Re: [R] Fwd: rarefy a matrix of counts

From: Petr Pikal <petr.pikal_at_precheza.cz>
Date: Wed 11 Oct 2006 - 14:43:23 GMT

Hi

a litle bit different story. But

x1 <- sample(c(rep("red",400),rep("green", 100), rep("black",300)),100)

is maybe close. With data frame (if it is not big)

> DF

  color sample1 sample2 sample3

1   red     400     300    2500
2 green     100       0     200
3 black     300    1000     500

x <- data.frame(matrix(NA,100,3))
for (i in 2:ncol(DF)) x[,i-1] <- sample(rep(DF[,1], DF[,i]),100) if you want result in data frame
or
x<-vector("list", 3)
for (i in 2:ncol(DF)) x[[,i-1]] <- sample(rep(DF[,1], DF[,i]),100)

if you want it in list. Maybe somebody is clever enough to discard for loop but you said you have 80 columns which shall be no problem.

HTH
Petr

On 11 Oct 2006 at 10:11, Brian Frappier wrote:

Date sent:      	Wed, 11 Oct 2006 10:11:33 -0400
From:           	"Brian Frappier" <brian.frappier@gmail.com>
To:             	"Petr Pikal" <petr.pikal@precheza.cz>
Subject:        	Fwd: [R] rarefy a matrix of counts

> ---------- Forwarded message ----------
> From: Brian Frappier <brian.frappier@gmail.com>
> Date: Oct 11, 2006 10:10 AM
> Subject: Re: [R] rarefy a matrix of counts
> To: r-help@stat.math.ethz.ch
>
> Hi Petr,
>
> Thanks for your response. I have data that looks like the following:
>
> sample 1 sample 2 sample 3 ....
> red candy 400 300 2500
> green candy 100 0 200
> black candy 300 1000 500
>
> I don't want to randomly select either the samples (columns) or the
> "candy" types (rows), which sample as you state would allow me.
> Instead, I want to randomly sample 100 candies from each sample and
> retain info on their associated type. I could make a list of all the
> candies in each sample:
>
> sample 1
> red
> red
> red
> red
> green
> green
> black
> red
> black
> ...
>
> and then randomly sample those rows. Repeat for each sample. But, I
> am not sure how to do that without alot of loops, and am wondering if
> there is an easier way in R. Thanks! I should have laid this out in
> the first email...sorry.
>
>
> On 10/11/06, Petr Pikal <petr.pikal@precheza.cz> wrote:
> >
> > Hi
> >
> > I am not experienced in Matlab and from your explanation I do not
> > understand what exactly do you want. It seems that you want randomly
> > choose a sample of 100 rows from your martix, what can be achived by
> > sample.
> >
> > DF<-data.frame(rnorm(100), 1:100, 101:200, 201:300)
> > DF[sample(1:100, 10),]
> >
> > If you want to do this several times, you need to save your result
> > and than it depends on what you want to do next. One suitable form
> > is list of matrices the other is array and you can use for loop for
> > completing it.
> >
> > HTH
> > Petr
> >
> >
> > On 10 Oct 2006 at 17:40, Brian Frappier wrote:
> >
> > Date sent: Tue, 10 Oct 2006 17:40:47 -0400
> > From: "Brian Frappier" <brian.frappier@gmail.com>
> > To: r-help@stat.math.ethz.ch Subject:
> > [R] rarefy a matrix of counts
> >
> > > Hi all,
> > >
> > > I have a matrix of counts for objects (rows) by samples (columns).
> > > I aimed for about 500 counts in each sample (I have about 80
> > > samples) and would now like to rarefy these down to 100 counts in
> > > each sample using simple random sampling without replacement. I
> > > plan on rarefying several times for each sample. I could do the
> > > tedious looping task of making a list of all objects (with its
> > > associated identifier) in each sample and then use the wonderful
> > > "sampling" package to select a sub-sample of 100 for each sample
> > > and thereby get a logical vector of inclusions. I would then
> > > regroup the resulting logical vector into a vector of counts by
> > > object, rinse and repeat several times for each sample.
> > >
> > > Alternately, using the same list, I could create a random index of
> > > integers between 1 and the number of objects for a sample (without
> > > repeats) and then select those objects from the list. Again,
> > > rinse and repeat several time for each sample.
> > >
> > > Is there a way to directly rarefy a matrix of counts without
> > > having to create a list of objects first? I am trying to switch
> > > to R from Matlab and am trying to pick up good programming habits
> > > from the start.
> > >
> > > Much appreciation!
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > ______________________________________________
> > > R-help@stat.math.ethz.ch 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.
> >
> > Petr Pikal
> > petr.pikal@precheza.cz
> >
> >
>

Petr Pikal
petr.pikal@precheza.cz



R-help@stat.math.ethz.ch 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. Received on Thu Oct 12 01:12:46 2006

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.1.8, at Wed 11 Oct 2006 - 15:30:09 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help. Please read the posting guide before posting to the list.