Hi Carlos,
With Bioconductor, this can simply be done with:
library(IRanges)
ID <- Rle(1:3, c(3,2,4))
x <- Rle(c(1,0,0,0,0,1,1,0,1))
groups <- split(x, ID)
idx <- groups == 0
Then:
> max(runLength(idx)[runValue(idx)])
1 2 3
2 2 1
Should be fast even with hundreds of thousands of groups (should take
< 10 sec).
HTH,
H.
On 10/31/2013 04:20 AM, Carlos Nasher wrote:
Dear R-helpers,
I need to count the maximum number of consecutive zero values of a variable
in a dataframe by different groups. My dataframe looks like this:
ID <- c(1,1,1,2,2,3,3,3,3)
x <- c(1,0,0,0,0,1,1,0,1)
df <- data.frame(ID=ID,x=x)
rm(ID,x)
So I want to get the max number of consecutive zeros of variable x for each
ID. I found rle() to be helpful for this task; so I did:
FUN <- function(x) {
rles <- rle(x == 0)
}
consec <- lapply(split(df[,2],df[,1]), FUN)
consec is now an rle object containing lists für each ID that contain
$lenghts: int as the counts for every consecutive number and $values: logi
indicating if the consecutive numbers are zero or not.
Unfortunately I'm not very experienced with lists. Could you help me how to
extract the max number of consec zeros for each ID and return the result as
a dataframe containing ID and max number of consecutive zeros?
Different approaches are also welcome. Since the real dataframe is quite
large, a fast solution is appreciated.
Best regards,
Carlos
______________________________________________
R-help@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.
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
______________________________________________
R-help@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.
