Holcombe:ProgrammingInR

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
Current revision (21:00, 13 September 2012) (view source)
(doing ANOVAs etc)
 
(42 intermediate revisions not shown.)
Line 1: Line 1:
{{Template:Holcombe}}
{{Template:Holcombe}}
-
R is an interactive programming language for statistics. The syntax is very idiosyncratic, try [http://www.johndcook.com/R_language_for_programmers.html R for programmers] for a description.
+
R is an interactive programming language for statistics. The syntax is very idiosyncratic, and not really in a good way. Try [http://www.johndcook.com/R_language_for_programmers.html R for programmers] for a description.
However it may have menu-driven versions maybe available  
However it may have menu-driven versions maybe available  
[http://socserv.mcmaster.ca/jfox/Misc/Rcmdr/ R commander] we haven't tried that and another one is pmg GTK [http://www.ggobi.org/rgtk2 maybe here]
[http://socserv.mcmaster.ca/jfox/Misc/Rcmdr/ R commander] we haven't tried that and another one is pmg GTK [http://www.ggobi.org/rgtk2 maybe here]
-
[[R_Statistics]] introduces you to R
+
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 [http://www.dlinares.org/Site/R_code.html personal website].
[http://www.rpad.org/Rpad/R-refcard.pdf R reference cheatsheet], also
[http://www.rpad.org/Rpad/R-refcard.pdf R reference cheatsheet], also
Line 10: Line 12:
[http://www.statmethods.net/advgraphs/axes.html plot parameters]
[http://www.statmethods.net/advgraphs/axes.html plot parameters]
-
In the lab we have the book ''Using R for Introductory Statistics''.
+
There is a wiki with some good tips [http://wiki.r-project.org/rwiki/doku.php?id=start here]. Also
 +
[http://rwiki.sciviews.org/doku.php?id=tips:tips#data Data frame tips],  [http://alittleknowledge.wordpress.com/2009/09/11/r-for-pedestrians/ list of R websites]
-
There is a wiki with some good tips [http://wiki.r-project.org/rwiki/doku.php?id=start here].
+
Functions in R can only return one parameter.
-
Examining your data matrix or object, let's say it's called ''datos''
+
 
 +
===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)
  head(datos)
  str(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==
 +
[http://ww2.coastal.edu/kingw/statistics/R-tutorials/formulae.html Understanding model formulae]
 +
 +
[http://ww2.coastal.edu/kingw/statistics/R-tutorials/repeated.html ANOVA with repeated measures] walk-through
-
Don't use the function ''attach''. It seems to leave lots of data in the 'environment' that can cause problems later. Also it makes the code harder to understand.
 
-
===doing ANOVAs etc===
 
[http://www.personality-project.org/r/r.anova.html some aov (ANOVA) explanation]
[http://www.personality-project.org/r/r.anova.html some aov (ANOVA) explanation]
Line 26: Line 73:
I think I had [http://tolstoy.newcastle.edu.au/R/help/04/08/2136.html too many error terms]
I think I had [http://tolstoy.newcastle.edu.au/R/help/04/08/2136.html too many error terms]
[http://books.google.com.au/books?id=ptbcCBSWvvQC&pg=PA359&lpg=PA359&dq=ANOVA+within-subjects++pooled+error+term&source=bl&ots=73eFDsaw8l&sig=ReTGWRjNFGnYQ4DF-D6qAE9qJgQ&hl=en&ei=cKu4Sd7CPIr2sAPSw4Q8&sa=X&oi=book_result&resnum=8&ct=result reducing error terms]
[http://books.google.com.au/books?id=ptbcCBSWvvQC&pg=PA359&lpg=PA359&dq=ANOVA+within-subjects++pooled+error+term&source=bl&ots=73eFDsaw8l&sig=ReTGWRjNFGnYQ4DF-D6qAE9qJgQ&hl=en&ei=cKu4Sd7CPIr2sAPSw4Q8&sa=X&oi=book_result&resnum=8&ct=result reducing error terms]
 +
 +
[http://blog.gribblelab.org/2009/03/09/repeated-measures-anova-using-r/ Anovas with repeated measures] can be complicated in R.
 +
 +
We have some R books in the lab
==Dealing with circular data==
==Dealing with circular data==
Line 33: Line 84:
==Setting up a proxy in R on a Mac==
==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" in your user directory (~ or Users/username/) with the line:
+
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:
<code>
<code>
   Sys.setenv(http_proxy=”http://username:password@tcdproxy.tcd.ie:8080″)
   Sys.setenv(http_proxy=”http://username:password@tcdproxy.tcd.ie:8080″)
Line 40: Line 91:
This information (and more) can be found on [http://www.kenbenoit.net/?p=261 Ken Benoit's webpage]
This information (and more) can be found on [http://www.kenbenoit.net/?p=261 Ken Benoit's webpage]
-
For Sydney Uni, use:
+
If you're at the Camperdown campus of the University of Sydney, use:
<code>
<code>
   Sys.setenv(http_proxy=”http://www-cache.usyd.edu.au:8080″)
   Sys.setenv(http_proxy=”http://www-cache.usyd.edu.au:8080″)
 +
</code>
 +
 +
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:
 +
<code>
 +
  Sys.setenv(http_proxy=”web-cache-ext.usyd.edu.au:8080″)
</code>
</code>

Current revision

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 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.

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″)
Views
Personal tools