Re: [R] Conditional read-in of data
That does not seem like a large data set. How are you reading it? How many columns does it have? What is a lot of time by your definition? You have provided minimal data for obtaining help. I common read in files with 300K rows in under 30 seconds. Maybe you need to consider a relational database for storing your data. On Wed, Nov 4, 2009 at 12:07 AM, mnstn pavan.n...@gmail.com wrote: Hello All, I have a 40k rows long data set that is taking a lot of time to be read-in. Is there a way to skip reading even/odd numbered rows or read-in only rows that are multiples of, say, 10? This way I get the general trend of the data w/o actually reading the entire thing. The option 'skip' in read.table simply skips the first n rows and reads the rest. I do understand that once the full data set (40k rows) is read-in, I can manipulate the data. But the bottle-neck here is the first read/scan of data. I searched in the forum using key words (conditional skip/skip reading rows/skip data/conditional data read) etc. but couldn't find relevant conversations. I apologize if this has already been discussed since it does seem hard to imagine that nobody has come across this problem yet. Any suggestions/comments are welcome. Thanks, mnstn -- View this message in context: http://old.nabble.com/Conditional-read-in-of-data-tp26191091p26191091.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Conditional read-in of data
1. You can pipe your data through gawk (or other scripting language) process as in: http://tolstoy.newcastle.edu.au/R/e5/help/08/09/2129.html 2. read.csv.sql in the sqldf package on CRAN will set up a database for you, read the file into the database automatically defining the layout of the table, extract a portion into R based on an sql statement that you provide and then destroy the database all in one statement. It uses the sqlite database which is included in the RSQLite R package that it depends on so there is nothing to separately install. See ?read.csv.sql in the package and also see example 13 on the home page: http://sqldf.googlecode.com On Wed, Nov 4, 2009 at 12:07 AM, mnstn pavan.n...@gmail.com wrote: Hello All, I have a 40k rows long data set that is taking a lot of time to be read-in. Is there a way to skip reading even/odd numbered rows or read-in only rows that are multiples of, say, 10? This way I get the general trend of the data w/o actually reading the entire thing. The option 'skip' in read.table simply skips the first n rows and reads the rest. I do understand that once the full data set (40k rows) is read-in, I can manipulate the data. But the bottle-neck here is the first read/scan of data. I searched in the forum using key words (conditional skip/skip reading rows/skip data/conditional data read) etc. but couldn't find relevant conversations. I apologize if this has already been discussed since it does seem hard to imagine that nobody has come across this problem yet. Any suggestions/comments are welcome. Thanks, mnstn -- View this message in context: http://old.nabble.com/Conditional-read-in-of-data-tp26191091p26191091.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Conditional read-in of data
Hello Jim and Gabor,
Thanks for your inputs. The lines:
a-as.matrix(read.table(pipe(awk -f cut.awk Data.file)))
cut.awk{for(i = 1; i = NF; i=i+10) print $i,}
solved my problem. I know that 40k lines is not a large data set. I have
about 150 files each of which has 40k rows and in each file I wanted to
visualize (basically to ensure nothing odd is going on) how the data behaves
in each quarter of the data w/o making 150 figures/pdf files. In future as
my data size increases I will consider using relational databases.
Thanks again,
mnstn
Gabor Grothendieck wrote:
1. You can pipe your data through gawk (or other scripting language)
process as in:
http://tolstoy.newcastle.edu.au/R/e5/help/08/09/2129.html
2. read.csv.sql in the sqldf package on CRAN will set up a database
for you, read the file into the database automatically defining the
layout of the table, extract a portion into R based on an sql
statement that you provide and then destroy the database all in one
statement. It uses the sqlite database which is included in the
RSQLite R package that it depends on so there is nothing to separately
install.
See ?read.csv.sql in the package and also see example 13 on the home page:
http://sqldf.googlecode.com
On Wed, Nov 4, 2009 at 12:07 AM, mnstn pavan.n...@gmail.com wrote:
Hello All,
I have a 40k rows long data set that is taking a lot of time to be
read-in.
Is there a way to skip reading even/odd numbered rows or read-in only
rows
that are multiples of, say, 10? This way I get the general trend of the
data
w/o actually reading the entire thing. The option 'skip' in read.table
simply skips the first n rows and reads the rest. I do understand that
once
the full data set (40k rows) is read-in, I can manipulate the data. But
the
bottle-neck here is the first read/scan of data.
I searched in the forum using key words (conditional skip/skip reading
rows/skip data/conditional data read) etc. but couldn't find relevant
conversations. I apologize if this has already been discussed since it
does
seem hard to imagine that nobody has come across this problem yet.
Any suggestions/comments are welcome.
Thanks,
mnstn
--
View this message in context:
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Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
View this message in context:
http://old.nabble.com/Conditional-read-in-of-data-tp26191091p26197793.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
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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.
