916.counts.at.size)
str(LFA31A.9916.counts.at.size) #15,546 RECORDS
unique(LFA31A.9916.counts.at.size$SIZE_CD) #SIZE 0-16; NO NA VALUES
##SIZE CLASS FREQUENCY TABLE
LFA31A.cpue.size = merge(LFA31A.9916.traps,LFA31A.9916.counts.at.size, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE"),all.x=T,all.y=F, sort=F)
LFA31A.0=which(LFA31A.cpue.size$SIZE_CD=='0')
LFA31A.size0=LFA31A.cpue.size[LFA31A.0,]
LFA31A.size0 = rename.df(LFA31A.size0,"Freq", "size0")
LFA31A.size0$SIZE_CD=NULL
LFA31A.2=which(LFA31A.cpue.size$SIZE_CD=='2')
LFA31A.size2=LFA31A.cpue.size[LFA31A.2,]
LFA31A.size2 = rename.df(LFA31A.size2,"Freq", "size2")
LFA31A.size2$SIZE_CD=NULL
LFA31A.0.2 = merge(LFA31A.size0,LFA31A.size2, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31A.3=which(LFA31A.cpue.size$SIZE_CD=='3')
LFA31A.size3=LFA31A.cpue.size[LFA31A.3,]
LFA31A.size3 = rename.df(LFA31A.size3, "Freq", "size3")
LFA31A.size3$SIZE_CD=NULL
LFA31A.0.3 = merge(LFA31A.0.2,LFA31A.size3, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31A.4=which(LFA31A.cpue.size$SIZE_CD=='4')
LFA31A.size4=LFA31A.cpue.size[LFA31A.4,]
LFA31A.size4 = rename.df(LFA31A.size4, "Freq", "size4")
LFA31A.size4$SIZE_CD=NULL
LFA31A.0.4 = merge(LFA31A.0.3,LFA31A.size4, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31A.5=which(LFA31A.cpue.size$SIZE_CD=='5')
LFA31A.size5=LFA31A.cpue.size[LFA31A.5,]
LFA31A.size5 = rename.df(LFA31A.size5, "Freq", "size5")
LFA31A.size5$SIZE_CD=NULL
LFA31A.0.5 = merge(LFA31A.0.4,LFA31A.size5, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31A.6=which(LFA31A.cpue.size$SIZE_CD=='6')
LFA31A.size6=LFA31A.cpue.size[LFA31A.6,]
LFA31A.size6 = rename.df(LFA31A.size6, "Freq", "size6")
LFA31A.size6$SIZE_CD=NULL
LFA31A.0.6 = merge(LFA31A.0.5,LFA31A.size6, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31A.7=which(LFA31A.cpue.size$SIZE_CD=='7')
LFA31A.size7=LFA31A.cpue.size[LFA31A.7,]
LFA31A.size7 = rename.df(LFA31A.size7, "Freq", "size7")
LFA31A.size7$SIZE_CD=NULL
LFA31A.0.7 = merge(LFA31A.0.6,LFA31A.size7, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31A.8=which(LFA31A.cpue.size$SIZE_CD=='8')
LFA31A.size8=LFA31A.cpue.size[LFA31A.8,]
LFA31A.size8 = rename.df(LFA31A.size8, "Freq", "size8")
LFA31A.size8$SIZE_CD=NULL
LFA31A.0.8 = merge(LFA31A.0.7,LFA31A.size8, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31A.9=which(LFA31A.cpue.size$SIZE_CD=='9')
LFA31A.size9=LFA31A.cpue.size[LFA31A.9,]
LFA31A.size9 = rename.df(LFA31A.size9, "Freq", "size9")
LFA31A.size9$SIZE_CD=NULL
LFA31A.0.9 = merge(LFA31A.0.8,LFA31A.size9, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31A.10.1=which(LFA31A.cpue.size$SIZE_CD=='10.1')
LFA31A.size10.1=LFA31A.cpue.size[LFA31A.10.1,]
LFA31A.size10.1 = rename.df(LFA31A.size10.1, "Freq", "size10.1")
LFA31A.size10.1$SIZE_CD=NULL
LFA31A.0.10.1 = merge(LFA31A.0.9,LFA31A.size10.1, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31A.10.2=which(LFA31A.cpue.size$SIZE_CD=='10.2')
LFA31A.size10.2=LFA31A.cpue.size[LFA31A.10.2,]
LFA31A.size10.2 = rename.df(LFA31A.size10.2, "Freq", "size10.2")
LFA31A.size10.2$SIZE_CD=NULL
LFA31A.0.10.2 = merge(LFA31A.0.10.1,LFA31A.size10.2, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31A.11=which(LFA31A.cpue.size$SIZE_CD=='11')
LFA31A.size11=LFA31A.cpue.size[LFA31A.11,]
LFA31A.size11 = rename.df(LFA31A.size11, "Freq", "size11")
LFA31A.size11$SIZE_CD=NULL
LFA31A.0.11 = merge(LFA31A.0.10.2,LFA31A.size11, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31A.12=which(LFA31A.cpue.size$SIZE_CD=='12')
LFA31A.size12=LFA31A.cpue.size[LFA31A.12,]
LFA31A.size12 = rename.df(LFA31A.size12, "Freq", "size12")
LFA31A.size12$SIZE_CD=NULL
LFA31A.0.12 = merge(LFA31A.0.11,LFA31A.size12, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31A.13=which(LFA31A.cpue.size$SIZE_CD=='13')
LFA31A.size13=LFA31A.cpue.size[LFA31A.13,]
LFA31A.size13 = rename.df(LFA31A.size13, "Freq", "size13")
LFA31A.size13$SIZE_CD=NULL
LFA31A.0.13 = merge(LFA31A.0.12,LFA31A.size13, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31A.14=which(LFA31A.cpue.size$SIZE_CD=='14')
LFA31A.size14=LFA31A.cpue.size[LFA31A.14,]
LFA31A.size14 = rename.df(LFA31A.size14, "Freq", "size14")
LFA31A.size14$SIZE_CD=NULL
LFA31A.0.14 = merge(LFA31A.0.13,LFA31A.size14, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31A.15=which(LFA31A.cpue.size$SIZE_CD=='15')
LFA31A.size15=LFA31A.cpue.size[LFA31A.15,]
LFA31A.size15 = rename.df(LFA31A.size15, "Freq", "size15")
LFA31A.size15$SIZE_CD=NULL
LFA31A.0.15 = merge(LFA31A.0.14,LFA31A.size15, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31A.16=which(LFA31A.cpue.size$SIZE_CD=='16')
LFA31A.size16=LFA31A.cpue.size[LFA31A.16,]
LFA31A.size16 = rename.df(LFA31A.size16, "Freq", "size16")
LFA31A.size16$SIZE_CD=NULL
LFA31A.0.16 = merge(LFA31A.0.15,LFA31A.size16, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31A.0.16[is.na(LFA31A.0.16)]=0
summary(LFA31A.0.16)
##SIZE CLASS SPECS FOR UNDERSIZED LOBSTERS
LFA31A.0.16$shorts=NA
LFA31A.0.16$shorts=LFA31A.0.16$size0+LFA31A.0.16$size2+LFA31A.0.16$size3+LFA31A.0.16$size4+LFA31A.0.16$size5+LFA31A.0.16$size6+
LFA31A.0.16$size7+LFA31A.0.16$size8+LFA31A.0.16$size9+LFA31A.0.16$size10.1
##SIZE CLASS SPECS FOR LEGAL LOBSTERS
LFA31A.0.16$legals=NA
LFA31A.0.16$legals=LFA31A.0.16$size10.2+LFA31A.0.16$size11+LFA31A.0.16$size12+LFA31A.0.16$size13+
LFA31A.0.16$size14+LFA31A.0.16$size15+LFA31A.0.16$size16
summary(LFA31A.0.16)
#Max shorts = 18; Max legals = 20
write.table(LFA31A.0.16, file=paste("rec.LFA31A.9916.SD1to5.nober.",Sys.Date(),".txt"), row.names=TRUE, col.names=TRUE, sep=" ")
#---------------------------------------LFA31B---------------------------------
#LFA 31B
LFA31B.9916=which(fsrs$LFA==31.2)
length(LFA31B.9916) #46,125 RECORDS JAN_2016
LFA31B.9916=fsrs[LFA31B.9916,]
unique(LFA31B.9916$HAUL_YEAR)
summary(LFA31B.9916)
##EMPTY TRAPS
e=which(LFA31B.9916$LOBSTER_NO==0)
length(e) #2,410 RECORDS
##VALIDATE SOAK DAYS:
>table(LFA31B.9916$SOAK_DAYS, LFA31B.9916$HAUL_YEAR)
1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015
1 282 889 856 1446 2590 2235 3035 4118 2700 3283 3741 2132 1925 2908 2310 2930 3709
2 106 237 188 300 392 155 290 629 174 275 193 172 116 121 302 219 222
3 32 36 37 48 40 7 108 57 24 32 44 0 69 86 81 80 15
4 0 6 5 20 0 0 0 0 0 0 0 0 6 0 0 30 0
5 0 0 0 14 0 0 13 0 0 0 0 0 8 0 0 0 0
6 0 0 0 0 3 0 0 0 0 0 0 0 12 0 0 0 0
7 0 6 0 0 0 0 6 0 0 0 0 0 0 0 0 0 6
8 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 7 0
>
write.table(LFA31B.9916, file=paste("rec.LFA31B 9916.Noremovals.from.datacheck.9916",Sys.Date(),".txt"), row.names=FALSE, col.names=TRUE, sep=" ")
#CPUE PREP FILE
##DAILY AGGREGATE FOR CPUE ANALYSIS
#SOAK DAY CONSTRAINT:
sd=which(LFA31B.9916$SOAK_DAYS > 5)
length(sd) #47 RECORDS
LFA31B.9916.sd=LFA31B.9916[-sd,]
##CALCULATE TRAP # PER DAY
LFA31B.9916.traps = compute.unique.lengths( x=LFA31B.9916.sd, var="TRAP_NO", index=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE"))
LFA31B.9916.traps = na.omit (LFA31B.9916.traps)
LFA31B.9916.traps = rename.df(LFA31B.9916.traps,"Freq", "TOT_TRAPS")
summary(LFA31B.9916.traps)
str(LFA31B.9916.traps) #8,597 RECORDS
#SHOWS NUMBER OF RECORDS WITH TRAP NUMBER DISTRIBUTION PER VESSEL
table(LFA31B.9916.traps$TOT_TRAPS,LFA31B.9916.traps$VESSEL_CD)
table(LFA31B.9916.traps$HAUL_YEAR,LFA31B.9916.traps$VESSEL_CD)
##SIZE CLASS ADJUSTMENT TO SPLIT THE SHORTS AND LEGAL SIZES IN CLASS 10
table(LFA31B.9916.sd$SIZE_CD,LFA31B.9916.sd$SHORT)
f1= which (LFA31B.9913.sd$SIZE_CD==10 & LFA31B.9913.sd$SHORT==1)
LFA31B.9913.sd[f1,"SIZE_CD"]=10.1
summary(LFA31B.9913.sd[f1,])
f2= which (LFA31B.9913.sd$SIZE_CD==10 & LFA31B.9913.sd$SHORT==0)
LFA31B.9913.sd[f2,"SIZE_CD"]=10.2
summary(LFA31B.9913.sd[f2,])
##REMOVE RECORDS FOR BERRIED BY INCLUDING IN SEX COLUMN - FOR CPUE ANALYSIS
b= which (LFA31B.9913.sd$SEX==3)
length (b) #2798 RECORDS
LFA31B.9913.sd.noberried=LFA31B.9913.sd[-b,]
str(LFA31B.9913.sd.noberried)
##CALCULATE TOTAL COUNT PER SIZE CLASS
LFA31B.9913.sd.noberried$VESSEL_CD <- as.factor(LFA31B.9913.sd.noberried$VESSEL_CD)
LFA31B.9913.sd.noberried$SIZE_CD <- as.factor(LFA31B.9913.sd.noberried$SIZE_CD)
LFA31B.9913.counts.at.size =aggregate(LFA31B.9913.sd.noberried[,1], by=as.list(LFA31B.9913.sd.noberried[c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "SIZE_CD")]), length, simplify = TRUE)
LFA31B.9913.counts.at.size = na.omit (LFA31B.9913.counts.at.size)
library(gdata)
LFA31B.9913.counts.at.size <- rename.vars(LFA31B.9913.counts.at.size, from="x", to="Freq")
summary(LFA31B.9913.counts.at.size)
str(LFA31B.9913.counts.at.size) #22,001 RECORDS
unique(LFA31B.9913.counts.at.size$SIZE_CD) #SIZE 0-16; NO NA VALUES
##SIZE CLASS FREQUENCY TABLE
LFA31B.cpue.size = merge(LFA31B.9913.traps,LFA31B.9913.counts.at.size, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE"),all.x=T,all.y=F, sort=F)
LFA31B.0=which(LFA31B.cpue.size$SIZE_CD=='0')
LFA31B.size0=LFA31B.cpue.size[LFA31B.0,]
LFA31B.size0 = rename.df(LFA31B.size0,"Freq", "size0")
LFA31B.size0$SIZE_CD=NULL
LFA31B.2=which(LFA31B.cpue.size$SIZE_CD=='2')
LFA31B.size2=LFA31B.cpue.size[LFA31B.2,]
LFA31B.size2 = rename.df(LFA31B.size2, "Freq", "size2")
LFA31B.size2$SIZE_CD=NULL
LFA31B.0.2 = merge(LFA31B.size0,LFA31B.size2, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31B.3=which(LFA31B.cpue.size$SIZE_CD=='3')
LFA31B.size3=LFA31B.cpue.size[LFA31B.3,]
LFA31B.size3 = rename.df(LFA31B.size3, "Freq", "size3")
LFA31B.size3$SIZE_CD=NULL
LFA31B.0.3 = merge(LFA31B.0.2,LFA31B.size3, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31B.4=which(LFA31B.cpue.size$SIZE_CD=='4')
LFA31B.size4=LFA31B.cpue.size[LFA31B.4,]
LFA31B.size4 = rename.df(LFA31B.size4, "Freq", "size4")
LFA31B.size4$SIZE_CD=NULL
LFA31B.0.4 = merge(LFA31B.0.3,LFA31B.size4, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31B.5=which(LFA31B.cpue.size$SIZE_CD=='5')
LFA31B.size5=LFA31B.cpue.size[LFA31B.5,]
LFA31B.size5 = rename.df(LFA31B.size5, "Freq", "size5")
LFA31B.size5$SIZE_CD=NULL
LFA31B.0.5 = merge(LFA31B.0.4,LFA31B.size5, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31B.6=which(LFA31B.cpue.size$SIZE_CD=='6')
LFA31B.size6=LFA31B.cpue.size[LFA31B.6,]
LFA31B.size6 = rename.df(LFA31B.size6, "Freq", "size6")
LFA31B.size6$SIZE_CD=NULL
LFA31B.0.6 = merge(LFA31B.0.5,LFA31B.size6, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31B.7=which(LFA31B.cpue.size$SIZE_CD=='7')
LFA31B.size7=LFA31B.cpue.size[LFA31B.7,]
LFA31B.size7 = rename.df(LFA31B.size7, "Freq", "size7")
LFA31B.size7$SIZE_CD=NULL
LFA31B.0.7 = merge(LFA31B.0.6,LFA31B.size7, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31B.8=which(LFA31B.cpue.size$SIZE_CD=='8')
LFA31B.size8=LFA31B.cpue.size[LFA31B.8,]
LFA31B.size8 = rename.df(LFA31B.size8, "Freq", "size8")
LFA31B.size8$SIZE_CD=NULL
LFA31B.0.8 = merge(LFA31B.0.7,LFA31B.size8, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31B.9=which(LFA31B.cpue.size$SIZE_CD=='9')
LFA31B.size9=LFA31B.cpue.size[LFA31B.9,]
LFA31B.size9 = rename.df(LFA31B.size9, "Freq", "size9")
LFA31B.size9$SIZE_CD=NULL
LFA31B.0.9 = merge(LFA31B.0.8,LFA31B.size9, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31B.10.1=which(LFA31B.cpue.size$SIZE_CD=='10.1')
LFA31B.size10.1=LFA31B.cpue.size[LFA31B.10.1,]
LFA31B.size10.1 = rename.df(LFA31B.size10.1, "Freq", "size10.1")
LFA31B.size10.1$SIZE_CD=NULL
LFA31B.0.10.1 = merge(LFA31B.0.9,LFA31B.size10.1, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31B.10.2=which(LFA31B.cpue.size$SIZE_CD=='10.2')
LFA31B.size10.2=LFA31B.cpue.size[LFA31B.10.2,]
LFA31B.size10.2 = rename.df(LFA31B.size10.2, "Freq", "size10.2")
LFA31B.size10.2$SIZE_CD=NULL
LFA31B.0.10.2 = merge(LFA31B.0.10.1,LFA31B.size10.2, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31B.11=which(LFA31B.cpue.size$SIZE_CD=='11')
LFA31B.size11=LFA31B.cpue.size[LFA31B.11,]
LFA31B.size11 = rename.df(LFA31B.size11, "Freq", "size11")
LFA31B.size11$SIZE_CD=NULL
LFA31B.0.11 = merge(LFA31B.0.10.2,LFA31B.size11, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31B.12=which(LFA31B.cpue.size$SIZE_CD=='12')
LFA31B.size12=LFA31B.cpue.size[LFA31B.12,]
LFA31B.size12 = rename.df(LFA31B.size12, "Freq", "size12")
LFA31B.size12$SIZE_CD=NULL
LFA31B.0.12 = merge(LFA31B.0.11,LFA31B.size12, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31B.13=which(LFA31B.cpue.size$SIZE_CD=='13')
LFA31B.size13=LFA31B.cpue.size[LFA31B.13,]
LFA31B.size13 = rename.df(LFA31B.size13, "Freq", "size13")
LFA31B.size13$SIZE_CD=NULL
LFA31B.0.13 = merge(LFA31B.0.12,LFA31B.size13, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31B.14=which(LFA31B.cpue.size$SIZE_CD=='14')
LFA31B.size14=LFA31B.cpue.size[LFA31B.14,]
LFA31B.size14 = rename.df(LFA31B.size14, "Freq", "size14")
LFA31B.size14$SIZE_CD=NULL
LFA31B.0.14 = merge(LFA31B.0.13,LFA31B.size14, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31B.15=which(LFA31B.cpue.size$SIZE_CD=='15')
LFA31B.size15=LFA31B.cpue.size[LFA31B.15,]
LFA31B.size15 = rename.df(LFA31B.size15, "Freq", "size15")
LFA31B.size15$SIZE_CD=NULL
LFA31B.0.15 = merge(LFA31B.0.14,LFA31B.size15, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31B.16=which(LFA31B.cpue.size$SIZE_CD=='16')
LFA31B.size16=LFA31B.cpue.size[LFA31B.16,]
LFA31B.size16 = rename.df(LFA31B.size16, "Freq", "size16")
LFA31B.size16$SIZE_CD=NULL
LFA31B.0.16 = merge(LFA31B.0.15,LFA31B.size16, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA31B.0.16[is.na(LFA31B.0.16)]=0
summary(LFA31B.0.16)
##SIZE CLASS SPECS FOR UNDERSIZED LOBSTERS FROM 1999-2013
LFA31B.0.16$shorts=NA
LFA31B.0.16$shorts=LFA31B.0.16$size0+LFA31B.0.16$size2+LFA31B.0.16$size3+LFA31B.0.16$size4+LFA31B.0.16$size5+LFA31B.0.16$size6+
LFA31B.0.16$size7+LFA31B.0.16$size8+LFA31B.0.16$size9+LFA31B.0.16$size10.1
##SIZE CLASS SPECS FOR LEGAL LOBSTERS FROM 1999-2013
LFA31B.0.16$legals=NA
LFA31B.0.16$legals=LFA31B.0.16$size10.2+LFA31B.0.16$size11+LFA31B.0.16$size12+LFA31B.0.16$size13+
LFA31B.0.16$size14+LFA31B.0.16$size15+LFA31B.0.16$size16
summary(LFA31B.0.16)
#Max shorts = 15; Max legals = 18
write.table(LFA31B.0.16, file=paste("rec.LFA31B.9913.SD1to5.nober.",Sys.Date(),".txt"), row.names=TRUE, col.names=TRUE, sep=" ")
#-------------------------------------LFA32-------------------------------------
#LFA 32
LFA32.9916=which(fsrs$LFA==32)
length(LFA32.9916) #45,019 RECORDS JAN_2016
LFA32.9916=fsrs[LFA32.9916,]
unique(LFA32.9916$HAUL_YEAR)
summary(LFA32.9916)
##EMPTY TRAPS
e=which(LFA32.9916$LOBSTER_NO==0)
length(e) #6,253 RECORDS
##VALIDATE SOAK DAYS:
>table(LFA32.9916$SOAK_DAYS, LFA32.9916$HAUL_YEAR)
1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015
1 854 1238 1158 1276 1715 1707 1945 2950 1594 2605 2885 2432 2522 3184 1972 4051 3152
2 222 337 211 295 213 325 290 376 188 321 431 337 559 518 272 431 492
3 39 36 46 46 46 9 57 102 56 71 121 102 90 146 173 157 49
4 17 1 25 18 2 2 11 4 23 36 37 37 52 37 36 18 2
5 2 1 8 2 2 0 24 4 0 2 0 2 39 7 14 0 0
6 0 0 4 1 2 0 30 2 5 18 0 0 0 0 0 14 4
7 0 0 1 0 2 0 10 4 6 0 0 2 13 0 0 0 0
8 0 0 0 0 2 0 0 2 0 2 0 0 10 0 0 0 0
9 0 2 0 0 2 0 6 0 0 0 0 0 0 0 0 0 0
10 0 0 0 0 3 0 3 0 0 0 0 0 0 0 0 0 0
>
write.table(LFA32.9916, file=paste("rec.LFA32 9916.Noremovals.from.datacheck.9916",Sys.Date(),".txt"), row.names=FALSE, col.names=TRUE, sep=" ")
#CPUE PREP FILE
##DAILY AGGREGATE FOR CPUE ANALYSIS
#SOAK DAY CONSTRAINT:
sd=which(LFA32.9916$SOAK_DAYS> 5)
length(sd) #150 RECORDS
LFA32.9916.sd=LFA32.9916[-sd,]
##CALCULATE TRAP # PER DAY
LFA32.9916.traps = ddply(LFA32.9916.sd,c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE"),summarize,TOT_TRAPS=length(unique(TRAP_NO)))
summary(LFA32.9916.traps)
str(LFA32.9916.traps) #11,772 RECORDS
#SHOWS NUMBER OF RECORDS WITH TRAP NUMBER DISTRIBUTION PER VESSEL
table(LFA32.9916.traps$TOT_TRAPS,LFA32.9916.traps$VESSEL_CD)
table(LFA32.9916.traps$HAUL_YEAR,LFA32.9916.traps$VESSEL_CD)
##SIZE CLASS ADJUSTMENT TO SPLIT THE SHORTS AND LEGAL SIZES IN CLASS 10
table(LFA32.9916.sd$SIZE_CD,LFA32.9916.sd$SHORT)
g1= which (LFA32.9916.sd$SIZE_CD==10 & LFA32.9916.sd$SHORT==1)
LFA32.9916.sd[g1,"SIZE_CD"]=10.1
summary(LFA32.9916.sd[g1,])
g2= which (LFA32.9916.sd$SIZE_CD==10 & LFA32.9916.sd$SHORT==0)
LFA32.9916.sd[g2,"SIZE_CD"]=10.2
summary(LFA32.9916.sd[g2,])
##REMOVE RECORDS FOR BERRIED BY INCLUDING IN SEX COLUMN - FOR CPUE ANALYSIS
b= which (LFA32.9916.sd$SEX==3)
length (b) #1,783 RECORDS
LFA32.9916.sd.noberried=LFA32.9916.sd[-b,]
str(LFA32.9916.sd.noberried)
##CALCULATE TOTAL COUNT PER SIZE CLASS
LFA32.9916.counts.at.size =aggregate(LFA32.9916.sd.noberried[,1], by=as.list(LFA32.9916.sd.noberried[c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "SIZE_CD")]), length, simplify = TRUE)
LFA32.9916.counts.at.size = na.omit (LFA32.9916.counts.at.size)
library(gdata)
LFA32.9916.counts.at.size <- rename.vars(LFA32.9916.counts.at.size, from="x", to="Freq")
summary(LFA32.9916.counts.at.size)
str(LFA32.9916.counts.at.size) #24,701 RECORDS
unique(LFA32.9916.counts.at.size$SIZE_CD) #SIZE 0-16; NO NA VALUES
##SIZE CLASS FREQUENCY TABLE
LFA32.cpue.size = merge(LFA32.9916.traps,LFA32.9916.counts.at.size, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE"),all.x=T,all.y=F, sort=F)
LFA32.0=which(LFA32.cpue.size$SIZE_CD=='0')
LFA32.size0=LFA32.cpue.size[LFA32.0,]
LFA32.size0 = rename.df(LFA32.size0,"Freq", "size0")
LFA32.size0$SIZE_CD=NULL
LFA32.2=which(LFA32.cpue.size$SIZE_CD=='2')
LFA32.size2=LFA32.cpue.size[LFA32.2,]
LFA32.size2 = rename.df(LFA32.size2, "Freq", "size2")
LFA32.size2$SIZE_CD=NULL
LFA32.0.2 = merge(LFA32.size0,LFA32.size2, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA32.3=which(LFA32.cpue.size$SIZE_CD=='3')
LFA32.size3=LFA32.cpue.size[LFA32.3,]
LFA32.size3 = rename.df(LFA32.size3, "Freq", "size3")
LFA32.size3$SIZE_CD=NULL
LFA32.0.3 = merge(LFA32.0.2,LFA32.size3, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA32.4=which(LFA32.cpue.size$SIZE_CD=='4')
LFA32.size4=LFA32.cpue.size[LFA32.4,]
LFA32.size4 = rename.df(LFA32.size4, "Freq", "size4")
LFA32.size4$SIZE_CD=NULL
LFA32.0.4 = merge(LFA32.0.3,LFA32.size4, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA32.5=which(LFA32.cpue.size$SIZE_CD=='5')
LFA32.size5=LFA32.cpue.size[LFA32.5,]
LFA32.size5 = rename.df(LFA32.size5, "Freq", "size5")
LFA32.size5$SIZE_CD=NULL
LFA32.0.5 = merge(LFA32.0.4,LFA32.size5, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA32.6=which(LFA32.cpue.size$SIZE_CD=='6')
LFA32.size6=LFA32.cpue.size[LFA32.6,]
LFA32.size6 = rename.df(LFA32.size6, "Freq", "size6")
LFA32.size6$SIZE_CD=NULL
LFA32.0.6 = merge(LFA32.0.5,LFA32.size6, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA32.7=which(LFA32.cpue.size$SIZE_CD=='7')
LFA32.size7=LFA32.cpue.size[LFA32.7,]
LFA32.size7 = rename.df(LFA32.size7, "Freq", "size7")
LFA32.size7$SIZE_CD=NULL
LFA32.0.7 = merge(LFA32.0.6,LFA32.size7, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA32.8=which(LFA32.cpue.size$SIZE_CD=='8')
LFA32.size8=LFA32.cpue.size[LFA32.8,]
LFA32.size8 = rename.df(LFA32.size8, "Freq", "size8")
LFA32.size8$SIZE_CD=NULL
LFA32.0.8 = merge(LFA32.0.7,LFA32.size8, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA32.9=which(LFA32.cpue.size$SIZE_CD=='9')
LFA32.size9=LFA32.cpue.size[LFA32.9,]
LFA32.size9 = rename.df(LFA32.size9, "Freq", "size9")
LFA32.size9$SIZE_CD=NULL
LFA32.0.9 = merge(LFA32.0.8,LFA32.size9, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA32.10.1=which(LFA32.cpue.size$SIZE_CD=='10.1')
LFA32.size10.1=LFA32.cpue.size[LFA32.10.1,]
LFA32.size10.1 = rename.df(LFA32.size10.1, "Freq", "size10.1")
LFA32.size10.1$SIZE_CD=NULL
LFA32.0.10.1 = merge(LFA32.0.9,LFA32.size10.1, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA32.10.2=which(LFA32.cpue.size$SIZE_CD=='10.2')
LFA32.size10.2=LFA32.cpue.size[LFA32.10.2,]
LFA32.size10.2 = rename.df(LFA32.size10.2, "Freq", "size10.2")
LFA32.size10.2$SIZE_CD=NULL
LFA32.0.10.2 = merge(LFA32.0.10.1,LFA32.size10.2, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA32.11=which(LFA32.cpue.size$SIZE_CD=='11')
LFA32.size11=LFA32.cpue.size[LFA32.11,]
LFA32.size11 = rename.df(LFA32.size11, "Freq", "size11")
LFA32.size11$SIZE_CD=NULL
LFA32.0.11 = merge(LFA32.0.10.2,LFA32.size11, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA32.12=which(LFA32.cpue.size$SIZE_CD=='12')
LFA32.size12=LFA32.cpue.size[LFA32.12,]
LFA32.size12 = rename.df(LFA32.size12, "Freq", "size12")
LFA32.size12$SIZE_CD=NULL
LFA32.0.12 = merge(LFA32.0.11,LFA32.size12, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA32.13=which(LFA32.cpue.size$SIZE_CD=='13')
LFA32.size13=LFA32.cpue.size[LFA32.13,]
LFA32.size13 = rename.df(LFA32.size13, "Freq", "size13")
LFA32.size13$SIZE_CD=NULL
LFA32.0.13 = merge(LFA32.0.12,LFA32.size13, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA32.14=which(LFA32.cpue.size$SIZE_CD=='14')
LFA32.size14=LFA32.cpue.size[LFA32.14,]
LFA32.size14 = rename.df(LFA32.size14, "Freq", "size14")
LFA32.size14$SIZE_CD=NULL
LFA32.0.14 = merge(LFA32.0.13,LFA32.size14, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA32.15=which(LFA32.cpue.size$SIZE_CD=='15')
LFA32.size15=LFA32.cpue.size[LFA32.15,]
LFA32.size15 = rename.df(LFA32.size15, "Freq", "size15")
LFA32.size15$SIZE_CD=NULL
LFA32.0.15 = merge(LFA32.0.14,LFA32.size15, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA32.16=which(LFA32.cpue.size$SIZE_CD=='16')
LFA32.size16=LFA32.cpue.size[LFA32.16,]
LFA32.size16 = rename.df(LFA32.size16, "Freq", "size16")
LFA32.size16$SIZE_CD=NULL
LFA32.0.16 = merge(LFA32.0.15,LFA32.size16, by=c("HAUL_YEAR", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA32.0.16[is.na(LFA32.0.16)]=0
summary(LFA32.0.16)
##SIZE CLASS SPECS FOR UNDERSIZED LOBSTERS FROM 1999-2013
LFA32.0.16$shorts=NA
LFA32.0.16$shorts=LFA32.0.16$size0+LFA32.0.16$size2+LFA32.0.16$size3+LFA32.0.16$size4+LFA32.0.16$size5+LFA32.0.16$size6+
LFA32.0.16$size7+LFA32.0.16$size8+LFA32.0.16$size9+LFA32.0.16$size10.1
##SIZE CLASS SPECS FOR LEGAL LOBSTERS FROM 1999-2013
LFA32.0.16$legals=NA
LFA32.0.16$legals=LFA32.0.16$size10.2+LFA32.0.16$size11+LFA32.0.16$size12+LFA32.0.16$size13+
LFA32.0.16$size14+LFA32.0.16$size15+LFA32.0.16$size16
summary(LFA32.0.16)
#Max shorts = 18; Max legals = 13
write.table(LFA32.0.16, file=paste("rec.LFA32.9916.SD1to5.nober.",Sys.Date(),".txt"), row.names=TRUE, col.names=TRUE, sep=" ")
#------------------------------------------LFA33-------------------------------
##LFA 33
LFA33.9916=which(fsrs$LFA==33)
length(LFA33.9916) #279,629 RECORDS JAN_2016
LFA33.9916=fsrs[LFA33.9916,]
summary(LFA33.9916)
##EMPTY TRAPS
e=which(LFA33.9916$LOBSTER_NO==0)
length(e) #15,085 RECORDS
##VALIDATE SOAK DAYS:
> table(LFA33.9916$SOAK_DAYS,LFA33.9916$S_LABEL) # A PORTION OF RECORDS HAVE TO HAVE LABEL ADDED - THESE ARE PAST NORMAL SEASON DATES
#LFA33.9916$S_LABEL<-recode(LFA33.9916$S_LABEL,"is.na='2004-2005'")
1998-1999 1999-2000 2000-2001 2001-2002 2002-2003 2003-2004 2004-2005 2005-2006 2006-2007 2007-2008 2008-2009 2009-2010 2010-2011 2011-2012 2012-2013 2013-2014
0.5 0 0 0 38 0 0 0 27 61 0 0 0 0 0 0 0
1 2583 5257 6864 8635 8108 8509 10908 11185 11008 8631 10414 13106 12111 10008 10598 11626
2 978 2682 2376 3144 3283 3190 4023 3875 4075 3200 5275 4503 3838 5452 4663 4108
3 240 1143 961 1308 1064 1349 1407 1667 1323 1329 1767 1861 2059 2083 3004 1637
4 25 461 396 351 347 622 598 811 596 325 681 1421 995 1073 879 609
5 12 92 176 251 270 362 277 425 379 339 489 511 1079 575 420 643
6 2 117 54 176 144 120 233 405 141 180 167 295 279 291 321 206
7 6 29 54 27 50 120 212 218 75 84 68 202 293 197 179 214
8 0 38 14 41 13 43 104 120 86 6 114 104 200 43 144 154
9 0 10 16 16 19 128 64 88 56 18 68 96 84 185 149 146
10 0 10 11 25 10 28 49 21 26 35 67 24 33 41 138 55
11 0 0 12 30 0 0 8 69 4 37 40 52 78 62 51 15
12 0 8 0 0 0 8 0 113 33 20 21 18 43 9 31 16
13 0 0 3 0 0 3 0 1 15 3 7 26 7 27 65 57
14 0 6 0 0 9 9 0 10 10 0 13 36 15 0 13 11
15 0 0 3 5 21 23 7 0 7 7 0 23 44 41 25 0
16 0 0 3 0 0 0 5 12 14 12 0 4 9 18 0 11
17 0 0 0 0 2 10 0 3 0 0 6 11 14 16 55 0
18 0 0 0 0 0 9 0 0 0 0 0 17 21 5 25 12
19 0 0 3 0 22 45 0 27 0 0 0 0 7 0 7 0
20 0 0 0 0 0 0 0 1 13 5 14 0 21 0 12 22
21 0 0 3 14 0 0 0 0 0 0 0 0 0 0 0 27
22 0 0 0 0 0 4 4 0 0 0 0 5 7 5 0 31
23 0 0 0 0 0 0 13 3 0 0 0 0 0 0 20 0
24 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0
25 0 0 0 0 0 3 0 0 0 0 10 3 0 0 6 0
26 0 0 0 0 0 0 0 3 0 0 33 0 0 0 0 19
27 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0 0
28 0 0 0 0 0 0 0 0 0 0 0 0 11 9 0 0
29 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 5
30 0 3 0 0 5 4 0 0 0 0 0 0 0 0 0 0
31 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0
32 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0
33 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0
34 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0
35 0 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0
36 0 0 0 0 0 0 0 0 0 0 0 0 0 21 0 0
37 0 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0
38 0 0 0 0 0 0 0 3 0 6 0 0 0 0 0 0
40 0 0 0 0 0 0 0 4 0 0 0 0 0 0 8 12
42 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0
43 0 0 0 0 0 5 4 0 0 0 0 0 3 0 0 0
48 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0
50 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0
57 0 0 0 0 0 20 0 0 0 0 0 0 0 0 0 0
59 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0
60 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0
64 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0
>
write.table(LFA33.9916, file=paste("rec.LFA33 9916.Noremovals.from.datacheck.9916",Sys.Date(),".txt"), row.names=FALSE, col.names=TRUE, sep=" ")
#CPUE PREP FILE:
##DAILY AGGREGATE FOR CPUE ANALYSIS
#SOAK DAY CONSTRAINT:
sd=which(LFA33.9916$SOAK_DAYS > 5)
length(sd) #10,355 RECORDS
LFA33.9916.sd=LFA33.9916[-sd,]
short.soak.days=which(LFA33.9916.sd$SOAK_DAYS < 1)
length(short.soak.days) # 126 RECORDS
LFA33.9916.sd=LFA33.9916.sd[-short.soak.days,]
##CALCULATE TRAP # PER DAY
LFA33.9916.traps<-ddply(LFA33.9916.sd,c("S_LABEL", "VESSEL_CD", "HAUL_DATE"),summarize, TOT_TRAPS=length(unique(TRAP_NO))) #27,647 RECORDS
str(LFA33.9916.traps) #27,647 RECORDS (SD 1 to 5 SELECTION) DEC.2014 SQL EXPORT
#SHOWS NUMBER OF RECORDS WITH TRAP NUMBER DISTRIBUTION PER VESSEL
table(LFA33.9916.traps$S_LABEL,LFA33.9916.traps$TOT_TRAPS)
table(LFA33.9916.traps$S_LABEL,LFA33.9916.traps$VESSEL_CD)
##SIZE CLASS ADJUSTMENT TO SPLIT THE SHORTS AND LEGAL SIZES IN CLASS 10
table(LFA33.9916.sd$SIZE_CD, LFA33.9916.sd$SHORT)
h1= which (LFA33.9916.sd$SIZE_CD==10 & LFA33.9916.sd$SHORT==1)
LFA33.9916.sd[h1,"SIZE_CD"]=10.1
summary(LFA33.9916.sd[h1,])
h2= which (LFA33.9916.sd$SIZE_CD==10 & LFA33.9916.sd$SHORT==0)
LFA33.9916.sd[h2,"SIZE_CD"]=10.2
summary(LFA33.9916.sd[h2,])
str(LFA33.9916.sd)
##REMOVE RECORDS FOR BERRIED BY INCLUDING IN SEX COLUMN - FOR CPUE ANALYSIS
b= which (LFA33.9916.sd$SEX==3)
length (b) #3861 RECORDS
LFA33.9916.sd.noberried=LFA33.9916.sd[-b,]
str(LFA33.9916.sd.noberried)
##CALCULATE TOTAL COUNT PER SIZE CLASS
LFA33.9916.counts.at.size =aggregate(LFA33.9916.sd.noberried[,1], by=as.list(LFA33.9916.sd.noberried[c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "SIZE_CD")]), length, simplify = TRUE)
LFA33.9916.counts.at.size = na.omit (LFA33.9916.counts.at.size)
library(gdata)
LFA33.9916.counts.at.size <- rename.vars(LFA33.9916.counts.at.size, from="x", to="Freq")
summary(LFA33.9916.counts.at.size)
str(LFA33.9916.counts.at.size) #100,527 RECORDS
unique(LFA33.9916.counts.at.size$SIZE_CD) #SIZE 0-16; NO NA VALUES
##SIZE CLASS FREQUENCY TABLE
LFA33.cpue.size = merge(LFA33.9916.traps,LFA33.9916.counts.at.size, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE"),all.x=T,all.y=F, sort=F)
LFA33.0=which(LFA33.cpue.size$SIZE_CD=='0')
LFA33.size0=LFA33.cpue.size[LFA33.0,]
LFA33.size0 = rename.df(LFA33.size0,"Freq", "size0")
LFA33.size0$SIZE_CD=NULL
LFA33.2=which(LFA33.cpue.size$SIZE_CD=='2')
LFA33.size2=LFA33.cpue.size[LFA33.2,]
LFA33.size2 = rename.df(LFA33.size2, "Freq", "size2")
LFA33.size2$SIZE_CD=NULL
LFA33.0.2 = merge(LFA33.size0,LFA33.size2, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA33.3=which(LFA33.cpue.size$SIZE_CD=='3')
LFA33.size3=LFA33.cpue.size[LFA33.3,]
LFA33.size3 = rename.df(LFA33.size3, "Freq", "size3")
LFA33.size3$SIZE_CD=NULL
LFA33.0.3 = merge(LFA33.0.2,LFA33.size3, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA33.4=which(LFA33.cpue.size$SIZE_CD=='4')
LFA33.size4=LFA33.cpue.size[LFA33.4,]
LFA33.size4 = rename.df(LFA33.size4, "Freq", "size4")
LFA33.size4$SIZE_CD=NULL
LFA33.0.4 = merge(LFA33.0.3,LFA33.size4, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA33.5=which(LFA33.cpue.size$SIZE_CD=='5')
LFA33.size5=LFA33.cpue.size[LFA33.5,]
LFA33.size5 = rename.df(LFA33.size5, "Freq", "size5")
LFA33.size5$SIZE_CD=NULL
LFA33.0.5 = merge(LFA33.0.4,LFA33.size5, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA33.6=which(LFA33.cpue.size$SIZE_CD=='6')
LFA33.size6=LFA33.cpue.size[LFA33.6,]
LFA33.size6 = rename.df(LFA33.size6, "Freq", "size6")
LFA33.size6$SIZE_CD=NULL
LFA33.0.6 = merge(LFA33.0.5,LFA33.size6, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA33.7=which(LFA33.cpue.size$SIZE_CD=='7')
LFA33.size7=LFA33.cpue.size[LFA33.7,]
LFA33.size7 = rename.df(LFA33.size7, "Freq", "size7")
LFA33.size7$SIZE_CD=NULL
LFA33.0.7 = merge(LFA33.0.6,LFA33.size7, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA33.8=which(LFA33.cpue.size$SIZE_CD=='8')
LFA33.size8=LFA33.cpue.size[LFA33.8,]
LFA33.size8 = rename.df(LFA33.size8, "Freq", "size8")
LFA33.size8$SIZE_CD=NULL
LFA33.0.8 = merge(LFA33.0.7,LFA33.size8, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA33.9=which(LFA33.cpue.size$SIZE_CD=='9')
LFA33.size9=LFA33.cpue.size[LFA33.9,]
LFA33.size9 = rename.df(LFA33.size9, "Freq", "size9")
LFA33.size9$SIZE_CD=NULL
LFA33.0.9 = merge(LFA33.0.8,LFA33.size9, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA33.10.1=which(LFA33.cpue.size$SIZE_CD=='10.1')
LFA33.size10.1=LFA33.cpue.size[LFA33.10.1,]
LFA33.size10.1 = rename.df(LFA33.size10.1, "Freq", "size10.1")
LFA33.size10.1$SIZE_CD=NULL
LFA33.0.10.1 = merge(LFA33.0.9,LFA33.size10.1, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA33.10.2=which(LFA33.cpue.size$SIZE_CD=='10.2')
LFA33.size10.2=LFA33.cpue.size[LFA33.10.2,]
LFA33.size10.2 = rename.df(LFA33.size10.2, "Freq", "size10.2")
LFA33.size10.2$SIZE_CD=NULL
LFA33.0.10.2 = merge(LFA33.0.10.1,LFA33.size10.2, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA33.11=which(LFA33.cpue.size$SIZE_CD=='11')
LFA33.size11=LFA33.cpue.size[LFA33.11,]
LFA33.size11 = rename.df(LFA33.size11, "Freq", "size11")
LFA33.size11$SIZE_CD=NULL
LFA33.0.11 = merge(LFA33.0.10.2,LFA33.size11, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA33.12=which(LFA33.cpue.size$SIZE_CD=='12')
LFA33.size12=LFA33.cpue.size[LFA33.12,]
LFA33.size12 = rename.df(LFA33.size12, "Freq", "size12")
LFA33.size12$SIZE_CD=NULL
LFA33.0.12 = merge(LFA33.0.11,LFA33.size12, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA33.13=which(LFA33.cpue.size$SIZE_CD=='13')
LFA33.size13=LFA33.cpue.size[LFA33.13,]
LFA33.size13 = rename.df(LFA33.size13, "Freq", "size13")
LFA33.size13$SIZE_CD=NULL
LFA33.0.13 = merge(LFA33.0.12,LFA33.size13, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA33.14=which(LFA33.cpue.size$SIZE_CD=='14')
LFA33.size14=LFA33.cpue.size[LFA33.14,]
LFA33.size14 = rename.df(LFA33.size14, "Freq", "size14")
LFA33.size14$SIZE_CD=NULL
LFA33.0.14 = merge(LFA33.0.13,LFA33.size14, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA33.15=which(LFA33.cpue.size$SIZE_CD=='15')
LFA33.size15=LFA33.cpue.size[LFA33.15,]
LFA33.size15 = rename.df(LFA33.size15, "Freq", "size15")
LFA33.size15$SIZE_CD=NULL
LFA33.0.15 = merge(LFA33.0.14,LFA33.size15, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA33.16=which(LFA33.cpue.size$SIZE_CD=='16')
LFA33.size16=LFA33.cpue.size[LFA33.16,]
LFA33.size16 = rename.df(LFA33.size16, "Freq", "size16")
LFA33.size16$SIZE_CD=NULL
LFA33.0.16 = merge(LFA33.0.15,LFA33.size16, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA33.0.16[is.na(LFA33.0.16)]=0
summary(LFA33.0.16)
##SIZE CLASS SPECS FOR UNDERSIZED LOBSTERS FROM 1999-2013
LFA33.0.16$shorts=NA
LFA33.0.16$shorts=LFA33.0.16$size0+LFA33.0.16$size2+LFA33.0.16$size3+LFA33.0.16$size4+LFA33.0.16$size5+LFA33.0.16$size6+
LFA33.0.16$size7+LFA33.0.16$size8+LFA33.0.16$size9+LFA33.0.16$size10.1
##SIZE CLASS SPECS FOR LEGAL LOBSTERS FROM 1999-2013
LFA33.0.16$legals=NA
LFA33.0.16$legals=LFA33.0.16$size10.2+LFA33.0.16$size11+LFA33.0.16$size12+LFA33.0.16$size13+
LFA33.0.16$size14+LFA33.0.16$size15+LFA33.0.16$size16
summary(LFA33.0.16)
#Max shorts = 95; Max legals = 33
write.table(LFA33.0.16, file=paste("rec.LFA33.9916.SD1to5.nober.",Sys.Date(),".txt"), row.names=TRUE, col.names=TRUE, sep=" ")
#------------------------------------------LFA34-------------------------------
##LFA 34
LFA34.9916=which(fsrs$LFA==34)
length(LFA34.9916) #308,726 RECORDS DEC_2014
LFA34.9916=fsrs[LFA34.9916,]
summary(LFA34.9916)
##EMPTY TRAPS
e=which(LFA34.9916$LOBSTER_NO==0)
length(e) #5129 RECORDS
##VALIDATE SOAK DAYS:
LFA34.9916$S_LABEL<-as.character(LFA34.9916$S_LABEL)
#out.of.season<-subset(LFA34.9916,S_LABEL=="")
#LFA34.9916$S_LABEL<-recode(LFA34.9916$S_LABEL,"''='2004-2005'")
> table(LFA34.9916$SOAK_DAYS,LFA34.9916$S_LABEL)# A PORTION OF RECORDS HAVE TO HAVE LABEL ADDED - THESE ARE PAST NORMAL SEASON DATES
1998-1999 1999-2000 2000-2001 2001-2002 2002-2003 2003-2004 2004-2005 2005-2006 2006-2007 2007-2008 2008-2009 2009-2010 2010-2011 2011-2012 2012-2013 2013-2014
0.5 0 0 0 129 0 0 0 27 78 13 0 0 0 0 0 0
1 197 3697 8964 12911 11168 7130 10171 10786 10222 6303 6117 7413 6611 8077 5305 4974
2 202 3541 7537 8088 7853 5069 8490 11545 6187 6168 6020 6331 4143 4774 5177 2536
3 37 2191 2481 3856 3683 3177 2833 4807 1727 1957 2030 1953 2105 2369 3242 1630
4 7 705 1237 1776 1803 1464 1128 2431 993 1053 1134 1559 1308 1136 1010 481
5 9 227 698 809 859 559 598 1348 914 861 454 637 749 682 864 525
6 0 192 443 571 533 532 635 717 300 200 361 273 398 379 631 222
7 0 69 462 271 108 616 641 785 142 294 284 204 331 299 319 169
8 0 52 194 374 216 236 268 210 97 121 169 112 247 201 228 148
9 0 105 123 33 167 158 90 230 61 31 32 31 82 280 323 41
10 0 39 75 267 57 62 53 340 40 55 79 10 94 167 287 76
11 0 53 78 42 172 17 99 97 57 30 12 47 40 83 191 18
12 0 42 41 98 39 62 10 110 47 59 4 85 34 131 105 68
13 0 36 55 59 3 52 73 77 4 26 13 27 14 35 34 21
14 0 14 15 13 34 104 21 116 66 13 28 26 5 49 51 4
15 0 2 31 17 66 88 57 28 34 18 12 2 20 11 2 33
16 0 37 43 19 3 34 46 10 15 11 2 0 4 33 7 24
17 0 11 10 0 34 6 0 3 52 13 9 2 5 18 53 31
18 0 0 20 12 33 0 2 8 15 17 4 9 29 38 11 9
19 0 7 17 7 43 6 22 8 15 0 9 30 4 9 14 13
20 0 0 11 8 35 9 14 5 13 2 8 13 0 0 0 34
21 0 3 15 0 4 4 9 0 7 11 7 0 4 0 0 8
22 0 3 13 5 7 0 3 6 3 0 0 0 5 0 0 0
23 0 0 9 4 2 21 5 0 0 3 0 0 23 0 0 6
24 0 4 0 0 12 34 10 0 2 2 2 0 0 2 0 0
25 0 4 0 0 8 16 4 0 0 0 2 5 2 0 0 0
26 0 0 0 0 3 0 0 0 24 0 0 0 8 3 0 0
27 0 8 0 7 19 0 0 0 0 4 0 15 0 4 19 0
28 0 5 7 0 11 38 0 0 0 3 0 0 0 0 15 7
29 0 0 0 0 0 12 0 0 17 0 0 0 0 0 0 0
30 0 0 4 0 23 9 32 24 2 0 2 6 2 0 26 0
31 0 0 0 0 8 0 2 0 2 0 2 0 0 0 0 0
32 0 0 0 0 0 0 0 0 0 7 13 0 7 0 0 0
33 0 0 0 8 0 0 0 0 2 0 0 0 0 0 0 0
34 0 0 0 0 8 0 0 3 0 0 0 0 0 0 0 0
35 0 0 2 3 7 12 0 0 17 0 2 0 3 0 8 0
36 0 0 0 0 0 10 0 0 4 0 2 0 0 0 0 0
37 0 0 0 0 0 2 9 0 0 0 0 0 0 0 0 0
38 0 0 0 0 23 3 16 0 0 0 0 0 12 0 0 0
39 0 0 0 39 0 11 0 0 0 0 0 0 0 0 0 0
40 0 0 0 0 0 16 2 0 3 0 0 0 0 0 11 33
41 0 0 0 0 0 11 0 0 0 0 0 0 0 0 0 0
42 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 0
43 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0
44 0 0 8 0 7 0 0 0 0 0 2 0 0 0 0 0
45 0 0 0 0 0 0 3 0 0 0 0 3 0 0 0 0
46 0 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0
47 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0
48 0 0 5 0 0 5 0 0 0 0 0 0 0 0 0 0
50 0 4 0 0 0 0 0 0 0 0 0 12 9 0 0 0
52 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0
53 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0
54 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0
55 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 0
56 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0
57 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0
59 0 0 16 4 0 0 0 0 0 0 0 0 0 0 0 0
60 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0
61 0 0 0 0 8 0 0 0 0 0 0 0 0 0 0 0
62 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0
65 0 0 0 0 2 0 0 0 0 0 7 0 0 0 0 0
68 0 0 0 0 13 0 0 7 0 0 0 0 0 0 0 0
70 0 0 0 0 10 0 0 14 0 0 19 0 0 0 0 0
72 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0
79 0 0 0 0 0 0 0 0 21 0 0 0 0 0 0 0
80 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0
83 0 0 0 0 18 0 0 0 0 0 0 0 0 0 0 0
84 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0
90 0 0 0 0 0 9 0 0 0 0 0 0 0 0 0 0
92 0 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0
>
write.table(LFA34.9916, file=paste("rec.LFA34 9916.Noremovals.from.datacheck.9916",Sys.Date(),".txt"), row.names=FALSE, col.names=TRUE, sep=" ")
#CPUE PREP FILE
##DAILY AGGREGATE FOR CPUE ANALYSIS:
#SOAK DAY CONSTRAINT:
sd=which(LFA34.9916$SOAK_DAYS > 5)
length(sd) #22,598 RECORDS
LFA34.9916.sd=LFA34.9916[-sd,]
short.soak.days=which(LFA34.9916.sd$SOAK_DAYS < 1)
length(short.soak.days) #247 RECORDS
LFA34.9916.sd=LFA34.9916.sd[-short.soak.days,]
##CALCULATE TRAP # PER DAY
LFA34.9913.traps = compute.unique.lengths( x=LFA34.9913.sd, var="TRAP_NO", index=c("S_LABEL", "VESSEL_CD", "HAUL_DATE") )
LFA34.9913.traps = na.omit (LFA34.9913.traps)
LFA34.9913.traps = rename.df(LFA34.9913.traps,"Freq", "TOT_TRAPS")
summary(LFA34.9913.traps)
str(LFA34.9913.traps) #24,819 RECORDS
#SHOWS NUMBER OF RECORDS WITH TRAP NUMBER DISTRIBUTION PER VESSEL
table(LFA34.9913.traps$TOT_TRAPS,LFA34.9913.traps$VESSEL_CD)
##SIZE CLASS ADJUSTMENT TO SPLIT THE SHORTS AND LEGAL SIZES IN CLASS 10
table(LFA34.9916.sd$SIZE_CD,LFA34.9916.sd$SHORT)
i1= which (LFA34.9913.sd$SIZE_CD==10 & LFA34.9913.sd$SHORT==1)
LFA34.9913.sd[i1,"SIZE_CD"]=10.1
summary(LFA34.9913.sd[i1,])
i2= which (LFA34.9913.sd$SIZE_CD==10 & LFA34.9913.sd$SHORT==0)
LFA34.9913.sd[i2,"SIZE_CD"]=10.2
summary(LFA34.9913.sd[i2,])
str(LFA34.9913.sd)
##REMOVE RECORDS FOR BERRIED BY INCLUDING IN SEX COLUMN - FOR CPUE ANALYSIS
b= which (LFA34.9913.sd$SEX==3)
length (b) #1631 RECORDS
LFA34.9913.sd.noberried=LFA34.9913.sd[-b,]
str(LFA34.9913.sd.noberried)
##CALCULATE TOTAL COUNT PER SIZE CLASS
LFA34.9913.sd.noberried$VESSEL_CD <- as.factor(LFA34.9913.sd.noberried$VESSEL_CD)
LFA34.9913.sd.noberried$SIZE_CD <- as.factor(LFA34.9913.sd.noberried$SIZE_CD)
LFA34.9913.counts.at.size =aggregate(LFA34.9913.sd.noberried[,1], by=as.list(LFA34.9913.sd.noberried[c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "SIZE_CD")]), length, simplify = TRUE)
LFA34.9913.counts.at.size = na.omit (LFA34.9913.counts.at.size)
library(gdata)
LFA34.9913.counts.at.size <- rename.vars(LFA34.9913.counts.at.size, from="x", to="Freq")
summary(LFA34.9913.counts.at.size)
str(LFA34.9913.counts.at.size) #104,705 RECORDS
unique(LFA34.9913.counts.at.size$SIZE_CD) #SIZE 0-16; NO NA VALUES
##SIZE CLASS FREQUENCY TABLE
LFA34.cpue.size = merge(LFA34.9913.traps,LFA34.9913.counts.at.size, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE"),all.x=T,all.y=F, sort=F)
LFA34.0=which(LFA34.cpue.size$SIZE_CD=='0')
LFA34.size0=LFA34.cpue.size[LFA34.0,]
LFA34.size0 = rename.df(LFA34.size0,"Freq", "size0")
LFA34.size0$SIZE_CD=NULL
LFA34.2=which(LFA34.cpue.size$SIZE_CD=='2')
LFA34.size2=LFA34.cpue.size[LFA34.2,]
LFA34.size2 = rename.df(LFA34.size2, "Freq", "size2")
LFA34.size2$SIZE_CD=NULL
LFA34.0.2 = merge(LFA34.size0,LFA34.size2, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA34.3=which(LFA34.cpue.size$SIZE_CD=='3')
LFA34.size3=LFA34.cpue.size[LFA34.3,]
LFA34.size3 = rename.df(LFA34.size3, "Freq", "size3")
LFA34.size3$SIZE_CD=NULL
LFA34.0.3 = merge(LFA34.0.2,LFA34.size3, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA34.4=which(LFA34.cpue.size$SIZE_CD=='4')
LFA34.size4=LFA34.cpue.size[LFA34.4,]
LFA34.size4 = rename.df(LFA34.size4, "Freq", "size4")
LFA34.size4$SIZE_CD=NULL
LFA34.0.4 = merge(LFA34.0.3,LFA34.size4, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA34.5=which(LFA34.cpue.size$SIZE_CD=='5')
LFA34.size5=LFA34.cpue.size[LFA34.5,]
LFA34.size5 = rename.df(LFA34.size5, "Freq", "size5")
LFA34.size5$SIZE_CD=NULL
LFA34.0.5 = merge(LFA34.0.4,LFA34.size5, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA34.6=which(LFA34.cpue.size$SIZE_CD=='6')
LFA34.size6=LFA34.cpue.size[LFA34.6,]
LFA34.size6 = rename.df(LFA34.size6, "Freq", "size6")
LFA34.size6$SIZE_CD=NULL
LFA34.0.6 = merge(LFA34.0.5,LFA34.size6, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA34.7=which(LFA34.cpue.size$SIZE_CD=='7')
LFA34.size7=LFA34.cpue.size[LFA34.7,]
LFA34.size7 = rename.df(LFA34.size7, "Freq", "size7")
LFA34.size7$SIZE_CD=NULL
LFA34.0.7 = merge(LFA34.0.6,LFA34.size7, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA34.8=which(LFA34.cpue.size$SIZE_CD=='8')
LFA34.size8=LFA34.cpue.size[LFA34.8,]
LFA34.size8 = rename.df(LFA34.size8, "Freq", "size8")
LFA34.size8$SIZE_CD=NULL
LFA34.0.8 = merge(LFA34.0.7,LFA34.size8, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA34.9=which(LFA34.cpue.size$SIZE_CD=='9')
LFA34.size9=LFA34.cpue.size[LFA34.9,]
LFA34.size9 = rename.df(LFA34.size9, "Freq", "size9")
LFA34.size9$SIZE_CD=NULL
LFA34.0.9 = merge(LFA34.0.8,LFA34.size9, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA34.10.1=which(LFA34.cpue.size$SIZE_CD=='10.1')
LFA34.size10.1=LFA34.cpue.size[LFA34.10.1,]
LFA34.size10.1 = rename.df(LFA34.size10.1, "Freq", "size10.1")
LFA34.size10.1$SIZE_CD=NULL
LFA34.0.10.1 = merge(LFA34.0.9,LFA34.size10.1, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA34.10.2=which(LFA34.cpue.size$SIZE_CD=='10.2')
LFA34.size10.2=LFA34.cpue.size[LFA34.10.2,]
LFA34.size10.2 = rename.df(LFA34.size10.2, "Freq", "size10.2")
LFA34.size10.2$SIZE_CD=NULL
LFA34.0.10.2 = merge(LFA34.0.10.1,LFA34.size10.2, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA34.11=which(LFA34.cpue.size$SIZE_CD=='11')
LFA34.size11=LFA34.cpue.size[LFA34.11,]
LFA34.size11 = rename.df(LFA34.size11, "Freq", "size11")
LFA34.size11$SIZE_CD=NULL
LFA34.0.11 = merge(LFA34.0.10.2,LFA34.size11, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA34.12=which(LFA34.cpue.size$SIZE_CD=='12')
LFA34.size12=LFA34.cpue.size[LFA34.12,]
LFA34.size12 = rename.df(LFA34.size12, "Freq", "size12")
LFA34.size12$SIZE_CD=NULL
LFA34.0.12 = merge(LFA34.0.11,LFA34.size12, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA34.13=which(LFA34.cpue.size$SIZE_CD=='13')
LFA34.size13=LFA34.cpue.size[LFA34.13,]
LFA34.size13 = rename.df(LFA34.size13, "Freq", "size13")
LFA34.size13$SIZE_CD=NULL
LFA34.0.13 = merge(LFA34.0.12,LFA34.size13, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA34.14=which(LFA34.cpue.size$SIZE_CD=='14')
LFA34.size14=LFA34.cpue.size[LFA34.14,]
LFA34.size14 = rename.df(LFA34.size14, "Freq", "size14")
LFA34.size14$SIZE_CD=NULL
LFA34.0.14 = merge(LFA34.0.13,LFA34.size14, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA34.15=which(LFA34.cpue.size$SIZE_CD=='15')
LFA34.size15=LFA34.cpue.size[LFA34.15,]
LFA34.size15 = rename.df(LFA34.size15, "Freq", "size15")
LFA34.size15$SIZE_CD=NULL
LFA34.0.15 = merge(LFA34.0.14,LFA34.size15, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA34.16=which(LFA34.cpue.size$SIZE_CD=='16')
LFA34.size16=LFA34.cpue.size[LFA34.16,]
LFA34.size16 = rename.df(LFA34.size16, "Freq", "size16")
LFA34.size16$SIZE_CD=NULL
LFA34.0.16 = merge(LFA34.0.15,LFA34.size16, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA34.0.16[is.na(LFA34.0.16)]=0
summary(LFA34.0.16)
##SIZE CLASS SPECS FOR UNDERSIZED LOBSTERS FROM 1999-2013
LFA34.0.16$shorts=NA
LFA34.0.16$shorts=LFA34.0.16$size0+LFA34.0.16$size2+LFA34.0.16$size3+LFA34.0.16$size4+LFA34.0.16$size5+LFA34.0.16$size6+
LFA34.0.16$size7+LFA34.0.16$size8+LFA34.0.16$size9+LFA34.0.16$size10.1
##SIZE CLASS SPECS FOR LEGAL LOBSTERS FROM 1999-2013
LFA34.0.16$legals=NA
LFA34.0.16$legals=LFA34.0.16$size10.2+LFA34.0.16$size11+LFA34.0.16$size12+LFA34.0.16$size13+
LFA34.0.16$size14+LFA34.0.16$size15+LFA34.0.16$size16
summary(LFA34.0.16)
#Max shorts = 146; Max legals = 35
write.table(LFA34.0.16, file=paste("rec.LFA34.9913.SD1to5.nober.",Sys.Date(),".txt"), row.names=TRUE, col.names=TRUE, sep=" ")
#------------------------------------------LFA35-------------------------------
##LFA 35
LFA35.9916=which(fsrs$LFA==35)
length(LFA35.9916) #58,406 RECORDS MAY_2014
LFA35.9916=fsrs[LFA35.9916,]
summary(LFA35.9916)
##EMPTY TRAPS
e=which(LFA35.9913$LOBSTER_NO==0)
length(e) #505 RECORDS
##VALIDATE SOAK DAYS:
LFA35.9916$S_LABEL<-as.character(LFA35.9916$S_LABEL)
> table(LFA35.9916$SOAK_DAYS,LFA35.9916$S_LABEL)
2007 2008 2009 2010 2011 2012 2013
1 1262 413 1438 886 1061 1916 1974
2 1480 1021 2390 1691 3237 2749 1862
3 661 355 3117 2878 2267 2804 1527
4 420 76 1435 1874 1290 1872 853
5 250 57 1233 974 1361 789 832
6 139 71 496 509 569 467 284
7 9 0 696 444 436 416 270
8 0 0 78 132 234 189 228
9 22 0 29 160 256 124 165
10 80 6 168 49 91 119 21
11 7 0 0 51 12 18 8
12 0 0 0 36 58 25 0
13 0 0 0 0 0 29 0
14 0 23 79 0 23 0 7
15 0 0 25 22 0 0 20
16 0 0 0 0 29 38 0
17 12 0 0 0 0 0 0
18 0 0 0 0 9 0 0
19 0 0 0 36 0 0 0
30 0 0 0 0 0 0 13
36 0 0 16 0 0 0 0
>
write.table(LFA35.9913f, file=paste("rec.LFA35 9913.Noremovals.from.datacheck.9913",Sys.Date(),".txt"), row.names=FALSE, col.names=TRUE, sep=" ")
#CPUE PREP FILE
#DAILY AGGREGATE FOR CPUE ANALYSIS
#SOAK DAY CONSTRAINT:
sd=which(LFA35.9913$SOAK_DAYS > 5)
length(sd) # 7584 RECORDS
LFA35.9913.sd=LFA35.9913[-sd,]
##CALCULATE TRAP # PER DAY
LFA35.9913.traps = compute.unique.lengths( x=LFA35.9913.sd, var="TRAP_NO", index=c("S_LABEL", "VESSEL_CD", "HAUL_DATE") )
LFA35.9913.traps = na.omit (LFA35.9913.traps)
LFA35.9913.traps = rename.df(LFA35.9913.traps,"Freq", "TOT_TRAPS")
summary(LFA35.9913.traps)
str(LFA35.9913.traps) # 1960 RECORDS
#SHOWS NUMBER OF RECORDS WITH TRAP NUMBER DISTRIBUTION PER VESSEL
table(LFA35.9913.traps$TOT_TRAPS,LFA35.9913.traps$VESSEL_CD)
##SIZE CLASS ADJUSTMENT TO SPLIT THE SHORTS AND LEGAL SIZES IN CLASS 10
table(LFA35.9913.sd$SIZE_CD,LFA35.9913.sd$SHORT)
j1= which (LFA35.9913.sd$SIZE_CD==10 & LFA35.9913.sd$SHORT==1)
LFA35.9913.sd[j1,"SIZE_CD"]=10.1
summary(LFA35.9913.sd[j1,])
j2= which (LFA35.9913.sd$SIZE_CD==10 & LFA35.9913.sd$SHORT==0)
LFA35.9913.sd[j2,"SIZE_CD"]=10.2
summary(LFA35.9913.sd[j2,])
str(LFA35.9913.sd)
##REMOVE RECORDS FOR BERRIED BY INCLUDING IN SEX COLUMN - FOR CPUE ANALYSIS
b= which (LFA35.9913.sd$SEX==3)
length (b) #521 RECORDS
LFA35.9913.sd.noberried=LFA35.9913.sd[-b,]
str(LFA35.9913.sd.noberried)
##CALCULATE TOTAL COUNT PER SIZE CLASS
LFA35.9913.sd.noberried$VESSEL_CD <- as.factor(LFA35.9913.sd.noberried$VESSEL_CD)
LFA35.9913.sd.noberried$SIZE_CD <- as.factor(LFA35.9913.sd.noberried$SIZE_CD)
LFA35.9913.counts.at.size =aggregate(LFA35.9913.sd.noberried[,1], by=as.list(LFA35.9913.sd.noberried[c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "SIZE_CD")]), length, simplify = TRUE)
LFA35.9913.counts.at.size = na.omit (LFA35.9913.counts.at.size)
library(gdata)
LFA35.9913.counts.at.size <- rename.vars(LFA35.9913.counts.at.size, from="x", to="Freq")
summary(LFA35.9913.counts.at.size)
str(LFA35.9913.counts.at.size) #12,982 RECORDS
unique(LFA35.9913.counts.at.size$SIZE_CD) #SIZE 2-16; NO NA VALUES
##SIZE CLASS FREQUENCY TABLE
LFA35.cpue.size = merge(LFA35.9913.traps,LFA35.9913.counts.at.size, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE"),all.x=T,all.y=F, sort=F)
LFA35.2=which(LFA35.cpue.size$SIZE_CD=='2')
LFA35.size2=LFA35.cpue.size[LFA35.2,]
LFA35.size2 = rename.df(LFA35.size2, "Freq", "size2")
LFA35.size2$SIZE_CD=NULL
LFA35.3=which(LFA35.cpue.size$SIZE_CD=='3')
LFA35.size3=LFA35.cpue.size[LFA35.3,]
LFA35.size3 = rename.df(LFA35.size3, "Freq", "size3")
LFA35.size3$SIZE_CD=NULL
LFA35.2.3 = merge(LFA35.2,LFA35.size3, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA35.4=which(LFA35.cpue.size$SIZE_CD=='4')
LFA35.size4=LFA35.cpue.size[LFA35.4,]
LFA35.size4 = rename.df(LFA35.size4, "Freq", "size4")
LFA35.size4$SIZE_CD=NULL
LFA35.2.4 = merge(LFA35.2.3,LFA35.size4, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA35.5=which(LFA35.cpue.size$SIZE_CD=='5')
LFA35.size5=LFA35.cpue.size[LFA35.5,]
LFA35.size5 = rename.df(LFA35.size5, "Freq", "size5")
LFA35.size5$SIZE_CD=NULL
LFA35.2.5 = merge(LFA35.2.4,LFA35.size5, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA35.6=which(LFA35.cpue.size$SIZE_CD=='6')
LFA35.size6=LFA35.cpue.size[LFA35.6,]
LFA35.size6 = rename.df(LFA35.size6, "Freq", "size6")
LFA35.size6$SIZE_CD=NULL
LFA35.2.6 = merge(LFA35.2.5,LFA35.size6, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA35.7=which(LFA35.cpue.size$SIZE_CD=='7')
LFA35.size7=LFA35.cpue.size[LFA35.7,]
LFA35.size7 = rename.df(LFA35.size7, "Freq", "size7")
LFA35.size7$SIZE_CD=NULL
LFA35.2.7 = merge(LFA35.2.6,LFA35.size7, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA35.8=which(LFA35.cpue.size$SIZE_CD=='8')
LFA35.size8=LFA35.cpue.size[LFA35.8,]
LFA35.size8 = rename.df(LFA35.size8, "Freq", "size8")
LFA35.size8$SIZE_CD=NULL
LFA35.2.8 = merge(LFA35.2.7,LFA35.size8, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA35.9=which(LFA35.cpue.size$SIZE_CD=='9')
LFA35.size9=LFA35.cpue.size[LFA35.9,]
LFA35.size9 = rename.df(LFA35.size9, "Freq", "size9")
LFA35.size9$SIZE_CD=NULL
LFA35.2.9 = merge(LFA35.2.8,LFA35.size9, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA35.10.1=which(LFA35.cpue.size$SIZE_CD=='10.1')
LFA35.size10.1=LFA35.cpue.size[LFA35.10.1,]
LFA35.size10.1 = rename.df(LFA35.size10.1, "Freq", "size10.1")
LFA35.size10.1$SIZE_CD=NULL
LFA35.2.10.1 = merge(LFA35.2.9,LFA35.size10.1, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA35.10.2=which(LFA35.cpue.size$SIZE_CD=='10.2')
LFA35.size10.2=LFA35.cpue.size[LFA35.10.2,]
LFA35.size10.2 = rename.df(LFA35.size10.2, "Freq", "size10.2")
LFA35.size10.2$SIZE_CD=NULL
LFA35.2.10.2 = merge(LFA35.2.10.1,LFA35.size10.2, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA35.11=which(LFA35.cpue.size$SIZE_CD=='11')
LFA35.size11=LFA35.cpue.size[LFA35.11,]
LFA35.size11 = rename.df(LFA35.size11, "Freq", "size11")
LFA35.size11$SIZE_CD=NULL
LFA35.2.11 = merge(LFA35.2.10.2,LFA35.size11, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA35.12=which(LFA35.cpue.size$SIZE_CD=='12')
LFA35.size12=LFA35.cpue.size[LFA35.12,]
LFA35.size12 = rename.df(LFA35.size12, "Freq", "size12")
LFA35.size12$SIZE_CD=NULL
LFA35.2.12 = merge(LFA35.2.11,LFA35.size12, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA35.13=which(LFA35.cpue.size$SIZE_CD=='13')
LFA35.size13=LFA35.cpue.size[LFA35.13,]
LFA35.size13 = rename.df(LFA35.size13, "Freq", "size13")
LFA35.size13$SIZE_CD=NULL
LFA35.2.13 = merge(LFA35.2.12,LFA35.size13, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA35.14=which(LFA35.cpue.size$SIZE_CD=='14')
LFA35.size14=LFA35.cpue.size[LFA35.14,]
LFA35.size14 = rename.df(LFA35.size14, "Freq", "size14")
LFA35.size14$SIZE_CD=NULL
LFA35.2.14 = merge(LFA35.2.13,LFA35.size14, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA35.15=which(LFA35.cpue.size$SIZE_CD=='15')
LFA35.size15=LFA35.cpue.size[LFA35.15,]
LFA35.size15 = rename.df(LFA35.size15, "Freq", "size15")
LFA35.size15$SIZE_CD=NULL
LFA35.2.15 = merge(LFA35.2.14,LFA35.size15, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA35.16=which(LFA35.cpue.size$SIZE_CD=='16')
LFA35.size16=LFA35.cpue.size[LFA35.16,]
LFA35.size16 = rename.df(LFA35.size16, "Freq", "size16")
LFA35.size16$SIZE_CD=NULL
LFA35.2.16 = merge(LFA35.2.15,LFA35.size16, by=c("S_LABEL", "VESSEL_CD", "HAUL_DATE", "TOT_TRAPS"),all.x=T,all.y=T, sort=F)
LFA35.2.16[is.na(LFA35.2.16)]=0
summary(LFA35.2.16)
##SIZE CLASS SPECS FOR UNDERSIZED LOBSTERS FROM 1999-2013
LFA35.2.16$shorts=NA
LFA35.2.16$shorts=LFA35.2.16$size0+LFA35.2.16$size2+LFA35.2.16$size3+LFA35.2.16$size4+LFA35.2.16$size5+LFA35.2.16$size6+
LFA35.2.16$size7+LFA35.2.16$size8+LFA35.2.16$size9+LFA35.2.16$size10.1
##SIZE CLASS SPECS FOR LEGAL LOBSTERS FROM 1999-2013
LFA35.2.16$legals=NA
LFA35.2.16$legals=LFA35.2.16$size10.2+LFA35.2.16$size11+LFA35.2.16$size12+LFA35.2.16$size13+
LFA35.2.16$size14+LFA35.2.16$size15+LFA35.2.16$size16
summary(LFA35.2.16)
#Max shorts = 146; Max legals = 35
write.table(LFA35.2.16, file=paste("rec.LFA35.9913.SD1to5.nober.",Sys.Date(),".txt"), row.names=TRUE, col.names=TRUE, sep=" ")
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