[R] Genstat into R - Randomisation test

[Mike Lawrence]

*sigh*

and the elapsed time line should be:

cat('Elapsed time:',proc.time()[1]-start.time)


On Wed, Apr 8, 2009 at 11:35 AM, Mike Lawrence <Mike.Lawrence at dal.ca> wrote:
> *Hits head*
> Of course, the approach taken by your Genstat code of only shuffling
> one variable is sufficient and faster:
>
> n.obs = 100
> ID=rnorm(n.obs)
> CD=rnorm(n.obs)
>
> obs.cor = cor(ID,CD)
>
> num.permutations = 1e4
> perm.cor = rep(NA,num.permutations)
> start.time=proc.time()[1]
> index = 1:n.obs
> for(i in 1:num.permutations){
>        IDorder = sample(index)
>        perm.cor[i] = .Internal(cor(ID[IDorder], CD, 4, FALSE))
> }
> cat('Elapsed time:',start.time-proc.time(1))
> sum(perm.cor>obs.cor)/num.permutations
>
>
> On Wed, Apr 8, 2009 at 11:33 AM, Mike Lawrence <Mike.Lawrence at dal.ca> wrote:
>> "Assuming you have a data frame with columns ID & CD, this should do it"
>>
>> Oops, the code I sent doesn't assume this. It assumes that you have
>> two vectors, ID & CD, as generated in the first 3 lines.
>>
>> On Wed, Apr 8, 2009 at 11:31 AM, Mike Lawrence <Mike.Lawrence at dal.ca> wrote:
>>> Looks like that code implements a non-exhaustive variant of the
>>> randomization test, sometimes called a permutation test. Assuming you
>>> have a data frame with columns ID & CD, this should do it:
>>>
>>> n.obs = 100
>>> ID=rnorm(n.obs)
>>> CD=rnorm(n.obs)
>>>
>>> obs.cor = cor(ID,CD)
>>>
>>> num.permutations = 1e4
>>> perm.cor = rep(NA,num.permutations)
>>> start.time=proc.time()[1]
>>> index = 1:n.obs
>>> for(i in 1:num.permutations){
>>>        IDorder = sample(index)
>>>        CDorder = sample(index)
>>>        perm.cor[i] = .Internal(cor(ID[IDorder], CD[CDorder], 4, FALSE))
>>> }
>>> cat('Elapsed time:',start.time-proc.time(1))
>>> sum(perm.cor>obs.cor)/num.permutations
>>>
>>>
>>> On Wed, Apr 8, 2009 at 10:02 AM, Anne Kempel <kempel at ips.unibe.ch> wrote:
>>>> Hello everybody,
>>>> I have a question. I would like to get a correlation between constitutive
>>>> and induced plant defence which I messured on 30 plant species. So I have
>>>> table with Species, Induced defence (ID), and constitutive defence (CD).
>>>> Since Induced and constitutive defence are not independant (so called
>>>> spurious correlation) I should do a randomisation test. I have a syntax of
>>>> my supervisor in Genstat, but I would really like to try this in R.
>>>>
>>>>
>>>> "data from trade-off.IDCD"
>>>> list
>>>> variate [nval=1000] slope
>>>> calc ID1=ID
>>>>
>>>> graph ID; CD
>>>> calc b=corr(ID; CD)
>>>> calc slope$[1]=b
>>>>
>>>> "slope$[1] is the correlation before permutating the data"
>>>>
>>>> for i=2...1000
>>>>    randomize ID1
>>>>    calc b=corr(CD1; ID1)
>>>>    calc slope$[i]=b
>>>> endfor
>>>>
>>>> hist slope
>>>> describe slope
>>>> quantile [proportion=!(0.0005,0.005, 0.025, 0.975, 0.995,0.9995)]slope
>>>> print slope$[1]
>>>> corr[p=corr] ID,CD
>>>>
>>>>
>>>> DHISTOGRAM [WINDOW=1; ORIENTATION=vertical; KEY=0; BARCOVERING=1.0] slope;
>>>> PEN=2
>>>>
>>>> Does anybody have done something similar and has any idea how to make the
>>>> randomisation part?
>>>> I would be very grateful for any help!!
>>>> Thanks in advance,
>>>> Anne
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Anne Kempel
>>>> Institute of Plant Sciences
>>>> University of Bern
>>>> Altenbergrain 21
>>>> CH-3103 Bern
>>>> kempel at ips.unibe.ch
>>>>
>>>> ______________________________________________
>>>> R-help at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>
>>>
>>>
>>>
>>> --
>>> Mike Lawrence
>>> Graduate Student
>>> Department of Psychology
>>> Dalhousie University
>>>
>>> Looking to arrange a meeting? Check my public calendar:
>>> http://tinyurl.com/mikes-public-calendar
>>>
>>> ~ Certainty is folly... I think. ~
>>>
>>
>>
>>
>> --
>> Mike Lawrence
>> Graduate Student
>> Department of Psychology
>> Dalhousie University
>>
>> Looking to arrange a meeting? Check my public calendar:
>> http://tinyurl.com/mikes-public-calendar
>>
>> ~ Certainty is folly... I think. ~
>>
>
>
>
> --
> Mike Lawrence
> Graduate Student
> Department of Psychology
> Dalhousie University
>
> Looking to arrange a meeting? Check my public calendar:
> http://tinyurl.com/mikes-public-calendar
>
> ~ Certainty is folly... I think. ~
>



-- 
Mike Lawrence
Graduate Student
Department of Psychology
Dalhousie University

Looking to arrange a meeting? Check my public calendar:
http://tinyurl.com/mikes-public-calendar

~ Certainty is folly... I think. ~