#
#  Basic R commands and examples
#
#=====================================================



#--- Getting Help --------------------------
  ?exponential
  ??"exponential distribution"
  apropos("keyword")
  RSiteSearch("keyword")


#--- Installing and loading packages -------
  install.packages("sos")
  require("sos")
  ???markov


#--- Combine two script lines into one ------------
  X <- 3
  X
  X <- 3; X



#--- Defining function -------------------------
  myFunc <- function( a ) {
    b <- (a+3)/2
    return(b)
  }




#--- Read/Write Files----------------------------
  DD <- read.csv("FrazierPARMA11residuals.csv")
  DD <- read.csv("FrazierPARMA11residuals.csv", stringsAsFactors=FALSE)

  DD <- read.table("FrazierPARMA11residuals.txt")
  unlist(DD)
  attach(DD)

  write.table(file="table.txt", X)



#--- Read table off of clipboard ---------------
  Data <- read.table(file = "clipboard", sep = " ", header=TRUE)
  attach(Data)



#--- define file or variable name by putting strings together -----
  infile <- paste("n",n,"_",k,".Rdata",sep="")
  load(infile)





#--- If else ---------------------------------------
  switch(a, { k <- "first" }, { k <- 4; j<- 2})

  ifelse(x>2, y<-"yes", y<-"no")
  if (x==0) {  } else { }

  if (X==0) {
      do X
  } else if (X==1) {
      do Y
  } else if (X==2) {
      do Z
  } else do W



  for (i in 1:10) {  }
  while ( i < 10 ) {  i <- i+1 }

  for (i in 1:1000) { 
    if (i %% 100==0) { print(c(i, date()) ) }
  }


  #--- if is not vectorized.  ifelse is.


#------------------------------------------------
  str(x)
  mode(x)

  x %%  y  remainder
  x %/% y  modulus

  options(warn = -1)

  all.equal(x, y)   # near equality
  identical(x, y)   # equality

  stage <- readline("stage:")



#--- Read Files----------------------------
  read.csv("FrazierPARMA11residuals.csv")
  read.table("FrazierPARMA11residuals.txt")
  unlist()

  save(x, y, file = "xy.Rdata")


  write.table(file="table.txt", X)

  sample(x,10, replace=T) # bootstrap sampling

  X.hw$drop2 <- apply(X.hw, 1, function(x) min((1:8)[x==min(x)]) ) # gives col # of min HW score for each row




#--- define file or variable name by putting strings together -----
  infile <- paste("n",n,"_",k,".Rdata",sep="")
  load(infile)



#--- keep track to computation time ---
  system.time( rnorm(100) )
  
  tic <- date()
  rnorm(100)
  tac <- date()
  rbind(tic, tac)




#--- Char and String -------------------------------
  x <- "10101001010100101010100101010101001001010"
  y <- 0
  for ( i in 1:nchar(x)) {
    y[i] <- as.integer( substr(x, start=i, stop=i) )
  }
  y <- rbinom(50, 1, .1)
  Box.test(y)




#--- Checking ---------------------------------------
  is.na(x)
  is.nan(x)
  exists("x")




#--- Printing values on screen ---------------------

  k=1
  print( paste("value of k is:  ", k), sep="" )


  k=10/23
  cat( sprintf( "\n    value of k is %.3f \n\n\n", k ) )