From f2c389c29e6d72c12ddd1be8629b0f154e93f1b6 Mon Sep 17 00:00:00 2001
From: Walmes Zeviani <walmeszeviani@gmail.com>
Date: Sat, 19 Sep 2015 23:33:18 -0300
Subject: [PATCH] Add dataset of a 2^3 experiment with NPK on korn yield,
Pimentel pg 115.
---
R/legTools.R | 87 +++++++++++++++++++++++--
data-raw/kornYield.R | 66 +++++++++++++++++++
data/kornYield.RData | Bin 0 -> 386 bytes
data/potatoYield.RData | Bin 464 -> 466 bytes
legTools.bmk | 77 +++++++++++++---------
man/kornYield.Rd | 76 +++++++++++++++++++++
man/plowing.Rd | 2 +-
man/{potatoyield.Rd => potatoYield.Rd} | 10 +--
man/sugarcaneYield3.Rd | 10 +--
9 files changed, 280 insertions(+), 48 deletions(-)
create mode 100644 data-raw/kornYield.R
create mode 100644 data/kornYield.RData
create mode 100644 man/kornYield.Rd
rename man/{potatoyield.Rd => potatoYield.Rd} (89%)
diff --git a/R/legTools.R b/R/legTools.R
index c6b3d2b..f062b1c 100644
--- a/R/legTools.R
+++ b/R/legTools.R
@@ -353,19 +353,19 @@ NULL
#' experimental unit.
#'
#' \itemize{
-#' \item \code{row} the rows of the latin square that controls in
+#' \item \code{row} the rows of the latin square that controls in
#' one dimention. A categorical unordered factor with 6 levels.
-#' \item \code{col} the columns of the latin square that controls in
+#' \item \code{col} the columns of the latin square that controls in
#' one dimention perpendicular to the previus. A categorical
#' unordered factor with 6 levels.
-#' \item \code{fertil} a categorical unordered factor with 6
+#' \item \code{fertil} a categorical unordered factor with 6
#' levels that is the fertilization strategy applied. These levels
#' are a result of treatment cells in a three incomplete factorial
#' arrangrment. See detais for more information.
-#' \item \code{yield} sugarcane yield (kg/plot).
+#' \item \code{yield} sugarcane yield (kg/plot).
#' }
#'
-#' @details The levels of fetilization are in fact a combination of a
+#' @details The levels of fertilization are in fact a combination of a
#' \eqn{3^2} factorial experiment but not all cells are present, so
#' this is a (intentional) incomplete three factorial
#' experiment. The factors used were limestone (A: present, a:
@@ -496,3 +496,80 @@ NULL
#' test=adjusted(type="single-step"))
#'
NULL
+
+#' @name kornYield
+#'
+#' @title Korn yield as function of fertilization with NPK
+#'
+#' @description These data are from an \eqn{2^3} factorial experiment
+#' studing the effect of Nitrogen (N), Phosporus (P) and Potassium
+#' (K) on korn yield in a randomized block design.
+#'
+#' \itemize{
+#' \item \code{block} a factor with 4 levels.
+#' \item \code{N} low (-1) and high (+1) levels of nitrogen.
+#' \item \code{P} low (-1) and high (+1) levels of phosporus.
+#' \item \code{K} low (-1) and high (+1) levels of potassium.
+#' \item \code{yield} korn yield (ton/ha).
+#' }
+#'
+#' @docType data
+#'
+#' @keywords datasets
+#'
+#' @usage data(kornYield)
+#'
+#' @format a \code{data.frame} with 32 records and 4 variables.
+#'
+#' @source Frederico, P. (2009). Curso de Estatística Experimental (15th
+#' ed.). Piracicaba, São Paulo: FEALQ. (page 115)
+#'
+#' @examples
+#'
+#' library(lattice)
+#' library(latticeExtra)
+#'
+#' data(kornYield)
+#' str(kornYield)
+#'
+#' xyplot(yield~N|P, groups=K,
+#' data=kornYield, type=c("p", "a"),
+#' ylab=expression(Yield~(ton~ha^{-1})),
+#' xlab="Nutrient level")
+#'
+#' xyplot(yield~N, groups=interaction(P, K),
+#' data=kornYield, type=c("p", "a"),
+#' auto.key=list(columns=2),
+#' ylab=expression(Yield~(ton~ha^{-1})),
+#' xlab="Nutrient level")
+#'
+#' m0 <- lm(yield~block+(N+P+K)^3, data=kornYield)
+#' par(mfrow=c(2,2)); plot(m0); layout(1)
+#' anova(m0)
+#'
+#' m1 <- update(m0, .~block+N+K)
+#' par(mfrow=c(2,2)); plot(m1); layout(1)
+#'
+#' anova(m0, m1)
+#' anova(m1)
+#'
+#' summary(m1)
+#'
+#' pred <- expand.grid(block="1",
+#' N=seq(-1, 1, by=0.1),
+#' K=seq(-1, 1, by=0.1))
+#' pred$mu <- predict(m1, newdata=pred)
+#'
+#' wireframe(mu~N+K, data=pred,
+#' scales=list(arrows=FALSE),
+#' zlab=list(expression(Yield~(ton~ha^{-1})), rot=90),
+#' drape=TRUE, cuts=20,
+#' col.regions=colorRampPalette(
+#' color=brewer.pal(n=11, name="Spectral"))(21))
+#'
+#' levelplot(mu~N+K, data=pred, aspect=1,
+#' main=expression(Yield~(ton~ha^{-1})),
+#' col.regions=colorRampPalette(
+#' color=brewer.pal(n=11, name="Spectral")))
+#'
+NULL
diff --git a/data-raw/kornYield.R b/data-raw/kornYield.R
new file mode 100644
index 0000000..bca2a49
--- /dev/null
+++ b/data-raw/kornYield.R
@@ -0,0 +1,66 @@
+##----------------------------------------------------------------------
+## Data generation.
+
+kornYield <- expand.grid(block=gl(4, 1), N=c(-1,1), P=c(-1,1),
+ K=c(-1,1), KEEP.OUT.ATTRS=FALSE)
+kornYield$yield <- c(1.32, 2.12, 1.75, 2.35, 1.80, 2.20, 2.95, 2.96,
+ 1.66, 2.66, 1.73, 2.58, 1.72, 3.85, 2.62, 3.00,
+ 2.58, 3.56, 2.86, 2.75, 2.72, 3.20, 2.25, 2.75,
+ 2.26, 2.08, 1.95, 2.70, 2.95, 3.28, 2.40, 3.35)
+str(kornYield)
+
+save(kornYield, file="../data/kornYield.RData")
+
+##----------------------------------------------------------------------
+## Examples.
+
+library(lattice)
+library(latticeExtra)
+
+data(kornYield)
+str(kornYield)
+
+xyplot(yield~N|P, groups=K,
+ data=kornYield, type=c("p", "a"),
+ ylab=expression(Yield~(ton~ha^{-1})),
+ xlab="Nutrient level")
+
+xyplot(yield~N, groups=interaction(P, K),
+ data=kornYield, type=c("p", "a"),
+ auto.key=list(columns=2),
+ ylab=expression(Yield~(ton~ha^{-1})),
+ xlab="Nutrient level")
+
+m0 <- lm(yield~block+(N+P+K)^3, data=kornYield)
+par(mfrow=c(2,2)); plot(m0); layout(1)
+anova(m0)
+
+m1 <- update(m0, .~block+N+K)
+par(mfrow=c(2,2)); plot(m1); layout(1)
+
+anova(m0, m1)
+anova(m1)
+
+summary(m1)
+
+pred <- expand.grid(block="1",
+ N=seq(-1, 1, by=0.1),
+ K=seq(-1, 1, by=0.1))
+pred$mu <- predict(m1, newdata=pred)
+
+wireframe(mu~N+K, data=pred,
+ scales=list(arrows=FALSE),
+ zlab=list(expression(Yield~(ton~ha^{-1})), rot=90),
+ drape=TRUE, cuts=20,
+ col.regions=colorRampPalette(
+ color=brewer.pal(n=11, name="Spectral"))(21))
+
+levelplot(mu~N+K, data=pred, aspect=1,
+ main=expression(Yield~(ton~ha^{-1})),
+ col.regions=colorRampPalette(
+ color=brewer.pal(n=11, name="Spectral")))
+
+rm(list=ls())
+load("../data/kornYield.RData")
+ls()
+str(kornYield)
diff --git a/data/kornYield.RData b/data/kornYield.RData
new file mode 100644
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diff --git a/data/potatoYield.RData b/data/potatoYield.RData
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diff --git a/legTools.bmk b/legTools.bmk
index bb8d9f9..93387a0 100644
--- a/legTools.bmk
+++ b/legTools.bmk
@@ -2,18 +2,31 @@
;;; This format is meant to be slightly human-readable;
;;; nevertheless, you probably don't want to edit it.
;;; -*- End Of Bookmark File Format Version Stamp -*-
-(#1=(#("wgpigs2" 0 7
+(#1=(#("kornYield" 0 9
(bmkp-full-record #1#))
(filename . "~/GitLab/legTools/R/legTools.R")
(buffer-name . "legTools.R")
- (front-context-string . "@name wgpigs2\n#'")
- (rear-context-string . "an)\n#'\nNULL\n\n#' ")
+ (front-context-string . "@name kornYield\n")
+ (rear-context-string . "\"))\n#'\nNULL\n\n#' ")
(front-context-region-string)
(rear-context-region-string)
(visits . 0)
- (time . #2=(22014 2449 877392 862000))
+ (time . #2=(22014 6386 355822 993000))
(created . #2#)
- (position . 14008))
+ (position . 16336))
+#1=(#("wgpigs2" 0 7
+ (bmkp-full-record #1#))
+ (end-position . 14001)
+ (filename . "~/GitLab/legTools/R/legTools.R")
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+ (front-context-string . "@name wgpigs2\n#'")
+ (rear-context-string . "an)\n#'\nNULL\n\n#' ")
+ (front-context-region-string)
+ (rear-context-region-string)
+ (visits . 3)
+ (time 22014 6373 782337 593000)
+ (created 22014 2449 877392 862000)
+ (position . 14001))
#1=(#("sugarcaneYield3" 0 15
(bmkp-full-record #1#))
(filename . "~/GitLab/legTools/R/legTools.R")
@@ -22,9 +35,9 @@
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(front-context-region-string)
(rear-context-region-string)
- (visits . 0)
- (time . #2=(22014 2438 565160 262000))
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+ (visits . 2)
+ (time 22014 6373 622489 1000)
+ (created 22014 2438 565160 262000)
(position . 11050))
#1=(#("sugarcaneYield2" 0 15
(bmkp-full-record #1#))
@@ -34,9 +47,9 @@
(rear-context-string . "y\")\n#'\nNULL\n\n#' ")
(front-context-region-string)
(rear-context-region-string)
- (visits . 0)
- (time . #2=(22014 2428 365189 950000))
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+ (visits . 1)
+ (time 22014 6373 470955 812000)
+ (created 22014 2428 365189 950000)
(position . 9217))
#1=(#("sugarcaneYield" 0 14
(bmkp-full-record #1#))
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(front-context-region-string)
(rear-context-region-string)
- (visits . 0)
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+ (visits . 1)
+ (time 22014 6373 318366 504000)
+ (created 22014 2414 357030 236000)
(position . 8152))
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(front-context-region-string)
(rear-context-region-string)
- (visits . 0)
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+ (created 22014 2401 421345 289000)
(position . 6963))
#1=(#("defoliation" 0 11
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(front-context-region-string)
(rear-context-region-string)
- (visits . 0)
- (time . #2=(22014 2377 645195 878000))
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+ (visits . 1)
+ (time 22014 6372 878551 941000)
+ (created 22014 2377 645195 878000)
(position . 2330))
#1=(#("potatoYield" 0 11
(bmkp-full-record #1#))
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(front-context-region-string)
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+ (created 22014 2364 877635 749000)
(position . 1285))
#1=(#("wgpigs" 0 6
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(front-context-region-string)
(rear-context-region-string)
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+ (created 22014 2268 166496 375000)
(position . 219))
#1=(#("legTools.R" 0 10
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(front-context-region-string)
(rear-context-region-string)
- (visits . 0)
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+ (created 22014 2255 246295 352000)
(position . 195))
#1=(#("DESCRIPTION" 0 11
(bmkp-full-record #1#))
diff --git a/man/kornYield.Rd b/man/kornYield.Rd
new file mode 100644
index 0000000..be35646
--- /dev/null
+++ b/man/kornYield.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{kornYield}
+\alias{kornYield}
+\title{Korn yield as function of fertilization with NPK}
+\format{a \code{data.frame} with 32 records and 4 variables.}
+\source{
+Frederico, P. (2009). Curso de Estatística Experimental (15th
+ ed.). Piracicaba, São Paulo: FEALQ. (page 115)
+}
+\usage{
+data(kornYield)
+}
+\description{
+These data are from an \eqn{2^3} factorial experiment
+ studing the effect of Nitrogen (N), Phosporus (P) and Potassium
+ (K) on korn yield in a randomized block design.
+
+\itemize{
+ \item \code{block} a factor with 4 levels.
+ \item \code{N} low (-1) and high (+1) levels of nitrogen.
+ \item \code{P} low (-1) and high (+1) levels of phosporus.
+ \item \code{K} low (-1) and high (+1) levels of potassium.
+ \item \code{yield} korn yield (ton/ha).
+}
+}
+\examples{
+library(lattice)
+library(latticeExtra)
+
+data(kornYield)
+str(kornYield)
+
+xyplot(yield~N|P, groups=K,
+ data=kornYield, type=c("p", "a"),
+ ylab=expression(Yield~(ton~ha^{-1})),
+ xlab="Nutrient level")
+
+xyplot(yield~N, groups=interaction(P, K),
+ data=kornYield, type=c("p", "a"),
+ auto.key=list(columns=2),
+ ylab=expression(Yield~(ton~ha^{-1})),
+ xlab="Nutrient level")
+
+m0 <- lm(yield~block+(N+P+K)^3, data=kornYield)
+par(mfrow=c(2,2)); plot(m0); layout(1)
+anova(m0)
+
+m1 <- update(m0, .~block+N+K)
+par(mfrow=c(2,2)); plot(m1); layout(1)
+
+anova(m0, m1)
+anova(m1)
+
+summary(m1)
+
+pred <- expand.grid(block="1",
+ N=seq(-1, 1, by=0.1),
+ K=seq(-1, 1, by=0.1))
+pred$mu <- predict(m1, newdata=pred)
+
+wireframe(mu~N+K, data=pred,
+ scales=list(arrows=FALSE),
+ zlab=list(expression(Yield~(ton~ha^{-1})), rot=90),
+ drape=TRUE, cuts=20,
+ col.regions=colorRampPalette(
+ color=brewer.pal(n=11, name="Spectral"))(21))
+
+levelplot(mu~N+K, data=pred, aspect=1,
+ main=expression(Yield~(ton~ha^{-1})),
+ col.regions=colorRampPalette(
+ color=brewer.pal(n=11, name="Spectral")))
+}
+\keyword{datasets}
+
diff --git a/man/plowing.Rd b/man/plowing.Rd
index 66fc799..30c69ca 100644
--- a/man/plowing.Rd
+++ b/man/plowing.Rd
@@ -29,7 +29,7 @@ These data are from an experiment done by the engineer
}
\examples{
library(lattice)
-data(potatoyield)
+data(plowing)
xyplot(yield~plow|block, data=plowing, type=c("p", "a"),
ylab=expression(Yield~(t~ha^{-1})),
diff --git a/man/potatoyield.Rd b/man/potatoYield.Rd
similarity index 89%
rename from man/potatoyield.Rd
rename to man/potatoYield.Rd
index 441fce5..3a07526 100644
--- a/man/potatoyield.Rd
+++ b/man/potatoYield.Rd
@@ -1,8 +1,8 @@
% Generated by roxygen2 (4.1.1): do not edit by hand
% Please edit documentation in R/legTools.R
\docType{data}
-\name{potatoyield}
-\alias{potatoyield}
+\name{potatoYield}
+\alias{potatoYield}
\title{Potato variety competition experiment}
\format{a \code{data.frame} with 32 records and 3 variables.}
\source{
@@ -10,7 +10,7 @@ Frederico, P. (2009). Curso de Estatística Experimental (15th
ed.). Piracicaba, São Paulo: FEALQ. (page 76)
}
\usage{
-data(potatoyield)
+data(potatoYield)
}
\description{
These data are from an experiment done by the engineer
@@ -27,9 +27,9 @@ These data are from an experiment done by the engineer
}
\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")
diff --git a/man/sugarcaneYield3.Rd b/man/sugarcaneYield3.Rd
index b7418bf..048af7a 100644
--- a/man/sugarcaneYield3.Rd
+++ b/man/sugarcaneYield3.Rd
@@ -18,20 +18,20 @@ These data are from an experiment done in a latin square
experimental unit.
\itemize{
- \item \code{row} the rows of the latin square that controls in
+ \item \code{row} the rows of the latin square that controls in
one dimention. A categorical unordered factor with 6 levels.
- \item \code{col} the columns of the latin square that controls in
+ \item \code{col} the columns of the latin square that controls in
one dimention perpendicular to the previus. A categorical
unordered factor with 6 levels.
- \item \code{fertil} a categorical unordered factor with 6
+ \item \code{fertil} a categorical unordered factor with 6
levels that is the fertilization strategy applied. These levels
are a result of treatment cells in a three incomplete factorial
arrangrment. See detais for more information.
- \item \code{yield} sugarcane yield (kg/plot).
+ \item \code{yield} sugarcane yield (kg/plot).
}
}
\details{
-The levels of fetilization are in fact a combination of a
+The levels of fertilization are in fact a combination of a
\eqn{3^2} factorial experiment but not all cells are present, so
this is a (intentional) incomplete three factorial
experiment. The factors used were limestone (A: present, a:
--
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