[R] Replace missing value within group with non-missing value
Rui Barradas
ruipbarradas at sapo.pt
Sat Apr 6 20:27:07 CEST 2013
Hello,
With the attached file, I could reproduce the error but I think the
added line does the trick.
Rui Barradas
Em 06-04-2013 19:20, arun escreveu:
> Hi,
>
> dat<- read.csv("test1.csv",sep=",",stringsAsFactors=FALSE)
> sp <- split(dat, list(dat$dn, dat$obs))
>
> sp1<-sp[lapply(sp,nrow)!=0] #added here
> names(sp1) <- NULL
>
>
> tmp<- lapply(sp1,function(x){
> idx<- which(!is.na(x$mth))[1]
> x$mth<- x$mth[idx]
> x
>
> }
> )
>
>
> res<- do.call(rbind,tmp)
> row.names(res)<-1:nrow(res)
> dim(res)
> #[1] 1200 6
> dim(dat)
> #[1] 1200 6
> head(res)
> # X dn obs choice br mth
> #1 1 4 1 0 1 487
> #2 2 4 1 0 2 487
> #3 3 4 1 0 3 487
> #4 4 4 1 0 4 487
> #5 5 4 1 0 5 487
> #6 6 4 1 1 6 487
>
> A.K.
>
> ----- Original Message -----
> From: "Leask, Graham" <g.leask at aston.ac.uk>
> To: Rui Barradas <ruipbarradas at sapo.pt>
> Cc: arun <smartpink111 at yahoo.com>; "r-help at r-project.org" <r-help at r-project.org>
> Sent: Saturday, April 6, 2013 1:44 PM
> Subject: RE: [R] Replace missing value within group with non-missing value
>
> Hi Rui,
>
> I have just pasted this direct and rerun. I still get the same error.
> I am running this on the full length dataset.
>
> dim [1] 255030 5
>
> I attach the first few rows of the file.
>
> Error pasted below.
> I am using version 2.15.2 on a windows 7 machine.
>
>> sp <- split(dat, list(dat$dn, dat$obs))
>> names(sp) <- NULL
>> tmp <- lapply(sp, function(x){
> + idx <- which(!is.na(x$mth))[1]
> + if(length(idx) > 0)
> + x$mth <- x$mth[idx]
> + x
> + })
> Error in `$<-.data.frame`(`*tmp*`, "mth", value = NA_real_) :
> replacement has 1 rows, data has 0
>> do.call(rbind,tmp)
> Error in do.call(rbind, tmp) : object 'tmp' not found
>
> Any thoughts on what could be causing this anomaly?
>
>
> -----Original Message-----
> From: Rui Barradas [mailto:ruipbarradas at sapo.pt]
> Sent: 06 April 2013 18:24
> To: Leask, Graham
> Cc: arun; r-help at r-project.org
> Subject: Re: [R] Replace missing value within group with non-missing value
>
> Hello,
>
> I've just run my code with your data and found no error. Anyway, try replacing the lapply instructi
>
>
> on with this.
>
>
> tmp <- lapply(sp, function(x){
> idx <- which(!is.na(x$mth))[1]
> if(length(idx) > 0)
> x$mth <- x$mth[idx]
> x
> })
>
>
> Rui Barradas
>
> Em 06-04-2013 18:12, Leask, Graham escreveu:
>> Hi Arun,
>>
>> How odd. Directly pasting the code from your email precisely repeats the error.
>> See below. Any thoughts on the cause of this anomaly?
>>
>>> dput(head(dat,50))
>> structure(list(dn = c(4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
>> 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
>> 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4), obs = c(1, 1,
>> 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4,
>> 4, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 8, 8,
>> 8, 8, 8, 8, 9, 9), choice = c(0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0,
>> 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0,
>> 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0), br = c(1,
>> 2, 3, 4, 5, 6, 1, 2, 3, 4, 5, 6, 1, 2, 3, 4, 5, 6, 1, 2, 3, 4,
>> 5, 6, 1, 2, 3, 4, 5, 6, 1, 2, 3, 4, 5, 6, 1, 2, 3, 4, 5, 6, 1,
>> 2, 3, 4, 5, 6, 1, 2), mth = c(NA, NA, NA, NA, NA, 487, NA, NA,
>> 488, NA, NA, NA, NA, NA, NA, NA, NA, 488, NA, NA, 489, NA, NA,
>> NA, NA, NA, NA, NA, NA, 489, NA, NA, NA, NA, NA, 489, NA, NA,
>> NA, NA, NA, 490, NA, NA, NA, NA, NA, 491, NA, NA)), .Names = c("dn",
>> "obs", "choice", "br", "mth"), row.names = c("1", "2", "3", "4",
>> "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15",
>> "16", "17", "18", "19", "20", "21", "22", "23", "24", "25", "26",
>> "27", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37",
>> "38", "39", "40", "41", "42", "43", "44", "45", "46", "47", "48",
>> "49", "50"), class = "data.frame")
>>> sp <- split(dat, list(dat$dn, dat$obs))
>>> names(sp) <- NULL
>>> tmp <- lapply(sp, function(x){
>> + idx <- which(!is.na(x$mth))[1]
>> + x$mth <- x$mth[idx]
>> + x
>> + })
>> Error in `$<-.data.frame`(`*tmp*`, "mth", value = NA_real_) :
>> replacement has 1 rows, data has 0
>>> head(do.call(rbind, tmp),7)
>> Error in do.call(rbind, tmp) : object 'tmp' not found
>>
>> Best wishes
>>
>>
>> Graham
>>
>> -----Original Message-----
>> From: arun [mailto:smartpink111 at yahoo.com]
>> Sent: 06 April 2013 17:25
>> To: Leask, Graham
>> Cc: Rui Barradas
>> Subject: Re: [R] Replace missing value within group with non-missing value
>>
>> Hello,
>> By running Rui's code, I am getting this:
>> sp <- split(dat, list(dat$dn, dat$obs))
>> names(sp) <- NULL
>> tmp <- lapply(sp, function(x){
>> idx <- which(!is.na(x$mth))[1]
>> x$mth <- x$mth[idx]
>> x
>> })
>> head(do.call(rbind, tmp),7)
>> dn obs choice br mth
>> 1 4 1 0 1 487
>> 2 4 1 0 2 487
>> 3 4 1 0 3 487
>> 4 4 1 0 4 487
>> 5 4 1 0 5 487
>> 6 4 1 1 6 487
>> 7 4 2 0 1 488
>>
>> Couldn't reproduce the error you cited.
>> A.K.
>>
>>
>>
>>
>> ----- Original Message -----
>> From: "Leask, Graham" <g.leask at aston.ac.uk>
>> To: Rui Barradas <ruipbarradas at sapo.pt>
>> Cc: "r-help at r-project.org" <r-help at r-project.org>
>> Sent: Saturday, April 6, 2013 12:16 PM
>> Subject: Re: [R] Replace missing value within group with non-missing value
>>
>> Hi Rui,
>>
>> Data as follows
>>
>> structure(list(dn = c(4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4), obs = c(1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 9, 9), choice = c(0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0), br = c(1, 2, 3, 4, 5, 6, 1, 2, 3, 4, 5, 6, 1, 2, 3, 4, 5, 6, 1, 2, 3, 4, 5, 6, 1, 2, 3, 4, 5, 6, 1, 2, 3, 4, 5, 6, 1, 2, 3, 4, 5, 6, 1, 2, 3, 4, 5, 6, 1, 2), mth = c(NA, NA, NA, NA, NA, 487, NA, NA, 488, NA, NA, NA, NA, NA, NA, NA, NA, 488, NA, NA, 489, NA, NA, NA, NA, NA, NA, NA, NA, 489, NA, NA, NA, NA, NA, 489, NA, NA, NA, NA, NA, 490, NA, NA, NA, NA, NA, 491, NA, NA)), .Names = c("dn", "obs", "choice", "br", "mth"), row.names = c("1", "2", "3", "4", "5", "6", "7",
> "8", "9", "10", "11",
> "12",
> "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46", "47", "48", "49", "50"), class = "data.frame")
>>
>> Best wishes
>>
>>
>> Graham
>>
>> -----Original Message-----
>> From: Rui Barradas [mailto:ruipbarradas at sapo.pt]
>> Sent: 06 April 2013 16:32
>> To: Leask, Graham
>> Cc: r-help at r-project.org
>> Subject: Re: [R] Replace missing value within group with non-missing value
>>
>> Hello,
>>
>> Can't you post a data example? If your dataset is named 'dat' use
>>
>> dput(head(dat, 50)) # paste the output of this in a post
>>
>>
>> Rui Barradas
>>
>> Em 06-04-2013 15:34, Leask, Graham escreveu:
>>> Hi Rui,
>>>
>>> Thank you for your suggestion which is very much appreciated. Unfortunately running this code produces the following error.
>>>
>>> error in '$<-.data.frame' ('*tmp*', "mth", value = NA_real_) :
>>> replacement has 1 rows, data has 0
>>>
>>> I'm sure there must be an elegant solution to this problem?
>>>
>>> Best wishes
>>>
>>>
>>>
>>> Graham
>>>
>>> On 6 Apr 2013, at 12:15, "Rui Barradas" <ruipbarradas at sapo.pt> wrote:
>>>
>>>> Hello,
>>>>
>>>> That's not a very good way of posting your data, preferably paste the output of ?dput in a post.
>>>> Some thing along the lines of the following might do what you want.
>>>> It seems that the groups are established by 'dn' and 'obs' numbers.
>>>> If so, try
>>>>
>>>>
>>>> # Make up some data
>>>> dat <- data.frame(dn = 4, obs = rep(1:5, each = 6), mth = NA)
>>>> dat$mth[6] <- 487 dat$mth[9] <- 488 dat$mth[18] <- 488 dat$mth[21] <-
>>>> 489 dat$mth[30] <- 489
>>>>
>>>>
>>>> sp <- split(dat, list(dat$dn, dat$obs))
>>>> names(sp) <- NULL
>>>> tmp <- lapply(sp, function(x){
>>>> idx <- which(!is.na(x$mth))[1]
>>>> x$mth <- x$mth[idx]
>>>> x
>>>> })
>>>> do.call(rbind, tmp)
>>>>
>>>>
>>>> Hope this helps,
>>>>
>>>> Rui Barradas
>>>>
>>>>
>>>> Em 06-04-2013 11:33, Leask, Graham escreveu:
>>>>> Dear List members
>>>>>
>>>>> I have a large dataset organised in choice groups see sample below
>>>>>
>>>>>
>>>>> +--------------------------------------------------------------------
>>>>> -----------------------------+
>>>>> | dn obs choice acid br date
>>>>> cdate situat~n mth year set |
>>>>>
>>>>> |--------------------------------------------------------------------
>>>>> -----------------------------|
>>>>> 1. | 4 1 0 LOSEC 1 .
>>>>> . . . 1 |
>>>>> 2. | 4 1 0 NEXIUM 2 .
>>>>> . . . 1 |
>>>>> 3. | 4 1 0 PARIET 3 .
>>>>> . . . 1 |
>>>>> 4. | 4 1 0 PROTIUM 4 .
>>>>> . . . 1 |
>>>>> 5. | 4 1 0 ZANTAC 5 .
>>>>> . . . 1 |
>>>>>
>>>>> |--------------------------------------------------------------------
>>>>> -----------------------------|
>>>>> 6. | 4 1 1 ZOTON 6 23aug2000 01:00:00
>>>>> 23aug2000 NS 487 2000 1 |
>>>>> 7. | 4 2 0 LOSEC 1 .
>>>>> . . . 2 |
>>>>> 8. | 4 2 0 NEXIUM 2 .
>>>>> . . . 2 |
>>>>> 9. | 4 2 1 PARIET 3 25sep2000 01:00:00
>>>>> 25sep2000 L 488 2000 2 | 10. | 4 2 0
>>>>> PROTIUM 4 . . . .
>>>>> 2 |
>>>>>
>>>>> |--------------------------------------------------------------------
>>>>> -----------------------------| 11. | 4 2 0 ZANTAC
>>>>> 5 . . . . 2 |
>>>>> 12. | 4 2 0 ZOTON 6 .
>>>>> . . . 2 | 13. | 4 3 0 LOSEC
>>>>> 1 . . . . 3 |
>>>>> 14. | 4 3 0 NEXIUM 2 .
>>>>> . . . 3 | 15. | 4 3 0 PARIET
>>>>> 3 . . . . 3 |
>>>>>
>>>>> |--------------------------------------------------------------------
>>>>> -----------------------------| 16. | 4 3 0 PROTIUM
>>>>> 4 . . . . 3 |
>>>>> 17. | 4 3 0 ZANTAC 5 .
>>>>> . . . 3 | 18. | 4 3 1 ZOTON
>>>>> 6 20sep2000 00:00:00 20sep2000 R 488 2000 3 |
>>>>> 19. | 4 4 0 LOSEC 1 .
>>>>> . . . 4 | 20. | 4 4 0 NEXIUM
>>>>> 2 . . . . 4 |
>>>>>
>>>>> |--------------------------------------------------------------------
>>>>> -----------------------------| 21. | 4 4 1 PARIET
>>>>> 3 27oct2000 00:00:00 27oct2000 NL 489 2000 4 |
>>>>> 22. | 4 4 0 PROTIUM 4 .
>>>>> . . . 4 | 23. | 4 4 0 ZANTAC
>>>>> 5 . . . . 4 |
>>>>> 24. | 4 4 0 ZOTON 6 .
>>>>> . . . 4 | 25. | 4 5 0 LOSEC
>>>>> 1 . . . . 5 |
>>>>>
>>>>> |--------------------------------------------------------------------
>>>>> -----------------------------| 26. | 4 5 0 NEXIUM
>>>>> 2 . . . . 5 |
>>>>> 27. | 4 5 0 PARIET 3 .
>>>>> . . . 5 | 28. | 4 5 0 PROTIUM
>>>>> 4 . . . . 5 |
>>>>> 29. | 4 5 0 ZANTAC 5 .
>>>>> . . . 5 | 30. | 4 5 1 ZOTON
>>>>> 6 23oct2000 03:00:00 23oct2000 NS 489 2000 5 |
>>>>>
>>>>> I wish to fill in the missing values in each choice set - delineated by dn (Doctor) obs (Observation number) and choices (1 to 6).
>>>>> For each choice set one choice is chosen which contains full time
>>>>> information for that choice set ie in set 1 choice 6 was chosen and shows the month 487. The other 5 choices show mth as missing. I want to fill these with the correct mth.
>>>>>
>>>>> I am sure there must be an elegant way to do this in R?
>>>>>
>>>>>
>>>>> Best wishes
>>>>>
>>>>>
>>>>>
>>>>> Graham
>>>>>
>>>>>
>>>>> [[alternative HTML version deleted]]
>>>>>
>>>>> ______________________________________________
>>>>> 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.
>>
>> ______________________________________________
>> 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.
>>
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