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.wein...@gmail.com > Sent: Mon, 25 May 2015 11:55:04 +0200 > To: jrkrid...@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.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) >>>>>> >>>> >>>> ____________________________________________________________ >>>> Can't remember your password? 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