Holcombe:ProgrammingInR

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Revision as of 18:59, 10 March 2011 by Alex O. Holcombe (Talk | contribs)
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Members

Alex Holcombe
Sarah McIntyre
Fahed Jbarah
• Shih-Yu Lo
• Patrick Goodbourn
Lizzy Nguyen
Alumni


Technical

Skills Checklist
Python Programming
Psychopy/VisionEgg Installation Notes
R analysis,plot,stats
Statistics
Buttonbox
Verifying timing
Programming Cheat Sheets


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 stuff

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
head(datos)
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

Check your counterbalancing in your results file. Make a contingency table,

table(dataRaw$speed,dataRaw$relPhaseOuterRing)

Creating Graphs (usu. ggplot2)

how I Holcombe:fit psychometric functions and bootstrap

See http://openwetware.org/wiki/Holcombe:Plotting

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

some aov (ANOVA) explanation

R will assume factor is regressor if numeric

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 note 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

For Sydney Uni, use:

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