Statistical Analysis: an Introduction using R/R/Packages
Some packages should always be available within R, and a number of these are automatically loaded at the start of an R session. These include the "base" package (which is where the max()
and sqrt()
functions are defined), the "utils" package (which is where RSiteSearch()
and citation()
are defined), the "graphics" package (which allows plots to be generated), and the "stats" package (which provides a broad range of statistical functionality). In total, the default packages allow you to do a considerable amount of statistics.
library()
function.library("datasets") #Load the already installed "datasets" package
cars #Having loaded "datasets", the "cars" object (containing a set of data) is now available
library("vioplot") #Try loading the "vioplot" package: will probably fail as it is not installed by default
install.packages("vioplot") #This is one way of installing the package. There are other ways too.
library("vioplot") #This should now work
example("vioplot") #produces some pretty graphics. Don't worry about what they mean for the time being
> library(datasets) #Load the datasets package (actually, it has probably been loaded already) > cars #Display one of the datasets: see ?car for more information
speed dist
1 4 2 2 4 10 3 7 4 4 7 22 5 8 16 6 9 10 7 10 18 8 10 26 9 10 34 10 11 17 11 11 28 12 12 14 13 12 20 14 12 24 15 12 28 16 13 26 17 13 34 18 13 34 19 13 46 20 14 26 21 14 36 22 14 60 23 14 80 24 15 20 25 15 26 26 15 54 27 16 32 28 16 40 29 17 32 30 17 40 31 17 50 32 18 42 33 18 56 34 18 76 35 18 84 36 19 36 37 19 46 38 19 68 39 20 32 40 20 48 41 20 52 42 20 56 43 20 64 44 22 66 45 23 54 46 24 70 47 24 92 48 24 93 49 24 120 50 25 85 > library(vioplot) #Try loading the "vioplot" package: this will probably fail as it is not installed by default Error in library(vioplot) : there is no package called 'vioplot' > install.packages("vioplot") #This is one way of installing the package. There are other ways too. also installing the dependency ‘sm’
trying URL 'http://cran.uk.r-project.org/bin/macosx/universal/contrib/2.8/sm_2.2-3.tgz' Content type 'application/x-gzip' length 306188 bytes (299 Kb) opened URL
=======================
downloaded 299 Kb
trying URL 'http://cran.uk.r-project.org/bin/macosx/universal/contrib/2.8/vioplot_0.2.tgz' Content type 'application/x-gzip' length 9677 bytes opened URL
=======================
downloaded 9677 bytes
The downloaded packages are in
/tmp/RtmpR28hpQ/downloaded_packages
> library(vioplot) #This should now work
Loading required package: sm
Package `sm', version 2.2-3; Copyright (C) 1997, 2000, 2005, 2007 A.W.Bowman & A.Azzalini
type help(sm) for summary information
> example(vioplot) #produces some pretty graphics. Don't worry about what they mean for the time being
vioplt> # box- vs violin-plot vioplt> par(mfrow=c(2,1))
vioplt> mu<-2
vioplt> si<-0.6
vioplt> bimodal<-c(rnorm(1000,-mu,si),rnorm(1000,mu,si))
vioplt> uniform<-runif(2000,-4,4)
vioplt> normal<-rnorm(2000,0,3)
vioplt> vioplot(bimodal,uniform,normal) Hit <Return> to see next plot:
vioplt> boxplot(bimodal,uniform,normal)
vioplt> # add to an existing plot vioplt> x <- rnorm(100)
vioplt> y <- rnorm(100)
vioplt> plot(x, y, xlim=c(-5,5), ylim=c(-5,5)) Hit <Return> to see next plot:
vioplt> vioplot(x, col="tomato", horizontal=TRUE, at=-4, add=TRUE,lty=2, rectCol="gray")
vioplt> vioplot(y, col="cyan", horizontal=FALSE, at=-4, add=TRUE,lty=2)
install.packages()
, should also install dependencies[1].
There are several other ways of installing packages. If you start R by typing "R" on a unix command-line, then you can install packages by running "R CMD INSTALL packagename" from the command-line instead (see ?INSTALL
). If you are running R using a graphical user interface (e.g. under Macintosh or Windows), then you can often install packages by using on-screen menus. Note that these methods may not install other, dependent packages.
You only need to read the following if you are are having problems installing packages. If a package is not installed already, and you encounter problems when trying to install it (e.g. when calling install.packages("vioplot") ), this may be for one of the following reasons:
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Notes
edit- ↑ Actually, the details are slightly more complex, depending on whether there is a default location to install the packages, see
?install.packages