[R] Vincentizing Reaction Time data in R
John Kane
jrkrideau at inbox.com
Fri May 22 13:17:58 CEST 2015
Hi, 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?
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)
ss1 <- data.frame(c1, s1)
vince1 <- ddply(ss1, .(c1), summarize, decile.mean = mean(s1) )
vince1
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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