[R] unable to get bigglm working, ATTN: Thomas Lumley

[Thomas Lumley]

Actually, I think the problem *is* reading in the data

If I try reading in your supplied lines of data with the read.table arguments() in your make.data() function I get your error message.
> data<-read.table(tmp<-textConnection(
+ "988887 2007-03-05 2007-06-01 90 3 5.450 205500.00 999.00 999.000 0.000 0 0
+ 988887 2007-03-06 2007-06-01 90 3 5.450 205500.00 999.00 999.000 0.000 1 0
+ 988887 2007-03-07 2007-06-01 90 3 5.450 205500.00 999.00 999.000 -0.100 2 0
+ 988887 2007-03-08 2007-06-01 90 3 5.450 205500.00 999.00 999.000 -0.100 3 0
+ 988887 2007-03-09 2007-06-01 90 3 5.450 205500.00 999.00 999.000 -0.100 4 0
+ 988887 2007-03-12 2007-06-01 90 3 5.450 205500.00 999.00 999.000 -0.100 7 0
+ 988887 2007-03-13 2007-06-01 90 3 5.450 205500.00 999.00 999.000 -0.100 8 0
+ 988887 2007-03-14 2007-06-01 90 3 5.450 205500.00 999.00 999.000 -0.100 9 0
+ 988887 2007-03-15 2007-06-01 90 3 5.450 205500.00 999.00 999.000 -0.100 10 0
+ 988887 2007-03-16 2007-06-01 90 3 5.450 205500.00 999.00 999.000 -0.100 11 0
+ "), colClasses = list ("NULL", "Date","Date", "integer",
+ "factor",rep("numeric",5),rep("integer",2)), 
+   col.names = c("id","dt", "promdt","term", "termfac",
+ "commintr","commbal","issuebal","intr","ri","loctime","resp") 
+ )
Error in is(object, Class) :
   trying to get slot "className" from an object of a basic class ("list") with no slots

My guess is that the problem is that you use list() instead of c() for constructing your colClasses argument.  In the code for reading the file that you didn't have a problem with, you used c().

    -thomas


On Fri, 2 Jul 2010, stephenb wrote:

>
> I am using an example posted in this help forum to work with a file. the head
> of the file looks like:
> 988887 2007-03-05 2007-06-01 90 3 5.450 205500.00 999.00 999.000 0.000 0 0
> 988887 2007-03-06 2007-06-01 90 3 5.450 205500.00 999.00 999.000 0.000 1 0
> 988887 2007-03-07 2007-06-01 90 3 5.450 205500.00 999.00 999.000 -0.100 2 0
> 988887 2007-03-08 2007-06-01 90 3 5.450 205500.00 999.00 999.000 -0.100 3 0
> 988887 2007-03-09 2007-06-01 90 3 5.450 205500.00 999.00 999.000 -0.100 4 0
> 988887 2007-03-12 2007-06-01 90 3 5.450 205500.00 999.00 999.000 -0.100 7 0
> 988887 2007-03-13 2007-06-01 90 3 5.450 205500.00 999.00 999.000 -0.100 8 0
> 988887 2007-03-14 2007-06-01 90 3 5.450 205500.00 999.00 999.000 -0.100 9 0
> 988887 2007-03-15 2007-06-01 90 3 5.450 205500.00 999.00 999.000 -0.100 10 0
> 988887 2007-03-16 2007-06-01 90 3 5.450 205500.00 999.00 999.000 -0.100 11 0
>
> the code is:
> make.data <- function (filename, chunksize, ...) {
>  conn<-NULL;
>  function (reset=FALSE) {
>    if (reset) {
>      if (!is.null(conn)) {
>        close(conn);
>      };
>      conn <<- file (description=filename, open="r");
>    } else {
>      rval <- read.table (conn, nrows=chunksize,sep=' ',
>        skip=0, header=FALSE,...);
>      if (nrow(rval)==0) {
>        close(conn);
>        conn<<-NULL;
>        rval<-NULL;
>      } else {
>        rval$relage <- rval$loctime/rval$term;
>
>      };
>    return(rval);
>    }
>  }
> };
>
> a <- make.data ( filename = "G:/sqldata/newf4.csv", chunksize = 100000,
>  colClasses = list ("NULL", "Date","Date", "integer",
> "factor",rep("numeric",5),rep("integer",2)),
>  col.names = c("id","dt", "promdt","term", "termfac",
> "commintr","commbal","issuebal","intr","ri","loctime","resp")
> )
> library(biglm);
>
> bigglm (formula = resp ~ poly(relage,2,raw=TRUE)+termfac+ri ,
>  data = a, family = binomial(link='logit'));
> ###   output:
>> bigglm (formula = resp ~ poly(relage,2,raw=TRUE)+termfac+ri ,
> +   data = a, family = binomial(link='logit'));
> Error in is(object, Class) :
>  trying to get slot "className" from an object of a basic class ("list")
> with no slots
>>
>
> ### the following can create a df, so the problem is not loading the data
> (maybe :-)
> a <- read.table ( "G:/sqldata/newf4.csv", nrows= 500000, sep=' ',head=F,
>  colClasses = c("NULL",
> "Date","Date","integer","factor",rep("numeric",5),rep("integer",2)),
>  col.names = ("id","dt", "promdt","term", "termfac",
> "commintr","commbal","issuebal","intr","ri","loctime","resp")
> )
>
> Thanks everybody.
> -- 
> View this message in context: http://r.789695.n4.nabble.com/unable-to-get-bigglm-working-ATTN-Thomas-Lumley-tp2276524p2276524.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

Thomas Lumley
Professor of Biostatistics
University of Washington, Seattle