History: Profile_r_test11_animation

            ! Displaying a ggplot2 map with Animation
Derived from http://www.analyticsandvisualization.com/2014/01/animated-choropleths-using-animation.html

{RR(cacheby="pagename", echo="TRUE", ln="1", caption="R Code - 1st part", loadandsave="1", wikisyntax="0")}
# We need to download data with Quandl to save it to a vcData.rda. 
# If you already have the required data in that file, don't run this code again any more.
if (!file.exists('vcData.rda')) {
  # Check if Quandl needs to be installed
  if(!require(Quandl)){ install.packages("Quandl", repos="http://ftp.heanet.ie/mirrors/cran.r-project.org/") }
  require(Quandl)
  # Not required but removes a warning message--- Quandl.auth('yourauthcode')
  # Quandl.search('violent crime')
  vcData = Quandl("FBI_UCR/USCRIME_TYPE_VIOLENTCRIMERATE")
  save(vcData,file='vcData.rda')
}
load("vcData.rda")

##dim(vcData)
##head(vcData, 2)
##tail(vcData, 2)

# There are 51 rows and 53 columns in the dataset. Data is for 51 years
# (2010-12-31 through 1960-12-31). 53 columns include a column for Year, each state and
# the District of Columbia, and the average for the country. Let's now do four things. 
# 1. Create a column denoting the year 
# 2. Drop the column involving date (the existing 'Year' column) 
# 3. Drop the column involving the average for the country 
# 4. Drop the column for District of Columbia, which is not a State.
vcData$Yearonly = 2010:1960  # Creating a new column with Year
vcData = vcData[, -1]  # Dropping the existing 'Year' column
vcData = vcData[, -52]  # Dropping the column with average for the country
vcData = vcData[, -9]  # Dropping the column for Washington DC, the 9th column

#Instead of looking at annual data, let's focus on different decades (2001-2010
#[rows 1-10], 1991-2000 [rows 11-20], 1981-1990 [rows 21-30], 1971-1980 [rows
#31-40], and 1961-1970 [rows 41-50]). Let us compute the mean violent crime
#rates for each state for each decade. Since 1960 does not fit in to our plans,
#let us drop that row.
vcData = vcData[-51, ]  # Removing the row for 1960, the 51st row
decades = data.frame(Decade2001_2010 = colMeans(vcData[1:10, ], na.rm = TRUE), 
                     Decade1991_2000 = colMeans(vcData[11:20, ], na.rm = TRUE), Decade1981_1990 = colMeans(vcData[21:30, 
                        ], na.rm = TRUE), Decade1971_1980 = colMeans(vcData[31:40, ], na.rm = TRUE), 
                     Decade1961_1970 = colMeans(vcData[41:50, ], na.rm = TRUE))
decades$State = row.names(decades)  # We needed a column for State and the row names provided that
decades = decades[-51, ]  # Remove the row for Yearonly, which is irrelevant.
##dim(decades)
##head(decades, 2)
##tail(decades, 2)

# Choropleths of different decades using ggplot2 and animation
# =============================================================
# The first order of business was to get a US map. A typical map file generated
# from the maps package does not include Alaska and Hawaii. Scouring the web for
# someone who might've addressed this issue took me to this post of Kristopher
# Kapphahn ( http://loloflargenumbers.com/blog/#.Up5D6sSkpS4 ). 
# The post was terrific and provided the complete code for generating
# such a map. This code, which is in a separate file for those interested in it
# ( https://github.com/patilv/choroplethanimation/tree/master/AllUSShapeFile ),
# was used to generated a file all_us.rda. We use this file below for the map.

# A preliminary choropleth for the 2001-2010 decade
# -------------------------------------------------
# You can fetch the data from github (359Kb) 
# Since data is in a url with https, we'll need to use the 'downloader' package
if(!require(downloader)){ install.packages("downloader", repos="http://ftp.heanet.ie/mirrors/cran.r-project.org/") }
require(downloader)
ur_l_all_us = "https://github.com/patilv/choroplethanimation/raw/master/AllUSShapeFile/all_us.rda"
file_all_us = "all_us.rda"
## For some reason this message is shown as of 2014 March when attempting to download the package with the method commented out below: 
## "WARNING: certificate common name `www.github.com' doesn't match requested host name `raw.githubusercontent.com'."
## "To connect to raw.githubusercontent.com insecurely, use `--no-check-certificate'."
#  downloader(ur_l_all_us, file_all_us, "auto", quiet = TRUE, mode = "w",
#                cacheOK = TRUE )
## Therefore, we will use wget directly with that param:
system(paste("wget", ur_l_all_us, "-c -O", file_all_us, "--no-check-certificate", sep=" "))
load("all_us.rda")
uslessdc = all_us[all_us$STATE_NAME != "District of Columbia", ]
uslessdc$STATE_NAME = factor(uslessdc$STATE_NAME)
uslessdc$CrimeRate = decades[, 1][match(uslessdc$STATE_NAME, decades$State)]  # bring value of decade to map data
if(!require(ggplot2)){ install.packages("ggplot2", repos="http://ftp.heanet.ie/mirrors/cran.r-project.org/") }
require(ggplot2)
ggplot(data = uslessdc, aes(x = x_proj, y = y_proj, group = DRAWSEQ, fill = CrimeRate)) + 
  geom_polygon(color = "black") + ggtitle(paste("Violent Crime Rate in", names(decades[1]))) + 
  xlab("") + ylab("")
{RR}

{RR(cacheby="pagename", echo="TRUE", ln="1", caption="R Code - 2nd part", loadandsave="1", wikisyntax="0")}
# Tweaking Data and Animating Choropleths
# ---------------------------------------
# To bring in more clarity, let us classify states into 3 different groups based
# on their violent crime rates for a decade and color code them differently. Top
# 1/3 in crime rates (high, denoted by number 3) are most dangerous and middle
# 1/3 (medium, denoted by number 2) are more dangerous than the bottom 1/3 (low,
# denoted by number 1).

# Create a new dataframe with crime rate data in decades classified into 3
# levels of crime rate for States for a decade.
# But make all this processing only once; if file already created, don't do it again :-)
if (!file.exists("decadespct.rda")) {
  decadespct = decades
  for (i in 1:5) {
    quantile = quantile(decades[, i], c(1/3, 2/3))
    decadespct[, i] = with(decades, factor(ifelse(decades[, i] < quantile[1], 
                                                  "1", ifelse(decades[, i] < quantile[2], "2", "3"))))
  }
  ##head(decadespct, 2)
  save(decadespct, file = "decadespct.rda")
}

# On to the animation.
if(!require(animation)){ install.packages("animation", repos="http://ftp.heanet.ie/mirrors/cran.r-project.org/") }
require(animation)
require(ggplot2)
saveHTML({
  for (i in 1:5) {
    uslessdc$CrimeRate = decadespct[, i][match(uslessdc$STATE_NAME, decadespct$State)]  # bring value of decade to map data
    mycols = c("#4daf4a", "#fc8d62", "red")  # Setting a color palette
    ggchoropleth = ggplot(data = uslessdc, aes(x = x_proj, y = y_proj, group = DRAWSEQ, 
        fill = CrimeRate)) + geom_polygon(color = "black") + ggtitle(paste("Violent Crime Rate in", 
        names(decadespct[i]))) + xlab("") + ylab("") + scale_fill_manual(values = mycols, 
        labels = c("Low", "Medium", "High")) + theme(legend.position = "top")
    print(ggchoropleth)
  }
}, img.name = "decadeplots", imgdir = "decadeplots", htmlfile = "decadeplots.html", 
outdir = getwd(), autobrowse = FALSE, ani.height = 400, ani.width = 600, 
verbose = FALSE, autoplay = TRUE, title = "Violent Crime Rates")
{RR}

{iframe name="myChart" width="850" height="500" align="middle" frameborder="0" marginheight="0" marginwidth="0" scrolling="auto" src="temp/cache/{{domainslash_if_multitiki}}R_{{page}}/decadeplots.html"}