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.wein...@gmail.com
Sent: Thu, 21 May 2015 17:50:02 +0200
To: jrkrid...@inbox.com, yishinlin...@gmail.com, gunter.ber...@gene.com,
djnordl...@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: yishinlin...@gmail.com
Sent: Thu, 21 May 2015 10:13:54 +0800
To: gabriel.wein...@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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