From 69448cbac456271fe42268819f70560e3824eff6 Mon Sep 17 00:00:00 2001
From: Walmes Zeviani <walmeszeviani@gmail.com>
Date: Sat, 19 Sep 2015 22:31:32 -0300
Subject: [PATCH] Add dataset of a LSD experiment about weight gain in pigs.
---
DESCRIPTION | 3 +-
R/legTools.R | 87 ++++++++++++++++++++++++++++++++++++++++++---
data-raw/wgpigs2.R | 63 ++++++++++++++++++++++++++++++++
data/wgpigs2.RData | Bin 0 -> 328 bytes
man/wgpigs2.Rd | 76 +++++++++++++++++++++++++++++++++++++++
5 files changed, 223 insertions(+), 6 deletions(-)
create mode 100644 data-raw/wgpigs2.R
create mode 100644 data/wgpigs2.RData
create mode 100644 man/wgpigs2.Rd
diff --git a/DESCRIPTION b/DESCRIPTION
index 1180dc1..5b665af 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -18,7 +18,8 @@ Depends:
gWidgetstcltk,
knitr,
markdown,
- RWordPress
+ RWordPress,
+ multcomp
License: GPL-3 | file LICENSE
URL: http://git.leg.ufpr.br/leg/legTools
BugReports: http://git.leg.ufpr.br/leg/legTools/issues
diff --git a/R/legTools.R b/R/legTools.R
index 75be3eb..c6b3d2b 100644
--- a/R/legTools.R
+++ b/R/legTools.R
@@ -47,7 +47,7 @@ NULL
#'
NULL
-#' @name potatoyield
+#' @name potatoYield
#'
#' @title Potato variety competition experiment
#'
@@ -67,7 +67,7 @@ NULL
#'
#' @keywords datasets
#'
-#' @usage data(potatoyield)
+#' @usage data(potatoYield)
#'
#' @format a \code{data.frame} with 32 records and 3 variables.
#'
@@ -76,9 +76,9 @@ NULL
#'
#' @examples
#' library(lattice)
-#' data(potatoyield)
+#' data(potatoYield)
#'
-#' plot(yield~variety, data=potatoyield,
+#' plot(yield~variety, data=potatoYield,
#' groups=block, type="o",
#' ylab=expression(Yield~(t~ha^{-1})),
#' xlab="Variety")
@@ -116,7 +116,7 @@ NULL
#'
#' @examples
#' library(lattice)
-#' data(potatoyield)
+#' data(plowing)
#'
#' xyplot(yield~plow|block, data=plowing, type=c("p", "a"),
#' ylab=expression(Yield~(t~ha^{-1})),
@@ -419,3 +419,80 @@ NULL
#' aggregate(yield~A+B+C, data=sugarcaneYield3, FUN=mean)
#'
NULL
+
+#' @name wgpigs2
+#'
+#' @title Age of castration in pig weight gain
+#'
+#' @description This is an artifial dataset corresponding a experiment
+#' to study the effect of feeding type (factor with 4 categorical
+#' nominal levels) in pig weight gain. The experiment was a
+#' randomized complete design with five experimental units per
+#' treatment level. The experimental unit was a pig. The response
+#' measured was weight gain from the beggining to the end of the
+#' experiment.
+#'
+#' \itemize{
+#' \item \code{litter} a categorical factor with 4 levels that
+#' represents the rows of the lattin square design and control for
+#' the differences among litters.
+#' \item code{size} a categorical ordered variable that represents the
+#' columns of latin square desing and control for the weight of the
+#' animals at the beggining of the experiment.
+#' \item \code{age} age of the animal (days) when castration was
+#' done. \code{controls} are the animals without castration.
+#' \item \code{wg} weight gain (kg) after 252 days.
+#' }
+#'
+#' @docType data
+#'
+#' @keywords datasets
+#'
+#' @usage data(wgpigs2)
+#'
+#' @format a \code{data.frame} with 16 records and 4 variables.
+#'
+#' @source Frederico, P. (2009). Curso de Estatística Experimental (15th
+#' ed.). Piracicaba, São Paulo: FEALQ. (page 110)
+#'
+#' @examples
+#'
+#' library(lattice)
+#'
+#' data(wgpigs2)
+#' str(wgpigs2)
+#'
+#' xyplot(wg~age, data=wgpigs2, groups=litter,
+#' ylab="Weight gain (kg)",
+#' xlab="Age at castration (days)")
+#'
+#' m0 <- lm(wg~litter+size+age, data=wgpigs2)
+#' par(mfrow=c(2,2)); plot(m0); layout(1)
+#' anova(m0)
+#'
+#' summary(m0)
+#'
+#' library(multcomp)
+#' summary(glht(m0, linfct=mcp(age="Dunnet")),
+#' test=adjusted(type="single-step"))
+#'
+#' m1 <- glm(wg~litter+size+age, data=wgpigs2, family=Gamma)
+#' m2 <- glm(wg~litter+size+age, data=wgpigs2,
+#' family=Gamma(link="log"))
+#' m3 <- glm(wg~litter+size+age, data=wgpigs2,
+#' family=Gamma(link="identity"))
+#'
+#' rbind(logLik(m0),
+#' logLik(m1),
+#' logLik(m2),
+#' logLik(m3))
+#'
+#' par(mfrow=c(2,2)); plot(m1); layout(1)
+#' anova(m1, test="F")
+#' anova(m2, test="F")
+#' anova(m3, test="F")
+#'
+#' summary(glht(m3, linfct=mcp(age="Dunnet")),
+#' test=adjusted(type="single-step"))
+#'
+NULL
diff --git a/data-raw/wgpigs2.R b/data-raw/wgpigs2.R
new file mode 100644
index 0000000..7c6fced
--- /dev/null
+++ b/data-raw/wgpigs2.R
@@ -0,0 +1,63 @@
+##----------------------------------------------------------------------
+## Data generation.
+
+wgpigs2 <- read.table("http://www.leg.ufpr.br/~walmes/data/pimentel_castracao.txt",
+ header=TRUE, sep="\t")
+names(wgpigs2) <- c("litter", "size", "age", "wg")
+wgpigs2 <- transform(wgpigs2, litter=factor(litter), size=factor(size))
+
+aggregate(wg~age, data=wgpigs2, FUN=mean)
+
+wgpigs2$age <- factor(wgpigs2$age,
+ levels=levels(wgpigs2$age)[c(4,3,1,2)],
+ labels=c("control", "7", "21", "56"))
+str(wgpigs2)
+
+save(wgpigs2, file="../data/wgpigs2.RData")
+
+##----------------------------------------------------------------------
+## Examples.
+
+library(lattice)
+
+data(wgpigs2)
+str(wgpigs2)
+
+xyplot(wg~age, data=wgpigs2, groups=litter,
+ ylab="Weight gain (kg)",
+ xlab="Age at castration (days)")
+
+m0 <- lm(wg~litter+size+age, data=wgpigs2)
+par(mfrow=c(2,2)); plot(m0); layout(1)
+anova(m0)
+
+summary(m0)
+
+library(multcomp)
+summary(glht(m0, linfct=mcp(age="Dunnet")),
+ test=adjusted(type="single-step"))
+
+m1 <- glm(wg~litter+size+age, data=wgpigs2, family=Gamma)
+m2 <- glm(wg~litter+size+age, data=wgpigs2,
+ family=Gamma(link="log"))
+m3 <- glm(wg~litter+size+age, data=wgpigs2,
+ family=Gamma(link="identity"))
+
+rbind(logLik(m0),
+ logLik(m1),
+ logLik(m2),
+ logLik(m3))
+
+par(mfrow=c(2,2)); plot(m1); layout(1)
+anova(m1, test="F")
+anova(m2, test="F")
+anova(m3, test="F")
+
+summary(glht(m3, linfct=mcp(age="Dunnet")),
+ test=adjusted(type="single-step"))
+
+rm(list=ls())
+load("../data/wgpigs2.RData")
+ls()
+str(wgpigs2)
+
diff --git a/data/wgpigs2.RData b/data/wgpigs2.RData
new file mode 100644
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diff --git a/man/wgpigs2.Rd b/man/wgpigs2.Rd
new file mode 100644
index 0000000..ef1ff36
--- /dev/null
+++ b/man/wgpigs2.Rd
@@ -0,0 +1,76 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/legTools.R
+\docType{data}
+\name{wgpigs2}
+\alias{wgpigs2}
+\title{Age of castration in pig weight gain}
+\format{a \code{data.frame} with 16 records and 4 variables.}
+\source{
+Frederico, P. (2009). Curso de Estatística Experimental (15th
+ ed.). Piracicaba, São Paulo: FEALQ. (page 110)
+}
+\usage{
+data(wgpigs2)
+}
+\description{
+This is an artifial dataset corresponding a experiment
+ to study the effect of feeding type (factor with 4 categorical
+ nominal levels) in pig weight gain. The experiment was a
+ randomized complete design with five experimental units per
+ treatment level. The experimental unit was a pig. The response
+ measured was weight gain from the beggining to the end of the
+ experiment.
+
+\itemize{
+ \item \code{litter} a categorical factor with 4 levels that
+ represents the rows of the lattin square design and control for
+ the differences among litters.
+ \item code{size} a categorical ordered variable that represents the
+ columns of latin square desing and control for the weight of the
+ animals at the beggining of the experiment.
+ \item \code{age} age of the animal (days) when castration was
+ done. \code{controls} are the animals without castration.
+ \item \code{wg} weight gain (kg) after 252 days.
+}
+}
+\examples{
+library(lattice)
+
+data(wgpigs2)
+str(wgpigs2)
+
+xyplot(wg~age, data=wgpigs2, groups=litter,
+ ylab="Weight gain (kg)",
+ xlab="Age at castration (days)")
+
+m0 <- lm(wg~litter+size+age, data=wgpigs2)
+par(mfrow=c(2,2)); plot(m0); layout(1)
+anova(m0)
+
+summary(m0)
+
+library(multcomp)
+summary(glht(m0, linfct=mcp(age="Dunnet")),
+ test=adjusted(type="single-step"))
+
+m1 <- glm(wg~litter+size+age, data=wgpigs2, family=Gamma)
+m2 <- glm(wg~litter+size+age, data=wgpigs2,
+ family=Gamma(link="log"))
+m3 <- glm(wg~litter+size+age, data=wgpigs2,
+ family=Gamma(link="identity"))
+
+rbind(logLik(m0),
+ logLik(m1),
+ logLik(m2),
+ logLik(m3))
+
+par(mfrow=c(2,2)); plot(m1); layout(1)
+anova(m1, test="F")
+anova(m2, test="F")
+anova(m3, test="F")
+
+summary(glht(m3, linfct=mcp(age="Dunnet")),
+ test=adjusted(type="single-step"))
+}
+\keyword{datasets}
+
--
GitLab