R help - Feb 2007 - setting a number of values to NA over a data.frame.

This is probably a simple problem but I don't see a
solution.

I have a data.frame with a number of columns where I
would like 0 <- NA

thus I have df1[,144:157] <- NA if df1[, 144: 157] ==0
and df1[, 190:198] <- NA if df1[, 190:198] ==0

but I cannot figure out a way do this.  

cata <- c( 1,1,6,1,1,NA)
catb <- c( 1,2,3,4,5,6)
doga <- c(3,5,3,6,4, 0)
dogb <- c(2,4,6,8,10, 12)
rata <- c (NA, 9, 9, 8, 9, 8)
ratb <- c( 1,2,3,4,5,6)
bata <- c( 12, 42,NA, 45, 32, 54)
batb <- c( 13, 15, 17,19,21,23)
id <- c('a', 'b', 'b', 'c', 'a',
'b')
site <- c(1,1,4,4,1,4)
mat1 <-  cbind(cata, catb, doga, dogb, rata, ratb,
bata, batb)

data1 <- data.frame(site, id, mat1)
data1

 # Obviously this works fine for one column

data1$site[data1$site ==1] <- NA  ; data1

but I cannot see how to do this with indices that
would allow me to do more than one column in the
data.frame.

At one point I even tried something like this
a <- c("site")
data1$a[data1$a ==1] <- NA

which seems to produce a corrupt data.frame.

I am sure it is simple but I don't see it.  

Any help would be much appreciated.

John -

Your initial problem uses 0, but the example uses 1 for the value that 
gets an NA.  My solution uses 1 to fit with your example.  There may be 
a better way, but try something like

data1[3:5] <- data.frame(lapply(data1[3:5], function(x) ifelse(x==1, NA, 
x)))

The data1[3:5] is just a test subset  of columns I chose from your data1 
example.  Notice it appears twice, once on each side of the assignment 
operator.

In English, apply to each column of the data frame (which is a list) a 
function that will return NA if the element is 1, and the value 
otherwise, and then turn the modified lists into a data.frame, and save 
it as data1.



See the help files for lapply and ifelse if you haven't seen those before.

Maybe someone has a better way?

Erik

John Kane wrote:
> This is probably a simple problem but I don't see a
> solution.
> 
> I have a data.frame with a number of columns where I
> would like 0 <- NA
> 
> thus I have df1[,144:157] <- NA if df1[, 144: 157] ==0
> and df1[, 190:198] <- NA if df1[, 190:198] ==0
> 
> but I cannot figure out a way do this.  
> 
> cata <- c( 1,1,6,1,1,NA)
> catb <- c( 1,2,3,4,5,6)
> doga <- c(3,5,3,6,4, 0)
> dogb <- c(2,4,6,8,10, 12)
> rata <- c (NA, 9, 9, 8, 9, 8)
> ratb <- c( 1,2,3,4,5,6)
> bata <- c( 12, 42,NA, 45, 32, 54)
> batb <- c( 13, 15, 17,19,21,23)
> id <- c('a', 'b', 'b', 'c', 'a',
'b')
> site <- c(1,1,4,4,1,4)
> mat1 <-  cbind(cata, catb, doga, dogb, rata, ratb,
> bata, batb)
> 
> data1 <- data.frame(site, id, mat1)
> data1
> 
>  # Obviously this works fine for one column
> 
> data1$site[data1$site ==1] <- NA  ; data1
> 
> but I cannot see how to do this with indices that
> would allow me to do more than one column in the
> data.frame.
> 
> At one point I even tried something like this
> a <- c("site")
> data1$a[data1$a ==1] <- NA
> 
> which seems to produce a corrupt data.frame.
> 
> I am sure it is simple but I don't see it.  
> 
> Any help would be much appreciated.
> 
> ______________________________________________
> R-help at stat.math.ethz.ch 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.

John Kane wrote:
> This is probably a simple problem but I don't see a
> solution.
> 
> I have a data.frame with a number of columns where I
> would like 0 <- NA
> 
Hi John,
You might have a look at "toNA" in the prettyR package. Wait for
version
1.0-4, just uploaded, as I have fixed a bug in that function.

Jim

Hi

Strange. It works for me without any problem.
> zeta
  tepl tio2 al2o3  iep
1   60    1   3.5 5.65
2   60    1   2.0 5.00
3   60    1   1.0 5.30
4   60    0   2.0 4.65
5   40    1   3.5 5.20
6   40    1   2.0 4.85
7   40    0   3.5 5.70
8   40    0   2.0 5.25
> zeta[zeta==1]<-NA
> zeta
  tepl tio2 al2o3  iep
1   60   NA   3.5 5.65
2   60   NA   2.0 5.00
3   60   NA    NA 5.30
4   60    0   2.0 4.65
5   40   NA   3.5 5.20
6   40   NA   2.0 4.85
7   40    0   3.5 5.70
8   40    0   2.0 5.25
> str(zeta)
'data.frame':   8 obs. of  4 variables:
 $ tepl : int  60 60 60 60 40 40 40 40
 $ tio2 : num  NA NA NA 0 NA NA 0 0
 $ al2o3: num  3.5 2 NA 2 3.5 2 3.5 2
 $ iep  : num  5.65 5 5.3 4.65 5.2 4.85 5.7 5.25
>
HTH
Petr



On 7 Feb 2007 at 16:57, Erik Iverson wrote:

Date sent:      	Wed, 07 Feb 2007 16:57:40 -0600
From:           	Erik Iverson <iverson at biostat.wisc.edu>
To:             	John Kane <jrkrideau at yahoo.ca>
Copies to:      	R R-help <r-help at stat.math.ethz.ch>
Subject:        	Re: [R] setting a number of values to NA over  a data.frame.
> John -
> 
> Your initial problem uses 0, but the example uses 1 for the value that
> gets an NA.  My solution uses 1 to fit with your example.  There may
> be a better way, but try something like
> 
> data1[3:5] <- data.frame(lapply(data1[3:5], function(x) ifelse(x==1,
> NA, x)))
> 
> The data1[3:5] is just a test subset  of columns I chose from your
> data1 example.  Notice it appears twice, once on each side of the
> assignment operator.
> 
> In English, apply to each column of the data frame (which is a list) a
> function that will return NA if the element is 1, and the value
> otherwise, and then turn the modified lists into a data.frame, and
> save it as data1.
> 
> 
> 
> See the help files for lapply and ifelse if you haven't seen those
> before.
> 
> Maybe someone has a better way?
> 
> Erik
> 
> John Kane wrote:
> > This is probably a simple problem but I don't see a
> > solution.
> > 
> > I have a data.frame with a number of columns where I
> > would like 0 <- NA
> > 
> > thus I have df1[,144:157] <- NA if df1[, 144: 157] ==0
> > and df1[, 190:198] <- NA if df1[, 190:198] ==0
> > 
> > but I cannot figure out a way do this.  
> > 
> > cata <- c( 1,1,6,1,1,NA)
> > catb <- c( 1,2,3,4,5,6)
> > doga <- c(3,5,3,6,4, 0)
> > dogb <- c(2,4,6,8,10, 12)
> > rata <- c (NA, 9, 9, 8, 9, 8)
> > ratb <- c( 1,2,3,4,5,6)
> > bata <- c( 12, 42,NA, 45, 32, 54)
> > batb <- c( 13, 15, 17,19,21,23)
> > id <- c('a', 'b', 'b', 'c',
'a', 'b')
> > site <- c(1,1,4,4,1,4)
> > mat1 <-  cbind(cata, catb, doga, dogb, rata, ratb,
> > bata, batb)
> > 
> > data1 <- data.frame(site, id, mat1)
> > data1
> > 
> >  # Obviously this works fine for one column
> > 
> > data1$site[data1$site ==1] <- NA  ; data1
> > 
> > but I cannot see how to do this with indices that
> > would allow me to do more than one column in the
> > data.frame.
> > 
> > At one point I even tried something like this
> > a <- c("site")
> > data1$a[data1$a ==1] <- NA
> > 
> > which seems to produce a corrupt data.frame.
> > 
> > I am sure it is simple but I don't see it.  
> > 
> > Any help would be much appreciated.
> > 
> > ______________________________________________
> > R-help at stat.math.ethz.ch 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 stat.math.ethz.ch 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.
Petr Pikal
petr.pikal at precheza.cz

Once again I forgot to reply to the whole list....
On Feb 9, 2007, at 8:39 AM, Charilaos Skiadas wrote:
> On Feb 9, 2007, at 8:13 AM, John Kane wrote:
>
>> The problem is that my dataframe has 1,s in about 50%
>> of the columns and I only want it to apply to a few
>> specified columns. My explanation may not have been
>> clear enough.
>>
>> Using your example,I want all values for tio2 set to 1
>> but not any values in al2o3 whereas zeta[zeta==1]<-NA
>> is also changing al2o3[3] to NA.
>>
>
> You need to index the zeta in zeta==1 in the same way as you do  
> with the zeta outside.
> I think the point is that if you do zeta[,cols][zeta==1] <- NA,  
> then the recycling of NA to obtain the correct number of elements  
> is done based on the elements in zeta[,cols]. But since zeta==1 is  
> a much longer vector than zeta[,cols], then zeta[,cols][zeta==1]  
> has a number of NA objects attached to its end, and hence has now   
> a longer length than the recycled NA that is supposed to replace it.
> But perhaps someone more expert in the internals can explain it in  
> greater detail, if the above is not right. In the mean time, the  
> following seems to work:
>
> > y <- rbinom(20, 1, 1/2)
> > dim(y) <- c(5,4)
> > colnames(y) <- c("one", "two",
"three", "four")
> > x <- as.data.frame(y)
> > cl <- c("two", "three")
> > x[,cl][x[,cl]==1] <- NA
> > x
>   one two three four
> 1   0   0    NA    0
> 2   0   0     0    0
> 3   1   0     0    0
> 4   0  NA     0    1
> 5   1   0     0    1
>
>> Thanks
>
> Haris
Haris

Jim Lemon <jim <at> bitwrit.com.au> writes:
> Hi John,
> You might have a look at "toNA" in the prettyR package. Wait for
version
> 1.0-4, just uploaded, as I have fixed a bug in that function.
There is also a set of generic functions exactly for such cases: unknownToNA(),
NAToUnknown() and isUnknown() in gdata package.

Gregor

--- Gregor Gorjanc <gregor.gorjanc at bfro.uni-lj.si>
wrote:
> Jim Lemon <jim <at> bitwrit.com.au> writes:
> > Hi John,
> > You might have a look at "toNA" in the prettyR
> package. Wait for version 
> > 1.0-4, just uploaded, as I have fixed a bug in
> that function.
> 
> There is also a set of generic functions exactly for
> such cases: unknownToNA(),
> NAToUnknown() and isUnknown() in gdata package.
> 
> Gregor
> 
Thanks very much.  I have a wealth of approaches now.