Count number of consecutive zeros by group

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Count number of consecutive zeros by group

Carlos Nasher
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


--
-----------------------------------------------------------------
Carlos Nasher
Buchenstr. 12
22299 Hamburg

tel:            +49 (0)40 67952962
mobil:        +49 (0)175 9386725
mail:          [hidden email]

        [[alternative HTML version deleted]]


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Re: Count number of consecutive zeros by group

S Ellison-2


> -----Original Message-----
> 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)

You're probably better off with tapply and a function that returns what you want. You're probably also better off with a data frame name that isn't a function name, so I'll use dfr instead of df...

dfr<- data.frame(x=rpois(500, 1.5), ID=gl(5,100)) #5 ID groups numbered 1-5, equal size but that doesn't matter for tapply

f2 <-   function(x) {
        max( rle(x == 0)$lengths )
}
with(dfr, tapply(x, ID, f2))


S Ellison


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Re: Count number of consecutive zeros by group

arun kirshna
In reply to this post by Carlos Nasher
Hi,
May be this helps:
fun1 <- function(dat){
 lst1 <- lapply(split(dat,dat$ID),function(y){
 rl <- rle(y$x)
 data.frame(ID=unique(y$ID),MAXZero=max(rl$lengths[rl$values==0]))
 })
 do.call(rbind,lst1)
 }

fun1(df)
#  ID MAXZero
#1  1       2
#2  2       2
#3  3       1

A.K.








On Thursday, October 31, 2013 7:22 AM, Carlos Nasher <[hidden email]> 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


--
-----------------------------------------------------------------
Carlos Nasher
Buchenstr. 12
22299 Hamburg

tel:            +49 (0)40 67952962
mobil:        +49 (0)175 9386725
mail:          [hidden email]

    [[alternative HTML version deleted]]

______________________________________________
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and provide commented, minimal, self-contained, reproducible code.


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Re: Count number of consecutive zeros by group

Carlos Nasher
In reply to this post by S Ellison-2
If I apply your function to my test data:

ID <- c(1,1,1,2,2,3,3,3,3)
x <- c(1,0,0,0,0,1,1,0,1)
data <- data.frame(ID=ID,x=x)
rm(ID,x)

f2 <-   function(x) {
  max( rle(x == 0)$lengths )
}
with(data, tapply(x, ID, f2))

the result is
1 2 3
2 2 2

which is not what I'm aiming for. It should be
1 2 3
2 2 1

I think f2 does not return the max of consecutive zeros, but the max of any
consecutve number... Any idea how to fix this?


2013/10/31 S Ellison <[hidden email]>

>
>
> > -----Original Message-----
> > 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)
>
> You're probably better off with tapply and a function that returns what
> you want. You're probably also better off with a data frame name that isn't
> a function name, so I'll use dfr instead of df...
>
> dfr<- data.frame(x=rpois(500, 1.5), ID=gl(5,100)) #5 ID groups numbered
> 1-5, equal size but that doesn't matter for tapply
>
> f2 <-   function(x) {
>         max( rle(x == 0)$lengths )
> }
> with(dfr, tapply(x, ID, f2))
>
>
> S Ellison
>
>
> *******************************************************************
> This email and any attachments are confidential. Any u...{{dropped:24}}

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Re: Count number of consecutive zeros by group

S Ellison-2
> If I apply your function to my test data:
>
....
> the result is
> 1 2 3
> 2 2 2
>
...
> I think f2 does not return the max of consecutive zeros, but the max of any
> consecutve number... Any idea how to fix this?

The toy example of tapply using f2 does indeed return the maximum run lengths irrespective of the value repeated.
If you want to select runs of a particular value, you can select according to use $values element of the rle object, again inside the function.
Modifying to accommodate that (and again avoiding a data frame name the same as a base R  function name - you managed it again!):

dfr <- data.frame(ID = c(1,1,1,2,2,3,3,3,3), x = c(1,0,0,0,0,1,1,0,1))

f3 <-   function(x) {
  runs <- rle(x == 0L) #Often wise to be careful with == and numbers ... see FAQ 7.31
  with(runs, max(lengths[values]))
        #This works because in this case the values in
        #$values are TRUE for x==0 and FALSE otherwise; see ?'[' for why those work
}
with(dfr, tapply(x, ID, f3))

or, more or less equivalently but a shade more generally

f4 <-   function(x, select=0L) {
  runs <- rle(x )
  with(runs, max(lengths[values == select]))
}
with(dfr, tapply(x, ID, f4))

None of this checks that runs of zero exist in a group; if they don't, you'll get warnings and -Inf in the output as max takes maxima of nothing. You can add extra checks inside the function if that bothers you.




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Re: Count number of consecutive zeros by group

Hervé Pagès
In reply to this post by Carlos Nasher
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
>
>
>
>
> ______________________________________________
> [hidden email] 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: [hidden email]
Phone:  (206) 667-5791
Fax:    (206) 667-1319

______________________________________________
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Re: Count number of consecutive zeros by group

William Dunlap
In reply to this post by S Ellison-2
> None of this checks that runs of zero exist in a group; if they don't, you'll get warnings
> and -Inf in the output as max takes maxima of nothing. You can add extra checks inside
> the function if that bothers you.

Just adding a second argument, 0, to the call to max() will take care of that.

Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com


> -----Original Message-----
> From: [hidden email] [mailto:[hidden email]] On Behalf
> Of S Ellison
> Sent: Thursday, October 31, 2013 11:27 AM
> To: Carlos Nasher; [hidden email]
> Subject: Re: [R] Count number of consecutive zeros by group
>
> > If I apply your function to my test data:
> >
> ....
> > the result is
> > 1 2 3
> > 2 2 2
> >
> ...
> > I think f2 does not return the max of consecutive zeros, but the max of any
> > consecutve number... Any idea how to fix this?
>
> The toy example of tapply using f2 does indeed return the maximum run lengths
> irrespective of the value repeated.
> If you want to select runs of a particular value, you can select according to use $values
> element of the rle object, again inside the function.
> Modifying to accommodate that (and again avoiding a data frame name the same as a
> base R  function name - you managed it again!):
>
> dfr <- data.frame(ID = c(1,1,1,2,2,3,3,3,3), x = c(1,0,0,0,0,1,1,0,1))
>
> f3 <-   function(x) {
>   runs <- rle(x == 0L) #Often wise to be careful with == and numbers ... see FAQ 7.31
>   with(runs, max(lengths[values]))
> #This works because in this case the values in
> #$values are TRUE for x==0 and FALSE otherwise; see ?'[' for why those work
> }
> with(dfr, tapply(x, ID, f3))
>
> or, more or less equivalently but a shade more generally
>
> f4 <-   function(x, select=0L) {
>   runs <- rle(x )
>   with(runs, max(lengths[values == select]))
> }
> with(dfr, tapply(x, ID, f4))
>
> None of this checks that runs of zero exist in a group; if they don't, you'll get warnings
> and -Inf in the output as max takes maxima of nothing. You can add extra checks inside
> the function if that bothers you.
>
>
>
>
> *******************************************************************
> This email and any attachments are confidential. Any use...{{dropped:8}}
>
> ______________________________________________
> [hidden email] 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.

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
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Re: Count number of consecutive zeros by group

PIKAL Petr
In reply to this post by Carlos Nasher
Hi

Another option is sapply/split/sum construction

with(data, sapply(split(x, ID), function(x) sum(x==0)))

Regards
Petr


> -----Original Message-----
> From: [hidden email] [mailto:r-help-bounces@r-
> project.org] On Behalf Of Carlos Nasher
> Sent: Thursday, October 31, 2013 6:46 PM
> To: S Ellison
> Cc: [hidden email]
> Subject: Re: [R] Count number of consecutive zeros by group
>
> If I apply your function to my test data:
>
> ID <- c(1,1,1,2,2,3,3,3,3)
> x <- c(1,0,0,0,0,1,1,0,1)
> data <- data.frame(ID=ID,x=x)
> rm(ID,x)
>
> f2 <-   function(x) {
>   max( rle(x == 0)$lengths )
> }
> with(data, tapply(x, ID, f2))
>
> the result is
> 1 2 3
> 2 2 2
>
> which is not what I'm aiming for. It should be
> 1 2 3
> 2 2 1
>
> I think f2 does not return the max of consecutive zeros, but the max of
> any consecutve number... Any idea how to fix this?
>
>
> 2013/10/31 S Ellison <[hidden email]>
>
> >
> >
> > > -----Original Message-----
> > > So I want to get the max number of consecutive zeros of variable x
> > > for
> > each
> > > ID. I found rle() to be helpful for this task; so I did:
> > >
> > > FUN <- function(x) {
> > >   rles <- rle(x == 0)
> > > }
> > > consec <- lapply(split(df[,2],df[,1]), FUN)
> >
> > You're probably better off with tapply and a function that returns
> > what you want. You're probably also better off with a data frame name
> > that isn't a function name, so I'll use dfr instead of df...
> >
> > dfr<- data.frame(x=rpois(500, 1.5), ID=gl(5,100)) #5 ID groups
> > numbered 1-5, equal size but that doesn't matter for tapply
> >
> > f2 <-   function(x) {
> >         max( rle(x == 0)$lengths )
> > }
> > with(dfr, tapply(x, ID, f2))
> >
> >
> > S Ellison
> >
> >
> > *******************************************************************
> > This email and any attachments are confidential. Any
> > u...{{dropped:24}}
>
> ______________________________________________
> [hidden email] 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.

______________________________________________
[hidden email] mailing list
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Re: Count number of consecutive zeros by group

arun kirshna
I think this gives a different result than the one OP asked for:

df1 <- structure(list(ID = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L,
2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), x = c(1, 0,
0, 1, 0, 0, 0, 1, 2, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0)), .Names = c("ID",
"x"), row.names = c(NA, -22L), class = "data.frame")

with(df1, sapply(split(x, ID), function(x) sum(x==0)))

with(df1,tapply(x,list(ID),function(y) {rl <- rle(!y); max(c(0,rl$lengths[rl$values]))}))


A.K.


On Friday, November 1, 2013 6:01 AM, PIKAL Petr <[hidden email]> wrote:
Hi

Another option is sapply/split/sum construction

with(data, sapply(split(x, ID), function(x) sum(x==0)))

Regards
Petr


> -----Original Message-----
> From: [hidden email] [mailto:r-help-bounces@r-
> project.org] On Behalf Of Carlos Nasher
> Sent: Thursday, October 31, 2013 6:46 PM
> To: S Ellison
> Cc: [hidden email]
> Subject: Re: [R] Count number of consecutive zeros by group
>
> If I apply your function to my test data:
>
> ID <- c(1,1,1,2,2,3,3,3,3)
> x <- c(1,0,0,0,0,1,1,0,1)
> data <- data.frame(ID=ID,x=x)
> rm(ID,x)
>
> f2 <-   function(x) {
>   max( rle(x == 0)$lengths )
> }
> with(data, tapply(x, ID, f2))
>
> the result is
> 1 2 3
> 2 2 2
>
> which is not what I'm aiming for. It should be
> 1 2 3
> 2 2 1
>
> I think f2 does not return the max of consecutive zeros, but the max of
> any consecutve number... Any idea how to fix this?
>
>
> 2013/10/31 S Ellison <[hidden email]>
>
> >
> >
> > > -----Original Message-----
> > > So I want to get the max number of consecutive zeros of variable x
> > > for
> > each
> > > ID. I found rle() to be helpful for this task; so I did:
> > >
> > > FUN <- function(x) {
> > >   rles <- rle(x == 0)
> > > }
> > > consec <- lapply(split(df[,2],df[,1]), FUN)
> >
> > You're probably better off with tapply and a function that returns
> > what you want. You're probably also better off with a data frame name
> > that isn't a function name, so I'll use dfr instead of df...
> >
> > dfr<- data.frame(x=rpois(500, 1.5), ID=gl(5,100)) #5 ID groups
> > numbered 1-5, equal size but that doesn't matter for tapply
> >
> > f2 <-   function(x) {
> >         max( rle(x == 0)$lengths )
> > }
> > with(dfr, tapply(x, ID, f2))
> >
> >
> > S Ellison
> >
> >
> > *******************************************************************
> > This email and any attachments are confidential. Any
> > u...{{dropped:24}}
>
> ______________________________________________
> [hidden email] 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.


______________________________________________
[hidden email] 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.


______________________________________________
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Re: Count number of consecutive zeros by group

PIKAL Petr
Hi

Yes you are right. This gives number of zeroes not max number of consecutive zeroes.

Regards
Petr


> -----Original Message-----
> From: arun [mailto:[hidden email]]
> Sent: Friday, November 01, 2013 2:17 PM
> To: R help
> Cc: PIKAL Petr; Carlos Nasher
> Subject: Re: [R] Count number of consecutive zeros by group
>
> I think this gives a different result than the one OP asked for:
>
> df1 <- structure(list(ID = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L,
> 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), x = c(1, 0, 0, 1, 0,
> 0, 0, 1, 2, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0)), .Names = c("ID",
> "x"), row.names = c(NA, -22L), class = "data.frame")
>
> with(df1, sapply(split(x, ID), function(x) sum(x==0)))
>
> with(df1,tapply(x,list(ID),function(y) {rl <- rle(!y);
> max(c(0,rl$lengths[rl$values]))}))
>
>
> A.K.
>
>
> On Friday, November 1, 2013 6:01 AM, PIKAL Petr
> <[hidden email]> wrote:
> Hi
>
> Another option is sapply/split/sum construction
>
> with(data, sapply(split(x, ID), function(x) sum(x==0)))
>
> Regards
> Petr
>
>
> > -----Original Message-----
> > From: [hidden email] [mailto:r-help-bounces@r-
> > project.org] On Behalf Of Carlos Nasher
> > Sent: Thursday, October 31, 2013 6:46 PM
> > To: S Ellison
> > Cc: [hidden email]
> > Subject: Re: [R] Count number of consecutive zeros by group
> >
> > If I apply your function to my test data:
> >
> > ID <- c(1,1,1,2,2,3,3,3,3)
> > x <- c(1,0,0,0,0,1,1,0,1)
> > data <- data.frame(ID=ID,x=x)
> > rm(ID,x)
> >
> > f2 <-   function(x) {
> >   max( rle(x == 0)$lengths )
> > }
> > with(data, tapply(x, ID, f2))
> >
> > the result is
> > 1 2 3
> > 2 2 2
> >
> > which is not what I'm aiming for. It should be
> > 1 2 3
> > 2 2 1
> >
> > I think f2 does not return the max of consecutive zeros, but the max
> > of any consecutve number... Any idea how to fix this?
> >
> >
> > 2013/10/31 S Ellison <[hidden email]>
> >
> > >
> > >
> > > > -----Original Message-----
> > > > So I want to get the max number of consecutive zeros of variable
> x
> > > > for
> > > each
> > > > ID. I found rle() to be helpful for this task; so I did:
> > > >
> > > > FUN <- function(x) {
> > > >   rles <- rle(x == 0)
> > > > }
> > > > consec <- lapply(split(df[,2],df[,1]), FUN)
> > >
> > > You're probably better off with tapply and a function that returns
> > > what you want. You're probably also better off with a data frame
> > > name that isn't a function name, so I'll use dfr instead of df...
> > >
> > > dfr<- data.frame(x=rpois(500, 1.5), ID=gl(5,100)) #5 ID groups
> > > numbered 1-5, equal size but that doesn't matter for tapply
> > >
> > > f2 <-   function(x) {
> > >         max( rle(x == 0)$lengths )
> > > }
> > > with(dfr, tapply(x, ID, f2))
> > >
> > >
> > > S Ellison
> > >
> > >
> > > *******************************************************************
> > > This email and any attachments are confidential. Any
> > > u...{{dropped:24}}
> >
> > ______________________________________________
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> > reproducible code.
>
>
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