Subscripting problem with is.na()
... actually, FWIW, I would say that this little discussion mostly demonstrates why the OP's request is probably not a good idea in the first place. Usually, NA's should be left as NA's to be dealt with properly by R and packages. In biological measurements, for example, NA's often mean "below the ability to reliably measure." Biologists with whom I've worked over many years often want to convert these to 0 or omit the cases, both of which lead to biased estimates and/or underestimates of variability and excess claims of "statistical significance" (for those who belong to this religious persuasion). One should never say never, but I suspect that there are relatively few circumstances where the conversion the OP requested is actually wise. Feel free to ignore/reject such extraneous comments of course. 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 12:14 PM, David L Carlson <dcarlson at tamu.edu> wrote:
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 ? 17:06, Bert Gunter a ?crit :
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 ? 16:27, Ivan Calandra a ?crit :
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$var1), "var1"] <- 0 It's the same problem with your 2nd and 4th tries (4th one has other problems). Your 3rd try does not change ds_test at all. HTH, Ivan -- Ivan Calandra, PhD Scientific Mediator University of Reims Champagne-Ardenne GEGENAA - EA 3795 CREA - 2 esplanade Roland Garros 51100 Reims, France +33(0)3 26 77 36 89 ivan.calandra at univ-reims.fr -- https://www.researchgate.net/profile/Ivan_Calandra https://publons.com/author/705639/ Le 23/06/2016 ? 15:57, G.Maubach at weinwolf.de a ?crit :
Hi All,
I would like to recode my NAs to 0. Using a single vector everything is
fine.
But if I use a data.frame things go wrong:
-- cut --
var1 <- c(1:3, NA, 5:7, NA, 9:10)
var2 <- c(1:3, NA, 5:7, NA, 9:10)
ds_test <-
data.frame(var1, var2)
test <- var1
test[is.na(test)] <- 0
test # NA recoded OK
# First try
ds_test[is.na(ds_test$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
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______________________________________________ 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.