version 1.0-7

DESCRIPTION

@@ -1,12 +1,26 @@
-Package: agricolae
-Type: Package
-Title: Statistical Procedures for Agricultural Research
-Version: 1.0-6
-Date: 2008-12-17
-Author: Felipe de Mendiburu
-Maintainer: Felipe de Mendiburu <f.mendiburu@cgiar.org>
-Suggests: akima, klaR, SuppDists, corpcor
-Description: Agricolae is a project in order to obtain the degree of master in Systems Engineering in the National University of Engineering in Lima-Peru (UNI in Spanish). These functions are currently utilized by the International Potato Center Research (CIP), the Universidad Nacional Agraria La Molina (UNALM-PERU), and the Instituto Nacional de Investigacion Agricola (INIA-PERU). It comprises the functionality of statistical analysis into experimental designs applied specially for field experiments in  agriculture and plant breeding: Lattice, factorial, complete and incomplete block, Latin Square, Greaco, Alpha designs, Cyclic designs, comparison of multi-location trials, comparison  between treatments, resampling, simulation, biodiversity indexes and consensus cluster.
-License: GPL
-URL: http://tarwi.lamolina.edu.pe/~fmendiburu
-Packaged: Wed Dec 17 09:47:13 2008; fdemendiburu
+Package: agricolae
+Type: Package
+Title: Statistical Procedures for Agricultural Research
+Version: 1.0-7
+Date: 2009-4-20
+Author: Felipe de Mendiburu
+Maintainer: Felipe de Mendiburu <f.mendiburu@cgiar.org>
+Suggests: akima, klaR, SuppDists, corpcor
+Description: Agricolae is a project in order to obtain the degree of
+        master in Systems Engineering in the National University of
+        Engineering in Lima-Peru (UNI in Spanish). These functions are
+        currently utilized by the International Potato Center Research
+        (CIP), the Universidad Nacional Agraria La Molina (UNALM-PERU),
+        and the Instituto Nacional de Investigacion Agricola
+        (INIA-PERU). It comprises the functionality of statistical
+        analysis into experimental designs applied specially for field
+        experiments in agriculture and plant breeding: Lattice,
+        factorial, complete and incomplete block, Latin Square, Greaco,
+        Alpha designs, Cyclic designs, comparison of multi-location
+        trials, comparison between treatments, resampling, simulation,
+        biodiversity indexes and consensus cluster.
+License: GPL
+URL: http://tarwi.lamolina.edu.pe/~fmendiburu
+Packaged: 2009-04-20 13:52:25 UTC; fdemendiburu
+Repository: CRAN
+Date/Publication: 2009-04-20 17:21:12

NAMESPACE

@@ -0,0 +1,3 @@
+exportPattern("^[[:alpha:]]+")
+S3method(summary,graph.freq)
+S3method(plot,graph.freq)

R/graph.freq.R

@@ -68,7 +68,7 @@ a<-breaks[1]-ancho[1]/2
 b<-breaks[k+1]+ancho[k]/2
 relative<-round(counts/sum(counts),4)
 density <- relative/ancho
-histogram<-list(breaks=breaks,counts=counts,mids=mids,relative=relative,density=density)
+histogram<-structure(list(breaks=breaks,counts=counts,mids=mids,relative=relative,density=density),class="graph.freq")
 
 if(plot) {
 x <- c(a, b)
@@ -90,5 +90,5 @@ for (j in 1:k) {
 suppressWarnings(warning(rect(breaks[j], 0, breaks[j + 1], density[j], ...)))
 }}
 }
-    return(histogram)
+    invisible(histogram)
 }

R/plot.graph.freq.R

@@ -0,0 +1,95 @@
+`plot.graph.freq` <-
+function (x, breaks="sturges",counts=NULL,frequency=1, plot=TRUE, nclass=NULL,xlab="",ylab="",...)
+{
+if (xlab=="") xlab= deparse(substitute(x))
+if (is.numeric(x) & is.null(counts)) {
+# histogram
+if (is.null(nclass)) {
+if (length(breaks)==1) {
+x<-na.omit(x)
+if(breaks== "sturges") breaks <- sturges.freq(x)$breaks
+}
+}
+else {
+amplitud <- max(x)-min(x)
+n <- length(x)
+z<-rep(0,n)
+y<- as.character(x)
+for (i in 1:n) {
+lc<-nchar(y[i])
+nd<-0
+for (j in 1:lc) {
+a <- substr(y[i],j,j)
+if(a!=".")nd=nd+1
+else break
+}
+z[i]<- lc-nd-1
+}
+d<-max(z)
+if(d<0) d=0
+tic <- round(amplitud/nclass + 0.5 * 10^(-d), d)
+breaks <-seq(min(x), by=tic, length=nclass+1)
+}
+
+k<-length(breaks)
+n<- length(x)
+counts <- rep(0,k-1)
+for (i in 1:n) {
+for (j in 1:(k-1)) {
+if( (x[i] >= breaks[j]) && (x[i] < breaks[j + 1])) counts[j]<-counts[j]+1
+}
+}
+    k <- length(counts)
+    mids <- rep(0, k)
+    ancho <- rep(0, k)
+    for (i in 1:k) {
+        mids[i] <- (breaks[i] + breaks[i + 1])/2
+        ancho[i] <- (breaks[i + 1] - breaks[i])
+    }
+    altura <- round(1.1 * max(counts), 0)
+}
+#############
+else  {
+if( is.list(x)) {
+breaks<- x$breaks
+counts <- x$counts
+}
+else breaks <- x
+k<-length(counts)
+mids<-rep(0,k)
+ancho<-rep(0,k)
+for (i in 1:k) {
+mids[i]<-(breaks[i]+breaks[i+1])/2
+ancho[i]<-(breaks[i+1]-breaks[i])
+}
+}
+################
+a<-breaks[1]-ancho[1]/2
+b<-breaks[k+1]+ancho[k]/2
+relative<-round(counts/sum(counts),4)
+density <- relative/ancho
+histogram<-list(breaks=breaks,counts=counts,mids=mids,relative=relative,density=density)
+
+if(plot) {
+x <- c(a, b)
+if(frequency==1)height<-round(1.1*max(counts),1)
+if(frequency==2)height<-round(1.1*max(relative),4)
+if(frequency==3)height<-round(1.1*max(density),4)
+y <- c(0, height)
+suppressWarnings(warning(plot(x,y, type = "n", xlab=xlab,ylab=ylab,...)))
+if (frequency==1) {
+for (j in 1:k) {
+suppressWarnings(warning(rect(breaks[j], 0, breaks[j + 1], counts[j], ...)))
+}}
+if (frequency==2) {
+for (j in 1:k) {
+suppressWarnings(warning(rect(breaks[j], 0, breaks[j + 1], relative[j], ...)))
+}}
+if (frequency==3) {
+for (j in 1:k) {
+suppressWarnings(warning(rect(breaks[j], 0, breaks[j + 1], density[j], ...)))
+}}
+}
+    invisible(histogram)
+}
+

R/summary.graph.freq.R

@@ -0,0 +1,25 @@
+`summary.graph.freq` <-
+function(object,...){
+xx<-object$mids
+yy<-object$counts
+y1<-sum(yy)
+zz<-object$breaks
+x<-length(xx)
+acum<-0
+z<-rep(0,7*x)
+dim(z)<-c(x,7)
+for (i in 1:x) {
+z[i,1]<-zz[i]
+z[i,2]<-zz[i+1]
+z[i,3]<-xx[i]
+z[i,4]<-yy[i]
+z[i,5]<-yy[i]/y1
+z[i,6]<-yy[i]+acum
+acum<-z[i,6]
+z[i,7]<-z[i,6]/y1
+}
+colnames(z)<-c("Inf","Sup","MC","fi","fri","Fi","Fri")
+rownames(z)<-rep(" ",x)
+return(z)
+}
+

R/table.freq.R

@@ -1,9 +1,9 @@
 `table.freq` <-
-function(histogram){
-xx<-histogram$mids
-yy<-histogram$counts
+function(object){
+xx<-object$mids
+yy<-object$counts
 y1<-sum(yy)
-zz<-histogram$breaks
+zz<-object$breaks
 x<-length(xx)
 acum<-0
 z<-rep(0,7*x)

man/agricolae.package.Rd

@@ -13,8 +13,8 @@ designs applied specially for field experiments in agriculture and plant breedin
 \tabular{ll}{
 Package: \tab agricolae\cr
 Type: \tab Package\cr
-Version: \tab 1.0-6\cr
-Date: \tab 2008-12-17\cr
+Version: \tab 1.0-7\cr
+Date: \tab 2009-04-20\cr
 License: \tab GPL\cr
 }
 Planning of field experiments: lattice, factorial, RCBD, CRD, Latin Square, Graeco, BIB, Alpha design, Cyclic Designs. 

man/cv.model.Rd

@@ -15,7 +15,7 @@ cv.model(x)
   \item{x}{ object of model lm() or AOV() }
 }
 \details{
-$\frac{sqrt(MSerror)}{mean(x)}\*100$
+sqrt(MSerror)*100/mean(x)
 }
 \value{
 

man/design.bib.Rd

@@ -42,7 +42,7 @@ library(agricolae)
 # 4 treatments and k=3 size block
 trt<-c("A","B","C","D")
 k<-3
-bib <-design.bib(trt,k,number=101,seed =41,kinds ="Super-Duper") # seed = 37
+bib <-design.bib(trt,k,number=101,seed =41,kinds ="Super-Duper") # seed = 41
 plots <-as.numeric(bib[,1])
 field <-as.character(bib[,3])
 t(matrix(plots,c(3,4)))

man/index.bio.Rd

@@ -30,7 +30,9 @@ index.bio(data, method = c("Margalef", "Simpson.Dom", "Simpson.Div", "Berger.Par
   \item{level }{ value 0-100 percentage }
   \item{nboot }{ size 100, 500,... }
 }
-\references{Efron, B., Tibshirani, R. (1993) An Introduction to the Boostrap. Chapman and Hall/CRC }
+\references{Magurran, A.E. (1988) Ecological diversity and its measurement. Princeton University Press
+Efron, B., Tibshirani, R. (1993) An Introduction to the Boostrap. Chapman and Hall/CRC 
+}
 \author{ Felipe de Mendiburu }
 \examples{
 library(agricolae)

man/index.smith.Rd

@@ -18,7 +18,7 @@ index.smith(data, ...)
 }
 \details{
 
- $V_{x}=\frac{V_{(x)}}{x^b}$
+ Vx=V(x)/x b
 
 
  V(x) is the between-plot variance,

man/kurtosis.Rd

@@ -13,13 +13,7 @@ kurtosis(x)
 \arguments{
   \item{x}{ a numeric vector }
 }
-\details{
 
-n = length(x)
-
-$\frac{n(n+1)}{(n-1)(n-2)(n-3)}\sum_{i}\left(\frac{x_i - mean(x)}{sd(x)}\right)^4 - \frac{3(n-1)^2}{(n-2)(n-3)}$
-
-}
 \value{
 
   \item{x }{ The kurtosis of x }

man/plot.graph.freq.Rd

@@ -0,0 +1,85 @@
+\name{plot.graph.freq}
+\alias{plot.graph.freq}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{ Histogram }
+\description{
+  In many situations it has intervals of class defined with its respective
+  frequencies. By means of this function, the graphic of frequency is obtained
+  and it is possible to superpose the normal distribution, polygon of frequency,
+  Ojiva and to construct the table of complete frequency.
+}
+\usage{
+plot.graph.freq(x, breaks="sturges",counts=NULL,frequency=1, plot=TRUE, nclass=NULL,xlab="",ylab="",...)
+
+}
+\arguments{
+  \item{x}{ a vector of values, a object hist(), graph.freq() }
+  \item{counts}{ frequency and x is class intervals}
+  \item{breaks}{ a vector giving the breakpoints between histogram cells }
+  \item{frequency}{ 1=counts, 2=relative, 3=density }
+  \item{plot}{ logic }
+  \item{nclass}{ number of classes }
+  \item{xlab}{ x labels}
+  \item{ylab}{ y labels}
+  \item{\dots}{ other parameters of graphic}
+}
+
+\value{
+  \item{x }{Numeric or list}
+  \item{plot }{TRUE or FALSE}
+  \item{counts }{Numeric}
+  \item{frequency}{ Numeric }
+
+}
+
+\author{ Felipe de Mendiburu }
+
+\seealso{\code{\link{polygon.freq}}, \code{\link{table.freq}}, \code{\link{stat.freq}},
+\code{\link{intervals.freq}}, \code{\link{sturges.freq}}, \code{\link{join.freq}},
+\code{\link{ojiva.freq}}, \code{\link{normal.freq} } }
+
+\examples{
+
+library(agricolae)
+data(genxenv)
+yield <- subset(genxenv$YLD,genxenv$ENV==2)
+yield <- round(yield,1)
+h<- graph.freq(yield,axes=FALSE, frequency=1, ylab="frequency",col="yellow")
+axis(1,h$breaks)
+axis(2,seq(0,20,0.1))
+# To reproduce histogram.
+h1 <- graph.freq(h, col="blue", frequency=2,border="red", density=8,axes=FALSE, xlab="YIELD",ylab="relative")
+axis(1,h$breaks)
+axis(2,seq(0,.4,0.1))
+# summary, only frecuency
+limits <-seq(10,40,5)
+frequencies <-c(2,6,8,7,3,4)
+#startgraph
+h<-graph.freq(limits,counts=frequencies,col="bisque",xlab="Classes")
+polygon.freq(h,col="red")
+title( main="Histogram and polygon of frequency",
+ylab="Frequency")
+#endgraph
+# Statistics
+measures<-stat.freq(h)
+print(measures)
+# frequency table full
+round(table.freq(h),2)
+#startgraph
+# Ojiva
+ojiva.freq(h,col="red",type="b",xlab="Variable",ylab="Accumulated relative frequency")
+# only frequency polygon
+h<-graph.freq(limits,counts=frequencies,border=FALSE,col=NULL,xlab="   ",ylab="")
+title( main="Polygon of frequency",
+xlab="Variable", ylab="Frecuency")
+polygon.freq(h,col="blue")
+grid(col="brown")
+#endgraph
+# Draw curve for Histogram
+h<- graph.freq(yield,axes=FALSE, frequency=3, ylab="f(yield)",col="yellow")
+axis(1,h$breaks)
+axis(2,seq(0,0.18,0.03),las=2)
+lines(density(yield), col = "red", lwd = 2)
+title("Draw curve for Histogram")
+}
+\keyword{ aplot }% at least one, from doc/KEYWORDS

man/skewness.Rd

@@ -12,13 +12,7 @@ skewness(x)
 \arguments{
   \item{x}{a numeric vector}
 }
-\details{
 
-n = length(x)
-
-$\frac{n}{(n-1)(n-2)}\sum_{i}\left(\frac{x_i - mean(x)}{sd(x)}\right)^3$
-
-}
 \value{
 
   \item{x }{The skewness of x}

man/summary.graph.freq.Rd

@@ -0,0 +1,31 @@
+\name{summary.graph.freq}
+\alias{summary.graph.freq}
+\title{ Frequency Table of a Histogram  }
+\description{
+  It finds the absolute, relative and accumulated frequencies with the class
+  intervals defined from a previously calculated histogram by "graph.freq".
+}
+\usage{
+summary.graph.freq(object,...)
+}
+
+\arguments{
+  \item{object}{Object by function graph.freq() }
+  \item{\dots}{ other parameters of graphic}
+}
+\value{
+  \item{object }{Object by graph.freq()}
+}
+\author{ Felipe de Mendiburu }
+
+\seealso{\code{\link{polygon.freq}}, \code{\link{stat.freq}}, \code{\link{graph.freq}},
+\code{\link{intervals.freq}}, \code{\link{sturges.freq}}, \code{\link{join.freq}},
+\code{\link{ojiva.freq}}, \code{\link{normal.freq} } }
+\examples{
+library(agricolae)
+data(growth)
+attach(growth)
+h2<-graph.freq(height,plot=FALSE)
+summary(h2)
+}
+\keyword{ distribution }% at least one, from doc/KEYWORDS