#for the dataset
data('mtcars')
mcor <-cor(mtcars)
# Print mcor and round to 2 digits
round(mcor,digits=2)

##        mpg   cyl  disp    hp  drat    wt  qsec    vs    am  gear  carb
## mpg   1.00 -0.85 -0.85 -0.78  0.68 -0.87  0.42  0.66  0.60  0.48 -0.55
## cyl  -0.85  1.00  0.90  0.83 -0.70  0.78 -0.59 -0.81 -0.52 -0.49  0.53
## disp -0.85  0.90  1.00  0.79 -0.71  0.89 -0.43 -0.71 -0.59 -0.56  0.39
## hp   -0.78  0.83  0.79  1.00 -0.45  0.66 -0.71 -0.72 -0.24 -0.13  0.75
## drat  0.68 -0.70 -0.71 -0.45  1.00 -0.71  0.09  0.44  0.71  0.70 -0.09
## wt   -0.87  0.78  0.89  0.66 -0.71  1.00 -0.17 -0.55 -0.69 -0.58  0.43
## qsec  0.42 -0.59 -0.43 -0.71  0.09 -0.17  1.00  0.74 -0.23 -0.21 -0.66
## vs    0.66 -0.81 -0.71 -0.72  0.44 -0.55  0.74  1.00  0.17  0.21 -0.57
## am    0.60 -0.52 -0.59 -0.24  0.71 -0.69 -0.23  0.17  1.00  0.79  0.06
## gear  0.48 -0.49 -0.56 -0.13  0.70 -0.58 -0.21  0.21  0.79  1.00  0.27
## carb -0.55  0.53  0.39  0.75 -0.09  0.43 -0.66 -0.57  0.06  0.27  1.00

library(corrplot)
corrplot(mcor)

library(igraph)

## Loading required package: methods

# Specify edges for a directed graph
gd <-graph(c(1,2, 2,3, 2,4, 1,4, 5,5, 3,6))
plot(gd)

# For an undirected graph
gu <-graph(c(1,2, 2,3, 2,4, 1,4, 5,5, 3,6),directed=FALSE)
# No labels
plot(gu,vertex.label=NA)

# ggplot2 examples
library(ggplot2)
#use color brewer as default discrete colors
scale_colour_discrete <- function(...) scale_color_brewer(palette="Set1", ...)
scale_fill_discrete <- function(...) scale_fill_brewer(palette="Set1", ...)

data('mtcars')
# create factors with value labels
mtcars$gear <- factor(mtcars$gear,levels=c(3,4,5),
     labels=c("3gears","4gears","5gears"))
mtcars$am <- factor(mtcars$am,levels=c(0,1),
     labels=c("Automatic","Manual"))
mtcars$cyl <- factor(mtcars$cyl,levels=c(4,6,8),
   labels=c("4cyl","6cyl","8cyl"))
head(mtcars)

##                    mpg  cyl disp  hp drat    wt  qsec vs        am   gear
## Mazda RX4         21.0 6cyl  160 110 3.90 2.620 16.46  0    Manual 4gears
## Mazda RX4 Wag     21.0 6cyl  160 110 3.90 2.875 17.02  0    Manual 4gears
## Datsun 710        22.8 4cyl  108  93 3.85 2.320 18.61  1    Manual 4gears
## Hornet 4 Drive    21.4 6cyl  258 110 3.08 3.215 19.44  1 Automatic 3gears
## Hornet Sportabout 18.7 8cyl  360 175 3.15 3.440 17.02  0 Automatic 3gears
## Valiant           18.1 6cyl  225 105 2.76 3.460 20.22  1 Automatic 3gears
##                   carb
## Mazda RX4            4
## Mazda RX4 Wag        4
## Datsun 710           1
## Hornet 4 Drive       1
## Hornet Sportabout    2
## Valiant              1

qplot(mpg, data=mtcars, geom="density", fill=gear, alpha=I(.5),
   main="Distribution of Gas Milage", xlab="Miles Per Gallon",
   ylab="Density")

qplot(hp, mpg, data=mtcars, shape=am, color=am,
   facets=gear~cyl, size=I(3),
   xlab="Horsepower", ylab="Miles per Gallon")

qplot(wt, mpg, data=mtcars, geom=c("point", "smooth"),
   method="lm", formula=y~x, color=cyl,
   main="Regression of MPG on Weight",
   xlab="Weight", ylab="Miles per Gallon")

qplot(gear, mpg, data=mtcars, geom=c("boxplot", "jitter"),
   fill=gear, main="Mileage by Gear Number",
   xlab="", ylab="Miles per Gallon")

library(ggplot2)

centre <- function(x, type, ...) {
  switch(type,
         mean = mean(x),
         median = median(x),
         trimmed = mean(x, trim = .1))
}

myVar1
myVar.2
data$x
foo "bar" baz
# test "test"
"test # test"

(123) (1) (10) (0.1) (.2) (1e-7)
(1.2e+7) (2e) (3e+10) (0x0) (0xa)
(0xabcdef1234567890) (123L) (1L)
(0x10L) (10000000L) (1e6L) (1.1L)
(1e-3L) (4123.381E-10i)
(3.) (3.E10) # BUG: .E10 should be part of number

# Numbers in some different contexts
1L
0x40
.234
3.
1L + 30
plot(cars, xlim=20)
plot(cars, xlim=0x20)
foo<-30
my.data.3 <- read() # not a number
c(1,2,3)
1%%2

"this is a quote that spans
multiple lines
\"

is this still a quote? it should be.
# even still!

" # now we're done.

'same for
single quotes #'

# keywords
NULL, NA, TRUE, FALSE, Inf, NaN, NA_integer_,
NA_real_, NA_character_, NA_complex_, function,
while, repeat, for, if, in, else, next, break,
..., ..1, ..2

# not keywords
the quick brown fox jumped over the lazy dogs
null na true false inf nan na_integer_ na_real_
na_character_ na_complex_ Function While Repeat
For If In Else Next Break .. .... "NULL" `NULL` 'NULL'

# operators
+, -, *, /, %%, ^, >, >=, <, <=, ==, !=, !, &, |, ~,
->, <-, <<-, $, :, ::

# infix operator
foo %union% bar
%"test"%
`"test"`

#!/bin/bash

###### BEGIN CONFIG
ACCEPTED_HOSTS="/root/.hag_accepted.conf"
BE_VERBOSE=false
###### END CONFIG

if [ "$UID" -ne 0 ]
then
 echo "Superuser rights is required"
 echo 'Printing the # sign'
 exit 2
fi

if test $# -eq 0
then
elif test [ $1 == 'start' ]
else
fi

genApacheConf(){
 if [[ "$2" = "www" ]]
 then
  full_domain=$1
 else
  full_domain=$2.$1
 fi
 host_root="${APACHE_HOME_DIR}$1/$2"
 echo -e "# Host $1/$2 :"
}

# loads object
sub load
{
  my $flds = $c->db_load($id,@_) || do {
    Carp::carp "Can`t load (class: $c, id: $id): '$!'"; return undef
  };
  my $o = $c->_perl_new();
  $id12 = $id / 24 / 3600;
  $o->{'ID'} = $id12 + 123;
  #$o->{'SHCUT'} = $flds->{'SHCUT'};
  my $p = $o->props;
  my $vt;
  $string =~ m/^sought_text$/;
  $items = split //, 'abc';
  for my $key (keys %$p)
  {
    if(${$vt.'::property'}) {
      $o->{$key . '_real'} = $flds->{$key};
      tie $o->{$key}, 'CMSBuilder::Property', $o, $key;
    }
  }
  $o->save if delete $o->{'_save_after_load'};
  return $o;
}

=head1 NAME
POD till the end of file

class A < B; def self.create(object = User) object end end
class Zebra; def inspect; "X#{2 + self.object_id}" end end

module ABC::DEF
  include Comparable

  # @param test
  # @return [String] nothing
  def foo(test)
    Thread.new do |blockvar|
      ABC::DEF.reverse(:a_symbol, :'a symbol', :<=>, 'test' + test)
    end.join
  end

  def [](index) self[index] end
  def ==(other) other == self end
end

anIdentifier = an_identifier
Constant = 1
render action: :new

@requires_authorization
def somefunc(param1='', param2=0):
    r'''A docstring'''
    if param1 > param2: # interesting
            print 'Gre\'ater'
        return (param2 - param1 + 1) or None

        class SomeClass:
            pass

        >>> message = '''interpreter
        ... prompt'''

library(grid)
rs <- expand.grid(x = seq(0, 1, 1/10), y = seq(0, 1, 1/10))
grid.rect(rs$x, rs$y, 1/10/2, 1/10/2, gp = gpar(fill = "black", col = NA))
grid.rect(rs$x + 1/10/4, rs$y + 1/10/2, 1/10/2, 1/10/2, gp = gpar(fill = "black", col = NA))
ls <- expand.grid(x = 0:1, y = seq(0, 1, 1/20) - 1/20/2)
grid.polyline(ls$x, ls$y, id = gl(nrow(ls)/2, 2), gp = gpar(col = "grey50", lwd = 1))

grid.newpage()
nx <- 10; ny <- 30
rs <- expand.grid(x = seq(0, 1, 1/nx/2), y = seq(0, 1, 1/ny/2))
grid.rect(rs$x, rs$y, 1/nx/2, 1/ny/2, gp = gpar(col = NA, fill = c("black", "white")))
rs <- expand.grid(x = seq(0.25, 0.75, 1/nx/2), y = seq(0.25, 0.75, 1/ny/2))
grid.rect(rs$y, rs$x, 1/ny/2, 1/nx/2, gp = gpar(col = NA, fill = c("black", "white")))

library(plyr)
grid.newpage()
n <- 10; ny <- 8; L <- 0.01; c <- seq(0, 1, length = n); d <- 1.2*diff(c)[1]/2
col <- c("black", "white")
x <- c(c-d, c, c+d, c)
y <- rep(c(0, -d, 0, d), each = n)
w <- c(c-d, c-d+L, c+d, c+d-L)
z <- c(0, L, 0, -L)
ys <- seq(0, 1, length = ny)
grid.rect(gp = gpar(fill = gray(0.5), col = NA))
l_ply(1:ny, function(i) {n
  if (i%%2==0) {
    co <- rev(col)
    z <- -z
  } else {
    co <- col
  }  
  grid.polygon(x, y + ys[i], id = rep(1:n, 4), gp = gpar(fill = co, col = NA))
  grid.polygon(w, rep(z, each = n) + ys[i], id = rep(1:n, 4), gp = gpar(fill = rev(co), col = NA))
})

grid.newpage()
No <- 3
wo <- 1/3/2
po <- seq(0, 1, by = wo)[(1:No) * 2]
Nc <- 8
tc <- seq(pi * 11/12, pi * 1/12, len = Nc)
px <- c(outer(wo * cos(tc), po, `+`))
wc <- rep(sin(tc), No)
ag <- rep(1:No, each = Nc)
dc <- 21
th <- seq(0, 2 * pi, len = dc)
grid.rect(gp = gpar(col = NA, fill = "#D2D200"))
for (y0 in seq(0, 1, len = 10)) {
  for (i in seq_along(px)) {
    th <- seq(pi/2, pi/2 + 2 * pi, len = 21)
    if (ag[i]%%2==0) th <- rev(th)
    x <- px[i] + 0.5 * 0.04 * cos(th) * wc[i]
    y <- y0 + 0.04 * sin(th)
    grid.polygon(x, y, gp = gpar(fill = "#3278FE"))
    grid.polyline(x[1:((dc + 1)/2)], y[1:((dc + 1)/2)], gp = gpar(lineend = "butt", lwd = 3, col = gray(0)))
    grid.polyline(x[-(1:((dc - 1)/2))], y[-(1:((dc - 1)/2))], gp = gpar(lineend = "butt", lwd = 3, col = gray(1)))
  }
}

x=1:100
y=1/log10(x)
y2=y+.2
plot(x,y, type='l', ylim=c(0,1.5))
lines(x,y2)

library(ggplot2)
crimes <- data.frame(state = tolower(rownames(USArrests)), USArrests)
library(reshape2) # for melt
crimesm <- melt(crimes, id = 1)
library(maps)
states_map <- map_data("state")
ggplot(crimes, aes(map_id = state)) + geom_map(aes(fill = Murder), map = states_map) + expand_limits(x = states_map$long, y = states_map$lat)
last_plot() + coord_map()
ggplot(crimesm, aes(map_id = state)) + geom_map(aes(fill = value), map = states_map) + expand_limits(x = states_map$long, y = states_map$lat) + facet_wrap( ~ variable)
great_lakes_states = c('michigan', 'illinois', 'ohio', 'wisconsin', 'indiana')
great_lakes_map = subset(states_map, region %in% great_lakes_states)
ggplot(subset(crimesm, state %in% great_lakes_states), aes(map_id = state)) + geom_map(aes(fill = value), map = great_lakes_map) + expand_limits(x=great_lakes_map$long, y=great_lakes_map$lat) + facet_wrap( ~ variable)

print('this is a print')

## [1] "this is a print"

cat('this is a cat\n')

## this is a cat

message('this is a message')

## this is a message

stop('this is an error')

## Error: this is an error

warning('this is a warning')

## Warning: this is a warning

print('this is a print')

## [1] "this is a print"

cat('this is a cat\n')

## this is a cat

message('this is a message')

## this is a message

warning('this is a warning')

## Warning: this is a warning

stop('this is an error')

## Error: this is an error