[R] How to globally convert NaN to NA in dataframe?

[PIKAL Petr]

Hi Luigi.

Weird. But maybe it is the desired behaviour of summary when calculating
mean of numeric column full of NAs.

See example

dat <- data.frame(x=rep(NA, 110), y=rep(1, 110), z= rnorm(110))

# change all values in second column to NA
dat[,2] <- NA
# change some of them to NAN
dat[5:6, 2:3] <- 0/0

# see summary
summary(dat)
    x                 y             z          
 Mode:logical   Min.   : NA   Min.   :-1.9798  
 NA's:110       1st Qu.: NA   1st Qu.:-0.4729  
                Median : NA   Median : 0.1745  
                Mean   :NaN   Mean   : 0.1856  
                3rd Qu.: NA   3rd Qu.: 0.8017  
                Max.   : NA   Max.   : 2.5075  
                NA's   :110   NA's   :2        

# change NAN values to NA
dat[sapply(dat, is.nan)] <- NA
*************************

#summary is same
summary(dat)
    x                 y             z          
 Mode:logical   Min.   : NA   Min.   :-1.9798  
 NA's:110       1st Qu.: NA   1st Qu.:-0.4729  
                Median : NA   Median : 0.1745  
                Mean   :NaN   Mean   : 0.1856  
                3rd Qu.: NA   3rd Qu.: 0.8017  
                Max.   : NA   Max.   : 2.5075  
                NA's   :110   NA's   :2        

# but no NAN value in data
dat[1:10,]
    x  y          z
1  NA NA -0.9148696
2  NA NA  0.7110570
3  NA NA -0.1901676
4  NA NA  0.5900650
5  NA NA         NA
6  NA NA         NA
7  NA NA  0.7987658
8  NA NA -0.5225229
9  NA NA  0.7673103
10 NA NA -0.5263897

So my "nice compact command"
dat[sapply(dat, is.nan)] <- NA

works as expected, but summary gives as mean NAN.

Cheers
Petr

> -----Original Message-----
> From: R-help <r-help-bounces using r-project.org> On Behalf Of Luigi Marongiu
> Sent: Thursday, September 2, 2021 3:46 PM
> To: Andrew Simmons <akwsimmo using gmail.com>
> Cc: r-help <r-help using r-project.org>
> Subject: Re: [R] How to globally convert NaN to NA in dataframe?
> 
> `data[sapply(data, is.nan)] <- NA` is a nice compact command, but I still
get
> NaN when using the summary function, for instance one of the columns give:
> ```
> Min.   : NA
> 1st Qu.: NA
> Median : NA
> Mean   :NaN
> 3rd Qu.: NA
> Max.   : NA
> NA's   :110
> ```
> I tried to implement the second solution but:
> ```
> df <- lapply(x, function(xx) {
>   xx[is.nan(xx)] <- NA
> })
> > str(df)
> List of 1
>  $ sd_ef_rash_loc___palm: logi NA
> ```
> What am I getting wrong?
> Thanks
> 
> On Thu, Sep 2, 2021 at 3:30 PM Andrew Simmons <akwsimmo using gmail.com>
> wrote:
> >
> > Hello,
> >
> >
> > I would use something like:
> >
> >
> > x <- c(1:5, NaN) |> sample(100, replace = TRUE) |> matrix(10, 10) |>
> > as.data.frame() x[] <- lapply(x, function(xx) {
> >     xx[is.nan(xx)] <- NA_real_
> >     xx
> > })
> >
> >
> > This prevents attributes from being changed in 'x', but accomplishes the
> same thing as you have above, I hope this helps!
> >
> > On Thu, Sep 2, 2021 at 9:19 AM Luigi Marongiu <marongiu.luigi using gmail.com>
> wrote:
> >>
> >> Hello,
> >> I have some NaN values in some elements of a dataframe that I would
> >> like to convert to NA.
> >> The command `df1$col[is.nan(df1$col)]<-NA` allows to work column-wise.
> >> Is there an alternative for the global modification at once of all
> >> instances?
> >> I have seen from
> >> https://stackoverflow.com/questions/18142117/how-to-replace-nan-
> value
> >> -with-zero-in-a-huge-data-frame/18143097#18143097
> >> that once could use:
> >> ```
> >>
> >> is.nan.data.frame <- function(x)
> >> do.call(cbind, lapply(x, is.nan))
> >>
> >> data123[is.nan(data123)] <- 0
> >> ```
> >> replacing o with NA, but I got
> >> ```
> >> str(df)
> >> > logi NA
> >> ```
> >> when modifying my dataframe df.
> >> What would be the correct syntax?
> >> Thank you
> >>
> >>
> >>
> >> --
> >> Best regards,
> >> Luigi
> >>
> >> ______________________________________________
> >> R-help using 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.
> 
> 
> 
> --
> Best regards,
> Luigi
> 
> ______________________________________________
> R-help using 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.