[Rd] importing explicitly declared missing values in read.spss (foreign)

[Jeroen Ooms]

There is a problem when importing an spss-file containing explicitly declared
missing values in R using the read.spss function from the foreign package.
I'm not sure these problems are the same in every version of spss, I am
using the latest version 16.0.2.

I included  http://www.nabble.com/file/p18776776/missingdata.sav
missingdata.sav  and  http://www.nabble.com/file/p18776776/frequencies.jpg
frequencies.jpg  as an example. The data contains 3 types of missing data: 2
are explicitly declared as a missing-value ('8' = NA and '9' = NAP), the
third type are the system missings. When this file is imported in R, only
the system missings are recognized as missing values, the others are just
imported as levels in the nominal case, and as (labeled) real values 8 and 9
in the continuous case. There are also no attributes in the object returned
by read.spss that contain information about which values/levels are the
missing values; their missingness seems to be completely ignored by the
function.

Is there some way or other function to be able to import spss files, with an
option that replaces all missing values with <NA>'s in R? Of course this
comes with the trade-off of losing the meaning of the missingness when there
are multiple types of missingness, but I think this is far less harmfull
than treating all missing values as normal values. 

[code]
> mydata <- read.spss("c:/users/jeroen/desktop/missingdata.sav",
> to.data.frame=T)
Warning messages:
1: In read.spss("c:/users/jeroen/desktop/missingdata.sav", to.data.frame =
T) :
  c:/users/jeroen/desktop/missingdata.sav: File-indicated character
representation code (1252) looks like a Windows codepage
2: In read.spss("c:/users/jeroen/desktop/missingdata.sav", to.data.frame =
T) :
  c:/users/jeroen/desktop/missingdata.sav: Unrecognized record type 7,
subtype 16 encountered in system file
3: In read.spss("c:/users/jeroen/desktop/missingdata.sav", to.data.frame =
T) :
  c:/users/jeroen/desktop/missingdata.sav: Unrecognized record type 7,
subtype 20 encountered in system file

> mydata
   SUBJECT CATEGORI CONTINUO
1        1      yes     3.11
2        2      yes     2.10
3        3      yes     5.34
4        4      yes     1.54
5        5      yes     3.89
6        6       no     2.98
7        7       no     4.53
8        8       no     1.98
9        9       no     3.68
10      10       no     2.94
11      11       NA     8.00
12      12       NA     8.00
13      13       NA     8.00
14      14       NA     8.00
15      15       NA     8.00
16      16      NAP     9.00
17      17      NAP     9.00
18      18      NAP     9.00
19      19      NAP     9.00
20      20      NAP     9.00
21      21     <NA>       NA
22      22     <NA>       NA
23      23     <NA>       NA
24      24     <NA>       NA
25      25     <NA>       NA

> is.na(mydata$CONTINUO)
 [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE  TRUE  TRUE 
TRUE

> is.na(mydata$CATEGORI)
 [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE  TRUE  TRUE 
TRUE

> summary(mydata)
    SUBJECT   CATEGORI    CONTINUO    
 Min.   : 1   yes :5   Min.   :1.540  
 1st Qu.: 7   no  :5   1st Qu.:3.078  
 Median :13   NA  :5   Median :6.670  
 Mean   :13   NAP :5   Mean   :5.854  
 3rd Qu.:19   NA's:5   3rd Qu.:8.250  
 Max.   :25            Max.   :9.000  
                       NA's   :5.000  
[/code]


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