I tried out everything but only one trick worked.
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34: | # ------------------------------------------
# Gabriel NEJM suppl data data
# m@wjst.de 29Sep10
# ------------------------------------------
d <- c("/Users/.../NEJM/")
f1 <- c("/Users/... /36studies_format_repository_NEJM.txt")
# all good tricks: NULL columns, explicit colclasses and comment characters
cc <- rep("NULL",276)
cc[c(2,4,5)] <- c("character")
ds <- read.table(file=f1, sep="\t", header=TRUE, na.string="", dec=".", comment.char="", colClasses=cc)
# but does not run due to memory problems with 567.589 rows and 276 cols
# another trick: read only certain columns
ds <- read.table( pipe("cut -f1,2,3,4 /Users/... /36studies_format_repository_NEJM.txt")
# this works but is not very handy...
# clever: make a SQL dataset on the fly - found at code.google.com/p/sqldf/#Example_6._File_Input
library(sqldf))
nejm <- file(f1)
ds <- sqldf("select * from nejm limit 10", file.format = list(header = TRUE) )
# but also this throws an error or silently crashes R
# converting to SQLITE outside R finally worked ...
try(system("sqlite nejm.sqlite3 <nejm_make.sql", intern = TRUE, ignore.stderr = TRUE))
library(RSQLite)
SQLite(max.con = 16, fetch.default.rec = 100000, force.reload = FALSE, shared.cache=FALSE)
con <- dbDriver("SQLite")
dbc <- dbConnect(con, dbname = "/Users/.../nejm.sqlite3")
SQL <- c("SELECT * FROM nejm")
rs <- dbSendQuery(dbc,SQL)
nejm <- fetch(rs, n = -1)
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