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### chunk number 1: setup
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#line 31 "/home/jimrc/classes/stat505/notes/introR3.Rnw"
options(width=60)


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### chunk number 2: 
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#line 40 "/home/jimrc/classes/stat505/notes/introR3.Rnw"
 methods(plot)


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#line 45 "/home/jimrc/classes/stat505/notes/introR3.Rnw"
getAnywhere("stack.data.frame")
getS3method("plot","factor")
require(arm)                ## load the books functions
getMethod("display","lm")   ## See G&H p 38-9


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#line 68 "/home/jimrc/classes/stat505/notes/introR3.Rnw"
Summrize <- function(x){               ## verbs are preferred function names
    ## function to plot BWplot, return fivenum, mean, sd
    boxplot(x, horizontal=TRUE)
    c( fivenum(x), mean(x), sd(x))  ## last thing created is returned
}
Summrize(rexp(50))


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#line 83 "/home/jimrc/classes/stat505/notes/introR3.Rnw"
Summrize <- function(x){
    s## function to plot BWplot, return fivenum, IQR, mean, sd
    ## check for numeric data
    if(!is.numeric(x))
         stop("Data must be numeric")  ## or convert it
    boxplot(x, horizontal=TRUE)
    list(fiveNum=fivenum(x),IQR=IQR(x),mean=mean(x),SD=sd(x))
}
# Summrize(rnorm(50,20,5))


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#line 97 "/home/jimrc/classes/stat505/notes/introR3.Rnw"
Summrize <- function(x,...){
    ## function to plot BWplot, return fivenum, IQR, mean, sd
    x <- as.numeric(x)  ## forced conversion to numeric
    boxplot(x, ... )       ## pass the extras on to boxplot
    list(fiveNum=fivenum(x),IQR=IQR(x),mean=mean(x),SD=sd(x))
}
# Summrize(rnorm(50,20,5), col="yellow")
# Summrize(rnorm(50,20,5), col="yellow",horizontal=TRUE)


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#line 113 "/home/jimrc/classes/stat505/notes/introR3.Rnw"
test.means <- function(y1, y2=NULL, paired=FALSE) {
    ##  see t.test for a better function to test means
    n1  <- length(y1)
    if(is.null(y2)){
        tst <- mean(y1)/sd(y1) * sqrt(n1)
    } else if(paired)
            tst <- test.means(y1-y2,NULL)
        else {
            n2  <- length(y2)
            yb1 <- mean(y1);       yb2 <- mean(y2)
            v1  <- var(y1);        v2  <- var(y2)
            sd <- sqrt((n1-1)*v1 + (n2-1)*v2)/(n1+n2-2)
            tst <- (yb1 - yb2)/(sd *sqrt(1/n1 + 1/n2))
       }
    tst
}
# test.means(rnorm(20))
# test.means(rnorm(20,3,4),rnorm(20,7,4))
# test.means(rnorm(20,3,4),rnorm(20,7,4),TRUE)


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#line 142 "/home/jimrc/classes/stat505/notes/introR3.Rnw"
 ruby <-  read.csv("../data/Ruby-AllFish.csv",head=TRUE) ##
 ruby.Ghrn.RBT2006 <- subset(ruby, species=="RBT" & site=="Ghorn" & 
                       year==2006 & length >100 )
 #summary(rubyRBT2006)
  out1 <- with(ruby.Ghrn.RBT2006, table(cut(length, seq(100,475,25)),mark,trip)) ## problem:  trip 1 is never marked
  cbind(out1[,,1],out1[,,2])


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#line 159 "/home/jimrc/classes/stat505/notes/introR3.Rnw"
 ruby.Ghrn.RBT2006$type <- with(ruby.Ghrn.RBT2006, ifelse(trip == 1,"pass1", 
                                ifelse(mark == 1,"both","pass2")))
  with(ruby.Ghrn.RBT2006, table(cut(length, seq(100,475,25)),type))


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### chunk number 10: fun1
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#line 187 "/home/jimrc/classes/stat505/notes/introR3.Rnw"
 fishTable <- function(data, yr, specs, ste, minLength=100, maxLength=500, increment=25){
   myData <- subset(data, species==specs & site==ste & 
                       year==yr & length > minLength & length < maxLength )
   type <- with(myData, ifelse(trip == 1, "pass1", 
                   ifelse(mark == 1, "both", "pass2")))
   results <- with(myData, table(cut(length, seq(minLength, maxLength, increment)), type))[,c(2,3,1)] ## reorder columns
   ## marks are included in pass1, not pass2
   results[,2] <- results[,3] + results[,2]
   results
 }


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### chunk number 11: fun2
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#line 204 "/home/jimrc/classes/stat505/notes/introR3.Rnw"
head( ruby.Canyon.RBT2006 <-  fishTable(ruby, specs ="RBT" , ste="Can", yr=2006))