[R] Need a vectorized way to avoid two nested FOR loops
Bert Gunter
gunter.berton at gene.com
Thu Oct 8 18:49:02 CEST 2009
If I understand your intent, I believe you can get what you want much faster
(no interpreted loops and linear times) by looking at this slightly
differently.
First of all, the choice of columns is unimportant, as indexing can be used
to create a data frame containing only the columns of interest. So I think
you can abstract your request to: group the rows of a data frame so that all
rows in a group "match." Now the problem here is exactly what you mean by
"match." If the data are numeric, finite precision arithmetic requires one
to ask whether you mean **exactly equal** or just equal within a tolerance.
I shall assume the former, but the latter is often what one wants. It is a
little more difficult to handle, but one way to do it with the present
approach is to first round to a few digits that represent the tolerance and
then proceed with the rounded values.
As always (and as recommended by the posting guide !) a small reproducible
example is helpful:
## Create a data frame with groups of identical rows.
z <- data.frame(matrix(rnorm(60),ncol=3))[sample(20,50,repl=TRUE),]
## now create a factor column of "id's" in which identical columns
## have identical id's (a hash)
id <- factor(do.call(paste,c(z,sep="+")))
## The levels of the factors now "index" groups of rows that "match"
## They can be easily accessed in a variety of way, e.g.
as.numeric(id)
## gives all rows of each group of matching rows
## the same integer index.
etc.
This all requires only linear time.
Hope this helps -- or my apologies if I have misinterpreted what was
requested.
Bert Gunter
Genentech Nonclinical Biostatistics
-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On
Behalf Of Dimitris Rizopoulos
Sent: Thursday, October 08, 2009 6:28 AM
To: joris meys
Cc: r-help at r-project.org; Rama Ramakrishnan
Subject: Re: [R] Need a vectorized way to avoid two nested FOR loops
Another approach is:
n <- 20
set.seed(2)
x <- as.data.frame(matrix(sample(1:2, n*6, TRUE), nrow = n))
x.col <- c(1, 3, 5)
values <- do.call(paste, c(x[x.col], sep = "\r"))
out <- lapply(seq_along(ind), function (i) {
ind <- which(values == values[i])
ind[!ind %in% i]
})
out
Best,
Dimitris
joris meys wrote:
> Neat piece of code, Jim, but it still uses a nested loop. If you order
> the matrix first, you only need one passage through the whole matrix
> to find the information you need.
>
> Off course I don't take into account the ordering. If the ordering
> algorithm doesn't work in linear time, then it doesn't really matter I
> guess. The limiting step would become the ordering algorithm.
>
> Kind regards
> Joris
>
>
>
> On Thu, Oct 8, 2009 at 2:24 PM, jim holtman <jholtman at gmail.com> wrote:
>> I answered the wrong question. Here is the code to find all the
>> matches for each row:
>>
>> n <- 20
>> set.seed(2)
>> # create test dataframe
>> x <- as.data.frame(matrix(sample(1:2,n*6, TRUE), nrow=n))
>> x
>> x.col <- c(1,3,5)
>>
>> # match against all the other rows
>> x.match1 <- apply(x[, x.col], 1, function(a){
>> .mat <- which(apply(x[, x.col], 1, function(z){
>> all(a == z)
>> }))
>> })
>>
>> # remove matches to itself
>> x.match2 <- lapply(seq(length(x.match1)), function(z){
>> x.match1[[z]][!(x.match1[[z]] %in% z)]
>> })
>> # x.match2 contains which rows indices match
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On Wed, Oct 7, 2009 at 3:52 PM, Rama Ramakrishnan <rama at alum.mit.edu>
wrote:
>>> Hi Friends,
>>>
>>> I have a data frame d. Let vars be the column indices for a subset of
the
>>> columns in d (e.g., vars <- c(1,3,4,8))
>>>
>>> For each row r in d, I want to collect all the other rows in d that
match
>>> the values in row r for just the columns in vars.
>>>
>>> The naive way to do this is to have a for loop stepping through each row
in
>>> d, and within the loop have another loop going through all the rows
again,
>>> checking for equality. This is quadratic in the number of rows and takes
way
>>> too long. Is there a better, "vectorized" way to do this?
>>>
>>> Thanks in advance!
>>>
>>> Rama Ramakrishnan
>>>
>>> ______________________________________________
>>> 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.
>>>
>>
>>
>> --
>> Jim Holtman
>> Cincinnati, OH
>> +1 513 646 9390
>>
>> What is the problem that you are trying to solve?
>>
>> ______________________________________________
>> 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.
>>
>
> ______________________________________________
> 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.
>
--
Dimitris Rizopoulos
Assistant Professor
Department of Biostatistics
Erasmus University Medical Center
Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands
Tel: +31/(0)10/7043478
Fax: +31/(0)10/7043014
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