library(dplyr)
library(ggplot2)
library(htmlTable)
library(pander)
library(xtable)
library(lubridate)
source("c:/Users/StanleyR/Documents/Github/bio/bio.surfclam/inst/FunctionList.R")
#load("c:/Users/StanleyR/Documents/Github/bio.data/bio.surfclam/data/Logdata.Rdata")
load("c:/Users/StanleyR/Documents/Surf clam/Assessment/processedLogdata.Rdata")
log.data <- processed.log.data
rm(processed.log.data)
load("c:/Users/StanleyR/Documents/Surf clam/Assessment/LFdata.Rdata")
## Define thresholds for figure captions
BB_cpue <- 75
BB_footprint <- 250
BB_percentlarge <- 120
BB_quota <- "24000"
GB_cpue <- 50
GB_footprint <- 125
GB_percentlarge <- 105
GB_quota <- "14756"
#What year is it?
currentyear <- 2017
#remove any observatiosn from the current year
log.data <- log.data[log.data$year<currentyear,]
Tabdata <- CatchTable(log.data=log.data,Sel.Bank=1,tableNames = T)
Tabdata2 <- CatchTable(log.data=log.data,Sel.Bank=2,tableNames = T)
Tabdata$Bank <- "Banquereau Bank"
Tabdata2$Bank <- "Grand Bank"
Labs <- c("Catch (t)", expression(paste("Effort (",km^2,")",sep=""))) # labels for the plots
Plotdata <- rbind(Tabdata,Tabdata2)
Plotdata <- reshape2::melt(Plotdata[,c(1:3,length(Plotdata))],id.vars=c("Year","Bank"))
Plotdata$Var=gl(2,nrow(Plotdata)/2,labels=Labs)
limits <- data.frame(x1=c(min(Tabdata$Year,na.rm=T),1995),
x2=c(1995,max(Tabdata$Year,na.rm=T)),
y1=c(30000,24000),y2=c(30000,24000))
limits$Bank <- "Banquereau Bank"
limits$Var=gl(2,2,length=2,labels=Labs)
limits2 <- data.frame(x1=c(min(CatchData$Year,na.rm=T),2010),
x2=c(2010,max(CatchData$Year,na.rm=T)),
y1=c(20000,14756),y2=c(20000,14756))
limits2$Bank <- "Grand Bank"
limits2$Var=gl(2,2,length=2,labels=Labs)
plotlimits <- rbind(limits,limits2)
p1 <- ggplot()+
geom_line(data=Plotdata,aes(x=Year,y=value,col=Bank,group=Bank),lwd=1)+
geom_point(data=Plotdata,aes(x=Year,y=value,col=Bank,group=Bank,fill=Bank),size=2.5,shape=21)+
geom_segment(data=plotlimits,aes(x=x1,y=y1,xend=x2,yend=y2,col=Bank),lty=2)+
facet_grid(Var~.,scales="free",labeller = "label_parsed")+
theme_bw()+
scale_x_continuous(breaks=seq(min(Plotdata$Year,na.rm=T),max(Plotdata$Year,na.rm=T),2))+
labs(x="",y="",fill="",group="",col="")+
theme(strip.background = element_rect(colour = "black", fill = "white"),
panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
axis.text.x=element_text(angle = 45,hjust=1),
legend.position = "bottom")+
scale_colour_manual(values=c("grey40","black"))+
scale_fill_manual(values=c("grey40","black"));p1
ggsave("c:/Users/StanleyR/Documents/Surf clam/Assessment/CatchEffort-TAC.png",height = 7,width=7,p1)
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