[R-lang] Re: Coding

Sat Jun 19 14:39:53 PDT 2010

Thanks for clearing that up!

If anyone comes across the UCLA Academic Techonlogy Services website when
searching for coding schemes be sure to pay close attention to what "method"
the coding table is under.  Always choose Method 2, otherwise you end up
setting up codes that appear to be for a SAS-specific way of setting up
coding variables for contrasts.

~Maureen

On Sat, Jun 19, 2010 at 4:16 PM, Reinhold Kliegl  <http://www.ats.ucla.edu/>
<kliegl@uni-potsdam.de> wrote:

> This is an incorrect contrast specification for successive differences! The
> correct specification depends on the number of levels. The simplest way to
> get the correct difference is to use contr.sdif from MASS. In this case:
>
> library(MASS)
> contr.sdif(3)
>
> I realize this is very counterintuitive for many people, but see Venerables
> & Ripley (2002, section 6.2 ).
>
> Reinhold Kliegl
>
> On 19.06.2010, at 21:15, Maureen Gillespie wrote:
>
> Hey Peter, Steve, and r-lang,
>    Not sure if I'm going to be able to answer your questions, but I'll give
> it a shot.  I think Steve is right in the sense that forward difference
> coding would get you the answers to the questions about whether one level is
> significantly different that the previous level (i.e., if D > E1, rather
> than is D > the mean of E1, F1, E2, F2, which is what Helmert tests).
> However, forward difference coding does not produce orthogonal coding
> variables - i.e., below, the sum of the dot products of AvB and BvC is != 0,
> same goes for BvC and CvD.  So, there will be some degree of colinearity
> among coding variables if you use this coding scheme, so that's an issue for
> getting estimates you can trust.
>
>     AvB    BvC     CvD
> A   .5        0          0
> B  -.5       .5          0
> C   0       -.5          .5
> D   0        0          -.5
>
>
> As for your second question about inferring whether E>F even though your
> EvF contrast isn't significant... I think that there is a problem doing that
> because in the first model where you established an order with Helmert
> coding, you could end up in a situation like Steve alluded to.  In the below
> hypothetical example, E1vF1E2F2 is likely to be significant  (.8 > .45), as
> well as F1vE2F2 (.78 > .29). But this asks nothing about whether E > F,
> overall.  In this example, it's likely there isn't a difference (.55 >
> .53).
>
> E1 =  .80
> F1 =  .78
> E2 =  .30
> F2 =  .28
>
>
> Without knowing your data, but following the adage that your model can only
> answer you what you ask it,  I would say that second model better tests your
> actual hypotheses --  it's the only one that actually asks the questions you
> want to know about EvF and 1v2. It also does ask some questions about order:
> Are ABC different than DE1F1E2F2?  Is D different than the Es and Fs
> combined?  If the theories/conditions you're testing only need to show those
> patterns to be supported/refuted, then you should be in good shape. :)
>
>
>
> As it seems that contrast coding questions regularly appear on this mailing
> list, I've listed references below that I have found useful when learning
> about these issues.   If anyone knows of any more, please add on!
>
> Cohen,  Cohen, West, Aiken (2002). Applied multiple regression/ correlation
> analysis for the behavioral sciences (Chapters 8 & 9).
>
> Kaufman & Sweet (1974). Contrast coding in least squares regression
> analysis. American Educational Research Journal, 11, 359-377.
>
> Serlin & Levin (1985). Teaching how to derive directly interpretable coding
> schemes for multiple regression. Journal of Educational Statistics, 10,
> 223-238.
>
> Wendorf (2004). Primer on multiple regression coding: Common forms and the
> additional case of repeated contrasts. Understanding Statistics, 3, 47-57.
>
>
> ~Maureen Gillespie
>
>
>
>
>
> On Fri, Jun 18, 2010 at 5:01 PM, Peter Graff <graff@mit.edu> wrote:
>
>> Dear R-lang,
>>
>> I have a question regarding the interpretation of different coding schemes
>> in a regression model. My experiment compares 8 different levels of a single
>> independent variable. Additionally, it is possible to conceive of 4 of these
>> 8 levels as a mini-2x2 within the 8 level variable:
>>
>> Cells: A, B, C, D, E-1, E-2, F-1, F-2
>>
>> I hypothesize the following ordering (which is substantiated by the
>> overall means in the different conditions):
>>
>> ABC>D>E1>F1>E2>F2
>>
>> Additionally, I hypothesize that E>F and 1>2. I have implemented 2
>> different models to test these hypotheses and I would like to hear your take
>> on what the correct interpretation of the results is. In model 1 have have
>> Helmert-coded the hypothesized ordering in terms of the following five
>> contrasts:
>>
>> ABCvDE1F1E2F2
>> DvE1F1E2F2
>> E1vF1E2F2
>> F1vE2F2
>> E2vF2
>>
>> All Helmert-contrasts are significant. In model 2 I have used the
>> following contrasts instead:
>>
>> ABCvDE1F1E2F2
>> DvE1F1E2F2
>> EvF
>> 1v2
>>
>> All contrasts except EvF are significant. Collinearity is minimal in both
>> models (all correlations below |.2|)
>>
>> Is it fair to say that the ABC>D>E1>F1>E2>F2 has been substantiated by the
>> experiment and thus infer that E>F, even though the EvF contrast is not
>> significant in a differently coded model?
>>
>> Thank you very much in advance for your help,
>>
>> Best,
>>
>> Peter Graff
>>
>
>
>
> --
> Maureen Gillespie, MA
>
> Graduate Student
> Northeastern University
> Department of Psychology
> 125 Nightingale Hall
> 360 Huntington Ave.
> Boston, MA 02115
> Office: 617-373-3077
> Cell: 603-397-7127
>
> http://sites.google.com/site/gillespiemaureen/
>
>
>   ----
> Reinhold Kliegl, Dept. of Psychology, University of Potsdam,
> Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
> phone: +49 331 977 2868, fax: +49 331 977 2793
> http://www.psych.uni-potsdam.de/people/kliegl/
>
>
>
>
>
>

-- 
Maureen Gillespie, MA

Graduate Student
Northeastern University
Department of Psychology
125 Nightingale Hall
360 Huntington Ave.
Boston, MA 02115
Office: 617-373-3077
Cell: 603-397-7127

http://sites.google.com/site/gillespiemaureen/
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