diff --git a/.Rbuildignore b/.Rbuildignore
index ec2fc7f29ce71c3f0c6b5784d6a84a13e21bb913..731e3ca5e58ab25f9d6793631aba9c8bfcd6c3c8 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -2,6 +2,7 @@ README.md
Rplots.pdf
contributing.md
buildPkg.R
+legTools.bmk
.#buildPkg.R
.gitignore
.Rprofile
diff --git a/DESCRIPTION b/DESCRIPTION
index bfcf1c9c2e6f9e65a0f0a5bb70334beffa763107..1431460bf315b4f8dfda64bd4c8641c6b96b69a4 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -9,21 +9,19 @@ Description: legTools is a collection of R functions and datasets used for
of them from books. It is maintained by the LEG group (Statistics and
Geoinformation Laboratory). Please visit http://www.leg.ufpr.br.
Depends:
- R (>= 3.2.1),
- gWidgets,
- gWidgetstcltk,
- knitr,
- markdown,
- RWordPress
-Imports:
+ R (>= 3.2.1)
+Imports:
lattice,
latticeExtra
Suggests:
+ gWidgets,
+ gWidgetstcltk,
knitr,
- rmarkdown
+ markdown,
+ RWordPress,
+ multcomp
License: GPL-3 | file LICENSE
URL: http://git.leg.ufpr.br/leg/legTools
BugReports: http://git.leg.ufpr.br/leg/legTools/issues
LazyData: true
Encoding: UTF-8
-VignetteBuilder: knitr
diff --git a/NAMESPACE b/NAMESPACE
index e7def8d305e7fdaea655ca4109a1d38fb49c49ea..e642272b0865c1350fd5c2a31fd2a334e127de27 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -10,11 +10,6 @@ export(polyGui)
export(runAllChunks)
export(subsetDropAll)
export(twoStripCombined)
-export(yscale.component.right)
-import(RWordPress)
-import(gWidgets)
-import(gWidgetstcltk)
-import(knitr)
+export(yscale.components.right)
import(lattice)
import(latticeExtra)
-import(markdown)
diff --git a/R/knit2wpCrayon.R b/R/knit2wpCrayon.R
index bb4c0b344e4df29b9ce3ad830c7999e9667540b5..6c4f45c99d27418628154967abf61e9c0054dc8b 100644
--- a/R/knit2wpCrayon.R
+++ b/R/knit2wpCrayon.R
@@ -25,7 +25,6 @@
#'
#' @author Walmes Zeviani, \email{walmes@@ufpr.br}
#'
-#' @import knitr markdown RWordPress
#' @export
#' @examples
#' \donttest{
@@ -66,17 +65,33 @@ knit2wpCrayon <- function(input, title="A post from knitr", ...,
stop("`markdown` needed for this function to work. Please install it.",
call.=FALSE)
}
- if (!requireNamespace("RWordPress", quietly=TRUE)){
+ if (!requireNamespace("RWordPress", quietly=TRUE)){
stop("`RWordPress` needed for this function to work. Please install it.",
call.=FALSE)
}
- out <- knit(input, encoding=encoding)
+ ##
+ ##-------------------------------------------
+ ## knitr:::native_encode().
+ ##
+ native_encode <- function (x, to = ""){
+ idx = Encoding(x) == "UTF-8"
+ x2 = iconv(x, if (any(idx)) "UTF-8" else "", to)
+ if (!any(is.na(x2)))
+ return(x2)
+ warning("some characters may not work under the current locale")
+ x
+ }
+ ##
+ ##-------------------------------------------
+ ## Modifed body of the knit2wp().
+ ##
+ out <- knitr::knit(input, encoding=encoding)
on.exit(unlink(out))
con <- file(out, encoding=encoding)
on.exit(close(con), add=TRUE)
content <- native_encode(readLines(con, warn=FALSE))
content <- paste(content, collapse="\n")
- content <- markdownToHTML(text=content, fragment.only=TRUE)
+ content <- markdown::markdownToHTML(text=content, fragment.only=TRUE)
content <- gsub(
pattern="<pre><code class=\"([[:alpha:]]+)\">(.+?)</code></pre>",
replacement="<pre class=\"lang:\\1 decode:true\">\\2</pre>",
@@ -97,3 +112,7 @@ knit2wpCrayon <- function(input, title="A post from knitr", ...,
print(do.call(action, args=WPargs))
}
}
+
+
+library(knitr)
+knitr:::native_encode
diff --git a/R/legTools.R b/R/legTools.R
index 75be3eb232c6eb00f09c70e15b3831d0ca9ade74..3915d62dbdbc5ae792d711610242a2124206d3b1 100644
--- a/R/legTools.R
+++ b/R/legTools.R
@@ -7,7 +7,7 @@
##' @name legTools
NULL
-#' @name wgpigs
+#' @name wgPigs
#'
#' @title Feeding type in pig weight gain
#'
@@ -29,7 +29,7 @@ NULL
#'
#' @keywords datasets
#'
-#' @usage data(wgpigs)
+#' @usage data(wgPigs)
#'
#' @format a \code{data.frame} with 20 records and 2 variables.
#'
@@ -39,15 +39,15 @@ NULL
#' @examples
#'
#' library(lattice)
-#' data(wgpigs)
+#' data(wgPigs)
#'
-#' xyplot(wg~ft, data=wgpigs,
+#' xyplot(wg~ft, data=wgPigs,
#' ylab="Weight gain (kg)",
#' xlab="Feeding type")
#'
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.
#'
@@ -75,10 +75,11 @@ NULL
#' ed.). Piracicaba, São Paulo: FEALQ. (page 76)
#'
#' @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")
@@ -115,8 +116,9 @@ NULL
#' ed.). Piracicaba, São Paulo: FEALQ. (page 91)
#'
#' @examples
+#'
#' library(lattice)
-#' data(potatoyield)
+#' data(plowing)
#'
#' xyplot(yield~plow|block, data=plowing, type=c("p", "a"),
#' ylab=expression(Yield~(t~ha^{-1})),
@@ -353,19 +355,19 @@ 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:
@@ -419,3 +421,347 @@ 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 EstatÃstica 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)")
+#'
+NULL
+
+#' @name cornYield
+#'
+#' @title Corn 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 corn 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} corn yield (ton/ha).
+#' }
+#'
+#' @docType data
+#'
+#' @keywords datasets
+#'
+#' @usage data(cornYield)
+#'
+#' @format a \code{data.frame} with 32 records and 4 variables.
+#'
+#' @source Frederico, P. (2009). Curso de EstatÃstica Experimental (15th
+#' ed.). Piracicaba, São Paulo: FEALQ. (page 115)
+#'
+#' @examples
+#'
+#' library(lattice)
+#' library(latticeExtra)
+#'
+#' data(cornYield)
+#' str(cornYield)
+#'
+#' xyplot(yield~N|P, groups=K,
+#' data=cornYield, type=c("p", "a"),
+#' ylab=expression(Yield~(ton~ha^{-1})),
+#' xlab="Nutrient level")
+#'
+#' xyplot(yield~N, groups=interaction(P, K),
+#' data=cornYield, type=c("p", "a"),
+#' auto.key=list(columns=2),
+#' ylab=expression(Yield~(ton~ha^{-1})),
+#' xlab="Nutrient level")
+#'
+NULL
+
+#' @name vinasseFert
+#'
+#' @title Fertilization with vinasse and mineral
+#'
+#' @description These data are from an \eqn{2^2} factorial experiment
+#' studing the effect of fertilizaton with vinasse (a residual from
+#' industrial processing of sugar cane) and complete mineral
+#' fertilization.
+#'
+#' \itemize{
+#' \item \code{block} a factor with 4 levels.
+#' \item \code{mineral} low (-1) and high (+1) levels of mineral
+#' fertilization.
+#' \item \code{vinasse} low (-1) and high (+1) levels of fetilization
+#' with vinasse.
+#' \item \code{y} some response variable. The text book doesn't give
+#' any information.
+#' }
+#'
+#' @docType data
+#'
+#' @keywords datasets
+#'
+#' @usage data(vinasseFert)
+#'
+#' @format a \code{data.frame} with 16 records and 4 variables.
+#'
+#' @source Frederico, P. (2009). Curso de EstatÃstica Experimental (15th
+#' ed.). Piracicaba, São Paulo: FEALQ. (page 119)
+#'
+#' @examples
+#'
+#' library(lattice)
+#' library(latticeExtra)
+#'
+#' data(vinasseFert)
+#' str(vinasseFert)
+#'
+#' xyplot(y~vinasse, groups=mineral,
+#' auto.key=list(title="Mineral", columns=2),
+#' data=vinasseFert, type=c("p", "a"),
+#' ylab="y",
+#' xlab="Vinasse level")
+#'
+NULL
+
+#' @name filterCake
+#'
+#' @title Fertilization with filter cake and mineral
+#'
+#' @description These data are from an \eqn{2^2} factorial experiment
+#' studing the effect of fertilizaton with filter cake (a residual
+#' from industrial processing of sugar cane) and traditional mineral
+#' fertilization.
+#'
+#' \itemize{
+#' \item \code{block} a factor with 4 levels.
+#' \item \code{mineral} low (-1) and high (+1) levels of mineral
+#' fertilization.
+#' \item \code{cake} low (-1) and high (+1) levels of fetilization
+#' with filter cake.
+#' \item \code{y} some response variable. The text book doesn't give
+#' any information.
+#' }
+#'
+#' @docType data
+#'
+#' @keywords datasets
+#'
+#' @usage data(filterCake)
+#'
+#' @format a \code{data.frame} with 16 records and 4 variables.
+#'
+#' @source Frederico, P. (2009). Curso de EstatÃstica Experimental (15th
+#' ed.). Piracicaba, São Paulo: FEALQ. (page 120)
+#'
+#' @examples
+#'
+#' library(lattice)
+#' library(latticeExtra)
+#'
+#' data(filterCake)
+#' str(filterCake)
+#'
+#' xyplot(y~cake, groups=mineral,
+#' auto.key=list(title="Mineral", columns=2),
+#' data=filterCake, type=c("p", "a"),
+#' ylab="y",
+#' xlab="Filter cake level")
+#'
+#'
+NULL
+
+#' @name sugarcaneYield4
+#'
+#' @title Triple factorial NPK fertilization on sugar cane yield
+#'
+#' @description These data are from an \eqn{3^3} factorial experiment
+#' studing the effect of NPK on the yield of sugar cane.
+#'
+#' \itemize{
+#' \item \code{block} a local control factor with 3 levels.
+#' \item \code{rept} factor with 2 levels.
+#' \item \code{N} integer coded nitrogen levels (0, 1, 2).
+#' \item \code{P} integer coded phosphorus levels (0, 1, 2).
+#' \item \code{K} integer coded potassium levels (0, 1, 2).
+#' \item \code{yield} sugar cane yield (ton/ha).
+#' }
+#'
+#' @details There is a missprint in the book for the 9th entry, which
+#' has yield 59.0, that is coded as 202 istead of 220.
+#'
+#' @docType data
+#'
+#' @keywords datasets
+#'
+#' @usage data(sugarcaneYield4)
+#'
+#' @format a \code{data.frame} with 54 records and 6 variables.
+#'
+#' @source Frederico, P. (2009). Curso de EstatÃstica Experimental (15th
+#' ed.). Piracicaba, São Paulo: FEALQ. (page 126)
+#'
+#' @examples
+#'
+#' library(lattice)
+#' library(latticeExtra)
+#'
+#' data(sugarcaneYield4)
+#' str(sugarcaneYield4)
+#'
+#' xyplot(yield~N|P, groups=K,
+#' auto.key=list(title="Potassim level", columns=3),
+#' strip=strip.custom(var.name="Phosphorus", strip.names=TRUE,
+#' strip.levels=TRUE, sep=": "),
+#' data=sugarcaneYield4, type=c("p", "a"),
+#' ylab=expression(Yield~(ton~ha^{-1})),
+#' xlab="Nitrogen level level")
+#'
+NULL
+
+#' @name mangoAcidity
+#'
+#' @title Acidity of mango fruits by varieties, years and months
+#'
+#' @description These data are from an observational study along 3 years
+#' where acidity in fruits of 6 varieties of mango was determined in
+#' Novermber, December and January.
+#'
+#' \itemize{
+#' \item \code{variety} a categorical variable with 6 levels that
+#' represents mango varieties studied.
+#' \item \code{year} the year of harvesting.
+#' \item \code{month} the month of harvesting.
+#' \item \code{acid} mean of the acidity determined in 3 fruits.
+#' }
+#'
+#' @docType data
+#'
+#' @keywords datasets
+#'
+#' @usage data(sugarcaneYield4)
+#'
+#' @format a \code{data.frame} with 54 records and 6 variables.
+#'
+#' @source Frederico, P. (2009). Curso de EstatÃstica Experimental (15th
+#' ed.). Piracicaba, São Paulo: FEALQ. (page 132)
+#'
+#' Simão, S. (1960). Estudo da planta e dos frutos da mangueira
+#' (\emph{Manginifera indica} L.). Piracicaba, 1960. Thesis.
+#'
+#' @examples
+#'
+#' library(lattice)
+#' library(latticeExtra)
+#'
+#' data(mangoAcidity)
+#' str(mangoAcidity)
+#'
+#' ## reshape::cast() can also be used.
+#' with(mangoAcidity,
+#' ftable(tapply(acid,
+#' list(variety, year, month),
+#' FUN=identity)))
+#'
+#' xyplot(acid~month|variety, groups=year,
+#' data=mangoAcidity, type=c("p", "a"),
+#' auto.key=TRUE,
+#' ylab="Acidity",
+#' xlab="Month")
+#'
+NULL
+
+#' @name cornYield2
+#'
+#' @title Axial factorial NPK experiment with added treatments
+#'
+#' @description These data are from an axial 3 factorial experiment
+#' studing NPK in the yield of corn. Tow controls were added, one is
+#' zer control (no NPK) and the other is central factorial point
+#' plus presence of limestone.
+#'
+#' \itemize{
+#' \item \code{N} content of nitrogen in the fertilizer.
+#' \item \code{P} content of phosphorus in the fertilizer.
+#' \item \code{K} content of potassium in the fertilizer.
+#' \item \code{limestone} presence (1) or absence of limestone (0).
+#' \item \code{acid} mean of corn yield in 16 locations (ton/ha).
+#' }
+#'
+#' @details The experiment was caried out in 16 different locations but
+#' only the mean by cell combinations were available in the text
+#' book.
+#'
+#' @docType data
+#'
+#' @keywords datasets
+#'
+#' @usage data(sugarcaneYield4)
+#'
+#' @format a \code{data.frame} with 9 records and 5 variables.
+#'
+#' @source Frederico, P. (2009). Curso de EstatÃstica Experimental (15th
+#' ed.). Piracicaba, São Paulo: FEALQ. (page 132)
+#'
+#' Simão, S. (1960). Estudo da planta e dos frutos da mangueira
+#' (\emph{Manginifera indica} L.). Piracicaba, 1960. Thesis.
+#'
+#' @examples
+#'
+#' library(lattice)
+#' library(latticeExtra)
+#'
+#' data(cornYield2)
+#' str(cornYield2)
+#'
+#' ## Axial triple factorial with 2 controls.
+#' ftable(xtabs(~N+P+K, data=cornYield2))
+#'
+#' xyplot(yield~N+P+K,
+#' groups=as.integer(limestone==1 | (N+P+K)==0),
+#' data=cornYield2, type=c("p", "a"),
+#' auto.key=TRUE,
+#' ylab=expression(Yield~(ton~ha^{-1})),
+#' xlab="Nutrient content")
+#'
+NULL
diff --git a/R/loessGui.R b/R/loessGui.R
index 2ec9d051e374c38de1a06045f5770021eda15804..20fcfd27f17af5a891d0be892a492ac385d46b6a 100644
--- a/R/loessGui.R
+++ b/R/loessGui.R
@@ -5,11 +5,11 @@
#' @description This function opens an interface to control the settings
#' of a loess regression:
#' \itemize{
-#' \item degree choose the local polynomial degree with a radio
+#' \item degree choose the local polynomial degree with a radio
#' selector;
-#' \item span set the span value that controls the degree of
+#' \item span set the span value that controls the degree of
#' smoothing;
-#' \item center move the x value to be predicted;
+#' \item center move the x value to be predicted;
#' }
#'
#' The elements of the interface change a plot that shows the observed
@@ -18,17 +18,13 @@
#' \code{gWidgets} and \code{gWidgetstcltk} packages are available.
#'
#' @param x,y independent and dependent (numeric) regression variables.
-#'
#' @param data an optional \code{data.frame}.
-#'
#' @param er stands for extend range. It is used to extend the plotting
-#' range by a fraction on both sides and directions. Default is
-#' 0.05. See \link[grDevices]{extendrange}.
+#' range by a fraction on both sides and directions. Default is
+#' 0.05. See \link[grDevices]{extendrange}.
#'
#' @return None is returned by the function, only a GUI is opened.
#'
-#' @import gWidgets gWidgetstcltk
-#'
#' @author Walmes Zeviani, \email{walmes@@ufpr.br}
#'
#' @export
@@ -116,8 +112,8 @@ loessGui <- function(x, y, data, er=0.05){
## Fit loess regression.
##
m0 <- loess(formula=y~x,
- span=svalue(SPAN),
- degree=as.integer(svalue(DEGREE)),
+ span=gWidgets::svalue(SPAN),
+ degree=as.integer(gWidgets::svalue(DEGREE)),
family="gaussian")
##
##-------------------------------------------
@@ -131,8 +127,8 @@ loessGui <- function(x, y, data, er=0.05){
##-------------------------------------------
## Weights to be used in local polynomial.
##
- x0 <- svalue(XCENTER)
- sp <- svalue(SPAN)
+ x0 <- gWidgets::svalue(XCENTER)
+ sp <- gWidgets::svalue(SPAN)
a <- abs(x-x0)
if (sp < 1){
q <- as.integer(sp*nx)
@@ -166,53 +162,56 @@ loessGui <- function(x, y, data, er=0.05){
sum(s), nx))
## NOTE: usar action aqui!
## xl <- c(min(c(xl[1], x0)), max(c(x0, xl[2])))
- do.call(what=paste0("f", svalue(DEGREE)),
+ do.call(what=paste0("f", gWidgets::svalue(DEGREE)),
args=list(w=w, xl=xl))
}
##
##-------------------------------------------
## Building the GUI.
##
- WDW <- gwindow(title="LOESS regression", visible=FALSE)
- GG <- ggroup(container=WDW, expand=TRUE, horizontal=FALSE)
- GF_DG <- gframe(text="Local polynomial degree:", container=GG)
- DEGREE <- gradio(items=0:2, selected=2L, horizontal=TRUE,
+ WDW <- gWidgets::gwindow(title="LOESS regression", visible=FALSE)
+ GG <- gWidgets::ggroup(container=WDW, expand=TRUE, horizontal=FALSE)
+ GF_DG <- gWidgets::gframe(text="Local polynomial degree:", container=GG)
+ DEGREE <- gWidgets::gradio(items=0:2, selected=2L, horizontal=TRUE,
handler=draw.loess,
container=GF_DG)
- GF_XC <- gframe(text="Predicted point:", expand=TRUE, container=GG)
- XCENTER <- gslider(from=erx[1], to=erx[2],
+ GF_XC <- gWidgets::gframe(text="Predicted point:", expand=TRUE,
+ container=GG)
+ XCENTER <- gWidgets::gslider(from=erx[1], to=erx[2],
value=mean(erx),
length.out=51,
handler=draw.loess,
expand=TRUE,
container=GF_XC)
- XCLABEL <- glabel(text=sprintf("%0.2f", svalue(XCENTER)),
+ XCLABEL <- gWidgets::glabel(text=sprintf("%0.2f",
+ gWidgets::svalue(XCENTER)),
container=GF_XC)
- addHandlerChanged(XCENTER,
+ gWidgets::addHandlerChanged(XCENTER,
action=XCLABEL,
handler=function(h, ...){
- svalue(h$action) <-
- sprintf("%0.2f", svalue(h$obj))
+ gWidgets::svalue(h$action) <-
+ sprintf("%0.2f", gWidgets::svalue(h$obj))
})
- GF_SP <- gframe(text="Span:", expand=TRUE,container=GG)
- SPAN <- gslider(from=0, to=1.5,
+ GF_SP <- gWidgets::gframe(text="Span:", expand=TRUE,container=GG)
+ SPAN <- gWidgets::gslider(from=0, to=1.5,
value=0.75, by=0.05,
handler=draw.loess,
expand=TRUE,
container=GF_SP)
- SPLABEL <- glabel(text=sprintf("%0.2f", svalue(SPAN)),
+ SPLABEL <- gWidgets::glabel(text=sprintf("%0.2f",
+ gWidgets::svalue(SPAN)),
container=GF_SP)
- addHandlerChanged(SPAN,
+ gWidgets::addHandlerChanged(SPAN,
action=SPLABEL,
handler=function(h, ...){
- svalue(h$action) <-
- sprintf("%0.2f", svalue(h$obj))
+ gWidgets::svalue(h$action) <-
+ sprintf("%0.2f", gWidgets::svalue(h$obj))
})
##-------------------------------------------
## Initializing.
- svalue(SPAN) <- 0.75
- svalue(DEGREE) <- 1L
- svalue(XCENTER) <- mean(erx)
+ gWidgets::svalue(SPAN) <- 0.75
+ gWidgets::svalue(DEGREE) <- 1L
+ gWidgets::svalue(XCENTER) <- mean(erx)
do.call(what=draw.loess, args=list(NA))
- visible(WDW) <- TRUE
+ gWidgets::visible(WDW) <- TRUE
}
diff --git a/R/polyGui.R b/R/polyGui.R
index f1e337c9b12f78ff139c63ab075d5d7f634a64c2..9d2a328d7af16df45b639cd368e8dde2aa4271e3 100644
--- a/R/polyGui.R
+++ b/R/polyGui.R
@@ -3,23 +3,20 @@
#' @name polyGui
#'
#' @description This function opens an interface to control the
-#' polynomial degree in linear regression. It shows the observed values
-#' and the corresponding fitted curve superimposed with confidence bands
-#' (for the fitted values) and also show the residuals plot. It assumes
-#' that \code{gWidgets} and \code{gWidgetstcltk} packages are available.
+#' polynomial degree in linear regression. It shows the observed
+#' values and the corresponding fitted curve superimposed with
+#' confidence bands (for the fitted values) and also show the
+#' residuals plot. It assumes that \code{gWidgets} and
+#' \code{gWidgetstcltk} packages are available.
#'
#' @param x,y independent and dependent (numeric) regression variables.
-#'
#' @param data an optional \code{data.frame}.
-#'
#' @param er stands for extend range. It is used to extend the plotting
-#' range by a fraction on both sides and directions. Default is
-#' 0.05. See \link[grDevices]{extendrange}.
+#' range by a fraction on both sides and directions. Default is
+#' 0.05. See \link[grDevices]{extendrange}.
#'
#' @return None is returned by the function.
#'
-#' @import gWidgets gWidgetstcltk
-#'
#' @author Walmes Zeviani, \email{walmes@@ufpr.br}
#'
#' @export
@@ -65,7 +62,7 @@ polyGui <- function(x, y, data, er=0.05){
mtext(side=3, adj=1, line=2.5, text=lastcoef)
mtext(side=3, adj=1, line=1.5,
text=sprintf("R^2 (adj. R^2): %0.2f (%0.2f)",
- 100*sm$r.squared, 100*sm$adj.r.squared))
+ 100*sm$r.squared, 100*sm$adj.r.squared))
}
##
##-------------------------------------------
@@ -87,17 +84,18 @@ polyGui <- function(x, y, data, er=0.05){
## Function controled by the GUI.
##
draw.poly <- function(h, ...){
- svalue(degree) <- min(c(
- max(c(1L, svalue(degree)+h$action$val)),
+ gWidgets::svalue(degree) <- min(c(
+ max(c(1L, gWidgets::svalue(degree)+h$action$val)),
maxd))
- m0 <- lm(y~poly(x, degree=svalue(degree)))
- switch(svalue(plottype),
+ m0 <- lm(y~poly(x, degree=gWidgets::svalue(degree)))
+ switch(gWidgets::svalue(plottype),
"Scatter plot"={
- cb <- predict(m0, newdata=newdata, interval="confidence")
+ cb <- predict(m0, newdata=newdata,
+ interval="confidence")
plot(y~x, xlim=xr, ylim=yr,
xlab=xlab, ylab=ylab)
- matlines(newdata$x, cb, lty=c(1,2,2), col=1)
- annotations(m0)
+ matlines(newdata$x, cb, lty=c(1,2,2), col=1)
+ annotations(m0)
},
"Residuals"={
par(mfrow=c(2,2))
@@ -109,30 +107,30 @@ polyGui <- function(x, y, data, er=0.05){
##-------------------------------------------
## Building the GUI.
##
- w <- gwindow(title="Polynomial regression", visible=FALSE)
- g <- ggroup(container=w, horizontal=FALSE)
- gg_label <- ggroup(container=g)
- dlabel <- glabel(text="Polynomial degree:",
- container=gg_label)
- degree <- gedit(text=1, width=2, coerce.with=as.integer,
- handler=draw.poly, action=list(val=0L),
- container=gg_label)
- gg_buttons <- ggroup(container=g)
- gminus <- gbutton(text="-",
- handler=draw.poly,
- action=list(val=-1L),
- container=gg_buttons)
- gplus <- gbutton(text="+",
- handler=draw.poly,
- action=list(val=1L),
- container=gg_buttons)
- gg_radio <- ggroup(container=g)
- plottype <- gradio(items=c("Scatter plot", "Residuals"),
- horizontal=TRUE,
- handler=draw.poly,
- action=list(val=0L),
- container=gg_radio)
+ w <- gWidgets::gwindow(title="Polynomial regression", visible=FALSE)
+ g <- gWidgets::ggroup(container=w, horizontal=FALSE)
+ gg_label <- gWidgets::ggroup(container=g)
+ dlabel <- gWidgets::glabel(text="Polynomial degree:",
+ container=gg_label)
+ degree <- gWidgets::gedit(text=1, width=2, coerce.with=as.integer,
+ handler=draw.poly, action=list(val=0L),
+ container=gg_label)
+ gg_buttons <- gWidgets::ggroup(container=g)
+ gminus <- gWidgets::gbutton(text="-",
+ handler=draw.poly,
+ action=list(val=-1L),
+ container=gg_buttons)
+ gplus <- gWidgets::gbutton(text="+",
+ handler=draw.poly,
+ action=list(val=1L),
+ container=gg_buttons)
+ gg_radio <- gWidgets::ggroup(container=g)
+ plottype <- gWidgets::gradio(items=c("Scatter plot", "Residuals"),
+ horizontal=TRUE,
+ handler=draw.poly,
+ action=list(val=0L),
+ container=gg_radio)
do.call(what=draw.poly, args=list(h=list(degree=1L)))
- visible(w) <- TRUE
+ gWidgets::visible(w) <- TRUE
invisible()
}
diff --git a/R/runAllChunks.R b/R/runAllChunks.R
index cc7ff57f028f42cfeddd4b718f60ab2b7d9e84fe..f7b974a910d2b6162bd167086cdab0e794c7eec1 100644
--- a/R/runAllChunks.R
+++ b/R/runAllChunks.R
@@ -3,13 +3,12 @@
#' @name runAllChunks
#'
#' @description This function was developed to run all chunks in a knitr
-#' Rmd (R markdown) file at once. Mainly for exploring and debugging
-#' purposes.
+#' Rmd (R markdown) file at once. Mainly for exploring and debugging
+#' purposes.
#'
#' @param Rmd the name of the Rmd file.
-#'
#' @param envir the environment in which the chunks will be
-#' evaluated. By default it is the GlobalEnv.
+#' evaluated. By default it is the GlobalEnv.
#'
#' @references This function was based on this
#' \href{http://stackoverflow.com/questions/24753969/knitr-run-all-chunks-in-an-rmarkdown-document}{SO
@@ -17,8 +16,6 @@
#'
#' @return Objects created in the chunks from the Rmd file.
#'
-#' @import knitr
-#'
#' @author Fernando Mayer, \email{fernando.mayer@@ufpr.br}
#'
#' @export
@@ -29,6 +26,6 @@ runAllChunks <- function(Rmd, envir = globalenv()){
}
tempR <- tempfile(tmpdir = ".", fileext = ".R")
on.exit(unlink(tempR))
- purl(Rmd, output = tempR)
+ knitr::purl(Rmd, output = tempR)
sys.source(tempR, envir = envir)
}
diff --git a/R/yscale.components.right.R b/R/yscale.components.right.R
index afbce1c98e725548dcc99440d8deb818de8aedcb..7e6995b9222209c014ae320e911f22ed4e9b14e3 100644
--- a/R/yscale.components.right.R
+++ b/R/yscale.components.right.R
@@ -37,7 +37,7 @@
#' p3 <- xyplot(yield~K|N+P, data=npk,
#' scales=list(y=list(relation="free", alternating=2)),
#' ylab=NULL, ylab.right="Yield",
-#' yscale.component=yscale.component.right,
+#' yscale.component=yscale.components.right,
#' between=list(x=0.5, y=0.2),
#' par.settings=list(
#' layout.widths=list(
@@ -48,7 +48,7 @@
#' )
#' useOuterStrips(p3)
#'
-yscale.component.right <- function(...){
+yscale.components.right <- function(...){
ans <- yscale.components.default(...)
ans$right <- ans$left
ans$left <- NULL
diff --git a/buildPkg.R b/buildPkg.R
index e531485abbcce063c25caf9a3a48e1240c407e47..367df497d444ae28b717cd66254fbe924ba4a528 100644
--- a/buildPkg.R
+++ b/buildPkg.R
@@ -1,3 +1,4 @@
+
## Script to build and verify the package
## Set working directory
@@ -44,10 +45,29 @@ build(manual = TRUE, vignettes = FALSE)
# build the binary version for windows (not used)
# build_win()
+##----------------------------------------------------------------------
+## Test installation.
+
## Test install with install.packages
pkg <- paste0("../legTools_", packageVersion("legTools"), ".tar.gz")
install.packages(pkg, repos = NULL)
+## Test using devtools::install_git().
+libTest <- "~/R/"
+if (file.exists(libTest)){
+ file.remove(libTest)
+}
+dir.create(path=libTest)
+
+.libPaths(new=libTest); .libPaths()
+
+install_git(url="http://git.leg.ufpr.br/leg/legTools.git",
+ branch="issue#9")
+
+library(legTools)
+packageVersion("legTools")
+ls("package:legTools")
+
##----------------------------------------------------------------------
## Package vignette.
## Based on: http://r-pkgs.had.co.nz/vignettes.html
@@ -55,6 +75,7 @@ install.packages(pkg, repos = NULL)
## Create the vignette template. Do just once.
use_vignette("PimentelGomes")
+
##======================================================================
## Sending package tarballs and manual to remote server to be
## downloadable
diff --git a/data-raw/cassavaYield.R b/data-raw/cassavaYield.R
index 249177652586b7e681d46791e5c219d2c827688f..28a39a046edc776dafaa6903ecac7d76f5a6f09a 100644
--- a/data-raw/cassavaYield.R
+++ b/data-raw/cassavaYield.R
@@ -6,6 +6,10 @@ cassavaYield <- read.table("http://www.leg.ufpr.br/~walmes/data/pimentel_mandioc
names(cassavaYield) <- c("block", "variety", "yield")
str(cassavaYield)
+levels(cassavaYield$variety) <-
+ c("Aipim bravo", "Escondida", "Mamão", "Milagrosa", "Salangó Preta",
+ "Sutinga")
+
cassavaYield <- cassavaYield[with(cassavaYield, order(block, variety)),]
save(cassavaYield, file="../data/cassavaYield.RData")
@@ -32,7 +36,3 @@ par(mfrow=c(2,2)); plot(m0); layout(1)
## ANOVA table.
anova(m0)
-
-library(doBy)
-ls <- LSmatrix(m0, effect="variety")
-dput(ls)
diff --git a/data-raw/cornYield.R b/data-raw/cornYield.R
new file mode 100644
index 0000000000000000000000000000000000000000..7bb2f73bec96ac9b10cd3d0a8e645db4936706fd
--- /dev/null
+++ b/data-raw/cornYield.R
@@ -0,0 +1,66 @@
+##----------------------------------------------------------------------
+## Data generation.
+
+cornYield <- expand.grid(block=gl(4, 1), N=c(-1,1), P=c(-1,1),
+ K=c(-1,1), KEEP.OUT.ATTRS=FALSE)
+cornYield$yield <- c(1.32, 2.12, 1.75, 2.35, 1.80, 2.20, 2.95, 2.96,
+ 1.66, 2.66, 1.73, 2.58, 1.72, 3.85, 2.62, 3.00,
+ 2.58, 3.56, 2.86, 2.75, 2.72, 3.20, 2.25, 2.75,
+ 2.26, 2.08, 1.95, 2.70, 2.95, 3.28, 2.40, 3.35)
+str(cornYield)
+
+save(cornYield, file="../data/cornYield.RData")
+
+##----------------------------------------------------------------------
+## Examples.
+
+library(lattice)
+library(latticeExtra)
+
+data(cornYield)
+str(cornYield)
+
+xyplot(yield~N|P, groups=K,
+ data=cornYield, type=c("p", "a"),
+ ylab=expression(Yield~(ton~ha^{-1})),
+ xlab="Nutrient level")
+
+xyplot(yield~N, groups=interaction(P, K),
+ data=cornYield, type=c("p", "a"),
+ auto.key=list(columns=2),
+ ylab=expression(Yield~(ton~ha^{-1})),
+ xlab="Nutrient level")
+
+m0 <- lm(yield~block+(N+P+K)^3, data=cornYield)
+par(mfrow=c(2,2)); plot(m0); layout(1)
+anova(m0)
+
+m1 <- update(m0, .~block+N+K)
+par(mfrow=c(2,2)); plot(m1); layout(1)
+
+anova(m0, m1)
+anova(m1)
+
+summary(m1)
+
+pred <- expand.grid(block="1",
+ N=seq(-1, 1, by=0.1),
+ K=seq(-1, 1, by=0.1))
+pred$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/cornYield.RData")
+ls()
+str(cornYield)
diff --git a/data-raw/cornYield2.R b/data-raw/cornYield2.R
new file mode 100644
index 0000000000000000000000000000000000000000..91ea8b902abe37477b93f48e3b9bd355da4d0f9c
--- /dev/null
+++ b/data-raw/cornYield2.R
@@ -0,0 +1,38 @@
+##----------------------------------------------------------------------
+## Data generation.
+
+## cornYield2 <- read.table("clipboard", header=TRUE, sep="\t")
+cornYield2 <- data.frame(
+ N=c(0L, 0L, 45L, 45L, 45L, 45L, 45L, 45L, 90L),
+ P=c(0L, 45L, 0L, 45L, 45L, 45L, 45L, 90L, 45L),
+ K=c(0L, 30L, 30L, 0L, 30L, 30L, 60L, 30L, 30L),
+ limestone=c(0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L),
+ yield=c(4.192, 4.427, 4.146, 5.029, 5.29, 5.325, 5.275, 5.465,
+ 5.39))
+str(cornYield2)
+
+save(cornYield2, file="../data/cornYield2.RData")
+
+##----------------------------------------------------------------------
+## Examples.
+
+library(lattice)
+library(latticeExtra)
+
+data(cornYield2)
+str(cornYield2)
+
+## Axial triple factorial with 2 controls.
+ftable(xtabs(~N+P+K, data=cornYield2))
+
+xyplot(yield~N+P+K,
+ groups=as.integer(limestone==1 | (N+P+K)==0),
+ data=cornYield2, type=c("p", "a"),
+ auto.key=TRUE,
+ ylab=expression(Yield~(ton~ha^{-1})),
+ xlab="Nutrient content")
+
+rm(list=ls())
+load("../data/cornYield2.RData")
+ls()
+str(cornYield2)
diff --git a/data-raw/filterCake.R b/data-raw/filterCake.R
new file mode 100644
index 0000000000000000000000000000000000000000..52aa6d39a650d1b02ad9ca24e672180f69b919e9
--- /dev/null
+++ b/data-raw/filterCake.R
@@ -0,0 +1,49 @@
+##----------------------------------------------------------------------
+## Data generation.
+
+filterCake <- expand.grid(block=gl(4, 1), mineral=c(-1, 1),
+ cake=c(-1, 1), KEEP.OUT.ATTRS=FALSE)
+
+filterCake$y <- c(18.0, 8.6, 9.4, 11.4, 20.6, 21.0, 18.6, 20.6, 19.6,
+ 15.0, 14.6, 15.8, 19.2, 19.6, 18.4, 20.2)
+
+str(filterCake)
+
+save(filterCake, file="../data/filterCake.RData")
+
+##----------------------------------------------------------------------
+## Examples.
+
+library(lattice)
+library(latticeExtra)
+
+data(filterCake)
+str(filterCake)
+
+xyplot(y~cake, groups=mineral,
+ auto.key=list(title="Mineral", columns=2),
+ data=filterCake, type=c("p", "a"),
+ ylab="y",
+ xlab="Filter cake level")
+
+m0 <- lm(y~block+(cake+mineral)^2, data=filterCake)
+par(mfrow=c(2,2)); plot(m0); layout(1)
+anova(m0)
+
+summary(m0)
+
+filterCake$Mineral <- factor(filterCake$mineral,
+ labels=c("absent", "present"))
+
+m1 <- aov(y~block+Mineral/cake, data=filterCake)
+anova(m1)
+
+## Split SS to see effect of cake in each level of mineral.
+summary(m1, split=list("Mineral:cake"=list("absent"=1, "present"=2)))
+
+summary.lm(m1)
+
+rm(list=ls())
+load("../data/filterCake.RData")
+ls()
+str(filterCake)
diff --git a/data-raw/mangoAcidity.R b/data-raw/mangoAcidity.R
new file mode 100644
index 0000000000000000000000000000000000000000..f42f67c8007267097eb1ad385bba960ead5727e1
--- /dev/null
+++ b/data-raw/mangoAcidity.R
@@ -0,0 +1,45 @@
+##----------------------------------------------------------------------
+## Data generation.
+
+mangoAcidity <- expand.grid(variety=c("Bourbon", "Brasil", "Extrema",
+ "Maçã", "Non Plus Ultra",
+ "Oliveira"),
+ year=c(1957:1959),
+ month=c("N", "D", "J"),
+ KEEP.OUT.ATTRS=FALSE)
+mangoAcidity$acid <- c(28.2, 38.3, 37.6, 47.2, 36.4, 40.0, 24.7, 32.0,
+ 39.0, 47.7, 35.3, 30.1, 16.4, 38.4, 50.3, 50.2,
+ 40.1, 30.0, 6.0, 5.0, 6.0, 6.2, 7.9, 6.0, 6.2,
+ 3.6, 6.6, 6.9, 10.2, 7.0, 6.9, 4.0, 6.9, 7.9,
+ 9.8, 8.4, 4.6, 4.6, 5.4, 5.2, 4.9, 6.1, 4.4,
+ 4.2, 5.4, 4.2, 6.8, 3.5, 5.0, 3.8, 5.0, 5.0,
+ 7.0, 4.8)
+str(mangoAcidity)
+
+save(mangoAcidity, file="../data/mangoAcidity.RData")
+
+##----------------------------------------------------------------------
+## Examples.
+
+library(lattice)
+library(latticeExtra)
+
+data(mangoAcidity)
+str(mangoAcidity)
+
+## reshape::cast() can also be used.
+with(mangoAcidity,
+ ftable(tapply(acid,
+ list(variety, year, month),
+ FUN=identity)))
+
+xyplot(acid~month|variety, groups=year,
+ data=mangoAcidity, type=c("p", "a"),
+ auto.key=TRUE,
+ ylab="Acidity",
+ xlab="Month")
+
+rm(list=ls())
+load("../data/mangoAcidity.RData")
+ls()
+str(mangoAcidity)
diff --git a/data-raw/potatoyield.R b/data-raw/potatoYield.R
similarity index 53%
rename from data-raw/potatoyield.R
rename to data-raw/potatoYield.R
index c1b160085614dd92684329514b6abec9644df9c2..6dea6d04af80644167d4cfdd90cfc6e8cb86f098 100644
--- a/data-raw/potatoyield.R
+++ b/data-raw/potatoYield.R
@@ -1,26 +1,26 @@
##----------------------------------------------------------------------
## Data generation.
-potatoyield <- read.table("http://www.leg.ufpr.br/~walmes/data/pimentel_batatinha.txt",
+potatoYield <- read.table("http://www.leg.ufpr.br/~walmes/data/pimentel_batatinha.txt",
header=TRUE, sep="\t")
-names(potatoyield) <- c("block", "variety", "yield")
-str(potatoyield)
+names(potatoYield) <- c("block", "variety", "yield")
+str(potatoYield)
-potatoyield <- potatoyield[with(potatoyield, order(block, variety)),]
+potatoYield <- potatoYield[with(potatoYield, order(block, variety)),]
-save(potatoyield, file="../data/potatoyield.RData")
+save(potatoYield, file="../data/potatoYield.RData")
##----------------------------------------------------------------------
## Examples.
require(lattice)
-xyplot(yield~variety, data=potatoyield,
+xyplot(yield~variety, data=potatoYield,
groups=block, type="o",
ylab=expression(Yield~(t~ha^{-1})),
xlab="Variety")
rm(list=ls())
-load("../data/potatoyield.RData")
+load("../data/potatoYield.RData")
ls()
-str(potatoyield)
+str(potatoYield)
diff --git a/data-raw/sugarcaneYield4.R b/data-raw/sugarcaneYield4.R
new file mode 100644
index 0000000000000000000000000000000000000000..3050b59eef4a0e8f857b92477eb8a8e316df9f2f
--- /dev/null
+++ b/data-raw/sugarcaneYield4.R
@@ -0,0 +1,85 @@
+##----------------------------------------------------------------------
+## Data generation.
+
+sugarcaneYield4 <- read.table("http://www.leg.ufpr.br/~walmes/data/pimentel_npk2.txt",
+ header=TRUE, sep="\t")
+names(sugarcaneYield4)[c(1,6)] <- c("block", "yield")
+sugarcaneYield4 <- transform(sugarcaneYield4, rept=factor(rept))
+str(sugarcaneYield4)
+
+sugarcaneYield4 <- sugarcaneYield4[
+ with(sugarcaneYield4, order(block, rept, N, P, K)),]
+
+save(sugarcaneYield4, file="../data/sugarcaneYield4.RData")
+
+##----------------------------------------------------------------------
+## Examples.
+
+library(lattice)
+library(latticeExtra)
+library(multcomp)
+
+data(sugarcaneYield4)
+str(sugarcaneYield4)
+
+xyplot(yield~N|P, groups=K,
+ auto.key=list(title="Potassim level", columns=3),
+ strip=strip.custom(var.name="Phosphorus", strip.names=TRUE,
+ strip.levels=TRUE, sep=": "),
+ data=sugarcaneYield4, type=c("p", "a"),
+ ylab=expression(Yield~(ton~ha^{-1})),
+ xlab="Nitrogen level level")
+
+## Sums in each cell combination.
+addmargins(with(sugarcaneYield4, tapply(yield, list(P, N), FUN=sum)))
+addmargins(with(sugarcaneYield4, tapply(yield, list(K, N), FUN=sum)))
+addmargins(with(sugarcaneYield4, tapply(yield, list(K, P), FUN=sum)))
+
+sugarcaneYield4 <- transform(sugarcaneYield4,
+ blockr=interaction(block, rept),
+ nitro=factor(N),
+ phosp=factor(P),
+ potas=factor(K))
+str(sugarcaneYield4)
+
+m0 <- lm(yield~blockr+(nitro+phosp+potas)^3, data=sugarcaneYield4)
+par(mfrow=c(2,2)); plot(m0); layout(1)
+anova(m0)
+
+m1 <- update(m0, .~blockr+(nitro+phosp)^2)
+par(mfrow=c(2,2)); plot(m1); layout(1)
+
+anova(m0, m1)
+anova(m1)
+
+m2 <- aov(yield~blockr+nitro/phosp, data=sugarcaneYield4)
+anova(m2)
+
+PinN <- sapply(paste0("nitro", levels(sugarcaneYield4$nitro)),
+ FUN=grep, x=names(coef(m2))[m2$assign==3L],
+ simplify=FALSE)
+
+summary(m2, split=list("nitro:phosp"=PinN))
+
+X <- model.matrix(m1)
+X
+
+aggregate(X~nitro+phosp, data=sugarcaneYield4, FUN=mean)
+
+## It is better use multcomp::LSmatrix().
+L <- aggregate(X~nitro+phosp, data=sugarcaneYield4, FUN=mean)
+rownames(L) <- with(L, paste0("N", nitro, ":P", phosp))
+L <- as.matrix(L[, colnames(X)])
+str(L)
+
+## Least squares means for N:P combinations.
+L%*%coef(m1)
+
+g1 <- glht(m1, linfct=L)
+
+confint(g1, calpha=univariate_calpha())
+
+rm(list=ls())
+load("../data/sugarcaneYield4.RData")
+ls()
+str(sugarcaneYield4)
diff --git a/data-raw/vinasseFert.R b/data-raw/vinasseFert.R
new file mode 100644
index 0000000000000000000000000000000000000000..be78f45e285e2a4c57869c6660cded7523392a86
--- /dev/null
+++ b/data-raw/vinasseFert.R
@@ -0,0 +1,45 @@
+##----------------------------------------------------------------------
+## Data generation.
+
+vinasseFert <- expand.grid(block=gl(4, 1), mineral=c(-1, 1),
+ vinasse=c(-1, 1), KEEP.OUT.ATTRS=FALSE)
+
+vinasseFert$y <- c(0.020, 0.630, 0.110, 0.115, 0.020, 2.005, 0.700,
+ 1.120, 3.040, 4.760, 5.860, 5.520, 5.150, 4.770,
+ 3.960, 5.230)
+
+str(vinasseFert)
+
+save(vinasseFert, file="../data/vinasseFert.RData")
+
+##----------------------------------------------------------------------
+## Examples.
+
+library(lattice)
+library(latticeExtra)
+
+data(vinasseFert)
+str(vinasseFert)
+
+xyplot(y~vinasse, groups=mineral,
+ auto.key=list(title="Mineral", columns=2),
+ data=vinasseFert, type=c("p", "a"),
+ ylab="y",
+ xlab="Vinasse level")
+
+m0 <- lm(y~block+(vinasse+mineral)^2, data=vinasseFert)
+par(mfrow=c(2,2)); plot(m0); layout(1)
+anova(m0)
+
+m1 <- update(m0, .~block+vinasse)
+par(mfrow=c(2,2)); plot(m1); layout(1)
+
+anova(m0, m1)
+anova(m1)
+
+summary(m1)
+
+rm(list=ls())
+load("../data/vinasseFert.RData")
+ls()
+str(vinasseFert)
diff --git a/data-raw/wgpigs.R b/data-raw/wgPigs.R
similarity index 58%
rename from data-raw/wgpigs.R
rename to data-raw/wgPigs.R
index 5a3cfe8076219634b0b57d7109c85ef40646b334..8beb3af0edf06bd2d3004d30aec9b4dbf608533a 100644
--- a/data-raw/wgpigs.R
+++ b/data-raw/wgPigs.R
@@ -1,38 +1,38 @@
##----------------------------------------------------------------------
## Data generation.
-wgpigs <- read.table("http://www.leg.ufpr.br/~walmes/data/pimentel_racoes.txt",
+wgPigs <- read.table("http://www.leg.ufpr.br/~walmes/data/pimentel_racoes.txt",
header=TRUE, sep="\t")
-names(wgpigs) <- c("ft","wg")
-str(wgpigs)
+names(wgPigs) <- c("ft","wg")
+str(wgPigs)
-save(wgpigs, file="../data/wgpigs.RData")
+save(wgPigs, file="../data/wgPigs.RData")
##----------------------------------------------------------------------
## Examples.
require(lattice)
-xyplot(wg~ft, data=wgpigs,
+xyplot(wg~ft, data=wgPigs,
ylab="Weight gain (kg)",
xlab="Feeding type")
rm(list=ls())
-load("../data/wgpigs.RData")
+load("../data/wgPigs.RData")
ls()
-str(wgpigs)
+str(wgPigs)
##----------------------------------------------------------------------
-write.table(x=wgpigs, file="wgpigs.txt",
+write.table(x=wgPigs, file="wgPigs.txt",
sep="\t", quote=FALSE, row.names=FALSE)
## Port and IP.
u <- scan(n=2, what=character())
-cmd <- paste0("scp -P ", u[1], " wgpigs.txt leg@", u[2],
+cmd <- paste0("scp -P ", u[1], " wgPigs.txt leg@", u[2],
":/home/leg/public_html/legTools/dataset")
system(cmd)
-url <- "http://blog.leg.ufpr.br/~leg/legTools/dataset/wgpigs.txt"
+url <- "http://blog.leg.ufpr.br/~leg/legTools/dataset/wgPigs.txt"
browseURL(url)
-wgpigs <- read.table(file=url, header=TRUE, sep="\t")
+wgPigs <- read.table(file=url, header=TRUE, sep="\t")
diff --git a/data-raw/wgPigs2.R b/data-raw/wgPigs2.R
new file mode 100644
index 0000000000000000000000000000000000000000..1e72f6b275fde66f0ed88e4c09acbb84a12fea4e
--- /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/cassavaYield.RData b/data/cassavaYield.RData
index 07cdb35446a418b6d57821875406864be2fff9a8..6fa7094064f95fc01ec7dc5f087b8d8fafb1b09a 100644
Binary files a/data/cassavaYield.RData and b/data/cassavaYield.RData differ
diff --git a/data/cornYield.RData b/data/cornYield.RData
new file mode 100644
index 0000000000000000000000000000000000000000..ee9c3dbf0c11c7172f7254b18bfeafe008b0aee8
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diff --git a/data/cornYield2.RData b/data/cornYield2.RData
new file mode 100644
index 0000000000000000000000000000000000000000..2fbd34fbf48dd46f8fadf8ddef7c60d6482574b7
Binary files /dev/null and b/data/cornYield2.RData differ
diff --git a/data/filterCake.RData b/data/filterCake.RData
new file mode 100644
index 0000000000000000000000000000000000000000..a0de62bd28138af476f33e6348a87bfd0ee00b62
Binary files /dev/null and b/data/filterCake.RData differ
diff --git a/data/mangoAcidity.RData b/data/mangoAcidity.RData
new file mode 100644
index 0000000000000000000000000000000000000000..d6dc2ed24a5e71f3bc05a1ef56396c99f5e479d6
Binary files /dev/null and b/data/mangoAcidity.RData differ
diff --git a/data/potatoYield.RData b/data/potatoYield.RData
new file mode 100644
index 0000000000000000000000000000000000000000..b640671588ce1ba3ab701862821577e03eda9e25
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diff --git a/data/potatoyield.RData b/data/potatoyield.RData
deleted file mode 100644
index c650a954d79af8e08247412563bcb3aa15f310ef..0000000000000000000000000000000000000000
Binary files a/data/potatoyield.RData and /dev/null differ
diff --git a/data/sugarcaneYield4.RData b/data/sugarcaneYield4.RData
new file mode 100644
index 0000000000000000000000000000000000000000..e8821cf112ad01881612e566986a55844359b73c
Binary files /dev/null and b/data/sugarcaneYield4.RData differ
diff --git a/data/vinasseFert.RData b/data/vinasseFert.RData
new file mode 100644
index 0000000000000000000000000000000000000000..68936a5086a615fd434fb664c2fe78942a8ab486
Binary files /dev/null and b/data/vinasseFert.RData differ
diff --git a/data/wgPigs.RData b/data/wgPigs.RData
new file mode 100644
index 0000000000000000000000000000000000000000..efecff0ddff82bc4119f7b5eb7ffbf6e7c191ddd
Binary files /dev/null and b/data/wgPigs.RData differ
diff --git a/data/wgPigs2.RData b/data/wgPigs2.RData
new file mode 100644
index 0000000000000000000000000000000000000000..f80771e612a39e20723c6ff3467ae4eb473d3950
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diff --git a/data/wgpigs.RData b/data/wgpigs.RData
deleted file mode 100644
index d44077aacfd23b90dfbc7f015257af67796e1c3c..0000000000000000000000000000000000000000
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new file mode 100644
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--- /dev/null
+++ b/legTools.bmk
@@ -0,0 +1,239 @@
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diff --git a/man/cornYield.Rd b/man/cornYield.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..7c7d0580367cb88c9d9e49a22fac3b7036e31580
--- /dev/null
+++ b/man/cornYield.Rd
@@ -0,0 +1,47 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/legTools.R
+\docType{data}
+\name{cornYield}
+\alias{cornYield}
+\title{Corn yield as function of fertilization with NPK}
+\format{a \code{data.frame} with 32 records and 4 variables.}
+\source{
+Frederico, P. (2009). Curso de EstatÃstica Experimental (15th
+ ed.). Piracicaba, São Paulo: FEALQ. (page 115)
+}
+\usage{
+data(cornYield)
+}
+\description{
+These data are from an \eqn{2^3} factorial experiment
+ studing the effect of Nitrogen (N), Phosporus (P) and Potassium
+ (K) on corn 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} corn yield (ton/ha).
+}
+}
+\examples{
+library(lattice)
+library(latticeExtra)
+
+data(cornYield)
+str(cornYield)
+
+xyplot(yield~N|P, groups=K,
+ data=cornYield, type=c("p", "a"),
+ ylab=expression(Yield~(ton~ha^{-1})),
+ xlab="Nutrient level")
+
+xyplot(yield~N, groups=interaction(P, K),
+ data=cornYield, type=c("p", "a"),
+ auto.key=list(columns=2),
+ ylab=expression(Yield~(ton~ha^{-1})),
+ xlab="Nutrient level")
+}
+\keyword{datasets}
+
diff --git a/man/cornYield2.Rd b/man/cornYield2.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..e6f18b139b10b52eb16a3583cb58d9c023e62644
--- /dev/null
+++ b/man/cornYield2.Rd
@@ -0,0 +1,55 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/legTools.R
+\docType{data}
+\name{cornYield2}
+\alias{cornYield2}
+\title{Axial factorial NPK experiment with added treatments}
+\format{a \code{data.frame} with 9 records and 5 variables.}
+\source{
+Frederico, P. (2009). Curso de EstatÃstica Experimental (15th
+ ed.). Piracicaba, São Paulo: FEALQ. (page 132)
+
+Simão, S. (1960). Estudo da planta e dos frutos da mangueira
+ (\emph{Manginifera indica} L.). Piracicaba, 1960. Thesis.
+}
+\usage{
+data(sugarcaneYield4)
+}
+\description{
+These data are from an axial 3 factorial experiment
+ studing NPK in the yield of corn. Tow controls were added, one is
+ zer control (no NPK) and the other is central factorial point
+ plus presence of limestone.
+
+\itemize{
+ \item \code{N} content of nitrogen in the fertilizer.
+ \item \code{P} content of phosphorus in the fertilizer.
+ \item \code{K} content of potassium in the fertilizer.
+ \item \code{limestone} presence (1) or absence of limestone (0).
+ \item \code{acid} mean of corn yield in 16 locations (ton/ha).
+}
+}
+\details{
+The experiment was caried out in 16 different locations but
+ only the mean by cell combinations were available in the text
+ book.
+}
+\examples{
+library(lattice)
+library(latticeExtra)
+
+data(cornYield2)
+str(cornYield2)
+
+## Axial triple factorial with 2 controls.
+ftable(xtabs(~N+P+K, data=cornYield2))
+
+xyplot(yield~N+P+K,
+ groups=as.integer(limestone==1 | (N+P+K)==0),
+ data=cornYield2, type=c("p", "a"),
+ auto.key=TRUE,
+ ylab=expression(Yield~(ton~ha^{-1})),
+ xlab="Nutrient content")
+}
+\keyword{datasets}
+
diff --git a/man/filterCake.Rd b/man/filterCake.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..6ddae712d3635d514921f43d8296b20c26f83a62
--- /dev/null
+++ b/man/filterCake.Rd
@@ -0,0 +1,45 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/legTools.R
+\docType{data}
+\name{filterCake}
+\alias{filterCake}
+\title{Fertilization with filter cake and mineral}
+\format{a \code{data.frame} with 16 records and 4 variables.}
+\source{
+Frederico, P. (2009). Curso de EstatÃstica Experimental (15th
+ ed.). Piracicaba, São Paulo: FEALQ. (page 120)
+}
+\usage{
+data(filterCake)
+}
+\description{
+These data are from an \eqn{2^2} factorial experiment
+ studing the effect of fertilizaton with filter cake (a residual
+ from industrial processing of sugar cane) and traditional mineral
+ fertilization.
+
+\itemize{
+ \item \code{block} a factor with 4 levels.
+ \item \code{mineral} low (-1) and high (+1) levels of mineral
+ fertilization.
+ \item \code{cake} low (-1) and high (+1) levels of fetilization
+ with filter cake.
+ \item \code{y} some response variable. The text book doesn't give
+ any information.
+}
+}
+\examples{
+library(lattice)
+library(latticeExtra)
+
+data(filterCake)
+str(filterCake)
+
+xyplot(y~cake, groups=mineral,
+ auto.key=list(title="Mineral", columns=2),
+ data=filterCake, type=c("p", "a"),
+ ylab="y",
+ xlab="Filter cake level")
+}
+\keyword{datasets}
+
diff --git a/man/loessGui.Rd b/man/loessGui.Rd
index 6c5ad1404e9efeed995a7de4eb7c4a52d76d0162..c2901e7a5d4e5320895527583114842648b106b3 100644
--- a/man/loessGui.Rd
+++ b/man/loessGui.Rd
@@ -12,8 +12,8 @@ loessGui(x, y, data, er = 0.05)
\item{data}{an optional \code{data.frame}.}
\item{er}{stands for extend range. It is used to extend the plotting
-range by a fraction on both sides and directions. Default is
-0.05. See \link[grDevices]{extendrange}.}
+ range by a fraction on both sides and directions. Default is
+ 0.05. See \link[grDevices]{extendrange}.}
}
\value{
None is returned by the function, only a GUI is opened.
@@ -22,11 +22,11 @@ None is returned by the function, only a GUI is opened.
This function opens an interface to control the settings
of a loess regression:
\itemize{
- \item degree choose the local polynomial degree with a radio
+ \item degree choose the local polynomial degree with a radio
selector;
- \item span set the span value that controls the degree of
+ \item span set the span value that controls the degree of
smoothing;
- \item center move the x value to be predicted;
+ \item center move the x value to be predicted;
}
The elements of the interface change a plot that shows the observed
diff --git a/man/mangoAcidity.Rd b/man/mangoAcidity.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..85fb633e3498df0486d95aac11912c4d51d5cb39
--- /dev/null
+++ b/man/mangoAcidity.Rd
@@ -0,0 +1,51 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/legTools.R
+\docType{data}
+\name{mangoAcidity}
+\alias{mangoAcidity}
+\title{Acidity of mango fruits by varieties, years and months}
+\format{a \code{data.frame} with 54 records and 6 variables.}
+\source{
+Frederico, P. (2009). Curso de EstatÃstica Experimental (15th
+ ed.). Piracicaba, São Paulo: FEALQ. (page 132)
+
+Simão, S. (1960). Estudo da planta e dos frutos da mangueira
+ (\emph{Manginifera indica} L.). Piracicaba, 1960. Thesis.
+}
+\usage{
+data(sugarcaneYield4)
+}
+\description{
+These data are from an observational study along 3 years
+ where acidity in fruits of 6 varieties of mango was determined in
+ Novermber, December and January.
+
+\itemize{
+ \item \code{variety} a categorical variable with 6 levels that
+ represents mango varieties studied.
+ \item \code{year} the year of harvesting.
+ \item \code{month} the month of harvesting.
+ \item \code{acid} mean of the acidity determined in 3 fruits.
+}
+}
+\examples{
+library(lattice)
+library(latticeExtra)
+
+data(mangoAcidity)
+str(mangoAcidity)
+
+## reshape::cast() can also be used.
+with(mangoAcidity,
+ ftable(tapply(acid,
+ list(variety, year, month),
+ FUN=identity)))
+
+xyplot(acid~month|variety, groups=year,
+ data=mangoAcidity, type=c("p", "a"),
+ auto.key=TRUE,
+ ylab="Acidity",
+ xlab="Month")
+}
+\keyword{datasets}
+
diff --git a/man/plowing.Rd b/man/plowing.Rd
index 66fc799e3e867bf1900a1f18a2de5c528d62150e..30c69cacc5761c0d39ad9463b2e461cf81dcf26b 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/polyGui.Rd b/man/polyGui.Rd
index 4b084c8f62269e04cc3dc5a0b1fdb6509a62f177..049c113c519ccc5f715232f86ae97fc5d1c72377 100644
--- a/man/polyGui.Rd
+++ b/man/polyGui.Rd
@@ -12,18 +12,19 @@ polyGui(x, y, data, er = 0.05)
\item{data}{an optional \code{data.frame}.}
\item{er}{stands for extend range. It is used to extend the plotting
-range by a fraction on both sides and directions. Default is
-0.05. See \link[grDevices]{extendrange}.}
+ range by a fraction on both sides and directions. Default is
+ 0.05. See \link[grDevices]{extendrange}.}
}
\value{
None is returned by the function.
}
\description{
This function opens an interface to control the
-polynomial degree in linear regression. It shows the observed values
-and the corresponding fitted curve superimposed with confidence bands
-(for the fitted values) and also show the residuals plot. It assumes
-that \code{gWidgets} and \code{gWidgetstcltk} packages are available.
+ polynomial degree in linear regression. It shows the observed
+ values and the corresponding fitted curve superimposed with
+ confidence bands (for the fitted values) and also show the
+ residuals plot. It assumes that \code{gWidgets} and
+ \code{gWidgetstcltk} packages are available.
}
\examples{
\donttest{
diff --git a/man/potatoyield.Rd b/man/potatoYield.Rd
similarity index 89%
rename from man/potatoyield.Rd
rename to man/potatoYield.Rd
index 441fce52b311a438c6aa1f1e765ccf9a585cdbe2..3a0752606e317a05121ac7558ed23f1a5014e590 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 EstatÃstica 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/runAllChunks.Rd b/man/runAllChunks.Rd
index 3602646e0ca20153358dd7f3bf75304c4902a54f..e8abbbe62431f8cd6e91f81ca19224c8c065bfc8 100644
--- a/man/runAllChunks.Rd
+++ b/man/runAllChunks.Rd
@@ -10,15 +10,15 @@ runAllChunks(Rmd, envir = globalenv())
\item{Rmd}{the name of the Rmd file.}
\item{envir}{the environment in which the chunks will be
-evaluated. By default it is the GlobalEnv.}
+ evaluated. By default it is the GlobalEnv.}
}
\value{
Objects created in the chunks from the Rmd file.
}
\description{
This function was developed to run all chunks in a knitr
-Rmd (R markdown) file at once. Mainly for exploring and debugging
-purposes.
+ Rmd (R markdown) file at once. Mainly for exploring and debugging
+ purposes.
}
\author{
Fernando Mayer, \email{fernando.mayer@ufpr.br}
diff --git a/man/sugarcaneYield3.Rd b/man/sugarcaneYield3.Rd
index b7418bf52cefa4b442e48191f3ac4cce9dedaa33..048af7a28000f61f627a4957d2ed5d733898fa35 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:
diff --git a/man/sugarcaneYield4.Rd b/man/sugarcaneYield4.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..b0a20021e4e7cf9284dde5a41e0adf2d7dd855d4
--- /dev/null
+++ b/man/sugarcaneYield4.Rd
@@ -0,0 +1,48 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/legTools.R
+\docType{data}
+\name{sugarcaneYield4}
+\alias{sugarcaneYield4}
+\title{Triple factorial NPK fertilization on sugar cane yield}
+\format{a \code{data.frame} with 54 records and 6 variables.}
+\source{
+Frederico, P. (2009). Curso de EstatÃstica Experimental (15th
+ ed.). Piracicaba, São Paulo: FEALQ. (page 126)
+}
+\usage{
+data(sugarcaneYield4)
+}
+\description{
+These data are from an \eqn{3^3} factorial experiment
+ studing the effect of NPK on the yield of sugar cane.
+
+\itemize{
+ \item \code{block} a local control factor with 3 levels.
+ \item \code{rept} factor with 2 levels.
+ \item \code{N} integer coded nitrogen levels (0, 1, 2).
+ \item \code{P} integer coded phosphorus levels (0, 1, 2).
+ \item \code{K} integer coded potassium levels (0, 1, 2).
+ \item \code{yield} sugar cane yield (ton/ha).
+}
+}
+\details{
+There is a missprint in the book for the 9th entry, which
+ has yield 59.0, that is coded as 202 istead of 220.
+}
+\examples{
+library(lattice)
+library(latticeExtra)
+
+data(sugarcaneYield4)
+str(sugarcaneYield4)
+
+xyplot(yield~N|P, groups=K,
+ auto.key=list(title="Potassim level", columns=3),
+ strip=strip.custom(var.name="Phosphorus", strip.names=TRUE,
+ strip.levels=TRUE, sep=": "),
+ data=sugarcaneYield4, type=c("p", "a"),
+ ylab=expression(Yield~(ton~ha^{-1})),
+ xlab="Nitrogen level level")
+}
+\keyword{datasets}
+
diff --git a/man/vinasseFert.Rd b/man/vinasseFert.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..c52ece6e40284557829e798b3e7279cf95c6783a
--- /dev/null
+++ b/man/vinasseFert.Rd
@@ -0,0 +1,45 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/legTools.R
+\docType{data}
+\name{vinasseFert}
+\alias{vinasseFert}
+\title{Fertilization with vinasse and mineral}
+\format{a \code{data.frame} with 16 records and 4 variables.}
+\source{
+Frederico, P. (2009). Curso de EstatÃstica Experimental (15th
+ ed.). Piracicaba, São Paulo: FEALQ. (page 119)
+}
+\usage{
+data(vinasseFert)
+}
+\description{
+These data are from an \eqn{2^2} factorial experiment
+ studing the effect of fertilizaton with vinasse (a residual from
+ industrial processing of sugar cane) and complete mineral
+ fertilization.
+
+\itemize{
+ \item \code{block} a factor with 4 levels.
+ \item \code{mineral} low (-1) and high (+1) levels of mineral
+ fertilization.
+ \item \code{vinasse} low (-1) and high (+1) levels of fetilization
+ with vinasse.
+ \item \code{y} some response variable. The text book doesn't give
+ any information.
+}
+}
+\examples{
+library(lattice)
+library(latticeExtra)
+
+data(vinasseFert)
+str(vinasseFert)
+
+xyplot(y~vinasse, groups=mineral,
+ auto.key=list(title="Mineral", columns=2),
+ data=vinasseFert, type=c("p", "a"),
+ ylab="y",
+ xlab="Vinasse level")
+}
+\keyword{datasets}
+
diff --git a/man/wgpigs.Rd b/man/wgPigs.Rd
similarity index 92%
rename from man/wgpigs.Rd
rename to man/wgPigs.Rd
index 3fc9a3ee41e441766520f2385b24fb0e11bb5095..e107692f914c6ec870518286efbb857f8a2c4e78 100644
--- a/man/wgpigs.Rd
+++ b/man/wgPigs.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{wgpigs}
-\alias{wgpigs}
+\name{wgPigs}
+\alias{wgPigs}
\title{Feeding type in pig weight gain}
\format{a \code{data.frame} with 20 records and 2 variables.}
\source{
@@ -10,7 +10,7 @@ Frederico, P. (2009). Curso de EstatÃstica Experimental (15th
ed.). Piracicaba, São Paulo: FEALQ. (page 62)
}
\usage{
-data(wgpigs)
+data(wgPigs)
}
\description{
This is an artifial dataset corresponding a experiment
@@ -29,9 +29,9 @@ This is an artifial dataset corresponding a experiment
}
\examples{
library(lattice)
-data(wgpigs)
+data(wgPigs)
-xyplot(wg~ft, data=wgpigs,
+xyplot(wg~ft, data=wgPigs,
ylab="Weight gain (kg)",
xlab="Feeding type")
}
diff --git a/man/wgPigs2.Rd b/man/wgPigs2.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..8ac1bb48b2aae8dae99418fa7113c493a9e978b3
--- /dev/null
+++ b/man/wgPigs2.Rd
@@ -0,0 +1,47 @@
+% 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 EstatÃstica 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)")
+}
+\keyword{datasets}
+
diff --git a/man/yscale.components.right.Rd b/man/yscale.components.right.Rd
index cfe1220fbe2e36861731f8125f1c16cdedb9552e..7d94a5b22589303ff4a3484844e7909042eff3e4 100644
--- a/man/yscale.components.right.Rd
+++ b/man/yscale.components.right.Rd
@@ -1,7 +1,6 @@
% Generated by roxygen2 (4.1.1): do not edit by hand
% Please edit documentation in R/yscale.components.right.R
\name{yscale.components.right}
-\alias{yscale.component.right}
\alias{yscale.components.right}
\title{y-axis annotations on the right side}
\source{
@@ -10,7 +9,7 @@ When such feature was necessary, a search in the web was done
\code{http://r.789695.n4.nabble.com/Spacing-between-lattice-panels-td855613.html}.
}
\usage{
-yscale.component.right(...)
+yscale.components.right(...)
}
\arguments{
\item{...}{arguments passed by the lattice function called. See
@@ -38,7 +37,7 @@ useOuterStrips(p2)
p3 <- xyplot(yield~K|N+P, data=npk,
scales=list(y=list(relation="free", alternating=2)),
ylab=NULL, ylab.right="Yield",
- yscale.component=yscale.component.right,
+ yscale.component=yscale.components.right,
between=list(x=0.5, y=0.2),
par.settings=list(
layout.widths=list(