R/figure.landings.timeseries.r

In jae0/bio.snowcrab: Snow crab assessment suite using aegis* and associated projects and data streams.

figure.landings.timeseries = function( yearmax, outdir=NULL, outfile=NULL, outfile2=NULL, type="line", plotmethod="default", 
  regions = c("cfanorth", "cfasouth", "cfa4x"), region_label = c("N-ENS", "S-ENS", "4X") ) {
     
  dir.create( outdir, recursive=T, showWarnings=F  )
  fn = file.path( outdir, paste( outfile, "pdf", sep="." ) )


  if (plotmethod=="default") {
    require(ggplot2)
    k = NULL

    for (i in 1:length(regions)) {
      res = get.fishery.stats.by.region(Reg=regions[i])
      res$region = region_label[i]
      k = rbind( k,  res[, c("yr", "landings", "region" )] )
    }

    k$region = factor(k$region, levels=region_label)
    k$landings = k$landings / 1000

    # The palette with grey: http://www.cookbook-r.com/Graphs/Colors_(ggplot2)/
    # cbPalette = c("#999999", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2", "#D55E00", "#CC79A7")
    color_map = c("#E69F00", "#56B4E9",  "#CC79A7" )
  

    out = ggplot(k, aes(x=yr, y=landings, fill=region, colour=region)) +
      geom_line( alpha=0.9, linewidth=1.2 ) +
      geom_point(aes(shape=region), size=5, alpha=0.7 )+
      labs(x="Year / Année", y="Landings (t) / Débarquements (t)", size = rel(1.5)) +
      theme_light( base_size = 22) + 
      # color_map = c("#E69F00", "#56B4E9",  "#CC79A7" )
      scale_colour_manual(values=color_map) +
      scale_fill_manual(values=color_map) +
      scale_shape_manual(values = c(15, 17, 19)) +
      theme( legend.position="inside", legend.position.inside=c(0.9, 0.9), legend.title=element_blank()) 
 
    out2=out %+% dplyr::filter(out$data, region %in% c("N-ENS", "4X") ) + 
      scale_colour_manual(values=color_map[c(1,3)]) +
      scale_fill_manual(values=color_map[c(1,3)]) +
      scale_shape_manual(values = c(15, 19)) +
      labs(x=NULL, y=NULL) +
      theme_light( base_size = 16) + 
      theme( legend.position="none") 
 
    require(cowplot)
    o = ggdraw( out ) +  draw_plot( out2, x=0.116, y=0.58, width=0.4, height=0.37 )

      # scale_y_continuous( limits=c(0, 300) )  
      ggsave(filename=fn, plot=o, device="pdf", width=12, height = 8)

    return( fn )
  }



  if (plotmethod=="old") {
        
      #variables = c("effort", "landings", "cpue")
      #for (v in variables) {
        #Extract data for the raster creation
        #M = K[, c("yr", "lon", "lat", v)]
        #M = M[is.finite(M[,v] *M[,"lon"] *M[,"lat"]),]
      
      l = NULL
      for (r in regions) {
        res = get.fishery.stats.by.region( Reg=r)
        print(r)
        print(res)
        l = cbind( l, res$landings  )
      }
      l = l / 1000

      l = as.data.frame( l )
      colnames(l) = regions
      rownames(l) = res$yr
    
      l = l[ which( as.numeric(rownames(l)) <= yearmax ), ] 
      uyrs = as.numeric(rownames(l) ) 
  
      fn2 = file.path( outdir, paste(outfile2,"pdf",sep="." ) )

      pdf(file=fn, width=7, height=7, bg='white')
    # png( file=fn,units='in', width=7,height=7,pointsize=10, res=350,type='cairo')

      if (type=="bar") {
        cols = c("grey10", "grey40",  "grey80")
        reverse = c(3,2,1)
        formed.data = t( l[,c(3,2,1)] ) # re-order for plot
        formed.data[ is.na(formed.data) ] = 0
        barplot( formed.data, space=0, xlab="Year", ylab="Landings (t)", col=cols)
        legend(x=1, y=10000, c("N-ENS", "S-ENS", "4X"), fill=cols[reverse], bty="n")
      }
      if (type=="line") {
        pts = c(19, 22, 24)
        lns = c(1, 1, 1)
        cols = c("grey10", "grey10",  "grey20") 
        yrange = range (l, na.rm=T)
        yrange[1] = 0
        xrange = range(uyrs)
        xrange[1] = xrange[1]
        xrange[2] = xrange[2]
        xlabels = seq(xrange[1] +1, xrange[2], 2)

        m=1; plot( uyrs, l[,m],  type="b", ylab="Landings (t)", xlab="Year", col=cols[m], lwd=4, lty=lns[m], pch=pts[m], xaxt="n", xlim=xrange, ylim=yrange)
        m=2; points(uyrs, l[,m], type="b", col=cols[m], lwd=3, lty=lns[m], pch=pts[m])
        m=3; points(uyrs, l[,m], type="b", col=cols[m], lwd=3, lty=lns[m], pch=pts[m])
        axis(1, at=xlabels, labels=FALSE)   
        text(x=xlabels+1, y=par('usr')[3], labels=xlabels, srt=45, adj=c(1.5,1), xpd=TRUE)
        axis( 2 )
        legend(x=1980, y=8500, c("N-ENS", "S-ENS", "4X"), bty="n", lty=lns, lwd=2, pch=pts, col=cols, cex=1.2)

        dev.off()
        pdf(file=fn2, width=7, height=7, bg='white')
        
        #png(file=fn2 ,units='in', width=7,height=7,pointsize=10, res=350,type='cairo')
        sm = l[, c(1, 3)]
        pts = c(19, 24)
        lns = c(1, 1)
        cols = c("grey10", "grey20")
        yrange = range (sm, na.rm=T)
        yrange[1] = 0
        xrange = range(uyrs)
        xrange[1] = xrange[1]
        xrange[2] = xrange[2]
        xlabels = seq(xrange[1]+1, xrange[2], 2)

        m=1; plot( uyrs, sm[,m],  type="b", ylab="Landings (t)", xlab="Year", col=cols[m], lwd=4, lty=lns[m], pch=pts[m], xaxt="n", xlim=xrange, ylim=yrange)
        m=2; points(uyrs, sm[,m], type="b", col=cols[m], lwd=3, lty=lns[m], pch=pts[m])
        axis( 1, at=xlabels, labels=FALSE )
        text(x=xlabels+1, y=par('usr')[3], labels=xlabels, srt=45, adj=c(1.5,1), xpd=TRUE)
        axis( 2 )
        legend(x=1985, y=1200, c("N-ENS", "4X"), bty="n", lty=lns, lwd=2, pch=pts, col=cols, cex=1.2 )
      }
      
    dev.off()
      #table.view( l )
    return( fn )
  }

}