[R] Vincentizing Reaction Time data in R

John Kane jrkrideau at inbox.com
Mon May 25 17:31:19 CEST 2015 

Thanks Gabriel, 
That new method you found looks interesting even if it is a long way from anything I am likely to be doing.

Re my code below.  It looks like  vincentization is actually straight-forward.  I used bins = 10 since it was a convenient number.  I imagine if one was to actually turn this into a function it would not be that hard to come up with some formula to calculate bin size although statisticians may be wincing when they read that last remark.

I played a little more with the idea and it really looks pretty easy to  vincentizatise a data.frame.  

John Kane
Kingston ON Canada


> -----Original Message-----
> From: gabriel.weindel at gmail.com
> Sent: Mon, 25 May 2015 11:55:04 +0200
> To: jrkrideau at inbox.com
> Subject: Re: [R] Vincentizing Reaction Time data in R
> 
> Hi John,
> 
> Sorry for the response delay.
> 
> I found a way to do it in a slight different way :
> http://www.nicebread.de/comparing-all-quantiles-of-two-distributions-simultaneously/
> 
> You're right with the application. I just put some comments in your post.
> 
> Thank you for your time. I will now use the quantile comparison for my
> statistic test, and perform vincentization later for my thesis result.
> If I create something useful I will share it on this topic.
> 
> Gabriel
> 
>> Do I  understand the idea behind 'vincentizing' reaction times?
>> I don't want to work through the Ratcliff, (1979)  paper unless I must.
>> 
>> Let's say we have a subject , s1, with 50 rt scores.
>> We sort the scores from high to low (or low to high , it makes no
>> difference) then we split the 50 scores into quantiles (let's say
>> deciles) and calculate the mean/decile?
>> 
>> Repeat for each subject.  We now have the 'vincentized' means.
>> 
>> That's it?
> 
> Yes, the point is to get rid of the shape blindness of, for example
> ANOVA sample mean, by using quantiles to also reduce influence of
> outliers.
>> 
>> Example, of what I understand for just for one subject (s1)
>> 
>> # install plyr package if not already installed
>> install.packages("plyr")
>> #=======================================
>> 
>> library(plyr)
>> 
>> # create some sciency looking sample data
>> rtmatter   <- c (seq(0.50 , 1.50, 0.01), seq(0.55, 1.55,  0.01) )
>> str(rtmatter)  # verify it looks sciencey
>> 
>> # create one subject
>> s1  <-  sample(rtmatter, 50, replace = TRUE)
>> 
>> # calculate 'vincentized' means for s1
>> s1  <-  sort(s1)
>> c1  <-  cut(s1, 10, right = TRUE)
> 
> You cut the distribution in 10, the use of vincentization fix the cut to
> n ≥ bins. So a formula should be used to compute it for each set of data
> 
>> ss1  <-  data.frame(c1,  s1)
>> vince1   <-   ddply(ss1, .(c1), summarize, decile.mean = mean(s1) )
>> vince1
>> 
> That's right too.
>> 
>> John Kane
>> Kingston ON Canada
>> 
>> 
>>> -----Original Message-----
>>> From: gabriel.weindel at gmail.com
>>> Sent: Thu, 21 May 2015 17:50:02 +0200
>>> To: jrkrideau at inbox.com, yishinlin001 at gmail.com,
>>> gunter.berton at gene.com,
>>> djnordlund at frontier.com
>>> Subject: Re: [R] Vincentizing Reaction Time data in R
>>> 
>>> Bert : Thank you for your advice, it would be a little bit difficult to
>>> do it for my master thesis but, if I want to go further with a PhD
>>> thesis (and I do want), I would probably follow your advice and get in
>>> touch with a statistician.
>>> 
>>> Yishin : Thank you very much for the references, I will definitively
>>> read the papers you quote. I'm already a little bit aware of the
>>> misuses
>>> possible with the vincentization in particular thanks to the paper of
>>> Rouder and Speckman (2004) and it seems to fit with my design. No
>>> problem if you want to keep the code but I have to tell you that it's
>>> our first semester using R and the teacher surely didn't thought that
>>> we
>>> will run out of available code with our experiment. Like John guessed
>>> the purpose of the course was to give a first view of R to get over the
>>> temptation of SPSS, my bad if I want to avoid biased statistics like
>>> sample mean ANOVA's on RT.
>>> 
>>> Dan : Thank you for your tip, this sure will help but I'm quiet at the
>>> beginning of my R skills so I hardly trust myself to do it on my own,
>>> but I can sure give it a try.
>>> 
>>> John : I had the same assumption but my research director warned me
>>> that
>>> I might run out of time for my first presentation by doing so but
>>> fairly
>>> enough for my master thesis. But again like I said to Dan I'm quiet
>>> concerned by my actual R skill.
>>> 
>>> Anyway I have to say that I'm really glad to see how much help you can
>>> get by using the r-help mailing-list.
>>> 
>>> Regards,
>>> Gabriel
>>> 
>>> Le 21/05/2015 15:52, John Kane a écrit :
>>>> In line
>>>> 
>>>> John Kane
>>>> Kingston ON Canada
>>>> 
>>>> 
>>>>> -----Original Message-----
>>>>> From: yishinlin001 at gmail.com
>>>>> Sent: Thu, 21 May 2015 10:13:54 +0800
>>>>> To: gabriel.weindel at gmail.com
>>>>> Subject: Re: [R] Vincentizing Reaction Time data in R
>>>>> 
>>>>> On Wed, 20 May 2015 18:13:17 +0800,
>>>>> Hi Gabriel,
>>>>> 
>>>>> As far as I could recall, there isn't an R package that has
>>>>> explicitly
>>>>> implemented "vincentization". You definitively can find some code
>>>>> segments/functions that have implemented "vincentize" on the web. But
>>>>> you
>>>>> should verify if they do exactly what you wish to do.  If you could
>>>>> look
>>>>> at the question from percentile/quantle perspective, it would not
>>>>> take
>>>>> you too much time to realise that they are similar.  I would suggest
>>>>> you
>>>>> to read, as John Kane suggested, Prof. Ratcliff's 1979 paper.
>>>>> Another
>>>>> paper that may be very helpful is Prof van Zandt's 2000 RT paper.
>>>>> 
>>>>> However, you should be aware that there are some different
>>>>> implementation
>>>>> of "vincentization", and it is debatable, if not problematic, to use
>>>>> it,
>>>>> rather than other more general quantile methods. It would help you to
>>>>> understand not only how to do vincentization, but also why/why not if
>>>>> you
>>>>> could read papers from Jeff Rouder's as well as from Heathcote's and
>>>>> Brown's lab.
>>>>> 
>>>>> Sorry that I hesitate to give you the code, because this looks like
>>>>> part
>>>>> of your course works.  It would be more rewarding for you, if you
>>>>> could
>>>>> figure out by yourself.
>>>>> 
>>>>> Yishin
>>>>> 
>>>> While I agree the exercise is likely to be a good learning experience
>>>> I
>>>> don't see this as the equivalent of course work.
>>>> 
>>>> If Gabriel (the OP) was tasked with implementing  "vincentization" in
>>>> R
>>>> then, strictly speaking it is course work but if I understand him the
>>>> requirement is to do his work in R rather than Minitab.  If such a
>>>> function existed in an existing R package than he could have simply
>>>> plugged in the numbers et voilà, done.
>>>> 
>>>> The tenor of the question did not suggest this and it would require
>>>> the
>>>> stats instructor to know that there was no  "vincentization" function
>>>> anywhere among the, what, a thousand or so packages? And if the OP was
>>>> working on his own data as part of the course then the instructor
>>>> might
>>>> have little or no idea of exactly what functions are needed
>>>> 
>>>> The course  strikes me more as an effort to get psychologists away
>>>> from
>>>> SPSS which often seems to be the only software package anyone knows.
>>>> 
>>>> 
>>>>> Gabriel WEINDEL wrote:
>>>>>> 
>>>>>> Dear all,
>>>>>> 
>>>>>> For my master thesis, I'm currently working in cognitive
>>>>>> neuroscience
>>>>>> on executive control through measurement of reaction time and I need
>>>>>> to get my data 'vincentized' with an exclusive use of R set by my
>>>>>> statistic teacher for a test purpose, for this reason I can't use
>>>>>> the
>>>>>> python code the lab team usually uses.
>>>>>> Despite a dozen hours of research I couldn't find any package or
>>>>>> R-code which would allow the use of vincentization, that's why I'm
>>>>>> querying help on the R forum.
>>>>>> 
>>>>>> So has anyone ever used vincentization in R ?
>>>>>> 
>>>>>> Best regards,
>>>>>> 
>>>>>> --
>>>>>> Gabriel Weindel
>>>>>> Master student in Neuropsychology - Aix-Marseille University
>>>>>> (France)
>>>>>> 
>>>> 
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