# useR-2010


# Credentials ====
# Account Name aaaaaa
# Account Number 1234-5678-1234 
#
# Access Key ID: AKIAIO445ARJMS4qwerty
# Secret Access Key: ISIu7OgJeEHQ6+0Pa8oJVCpyIaDCZW3E4r5t^


# Win pwd:        

#Check web server is running

# Example 1. (Xming, PuTTY)
plot(1:4)
plot(5:1)
x11()
plot(1:3)

#  vnc - also slow
  
#now WinSCP (no need in display tunneling)

# Example 2. www – pdf()

setwd("/var/www/html")
# or
setwd("/var/www/")

#rename index.html

pdf(’z.pdf’)
plot(1:4)
plot(5:1)
dev.off()


# Example 3.  www – R2HTML()

install.packages("R2HTML", repos = "http://cran.stat.ucla.edu/")
library(R2HTML)



file.remove("/var/www/z.html")
fout= HTMLInitFile(outdir = "/var/www/",	filename="z",
	CSSFile="http://www.stat.ucl.ac.be/R2HTML/Pastel.css")
data(iris)
HTML(as.title("Fisher Iris dataset / Correlation 1"),file=fout)
HTML(cor(iris[,1:4]), file=fout)
HTML(as.title("Fisher Iris dataset / Correlation 2"),file=fout)
HTML.cormat(cor(iris[,1:4]), file=fout) 

png("gr1.png")
plot(exp,-1,2)
#dev.off()

png("gr2.png")
plot(sin,-9,9)
dev.off()

HTML('exp')
HTMLInsertGraph("gr1.png", file=fout, caption="plot exp")
#HTML.title('sinus')
HTMLInsertGraph("gr2.png", file=fout, caption="plot sin")
dev.off()


# Example 4. SVG  
install.packages("RSvgDevice", repos = "http://cran.stat.ucla.edu/")
library(RSvgDevice)
devSVG(file = "zRplots.svg")
#devSVG(file = "zRplots2.svg", width = 10, height = 8,
#       bg = "white", fg = "black", onefile=F, xmlHeader=TRUE)


plot(1:9)
#see

plot(4:1)
dev.off()

  




  

# local ===
n=100
x= data.frame(x1= sample(2,n, replace = T) + rnorm(n, 0, .1)
            , x2= sample(2,n, replace = T) + rnorm(n, 0, .3))
plot(x2~x1, data=x)
write.table(x, 'Z:/work/29_Conferences/1101_R/x.txt')
y= read.table('Z:/work/29_Conferences/1101_R/x.txt')

# remote ===
y= read.table('x.txt')

attach(y)
plot(x2~x1)

install.packages("cluster", repos = "http://cran.stat.ucla.edu/")
library(cluster)

pamr <- pam(y, k=4)
pamc <- pamr$clustering

plot(x1, x2, col=pamc)
#clusplot(pamr, color=TRUE, col.clus = 1:4, shade = TRUE, axes=T, labels=0) #  names(pamr$ clustering))
clusplot(pamr, color=TRUE, col.clus = 1:4, shade = TRUE, labels=0) #  names(pamr$ clustering))




#== Saving a Customised Linux Amazon Instance (EC2 and S3)

1) copy  private key and cert key over to the EC2 instance /mnt 
2) install a  Amazon tool on the instance to allow you to 
create another AMI and store it

# apt-get install unzip 

#Download the Amazon AMI tools onto the instance.

mkdir ~/ec2
cd ~/ec2
wget http://s3.amazonaws.com/ec2-downloads/ec2-ami-tools.zip 
unzip ec2-ami-tools.zip
ln -s ec2-ami-tools-* current
vi ~/.bashrc
#add the following lines to the end of the .bashrc file

export EC2_AMITOOL_HOME=~/ec2/current
export PATH=${PATH}:~/ec2/current/bin
#And then re-initialise the configuration file

source ~/.bashrc
#should be able to run w/o error:

# ec2-bundle-vol --help

#Create your AMI.. While still on the server run the following command:

ec2-bundle-vol -d /mnt -k /mnt/pk-STRINGOFTHIRTYTWOLETTERSORDIGITS.pem -c /mnt/cert-STRINGOFTHIRTYTWOLETTERSORDIGITS.pem -u XXXXXXXXXXXX
# XXXXXXXXXXXX is your Amazon account number without the dashes.
# wait 15 min :(

#Save your new AMI to S3.

ec2-upload-bundle -b [your-s3-bucket] -m /mnt/image.manifest.xml -a [aws-access-key-id] -s [aws-secret-access-key]

#If the bucket doesn’t exist, it should create the bucket for you though. The keys are those crazy long keys you use to access S3.

#== Register the AMI via GUI or command tool 
#Go back to your desktop, and issue the command:

ec2-register [your_bucket]/image.manifest.xml


# Install R on DEBIAN 

apt-cache search ^r-.*
#should get you started with a list of available packages.

#add to the file /etc/apt/sources.list on your computer line 
deb http://cran.mtu.edu/bin/linux/debian lenny-cran/

#or other CRAN  mirror URLs listed in  http://cran.r-project.org/mirrors.html


# After installing R 2.11.0 from CRAN, you will have to update or reinstall all 
# R packages that have been installed with an R version lower than R 2.10.X

apt-get update
apt-get install r-base r-base-dev