[R] Problem passing data into read.table()

dmcwilli dmcwilli at utk.edu
Tue Apr 23 20:51:04 CEST 2002

Sorry for the delay, only just now got back to it ...

1. debug() did not help, would not show state of nrows inside read.table()
2. fill=T did help, could have dropped the last 2 rows (footer).

By accident I found the problem.  read.table() returns a dataframe and the 
result of the calculation of the number of rows has mode "list".  Coercing it 
to numeric solves the problem.

Working solution:

function(fname) {

# my.func(fname)
# Function to read file with header and footer
# Number of rows calculable from header row 8

grid.layout <- read.table(fname, as.is=T, header=F, sep="\t", comment.char="", 
skip=7, nrows=1)

# coerce rows calculation to numeric
row.ctr <- 

#read.table now sees row.ctr
tmp.df <- read.table(fname, as.is=T, header=T, sep="\t", comment.char="", 
skip=20, nrows=row.ctr )

# drop empty first column
tmp.df <- tmp.df[, -1 ]


#  end of my.func()

Thanks to all who helped.


>===== Original Message From Jason Turner <jasont at indigoindustrial.co.nz> 
>On Mon, Apr 22, 2002 at 03:21:34PM -0400, David R. McWillliams wrote:
>> I thought about scan(), but I think that would require knowing the number
>> of columns beforehand.
>Sounds like you need file(),readLines(), and strsplit(), with
>a home-brewed data frame filler loop.
>Something like (untested - just giving the idea here):
>con <- file(fname)
>header <- readLines(con, n=21)
>#some magic here, to get the max number of columns
>max.cols <- magic stuff
>my.data <- readLines(con)
>#and let's be hygenic
>#chop off the last 2 lines, as they're footer stuff we don't want
>#pushBack would probably work too, but I'm less familiar with it.
>last.two <- ( length(my.data)-1 ):length(my.data)
>my.data <- my.data[-last.two]
>#split by tabs
>my.data <- strsplit(my.data,"\t")
>my.mat <- matrix(NA,ncol=max.cols,nrow=length(my.data))
>for(i in seq(along=my.data)) {
>	for(j in seq(along=my.data[[i]]) {
>		my.mat[i][j] <- as.numeric(my.data[[i]][j])
>	}
>> As I noted before, if I put in the number of
>> rows in the second call to read.table(), say 'nrows=2000', it correctly
>> detects the number of columns and rows.  I just can't get it to see the
>> calculated value as in 'nrows=row.ctr'.  The intervening print() can fetch
>> the value of row.ctr, so I don't understand why read.table() can't get it.
>Not sure.  Have you played with debug() ?  I've found that very, very
>handy for when I lose values - just walk slowly through the function,
>one step at a time, and print out values as you think they might be
>Indigo Industrial Controls Ltd.
>jasont at indigoindustrial.co.nz

David McWilliams

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