Building package - tab delimited example data issue

Johannes Graumann wrote:

  

On Thursday 06 December 2007 11:52:46 Peter Dalgaard wrote:
    

Johannes Graumann wrote:
      

Hello,

I'm trying to integrate example data in the shape of a tab delimited
ASCII file into my package and therefore dropped it into the data
subdirectory. The build works out just fine, but when I attempt to
install I get:

** building package indices ...
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines,
na.strings,  :
  line 1 did not have 500 elements
Calls: <Anonymous> ... <Anonymous> -> switch -> assign -> read.table ->
scan Execution halted
ERROR: installing package indices failed
** Removing '/usr/local/lib/R/site-library/MaxQuantUtils'
** Restoring previous '/usr/local/lib/R/site-library/MaxQuantUtils'

Accordingly the check delivers:

...
* checking whether package 'MaxQuantUtils' can be installed ... ERROR

Can anyone tell me what I'm doing wrong? build/install witout the ASCII
file works just fine.

Joh
        

If you had looked at help(data), you would have found a list of which
file formats it supports and how they are read. Hint: TAB-delimited
files are not among them. *Whitespace* separated files work, using
read.table(filename, header=TRUE), but that is not a superset of
TAB-delimited data if there are empty fields.

A nice trick is to figure out how to read the data from the command line
and drop the relevant code into a mydata.R file (assuming that the
actual data file is mydata.txt). This gets executed when the data is
loaded (by data(mydata) or when building the lazyload database) because
.R files have priority over .txt.

This is quite general and allows a nice way of incorporating data

management while retaining the original data source:
      

more ISwR/data/stroke.R
        

stroke <-  read.csv2("stroke.csv", na.strings=".")
names(stroke) <- tolower(names(stroke))
stroke <-  within(stroke,{
    sex <- factor(sex,levels=0:1,labels=c("Female","Male"))
    dgn <- factor(dgn)
    coma <- factor(coma, levels=0:1, labels=c("No","Yes"))
    minf <- factor(minf, levels=0:1, labels=c("No","Yes"))
    diab <- factor(diab, levels=0:1, labels=c("No","Yes"))
    han <- factor(han, levels=0:1, labels=c("No","Yes"))
    died <- as.Date(died, format="%d.%m.%Y")
    dstr <- as.Date(dstr,format="%d.%m.%Y")
    dead <- !is.na(died) & died < as.Date("1996-01-01")
    died[!dead] <- NA
})

      

head ISwR/data/stroke.csv
        

SEX;DIED;DSTR;AGE;DGN;COMA;DIAB;MINF;HAN
1;7.01.1991;2.01.1991;76;INF;0;0;1;0
1;.;3.01.1991;58;INF;0;0;0;0
1;2.06.1991;8.01.1991;74;INF;0;0;1;1
0;13.01.1991;11.01.1991;77;ICH;0;1;0;1
0;23.01.1996;13.01.1991;76;INF;0;1;0;1
1;13.01.1991;13.01.1991;48;ICH;1;0;0;1
0;1.12.1993;14.01.1991;81;INF;0;0;0;1
1;12.12.1991;14.01.1991;53;INF;0;0;1;1
0;.;15.01.1991;73;ID;0;0;0;1
      

Thanks for your help. Very insightfull and your version of "RTFM" was not
to harsh either ;0)
Part of what I want to achieve with the inclusion of the file is to be
able to showcase a read-in function for the particular data type. Is there
a slick way - sticking to your example - to reference the 'stroke.csv'
directly? I'd like to put in the example of some function.Rd something
analogous to # Use function to read in file:
result <- function(<link to 'stroke.csv' in installed ISwR package>)
Without having to resort to accepting the example as "No Run".
    

Answering to myself and staying with the same example:
        system.file("data/stroke.csv",package="ISwR")
allows direct access to the example file (name).