# I. More on vectors
# 1. contain elements of just 1 type, either numeric, logical, or character
#   a. numeric
       y <- 18
       y <- c(-3.6,1.58)
       y <- 1:9
       y <- seq(from=0,to=10,by=0.02)     #seq() a function w/ args from, to,..
					  #by argument gives distance
       y <- seq(0,10,by=0.02)             #if know where args are, no need to specify name
					  
       y <- seq(-3,25,length=6)           #length option 
       x <- c(3,3,9,12,1)
       y <- seq(0,10,along=x)             #will return seq w/ length(x)

       y <- rep(x=3,times=7)              #replicate the value in x, namely 3, seven times
       y <- rep(x=c(3,5),times=7)         # same
       y <- rep(x=c(3,5),times=c(2,6))    #repeat 3 two times, then 5 six times
 
#   b. character
       y <- "San Diego"
       y <- c("LA","NY","San Fran")

#   c. logical
       y <- T
       y <- c(F,F,T)
       x <- 1:7
       y <- (x<5)

#  2. Accessing elements of a vector in 1 of 4 ways
       y <- c(18,32,15,-7,12,19)
#   a. position in vector as positive integer
      y[3:5]

#   b. excluding elements, position as negative integers
      y[-c(1,5,6)]

#   c. by element name
      names(y) <- c("Joe","Bill","Karen","Helen","Ray","Paul")
      y[c("Helen","Ray")]
 
#   d. by logical conditions
      y[y<15]

#  3. Matrices, arrays, and factors
#   a. Matrices
      y <- c(18,32,15,-7,12,19)
      x <- matrix(data=y,nrow=2,ncol=3)           #fill columns first (column major order)
						  #  -the default
      x <- matrix(data=y,nrow=2,ncol=3,byrow=T)   #fill rows first
      dimnames(x) <- list(c("r1","r2"),c("a","b","c"))

#   b. Arrays
        # creates a 2 by 4 by 3 array
      y <- c(1:8, 11:18, 111:118)
      x <- array(y, dim = c(2,4,3))    #first dimension changes fastest

#   c. Factors
      color <- c("red", "red", "red", "green", "blue")  #character valued vector
      colors <- factor(color, c("red","green","blue"))
      table(colors)  # table counting occurrences of colors
               #one use: when building models where "dummy" variables needed

#  4. Vector attributes
#   every vector (and object) has 2 "implicit" attributes, mode and length
#      some modes, e.g.  "numeric",  "list",  "logical", "NULL"

#   other attributes- name, dimension,levels, class
     attributes(y)        #for "plain" vector doesn't report anything
     attributes(x)
     attributes(colors)

#II. More on lists
    x <- list(one=c(18:36),two=c("AK","AL","AZ"),three=c(T,T,F,T),four=matrix(1:12,3,4))
#  1. access to components
    x[[1]]          #by order
    x$one           #by name

#  2. access to elements within components
    x[[1]][3:6]
    x$one[3:6]

#  3. unlist()        #convert a list to a vector
    unlist(x)        #handy for printing out returned values from function

#  4. attach(what,...)       #makes components of list directly accessible       
    attach(x)
    one
    detach(x)       #no longer make this direct access possible

#    Note- attach(name="mydirectory",pos=2) will put a directory named
#       mydirectory, say, in the first position of the search list
#       - the directory name must be in quotes to distinguish it from an
#	 ordinary object

#   5. data frames- a special kind of list object; number of elements must
#       be the same for all components
#	- handy for regression modeling

      muscle <- rnorm(n=10,mean=3,sd=1)
      sex <- factor(rep(c("M","F"),c(6,4)))
      speed  <- rep(0,10)
      speed[1:6] <- rnorm(6,30-2*muscle[1:6],2)
      speed[7:10] <- rnorm(4,40-2*muscle[7:10],2)
      mydata <- data.frame(y=speed,x1=muscle,x2=sex)
      temp <- lm(y~x1+x2,data=mydata)  #we will work with linear models later
      summary(temp)

#III. More on functions
#   1. specified or unspecified arguments
#     a. unspecified   c <- function(...)
#     b. specified   
	  mysd <- function(x) {return(sqrt(var(x)))}

          dumplot <- function(x,y) {
		      plot(x,y)
		      abline(0,1)
		     }

#    2. argument passing for specified case
#       if don't use names, call function by passing arguments in proper order
          dumplot(my.x,my.y)	   
#       if use names, then any order ok
	  dumplot(y=my.y, x = my.x)

#    3. default values for specified case
	dumplot <- function(x,y,my.line=T) {
	        plot(x,y)
	       if(my.line) {
		abline(lm(y~x))
               } 
	     }