From 544594a32eb4ec32997517fdb20b8c231ac2fd86 Mon Sep 17 00:00:00 2001
From: Walmes Zeviani <walmes@ufpr.br>
Date: Wed, 7 Oct 2015 11:07:52 -0300
Subject: [PATCH] Add *.R to prepare datasets of chapter 10.
---
data-raw/bib1.R | 52 +++++++++++++++++++++++++++++++++++
data-raw/bib2.R | 49 +++++++++++++++++++++++++++++++++
data-raw/bib3.R | 53 +++++++++++++++++++++++++++++++++++
data-raw/bib3asin.R | 67 +++++++++++++++++++++++++++++++++++++++++++++
4 files changed, 221 insertions(+)
create mode 100644 data-raw/bib1.R
create mode 100644 data-raw/bib2.R
create mode 100644 data-raw/bib3.R
create mode 100644 data-raw/bib3asin.R
diff --git a/data-raw/bib1.R b/data-raw/bib1.R
new file mode 100644
index 0000000..9688a6b
--- /dev/null
+++ b/data-raw/bib1.R
@@ -0,0 +1,52 @@
+##----------------------------------------------------------------------
+## Data generation. Pimentel page 190.
+
+## bib1 <- read.table("clipboard", header=TRUE, sep="\t")
+## names(bib1) <- c("rept", "treat", "block", "y")
+## bib1 <- transform(bib1, rept=factor(rept),
+## block=factor(block), treat=factor(treat))
+
+bib1 <-
+structure(list(rept = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L,
+1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
+3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L,
+5L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 7L, 7L, 7L, 7L, 7L, 7L, 7L,
+7L), .Label = c("1", "2", "3", "4", "5", "6", "7"), class = "factor"),
+ treat = structure(c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 1L, 3L,
+ 2L, 8L, 4L, 5L, 6L, 7L, 1L, 4L, 2L, 7L, 3L, 6L, 5L, 8L, 1L,
+ 5L, 2L, 3L, 4L, 7L, 6L, 8L, 1L, 6L, 2L, 4L, 3L, 8L, 5L, 7L,
+ 1L, 7L, 2L, 6L, 3L, 5L, 4L, 8L, 1L, 8L, 2L, 5L, 3L, 7L, 4L,
+ 6L), .Label = c("1", "2", "3", "4", "5", "6", "7", "8"), class = "factor"),
+ block = structure(c(1L, 1L, 2L, 2L, 3L, 3L, 4L, 4L, 1L, 1L,
+ 2L, 2L, 3L, 3L, 4L, 4L, 1L, 1L, 2L, 2L, 3L, 3L, 4L, 4L, 1L,
+ 1L, 2L, 2L, 3L, 3L, 4L, 4L, 1L, 1L, 2L, 2L, 3L, 3L, 4L, 4L,
+ 1L, 1L, 2L, 2L, 3L, 3L, 4L, 4L, 1L, 1L, 2L, 2L, 3L, 3L, 4L,
+ 4L), .Label = c("1", "2", "3", "4"), class = "factor"), y = c(20L,
+ 18L, 15L, 16L, 14L, 15L, 16L, 18L, 24L, 18L, 25L, 19L, 13L,
+ 16L, 12L, 16L, 23L, 17L, 26L, 18L, 15L, 17L, 13L, 16L, 21L,
+ 13L, 23L, 16L, 10L, 12L, 13L, 11L, 28L, 14L, 27L, 18L, 18L,
+ 15L, 16L, 17L, 22L, 17L, 24L, 16L, 18L, 14L, 15L, 17L, 23L,
+ 15L, 21L, 13L, 15L, 12L, 13L, 16L)), .Names = c("rept", "treat",
+"block", "y"), row.names = c(NA, -56L), class = "data.frame")
+
+str(bib1)
+
+bib <- bib1[with(bib1, order(rept, block, treat)), ]
+
+save(bib1, file="../data/bib1.RData")
+
+##----------------------------------------------------------------------
+## Examples.
+
+require(lattice)
+
+xyplot(y~treat|rept, groups=block, data=bib1, type="b",
+ ylab="Y", xlab="Treatment")
+
+xyplot(y~treat, data=bib1, jitter.x=TRUE,
+ ylab="Y", xlab="Treatment")
+
+rm(list=ls())
+load("../data/bib1.RData")
+ls()
+str(bib1)
diff --git a/data-raw/bib2.R b/data-raw/bib2.R
new file mode 100644
index 0000000..9fd0903
--- /dev/null
+++ b/data-raw/bib2.R
@@ -0,0 +1,49 @@
+##----------------------------------------------------------------------
+## Data generation. Pimentel page 192.
+
+## bib2 <- read.table("clipboard", header=TRUE, sep="\t")
+## bib2$y <- as.numeric(sub(x=bib2$y, ",", "."))
+## names(bib2) <- c("rept", "block", "treat", "y")
+## bib2 <- transform(bib2, rept=factor(rept),
+## block=factor(block), treat=factor(treat))
+## dput(bib2)
+
+bib2 <-
+structure(list(rept = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L,
+1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
+2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
+3L, 3L, 3L), .Label = c("1", "2", "3"), class = "factor"), block = structure(c(1L,
+1L, 2L, 2L, 3L, 3L, 4L, 4L, 5L, 5L, 6L, 6L, 7L, 7L, 1L, 1L, 2L,
+2L, 3L, 3L, 4L, 4L, 5L, 5L, 6L, 6L, 7L, 7L, 1L, 1L, 2L, 2L, 3L,
+3L, 4L, 4L, 5L, 5L, 6L, 6L, 7L, 7L), .Label = c("1", "2", "3",
+"4", "5", "6", "7"), class = "factor"), treat = structure(c(1L,
+2L, 2L, 3L, 3L, 4L, 4L, 5L, 5L, 6L, 6L, 7L, 7L, 1L, 1L, 3L, 3L,
+5L, 5L, 7L, 7L, 2L, 2L, 4L, 4L, 6L, 6L, 1L, 1L, 4L, 4L, 7L, 7L,
+3L, 3L, 6L, 6L, 2L, 2L, 5L, 5L, 1L), .Label = c("1", "2", "3",
+"4", "5", "6", "7"), class = "factor"), y = c(3.5, 2.8, 3.2,
+3.7, 3.5, 2.5, 2.8, 2.7, 3, 3.2, 2.4, 2.6, 3.1, 2.7, 3.8, 4,
+3.6, 2.7, 2.3, 3, 2.8, 2.5, 2.6, 2.8, 2.3, 2.4, 2.8, 3.3, 3,
+2.2, 2.7, 3.4, 3.2, 3.9, 3.3, 2.4, 2.8, 3.4, 2.9, 2.6, 2.3, 3.3
+)), .Names = c("rept", "block", "treat", "y"), row.names = c(NA,
+-42L), class = "data.frame")
+str(bib2)
+
+bib <- bib2[with(bib2, order(rept, block, treat)), ]
+
+save(bib2, file="../data/bib2.RData")
+
+##----------------------------------------------------------------------
+## Examples.
+
+require(lattice)
+
+xyplot(y~treat|rept, groups=block, data=bib2, type="b",
+ ylab="Y", xlab="Treatment")
+
+xyplot(y~treat, data=bib2, jitter.x=TRUE,
+ ylab="Y", xlab="Treatment")
+
+rm(list=ls())
+load("../data/bib2.RData")
+ls()
+str(bib2)
diff --git a/data-raw/bib3.R b/data-raw/bib3.R
new file mode 100644
index 0000000..a5d9207
--- /dev/null
+++ b/data-raw/bib3.R
@@ -0,0 +1,53 @@
+##----------------------------------------------------------------------
+## Data generation. Pimentel page 185.
+
+## bib3 <- read.table("clipboard", header=TRUE, sep="\t")
+## names(bib3) <- c("block", "treat", "y")
+## bib3 <- transform(bib3,
+## block=factor(block), treat=factor(treat))
+## dput(bib3)
+
+bib3 <-
+structure(list(block = structure(c(1L, 1L, 1L, 2L, 2L, 2L, 3L,
+3L, 3L, 4L, 4L, 4L, 5L, 5L, 5L, 6L, 6L, 6L, 7L, 7L, 7L, 8L, 8L,
+8L, 9L, 9L, 9L, 10L, 10L, 10L), .Label = c("1", "2", "3", "4",
+"5", "6", "7", "8", "9", "10"), class = "factor"), treat = structure(c(1L,
+2L, 3L, 1L, 2L, 4L, 1L, 2L, 5L, 1L, 3L, 4L, 1L, 3L, 5L, 1L, 4L,
+5L, 2L, 3L, 4L, 2L, 3L, 5L, 2L, 4L, 5L, 3L, 4L, 5L), .Label = c("1",
+"2", "3", "4", "5"), class = "factor"), y = c(35L, 28L, 27L,
+30L, 20L, 22L, 28L, 16L, 18L, 36L, 29L, 30L, 29L, 19L, 22L, 25L,
+16L, 19L, 26L, 30L, 28L, 27L, 29L, 27L, 29L, 29L, 27L, 27L, 26L,
+29L)), .Names = c("block", "treat", "y"), row.names = c(NA, -30L
+), class = "data.frame")
+
+bib <- bib3[with(bib3, order(block, treat)), ]
+
+save(bib3, file="../data/bib3.RData")
+
+##----------------------------------------------------------------------
+## Examples.
+
+require(lattice)
+
+xyplot(y~treat|block, data=bib3,
+ ylab="Y",
+ xlab="Treatment")
+
+g <- nlevels(bib3$treat)
+a <- seq(0, by=(2*pi)/(g), length.out=g)
+y <- sin(a)
+x <- cos(a)
+plot(y~x, asp=1, xlim=c(-1,1), ylim=c(-1,1))
+
+for (b in levels(bib3$block)){
+ cbn <- combn(x=as.integer(bib3$treat[bib3$block==b]),
+ m=2)
+ segments(
+ x0=x[cbn[1,]], y0=y[cbn[1,]],
+ x1=x[cbn[2,]], y1=y[cbn[2,]], col=b)
+}
+
+rm(list=ls())
+load("../data/bib3.RData")
+ls()
+str(bib3)
diff --git a/data-raw/bib3asin.R b/data-raw/bib3asin.R
new file mode 100644
index 0000000..1f771d1
--- /dev/null
+++ b/data-raw/bib3asin.R
@@ -0,0 +1,67 @@
+##----------------------------------------------------------------------
+## Data generation. Pimentel page 198.
+
+## bib3asin <- read.table("clipboard", header=TRUE, sep="\t")
+## bib3asin[, 3] <- as.numeric(sub(x=bib3asin[, 3], ",", "."))
+## names(bib3asin) <- c("block", "treat", "z")
+## bib3asin <- transform(bib3asin,
+## block=factor(block), treat=factor(treat))
+## dput(bib3asin)
+
+bib3asin <-
+structure(list(block = structure(c(1L, 2L, 3L, 4L, 5L, 6L, 7L,
+8L, 9L, 10L, 11L, 12L, 13L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L,
+10L, 11L, 12L, 13L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L,
+11L, 12L, 13L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L,
+12L, 13L), .Label = c("1", "2", "3", "4", "5", "6", "7", "8",
+"9", "10", "11", "12", "13"), class = "factor"), treat = structure(c(1L,
+2L, 1L, 3L, 4L, 1L, 2L, 1L, 6L, 3L, 5L, 4L, 2L, 2L, 8L, 7L, 4L,
+8L, 3L, 3L, 5L, 10L, 7L, 9L, 5L, 6L, 4L, 12L, 11L, 6L, 9L, 9L,
+5L, 6L, 11L, 8L, 10L, 7L, 7L, 10L, 13L, 12L, 12L, 11L, 13L, 11L,
+8L, 13L, 10L, 12L, 13L, 9L), .Label = c("1", "2", "3", "4", "5",
+"6", "7", "8", "9", "10", "11", "12", "13"), class = "factor"),
+ z = c(52.7, 71.6, 58.9, 75, 71.6, 56.8, 75, 48.8, 63.4, 71.6,
+ 75, 63.4, 71.6, 79.5, 56.8, 75, 65.9, 75, 65.9, 65.9, 68.6,
+ 90, 63.4, 68.6, 61.1, 63.4, 63.4, 71.6, 75, 79.5, 71.6, 71.6,
+ 65.9, 63.4, 90, 61.1, 75, 50.8, 61.1, 65.9, 65.9, 71.6, 79.5,
+ 79.5, 65.9, 90, 61.1, 71.6, 58.9, 75, 79.5, 75)), .Names = c("block",
+"treat", "z"), row.names = c(NA, -52L), class = "data.frame")
+
+bib <- bib3asin[with(bib3asin, order(block, treat)), ]
+
+save(bib3asin, file="../data/bib3asin.RData")
+
+##----------------------------------------------------------------------
+## Examples.
+
+require(lattice)
+
+xyplot(z~treat|block, data=bib3asin,
+ ylab="Arc sin of heathy plants fraction",
+ xlab="Treatment")
+
+## Why not consider a beta distribution for p?
+bib3asin$p <- sin(bib3asin$z*pi/180)^2
+
+xyplot(p~treat|block, data=bib3asin,
+ ylab="Fraction of healthy plants",
+ xlab="Treatment")
+
+g <- nlevels(bib3asin$treat)
+a <- seq(0, by=(2*pi)/(g), length.out=g)
+y <- sin(a)
+x <- cos(a)
+plot(y~x, asp=1, xlim=c(-1,1), ylim=c(-1,1))
+
+for (b in levels(bib3asin$block)){
+ cbn <- combn(x=as.integer(bib3asin$treat[bib3asin$block==b]),
+ m=2)
+ segments(
+ x0=x[cbn[1,]], y0=y[cbn[1,]],
+ x1=x[cbn[2,]], y1=y[cbn[2,]], col=b)
+}
+
+rm(list=ls())
+load("../data/bib3asin.RData")
+ls()
+str(bib3asin)
--
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