Holcombe:ProgrammingInR

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Members

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



Technical

Skills Checklist
Python Programming
Psychopy/VisionEgg Installation Notes
R analysis,plot,stats
Statistics
Buttonbox
Buttonbox with photocell
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 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
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)

Replace certain value with another

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

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

Understanding model formulae

ANOVA with repeated measures walk-through

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.