R help - Jul 2014 - combining data from multiple read.delim() invocations.

Is there a better way to do the following? I have data in a number of tab
delimited files. I am using read.delim() to read them, in a loop. I am
invoking my code on Linux Fedora 20, from the BASH command line, using
Rscript. The code I'm using looks like:

arguments <- commandArgs(trailingOnly=TRUE);
# initialize the capped_data data.frame
capped_data <- data.frame(lpar="NULL",
                       started=Sys.time(),
                       ended=Sys.time(),
                       stringsAsFactors=FALSE);
# and empty it.
capped_data <- capped_data[-1,];
#
# Read in the data from the files listed
for (file in arguments) {
    data <- read.delim(file,
                    header=FALSE,
                   
col.names=c("lpar","started","ended"),
                    as.is=TRUE,
                    na.strings='\\N',
                   
colClasses=c("character","POSIXct","POSIXct"));
    capped_data <- rbind(capped_data,data)
}
#

I.e. is there an easier way than doing a read.delim/rbind in a loop?


-- 
There is nothing more pleasant than traveling and meeting new people!
Genghis Khan

Maranatha! <><
John McKown

	[[alternative HTML version deleted]]

There is a better way. First we need some data. This creates three files in your
home directory, each with five rows:

write.table(data.frame(rep("A", 5), Sys.time(), Sys.time()),
	"A.tab", sep="\t", row.names=FALSE, col.names=FALSE)
write.table(data.frame(rep("B", 5), Sys.time(), Sys.time()),
	 "B.tab", sep="\t", row.names=FALSE, col.names=FALSE)
write.table(data.frame(rep("C", 5), Sys.time(), Sys.time()),
	"C.tab", sep="\t", row.names=FALSE, col.names=FALSE)

Now to read and combine them into a single data.frame:

fls <- c("A.tab", "B.tab", "C.tab")
df.list <- lapply(fls, read.delim, header=FALSE,
col.names=c("lpar","started","ended"),
           as.is=TRUE, na.strings='\\N',
colClasses=c("character","POSIXct","POSIXct"))
df.all <- do.call(rbind, df.list)
> str(df.all)
'data.frame':   15 obs. of  3 variables:
 $ lpar   : chr  "A" "A" "A" "A" ...
 $ started: POSIXct, format: "2014-07-01 11:25:05" "2014-07-01
11:25:05" ...
 $ ended  : POSIXct, format: "2014-07-01 11:25:05" "2014-07-01
11:25:05" ...

-------------------------------------
David L Carlson
Department of Anthropology
Texas A&M University
College Station, TX 77840-4352

-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
On Behalf Of John McKown
Sent: Tuesday, July 1, 2014 7:07 AM
To: r-help at r-project.org
Subject: [R] combining data from multiple read.delim() invocations.

Is there a better way to do the following? I have data in a number of tab
delimited files. I am using read.delim() to read them, in a loop. I am
invoking my code on Linux Fedora 20, from the BASH command line, using
Rscript. The code I'm using looks like:

arguments <- commandArgs(trailingOnly=TRUE);
# initialize the capped_data data.frame
capped_data <- data.frame(lpar="NULL",
                       started=Sys.time(),
                       ended=Sys.time(),
                       stringsAsFactors=FALSE);
# and empty it.
capped_data <- capped_data[-1,];
#
# Read in the data from the files listed
for (file in arguments) {
    data <- read.delim(file,
                    header=FALSE,
                   
col.names=c("lpar","started","ended"),
                    as.is=TRUE,
                    na.strings='\\N',
                   
colClasses=c("character","POSIXct","POSIXct"));
    capped_data <- rbind(capped_data,data)
}
#

I.e. is there an easier way than doing a read.delim/rbind in a loop?


-- 
There is nothing more pleasant than traveling and meeting new people!
Genghis Khan

Maranatha! <><
John McKown

	[[alternative HTML version deleted]]

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