[R] Vincentizing Reaction Time data in R
Gabriel WEINDEL
gabriel.weindel at gmail.com
Mon May 25 11:55:04 CEST 2015
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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