First commit

.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$

.gitignore

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+.Rproj.user
+.Rhistory
+.RData

DESCRIPTION

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+Package: factoextra
+Type: Package
+Title: Visualization of FactoMineR outputs (PCA, CA, MCA) using ggplot2
+Version: 1.0.0
+Date: 2015-02-21
+Author: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
+Maintainer: Alboukadel kassambara <alboukadel.kassambara@gmail.com>
+Description: Provide easy to use functions to visualize FactoMineR PCA, CA and MCA outputs using ggplot2
+License: GPL-3
+Depends: FactoMineR, ggplot2
+Imports: FactoMineR, ggplot2
+VignetteBuilder: knitr
+URL: htt://www.sthda.com 
+BugReports:https://github.com/kassambara/factoextra/issues

NAMESPACE

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+exportPattern("^[[:alpha:]]+")

R/fviz_screeplot.R

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+#' Screeplot : Plots the variances/eigenvalues against the number of dimensions
+#' 
+#' @param X Object of class PCA, MCA, CA (from FactoMineR)
+#' @param choice Character specifing the type of the data to be plotted.
+#'  Allowed values are "variance" or "eigenvalue"
+#' @param geom Character specifing the geometry to be used for the graph.
+#'  Allowed values are "bar" for barplot, "line" for lineplot or c("bar", "line") to use both type
+#' @param barfill Fill color for bar plot
+#' @param barcolor Outline color for bar plot
+#' @param linecolor Color for line plot (when geom contains "line")
+#' @param ncp Numeric value specifing the number of components to be shown
+#' @param addlabels Logical value. If TRUE, labels are added at the top of bars or points
+#'  showing the information retained by each dimension
+#'  
+#' @return a ggplot2 plot
+#' @author Alboukadel Kassambara \email{alboukadel.kassambara@@gmail.com}
+#' @references http://www.sthda.com
+#' @examples
+#' \donttest{
+#'  library("FactoMineR")
+#'  data(decathlon)
+#'  res.pca <- PCA(decathlon, quanti.sup = 11:12, quali.sup=13)
+#'  fviz_screeplot(res.pca)
+#'  }
+fviz_screeplot<-function(X, choice=c("variance", "eigenvalue"), geom=c("bar", "line"),
+                         barfill="steelblue", barcolor="steelblue", linecolor = "black",
+                         ncp=5, addlabels=FALSE, ...)
+{
+  library("ggplot2")
+
+  eig <- X$eig
+  if(ncp > 0 & nrow(eig) > ncp) eig <- eig[1:ncp, , drop=FALSE]
+
+  title <- "Scree plot"
+  xlab <- "Dimensions"
+  ylab <- "Percentage of variances"
+  if(inherits(X, "PCA")) xlab = "Principal Components"
+
+  choice <- choice[1]
+  if(choice=="eigenvalue") {
+    eig <- eig[,1]
+    text_labels <- round(eig,1)
+    ylab <- "Eigenvalue"
+  }
+  else if(choice=="variance") {
+    eig <- eig[,2]
+    text_labels <- paste0(round(eig,1), "%")
+  }
+  else stop("Allowed values for the argument choice are : 'variance' or 'eigenvalue'")
+
+  if(length(intersect(geom, c("bar", "line"))) == 0)
+    stop("The specified value(s) for the argument geom are not allowed ")
+
+  df.eig <- data.frame(dim = factor(1:length(eig)), eig=eig )
+  p <- ggplot(df.eig, aes(dim, eig, group=1 ))
+  if("bar" %in% geom) p <- p + geom_bar(stat="identity", fill=barfill, color = barcolor,...)
+  if("line" %in% geom) p <- p + geom_line(color = linecolor, ...)+
+    geom_point(shape=19, color=linecolor)
+  if(addlabels) p <- p + geom_text(label = text_labels,
+                                   vjust=-0.4, ...)
+  p <- p + labs(title = title, x = xlab, y = ylab)
+
+  p 
+}

factoextra.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source

man/factoextra-package.Rd

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+\name{factoextra-package}
+\alias{factoextra-package}
+\alias{factoextra}
+\docType{package}
+\title{
+Visualization of FactoMineR outputs (PCA, CA, MCA) using ggplot2
+}
+\description{
+Provide easy to use functions to visualize FactoMineR PCA, CA and MCA outputs using ggplot2
+}
+\details{
+\tabular{ll}{
+Package: \tab factoextra\cr
+Type: \tab Package\cr
+Version: \tab 1.0.0\cr
+Date: \tab 2015-02-21\cr
+License: \tab GPL-3\cr
+}
+~~ An overview of how to use the package, including the most important functions ~~
+}
+\author{
+Alboukadel Kassambara
+
+Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
+}
+\references{
+http://www.sthda.com
+}
+~~ Optionally other standard keywords, one per line, from file KEYWORDS in the R documentation directory ~~
+\keyword{ package }
+\seealso{
+}
+\examples{
+library("FactoMineR")
+ data(decathlon)
+ res.pca <- PCA(decathlon, quanti.sup = 11:12, quali.sup=13)
+
+ # Screeplot
+ fviz_screeplot(res.pca)
+}

man/fviz_screeplot.Rd

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+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/fviz_screeplot.R
+\name{fviz_screeplot}
+\alias{fviz_screeplot}
+\title{Screeplot : Plots the variances against the number of dimensions}
+\usage{
+fviz_screeplot(X, choice = c("variance", "eigenvalue"), geom = c("bar",
+  "line"), barfill = "steelblue", barcolor = "steelblue",
+  linecolor = "black", ncp = 5, addlabels = FALSE, ...)
+}
+\arguments{
+\item{X}{Object of class PCA, MCA, CA (from FactoMineR)}
+
+\item{choice}{Character specifing the type of the data to be plotted.
+Allowed values are "variance" or "eigenvalue"}
+
+\item{geom}{Character specifing the geometry to be used for the graph.
+Allowed values are "bar" for barplot, "line" for lineplot or c("bar", "line") to use both type}
+
+\item{barfill}{Fill color for bar plot}
+
+\item{barcolor}{Outline color for bar plot}
+
+\item{linecolor}{Color for line plot (when geom contains "line")}
+
+\item{ncp}{Numeric value specifing the number of components to be shown}
+
+\item{addlabels}{Logical value. If TRUE, labels are added at the top of bars or points
+ showing the information retained by each dimension}
+}
+\value{
+a ggplot2 plot
+}
+\description{
+Screeplot : Plots the variances against the number of dimensions
+}
+\examples{
+\donttest{
+ library("FactoMineR")
+ data(decathlon)
+ res.pca <- PCA(decathlon, quanti.sup = 11:12, quali.sup=13)
+ fviz_screeplot(res.pca)
+ }
+}
+\author{
+Alboukadel Kassambara \email{alboukadel.kassambara@gmail.com}
+}
+\references{
+http://en.sthda.com
+}
+