inst/OldPotentiallyDepricatedCode/3.SurveyDesignScript.r
In LobsterScience/bio.lobster: Lobster Stock Assessment Tools for DFO Maritimes
#------------------------- ecosystem survey data
p = bio.lobster::load.environment()
p = bio.groundfish::load.groundfish.environment(assessment.year = 2016)
odbc.data.yrs=1970:2015
groundfish.db( DS="gscat.redo" )
groundfish.db( DS="gsdet.redo" )
groundfish.db( DS="gsinf.redo" )
gi = groundfish.db('gsinf')
gc = groundfish.db('gscat')
gc = gc[which(gc$spec==2550),]
gic = merge(gi,gc,by='id',all.x=T)
i = which(is.na(gic$spec))
gic$spec[i] = 2550
gic$totno[i] = 0
gic$totwgt[i] = 0
gic = makePBS(gic,polygon=F)
#abundance and weight in per km2
gic$totwgt = gic$totwgt / gic$dist_km
gic$totno = gic$totno / gic$dist_km
# select for LFA 34
LFAs<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFAPolys.csv"))
LFAgrid<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","GridPolys.csv"))
LFAgrid<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFAgridPolys.csv"))
# Multibeam
gerbk50 <-read.csv(file.path( project.datadirectory("bio.bathymetry"),"data","GermanBathy","gerbk_50.txt"))
key<-read.csv(file.path( project.datadirectory("bio.bathymetry"),"data","GermanBathy","fileKey.csv"))
# groundfish survey
gfkey<-findPolys(na.omit(gic[c('X','Y','EID')]),LFAs)
gic=merge(gic,gfkey[c('EID','PID')],all=T)
gic34=subset(gic,PID==34)
### create Map1
pdf('SDlfa34map1.pdf')
assignStation(subset(gic34,yr>1970,c('EID','X','Y')),maxdist=0.07,res=0.005,expwin=0.05,map='34')
noRVgrids=c(69,81,92,103,114,125:127,137:141,153:159,170:177,188:193,207:210)
addPolys(subset(LFA34grid,SID%in%noRVgrids),col=rgb(1,0,0,0.2))
median(with(subset(gic34,yr>=1999),tapply(EID,yr,length)))
stations= read.csv(file.path(project.datadirectory('bio.lobster'),"data","products","surveyStations.csv"))
stations$EID=stations$SID
addPoints(stations,pch=16)
Stns32<-read.csv(file.path(project.datadirectory('bio.lobster'),'data',"survey32Stations.csv"))
indexStns=subset(stations,SID%in%Stns32$SID)
addPoints(indexStns,pch=16,col='green')
with(indexStns,text(X,Y,SID,pos=4,col='darkgreen',cex=0.5))
dev.off()
#typical number of RV tow in 34
median(with(subset(gic34,yr>=1999),tapply(EID,yr,length)))
LFA34poly=subset(LFAs,PID==34)
LFA34grid=subset(LFAgrid,PID==34)
###-------------- Create polygons
LobsterMap('34',labels='grid',labcex=0.5)
innerGrids=c(69,81,92,101:103,112:114,123:127,136:141,152:159,170:177,188:193,207:210)
addPolys(subset(LFA34grid,SID%in%innerGrids),col=rgb(1,0,0,0.2))
junk<-data.frame(PID=1,POS=1:4,X=c(162,161,161,162),Y=c(-41,-41,-40,-40))
innerGridPoly1=joinPolys(subset(LFA34grid,SID%in%innerGrids),junk,operation="DIFF")
LFA34poly=subset(LFAs,PID==34)
innerGridPoly<-joinPolys(innerGridPoly1,LFA34poly,operation="INT")
outerGridPoly<-joinPolys(LFA34poly,innerGridPoly,operation="DIFF")
MBpoly=outerBounds(gerbk50)
# map of survey polygons
pdf(file.path(project.datadirectory("lobster"),"figures","SurveyDesign","LFA34SurveyPolygons.pdf"),9,9)
LobsterMap('34',labels='grid',labcex=0.5)
addPolys(innerGridPoly,col=rgb(1,0,0,0.3))
addPolys(outerGridPoly,col=rgb(0,0,1,0.3))
addPolys(MBpoly,col=rgb(0,1,0,0.3))
#with(gerbk50,points(X,Y,pch='.'))
addPoints(indexStns,pch=21,bg='yellow')
with(indexStns,text(X,Y,SID,pos=4,cex=0.5))
dev.off()
innerGridPoly<-joinPolys(innerGridPoly,MBpoly,operation="DIFF")
outerGridPoly<-joinPolys(outerGridPoly,MBpoly,operation="DIFF")
innerGridPoly$PID=1
outerGridPoly$PID=3
LFA34surveyPolys=rbind(innerGridPoly,MBpoly,outerGridPoly)
write.csv(LFA34surveyPolys,file.path(project.datadirectory('bio.lobster'),"data","products","LFA34surveyPolys.csv"),row.names=F)
LFA34surveyPolys = read.csv(file.path(project.datadirectory('bio.lobster'),"data","products","LFA34surveyPolys.csv"))
###-------------- Determine allocation
attr(LFA34surveyPolys,"projection")<-"LL"
polyAreas=calcArea(LFA34surveyPolys,1)
areaAlloc=round(polyAreas$area/sum(polyAreas$area)*120)
areaAlloc[3]=areaAlloc[3]-20
iStnkey=findPolys(indexStns,LFA34surveyPolys)
iStnAlloc=with(iStnkey,tapply(EID,PID,length))
newAlloc=areaAlloc-iStnAlloc
otherStns=subset(stations,!SID%in%Stns32$SID)
oStnkey=findPolys(otherStns,LFA34surveyPolys)
oStnAlloc=with(oStnkey,tapply(EID,PID,length))
P3adds=otherStns[c(4, 5, 7, 8, 10, 12, 14, 18, 19, 23, 24, 30, 38, 42),]
P1adds=otherStns[c(17, 20, 27, 28, 29, 33, 34, 41, 44, 45, 47, 48, 49, 55, 61),]
LobsterMap('34',labels='grid',labcex=0.5)
addPolys(innerGridPoly,col=rgb(1,0,0,0.3))
addPolys(outerGridPoly,col=rgb(0,0,1,0.3))
addPolys(MBpoly,col=rgb(0,1,0,0.3))
addPoints(indexStns,pch=21,bg='yellow')
addPoints(otherStns,pch=16,col='grey')
addPoints(P1adds,pch=21,bg='orange')
addPoints(P3adds,pch=21,bg='orange')
repeatStns=rbind(indexStns,P1adds,P3adds)
rStnkey=findPolys(repeatStns,LFA34surveyPolys)
repeatStns=with(merge(repeatStns,rStnkey,by='EID',all=T),data.frame(EID,X,Y,PID))
rStnAlloc=with(rStnkey,tapply(EID,PID,length))
newAlloc=areaAlloc-rStnAlloc
LFA34surveyPolyData=data.frame(PID=1:3,col=c(rgb(1,0,0,0.3),rgb(0,1,0,0.3),rgb(0,0,1,0.3)),PName=c("inner","multibeam","outer"),allocation=newAlloc,repeats=rStnAlloc)
towlst<-alloc.poly(poly.lst=list(LFA34surveyPolys, LFA34surveyPolyData),ntows=100,pool.size=3,mindist=5,repeated.tows=repeatStns,map='34',show.pool=T,UTMzone=20)
file.key<-read.csv(file.path( project.datadirectory("bathymetry"),"data","GermanBathy","fileKey.csv"))
Relief.plots(subset(towlst$Tows$new.tows,STRATA=='multibeam'),graphic="pdf",file=file.path(project.datadirectory('lobster'),'figures','SurveyDesign','SurveyMB','2016','Tow'),digits=4,gerfiles=1:77,key=file.key)
save.image(file.path(project.datadirectory("lobster"),"R","LFA34SurveyDesign2016.Rdata"))
load(file.path(project.datadirectory("lobster"),"R","LFA34SurveyDesign2016.Rdata"))
pdf("Survey2016.pdf",8,11)
LobsterMap('34',labels='grid',labcex=0.5)
addPolys(innerGridPoly,col=rgb(1,0,0,0.3))
addPolys(outerGridPoly,col=rgb(0,0,1,0.3))
addPolys(MBpoly,col=rgb(0,1,0,0.3))
addPoints(towlst$Tows$new.tows,pch=21,cex=0.5,bg='orange')
addPoints(towlst$Tows$repeated.tows,pch=21,cex=0.5,bg='orange')
MBtows=subset(towlst$Tows$new.tows,Poly.ID==2)
MBtows$label=MBtows$EID
MBtows$Y= MBtows$Y-0.03
addLabels(as.EventData(MBtows),cex=0.7)
dev.off()
MBEIDs=c(5,6,9,10,13,15,18,23,24,25,27,28,29,30,31,34,35,36,38,40)
new.tows <- rbind(subset(towlst$Tows$new.tows,Poly.ID==2&EID%in%MBEIDs),subset(towlst$Tows$new.tows,Poly.ID!=2&!EID%in%c(2,51,56)),data.frame(EID=c(2,51,56),X=c(-66.312,-67.031,-66.854),Y=c(42.969,43.5,43.854),Poly.ID=c(1,3,3),STRATA=c("inner","outer","outer"),nndist=NA))
pdf(file.path(project.datadirectory('lobster'),'figures','SurveyDesign','SurveyMB','2016',"Survey2016.pdf"),8,11)
LobsterMap('34',labels='grid',labcex=0.5)
addPolys(innerGridPoly,col=rgb(1,0,0,0.3))
addPolys(outerGridPoly,col=rgb(0,0,1,0.3))
addPolys(MBpoly,col=rgb(0,1,0,0.3))
addPoints(new.tows,pch=21,cex=0.6,bg='orange')
addPoints(towlst$Tows$repeated.tows,pch=21,cex=0.6,bg='red')
labtows=rbind(new.tows[,-6],towlst$Tows$repeated.tows)
labtows$label=labtows$EID
labtows$Y= labtows$Y-0.03
addLabels(as.EventData(labtows),cex=0.7)
dev.off()
test.tow=data.frame(EID=1:2,X=c(-66.34800,),Y=c(43.27362,)
new.tows
file.key<-read.csv(file.path( project.datadirectory("bathymetry"),"data","GermanBathy","fileKey.csv"))
Relief.plots(subset(new.tows,STRATA=='multibeam'),graphic="pdf",file=file.path(project.datadirectory('lobster'),'figures','SurveyDesign','SurveyMB','2016','Tow'),digits=4,gerfiles=1:77,key=file.key)
Relief.plots(subset(towlst$Tows$repeated.tows,STRATA=='multibeam'),graphic="pdf",file=file.path(project.datadirectory('lobster'),'figures','SurveyDesign','SurveyMB','2016','Tow'),digits=4,gerfiles=1:77,key=file.key)
################################################################################################################################################################################################################
#
# extra stuff
#
#####################################################
# # key to files for german MB res 5m
# pdf(file.path(project.datadirectory("lobster"),"figures","SurveyDesign","LFA34MultibeamExtent.pdf"),9,9)
# key<-read.csv(file.path( project.datadirectory("bathymetry"),"data","GermanBathy","fileKey.csv"))
# LobsterMap('34',labels='grid',labcex=0.5,isobath=c(50,100,200),bathy.source='bathy')
# with(key,rect(X1,Y1,X2,Y2,col='black'))
# dev.off()
#
#
#
# calcArea(LFA34grid2)
# key<-findPolys(na.omit(gic[c('X','Y','EID')]),LFAs)
# gic=merge(gic,key[c('EID','PID')],all=T)
# gic34=subset(gic,PID==34)
#
# assignStation(subset(gic34,yr>1970,c('EID','X','Y')),maxdist=0.07,res=0.005,expwin=0.05,map='34')
# median(with(subset(gic34,yr>=1999),tapply(EID,yr,length)))
# gfpoly<-gic34[chull(gic34$X,gic34$Y),c("X","Y")]
# gfpoly$PID=1
# gfpoly$POS=1:nrow(gfpoly)
# addPolys(gfpoly)
# innerGrids=c(69,81,92,101:103,112:114,123:127,136:141,152:159,170:177,188:193,207:210)
# addPolys(subset(LFA34grid,SID%in%innerGrids),col=rgb(1,0,0,0.2))
# junk<-data.frame(PID=1,POS=1:4,X=c(162,161,161,162),Y=c(-41,-41,-40,-40))
# innerGridPoly=joinPolys(subset(LFA34grid,SID%in%innerGrids),junk,operation="DIFF")
# coastalGrids=c(69,81,92,103,114,125:127,137:141,153:159,170:177,188:193,207:210)
# LobsterMap('34',labels='grid',labcex=0.5)
# addPoints(na.omit(gic[which(gic$yr==2015),c('X','Y','EID')]),pch=16,col='red',cex=0.75)
# addPoints(na.omit(gic[which(gic$yr>=1999),c('X','Y','EID')]),pch=16,col='red',cex=0.75)
# addPoints(na.omit(gic[which(gic$yr>=1999 & gic$totno>0),c('X','Y','EID')]),pch=16,col='green',cex=0.75) #lobster only
#
#require(PBSmapping)
#require(RColorBrewer)
#loadfunctions('lobster')
#
#extent<-data.frame(PID=1,POS=1:4,X=c(-66.3,-65.4,-65.4,-66.3),Y=c(43.15,43.15,43.8,43.8))
#attr(extent,"projection")<-"LL"
#
#
#load(file.path(project.datadirectory("substrate"),"data","InshoreSubstrate.rdata"))
#
#subpoly.data<-read.csv(file.path(project.datadirectory("substrate"),"data","SubPolyData.csv"))
#subpoly.data$col<-brewer.pal(10,"Set3")
#subpoly.data$border<-NA
#
#attr(substrate,"projection")<-"UTM"
#attr(substrate,"zone")<-20
#substrate<-convUL(substrate,km=F)
#
#LBsubstrate<-joinPolys(substrate,extent,operation="INT")
#
#pdf(file.path(project.datadirectory("lobster"),"R","LobsterBaySubstrate.pdf"),9,9)
#LobsterMap(xlim=c(-66.35,-65.35),ylim=c(43.1,43.85),poly.lst=list(LBsubstrate,subpoly.data),isobath=40,bathcol='blue',bathy.source='bathy',mapRes="UR")
#with(subset(subpoly.data,PID%in%unique(LBsubstrate$PID)),legend('topright',PName,fill=col,inset=0.02,cex=0.8,bg='white'))
#dev.off()
#
#load(file.path( project.datadirectory("lobster"), "data","maps", "bathy", "bathyPoly1.rdata"))
#LBsubstrate<-joinPolys(LBsubstrate,subset(bathy.poly,Z==40),operation="INT")
#LFAs<-read.csv(file.path(project.datadirectory('lobster'),'data','maps','Polygons_LFA.csv'))
#LBsubstrate<-joinPolys(LBsubstrate,subset(LFAs,LFA=='34'),operation="INT")
#
#
## repeated index stations
#LFA34TrawlStations2015<-read.csv(file.path(project.datadirectory("lobster"),"data","LFA34TrawlStations2015.csv"))
#LFA34TrawlStations2015$EID<-1:nrow(LFA34TrawlStations2015)
#names(LFA34TrawlStations2015)[2:3]<-c("Y","X")
#key<-findPolys(LFA34TrawlStations2015,LBsubstrate)
#repeatStations<-merge(LFA34TrawlStations2015,key)
#
#LB.towlst<-alloc.poly(poly.lst=list(LBsubstrate, subpoly.data),ntows=20,mindist=2)
#
#pdf(file.path(project.datadirectory("lobster"),"R","LobsterBaySurvey2015.pdf"),9,9)
#LobsterMap(xlim=c(-66.35,-65.35),ylim=c(43.1,43.85),poly.lst=list(LBsubstrate,subpoly.data),isobath=c(20,40,70,100),bathy.source='bathy',mapRes="UR")
#with(subset(subpoly.data,PID%in%unique(LBsubstrate$PID)),legend('topright',paste(PID,PName),fill=col,inset=0.02,cex=0.8,bg='white'))
#addPoints(LB.towlst$Tows)
#points(Y~X,repeatStations,pch=2)
#dev.off()
#write.csv(LB.towlst$Tows,file.path(project.datadirectory('lobster'),'R','LFA34extraSurveyStation2015.csv'))
#
## Take 2
#
#extent<-data.frame(PID=1,POS=1:4,X=c(-66.05,-65.7,-65.7,-66.05),Y=c(43.15,43.15,43.8,43.8))
#attr(extent,"projection")<-"LL"
#
#
#load(file.path(project.datadirectory("substrate"),"data","InshoreSubstrate.rdata"))
#
#bathpoly.data<-data.frame
#subpoly.data$col<-brewer.pal(10,"Set3")
#subpoly.data$border<-NA
#
#attr(substrate,"projection")<-"UTM"
#attr(substrate,"zone")<-20
#substrate<-convUL(substrate,km=F)
#
#LBsubstrate<-joinPolys(substrate,extent,operation="INT")
#
#pdf(file.path(project.datadirectory("lobster"),"R","LobsterBaySubstrate.pdf"),9,9)
#LobsterMap(xlim=c(-66.35,-65.35),ylim=c(43.1,43.85),poly.lst=list(LBsubstrate,subpoly.data),isobath=40,bathcol='blue',bathy.source='bathy',mapRes="UR")
#with(subset(subpoly.data,PID%in%unique(LBsubstrate$PID)),legend('topright',PName,fill=col,inset=0.02,cex=0.8,bg='white'))
#dev.off()
#
#
#
#load(file.path( project.datadirectory("lobster"), "data","maps", "bathy", "bathy1Poly1.rdata"))
# junk<-data.frame(PID=1,POS=1:4,X=c(162,161,161,162),Y=c(-41,-41,-40,-40))
#
#LBbathy<-joinPolys(subset(bathy.poly,Z%in%c(10,25,40)),extent,operation="INT")
#bathpoly.data<-data.frame(PID=c(10,25,40),PName=c("<10m","10-25m","25-40m"),col=brewer.pal(3,"Blues"),border=NA)
#
#pdf(file.path(project.datadirectory("lobster"),"R","LobsterBayDepth.pdf"),9,9)
#LobsterMap(xlim=c(-66.2,-65.5),ylim=c(43.1,43.85),poly.lst=list(LBbathy,bathpoly.data),isobath=c(10,25,40,70,100),bathy.source='bathy',mapRes="UR")
#with(bathpoly.data,legend('topright',legend=paste(PID[-length(PID)],'-',PID[-1],sep=''),fill=col[-1],inset=0.02,cex=0.8,bg='white'))
#dev.off()
#
#b40<-joinPolys(subset(LBbathy,PID==40),junk,operation="DIFF")
#b25<-joinPolys(subset(LBbathy,PID==25),junk,operation="DIFF")
#b10<-joinPolys(subset(LBbathy,PID==10),junk,operation="DIFF")
#
#strata2<-joinPolys(b40,b25,operation="DIFF")
#strata2<-joinPolys(strata2,junk,operation="DIFF")
#strata2<-joinPolys(strata2,strata1,operation="DIFF")
#
#strata1<-joinPolys(b25,b10,operation="DIFF")
#strata1<-joinPolys(strata1,junk,operation="DIFF")
#strata1<-joinPolys(strata1,strata2,operation="DIFF")
#
#
#LBbathy<-rbind(strata1,strata2)
#LBbathy<-joinPolys(LBbathy,junk,operation="DIFF")
#
#LBsubstrate<-joinPolys(LBsubstrate,subset(bathy.poly,Z==40),operation="INT")
#LFAs<-read.csv(file.path(project.datadirectory('lobster'),'data','maps','Polygons_LFA.csv'))
#LBsubstrate<-joinPolys(LBsubstrate,subset(LFAs,LFA=='34'),operation="INT")
#
#
## repeated index stations
#LFA34TrawlStations2015<-read.csv(file.path(project.datadirectory("lobster"),"data","LFA34TrawlStations2015.csv"))
#LFA34TrawlStations2015$EID<-1:nrow(LFA34TrawlStations2015)
#names(LFA34TrawlStations2015)[2:3]<-c("Y","X")
#key<-findPolys(LFA34TrawlStations2015,LBsubstrate)
#repeatStations<-merge(LFA34TrawlStations2015,key)
#
#LB.towlst<-alloc.poly(poly.lst=list(LBbathy, bathpoly.data),ntows=40,mindist=2)
#
#pdf(file.path(project.datadirectory("lobster"),"R","LobsterBaySurvey2015.pdf"),8,10)
#LobsterMap(xlim=c(-66.2,-65.5),ylim=c(43.1,43.85),poly.lst=list(LBbathy,bathpoly.data),isobath=c(10,25,40,70,100),bathy.source='bathy',mapRes="UR")
#with(bathpoly.data,legend('topright',legend=paste(PID[-length(PID)],'-',PID[-1],sep=''),fill=col[-1],inset=0.02,cex=0.8,bg='white'))
#addPoints(LB.towlst$Tows)
#points(Y~X,repeatStations,pch=2)
#dev.off()
#write.csv(LB.towlst$Tows,file.path(project.datadirectory('lobster'),'R','LFA34extraSurveyStation2015.csv'),row.names=F)
#
#
#LB.towlst$Tows$EID<-LB.towlst$Tows$EID+100
#
#LB.towlst$Tows$STATION<-paste0('extra',1:40)
#allTows<-merge(LFA34TrawlStations2015,LB.towlst$Tows,all=T)
#allTows<-allTows[order(allTows$EID),]
#
# Relief.plots(allTows,graphic="pdf",file=file.path(project.datadirectory('lobster'),'R','SurveyMB','Tow'),digits=4,gerfiles=1:77,key=file.key)
#
########### 2017 ##########################3
surveyLobsters34<-LobsterSurveyProcess(lfa="34",yrs=1996:2016,bin.size=5)
primary = subset(surveyLobsters34,YEAR==2016&GEAR!="NEST",c("STATION","SID","SET_LONG","SET_LAT"))
names(primary)[3:4] = c("X","Y")
#write.csv(primary,file.path(project.datadirectory('bio.lobster'),"data","survey","2017","primary.csv"),row.names=F)
LobsterMap('34')
with(subset(surveyLobsters34),points(SET_LONG,SET_LAT))
with(primary,points(SET_LONG,SET_LAT,pch=16,col='green'))
with(subset(surveyLobsters34),identify(SET_LONG,SET_LAT))
with(secondary,identify(SET_LONG,SET_LAT))
a=surveyLobsters34[c(28, 37, 449, 467, 617, 623, 651, 749, 808, 814, 815, 845, 868, 881, 922, 971, 1175, 1181, 1218, 1223),]
secondary = subset(a,select=c("STATION","SID","SET_LONG","SET_LAT"))
names(secondary)[3:4] = c("X","Y")
#write.csv(secondary,file.path(project.datadirectory('bio.lobster'),"data","survey","2017","secondary.csv"),row.names=F)
LFA34surveyPolys = read.csv(file.path(project.datadirectory('bio.lobster'),"data","products","LFA34surveyPolys.csv"))
LFA34surveyPolyData=data.frame(PID=1:3,col=c(rgb(1,0,0,0.3),rgb(0,1,0,0.3),rgb(0,0,1,0.3)),PName=c("inner","multibeam","outer"))
SurveyStation2016 = subset(read.csv(file.path(project.datadirectory('bio.lobster'),"data","survey","2016","SurveyStationAssignOriginal.csv")),TOW_ID!="Pre2016")
with(SurveyStation2016,identify(X,Y))
SurveyStation2016[c(3, 4, 6, 7, 8, 9, 13, 14, 17, 18, 19, 20, 23, 29, 31, 34, 36),]
tertiary = SurveyStation2016[c(3, 4, 6, 7, 8, 9, 13, 14, 17, 18, 19, 20, 23, 29, 31, 34, 36),c("STATION","SID","X","Y")]
repeatStns=rbind(primary,secondary,tertiary)
repeatStns$EID = 1:nrow(repeatStns)
rStnkey=findPolys(repeatStns,LFA34surveyPolys)
repeatStns=with(merge(repeatStns,rStnkey,by='EID',all=T),data.frame(EID,X,Y,PID))
rStnAlloc=with(rStnkey,tapply(EID,PID,length))
newAlloc=c(20,20,10)
LFA34surveyPolyData$allocation=newAlloc
LFA34surveyPolyData$repeats=rStnAlloc
towlst<-allocPoly(poly.lst=list(LFA34surveyPolys, LFA34surveyPolyData),ntows=100,pool.size=3,mindist=5,repeated.tows=repeatStns,map='lfa34',show.pool=T,UTMzone=20)
tertiary = rbind(tertiary, data.frame(STATION=304:353,SID=304:353, towlst$Tows$new.tows[,c("X","Y")]))
with(tertiary,identify(X,Y))
tertiary[c(21,27,34),'X'] = c(-66.42397,-66.13020,-66.5143)
tertiary[c(21,27,34),'Y'] = c(43.21405,43.0097,43.58518)
write.csv(tertiary,file.path(project.datadirectory('bio.lobster'),"data","survey","2017","tertiary.csv"),row.names=F)
pdf(file.path(project.datadirectory('bio.lobster'),'figures','SurveyDesign',"Survey2017.pdf"),8,11)
LobsterMap('34',labels='grid',labcex=0.5)
addPolys(LFA34surveyPolys,polyProps=LFA34surveyPolyData)
points(Y~X,primary,pch=21,bg='green')
points(Y~X,secondary,pch=21,bg='orange')
points(Y~X,tertiary,pch=21,bg='purple')
legend('bottomleft',c('primary','secondary','tertiary'),pch=21,pt.bg=c('green','orange','purple'),bg='white')
dev.off()
primary$priority='primary'
secondary$priority='secondary'
tertiary$priority='tertiary'
tows2017=rbind(primary,secondary,tertiary)
tows2017$EID = 1:nrow(tows2017)
write.csv(tows2017,file.path(project.datadirectory('bio.lobster'),"data","survey","2017","tows2017.csv"),row.names=F)
rStnkey=findPolys(tows2017,LFA34surveyPolys)
tows2017=with(merge(tows2017,rStnkey,by='EID',all=T),data.frame(EID,X,Y,PID))
file.key<-read.csv(file.path( project.datadirectory("bio.bathymetry"),"data","GermanBathy","fileKey.csv"))
Relief.plots(subset(tows2017,PID==2),graphic="pdf",file=file.path(project.datadirectory('bio.lobster'),'figures','SurveyDesign','SurveyMB','2017','Tow'),digits=4,gerfiles=1:77,key=file.key)
LobsterScience/bio.lobster documentation built on Feb. 14, 2025, 3:28 p.m.
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#------------------------- ecosystem survey data
p = bio.lobster::load.environment()
p = bio.groundfish::load.groundfish.environment(assessment.year = 2016)
odbc.data.yrs=1970:2015
groundfish.db( DS="gscat.redo" )
groundfish.db( DS="gsdet.redo" )
groundfish.db( DS="gsinf.redo" )
gi = groundfish.db('gsinf')
gc = groundfish.db('gscat')
gc = gc[which(gc$spec==2550),]
gic = merge(gi,gc,by='id',all.x=T)
i = which(is.na(gic$spec))
gic$spec[i] = 2550
gic$totno[i] = 0
gic$totwgt[i] = 0
gic = makePBS(gic,polygon=F)
#abundance and weight in per km2
gic$totwgt = gic$totwgt / gic$dist_km
gic$totno = gic$totno / gic$dist_km
# select for LFA 34
LFAs<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFAPolys.csv"))
LFAgrid<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","GridPolys.csv"))
LFAgrid<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFAgridPolys.csv"))
# Multibeam
gerbk50 <-read.csv(file.path( project.datadirectory("bio.bathymetry"),"data","GermanBathy","gerbk_50.txt"))
key<-read.csv(file.path( project.datadirectory("bio.bathymetry"),"data","GermanBathy","fileKey.csv"))
# groundfish survey
gfkey<-findPolys(na.omit(gic[c('X','Y','EID')]),LFAs)
gic=merge(gic,gfkey[c('EID','PID')],all=T)
gic34=subset(gic,PID==34)
### create Map1
pdf('SDlfa34map1.pdf')
assignStation(subset(gic34,yr>1970,c('EID','X','Y')),maxdist=0.07,res=0.005,expwin=0.05,map='34')
noRVgrids=c(69,81,92,103,114,125:127,137:141,153:159,170:177,188:193,207:210)
addPolys(subset(LFA34grid,SID%in%noRVgrids),col=rgb(1,0,0,0.2))
median(with(subset(gic34,yr>=1999),tapply(EID,yr,length)))
stations= read.csv(file.path(project.datadirectory('bio.lobster'),"data","products","surveyStations.csv"))
stations$EID=stations$SID
addPoints(stations,pch=16)
Stns32<-read.csv(file.path(project.datadirectory('bio.lobster'),'data',"survey32Stations.csv"))
indexStns=subset(stations,SID%in%Stns32$SID)
addPoints(indexStns,pch=16,col='green')
with(indexStns,text(X,Y,SID,pos=4,col='darkgreen',cex=0.5))
dev.off()
#typical number of RV tow in 34
median(with(subset(gic34,yr>=1999),tapply(EID,yr,length)))
LFA34poly=subset(LFAs,PID==34)
LFA34grid=subset(LFAgrid,PID==34)
###-------------- Create polygons
LobsterMap('34',labels='grid',labcex=0.5)
innerGrids=c(69,81,92,101:103,112:114,123:127,136:141,152:159,170:177,188:193,207:210)
addPolys(subset(LFA34grid,SID%in%innerGrids),col=rgb(1,0,0,0.2))
junk<-data.frame(PID=1,POS=1:4,X=c(162,161,161,162),Y=c(-41,-41,-40,-40))
innerGridPoly1=joinPolys(subset(LFA34grid,SID%in%innerGrids),junk,operation="DIFF")
LFA34poly=subset(LFAs,PID==34)
innerGridPoly<-joinPolys(innerGridPoly1,LFA34poly,operation="INT")
outerGridPoly<-joinPolys(LFA34poly,innerGridPoly,operation="DIFF")
MBpoly=outerBounds(gerbk50)
# map of survey polygons
pdf(file.path(project.datadirectory("lobster"),"figures","SurveyDesign","LFA34SurveyPolygons.pdf"),9,9)
LobsterMap('34',labels='grid',labcex=0.5)
addPolys(innerGridPoly,col=rgb(1,0,0,0.3))
addPolys(outerGridPoly,col=rgb(0,0,1,0.3))
addPolys(MBpoly,col=rgb(0,1,0,0.3))
#with(gerbk50,points(X,Y,pch='.'))
addPoints(indexStns,pch=21,bg='yellow')
with(indexStns,text(X,Y,SID,pos=4,cex=0.5))
dev.off()
innerGridPoly<-joinPolys(innerGridPoly,MBpoly,operation="DIFF")
outerGridPoly<-joinPolys(outerGridPoly,MBpoly,operation="DIFF")
innerGridPoly$PID=1
outerGridPoly$PID=3
LFA34surveyPolys=rbind(innerGridPoly,MBpoly,outerGridPoly)
write.csv(LFA34surveyPolys,file.path(project.datadirectory('bio.lobster'),"data","products","LFA34surveyPolys.csv"),row.names=F)
LFA34surveyPolys = read.csv(file.path(project.datadirectory('bio.lobster'),"data","products","LFA34surveyPolys.csv"))
###-------------- Determine allocation
attr(LFA34surveyPolys,"projection")<-"LL"
polyAreas=calcArea(LFA34surveyPolys,1)
areaAlloc=round(polyAreas$area/sum(polyAreas$area)*120)
areaAlloc[3]=areaAlloc[3]-20
iStnkey=findPolys(indexStns,LFA34surveyPolys)
iStnAlloc=with(iStnkey,tapply(EID,PID,length))
newAlloc=areaAlloc-iStnAlloc
otherStns=subset(stations,!SID%in%Stns32$SID)
oStnkey=findPolys(otherStns,LFA34surveyPolys)
oStnAlloc=with(oStnkey,tapply(EID,PID,length))
P3adds=otherStns[c(4, 5, 7, 8, 10, 12, 14, 18, 19, 23, 24, 30, 38, 42),]
P1adds=otherStns[c(17, 20, 27, 28, 29, 33, 34, 41, 44, 45, 47, 48, 49, 55, 61),]
LobsterMap('34',labels='grid',labcex=0.5)
addPolys(innerGridPoly,col=rgb(1,0,0,0.3))
addPolys(outerGridPoly,col=rgb(0,0,1,0.3))
addPolys(MBpoly,col=rgb(0,1,0,0.3))
addPoints(indexStns,pch=21,bg='yellow')
addPoints(otherStns,pch=16,col='grey')
addPoints(P1adds,pch=21,bg='orange')
addPoints(P3adds,pch=21,bg='orange')
repeatStns=rbind(indexStns,P1adds,P3adds)
rStnkey=findPolys(repeatStns,LFA34surveyPolys)
repeatStns=with(merge(repeatStns,rStnkey,by='EID',all=T),data.frame(EID,X,Y,PID))
rStnAlloc=with(rStnkey,tapply(EID,PID,length))
newAlloc=areaAlloc-rStnAlloc
LFA34surveyPolyData=data.frame(PID=1:3,col=c(rgb(1,0,0,0.3),rgb(0,1,0,0.3),rgb(0,0,1,0.3)),PName=c("inner","multibeam","outer"),allocation=newAlloc,repeats=rStnAlloc)
towlst<-alloc.poly(poly.lst=list(LFA34surveyPolys, LFA34surveyPolyData),ntows=100,pool.size=3,mindist=5,repeated.tows=repeatStns,map='34',show.pool=T,UTMzone=20)
file.key<-read.csv(file.path( project.datadirectory("bathymetry"),"data","GermanBathy","fileKey.csv"))
Relief.plots(subset(towlst$Tows$new.tows,STRATA=='multibeam'),graphic="pdf",file=file.path(project.datadirectory('lobster'),'figures','SurveyDesign','SurveyMB','2016','Tow'),digits=4,gerfiles=1:77,key=file.key)
save.image(file.path(project.datadirectory("lobster"),"R","LFA34SurveyDesign2016.Rdata"))
load(file.path(project.datadirectory("lobster"),"R","LFA34SurveyDesign2016.Rdata"))
pdf("Survey2016.pdf",8,11)
LobsterMap('34',labels='grid',labcex=0.5)
addPolys(innerGridPoly,col=rgb(1,0,0,0.3))
addPolys(outerGridPoly,col=rgb(0,0,1,0.3))
addPolys(MBpoly,col=rgb(0,1,0,0.3))
addPoints(towlst$Tows$new.tows,pch=21,cex=0.5,bg='orange')
addPoints(towlst$Tows$repeated.tows,pch=21,cex=0.5,bg='orange')
MBtows=subset(towlst$Tows$new.tows,Poly.ID==2)
MBtows$label=MBtows$EID
MBtows$Y= MBtows$Y-0.03
addLabels(as.EventData(MBtows),cex=0.7)
dev.off()
MBEIDs=c(5,6,9,10,13,15,18,23,24,25,27,28,29,30,31,34,35,36,38,40)
new.tows <- rbind(subset(towlst$Tows$new.tows,Poly.ID==2&EID%in%MBEIDs),subset(towlst$Tows$new.tows,Poly.ID!=2&!EID%in%c(2,51,56)),data.frame(EID=c(2,51,56),X=c(-66.312,-67.031,-66.854),Y=c(42.969,43.5,43.854),Poly.ID=c(1,3,3),STRATA=c("inner","outer","outer"),nndist=NA))
pdf(file.path(project.datadirectory('lobster'),'figures','SurveyDesign','SurveyMB','2016',"Survey2016.pdf"),8,11)
LobsterMap('34',labels='grid',labcex=0.5)
addPolys(innerGridPoly,col=rgb(1,0,0,0.3))
addPolys(outerGridPoly,col=rgb(0,0,1,0.3))
addPolys(MBpoly,col=rgb(0,1,0,0.3))
addPoints(new.tows,pch=21,cex=0.6,bg='orange')
addPoints(towlst$Tows$repeated.tows,pch=21,cex=0.6,bg='red')
labtows=rbind(new.tows[,-6],towlst$Tows$repeated.tows)
labtows$label=labtows$EID
labtows$Y= labtows$Y-0.03
addLabels(as.EventData(labtows),cex=0.7)
dev.off()
test.tow=data.frame(EID=1:2,X=c(-66.34800,),Y=c(43.27362,)
new.tows
file.key<-read.csv(file.path( project.datadirectory("bathymetry"),"data","GermanBathy","fileKey.csv"))
Relief.plots(subset(new.tows,STRATA=='multibeam'),graphic="pdf",file=file.path(project.datadirectory('lobster'),'figures','SurveyDesign','SurveyMB','2016','Tow'),digits=4,gerfiles=1:77,key=file.key)
Relief.plots(subset(towlst$Tows$repeated.tows,STRATA=='multibeam'),graphic="pdf",file=file.path(project.datadirectory('lobster'),'figures','SurveyDesign','SurveyMB','2016','Tow'),digits=4,gerfiles=1:77,key=file.key)
################################################################################################################################################################################################################
#
# extra stuff
#
#####################################################
# # key to files for german MB res 5m
# pdf(file.path(project.datadirectory("lobster"),"figures","SurveyDesign","LFA34MultibeamExtent.pdf"),9,9)
# key<-read.csv(file.path( project.datadirectory("bathymetry"),"data","GermanBathy","fileKey.csv"))
# LobsterMap('34',labels='grid',labcex=0.5,isobath=c(50,100,200),bathy.source='bathy')
# with(key,rect(X1,Y1,X2,Y2,col='black'))
# dev.off()
#
#
#
# calcArea(LFA34grid2)
# key<-findPolys(na.omit(gic[c('X','Y','EID')]),LFAs)
# gic=merge(gic,key[c('EID','PID')],all=T)
# gic34=subset(gic,PID==34)
#
# assignStation(subset(gic34,yr>1970,c('EID','X','Y')),maxdist=0.07,res=0.005,expwin=0.05,map='34')
# median(with(subset(gic34,yr>=1999),tapply(EID,yr,length)))
# gfpoly<-gic34[chull(gic34$X,gic34$Y),c("X","Y")]
# gfpoly$PID=1
# gfpoly$POS=1:nrow(gfpoly)
# addPolys(gfpoly)
# innerGrids=c(69,81,92,101:103,112:114,123:127,136:141,152:159,170:177,188:193,207:210)
# addPolys(subset(LFA34grid,SID%in%innerGrids),col=rgb(1,0,0,0.2))
# junk<-data.frame(PID=1,POS=1:4,X=c(162,161,161,162),Y=c(-41,-41,-40,-40))
# innerGridPoly=joinPolys(subset(LFA34grid,SID%in%innerGrids),junk,operation="DIFF")
# coastalGrids=c(69,81,92,103,114,125:127,137:141,153:159,170:177,188:193,207:210)
# LobsterMap('34',labels='grid',labcex=0.5)
# addPoints(na.omit(gic[which(gic$yr==2015),c('X','Y','EID')]),pch=16,col='red',cex=0.75)
# addPoints(na.omit(gic[which(gic$yr>=1999),c('X','Y','EID')]),pch=16,col='red',cex=0.75)
# addPoints(na.omit(gic[which(gic$yr>=1999 & gic$totno>0),c('X','Y','EID')]),pch=16,col='green',cex=0.75) #lobster only
#
#require(PBSmapping)
#require(RColorBrewer)
#loadfunctions('lobster')
#
#extent<-data.frame(PID=1,POS=1:4,X=c(-66.3,-65.4,-65.4,-66.3),Y=c(43.15,43.15,43.8,43.8))
#attr(extent,"projection")<-"LL"
#
#
#load(file.path(project.datadirectory("substrate"),"data","InshoreSubstrate.rdata"))
#
#subpoly.data<-read.csv(file.path(project.datadirectory("substrate"),"data","SubPolyData.csv"))
#subpoly.data$col<-brewer.pal(10,"Set3")
#subpoly.data$border<-NA
#
#attr(substrate,"projection")<-"UTM"
#attr(substrate,"zone")<-20
#substrate<-convUL(substrate,km=F)
#
#LBsubstrate<-joinPolys(substrate,extent,operation="INT")
#
#pdf(file.path(project.datadirectory("lobster"),"R","LobsterBaySubstrate.pdf"),9,9)
#LobsterMap(xlim=c(-66.35,-65.35),ylim=c(43.1,43.85),poly.lst=list(LBsubstrate,subpoly.data),isobath=40,bathcol='blue',bathy.source='bathy',mapRes="UR")
#with(subset(subpoly.data,PID%in%unique(LBsubstrate$PID)),legend('topright',PName,fill=col,inset=0.02,cex=0.8,bg='white'))
#dev.off()
#
#load(file.path( project.datadirectory("lobster"), "data","maps", "bathy", "bathyPoly1.rdata"))
#LBsubstrate<-joinPolys(LBsubstrate,subset(bathy.poly,Z==40),operation="INT")
#LFAs<-read.csv(file.path(project.datadirectory('lobster'),'data','maps','Polygons_LFA.csv'))
#LBsubstrate<-joinPolys(LBsubstrate,subset(LFAs,LFA=='34'),operation="INT")
#
#
## repeated index stations
#LFA34TrawlStations2015<-read.csv(file.path(project.datadirectory("lobster"),"data","LFA34TrawlStations2015.csv"))
#LFA34TrawlStations2015$EID<-1:nrow(LFA34TrawlStations2015)
#names(LFA34TrawlStations2015)[2:3]<-c("Y","X")
#key<-findPolys(LFA34TrawlStations2015,LBsubstrate)
#repeatStations<-merge(LFA34TrawlStations2015,key)
#
#LB.towlst<-alloc.poly(poly.lst=list(LBsubstrate, subpoly.data),ntows=20,mindist=2)
#
#pdf(file.path(project.datadirectory("lobster"),"R","LobsterBaySurvey2015.pdf"),9,9)
#LobsterMap(xlim=c(-66.35,-65.35),ylim=c(43.1,43.85),poly.lst=list(LBsubstrate,subpoly.data),isobath=c(20,40,70,100),bathy.source='bathy',mapRes="UR")
#with(subset(subpoly.data,PID%in%unique(LBsubstrate$PID)),legend('topright',paste(PID,PName),fill=col,inset=0.02,cex=0.8,bg='white'))
#addPoints(LB.towlst$Tows)
#points(Y~X,repeatStations,pch=2)
#dev.off()
#write.csv(LB.towlst$Tows,file.path(project.datadirectory('lobster'),'R','LFA34extraSurveyStation2015.csv'))
#
## Take 2
#
#extent<-data.frame(PID=1,POS=1:4,X=c(-66.05,-65.7,-65.7,-66.05),Y=c(43.15,43.15,43.8,43.8))
#attr(extent,"projection")<-"LL"
#
#
#load(file.path(project.datadirectory("substrate"),"data","InshoreSubstrate.rdata"))
#
#bathpoly.data<-data.frame
#subpoly.data$col<-brewer.pal(10,"Set3")
#subpoly.data$border<-NA
#
#attr(substrate,"projection")<-"UTM"
#attr(substrate,"zone")<-20
#substrate<-convUL(substrate,km=F)
#
#LBsubstrate<-joinPolys(substrate,extent,operation="INT")
#
#pdf(file.path(project.datadirectory("lobster"),"R","LobsterBaySubstrate.pdf"),9,9)
#LobsterMap(xlim=c(-66.35,-65.35),ylim=c(43.1,43.85),poly.lst=list(LBsubstrate,subpoly.data),isobath=40,bathcol='blue',bathy.source='bathy',mapRes="UR")
#with(subset(subpoly.data,PID%in%unique(LBsubstrate$PID)),legend('topright',PName,fill=col,inset=0.02,cex=0.8,bg='white'))
#dev.off()
#
#
#
#load(file.path( project.datadirectory("lobster"), "data","maps", "bathy", "bathy1Poly1.rdata"))
# junk<-data.frame(PID=1,POS=1:4,X=c(162,161,161,162),Y=c(-41,-41,-40,-40))
#
#LBbathy<-joinPolys(subset(bathy.poly,Z%in%c(10,25,40)),extent,operation="INT")
#bathpoly.data<-data.frame(PID=c(10,25,40),PName=c("<10m","10-25m","25-40m"),col=brewer.pal(3,"Blues"),border=NA)
#
#pdf(file.path(project.datadirectory("lobster"),"R","LobsterBayDepth.pdf"),9,9)
#LobsterMap(xlim=c(-66.2,-65.5),ylim=c(43.1,43.85),poly.lst=list(LBbathy,bathpoly.data),isobath=c(10,25,40,70,100),bathy.source='bathy',mapRes="UR")
#with(bathpoly.data,legend('topright',legend=paste(PID[-length(PID)],'-',PID[-1],sep=''),fill=col[-1],inset=0.02,cex=0.8,bg='white'))
#dev.off()
#
#b40<-joinPolys(subset(LBbathy,PID==40),junk,operation="DIFF")
#b25<-joinPolys(subset(LBbathy,PID==25),junk,operation="DIFF")
#b10<-joinPolys(subset(LBbathy,PID==10),junk,operation="DIFF")
#
#strata2<-joinPolys(b40,b25,operation="DIFF")
#strata2<-joinPolys(strata2,junk,operation="DIFF")
#strata2<-joinPolys(strata2,strata1,operation="DIFF")
#
#strata1<-joinPolys(b25,b10,operation="DIFF")
#strata1<-joinPolys(strata1,junk,operation="DIFF")
#strata1<-joinPolys(strata1,strata2,operation="DIFF")
#
#
#LBbathy<-rbind(strata1,strata2)
#LBbathy<-joinPolys(LBbathy,junk,operation="DIFF")
#
#LBsubstrate<-joinPolys(LBsubstrate,subset(bathy.poly,Z==40),operation="INT")
#LFAs<-read.csv(file.path(project.datadirectory('lobster'),'data','maps','Polygons_LFA.csv'))
#LBsubstrate<-joinPolys(LBsubstrate,subset(LFAs,LFA=='34'),operation="INT")
#
#
## repeated index stations
#LFA34TrawlStations2015<-read.csv(file.path(project.datadirectory("lobster"),"data","LFA34TrawlStations2015.csv"))
#LFA34TrawlStations2015$EID<-1:nrow(LFA34TrawlStations2015)
#names(LFA34TrawlStations2015)[2:3]<-c("Y","X")
#key<-findPolys(LFA34TrawlStations2015,LBsubstrate)
#repeatStations<-merge(LFA34TrawlStations2015,key)
#
#LB.towlst<-alloc.poly(poly.lst=list(LBbathy, bathpoly.data),ntows=40,mindist=2)
#
#pdf(file.path(project.datadirectory("lobster"),"R","LobsterBaySurvey2015.pdf"),8,10)
#LobsterMap(xlim=c(-66.2,-65.5),ylim=c(43.1,43.85),poly.lst=list(LBbathy,bathpoly.data),isobath=c(10,25,40,70,100),bathy.source='bathy',mapRes="UR")
#with(bathpoly.data,legend('topright',legend=paste(PID[-length(PID)],'-',PID[-1],sep=''),fill=col[-1],inset=0.02,cex=0.8,bg='white'))
#addPoints(LB.towlst$Tows)
#points(Y~X,repeatStations,pch=2)
#dev.off()
#write.csv(LB.towlst$Tows,file.path(project.datadirectory('lobster'),'R','LFA34extraSurveyStation2015.csv'),row.names=F)
#
#
#LB.towlst$Tows$EID<-LB.towlst$Tows$EID+100
#
#LB.towlst$Tows$STATION<-paste0('extra',1:40)
#allTows<-merge(LFA34TrawlStations2015,LB.towlst$Tows,all=T)
#allTows<-allTows[order(allTows$EID),]
#
# Relief.plots(allTows,graphic="pdf",file=file.path(project.datadirectory('lobster'),'R','SurveyMB','Tow'),digits=4,gerfiles=1:77,key=file.key)
#
########### 2017 ##########################3
surveyLobsters34<-LobsterSurveyProcess(lfa="34",yrs=1996:2016,bin.size=5)
primary = subset(surveyLobsters34,YEAR==2016&GEAR!="NEST",c("STATION","SID","SET_LONG","SET_LAT"))
names(primary)[3:4] = c("X","Y")
#write.csv(primary,file.path(project.datadirectory('bio.lobster'),"data","survey","2017","primary.csv"),row.names=F)
LobsterMap('34')
with(subset(surveyLobsters34),points(SET_LONG,SET_LAT))
with(primary,points(SET_LONG,SET_LAT,pch=16,col='green'))
with(subset(surveyLobsters34),identify(SET_LONG,SET_LAT))
with(secondary,identify(SET_LONG,SET_LAT))
a=surveyLobsters34[c(28, 37, 449, 467, 617, 623, 651, 749, 808, 814, 815, 845, 868, 881, 922, 971, 1175, 1181, 1218, 1223),]
secondary = subset(a,select=c("STATION","SID","SET_LONG","SET_LAT"))
names(secondary)[3:4] = c("X","Y")
#write.csv(secondary,file.path(project.datadirectory('bio.lobster'),"data","survey","2017","secondary.csv"),row.names=F)
LFA34surveyPolys = read.csv(file.path(project.datadirectory('bio.lobster'),"data","products","LFA34surveyPolys.csv"))
LFA34surveyPolyData=data.frame(PID=1:3,col=c(rgb(1,0,0,0.3),rgb(0,1,0,0.3),rgb(0,0,1,0.3)),PName=c("inner","multibeam","outer"))
SurveyStation2016 = subset(read.csv(file.path(project.datadirectory('bio.lobster'),"data","survey","2016","SurveyStationAssignOriginal.csv")),TOW_ID!="Pre2016")
with(SurveyStation2016,identify(X,Y))
SurveyStation2016[c(3, 4, 6, 7, 8, 9, 13, 14, 17, 18, 19, 20, 23, 29, 31, 34, 36),]
tertiary = SurveyStation2016[c(3, 4, 6, 7, 8, 9, 13, 14, 17, 18, 19, 20, 23, 29, 31, 34, 36),c("STATION","SID","X","Y")]
repeatStns=rbind(primary,secondary,tertiary)
repeatStns$EID = 1:nrow(repeatStns)
rStnkey=findPolys(repeatStns,LFA34surveyPolys)
repeatStns=with(merge(repeatStns,rStnkey,by='EID',all=T),data.frame(EID,X,Y,PID))
rStnAlloc=with(rStnkey,tapply(EID,PID,length))
newAlloc=c(20,20,10)
LFA34surveyPolyData$allocation=newAlloc
LFA34surveyPolyData$repeats=rStnAlloc
towlst<-allocPoly(poly.lst=list(LFA34surveyPolys, LFA34surveyPolyData),ntows=100,pool.size=3,mindist=5,repeated.tows=repeatStns,map='lfa34',show.pool=T,UTMzone=20)
tertiary = rbind(tertiary, data.frame(STATION=304:353,SID=304:353, towlst$Tows$new.tows[,c("X","Y")]))
with(tertiary,identify(X,Y))
tertiary[c(21,27,34),'X'] = c(-66.42397,-66.13020,-66.5143)
tertiary[c(21,27,34),'Y'] = c(43.21405,43.0097,43.58518)
write.csv(tertiary,file.path(project.datadirectory('bio.lobster'),"data","survey","2017","tertiary.csv"),row.names=F)
pdf(file.path(project.datadirectory('bio.lobster'),'figures','SurveyDesign',"Survey2017.pdf"),8,11)
LobsterMap('34',labels='grid',labcex=0.5)
addPolys(LFA34surveyPolys,polyProps=LFA34surveyPolyData)
points(Y~X,primary,pch=21,bg='green')
points(Y~X,secondary,pch=21,bg='orange')
points(Y~X,tertiary,pch=21,bg='purple')
legend('bottomleft',c('primary','secondary','tertiary'),pch=21,pt.bg=c('green','orange','purple'),bg='white')
dev.off()
primary$priority='primary'
secondary$priority='secondary'
tertiary$priority='tertiary'
tows2017=rbind(primary,secondary,tertiary)
tows2017$EID = 1:nrow(tows2017)
write.csv(tows2017,file.path(project.datadirectory('bio.lobster'),"data","survey","2017","tows2017.csv"),row.names=F)
rStnkey=findPolys(tows2017,LFA34surveyPolys)
tows2017=with(merge(tows2017,rStnkey,by='EID',all=T),data.frame(EID,X,Y,PID))
file.key<-read.csv(file.path( project.datadirectory("bio.bathymetry"),"data","GermanBathy","fileKey.csv"))
Relief.plots(subset(tows2017,PID==2),graphic="pdf",file=file.path(project.datadirectory('bio.lobster'),'figures','SurveyDesign','SurveyMB','2017','Tow'),digits=4,gerfiles=1:77,key=file.key)
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