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jeff6868

2012-Apr-03 08:52 UTC

[R] filling small gaps of N/A

Hi everybody,

I'm a new R french user. Sorry if my english is not perfect. Hope you'll
understand my problem ;)

I have to work on temperature data (35000 lines in one file) containing some
missing data (N/A). Sometimes I have only 2 or 3 N/A following each other,
but I have also sometimes 100 or 200 N/A following each other. Here's an
example of my data, when I have only small gaps of missing data (2 or 3
N/A):

09/01/2008 12:00   2   1.93   2.93   4.56   5.43
09/01/2008 12:15   2   *3.93*   3.25   4.93   5.56
09/01/2008 12:30   2    NA   3.5   5.06   5.56
09/01/2008 12:45   2    NA   3.68 5.25   5.68
09/01/2008 13:00   2   *4.93 *  3.87   5.56   5.93
09/01/2008 13:15   2   5.93   4.25   5.75   6.06
09/01/2008 13:30   2   3.93   4.56   5.93   6.18

My question is: how can I replace these small gaps of N/A by numeric values?
I would like a fonction which only replace the small gaps (2 or 3 N/A) in my
data, but not the big gaps (more than 5 N/A following each other).

For the moment, i'm trying to do it by working with the time gap between the
2 numeric values surrounding the N/A as following:

imputation <- function(x){
    met = NULL
    
    temp <- met[1] <- x[1]
    
    ind_temp <- 1
    
    tps <- time(x)
   
    for (i in 2:(length(x)) ){
    if((tps[i]-tps[ind_temp] > 1)&(tps[i]-tps[ind_temp]
<4)&(is.na(x[i]))){
    met[i] <- na.approx(x)
    }
    else {
    temp <- met[i] <- x[i]
    ind_temp <- i
    }   
    }

    return(met)
    }

In this example, I would like to apply the function: na.approx(x) on my N/A,
but only when I have maximum 4 N/A following each other.
There's no error, but it doesn't work (it was working in the other way,
when
I had to detect aberrant data and replace it by N/A, but not now). It is
maybe not the good way to solve this problem. I don't have a lot of
experience in R. Maybe there is an easier way to do it...
Does somebody have an idea about it for helping me?
Thanks a lot!


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R. Michael Weylandt

2012-Apr-03 13:24 UTC

head link

[R] filling small gaps of N/A

It seems like you could benefit from using a zoo [time series] object
to hold your data -- then you have a variety of NA filling functions
which work for arbitrarily long gaps. E.g.,

library(zoo)
x <- zoo(1:100, Sys.Date() + 1:100)
x[2:60] <- NA

# Most of these look the same because the data is simple: will give
different results for more complicated examples
na.approx(x)
na.locf(x)
na.spline(x)
na.aggregate(x)
na.fill # Takes more arguments

Hope this helps,
Michael

On Tue, Apr 3, 2012 at 4:52 AM, jeff6868
<geoffrey_klein at etu.u-bourgogne.fr> wrote:> Hi everybody,
>
> I'm a new R french user. Sorry if my english is not perfect. Hope
you'll
> understand my problem ;)
>
> I have to work on temperature data (35000 lines in one file) containing
some
> missing data (N/A). Sometimes I have only 2 or 3 N/A following each other,
> but I have also sometimes 100 or 200 N/A following each other. Here's
an
> example of my data, when I have only small gaps of missing data (2 or 3
> N/A):
>
> 09/01/2008 12:00 ? 2 ? 1.93 ? 2.93 ? 4.56 ? 5.43
> 09/01/2008 12:15 ? 2 ? *3.93* ? 3.25 ? 4.93 ? 5.56
> 09/01/2008 12:30 ? 2 ? ?NA ? 3.5 ? 5.06 ? 5.56
> 09/01/2008 12:45 ? 2 ? ?NA ? 3.68 5.25 ? 5.68
> 09/01/2008 13:00 ? 2 ? *4.93 * ?3.87 ? 5.56 ? 5.93
> 09/01/2008 13:15 ? 2 ? 5.93 ? 4.25 ? 5.75 ? 6.06
> 09/01/2008 13:30 ? 2 ? 3.93 ? 4.56 ? 5.93 ? 6.18
>
> My question is: how can I replace these small gaps of N/A by numeric
values?
> I would like a fonction which only replace the small gaps (2 or 3 N/A) in
my
> data, but not the big gaps (more than 5 N/A following each other).
>
> For the moment, i'm trying to do it by working with the time gap
between the
> 2 numeric values surrounding the N/A as following:
>
> imputation <- function(x){
> ? ?met = NULL
>
> ? ?temp <- met[1] <- x[1]
>
> ? ?ind_temp <- 1
>
> ? ?tps <- time(x)
>
> ? ?for (i in 2:(length(x)) ){
> ? ?if((tps[i]-tps[ind_temp] > 1)&(tps[i]-tps[ind_temp] <>
4)&(is.na(x[i]))){
> ? ?met[i] <- na.approx(x)
> ? ?}
> ? ?else {
> ? ?temp <- met[i] <- x[i]
> ? ?ind_temp <- i
> ? ?}
> ? ?}
>
> ? ?return(met)
> ? ?}
>
> In this example, I would like to apply the function: na.approx(x) on my
N/A,
> but only when I have maximum 4 N/A following each other.
> There's no error, but it doesn't work (it was working in the other
way, when
> I had to detect aberrant data and replace it by N/A, but not now). It is
> maybe not the good way to solve this problem. I don't have a lot of
> experience in R. Maybe there is an easier way to do it...
> Does somebody have an idea about it for helping me?
> Thanks a lot!
>
>
> --
> View this message in context:
http://r.789695.n4.nabble.com/filling-small-gaps-of-N-A-tp4528184p4528184.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> 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.

Gabor Grothendieck

2012-Apr-03 17:30 UTC

head link

[R] filling small gaps of N/A

On Tue, Apr 3, 2012 at 4:52 AM, jeff6868
<geoffrey_klein at etu.u-bourgogne.fr> wrote:> Hi everybody,
>
> I'm a new R french user. Sorry if my english is not perfect. Hope
you'll
> understand my problem ;)
>
> I have to work on temperature data (35000 lines in one file) containing
some
> missing data (N/A). Sometimes I have only 2 or 3 N/A following each other,
> but I have also sometimes 100 or 200 N/A following each other. Here's
an
> example of my data, when I have only small gaps of missing data (2 or 3
> N/A):
>
> 09/01/2008 12:00 ? 2 ? 1.93 ? 2.93 ? 4.56 ? 5.43
> 09/01/2008 12:15 ? 2 ? *3.93* ? 3.25 ? 4.93 ? 5.56
> 09/01/2008 12:30 ? 2 ? ?NA ? 3.5 ? 5.06 ? 5.56
> 09/01/2008 12:45 ? 2 ? ?NA ? 3.68 5.25 ? 5.68
> 09/01/2008 13:00 ? 2 ? *4.93 * ?3.87 ? 5.56 ? 5.93
> 09/01/2008 13:15 ? 2 ? 5.93 ? 4.25 ? 5.75 ? 6.06
> 09/01/2008 13:30 ? 2 ? 3.93 ? 4.56 ? 5.93 ? 6.18
>
> My question is: how can I replace these small gaps of N/A by numeric
values?
> I would like a fonction which only replace the small gaps (2 or 3 N/A) in
my
> data, but not the big gaps (more than 5 N/A following each other).
>
Try na.locf, na.approx or na.spline in the zoo package noting the
maxgap= argument on each.

-- 
Statistics & Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com

jeff6868

2012-Apr-04 08:20 UTC

head link

[R] filling small gaps of N/A

Wow, thank you for all your answers.

You were completely right michael. Well, it's my fault. I didn't
understood
your 2nd reply, when you were talking about arguments for larger gaps. I
thought it was for deleting big gaps too. I apologize.
It was too easy in fact. I also didn't noticed the argument
"maxgap" of the
function. 
Finally, it works perfectly only with this:

require(zoo)

    imputation <- function(x){
    met <- na.approx(x, maxgap = 4)

    return(met)
    }
    
    data <- myts[,2:5]
    myts[,2:5]<-apply(data,2,imputation)

Sorry for my stupidity. I'll try to be more careful next time, for such
small problems (when I was thinking it would be a big one) ;).
Well, thank you very much michael and the other repliers, and thank you for
having spared a bit of your time for me!

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View this message in context:
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