R/PlotLengthData.R

In DanOvando/DLSA: Library Data Limited Stock Assessment Modules

#' Plot Length Data
#'
#' @param LengthDat
#' @param FigureFolder
#' @param Fish
#' @param Species
#' @param Site
#' @param Theme
#'
#' @return
#' @export

PlotLengthData<- function(LengthDat,FigureFolder,Fish,Species,Site,Theme)
{
#   LengthDat<- LengthData

  LengthDat<- subset(LengthDat,is.na(Length)==F & Length>0)

  LengthDat$SiteType[LengthDat$MPA==0]<- 'Fished'

  LengthDat$SiteType[LengthDat$MPA==1]<- 'MPA'

  pdf(file=paste(FigureFolder,Species,'-',Site,'Length Data.pdf',sep=''),width=5,height=5)

  LengthDist<- (ggplot(data=LengthDat,aes(Length,fill=(SiteType)))+geom_density(alpha=0.6,aes(y=..count..))
  +scale_fill_manual(name='',values=c(FishedColor,MPAColor))
  +geom_vline(xintercept=Fish$Mat50,linetype='longdash')+
    geom_vline(xintercept=Fish$Linf,linetype='longdash',color='red2')+
    facet_wrap(~Year,as.table=F, scales = 'free_y')+ggtitle(paste(Species,Site,sep='-'))+Theme)

  print(LengthDist)

# pdf(file=paste(FigureFolder,Species,'-',Site,'Length Data.pdf',sep=''))
# print(ggplot(data=LengthDat,aes(Length,fill=(SiteType)))+geom_density(alpha=0.6,aes(y=..count..))
#       +scale_fill_manual(name='',values=c(FishedColor,MPAColor))
#       +geom_vline(xintercept=Fish$Mat50,linetype='longdash')+
#         geom_vline(xintercept=Fish$Linf,linetype='longdash',color='red2')+
#         facet_wrap(~Year,as.table=F)+ggtitle(paste(Species,Site,sep='-')))
# dev.off()

LengthBox<- (ggplot(data=LengthDat,aes(factor(Year),Length,fill=SiteType))
+geom_boxplot(varwidth=F,alpha=1)+scale_fill_manual(name='',values=c(FishedColor,MPAColor))+Theme+xlab('Year')+
  ylab('Length (cm)'))

print(LengthBox)
  dev.off()

save(LengthDist,LengthBox,file=paste(FigureFolder,Species,'-',Site,'Length Data.Rdata',sep=''))

}