# Holcombe:ProgrammingInR

(Difference between revisions)

## Revision as of 21:00, 13 September 2012

### Members

Alex Holcombe
Polly Barr
• Charlie Ludowici
• Kim Ransley
• Ingrid Van Tongeren
William Ngiam
Fahed Jbarah
• Patrick Goodbourn
Alumni

### Other

R is an interactive programming language for statistics. The syntax is very idiosyncratic, and not really in a good way. Try R for programmers for a description. However it may have menu-driven versions maybe available R commander we haven't tried that and another one is pmg GTK maybe here

In the lab we have the book Using R for Introductory Statistics. R_Statistics introduces you to R

Dani has posted some example code and graphs on his personal website.

R reference cheatsheet, also a file here Media:Matlab-python-xref.pdf‎ that gives equivalent code for doing array operations in MATLAB, Python, and R plot parameters

There is a wiki with some good tips here. Also Data frame tips, list of R websites

Functions in R can only return one parameter.

### dataframe tips

Examining your data frame or object, let's say it's called datos

```typeof(datos) #returns "list!"
str(datos) #tells you it's a dataframe, number of observations, columns, etc
str(datos)
summary(datos) #good for ggplot objects also
```
```df\$varWithExtraLevels = factor(df\$varWithExtraLevels)
```
```length(df) #number of columns of dataframe
```
```names(df) #names of columns of dataframe
```
```library(Hmisc);
describe(df)
```
```#Calling typeof() on a dataframe returns "list"
```
```rm(objectToBeDeleted)
rm(list = ls())  #Delete nearly everything in memory
```

expand.grid() to create dataframe with every combination of some factors

```table(dataRaw\$speed,dataRaw\$relPhaseOuterRing)
```

Replace certain value with another

```thr\$thresh[  thr\$task=='ident' ] = NA
```

## Creating Graphs (usu. ggplot2)

how I Holcombe:fit psychometric functions and bootstrap

## Debugging in R

How to examine and try things with a questionable variable within a function?

``` ee <<- resultsMeans #make global, violating all principles of good coding #DEBUG
STOP
```

After an error, calling traceback() gives you the stack

## doing ANOVAs etc

ANOVA with repeated measures walk-through

I think I had too many error terms reducing error terms

Anovas with repeated measures can be complicated in R.

We have some R books in the lab

## Dealing with circular data

von Mises vs. wrapped Gaussian,

see Swindale, N. V. (1998). Orientation tuning curves: empirical description and estimation of parameters. Biol Cybern, 78(1), 45-56.

## Setting up a proxy in R on a Mac

The easiest way to set up a proxy is simply to create a file called ".Rprofile" (make sure the file does not have a .txt or .rtf extension. Textwrangler will automatically give it an extension, it may be best to create the file using Vi in a terminal - using emacs probably won't work) in your user directory (~ or /Users/username/) with the line: ``` ```

``` Sys.setenv(http_proxy=”http://username:password@tcdproxy.tcd.ie:8080″) ```

Then restart R. This information (and more) can be found on Ken Benoit's webpage

If you're at the Camperdown campus of the University of Sydney, use: ``` ```

``` Sys.setenv(http_proxy=”http://www-cache.usyd.edu.au:8080″) ```

Note: The following may not necessarily be true anymore. If the below address does not work, use the same one as for Camperdown above. The Cumberland Campus of the University of Sydney, use: ``` ```

``` Sys.setenv(http_proxy=”web-cache-ext.usyd.edu.au:8080″) ```