[R] Subscripting problem with is.na()
David L Carlson
dcarlson at tamu.edu
Thu Jun 23 21:14:06 CEST 2016
Good point. I did not think about factors. Also your example raises another issue since column c is logical, but gets silently converted to numeric. This would seem to get the job done assuming the conversion is intended for numeric columns only:
> test <- data.frame(a=c(1,NA,2), b = c("A","b",NA), c= rep(NA,3))
> sapply(test, class)
a b c
"numeric" "factor" "logical"
> num <- sapply(test, is.numeric)
> test[, num][is.na(test[, num])] <- 0
> test
a b c
1 1 A NA
2 0 b NA
3 2 <NA> NA
David C
-----Original Message-----
From: Bert Gunter [mailto:bgunter.4567 at gmail.com]
Sent: Thursday, June 23, 2016 1:48 PM
To: David L Carlson
Cc: Ivan Calandra; R Help
Subject: Re: [R] Subscripting problem with is.na()
Not in general, David:
e.g.
> test <- data.frame(a=c(1,NA,2), b = c("A","b",NA), c= rep(NA,3))
> is.na(test)
a b c
[1,] FALSE FALSE TRUE
[2,] TRUE FALSE TRUE
[3,] FALSE TRUE TRUE
> test[is.na(test)]
[1] NA NA NA NA NA
> test[is.na(test)] <- 0
Warning message:
In `[<-.factor`(`*tmp*`, thisvar, value = 0) :
invalid factor level, NA generated
> test
a b c
1 1 A 0
2 0 b 0
3 2 <NA> 0
The problem is the default conversion to factors and the replacement
operation for factors. So:
> test <- data.frame(a=c(1,NA,2), b = I(c("A","b",NA_character_)), c= rep(NA,3))
> class(test$b)
[1] "AsIs" ## so NOT a factor
> test[is.na(test)] <- 0 # now works as you describe
> test
a b c
1 1 A 0
2 0 b 0
3 2 0 0
Of course the OP (and you) probably had a data frame of all numerics
in mind, so the problem doesn't arise. But I think one needs to make
the distinction and issue clear.
Cheers,
Bert
Bert Gunter
"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
On Thu, Jun 23, 2016 at 8:46 AM, David L Carlson <dcarlson at tamu.edu> wrote:
> The function is.na() returns a matrix when applied to a data.frame so you can easily convert all the NAs to 0's:
>
>> ds_test
> var1 var2
> 1 1 1
> 2 2 2
> 3 3 3
> 4 NA NA
> 5 5 5
> 6 6 6
> 7 7 7
> 8 NA NA
> 9 9 9
> 10 10 10
>> is.na(ds_test)
> var1 var2
> [1,] FALSE FALSE
> [2,] FALSE FALSE
> [3,] FALSE FALSE
> [4,] TRUE TRUE
> [5,] FALSE FALSE
> [6,] FALSE FALSE
> [7,] FALSE FALSE
> [8,] TRUE TRUE
> [9,] FALSE FALSE
> [10,] FALSE FALSE
>> ds_test[is.na(ds_test)] <- 0
>> ds_test
> var1 var2
> 1 1 1
> 2 2 2
> 3 3 3
> 4 0 0
> 5 5 5
> 6 6 6
> 7 7 7
> 8 0 0
> 9 9 9
> 10 10 10
>
> -------------------------------------
> David L Carlson
> Department of Anthropology
> Texas A&M University
> College Station, TX 77840-4352
>
> -----Original Message-----
> From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Ivan Calandra
> Sent: Thursday, June 23, 2016 10:14 AM
> To: R Help
> Subject: Re: [R] Subscripting problem with is.na()
>
> Thank you Bert for this clarification. It is indeed an important point.
>
> Ivan
>
> --
> Ivan Calandra, PhD
> Scientific Mediator
> University of Reims Champagne-Ardenne
> GEGENAA - EA 3795
> CREA - 2 esplanade Roland Garros
> 51100 Reims, France
> +33(0)3 26 77 36 89
> ivan.calandra at univ-reims.fr
> --
> https://www.researchgate.net/profile/Ivan_Calandra
> https://publons.com/author/705639/
>
> Le 23/06/2016 à 17:06, Bert Gunter a écrit :
>> Sorry, Ivan, your statement is incorrect:
>>
>> "When you use a single bracket on a list with only one argument in
>> between, then R extracts "elements", i.e. columns in the case of a
>> data.frame. This explains your errors. "
>>
>> e.g.
>>
>>> ex <- data.frame(a = 1:3, b = letters[1:3])
>>> a <- 1:3
>>> identical(ex[1], a)
>> [1] FALSE
>>
>>> class(ex[1])
>> [1] "data.frame"
>>> class(a)
>> [1] "integer"
>>
>> Compare:
>>
>>> identical(ex[[1]], a)
>> [1] TRUE
>>
>> Why? Single bracket extraction on a list results in a list; double
>> bracket extraction results in the element of the list ( a "column" in
>> the case of a data frame, which is a specific kind of list). The
>> relevant sections of ?Extract are:
>>
>> "Indexing by [ is similar to atomic vectors and selects a **list** of
>> the specified element(s).
>>
>> Both [[ and $ select a **single element of the list**. "
>>
>>
>> Hope this clarifies this often-confused issue.
>>
>>
>> Cheers,
>> Bert
>> Bert Gunter
>>
>> "The trouble with having an open mind is that people keep coming along
>> and sticking things into it."
>> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>>
>>
>> On Thu, Jun 23, 2016 at 7:34 AM, Ivan Calandra
>> <ivan.calandra at univ-reims.fr> wrote:
>>> My statement "Using a single bracket '[' on a data.frame does the same as
>>> for matrices: you need to specify rows and columns" was not correct.
>>>
>>>
>>> When you use a single bracket on a list with only one argument in between,
>>> then R extracts "elements", i.e. columns in the case of a data.frame. This
>>> explains your errors.
>>>
>>> But it is possible to use a single bracket on a data.frame with 2 arguments
>>> (rows, columns) separated by a comma, as with matrices. This is the solution
>>> you received.
>>>
>>> Ivan
>>>
>>>
>>> --
>>> Ivan Calandra, PhD
>>> Scientific Mediator
>>> University of Reims Champagne-Ardenne
>>> GEGENAA - EA 3795
>>> CREA - 2 esplanade Roland Garros
>>> 51100 Reims, France
>>> +33(0)3 26 77 36 89
>>> ivan.calandra at univ-reims.fr
>>> --
>>> https://www.researchgate.net/profile/Ivan_Calandra
>>> https://publons.com/author/705639/
>>>
>>> Le 23/06/2016 à 16:27, Ivan Calandra a écrit :
>>>> Dear Georg,
>>>>
>>>> You need to learn a bit more about the subsetting methods, depending on
>>>> the object structure you're trying to subset.
>>>>
>>>> More specifically, when you run this: ds_test[is.na(ds_test$var1)]
>>>> you get this error: "Error in `[.data.frame`(ds_test, is.na(ds_test$var1))
>>>> : undefined columns selected"
>>>>
>>>> This means that R does not understand which column you're trying to
>>>> select. But you're actually trying to select rows.
>>>>
>>>> Using a single bracket '[' on a data.frame does the same as for matrices:
>>>> you need to specify rows and columns, like this:
>>>> ds_test[is.na(ds_test$var1), ] ## notice the last comma
>>>> ds_test[is.na(ds_test$var1), ] <- 0 ## works on all columns because you
>>>> didn't specify any after the comma
>>>>
>>>> If you want it only for "var1", then you need to specify the column:
>>>> ds_test[is.na(ds_test$var1), "var1"] <- 0
>>>>
>>>> It's the same problem with your 2nd and 4th tries (4th one has other
>>>> problems). Your 3rd try does not change ds_test at all.
>>>>
>>>> HTH,
>>>> Ivan
>>>>
>>>> --
>>>> Ivan Calandra, PhD
>>>> Scientific Mediator
>>>> University of Reims Champagne-Ardenne
>>>> GEGENAA - EA 3795
>>>> CREA - 2 esplanade Roland Garros
>>>> 51100 Reims, France
>>>> +33(0)3 26 77 36 89
>>>> ivan.calandra at univ-reims.fr
>>>> --
>>>> https://www.researchgate.net/profile/Ivan_Calandra
>>>> https://publons.com/author/705639/
>>>>
>>>> Le 23/06/2016 à 15:57, G.Maubach at weinwolf.de a écrit :
>>>>> Hi All,
>>>>>
>>>>> I would like to recode my NAs to 0. Using a single vector everything is
>>>>> fine.
>>>>>
>>>>> But if I use a data.frame things go wrong:
>>>>>
>>>>> -- cut --
>>>>>
>>>>> var1 <- c(1:3, NA, 5:7, NA, 9:10)
>>>>> var2 <- c(1:3, NA, 5:7, NA, 9:10)
>>>>> ds_test <-
>>>>> data.frame(var1, var2)
>>>>>
>>>>> test <- var1
>>>>> test[is.na(test)] <- 0
>>>>> test # NA recoded OK
>>>>>
>>>>> # First try
>>>>> ds_test[is.na(ds_test$var1)] <- 0 # duplicate subscripts WRONG
>>>>>
>>>>> # Second try
>>>>> ds_test[is.na("var1")] <- 0
>>>>> ds_test$var1 # not recoded WRONG
>>>>>
>>>>> # Third try: to me the most intuitive approach
>>>>> is.na(ds_test["var1"]) <- 0 # attempt to select less than one element in
>>>>> integerOneIndex WRONG
>>>>>
>>>>> # Fourth try
>>>>> ds_test[is.na(var1)] <- 0 # duplicate subscripts for columns WRONG
>>>>>
>>>>> -- cut --
>>>>> How can I do it correctly?
>>>>>
>>>>> Where could I have found something about it?
>>>>>
>>>>> Kind regards
>>>>>
>>>>> Georg
>>>>>
>>>>> ______________________________________________
>>>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>>>> 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 -- To UNSUBSCRIBE and more, see
>>>> 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 -- To UNSUBSCRIBE and more, see
>>> 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 -- To UNSUBSCRIBE and more, see
> 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 -- To UNSUBSCRIBE and more, see
> 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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