R help - Aug 2007 - Replace NAs in dataframe: what am I doing wrong

Dear R-users,

My script imports a dataset from a csv file, in which missing values are 
represented by ".". This importation is done into a dataframe using
the
read.table function with na.strings = "."  Then I want to replace the 
NAs in the first column of the dataframe by "Missing data". I am using
the following code to do so :

mydata<-data.frame(read.table(myFile,sep=",",header=TRUE,na.strings="."))
   # myFile is the full path of the source file

mydata[,1][is.na(mydata[,1])]<-"Missing value"

This code works perfectly fine if this first column contains only 
missing values, i.e. ".". As soon as it contains multiple levels and 
missing values, things start to get wrong. I get the following error 
message and the replacement is not done.

Warning message:
invalid factor level, NAs generated in: `[<-.factor`(`*tmp*`, 
is.na(mydata[, 1]), value = "Missing value")

Is there an error in my code or is that a bug (I doubt about it) ?

Thanks in advance.

The problem is that the first column is probably a factor and you are
trying to assign a value that is not already a 'level' in the factor.
One way is to read the data with as.is=TRUE to keep it as character,
replace the NAs and then convert back to factors if you want to:
> x <- read.csv(textConnection("A,B
+ a,3
+ b,4
+ .,.
+ c,5"), na.strings='.', as.is=TRUE)  # keep as
character
> # replace NAs
> x[is.na(x[,1]), 1] <- "Missing Value"
> # convert back to factors if you want to
> x[[1]] <- factor(x[[1]])
> str(x)
'data.frame':   4 obs. of  2 variables:
 $ A: Factor w/ 4 levels "a","b","c","Missing
Value": 1 2 4 3
 $ B: int  3 4 NA 5
>
>

On 8/11/07, S?bastien <pomchip at free.fr> wrote:
> Dear R-users,
>
> My script imports a dataset from a csv file, in which missing values are
> represented by ".". This importation is done into a dataframe
using the
> read.table function with na.strings = "."  Then I want to replace
the
> NAs in the first column of the dataframe by "Missing data". I am
using
> the following code to do so :
>
>
mydata<-data.frame(read.table(myFile,sep=",",header=TRUE,na.strings="."))
>   # myFile is the full path of the source file
>
> mydata[,1][is.na(mydata[,1])]<-"Missing value"
>
> This code works perfectly fine if this first column contains only
> missing values, i.e. ".". As soon as it contains multiple levels
and
> missing values, things start to get wrong. I get the following error
> message and the replacement is not done.
>
> Warning message:
> invalid factor level, NAs generated in: `[<-.factor`(`*tmp*`,
> is.na(mydata[, 1]), value = "Missing value")
>
> Is there an error in my code or is that a bug (I doubt about it) ?
>
> Thanks in advance.
>
> ______________________________________________
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http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem you are trying to solve?