Second R workshop

Mike Hammond
U. of Arizona

Last time
1. Basic interaction: q(), help(), etc.
2. Importing data: data.frame(), fix(), read.table().
3. Objects: ls(), summary(), rm().
4. Accessing a dataframe: x$column, x[[n]], x[,n], x[n,], attach(), detach(), search().
5. Basic stats: mean(), sd(), var().
6. Manipulating dataframes: tapply(), t(), transform(), aggregate(), as.factor(), is.factor(), cut().
7. Plotting: plot(), barplot(), hist(), interaction.plot(), etc.
8. Big stats: aov() and lm().
9. Scripting: function() {}.

An example

More data: tai.txt

td <- read.table('tai.txt', header=T)
summary(td)
attach(td)
tapply(response, list(native, nasal), mean)
plot(response ~ nasal)
summary(aov(response ~ native * nasal +
   Error(subject/nasal)))
summary(aov(response ~ native * nasal +
   Error(item/native)))

Other Tests
1. chisq.test() — χ² test.
  
  total number of words 1,026,595
  words beginning with [mn] 62,415
  words beginning with [bd] 77,262
```
chisq.test(c(62415, 77262))
```
2. t.test() — Student's t-test.
```
t.test(response ~ nasal, data=td,
   subset=td$native=='no')
```
Fixing Problems
Adding and Loading Libraries/Packages
1. Any of 1402 packages can be downloaded from CRAN directly and then installed on the command line (not recommended).
```
R CMD INSTALL /path/to/pkg_version.tar.gz
```
2. Packages can be downloaded and installed from within R (not recommended).
```
install.packages(c('packagename.tar.gz'))
```
3. Packages can be downloaded and installed from the appropriate menu in the GUI versions of R.
4. We'll download and install languageR.
5. library(packagename) — loading packages.
```
library(lme4)
library(languageR)
```
6. data(name, package='somepackage') — reads a dataset from some package.
7. Some interesting packages:
  1. corpora — Statistics for corpus linguists.
  2. languageR — Package for Harald Baayen's book on statistics for linguists.
  3. matlab — MATLAB emulation package.
  4. neural — Neural Networks.
  5. neuralnet — Training of neural networks.
  6. Rcmdr — R Commander. A platform-independent basic-statistics GUI (graphical user interface) for R.
  7. sound — Basic functions for dealing with wav files and sound samples.
  8. tm — Text mining package.
  9. xtable — Export tables to LaTeX or HTML.
  10. zipfR — Statistical models for word frequency distributions.
Linear Mixed Effects Models
1. lmer() — function from the lme4 package to calculate a linear mixed effects model.
2. pvals.fnc() — function from the languageR package to calculate p-values from a linear mixed effects model.
```
summary(lmer(response ~ size * sonority +
   (1|subject) + (1|item), sn))
pvals.fnc(lmer(response ~ size * sonority +
   (1|subject) + (1|item), sn))$fixed
```
Using R in papers
1. postscript() — export a plot as postscript.
```
postscript('filename.ps')
plot(age ~ weight, data=g)
dev.off()
```
2. Exporting a plot using the GUI menus.
3. xtable() — converts an R object into something that can be printed as LaTeX or as HTML.
```
library(xtable)
g.lm <- lm(age ~ weight)
print(xtable(g.lm))
print(xtable(g.lm), type='HTML')
```
4. R CMD Sweave filename.Rnw — converts a sweave file into a LaTeX file. For example: swtest.Rnw can be converted to swtest.pdf.
```
R CMD Sweave swtest.Rnw
latex swtest
latex swtest
dvipdf swtest
```
More Links
1. http://www.r-project.org Main R site. R can be downloaded from here, lots and lots of documentation, tutorials, etc.
2. http://www.statistik.lmu.de/~leisch/Sweave/ Sweave homepage.
3. http://dingo.sbs.arizona.edu/~psycol/tools/?v=1 R links from Adam & Andy.
4. http://dingo.sbs.arizona.edu/~hammond/Rwkshp/ URL for workshop materials.

total number of words	1,026,595
words beginning with [mn]	62,415
words beginning with [bd]	77,262