R Script to Build Animation of Arctic Sea Ice Extent – Update 12/20/13

In my previous post I showed an animation of Arctic Sea Ice Extent from the 1980′s through August, 2012 (link).  In this post, I show how to build this Arctic Sea ice Extent  animated chart.

Source Data

The Arctic Ice Sea Monitor (link)   updates their daily csv file with the latest satellite based arctic sea ice measurements.  Here is the daily csv file link.

R script

To develop my animation of the daily Arctic Sea Ice extent, I decided to produce a plot for each year that showed the current year in red and the previous years in grey.  I go this idea from Tamino at Open Mind.

Here is my R script:
Be sure to set your working directory to appropriate location!!

library(animation)
  ani.options(convert=shQuote('C:\\Program Files (x86)\\ImageMagick-6.7.9-Q16\\convert.exe'))
## Use setwd() to specify directory where you want png images to be saved
  setwd("<strong>C:\\R_Home\\Charts & Graphs Blog\\RClimateTools\\Arctic_sea-ice_extent</strong><em>")
# use png_yn to toggle between plot output to png file or screen
  png_yn <- "y"
# Establish chart series patterns and colors to be able to distinguish current yr from previous years in plot
  pattern <- c(rep("dashed", 5), rep("solid", 12))
  ser_col <- c(rep("black",5),rep("grey",12))
# Establish chart annotations for date, chart title,
  what_date <- format(Sys.Date(), "%b %d, %Y")  # with month as a word
  title <- paste("IARC-JAXA Daily Arctic Sea Ice Extent*\n", what_date)
  note_1 <- "*Extent - Area of Ocean with at least 15% Sea Ice"
  par(oma=c(2,1,1,1)); par(mar=c(2,4,2,1))
#  Day of year axis setup
## Set up basic day of year vectors (mon_names, 1st day of mon)
  mon_names <- c("Jan", "Feb", "Mar", "April", "May", "June", "July", "Aug", "Sept", "Oct","Nov","Dec")
  mon_doy <- c(1,32,60,91,121,151,182,213,244,274,305,335,366)
  mon_pos <- c(16, 46, 75, 106,135, 165, 200, 228, 255, 289, 320, 355)
# Read JAXA Arctic Sea ice Extent csv file
# Data File: Month,Day,1980's Avg,1990's Avg,2000's Average,2002:2012
  link <- "http://www.ijis.iarc.uaf.edu/seaice/extent/plot.csv"
  j_data <- read.csv(link, header = F, skip=1, na.strings = c(-9999))
 series_id <-  c("mo", "day", "1980s", "1990s", "2000s","2002", "2003", "2004", "2005", "2006", "2007", "2008", "2009",
                "2010", "2011", "2012", "2013")
 colnames(j_data) <- series_id
# File has data for each day in 366 day year
# Establish Day of year
  for (i in 1:366)   j_data$yr_frac[i] <- i
    #convert ASIE to millions Km^2
   j_data[,c(3:17)] <- j_data[,c(3:17)]/1000000
# Loop through years
   for (j in 3:17)
  {
     png_name <- paste("asie",series_id[j],".png",sep="")
      if (png_yn =="y") png(filename=png_name)
      which_yr <- j
      no_yrs <- j
  # Calc min asie for year
    min_asie <- min(j_data[,j], na.rm = T)  # must remove na's to get valid answer
    lab_asie <- round(min_asie,3)
    min_r <- which(j_data[,j] == min_asie)
    min_d <- j_data[min_r,2]
    min_m <- j_data[min_r,1]
    min_date <- paste(min_m,"/",min_d,"/",series_id[j], sep="")
    plot(j_data[,17],  type="n", col = "grey",axes=F, xlab="",
       ylab="Arctic Sea Ice Extent - Millions Sq KM",
       ylim=c(0,15),xaxs="i", yaxs = "i",
       main=title)
    text(20, 1.5, note_1, cex = 0.8, adj=0, col = "black")
    text(20,1,"Data Source: http://www.ijis.iarc.uaf.edu/seaice/extent/plot.csv", cex = 0.8, adj=0,col = "black")
    mtext("D Kelly O'Day - http://chartsgraphs.wordpress.com", 1,0.5, adj = 0, cex = 0.8, outer=T)
  # custom x & y axes
    axis(side = 1, at=mon_doy, labels=F, xaxs="i")
    axis(side=1, at= mon_pos, labels=mon_names, tick=F, line=F, xaxs="i")
    axis(side=2,  yaxs="i", las=1)
    points(70, min_asie, col = "red",pch=19, cex = 2)
  # Add each previous yr data series as light grey line
  for (n in 3:no_yrs)
  {
    points(j_data[,18], j_data[,n], type="l",lwd=1,lty=pattern[j], col=ser_col[j])
    text(182,14,series_id[j], col = "red", cex = 1.1)
  }
  points(j_data[,18], j_data[,j], col="red", type="l",lwd=2.5)
  text(182,14,series_id[j], col = "red", cex = 1.1)
  text(120,min_asie+0.5, min_date, col="red", cex=0.9)
  text(120,min_asie, lab_asie, col="red", cex=0.9)
  if(png_yn == "y") dev.off()
}
## copy last png file 3 times to provide pause in animation
if(png_yn== "y")
{
  for (c in 1:2)
  {
    file_name <- paste("asie2012",c, ".png",sep="")
    file.copy(from= "asie2012.png", to = file_name, overwrite=T)
  }
  ani.options(outdir = getwd())    # direct gif output file to working dir
  ani.options(interval= 0.80)
  im.convert("asie*.png", "last_animation.gif")
}
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4 responses to “R Script to Build Animation of Arctic Sea Ice Extent – Update 12/20/13

  1. Pingback: Animated Images of Arctic Sea Ice Extent Decline | Climate Charts & Graphs

  2. Manuel Gonzalez Canche

    Wonderful, I simply love your post, thank you for sharing!!!

  3. Hello !
    Nice animation
    I believe there is a package that enables to easily build gif and videos like this one in R
    It’s the “animation” package by Yihui Xie
    IIRC it’s well writen and will save you some time in the future if you want to produce this kind of outputs
    Cheers

    • Pierre – Based on your comment, I retried the animation package. The Windows workaround was easy! I now use the animation package instead of Photoshop Elements, it saves me time and effort.

      Thanks!! Kelly

      Pierre

      I tried to use ‘animation” package, however, I use Windows and ran into problem with ImageMagic.

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