[R] ggplot2
I just updated to R 2.14 with ggplot2 0.9 and am finding bugs. ggplot2 GPL-2 2.14.0 This example is taken from pg 101 in the ggplot book. plot - qplot(date, psavert, data = economics, geom = line) + ylab(Personal savings rate) + geom_hline(xintercept = 0, colour = grey50)' plot + scale_x_date(major = 10 years) Error in continuous_scale(aesthetics, date, identity, breaks = breaks, : unused argument(s) (major = 10 years) plot + scale_x_date(limits = as.Date(c(2004-01-01, 2005-01-01)),format = %Y-%m-%d) plot + scale_x_date(limits = as.Date(c(2004-01-01, 2005-01-01)),format = %Y-%m-%d) Error in continuous_scale(aesthetics, date, identity, breaks = breaks, : unused argument(s) (format = %Y-%m-%d) -- View this message in context: http://r.789695.n4.nabble.com/ggplot2-tp4447745p4447745.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.
Re: [R] ggplot2
I found the addendum. http://cloud.github.com/downloads/hadley/ggplot2/guide-col.pdf -- View this message in context: http://r.789695.n4.nabble.com/ggplot2-tp4447745p4448150.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.
Re: [R] X11 graphics windows under CMD BATCH
I had this same issue. My quick and dirty solution was to create an infinite loop at the end of my R plotting script and then manually kill the job with Ctrl+C once I was done looking at the plot. -- View this message in context: http://r.789695.n4.nabble.com/X11-graphics-windows-under-CMD-BATCH-tp838015p3335922.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.
Re: [R] Parallel Scan of Large File
Hi Jim,
Thanks for your insight. I used Linux split to split my large file into
smaller partitions. On the server I work on, multipath I/O access is enabled
and we use RAID for storage; thus, I don't think I can put each partition on
a spindle. I'm able to open multiple files at a time into stdin from the
command line:
cat file1.txt | wc -l
cat file2.txt | wc -l
cat file3.txt | wc -l
cat file4.txt | wc -l
But I'm still not sure how to read each partition in parallel. When I run
this code, it doesn't run in parallel, instead file.list gets filled with 1
cpu doing all the work.
R library(doMC)
R files - Sys.glob(x*) #
Grabs all the file partitions created by split
R file.list - lapply(files,function(x){file(x,r)}) #
Creates all the file partitions connections
R master - foreach (i = icount(length(open))) %dopar% # Attempt at
parallel readLines
+{
+ readLines(file.list[[i]],100)
+}
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[R] Parallel Scan of Large File
Is it possible to parallel scan a large file into a character vector in 1M
chunks using scan() with the doMC package? Furthermore, can I specify the
tasks for each child?
i.e. I'm working on a Linux box with 8 cores and would like to scan in 8M
records at time (all 8 cores scan 1M records at a time) from a file with 40M
records total.
file - file(data.txt,r)
child - foreach(i = icount(40)) %dopar%
{
scan(file,what = character,sep = \n,skip = 0,nlines = 1e6)
}
Thus, each child would have a different skip argument. child[[1]]: skip = 0,
child[[2]]: skip = 1e6 + 1, child[[3]]: skip = 2e6 + 1, ... ,child[[40]]:
skip = 39e6 + 1. I would then end up with a list of 40 vectors with
child[[1]] containing records 1 to 100, child[[2]] containing records
101 to 200, ... ,child[[40]] containing records 3901 to
4000.
Also, would one file connection suffice or does their need to be a file
connection that opens and closes for each child?
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Re: [R] R cmd batch with parameters
http://projects.uabgrid.uab.edu/r-group/wiki/CommandLineProcessing -- View this message in context: http://r.789695.n4.nabble.com/R-cmd-batch-with-parameters-tp3075376p3075587.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.
Re: [R] Non-visible functions: merge.data.table
Thanks Jim! I posted the specifics of what I'm trying to accomplish here: http://r.789695.n4.nabble.com/Slow-Data-Table-Merge-td3072027.html -- View this message in context: http://r.789695.n4.nabble.com/Non-visible-functions-merge-data-table-tp3072051p3072075.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] Non-visible functions: merge.data.table
I've downloaded the data.table package from CRAN and R-Forge and still can't utilize merge.data.table for faster merges. How do I make this function visible? install.packages(data.table,repos=http://R-Forge.R-project.org;) trying URL 'http://R-Forge.R-project.org/src/contrib/data.table_1.5.1.tar.gz' Content type 'application/x-gzip' length 616492 bytes (602 Kb) opened URL library(data.table) methods(merge) [1] merge.data.frame merge.data.table* merge.default Non-visible functions are asterisked -- View this message in context: http://r.789695.n4.nabble.com/Non-visible-functions-merge-data-table-tp3071879p3071879.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.
Re: [R] Subset POSIXlt Field
This should work: test -subset(wild,ID==2830 Date==as.POSIXlt(2010-08-17)) If not, here's another solution: dates - c(2010-05-28,2010-08-17) dates - as.POSIXlt(dates) id - c(2830,2830) data - data.frame(id,dates) test - data[data$id == 2830 data$dates == as.POSIXlt(2010-08-17), ] test id dates 2 2830 2010-08-17 -- View this message in context: http://r.789695.n4.nabble.com/Subset-POSIXlt-Field-tp2956822p2956890.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.
Re: [R] Linux System Function
Clever solution. I use paste alot and didn't think to use it for this problem. Thanks! -- View this message in context: http://r.789695.n4.nabble.com/Linux-System-Function-tp2063058p2063113.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] Linux System Function
How do I pass a filename as an argument to the system command to count the number of records in that file? I only know how to do it by hardcoding it. HARDCODING EXAMPLE test - matrix(1:20,ncol=5) write(x = test,file = test.txt) records - as.numeric(system(cat test.txt | wc -l,intern = TRUE)) records [1] 4 ??? NON-HARCODING EXAMPLE ??? file = test.txt records - as.numeric(system(cat file | wc -l,intern = TRUE)) cat: file: No such file or directory records - as.numeric(system(cat test.txt | wc -l,intern = TRUE)) Error: unexpected symbol in records - as.numeric(system(cat test.txt TFYH -- View this message in context: http://r.789695.n4.nabble.com/Linux-System-Function-tp2063058p2063058.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] GGPLOT2: Reverse order of legend to match order of x-axis
How do I reverse the order of the legend in a bar plot to match order of the x-axis? In other words, I want the stacked colors of the legend to match the stacked colors of the bar plot. I tried this, but it didn't work. colors - c(5 = red,4 = blue,3 = darkgreen) p - qplot(factor(cyl), data=mtcars, geom=bar, fill=factor(gear)) p + scale_colour_manual(name = gear,values = colors,breaks = c(5,4,3),labels = c(5 speed,4 speed,3 speed)) http://n4.nabble.com/file/n1689526/plot.jpeg -- View this message in context: http://n4.nabble.com/GGPLOT2-Reverse-order-of-legend-to-match-order-of-x-axis-tp1689526p1689526.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.
Re: [R] GGPLOT2: Reverse order of legend to match order of x-axis
Hadley, it doesn't work. Here is my step by step sequence following the Wordpress site instructions. R version 2.10.1 (2009-12-14) Copyright (C) 2009 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. library(ggplot2) Loading required package: proto Loading required package: grid Loading required package: reshape Loading required package: plyr Loading required package: digest ggplot(diamonds, aes(clarity, fill = cut)) + geom_bar() http://n4.nabble.com/file/n1689957/plot1.jpeg levels(diamonds$cut) [1] Fair Good Very Good Premium Ideal diamonds$cut - factor(diamonds$cut, levels = rev(levels(diamonds$cut))) levels(diamonds$cut) [1] Ideal Premium Very Good Good Fair http://n4.nabble.com/file/n1689957/plot2.jpeg ggplot(diamonds, aes(clarity, fill = cut, order = -as.numeric(cut))) + geom_bar() http://n4.nabble.com/file/n1689957/plot3.jpeg diamonds$cut - factor(diamonds$cut, levels = rev(levels(diamonds$cut))) ggplot(diamonds, aes(clarity, fill = cut, order = -as.numeric(cut))) + geom_bar() http://n4.nabble.com/file/n1689957/plot4.jpeg -- View this message in context: http://n4.nabble.com/GGPLOT2-Reverse-order-of-legend-to-match-order-of-x-axis-tp1689526p1689957.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.
Re: [R] GGPLOT2: Reverse order of legend to match order of x-axis
Hah, my previous post was from my attempt on Windows Vista. It works fine on Linux though. -- View this message in context: http://n4.nabble.com/GGPLOT2-Reverse-order-of-legend-to-match-order-of-x-axis-tp1689526p1689997.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] Redhat Linux Install
I just installed R on Redhat Linux at work for the first time and have two questions. 1. I tried to install R to have png and cairo capabilities and was unsuccessful. Before running make, I ran ./configure --with-libpng=yes --with-x=no --with-cairo=yes --with-readline-yes . R installed fine, but when I run R and type capabilities() capabilities() jpeg pngtiff tcltk X11 aqua http/ftp sockets TRUE TRUE TRUE TRUEFALSEFALSE TRUE TRUE l ibxmlfifo cledit iconv NLS profmemcairo TRUEFALSE TRUE TRUE TRUE TRUEFALSE Why are png and cairo still FALSE? 2. I would also like to have X11 enabled. From reading the message board, the consesus seems to be to install xorg-dev. I'm unable to do this because I don't have root or super user priveleges. But if I'm able to log into my work servers with PuTTY and Xming and run xemacs or xvim, does this mean that X11 is already installed somewhere? If so, how do I specify this when doing ./configure? -- View this message in context: http://n4.nabble.com/Redhat-Linux-Install-tp1580181p1580181.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] ggsave in Linux
I have a script that creates a qplot that is then saved as a .png file which works fine on Windows. But I also work on Linux servers via Putty and would like to be able to create and save my plots to my working directory. Is there a way I can ggsave my qplot without utilizing X11 in Linux? I don't need to view the plot in Linux, I just want the plot created and immediately saved to my working directory. I get this error: Error in grDevices::png(..., width = width, height = height, res = dpi, : X11 is not available -- View this message in context: http://n4.nabble.com/ggsave-in-Linux-tp1567860p1567860.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] Unordered Factors For ggplot?
I have data that comes into R already ordered. When I use ggplot, it orders them which I don't want. How do I fix this without changing options(contrast)? The data I have is number of days: 30 29 ... 20 19 ... 10 9 ... 1 When I plot with ggplot, it orders them by the first number only. So 3 ends up coming before 29. -- View this message in context: http://n4.nabble.com/Unordered-Factors-For-ggplot-tp1559146p1559146.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] ggplot stacked bar chart help
I'm trying to create a stacked bar chart with x=month, y=volume, and factor=type. volume type month 100A SEP09 200A OCT09 300A DEC09 400B SEP09 500B OCT09 600B DEC09 700C SEP09 800C OCT09 900C DEC09 Following Hadley's examples, I get 3 bars with SEP09: 3-A, 3-B, 3-C, OCT09: 3-A, 3-B, 3-C, and NOV09: 3-A, 3-B, 3-C. I need SEP09: 100-A, 400-B, 700-C, OCT09: 200-A, 500-B, 800-C, and NOV09: 300-A, 600-B, 900-C. -- View this message in context: http://n4.nabble.com/ggplot-stacked-bar-chart-help-tp1470582p1470582.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.
Re: [R] ggplot stacked bar chart help
Almost there! So my previous data example was just a small subset of my true data. I have all the months from 2007-2009 in order. So when I create the barplot following your script, it bins all 12 months for each year -- a stacked barplot with 3 bars (2007,2008,2009), which I don't want. I want each month to be a seperate bin. i.e. JAN07,FEB07,...,DEC09. Thanks for your help. volume type month 100 A JAN07 100 A FEB07 100 A DEC09 100 B JAN07 100 B FEB07 100 C DEC09 100 C JAN07 100 C FEB07 100 C DEC09 -- View this message in context: http://n4.nabble.com/ggplot-stacked-bar-chart-help-tp1470582p1470725.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.
