Re: [R] Calculating distance matrix for large dataset
I have a version that uses bigmemory on my blog, but looks at distance on a sphere for a 36k * 36K matrix not hundreds of Gb so I dont know if the approach will work for you http://stevemosher.wordpress.com/2012/04/12/nick-stokes-distance-code-now-with-big-memory/ Steve However, I never tested it with On May 2, 2013 9:40 PM, HJ YAN yhj...@googlemail.com wrote: Dear R users I wondered if any of you ever tried to calculate distance matrix with very large data set, and if anyone out there can confirm this error message I got actually mean that my data is too large for this task. negative length vectors are not allowed My data size and code used dim(mydata_nor)[1] 365000144 d - dist(mydata_nor, method = euclidean) Here my data has 1000 samples each has a year data observed by 10 minutes interval daily, so the size is (365* 1000) * 144. I checked the manual of function 'dist' but can not see the upper limit size allowed, and I bet there should be one, so any hints is appreciated. I would also be grateful if any other method for calculating distance matrix for large dataset could be advised. I appreciate reproducible code should be provided for your advice, so try below if needed: A-matrix(1:365000*144,nrow=365000,ncol=144) dim(A)[1] 365000144 d1-dist(A,method=euclidean)Error in dist(A, method = euclidean) : negative length vectors are not allowed Many thanks in advance! HJ [[alternative HTML version deleted]] __ 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. [[alternative HTML version deleted]] __ 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] How can I map numbers to colours with raster?
see the function level() in raster. also levelplot in rastervis package. you basically create a raster attribute table coerce the raster to factor class and plot. check geo sig i have posted the same question there On Oct 29, 2012 2:15 AM, Jonsson amen.alya...@bordeaux.inra.fr wrote: This code will read binary file and display it as a map. may problem is that this code is using a continuous colour scheme, even though I have discrete data (which is a classification scheme). How can I map numbers to colours with raster? Please require(raster) conne - file(C:\\lai.bin, rb) sd- readBin(conne, integer(), size=1, n=360*720, signed=F) y-t(matrix((data=sd), ncol=360, nrow=720)) r = raster(y) extent(r) = extent(c(xmn=-180,xmx=180,ymn=-90,ymx=90)) plot(r) -- View this message in context: http://r.789695.n4.nabble.com/How-can-I-map-numbers-to-colours-with-raster-tp4647742.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. [[alternative HTML version deleted]] __ 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] bigmemory for dataframes?
i believe ff has a dataframe class. as for your object data im less clear. how big is it On Oct 18, 2012 12:45 PM, Alexander Shenkin ashen...@ufl.edu wrote: Hi Folks, I've been bumping my head against the 4GB limit for 32-bit R. I can't go to 64-bit R due to package compatibility issues (ROBDC - possible but painful, xlsReadWrite - not possible, and others). I have a number of big dataframes whose columns all sorts of data types - factor, character, integer, etc. I run and save models that keep copies of the modeled data inside the model objects as well (mle2 objects, to be specific). I'm searching for a way to cache some of these dataframes and objects to virtual memory (I think I'm using the right terminology...). I've read around, and while bigmemory and ff and the like would likely suit my purposes if I were just dealing with numeric matricies, I'm dealing with dataframes and objects. Any thoughts would be greatly appreciated! Thanks, Allie __ 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. [[alternative HTML version deleted]] __ 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] R process must die - can I save history?
thanks Dr. R. this will come in handy in the future as I have a knack for hanging R. On Oct 2, 2012 12:01 PM, Prof Brian Ripley rip...@stats.ox.ac.uk wrote: On 02/10/2012 18:29, Bert Gunter wrote: ?history in a fresh R session, to see what might be possible. I'll bet the answer is, No, you're screwed, though. Nevertheless, maybe Linux experts can save you. Maybe not. On a Unix-alike see ?Signals. If you can find the pid of the R process and it is still running (and not e.g. suspended), kill -USR1 pid will save the workspace and history. May the Force be with you. -- Bert On Tue, Oct 2, 2012 at 10:17 AM, Mike Miller mbmille...@gmail.com wrote: I connected from my desktop Linux box to a Linux server using ssh in an xterm, but that xterm was running in Xvnc. I'm running R on the server in that xterm (over ssh). Something went wrong with Xvnc that has caused it to hang, probably this bug: https://bugs.launchpad.net/**ubuntu/+source/vnc4/+bug/**819473https://bugs.launchpad.net/ubuntu/+source/vnc4/+bug/819473 So I can't get back to that ssh session or to R. I had done a bunch of work in R but the command history hasn't been written out. If I kill R, I assume the command history is gone. I wish I could somehow cause R to dump the command history. Is there any way to tell the running R process to write the history somewhere? Thanks in advance. Mike -- Michael B. Miller, Ph.D. Minnesota Center for Twin and Family Research Department of Psychology University of Minnesota __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/** posting-guide.html http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~**ripley/http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/** posting-guide.html http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ 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] How to arrange the GUI's in window in tcltk package???
1. get programming grapgical user interfaces in R. lawrence and verzani. 2. if you used gwidgets on gtk i could tell you exactly what to do. 3. with the toolkit youve selected i think tlpack controls the way children are placed in a container. default is top to bottom On Aug 24, 2012 11:27 PM, punitha punitha@wipro.com wrote: Hi, I am new to R, I need your help. I have been said to create a GUI in R, I started using Tcltk package which was very easy to learn and code, but i am unable to arrange the GUI's in proper order in the window they are always arranged one below the other, please can anyone help me in solving this problem, Is there any links which will help me solve this problem with example. Thanks in advance. with regards, Punitha -- View this message in context: http://r.789695.n4.nabble.com/How-to-arrange-the-GUI-s-in-window-in-tcltk-package-tp4641279.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. [[alternative HTML version deleted]] __ 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] building binary tree
I believe chambers book has an example using S4 classes. which isnt much help for a beginner. you can do it the old school way. build it by hand with one vector of pointers and another data structure of leaf nodes. there is nothing magical about a tree. you can build one in basic or fortran. painful but good for ur character. On Jun 27, 2012 10:09 PM, Peppino giuseppel...@hotmail.com wrote: Hi I am new with R I Have to build a binary tree with R. I'm very confused was wondering if anyone had any R sample code they would share. I've come across a lot of C++ code(nothing in R) and this is not helping. Any bady can help me? Bye Giuseppe -- View this message in context: http://r.789695.n4.nabble.com/building-binary-tree-tp4634592.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. [[alternative HTML version deleted]] __ 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] A basic design question for R
use a list. or create new class which is a list On Jun 16, 2012 8:52 AM, Onur Uncu onuru...@gmail.com wrote: Hello R Community, I have the following design question. I have a data set that looks like this (shortened for the sake of example). Gender Age M 70 F 65 M 70 Each row represents a person with an age/gender combination. We could put this data into a data frame. Now, I would like to do some actuarial analysis on this data set. To do so, I need to create and store a mortality curve for each person in the table (a mortality curve is a matrix with 2 columns: date and survival probability). I can write a function that returns a mortality curve given gender and age. The question is the following: In what data format should I store all these mortality curve objects? Should I add a column to the data frame and each entry in that column is a matrix (a mortality curve)? This way, the mortality curve would be stored next to age/gender data in the data frame. However, I read in several places that putting vectors/matrices as elements of a data frame is a bad idea. I do not know why. What is a good design choice in this instance please? How should I store the mortality curves? Thank you for your help. __ 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. [[alternative HTML version deleted]] __ 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] Converting to XTS loses data.frame structure
is there a statement of work for the summer of code work. On May 29, 2012 12:19 PM, Joshua Ulrich josh.m.ulr...@gmail.com wrote: On Tue, May 29, 2012 at 2:11 PM, Noah Silverman noahsilver...@ucla.edu wrote: Hello, I noticed something odd when working with data frames and xts objects. If I read in a CSV file, R creates a nice data.frame. This works well. If I then convert to an XTS object, I see that all the values in the data are now quoted. My data is a mix of numeric and character. This is usually seen when converting a data.frame to a matrix, as R will treat all the data as the same class. (character) How can I ensure that R creates an XTS object that is still a data.frame so that all the data are the correct type?? You can't. xts/zoo objects are a matrix with an index attribute. Since you can't mix types in a matrix, you can't mix types in an xts/zoo object. That said, part of the xts Google Summer of Code project is to create an xts-like object that allows mixed types. Best, -- Joshua Ulrich | FOSS Trading: www.fosstrading.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. [[alternative HTML version deleted]] __ 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] Failure building any package
Did you edit the description file and the namespace file and the Rd files?
Although my tutorial is for windows if you follow steps 8 thru 10 on mac it
should work
http://stevemosher.wordpress.com/step-8-the-sample-package/
On Thu, May 17, 2012 at 7:44 PM, Noah Silverman noahsilver...@ucla.eduwrote:
Hello,
I'm attempting to build a package using R 2.15.0 on OS X
I am getting a generic failure when performing a cran type check on the
package. Even with a very simple test package, it still fails int he same
place.
Example:
In R:
rm(list=ls())
foo - function(x){print(x)}
package.skeleton(name=foo)
Then, at the command line:
R CMD build foo
R CMD check --as-cran foo_1.0.tar.gz
Some output not included here
* checking whether package foo can be installed
ERROR
Installation failed.
See foo.Rcheck/00install.out for details.
Looking at the 00install.out file, I see:
* installing *source* package foo ...
** R
Error in parse(outFile) : 5949:10: unexpected symbol
5948: c(01, 00, 00, 00, 01, 00, 00, 00, 00, 00, 00, 00, 00, 00,
5949: e0, 3f
^
ERROR: unable to collate and parse R files for package foo
Can anyone help explain what is happening here? This is the most generic
and empty package I can think of, so not sure why a build is failing.
Thanks!
--
Noah Silverman
UCLA Department of Statistics
8117 Math Sciences Building
Los Angeles, CA 90095
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Re: [R] using wildcards in download.file?
one way to solve your problem is to fetch the directory using rcurl. then mapply using the dirlist as a parameter passed to download file On Apr 13, 2012 9:24 AM, MacQueen, Don macque...@llnl.gov wrote: If you take a thorough look at the help page for download.file, and follow its advice, you may find a solution. Hint: The help page for download.file says, -- quote -- The function 'download.file' can be used to download a single file as described by 'url' from the internet and store it in 'destfile'. -- end quote -- I'd say that makes it pretty clear the answer is no. Further on in the help page in the See Also section it refers to another package. Hint: A help page for one of the functions in that packages says, -- quote -- # FTP # Download the files within a directory. -- end quote -- which looks promising. -- Don MacQueen Lawrence Livermore National Laboratory 7000 East Ave., L-627 Livermore, CA 94550 925-423-1062 On 4/12/12 2:07 PM, jt...@mappi.helsinki.fi jt...@mappi.helsinki.fi wrote: Hi, Do you know whether it is possible to use wildcards in download.file()? For example: url = ftp://abc.com/*.*; # to download all the files in the ftp folder download.file(url,destfile=...) # does not work, any solutions? Thanks! JIng __ 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. [[alternative HTML version deleted]] __ 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] Help - Importing data from txt and xlsx files
read your file with readLines(). copy the first few lines for me to read here test - readLines(yur filename) test[1:5] post the result. we can figure it out from there On Apr 13, 2012 11:46 AM, AMFTom the.quiet.r...@gmail.com wrote: Dear Thierry, Thanks for your help. Now though, I try to import data from a txt file, and it says either mydataframe - read.table(Lv2.8.txt) Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 3 did not have 15 elements or mydataframe - read.table(Lv2.8.txt, header = TRUE) Error in read.table(Lv2.8.txt, header = TRUE) : more columns than column names even though I seem to have put a column name into the txt file for each column. Any ideas? Thanks again! Tom -- View this message in context: http://r.789695.n4.nabble.com/Help-Importing-data-from-txt-and-xlsx-files-tp4554622p4555001.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. [[alternative HTML version deleted]] __ 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] Applying a function to categorized data?
Welcome to R and the list.
Others may suggest books ( Nutshell was my first ) but first there are
some things that will help you
both in programming and getting help on the list.
You should post executable code in your question. So, build a toy example
of the data.frame you have
and show what you tried. Folks here should be able to run your toy example
and show you how to get the answer you want.
For your problem I'm guessing that aggregate() would be one path
?aggregate
you will need to specify by to aggregate by month
Steve
On Thu, Apr 12, 2012 at 7:10 AM, Robert Latest boblat...@gmail.com wrote:
Hi all,
I'm just getting started in R. My problem is the following:
I have a data frame (v1) with lots of production data measurements.
Each row contains a single measurement ('ARI_MIT') with a timestamp. I
want to lump the data by months with their mean and standard
deviation.
I have already successfully managed to do the lumping by adding
another column to my data frame:
v1$MONTH = strftime(v1$TIMESTAMP, %y%m)
This makes a nice month-wise boxplot of my data, although I don't have
an idea why:
boxplot(v1$ARI_MIT ~ v1$MONTH)
I don't need this plotted, though, but in the form of a new data frame
with three columns: the month, the mean, and the standard deviation of
all values from that month.
I tried un-stacking v1 into a list of vectors and then looping over
its elements, calculating the mean of each group:
for (i in unstack(v1, v1$ARI_MIT ~ v1$MONTH)) { write(mean(i), ) }
This works, but how do I get the data into a data frame? With the
month labels in a column? They are not avaliable inside the loop body.
I know I need to get a book on R.
Thanks,
robert
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Re: [R] Listing the contents of an FTP directory via R?
A couple of ways. using Rcurl you can use the curlOption of dirlistonly. otherwise you can read the page and parse. I've got some code around here to do that. Steve On Mon, Apr 9, 2012 at 11:27 AM, Jonathan Greenberg j...@illinois.eduwrote: R-helpers: I'd like to be able to store all the file information from an ftp site (e.g. file and foldernames) through an R command. Any ideas how to do this? Here's an example site to use: ftp://e4ftl01.cr.usgs.gov/MOTA/MCD15A3.005 --j -- Jonathan A. Greenberg, PhD Assistant Professor Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 607 South Mathews Avenue, MC 150 Urbana, IL 61801 Phone: 415-763-5476 AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 http://www.geog.illinois.edu/people/JonathanGreenberg.html __ 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. [[alternative HTML version deleted]] __ 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] Listing the contents of an FTP directory via R?
Ya I hit the same error with my code that reads directories. I'll try some other stuff . I think I hit this error before I with usgs. On Mon, Apr 9, 2012 at 11:40 AM, Jonathan Greenberg j...@illinois.eduwrote: Steven: Thanks -- I seem to be running into the problem with the link I sent along: getURL(ftp://e4ftl01.cr.usgs.gov/MOTA/MCD15A3.005/,verbose=TRUE,dirlistonly = TRUE) Error in function (type, msg, asError = TRUE) : RETR response: 550 I'm wondering if it might be a passive ftp issue, but: getURL(ftp://e4ftl01.cr.usgs.gov/MOTA/MCD15A3.005/,verbose=TRUE,ftp.use.epsv=TRUE, dirlistonly = TRUE) Error in function (type, msg, asError = TRUE) : FTP response reading failed Does not seem to work... Thoughts? --j On Mon, Apr 9, 2012 at 1:32 PM, steven mosher mosherste...@gmail.com wrote: A couple of ways. using Rcurl you can use the curlOption of dirlistonly. otherwise you can read the page and parse. I've got some code around here to do that. Steve On Mon, Apr 9, 2012 at 11:27 AM, Jonathan Greenberg j...@illinois.edu wrote: R-helpers: I'd like to be able to store all the file information from an ftp site (e.g. file and foldernames) through an R command. Any ideas how to do this? Here's an example site to use: ftp://e4ftl01.cr.usgs.gov/MOTA/MCD15A3.005 --j -- Jonathan A. Greenberg, PhD Assistant Professor Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 607 South Mathews Avenue, MC 150 Urbana, IL 61801 Phone: 415-763-5476 AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 http://www.geog.illinois.edu/people/JonathanGreenberg.html __ 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. -- Jonathan A. Greenberg, PhD Assistant Professor Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 607 South Mathews Avenue, MC 150 Urbana, IL 61801 Phone: 415-763-5476 AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 http://www.geog.illinois.edu/people/JonathanGreenberg.html [[alternative HTML version deleted]] __ 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] Listing the contents of an FTP directory via R?
Directory A HREF=/MOTA/MCD15A3.005/2003.07.04/B2003.07.04/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.07.08/B2003.07.08/B/A 10/18/2011 06:00PM Directory A HREF=/MOTA/MCD15A3.005/2003.07.12/B2003.07.12/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.07.16/B2003.07.16/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.07.20/B2003.07.20/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.07.24/B2003.07.24/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.07.28/B2003.07.28/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.08.01/B2003.08.01/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.08.05/B2003.08.05/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.08.09/B2003.08.09/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.08.13/B2003.08.13/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.08.17/B2003.08.17/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.08.21/B2003.08.21/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.08.25/B2003.08.25/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.08.29/B2003.08.29/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.09.02/B2003.09.02/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.09.06/B2003.09.06/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.09.10/B2003.09.10/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.09.14/B2003.09.14/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.09.18/B2003.09.18/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.09.22/B2003.09.22/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.09.26/B2003.09.26/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.09.30/B2003.09.30/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.10.04/B2003.10.04/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.10.08/B2003.10.08/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.10.12/B2003.10.12/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.10.16/B2003.10.16/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.10.20/B2003.10.20/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.10.24/B2003.10.24/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.10.28/B2003.10.28/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.11.01/B2003.11.01/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.11.05/B2003.11.05/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.11.09/B2003.11.09/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.11.13/B2003.11.13/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.11.17/B2003.11.17/B/A 10/18/2011 06:00PM Directory A HREF=/MOTA/MCD15A3.005/2003.11.21/B2003.11.21/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.11.25/B2003.11.25/B/A 10/18/2011 06:00PM Directory A HREF=/MOTA/MCD15A3.005/2003.11.29/B2003.11.29/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.12.03/B2003.12.03/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.12.07/B2003.12.07/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.12.11/B2003.12.11/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.12.15/B2003.12.15/B/A 10/18/2011 06:01PM Directory A HREF=/MOTA/MCD15A3.005/2003.12.23/B2003.12.23/B/A On Mon, Apr 9, 2012 at 11:40 AM, Jonathan Greenberg j...@illinois.eduwrote: Steven: Thanks -- I seem to be running into the problem with the link I sent along: getURL(ftp://e4ftl01.cr.usgs.gov/MOTA/MCD15A3.005/,verbose=TRUE,dirlistonly = TRUE) Error in function (type, msg, asError = TRUE) : RETR response: 550 I'm wondering if it might be a passive ftp issue, but: getURL(ftp://e4ftl01.cr.usgs.gov/MOTA/MCD15A3.005/,verbose=TRUE,ftp.use.epsv=TRUE, dirlistonly = TRUE) Error in function (type, msg, asError = TRUE) : FTP response reading failed Does not seem to work... Thoughts? --j On Mon, Apr 9, 2012 at 1:32 PM, steven mosher mosherste...@gmail.com wrote: A couple of ways. using Rcurl you can use the curlOption of dirlistonly. otherwise you can read the page and parse. I've got some code around here to do that. Steve On Mon, Apr 9, 2012 at 11:27 AM, Jonathan Greenberg j...@illinois.edu wrote: R-helpers: I'd like to be able to store all the file information from an ftp site (e.g. file and foldernames) through an R command. Any ideas how to do this? Here's an example site to use: ftp://e4ftl01.cr.usgs.gov/MOTA/MCD15A3.005 --j -- Jonathan A. Greenberg, PhD Assistant Professor Department
Re: [R] Handling 8GB .txt file in R?
As the other poster noted, you can just skip lines. Big matrix should work just fine, except I am not sure how the dates will be handled Here is some sample code from my stuff txtName is the file name of the file you are reading Directory is the path where you want to write the file.backed matrix filenameis the file.backed big matrix dname is a filename for describing the data sep What's your separator, comma or space? below I use tab, because my file is tab delimited replace my column names with yours PERMNO DATETICKERPERMCO PRC VOLNUMTRDvwretdewretd Your dates may be coerced in factors. Not sure how that will work. You can also try ff options(bigmemory.allow.dimnames=TRUE) D- read.big.matrix(txtName, skip = 5, backingpath = Directory, backingfile = filename, descriptorfile = dname, sep = \t, type = double, col.names = c(Id,SeriesNo,Date,Temp,Unc,Obs,Tobs) ) On Sat, Mar 24, 2012 at 9:20 PM, iliketurtles isaacm...@gmail.com wrote: Thanks to all the suggestions. To the first individual that replied, I can't do any stuff with unix or perl. All I know is R. @KEN: I'm using Windows 7, 64 bit. @Steve: Here's the readLines output.. As we can see, lines 1-3 are empty and line 5 is empty, and there's also empty elements after line 5!. [1] [2] [3] [4] PERMNO DATETICKERPERMCO PRC VOLNUMTRDvwretdewretd [5] [6]106/01/19867952 . . . -0.000138 0.001926 [7]107/01/1986OMFGA 7952-2.56250 1000 . 0.013809 0.011061 [8]108/01/1986OMFGA 7952-2.5 12800 . -0.020744 -0.005117 [9]109/01/1986OMFGA 7952-2.5 1400 . -0.011219 -0.011588 [10]110/01/1986OMFGA 7952-2.5 8500 . 0.83 0.003651 [11]113/01/1986OMFGA 7952-2.62500 5450 . 0.002749 0.002433 - Isaac Research Assistant Quantitative Finance Faculty, UTS -- View this message in context: http://r.789695.n4.nabble.com/Handling-8GB-txt-file-in-R-tp4500971p4502706.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. [[alternative HTML version deleted]] __ 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] video recorded simulations in R?
see the package animate On Mar 24, 2012 7:37 AM, Sarah Goslee sarah.gos...@gmail.com wrote: The easiest approach is to save your plot as a bitmap every x-th iteration, and then use other tools to animate them. I use ImageMagick for this, but I'm sure there are other options. Sarah On Mar 23, 2012, at 11:28 PM, C W tmrs...@gmail.com wrote: Hi everyone, Is it possible to video record simulations in R? Say, for instance, I am plotting samples using MCMC algorithm, and then showing its convergence after 1 iterations. I was wondering if anyone has done this before? __ 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. [[alternative HTML version deleted]] __ 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] Memory issue. XXXX
1. How much RAM do you have (looks like 2GB ) . If you have more than 2GB then you can allocate more memory with memory.size() 2. If you have 2GB or less then you have a couple options a) make sure your session is clean of unnecessary objects. b) Dont read in all the data if you dont need to ( see colClasses to control this ) c) use the bigmemory package or ff package d) buy more RAM On Fri, Mar 2, 2012 at 6:57 AM, Dan Abner dan.abne...@gmail.com wrote: Hi everyone, Any ideas on troubleshooting this memory issue: d1-read.csv(arrears.csv) Error: cannot allocate vector of size 77.3 Mb In addition: Warning messages: 1: In class(data) - data.frame : Reached total allocation of 1535Mb: see help(memory.size) 2: In class(data) - data.frame : Reached total allocation of 1535Mb: see help(memory.size) 3: In class(data) - data.frame : Reached total allocation of 1535Mb: see help(memory.size) 4: In class(data) - data.frame : Reached total allocation of 1535Mb: see help(memory.size) Thanks! Dan __ 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. [[alternative HTML version deleted]] __ 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] Question about tables in bigtabulate
I have a large file backed big. matrix, with millions of rows and 20 columns. The columns contain data that I simply need to tabulate. There are a few dozen unique values. and I just want a frequency count Test code with a small big matrix. library(bigmemory) library(bigtabulate) test - big.matrix(nrow = 100, ncol = 10) test[,1:3]- sample(150) test[,4:6]- sample(100) test[,7:10]- sample(100) ##so we have sample big memory matrix. Its not file backed but will do for testing. ##the result we want is one that you would get if you could run table() on the bigmatrix ##thats emulated in this example by coercing the bigmatrix to a matrix. ##in the real application that is not possible, because of RAM limits P - table(as.matrix(test)) ## the package big tabulate has a version of table called bigtable. ## you can run table on an individual column. ## I want to run it on all the columns. basically combine the results of running it on individual columns ## if you try to specify multiple columns, you get a contingency table, and if you use too many ## columns you will hang your system hard .. so dont try the line below . Well at least I hung my system # Ouch - bigtable(test, ccols = seq(1,10)) So, is there a simple way to get the answer as emulated by P-table(as.matrix(test)) without coercing to a matrix. TIA [[alternative HTML version deleted]] __ 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] best option for big 3D arrays?
Thanks,
That helped. Maybe when I get a chance I will do some blog posts on the
basics of ff
I think some tutorials would be a good idea
Steve
On Mon, Feb 27, 2012 at 3:47 AM, Djordje Bajic je.li@gmail.com wrote:
Steven, sorry for the delay in responding,
I have been investigating this also and here is the way I do it (though
probably not the best way):
# .. define a 3D array
ngen = 904
gratios - ff(NA, dim=rep(ngen,3), vmode=double)
# .. fill the array with standard R functions
ffsave (gratios, file=mydir/myfile)# without extension
finalizer(gratios) - delete
# ..
so, you firstly define the ff object, you put the data inside, and you
ffsave it. The ffsave function will generate two files, with extensions
ffdata and a Rdata. Then you set 'delete' to be the 'finalizer' of the
object; in this way you avoid ff to save it in some tmp dir and occupy disk
space forever. Then, you can access your object in the next R session:
ffload(mydir/myfile)# also without extension
I hope this helped.
Cheers,
djordje
2012/2/23 steven mosher mosherste...@gmail.com
Did you have to use a particular filename? or extension.
I created a similar file but then could not read it back in
Steve
On Mon, Feb 13, 2012 at 6:45 AM, Djordje Bajic je.li@gmail.com
wrote:
I've been investigating and I partially respond myself. I tried the
packages 'bigmemory' and 'ff' and for me the latter did the work I need
pretty straightforward. I create the array in filebacked form with the
function ff, and it seems that the usual R indexing works well. I have
yet
to see the limitations, but I hope it helps.
a foo example:
myArr - ff(NA, dim=rep(904,3), filename=arr.ffd, vmode=double)
myMat - matrix(1:904^2, ncol=904)
for ( i in 1:904 ) {
myArr[,,i] - myMat
}
Thanks all,
2012/2/11 Duncan Murdoch murdoch.dun...@gmail.com
On 12-02-10 9:12 AM, Djordje Bajic wrote:
Hi all,
I am trying to fill a 904x904x904 array, but at some point of the
loop
R
states that the 5.5Gb sized vector is too big to allocate. I have
looked
at
packages such as bigmemory, but I need help to decide which is the
best
way to store such an object. It would be perfect to store it in this
cube
form (for indexing and computation purpouses). If not possible, maybe
the
best is to store the 904 matrices separately and read them
individually
when needed?
Never dealed with such a big dataset, so any help will be appreciated
(R+ESS, Debian 64bit, 4Gb RAM, 4core)
I'd really recommend getting more RAM, so you can have the whole thing
loaded in memory. 16 Gb would be nice, but even 8Gb should make a
substantial difference. It's going to be too big to store as an array
since arrays have a limit of 2^31-1 entries, but you could store it
as a
list of matrices, e.g.
x - vector(list, 904)
for (i in 1:904)
x[[i]] - matrix(0, 904,904)
and then refer to entry i,j,k as x[[i]][j,k].
Duncan Murdoch
[[alternative HTML version deleted]]
__
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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.
[[alternative HTML version deleted]]
__
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.
[[alternative HTML version deleted]]
__
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] best option for big 3D arrays?
Did you have to use a particular filename? or extension.
I created a similar file but then could not read it back in
Steve
On Mon, Feb 13, 2012 at 6:45 AM, Djordje Bajic je.li@gmail.com wrote:
I've been investigating and I partially respond myself. I tried the
packages 'bigmemory' and 'ff' and for me the latter did the work I need
pretty straightforward. I create the array in filebacked form with the
function ff, and it seems that the usual R indexing works well. I have yet
to see the limitations, but I hope it helps.
a foo example:
myArr - ff(NA, dim=rep(904,3), filename=arr.ffd, vmode=double)
myMat - matrix(1:904^2, ncol=904)
for ( i in 1:904 ) {
myArr[,,i] - myMat
}
Thanks all,
2012/2/11 Duncan Murdoch murdoch.dun...@gmail.com
On 12-02-10 9:12 AM, Djordje Bajic wrote:
Hi all,
I am trying to fill a 904x904x904 array, but at some point of the loop R
states that the 5.5Gb sized vector is too big to allocate. I have looked
at
packages such as bigmemory, but I need help to decide which is the
best
way to store such an object. It would be perfect to store it in this
cube
form (for indexing and computation purpouses). If not possible, maybe
the
best is to store the 904 matrices separately and read them individually
when needed?
Never dealed with such a big dataset, so any help will be appreciated
(R+ESS, Debian 64bit, 4Gb RAM, 4core)
I'd really recommend getting more RAM, so you can have the whole thing
loaded in memory. 16 Gb would be nice, but even 8Gb should make a
substantial difference. It's going to be too big to store as an array
since arrays have a limit of 2^31-1 entries, but you could store it as a
list of matrices, e.g.
x - vector(list, 904)
for (i in 1:904)
x[[i]] - matrix(0, 904,904)
and then refer to entry i,j,k as x[[i]][j,k].
Duncan Murdoch
[[alternative HTML version deleted]]
__
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.
[[alternative HTML version deleted]]
__
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.
Re: [R] package.skeleton()
Here ben I have a tutorial on how to do it http://stevemosher.wordpress.com/step-8-the-sample-package/ On Sun, Dec 18, 2011 at 11:49 PM, Petr PIKAL petr.pi...@precheza.cz wrote: Hi If I remember correctly I do start clear R -vanilla session copy my functions to it. run package.skeleton(some.name) which creates the some.name directory. Regards Petr Hi Duncan, Thanks for your response. That's the confusing thing, I didn't receive a message and I can't seem to find the new source package directory anywhere. I would greatly appreciate any advice about what I might be doing wrong. Happy Holidays, Ben On Fri, Dec 16, 2011 at 7:12 PM, Duncan Murdoch murdoch.dun...@gmail.comwrote: On 11-12-16 4:12 PM, Ben Ganzfried wrote: Hi-- I'm creating an R package, I've read through Writing R Extensions and the package.skeleton() R page-- and I'm still running into a little confusion. I would greatly appreciate any advice you can provide. Where do I run my following line of code from?: package.skeleton(name = a, code_files = EsetObject.r I'm currently running it from Rgui, but when I type the line above nothing happens. What is supposed to happen is that a new source package directory will be created in the current directory (what getwd() gives you). Did that happen? (I thought a message would also be printed and apparently you're not seeing that, but maybe it just worked without telling you.) Duncan Murdoch Thank you very much. Ben [[alternative HTML version deleted]] __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/ mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/** posting-guide.html http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ 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. [[alternative HTML version deleted]] __ 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] Levenshtein-Distance
check the help archives. hclust with method=ward might be what you are looking for On Wed, Oct 19, 2011 at 2:43 PM, Jörg Reuter jo...@reuter.at wrote: I am very new to R, so sorry that I ask stupid things. I want compare a Matrix row by row and at the end I want to a Matrix with the Levenshtein-Distance. Example: The Data (Learningpath in a E-Learning-System): 5 12 24 35 1 24 35 3 35 35 45 35 Now I need a comand, which compare the first line with the second, then with the third and write the result in a new Matrix. I found many Funktion in R, but all compare Strings, but I have numbers. After that I want to use the ward-argorithm at the result. Can anyone give me a hint, I am at the end with my nervs. Joerg __ 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] Problem with twitteR package
check the version of libcurl you have installed. If you have an older version some of the options may not be present. On Sun, Oct 9, 2011 at 10:39 AM, Steven Oliver s1oli...@ucsd.edu wrote: Hey Guys, I just started fooling around with the twitteR package in order to get a record of all tweets from a single public account. When I run userTimeline, I get the default 20 most recent tweets just fine. However, when I specify an arbitrary number of tweets (as described in the documentation from June 14th, 2011), I get the following warning: bjaTweets-userTimeline(BeijingAir, n=50) Warning message: In mapCurlOptNames(names(.els), asNames = TRUE) : Unrecognized CURL options: n Does anyone familiar with the twitteR package know what is going on with options? Alternatively, if there are any other simple means for getting this sort of data? Steve __ 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] Best Package to Extract Numbers from this Image?
You can probably use the package jpg , It will be a pain. You will have to read it in as a jpg then isolate the numbers ( by row and column ) then figure out some way ( probably not that hard) to identify the numbers from the bit pattern. I tried something similar with the png package. it was not elegant On Thu, Oct 6, 2011 at 6:28 PM, Jason Rupert jasonkrup...@yahoo.com wrote: I've done a bit of searching around on the forums looking for an R Package to extract the numbers from an image like the following: http://www.whnt.com/extras/whnt/weather/7day_640.jpg I would like to be able to do this in an automated way, so thanks for any hints and tips. [[alternative HTML version deleted]] __ 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] Hourly data with zoo
Gabor.. thanks. zr - zooreg(rnorm(24), as.chron(2011-01-01), frequency = 24) a couple issues: my date data has missing days and missing hours.. Sorry if I was not clear on that.. I input it to a data frame and dates are of the form 20110101 and hours are in the format 0,100,200 The end goal is to create a data structure for around 200 series aligned by time On Mon, Sep 12, 2011 at 3:48 AM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Mon, Sep 12, 2011 at 1:58 AM, steven mosher mosherste...@gmail.com wrote: I have date data as a numeric and hourly data in 0 to 2300 hours in a dataframe. d - rep(20110101,24) h - seq(from = 0, to = 2300, by = 100) df - data.frame(LST_DATE = d, LST_TIME = h, data = rnorm(24, 0, 1)) S - chron(dates. = as.character(df$LST_DATE), times. = paste(as.character(df$LST_TIME/100), :0:0, sep = ), format = c(dates = Ymd, times = h:m:s)) X - zoo(df$data, order.by = S) And I want to create a regular zoo series, The above works but its pretty ugly. Is there a more elegant way to do this. You probably want to create a zooreg object: library(zoo) library(chron) zr - zooreg(rnorm(24), as.chron(2011-01-01), frequency = 24) although if you really do want a zoo object that is not a zooreg object then you can do it like this: z - as.zoo(zr) -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Hourly data with zoo
worked beautifully. Thanks. On Mon, Sep 12, 2011 at 9:45 AM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Mon, Sep 12, 2011 at 11:57 AM, steven mosher mosherste...@gmail.com wrote: Gabor.. thanks. zr - zooreg(rnorm(24), as.chron(2011-01-01), frequency = 24) a couple issues: my date data has missing days and missing hours.. Sorry if I was not clear on that.. I input it to a data frame and dates are of the form 20110101 and hours are in the format 0,100,200 The end goal is to create a data structure for around 200 series aligned by time Try this: v - df$data z - zoo(v, as.chron(d, format = %Y%m%d) + h / 2400) -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.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] Hourly data with zoo
I have date data as a numeric and hourly data in 0 to 2300 hours in a dataframe. d - rep(20110101,24) h - seq(from = 0, to = 2300, by = 100) df - data.frame(LST_DATE = d, LST_TIME = h, data = rnorm(24, 0, 1)) S - chron(dates. = as.character(df$LST_DATE), times. = paste(as.character(df$LST_TIME/100), :0:0, sep = ), format = c(dates = Ymd, times = h:m:s)) X - zoo(df$data, order.by = S) And I want to create a regular zoo series, The above works but its pretty ugly. Is there a more elegant way to do this. __ 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] Elegant way to subtract matrix from array
there are really two related problems here I have a 2D matrix A - matrix(1:100,nrow=20,ncol =5) S - matrix(1:10,nrow=2,ncol =5) #I want to subtract S from A. so that S would be subtracted from the first 2 rows of #A, then the next two rows and so on. #I have a the same problem with a 3D array # where I want to subtract Q for every layer (1-10) in Z # I thought I solved this one with array(mapply(-,Z,Q),dim=dim(Z)) # but got the wrong answers Z - array(1:100,dim=c(2,5,10)) Q - matrix(1:10,nrow=2,ncol =5) [[alternative HTML version deleted]] __ 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] Elegant way to subtract matrix from array
Cool, I looked at sweep but didnt consider it as I thought it was restricted to certain functions. So thanks for that solution. yes the data is very large and the future work will increase 10 fold, as for the matrix one I'm not too keen on replicating the smaller matrix, I've had one guy using the package who has hit the memory limits.. I have one more thing to try Thanks! Steve On Wed, Jul 27, 2011 at 1:42 AM, Gavin Simpson gavin.simp...@ucl.ac.ukwrote: On Wed, 2011-07-27 at 01:06 -0700, steven mosher wrote: there are really two related problems here I have a 2D matrix A - matrix(1:100,nrow=20,ncol =5) S - matrix(1:10,nrow=2,ncol =5) #I want to subtract S from A. so that S would be subtracted from the first 2 rows of #A, then the next two rows and so on. For this one, I have used the following trick to replication a matrix do.call(rbind, rep(list(mat), N) where we convert the matrix, `mat`, to a list and repeat that list `N` times, and arrange for the resulting list to be rbind-ed. For your example matrices, the following does what you want: A - do.call(rbind, rep(list(S), nrow(A)/nrow(S))) Whether this is useful will depend on the dimension of A and S - from your posts on R-Bloggers, I can well imagine you are dealing with large matrices. #I have a the same problem with a 3D array # where I want to subtract Q for every layer (1-10) in Z # I thought I solved this one with array(mapply(-,Z,Q),dim=dim(Z)) # but got the wrong answers Z - array(1:100,dim=c(2,5,10)) Q - matrix(1:10,nrow=2,ncol =5) For this one, consider the often overlooked function `sweep()`: sweep(Z, c(1,2), Q, -) does what you wanted. c(1,2) is the `MARGIN` argument over the dimensions that Q will be swept from. HTH G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% [[alternative HTML version deleted]] __ 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] Elegant way to subtract matrix from array
Thanks Gabor! On Wed, Jul 27, 2011 at 3:08 AM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Wed, Jul 27, 2011 at 4:06 AM, steven mosher mosherste...@gmail.com wrote: there are really two related problems here I have a 2D matrix A - matrix(1:100,nrow=20,ncol =5) S - matrix(1:10,nrow=2,ncol =5) #I want to subtract S from A. so that S would be subtracted from the first 2 rows of #A, then the next two rows and so on. #I have a the same problem with a 3D array # where I want to subtract Q for every layer (1-10) in Z # I thought I solved this one with array(mapply(-,Z,Q),dim=dim(Z)) # but got the wrong answers Z - array(1:100,dim=c(2,5,10)) Q - matrix(1:10,nrow=2,ncol =5) For the first one: matrix(c(t(A)) - c(t(S)), nrow(A), byrow = TRUE) or this version which may seem a bit more complex but has the advantage that it shows the general form of which both your questions are special cases: ix - 2:1 aperm(array(c(aperm(A, ix)) - c(t(S)), dim(A)[ix]), ix) Now, as mentioned, the answer to second question is the same except for ix: ix - c(2, 1, 3) aperm(array(c(aperm(Z, ix)) - c(t(Q)), dim(Z)[ix]), ix) -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com [[alternative HTML version deleted]] __ 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] How to convert number (matlab) to date
Thanks, I just upgraded to 1.7.1 Also thanks for adding the t() function. On Mon, Jul 18, 2011 at 12:38 PM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Mon, Jul 18, 2011 at 2:57 PM, peter dalgaard pda...@gmail.com wrote: On Jul 18, 2011, at 20:19 , Gabor Grothendieck wrote: On Mon, Jul 18, 2011 at 1:59 PM, peter dalgaard pda...@gmail.com wrote: On Jul 18, 2011, at 16:36 , Gabor Grothendieck wrote: . However, this was after reinstalling and reloading zoo. Restarting R and retrying did indeed make things work. Does the fact that it worked if R was restarted, but not without, imply that there is something in R that needs to be fixed? Well, zoo is rewriting code in base. Apparently, it didn't do it again on the second library(zoo). Not really sure who to blame for what... Its done in the .onLoad function in zzz.R in zoo. It seems that if one re-installs zoo and then runs it that the .onLoad is not rerun. I would have thought it would reload the package and therefore .onLoad would be run again.. Also there exists .onAttach but its not used by zoo. Should the code for as.Date.numeric be put in an .onAttach instead or in both .onLoad and .onAttach? Or perhaps not at all! I'll leave this discussion for others. An INSTALL file has been added to zoo to ask users to restart R after installing zoo. -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.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. [[alternative HTML version deleted]] __ 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] Storing and managing custom R functions for re-use
Same here. Just made my first package and regret not having learned how to do it from the very beginning. Steve On Sun, Jul 10, 2011 at 3:27 AM, Michael Dewey i...@aghmed.fsnet.co.ukwrote: At 12:30 09/07/2011, Simon Chamaillé-Jammes wrote: Dear all, sorry if this is a bit on the sidetrack for R-help. As a regular R user I have developed quite a lot of custom R functions, to the point of not always remembering what I have already programmed, where the file is and so on. I was wondering what other people do in this regards. A basic file with all your functions, or a custom R package, or directly integrated into a profile file ??? I'm considering that a blog with tagged posts may be a good solution (and really good ones could join R-bloggers maybe). If someone is happy to share what (s)he considers good practice, thanks. I spent too many years doing what you say you are doing because creating a package seemed quite complicated. Once I took the plunge I found it well worth the effort. You do have to invest time and effort to begin with. You will find ?package.skeleton ?prompt rewarding reading as well as those sections of the R extensions document which are relevant to your use. Good luck simon Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/**home.htmlhttp://www.aghmed.fsnet.co.uk/home.html __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/** posting-guide.html http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ 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] Package warnings
Thanks Duncan, I'll join Dev and ask the questions over there. Steve On Wed, Jun 22, 2011 at 7:19 AM, Duncan Murdoch murdoch.dun...@gmail.comwrote: On 11-06-21 11:58 PM, steven mosher wrote: Thanks to all your help I've just finished my first package and I have a couple of questions I want to submit to CRAN but I have 1 warning checking for code/documentation mismatches ... WARNING Data sets with usage in documentation object 'FILE.PARAMETERS' but not in code: FILE.PARAMETERS I actually have a few instances with the same issue. I have a handful of data objects, things like URLs and some file parameters ( like column widths etc). These are declared in an R file and then loaded (lazyData no) There are help files for all these objects, and some of them get used in the code as defaults for when functions are called foo- function( x, y=FILE.PARAMETERS) So why do I get this warning? is it one I have to fix? and should I be asking this on the dev list? Yes, you should fix almost all warnings, and yes, questions like this belong on the R-devel list. When you ask there, it would be helpful to be very specific: show us the start of the Rd file that is being complained about (the \usage and \docType sections are of particular interest), and give us the exact details about how the data object is being created. Duncan Murdoch Thanks again for all your help, hope this is right place to ask. [[alternative HTML version deleted]] __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/** posting-guide.html http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ 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] Package warnings
Thanks all the issue is closed.
in this case I had a data element FILE.PARAMETERS = list()
the .Rd files created by package.skelton() for data objects had the
following for \usage.
\usage{data(FILE.PARAMETERS)}
I left that as is and CHECK throws a warning.
checking for code/documentation mismatches ... WARNING
Data sets with usage in documentation object 'FILE.PARAMETERS' but not in
code:
changing \usage cleared the warning
\usage{FILE.PARAMETERS}
clears check! crantastic, no warnings, no errors!
On Wed, Jun 22, 2011 at 8:29 AM, steven mosher mosherste...@gmail.comwrote:
Thanks Duncan, I'll join Dev and ask the questions over there.
Steve
On Wed, Jun 22, 2011 at 7:19 AM, Duncan Murdoch
murdoch.dun...@gmail.comwrote:
On 11-06-21 11:58 PM, steven mosher wrote:
Thanks to all your help I've just finished my first package and I have a
couple of questions
I want to submit to CRAN but I have 1 warning
checking for code/documentation mismatches ... WARNING
Data sets with usage in documentation object 'FILE.PARAMETERS' but not in
code:
FILE.PARAMETERS
I actually have a few instances with the same issue. I have a handful of
data objects, things like URLs
and some file parameters ( like column widths etc). These are declared in
an
R file and then loaded
(lazyData no)
There are help files for all these objects, and some of them get used in
the
code as defaults for when
functions are called
foo- function( x, y=FILE.PARAMETERS)
So why do I get this warning? is it one I have to fix? and should I be
asking this on the dev list?
Yes, you should fix almost all warnings, and yes, questions like this
belong on the R-devel list.
When you ask there, it would be helpful to be very specific: show us the
start of the Rd file that is being complained about (the \usage and \docType
sections are of particular interest), and give us the exact details about
how the data object is being created.
Duncan Murdoch
Thanks again for all your help, hope this is right place to ask.
[[alternative HTML version deleted]]
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https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/**
posting-guide.html http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
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] Package warnings
Thanks to all your help I've just finished my first package and I have a couple of questions I want to submit to CRAN but I have 1 warning checking for code/documentation mismatches ... WARNING Data sets with usage in documentation object 'FILE.PARAMETERS' but not in code: FILE.PARAMETERS I actually have a few instances with the same issue. I have a handful of data objects, things like URLs and some file parameters ( like column widths etc). These are declared in an R file and then loaded (lazyData no) There are help files for all these objects, and some of them get used in the code as defaults for when functions are called foo - function( x, y=FILE.PARAMETERS) So why do I get this warning? is it one I have to fix? and should I be asking this on the dev list? Thanks again for all your help, hope this is right place to ask. [[alternative HTML version deleted]] __ 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] Permission denied in Windows 7
Prof, Ripley. I think I figured it out. I took the instructions for code_files to mean that you had to supply the path to the directory and not the paths to all the files within that directory. I'll show my work below which should make clear the mistake that I made sessionInfo()R version 2.13.0 (2011-04-13) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] R.utils_1.7.5 R.oo_1.8.0R.methodsS3_1.2.1 loaded via a namespace (and not attached): [1] tools_2.13.0 getwd()[1] C:/Users/steve/Documents/GHCNPackage list.files(full.names=TRUE)[1] ./d.R ./f.R filePath - getwd() filePath[1] C:/Users/steve/Documents/GHCNPackage package.skeleton(name=testpackage,code_files=filePath)Error in file(file, r) : cannot open the connectionIn addition: Warning message:In file(file, r) : cannot open file 'C:/Users/steve/Documents/GHCNPackage': Permission denied # Looks like I need a path all the way to the file. # start with one file to test testFile -file.path(filePath,d.R,fsep=.Platform$file.sep) package.skeleton(name=testpackage,code_files=testFile)Creating directories ...Creating DESCRIPTION ...Creating Read-and-delete-me ...Copying code files ...Making help files ...Done.Further steps are described in './testpackage/Read-and-delete-me'. ?package.skeleton() testFile2 -file.path(filePath,f.R,fsep=.Platform$file.sep) package.skeleton(name=testpackage,code_files=c(testFile,testFile2))Creating directories ...Error in package.skeleton(name = testpackage, code_files = c(testFile, : directory './testpackage' already exists package.skeleton(name=testpackage,code_files=c(testFile,testFile2))Creating directories ...Creating DESCRIPTION ...Creating Read-and-delete-me ...Copying code files ...Making help files ...Done.Further steps are described in './testpackage/Read-and-delete-me'. Success. I assumed that you just passed in the directory that contained all the source Files and that all the files in that directory ending in .R would be used. Thanks On Wed, Jun 8, 2011 at 11:44 PM, Prof Brian Ripley rip...@stats.ox.ac.ukwrote: On Wed, 8 Jun 2011, steven mosher wrote: I'm using package.skeleton() windows 7, 64 bit. When I try to specify the code_files package_skeleton(code_files = some directory) I get a warning that that the connection cannot be opened and I get a Permissions denied error. Which connection? Please copy-and-paste exactly what you did and what the output was. I'm running R as admin and I've given everybody full permissions on the folder. What am I missing There can be more to that on Windows 7. Is it read-only, for example? One thing which often catches users of POSIX operating systems (like me) is that read-only files are also no-delete files. [[alternative HTML version deleted]] Please don't keep sending HTML when the posting guide expressly asked you not to. __ 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. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 [[alternative HTML version deleted]] __ 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] Permission denied in Windows 7
I'm using package.skeleton() windows 7, 64 bit. When I try to specify the code_files package_skeleton(code_files = some directory) I get a warning that that the connection cannot be opened and I get a Permissions denied error. I'm running R as admin and I've given everybody full permissions on the folder. What am I missing [[alternative HTML version deleted]] __ 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] Questions about building R packages
here i wrote a step by step tutorial. http://stevemosher.wordpress.com/2011/06/09/making-simple-packages-in-r-on-windows/ On Wed, Jun 8, 2011 at 1:17 PM, Xia.Li oddity...@gmail.com wrote: Hello R users, I have difficulties when trying to make R packages. I tried to read many tutorials but still could not find out the right way. Could any one help me out please? (I'm using Windows xp.) After running package.skeleton() and edit those RD files, I don't know how to use Rtools (or CMD shell?) to build the zip file. I installed the Rtools from Murdoch's link, but it doesn't look like a software... Anyone could give me a tutorial with more details about Rtools (or CMD shell)? I've already have MikTex installed. Thanks! -- View this message in context: http://r.789695.n4.nabble.com/Questions-about-building-R-packages-tp3583510p3583510.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. [[alternative HTML version deleted]] __ 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] Problem with package development
I hope you're successful because I'm having issues as well building a simple
package on
windows. maybe when you're finished you can share back a step by step
guide.
On Thu, Jun 2, 2011 at 12:21 PM, Nipesh Bajaj bajaj141...@gmail.com wrote:
I have run R CMD check trial1 and saw an error. This says that:
* checking pdf version of manual without hyperrefs or index ... ERROR
Re-running with no redirection of stdout/stderr.
Hmm... looks like a package
Error in texi2dvi(Rd2.tex, pdf = (out_ext == pdf), quiet = FALSE, :
pdflatex is not available
Error in running tools:: texi2dvi
Does this information hwlp you to suggest something? Please let me
know what else I can provide.
Thanks,
On Fri, Jun 3, 2011 at 12:00 AM, Nipesh Bajaj bajaj141...@gmail.com
wrote:
What else I need to do? In the Read-and-delete-me file following steps
are asked to perform:
* Edit the help file skeletons in 'man', possibly combining help files
for multiple functions.
* Edit the exports in 'NAMESPACE', and add necessary imports.
* Put any C/C++/Fortran code in 'src'.
* If you have compiled code, add a useDynLib() directive to 'NAMESPACE'.
* Run R CMD build to build the package tarball.
* Run R CMD check to check the package tarball.
I editied the help page for fn1() function (as I already communicated
in previous mail) as follows:
\name{fn1}
\alias{fn1}
\title{
A function.
}
\description{
A function.
}
\usage{
A function.
}
\arguments{
A function.
}
\value{
A function.
}
\author{
\bold{Me}
\cr
\email{m...@me.com}
}
And regarding th Namespace file, this time I put
package.skeleton(trial1,namespace = FALSE, code_files =
f:/trial.r)
I do not have any C/C++ code so I ignored 3rd step.
then Read-and-delete-me file asking me to build the package, so in
cmd, I run following:
cd C:\R_PackageBuild
Rcmd build âbinary trial1
What I am missing in this entire process? Do you please point me?
Thanks,
On Thu, Jun 2, 2011 at 11:40 PM, Duncan Murdoch
murdoch.dun...@gmail.com wrote:
On 02/06/2011 2:03 PM, Nipesh Bajaj wrote:
Thanks Prof. Ripley and Duncan for your pointers. Noting down your
points I have modified my way of building package and have done
following so far:
1. In my C: drive I create one working folder naming R_PackageBuild
2. In R console I have written following codes:
setwd(c:/R_packageBuild)
package.skeleton(trial1,namespace = TRUE, code_files =
f:/trial.r)
3. then I opened cmd and wrote following:
cd C:\R_PackageBuild
Rcmd build âbinary trial1
This process halted with following error:
Error: unexpected symbol in
âtools:::.test_load_package(âtrial1â²,â¦.)â
Execution halted
ERROR: loading failed
What I have missed in this process? Can you please help me how to
solve this issue?
You haven't done the manual changes required between steps 2 and 3.
package.skeleton() creates the skeleton of a package; you run it once
as
you are starting development, the do a lot of manual updates, described
on
the ?package.skeleton help page, and in the âRead-and-delete-meâ file.
Once those are done, step 3 should succeed.
Duncan Murdoch
Thanks,
PS: I am sorry I missplet 'Program Files'. Thanks Prof. Ripley for this
pointer.
On Wed, Jun 1, 2011 at 11:41 AM, Prof Brian Ripley
rip...@stats.ox.ac.uk wrote:
On Wed, 1 Jun 2011, Nipesh Bajaj wrote:
I have been struggling for last one hour but not yet any through.
However again I recreate the package.skeleton and run R CMD check
trial3
Here are the errors:
warning in dir.create(pkgoutdir, mode = 0755):
cannot create dir 'c:\Program files\R\R-2.13.0\bin\trial3.Rcheck',
reason .
Error in printLog(Log, , text, \n): object 'Log' not found
Execution haulted
Why I am getting this error? what is that Log. I will really
appreciate if somebody please help me to figure out.
R CMD check writes a (in your case) trial3.Rcheck directory, and in
there in
file 00check.log a copy of the log. If it cannot create
trial3.Rcheck
it
cannot write the log.
I would be surprised that even on Windows Vista the message was
literally
reason .
but if it was, blame Microsoft for their error messages.
But
cannot create dir 'c:\Program files\R\R-2.13.0\bin\trial3.Rcheck',
is clear enough. You need to run 'R CMD check' in your user area.
In case you did this because that is where you though 'R' was, it is
not the
correct R.exe. You may need to add
c:\Program Files\R\R-2.13.0\bin\i386
(assuming 32-bit R) to your path.
However, your use of e.g. 'Program files' suggests you are not
accurately
transmitting the messages you got.
Thanks,
On Wed, Jun 1, 2011 at 1:20 AM, Nipesh
Re: [R] help with barplot
Thanks,
ggplot is on my list of things to learn before Hadley comes here to the
bay area
to give a session on interactive graphics in R
On Fri, May 27, 2011 at 10:29 PM, Joshua Wiley jwiley.ps...@gmail.comwrote:
Hi Steven,
This is not, strictly speaking, the answer to your question (hopefully
Tom already answered that). Rather, it is the answer to questions you
*might* have asked (and perhaps one of them will be one you wished you
had asked).
Barplots have a low data:ink ratio...you are using an entire plot to
convey 8 means. A variety of alternatives exist. As a minimal first
step, you could just use points to show the means and skip all the
wasted bar space, and you might add error bars in (A). You could also
use boxplots to give your viewers (or just yourself) a sense of the
distribution along with the medians (B). Another elegant option is
violin plots. These are kind of like (exactly like?) mirrored density
plots. A measure of central tendency is not explicitly shown, but the
*entire* distribution and range is shown (C).
Cheers,
Josh
(P.S. I hit send too soon before and sent you an offlist message with
PDF examples)
## Create your data
DF - data.frame(
Incidents = factor(rep(c(a, b, d, e), each = 25)),
Months = factor(rep(1:2, each = 10)),
Time = rnorm(100))
## Load required packages
require(ggplot2)
require(Hmisc)
## Option A
ggplot(DF, aes(x = Incidents, y = Time, colour = Months)) +
stat_summary(fun.y = mean, geom = point,
position = position_dodge(width = .90), size = 3) +
stat_summary(fun.data = mean_cl_normal, geom = errorbar,
position = dodge)
## Option B
ggplot(DF, aes(x = Incidents, y = Time, fill = Months)) +
geom_boxplot(position = position_dodge(width = .8))
## Option C
ggplot(DF, aes(x = Time, fill = Months)) +
geom_ribbon(aes(ymax = ..density.., ymin = -..density..),
alpha = .2, stat = density) +
facet_grid( ~ Incidents) +
coord_flip()
## Option C altered
ggplot(DF, aes(x = Time, fill = Months)) +
geom_ribbon(aes(ymax = ..density.., ymin = -..density..),
alpha = .2, stat = density) +
facet_grid( ~ Incidents + Months) +
scale_y_continuous(name = density, breaks = NA, labels = NA) +
coord_flip()
On Fri, May 27, 2011 at 3:08 PM, steven mosher mosherste...@gmail.com
wrote:
Hi,
I'm really struggling with barplot
I have a data.frame with 3 columns. The first column represents an
incident type
The second column represents a month
The third column represents a time
Code for a sample data.frame
incidents - rep(c('a','b','d','e'), each =25)
months- rep(c(1,2), each =10)
times -rnorm(100)
# make my sample data
DF-
data.frame(Incidents=as.factor(incidents),Months=as.factor(months),Time=times)
# now calculate a mean for the by groups of incident type and month
pivot -
aggregate(DF$Time,by=list(Incidents=DF$Incidents,Months=DF$Month),FUN=mean,simplify=TRUE)
What I want to create is a bar plot where I have groupings by incident
type
( a,b,d,e) and within each group
I have the months in order.
So group 1 would be Type a; month 1,2;
group 2 would be Type b; month 1,2;
group 3 would be Type d; month 1,2;
group 4 would be Type 3; month 1,2;
I know barplot is probably the right function but I'm a bit lost on how
to
specify groupings etc
TIA
[[alternative HTML version deleted]]
__
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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.
--
Joshua Wiley
Ph.D. Student, Health Psychology
University of California, Los Angeles
http://www.joshuawiley.com/
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] help with barplot
Thanks Thomas.
On Sat, May 28, 2011 at 11:29 AM, Thomas Levine thomas.lev...@gmail.comwrote:
You can do pretty well without ggplot actually.
boxplot(Time~paste(Incidents,Months),data=DF,border=c('grey20','red'))
On Sat, May 28, 2011 at 2:55 AM, steven mosher mosherste...@gmail.com
wrote:
Thanks,
ggplot is on my list of things to learn before Hadley comes here to the
bay area
to give a session on interactive graphics in R
On Fri, May 27, 2011 at 10:29 PM, Joshua Wiley jwiley.ps...@gmail.com
wrote:
Hi Steven,
This is not, strictly speaking, the answer to your question (hopefully
Tom already answered that). Rather, it is the answer to questions you
*might* have asked (and perhaps one of them will be one you wished you
had asked).
Barplots have a low data:ink ratio...you are using an entire plot to
convey 8 means. A variety of alternatives exist. As a minimal first
step, you could just use points to show the means and skip all the
wasted bar space, and you might add error bars in (A). You could also
use boxplots to give your viewers (or just yourself) a sense of the
distribution along with the medians (B). Another elegant option is
violin plots. These are kind of like (exactly like?) mirrored density
plots. A measure of central tendency is not explicitly shown, but the
*entire* distribution and range is shown (C).
Cheers,
Josh
(P.S. I hit send too soon before and sent you an offlist message with
PDF examples)
## Create your data
DF - data.frame(
Incidents = factor(rep(c(a, b, d, e), each = 25)),
Months = factor(rep(1:2, each = 10)),
Time = rnorm(100))
## Load required packages
require(ggplot2)
require(Hmisc)
## Option A
ggplot(DF, aes(x = Incidents, y = Time, colour = Months)) +
stat_summary(fun.y = mean, geom = point,
position = position_dodge(width = .90), size = 3) +
stat_summary(fun.data = mean_cl_normal, geom = errorbar,
position = dodge)
## Option B
ggplot(DF, aes(x = Incidents, y = Time, fill = Months)) +
geom_boxplot(position = position_dodge(width = .8))
## Option C
ggplot(DF, aes(x = Time, fill = Months)) +
geom_ribbon(aes(ymax = ..density.., ymin = -..density..),
alpha = .2, stat = density) +
facet_grid( ~ Incidents) +
coord_flip()
## Option C altered
ggplot(DF, aes(x = Time, fill = Months)) +
geom_ribbon(aes(ymax = ..density.., ymin = -..density..),
alpha = .2, stat = density) +
facet_grid( ~ Incidents + Months) +
scale_y_continuous(name = density, breaks = NA, labels = NA) +
coord_flip()
On Fri, May 27, 2011 at 3:08 PM, steven mosher mosherste...@gmail.com
wrote:
Hi,
I'm really struggling with barplot
I have a data.frame with 3 columns. The first column represents an
incident type
The second column represents a month
The third column represents a time
Code for a sample data.frame
incidents - rep(c('a','b','d','e'), each =25)
months- rep(c(1,2), each =10)
times -rnorm(100)
# make my sample data
DF-
data.frame(Incidents=as.factor(incidents),Months=as.factor(months),Time=times)
# now calculate a mean for the by groups of incident type and month
pivot -
aggregate(DF$Time,by=list(Incidents=DF$Incidents,Months=DF$Month),FUN=mean,simplify=TRUE)
What I want to create is a bar plot where I have groupings by
incident
type
( a,b,d,e) and within each group
I have the months in order.
So group 1 would be Type a; month 1,2;
group 2 would be Type b; month 1,2;
group 3 would be Type d; month 1,2;
group 4 would be Type 3; month 1,2;
I know barplot is probably the right function but I'm a bit lost on
how
to
specify groupings etc
TIA
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Joshua Wiley
Ph.D. Student, Health Psychology
University of California, Los Angeles
http://www.joshuawiley.com/
[[alternative HTML version deleted]]
__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] help with barplot
Hi,
I'm really struggling with barplot
I have a data.frame with 3 columns. The first column represents an
incident type
The second column represents a month
The third column represents a time
Code for a sample data.frame
incidents - rep(c('a','b','d','e'), each =25)
months- rep(c(1,2), each =10)
times -rnorm(100)
# make my sample data
DF-
data.frame(Incidents=as.factor(incidents),Months=as.factor(months),Time=times)
# now calculate a mean for the by groups of incident type and month
pivot -
aggregate(DF$Time,by=list(Incidents=DF$Incidents,Months=DF$Month),FUN=mean,simplify=TRUE)
What I want to create is a bar plot where I have groupings by incident type
( a,b,d,e) and within each group
I have the months in order.
So group 1 would be Type a; month 1,2;
group 2 would be Type b; month 1,2;
group 3 would be Type d; month 1,2;
group 4 would be Type 3; month 1,2;
I know barplot is probably the right function but I'm a bit lost on how to
specify groupings etc
TIA
[[alternative HTML version deleted]]
__
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] Understanding tryCatch
I've read the help and the archives on tryCatch but I'm still stuggling trying to understand how it works exactly and how I can use it to get the result I need. I have a data.frame of urls which point to 11 .zip files. Basically I use RCurl to get the list of files from a ftp and then reduce that directory dump to the 11 zip files I want to download. Its easy enough to do that in a loop over the elements in data.frame. The problem is that the site is very inconsistent. All 11 files will download, but I will get random warnings that the size of some of the files does not match what was downloaded. So at the end of the loop I may get 5 warnings about the file size not matching. These files, when tried a second or third time, will eventually download properly. What I want to do is record which files had this download warning. [[alternative HTML version deleted]] __ 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] Understanding tryCatch
That works
# hydeUrls = vector of urls to file names
#destList = vector of destination file names
for(files in 1:length(hydeUrls)){
filesFailed[files]- FALSE
filesFailed[files] -
tryCatch(download.file(url=hydeUrls[files],destfile=destList[files],quiet=FALSE,mode=wb),warning=function(m)
m-TRUE)
print(filesFailed[files])
}
And below I get the result I want which has flagged this file as improperly
downloaded.
note the difference between the file length and the amount downloaded.
trying URL 'ftp://ftp.mnp.nl/hyde/hyde31_final/1870ad_pop.zip'ftp data
connection made, file length 14394402 bytesopened URLdownloaded 2.8 Mb
[1] 1
And on successful download
trying URL 'ftp://ftp.mnp.nl/hyde/hyde31_final/1910ad_pop.zip'ftp data
connection made, file length 14694703 bytesopened URLdownloaded 14.0
Mb
[1] 0
On Fri, Mar 18, 2011 at 12:17 PM, Henrique Dallazuanna www...@gmail.comwrote:
Try this:
tryCatch(log(rnorm(10)), warning = function(m)deparse(m$call[[2]]))
Where log(rnorm(10)) is your expr to evaluate.
On Fri, Mar 18, 2011 at 4:04 PM, steven mosher mosherste...@gmail.com
wrote:
I've read the help and the archives on tryCatch but I'm still stuggling
trying to understand how it
works exactly and how I can use it to get the result I need.
I have a data.frame of urls which point to 11 .zip files. Basically I use
RCurl to get the list of
files from a ftp and then reduce that directory dump to the 11 zip files
I
want to download.
Its easy enough to do that in a loop over the elements in data.frame.
The problem is that the site is very inconsistent. All 11 files will
download, but I will get random
warnings that the size of some of the files does not match what was
downloaded.
So at the end of the loop I may get 5 warnings about the file size not
matching.
These files, when tried a second or third time, will eventually download
properly.
What I want to do is record which files had this download warning.
[[alternative HTML version deleted]]
__
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.
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
[[alternative HTML version deleted]]
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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.
Re: [R] s3 methods on S4 objects
On Thu, Jan 13, 2011 at 6:46 AM, Martin Morgan mtmor...@fhcrc.org wrote:
On 01/12/2011 10:54 PM, steven mosher wrote:
I have J Chambers wonderful text ( Software for data Analysis) and I've
been
trying
my hand at some very routine S4 OOP development.
One of the things I was trying to do was to create some very basic S4
classes. The first
was simply a class that had a data.frame as part of its representation.
setClass(df,representation(dirframe=data.frame))
The object basically contains a data.frame that represents a file
directory
listing
with a column named filename, size, time, etc.
And then I have methods for doing various things with this object.
I then tried to tackle the problem of coercing this S4 object to a
data.frame. Again just a learning exercise.
The goal would be able to make a call like this
testFrame - as.data.frame(x)
where x, was an object of class df
If I try to define as.data.frame as a S4 method, then I can make it
work,
but I then destroy the S3 functionality
of as.data.frame, so that if I were to try to coerce a matrix to a
data.frame it would work.
Hi Steven --
This works for me
setClass(A, representation=representation(df=data.frame))
setMethod(as.data.frame, A,
function(x, row.names=NULL, optional=FALSE, ...)
{
## implementation, e.g.,
callGeneric(x@df, row.names=row.names, optional=optional, ...)
})
this makes no sense to me.
Looking at this in the manual:
A call to callGeneric can only appear inside a method definition. It then
results in a call to the current generic function. The value of that call is
the value of callGeneric. While it can be called from any method, it is
useful and typically used in methods for group generic functions.
I'm further confused. what is the current generic function?
as.data.frame(new(A))
Object of class data.frame
data frame with 0 columns and 0 rows
as.data.frame(matrix(0, 3, 5))
V1 V2 V3 V4 V5
1 0 0 0 0 0
2 0 0 0 0 0
3 0 0 0 0 0
Maybe you call setGeneric (no need to, setMethod will promote
as.data.frame automatically) in a way that does not specify the default
(arg useAsDefault) correctly?
I think that may have been the mistake.. what do you mean by
no need to call setGeneric?
I really like chambers book, but there are certain parts where the lack of
simple examples
really makes it difficult to follow.
Martin
So, I guess my question is what do I do, write an s3 method for
as.data.frame that takes a df object as a paramter?
The book wasn't exactly clear ( or I'm not that bright), or is there a
way
to make the S4 method I wrote as.data.frame
call the S3 method if needed?
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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.
--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
Location: M1-B861
Telephone: 206 667-2793
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] s3 methods on S4 objects
Martin, that helps. I
I made the mistake you outlined below
setGeneric(as.data.frame,
function(x) standardGeneric(as.data.frame))
Creating a generic for 'as.data.frame' in package '.GlobalEnv'
(the supplied definition differs from and overrides the implicit generic
in package 'base': Formal arguments differ: (x), (x, row.names,
optional, ...))
[1] as.data.frame
then I'm in trouble -- I've created a generic 'as.data.frame', but since
the signature of my generic differs from the signature of
base::as.data.frame, the default behavior does NOT create a
as.data.frame,ANY method.
this, as you note leads to trouble
And of course got in trouble.
setClass(Class=ftpdir,
representation = list(dirframe=data.frame))
if (!isGeneric(as.data.frame)) {
setGeneric(as.data.frame, function(dirlist )
standardGeneric(as.data.frame))
}
setMethod(as.data.frame,
signature(dirlist = ftpdir ),
function (dirlist )
{
return( dirlist@dirframe)
}
)
On Thu, Jan 13, 2011 at 10:33 AM, Martin Morgan mtmor...@fhcrc.org wrote:
On 01/13/2011 09:49 AM, steven mosher wrote:
On Thu, Jan 13, 2011 at 6:46 AM, Martin Morgan mtmor...@fhcrc.org
mailto:mtmor...@fhcrc.org wrote:
On 01/12/2011 10:54 PM, steven mosher wrote:
I have J Chambers wonderful text ( Software for data Analysis) and
I've been
trying
my hand at some very routine S4 OOP development.
One of the things I was trying to do was to create some very basic
S4
classes. The first
was simply a class that had a data.frame as part of its
representation.
setClass(df,representation(dirframe=data.frame))
The object basically contains a data.frame that represents a file
directory
listing
with a column named filename, size, time, etc.
And then I have methods for doing various things with this object.
I then tried to tackle the problem of coercing this S4 object to a
data.frame. Again just a learning exercise.
The goal would be able to make a call like this
testFrame - as.data.frame(x)
where x, was an object of class df
If I try to define as.data.frame as a S4 method, then I can make
it work,
but I then destroy the S3 functionality
of as.data.frame, so that if I were to try to coerce a matrix to a
data.frame it would work.
Hi Steven --
This works for me
setClass(A, representation=representation(df=data.frame))
setMethod(as.data.frame, A,
function(x, row.names=NULL, optional=FALSE, ...)
{
## implementation, e.g.,
callGeneric(x@df, row.names=row.names, optional=optional, ...)
})
this makes no sense to me.
Looking at this in the manual:
A call to callGeneric can only appear inside a method definition. It
then results in a call to the current generic function. The value of
that call is the value of callGeneric. While it can be called from any
method, it is useful and typically used in methods for group generic
functions.
callGeneric is not necessary, and I should just have said
as.data.frame(x@df, row.names=row.names, optional=optional, ...)
I'm further confused. what is the current generic function?
I think of a generic 'foo' as a function, and inside that function are
functions foo,A-method, foo,B-method etc for classes A, B, When in
one of these methods, foo,A-method, the current generic is the function
'foo'. For as.data.frame, the generic is unambiguous ('as.data.frame' !)
and the interesting case are the group generics (?Logic, for instance),
where a single method
setMethod(Logic, function(e1, e2) callGeneric(YOUR CODE HERE))
and you'll have in effect written 'methods' for all the operators
defined in the 'Logic' group. Cool.
as.data.frame(new(A))
Object of class data.frame
data frame with 0 columns and 0 rows
as.data.frame(matrix(0, 3, 5))
V1 V2 V3 V4 V5
1 0 0 0 0 0
2 0 0 0 0 0
3 0 0 0 0 0
Maybe you call setGeneric (no need to, setMethod will promote
as.data.frame automatically) in a way that does not specify the
default
(arg useAsDefault) correctly?
I think that may have been the mistake.. what do you mean by
no need to call setGeneric?
The only code I had was what was written above -- setClass and
setMethod. I could also have
setGeneric(as.data.frame)
and would have been ok -- the default behavior of setGeneric in this
case is to make a generic function as.data.frame, AND a method
as.data.frame,ANY-method. The as.data.frame,ANY-method is implemented as
base::as.data.frame, and is where objects not handled by methods I
implement might end up being dispatched to. In a new R session, try
setGeneric(as.data.frame)
showMethods(as.data.frame
[R] s3 methods on S4 objects
I have J Chambers wonderful text ( Software for data Analysis) and I've been trying my hand at some very routine S4 OOP development. One of the things I was trying to do was to create some very basic S4 classes. The first was simply a class that had a data.frame as part of its representation. setClass(df,representation(dirframe=data.frame)) The object basically contains a data.frame that represents a file directory listing with a column named filename, size, time, etc. And then I have methods for doing various things with this object. I then tried to tackle the problem of coercing this S4 object to a data.frame. Again just a learning exercise. The goal would be able to make a call like this testFrame - as.data.frame(x) where x, was an object of class df If I try to define as.data.frame as a S4 method, then I can make it work, but I then destroy the S3 functionality of as.data.frame, so that if I were to try to coerce a matrix to a data.frame it would work. So, I guess my question is what do I do, write an s3 method for as.data.frame that takes a df object as a paramter? The book wasn't exactly clear ( or I'm not that bright), or is there a way to make the S4 method I wrote as.data.frame call the S3 method if needed? [[alternative HTML version deleted]] __ 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] Accessing data via url
https your second link is an https that's not supported as I recall. ?url On Thu, Jan 6, 2011 at 11:53 AM, John Kane jrkrid...@yahoo.ca wrote: # Can anyone suggest why this works datafilename - http://personality-project.org/r/datasets/maps.mixx.epi.bfi.data; person.data - read.table(datafilename,header=TRUE) # but this does not? dd - https://sites.google.com/site/jrkrideau/home/general-stores/trees.txt; treedata - read.table(dd, header=TRUE) === Error in file(file, rt) : cannot open the connection In addition: Warning message: In file(file, rt) : unsupported URL scheme # I can access both through a hyperlink in OOO Calc. t # Thanks __ 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. [[alternative HTML version deleted]] __ 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] Accessing data via url
Here John, from the manual URLs A note on file:// URLs. The most general form (from RFC1738) is file://host/path/to/file, but R only accepts the form with an empty host field referring to the local machine. This is then file:///path/to/file, where path/to/file is relative to /. So although the third slash is strictly part of the specification not part of the path, this can be regarded as a way to specify the file /path/to/file. It is not possible to specify a relative path using a file URL. No attempt is made to decode an encoded URL: call URLdecode if necessary. Note that https:// connections are not supported. So, when you use a https Url as opposed to a http url the former is not supported. You might try RCurl package getURL() which has support for HTTPS, provided your libcurl has support for SSL ( as I recall) On Thu, Jan 6, 2011 at 11:53 AM, John Kane jrkrid...@yahoo.ca wrote: # Can anyone suggest why this works datafilename - http://personality-project.org/r/datasets/maps.mixx.epi.bfi.data; person.data - read.table(datafilename,header=TRUE) # but this does not? dd - https://sites.google.com/site/jrkrideau/home/general-stores/trees.txt; treedata - read.table(dd, header=TRUE) === Error in file(file, rt) : cannot open the connection In addition: Warning message: In file(file, rt) : unsupported URL scheme # I can access both through a hyperlink in OOO Calc. t # Thanks __ 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. [[alternative HTML version deleted]] __ 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] Navigating web pages using R
Hmm, Rcurl may be able to help you. Not sure I have not played with the query abilities. On Tue, Jan 4, 2011 at 10:54 AM, Erik Gregory egregory2...@yahoo.comwrote: R-Help, I'm trying to obtain some data from a webpage which masks the URL from the user, so an explicit URL will not work. For example, when one navigates to the web page the URL looks something like: http://137.113.141.205/rpt34s.php?flags=1 (changed for privacy, but i'm not sure you could access it anyways since it's internal to the agency I work for). The site has three drop-down menus for Site, Month, and Year. When a combination is selected of these, the resulting URL is always http://137.113.141.205/rpt34s (nothing changes, except flags=1 is dropped, so what I need to be able to do is write something that will navigate to the original URL, then select some combination of Site, Month, and Year, and then submit the query to the site to navigate to the page with the data. Is this a capability that R has as a language? Unfortunately, I'm unfamiliar with html or php programming, so if this question belongs in a forum on that I apologize. I'm trying to centralize all of my code for my analysis in R! Thank you, -Erik Gregory Student Assistant, California EPA CSU Sacramento, Mathematics __ 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. [[alternative HTML version deleted]] __ 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] lm() on a matrix of zoo series
I have a matrix of zoo series. each series is in a column. x - as.yearmon(2000 + seq(0, 23)/12) # 24 months of data, lets make 20 sets of random data testData - matrix(rnorm(480),ncol=20) # make a zoo object and columns will hold the 20 series TestZoo - zoo(testData,order.by=x) # now run lm for just one series. m - lm(TestZoo[,1]~time(TestZoo))$coeff[2] m time(TestZoo) 0.3443124 m2 - lm(TestZoo[,2]~time(TestZoo))$coeff[2] m2 time(TestZoo) -0.1192866 I've been struggling trying to use apply ( or something equally suitable) to get a vector of m for this entire matrix without resorting to a loop. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] lm() on a matrix of zoo series
Thanks, I was trying apply(TestZoo,2,lm,TestZoo~time(TestZoo)) which was throwing a formula error. On Tue, Dec 21, 2010 at 12:21 PM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Tue, Dec 21, 2010 at 3:02 PM, steven mosher mosherste...@gmail.com wrote: I have a matrix of zoo series. each series is in a column. x - as.yearmon(2000 + seq(0, 23)/12) # 24 months of data, lets make 20 sets of random data testData - matrix(rnorm(480),ncol=20) # make a zoo object and columns will hold the 20 series TestZoo - zoo(testData,order.by=x) # now run lm for just one series. m - lm(TestZoo[,1]~time(TestZoo))$coeff[2] m time(TestZoo) 0.3443124 m2 - lm(TestZoo[,2]~time(TestZoo))$coeff[2] m2 time(TestZoo) -0.1192866 I've been struggling trying to use apply ( or something equally suitable) to get a vector of m for this entire matrix without resorting to a loop. Try this: lm(TestZoo ~ time(TestZoo)) -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] selecting certain rows from data frame
Hi, Next time give folks code to produce a toy sample of your problem DF -data.frame(ID=rep(1:5,each=3),Data=rnorm(15),Stuff=seq(1:15)) DF ID Data Stuff 1 1 2.0628225 1 2 1 0.6599165 2 3 1 0.5672595 3 4 2 -0.5308823 4 5 2 -0.5358471 5 6 2 -0.1414992 6 7 3 -0.1679643 7 8 3 0.9220922 8 9 3 0.8863018 9 10 4 -0.725591610 11 4 -1.244675311 12 4 0.816556712 13 5 0.092500813 14 5 -0.853480314 15 5 -0.653501615 # now I want to select rows where ID = 2 or 5 # Assign DF2 to those elements of DF where the ID variable=2 or 5 DF2 - DF[which(DF$ID==2 | DF$ID==5), ] DF2 ID Data Stuff 4 2 -0.5308823 4 5 2 -0.5358471 5 6 2 -0.1414992 6 13 5 0.092500813 14 5 -0.853480314 15 5 -0.653501615 On Tue, Dec 14, 2010 at 10:10 PM, Hrithik R rit...@yahoo.com wrote: Hi, if I have a dataframe such that ID Time Earn 1110 1250 1368 2140 2278 24 88 3150 3260 3398 4133 4248 44 58 . . Now if I have to select the all the rows from the data frame which does not include rows with certain IDs, say for example (prime) ID == 2 3, how do I do it Thanks Rith [[alternative HTML version deleted]] __ 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. [[alternative HTML version deleted]] __ 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] how to know if a file exists on a remote server?
I would use RCurl. if you have, for example, the url of an ftp site you can merely do a getURL() and the contents will be returned. That call will return data that can be coerced into a data.frame that will look like a directory structure listing the file names. If you need code just ask, but the RCurl docs are pretty good. On Tue, Nov 30, 2010 at 8:10 AM, Baoqiang Cao bqcaom...@gmail.com wrote: Hi, I'd like to download some data files from a remote server, the problem here is that some of the files actually don't exist, which I don't know before try. Just wondering if a function in R could tell me if a file exists on a remote server? I searched this mailing list and after read severals mails, still clueless. Any help will be highly appreciated. B.C. __ 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. [[alternative HTML version deleted]] __ 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] how to know if a file exists on a remote server?
using RCurl
getFtpList - function(ftp){
# the structure returned is dependent on the ftp site as there are
# various formats for directory listings dependent upon the server
# and the OS. you will need to play with this.
# have a look at the ftp with your browser first and adjust accordingly.
# some formats only return 4 columns.
# column 1= literal string first position mean file
# column 2= number 1
# column 3 =owner
# column 4 = group
# column 5 =file size
# colmn 6 =Month
# column 7 =Day
# column 8 =Time (year)
# column 9 =FileName
#
txt - getURL(ftp)
dir - read.table( textConnection(txt),as.is=TRUE)
out - data.frame(Dir=ftp,Filename=dir[, ncol(dir)],Size=dir[ ,5],
Month=dir[ ,6],Day=dir[ ,7],Time=dir[
,8],stringsAsFactors=FALSE)
closeAllConnections()
return(out)
}
On Tue, Nov 30, 2010 at 8:10 AM, Baoqiang Cao bqcaom...@gmail.com wrote:
Hi,
I'd like to download some data files from a remote server, the problem
here is that some of the files actually don't exist, which I don't
know before try. Just wondering if a function in R could tell me if a
file exists on a remote server? I searched this mailing list and after
read severals mails, still clueless. Any help will be highly
appreciated.
B.C.
__
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http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
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Re: [R] how to know if a file exists on a remote server?
No problem, you can also get the directory with a curlOption of dirlistonly see the example code in the package. This will depend on the version of libcurl that you have. If you have an older version, my code will get you the directory. From the Rcurl examples: the files within a directory. url = ' ftp://ftp.wcc.nrcs.usda.gov/data/snow/snow_course/table/history/idaho/' filenames = getURL(url, ftp.use.epsv = FALSE, dirlistonly = TRUE) # Deal with newlines as \n or \r\n. (BDR) # Or alternatively, instruct libcurl to change \n's to \r\n's for us with crlf = TRUE # filenames = getURL(url, ftp.use.epsv = FALSE, ftplistonly = TRUE, crlf = TRUE) filenames = paste(url, strsplit(filenames, \r*\n)[[1]], sep = ) con = getCurlHandle( ftp.use.epsv = FALSE) contents = sapply(filenames[1:5], getURL, curl = con) names(contents) = filenames[1:length(contents)] On Tue, Nov 30, 2010 at 9:56 AM, Baoqiang Cao bqcaom...@gmail.com wrote: Thanks Steven! It is excellent code indeed! On Tue, Nov 30, 2010 at 11:26 AM, steven mosher mosherste...@gmail.com wrote: I would use RCurl. if you have, for example, the url of an ftp site you can merely do a getURL() and the contents will be returned. That call will return data that can be coerced into a data.frame that will look like a directory structure listing the file names. If you need code just ask, but the RCurl docs are pretty good. On Tue, Nov 30, 2010 at 8:10 AM, Baoqiang Cao bqcaom...@gmail.com wrote: Hi, I'd like to download some data files from a remote server, the problem here is that some of the files actually don't exist, which I don't know before try. Just wondering if a function in R could tell me if a file exists on a remote server? I searched this mailing list and after read severals mails, still clueless. Any help will be highly appreciated. B.C. __ 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. [[alternative HTML version deleted]] __ 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] how to know if a file exists on a remote server?
here:
getFtpList - function(ftp){
# column 1= literal string first position mean file
# column 2= number 1
# column 3 =owner
# column 4 = group
# column 5 =file size
# colmn 6 =Month
# column 7 =Day
# column 8 =Time (year)
# column 9 =FileName
#
txt - getURL(ftp)
dir - read.table( textConnection(txt),as.is=TRUE)
if(ncol(dir)==9)out - data.frame(Dir=ftp,Filename=dir[,
ncol(dir)],Size=dir[ ,5],
Month=dir[ ,6],Day=dir[ ,7],Time=dir[
,8],stringsAsFactors=FALSE)
if(ncol(dir)==4)out - data.frame(Dir=ftp,Filename=dir[,
ncol(dir)],Size=dir[ ,3],
Month=dir[ ,1],Time=dir[ ,2],stringsAsFactors=FALSE)
closeAllConnections()
return(out)
}
On Tue, Nov 30, 2010 at 9:56 AM, Baoqiang Cao bqcaom...@gmail.com wrote:
Thanks Steven!
It is excellent code indeed!
On Tue, Nov 30, 2010 at 11:26 AM, steven mosher mosherste...@gmail.com
wrote:
I would use RCurl.
if you have, for example, the url of an ftp site you can merely do a
getURL() and the contents will be returned. That call will return data
that
can be coerced into a data.frame that will look like a directory
structure
listing the file names.
If you need code just ask, but the RCurl docs are pretty good.
On Tue, Nov 30, 2010 at 8:10 AM, Baoqiang Cao bqcaom...@gmail.com
wrote:
Hi,
I'd like to download some data files from a remote server, the problem
here is that some of the files actually don't exist, which I don't
know before try. Just wondering if a function in R could tell me if a
file exists on a remote server? I searched this mailing list and after
read severals mails, still clueless. Any help will be highly
appreciated.
B.C.
__
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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.
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to know if a file exists on a remote server?
study trycatch()
also, be awre that even with RCurl, that you may find the file there and
then fail or lose
the connection.
worse still you may get a currupt file on download. So there is a lot of
checking to do
to make bullet proof code that downloads files.
On Tue, Nov 30, 2010 at 3:16 PM, Baoqiang Cao bqcaom...@gmail.com wrote:
Hi Georg,
Your code does work, I mean, it doesn't give me any error message,
which is critical for me because I need use it in a loop and plus I
don't know how to catch error message. Before your message, I was
using download.file but the loop was stopped because of the error
message when a file doesn't exist. So I guess, the option
method=wget made the difference.
To summarize (in case it is useful to others), there are (at least)
two ways to download files:
1) Georg Ruß:
v = download.file(url,destf,method=wget)
if(v!=0) {
#download.file failed
}
#no error message though
2)
Henrique Dallazuanna and Steven Mosher both suggested using RCurl,
here is an example code from Henrique for checking if a file exists on
a server:
library(RCurl)
h = basicHeaderGatherer()
Lines - getURI(http://www.pdb.org/pdb/files/2J0S.1001;,
headerfunction = h$update)
h$value()[['status']]
If the status is 404, then not found. If exists then status should be 200.
What a productive day!
BC
On Tue, Nov 30, 2010 at 1:34 PM, Georg Ruß resea...@georgruss.de wrote:
On 30/11/10 10:10:07, Baoqiang Cao wrote:
I'd like to download some data files from a remote server, the problem
here is that some of the files actually don't exist, which I don't
know before try. Just wondering if a function in R could tell me if a
file exists on a remote server?
Hi Baoqiang,
try downloading the file with R's download.file() function. Then you
should examine the returned value.
Citing a part of ?download.file below:
Value:
An (invisible) integer code, 0 for success and non-zero for
failure. For the wget and lynx methods this is the status
code returned by the external program. The internal method can
return 1, but will in most cases throw an error.
So if you call your download via
v - download.file(url, destfile, method=wget)
and v is not equal to zero, then the file is likely to be non-existent
(at
least the download failed). Note: the method internal doesn't really
change the value of v, I just tried that. With wget it returns 0 for
success and 2048 (or some other value) for non-success.
Regards,
Georg.
--
Research Assistant
Otto-von-Guericke-Universität Magdeburg
resea...@georgruss.de
http://research.georgruss.de
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[R] Reverting to previous version
R 2.12 is not functioning for me On the MAC what the most painless way of reverting [[alternative HTML version deleted]] __ 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] spliting first 10 words in a string
Thanks david. Matevz, maybe I can help explain by doing a very simple and brute force approach as opposed to the way david did it. But you should learn his methods. I will just do a subset of your problem and if you understand how it works then you should be able to get something done and then make it more elegant. First, I simplify the problem by separating out the sentence column. You can do this with your data frame by simply doing this MySentence -data.frame(sentence=yourbigDF$Opis,stringsAsFactors=FALSE) so I take your original data.frame (yourbigDF) and I just create a copy of that one column $Opis Later we can merge the two back together after I add 10 columns for the words Lets make some dummy data with just 10 rows sentence- this is a sentence with ten words or maybe more than ten words sentV-rep(sentence,10) # now I just made 10 rows of the same sentence # NEXT because I am going to create 10 new colums of 10 rows I create # 10 vectors each is named and each has 10 elements For the rows. # they have NO DATA in them first=second=third=fourth=fifth=sixth=seventh=eighth=ninth=tenth-vector(length=10) #Next I create a dataframe with Sentence in the first column and 10 blank colums. # NOTE I use stringsAsFactors=False DF -data.frame(Sentence=sentence,first,second,third,fourth,fifth,sixth,seventh,eighth,ninth,tenth,stringsAsFactors=FALSE) # This is what it would look like ( the first row) DF[1,] Sentence first second third fourth fifth sixth seventh eighth ninth tenth 1 this is a sentence with ten words or maybe more than ten words FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE Next, I will show you how to assign the first ten words to the 10 blank columns DF[1,2:11]-strsplit(DF[1,1], )[[1]][1:10] #DF[1,2:11] selects the columns 2-11 of the first row #strsplit returns the first 10 words [1:10] and place them in the columsn2-11 If you want to do this the slow way you can just loop through your dataframe row by row or you can probably use apply. Make more sense? DF[1,2:11]-strsplit(DF[1,1], )[[1]][1:10] DF[1,] Sentence first second third fourth fifth sixth seventh eighth ninth tenth 1 this is a sentence with ten words or maybe more than ten words this is a sentence with ten words or maybe more DF[1,first] [1] this On Tue, Nov 2, 2010 at 12:22 PM, David Winsemius dwinsem...@comcast.netwrote: On Nov 2, 2010, at 3:01 PM, Matevž PavliÄ wrote: Hi all, Thanks for all the help. I managed to do it with what Gaj suggested (Excel :(). The last solution from David is also freat i just don't undestand why R put the words in 14 columns and thre rows? Because the maximum number of words was 14 and the fill argument was TRUE. There were three rows because there were three items in the supplied character vector. I would like it to put just the first 10 words in source field to 10 diefferent destiantion fields, but the same row. And so on...is that possible? I don't know what a destination field might be. Those are not R data types. This would trim the extra columns (in this example set to those greater than 8) by adding a lot of NULL's to the end of a colClasses specification at the expense of a warning message which can be ignored: read.table(textConnection(words), fill=T, colClasses = c(rep(character, 8), rep(NULL, 30) ) , stringsAsFactors=FALSE ) V1V2V3 V4V5V6V7 V8 1 I have a columnn with text that has 2 I would like to split these words in 3 but just first ten wordsin the string. Warning message: In read.table(textConnection(words), fill = T, colClasses = c(rep(character, : cols = 14 != length(data) = 38 If you want to assign the first column to a variable then just: first8 - read.table(textConnection(words), fill=T, colClasses = c(rep(character, 8), rep(NULL, 30) ) , stringsAsFactors=FALSE) var1 - first8[[1]] var1 [1] I I but -- David. Thank you, m -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of David Winsemius Sent: Tuesday, November 02, 2010 3:47 PM To: Gaj Vidmar Cc: r-h...@stat.math.ethz.ch Subject: Re: [R] spliting first 10 words in a string On Nov 2, 2010, at 6:24 AM, Gaj Vidmar wrote: Though forbidden in this list, in Excel it's just (literally!) five clicks away! (with the column in question selected) Data - Text to Columns - Delimited - tick Space - Finish Pa je! (~Voila in Slovenian) (then import back to R, keeping only the first 10 columns if so desired) You could do the same thing without needing to leave R. Just read.table( textConnection(..), header=FALSE, fill=TRUE) read.table(textConnection(words), fill=T) V1V2V3 V4V5V6V7 V8 V9 V10 V11 V12 V13 V14 1 I have a columnn with text that
Re: [R] splitting First 10 words in a string
That's easy you are confusing the dummy code I sent.
Do this:
lit-read.csv(litologija.csv, sep=;, dec=.)
sent -data.frame(sentence=lit$Opis,stringsAsFactors=FALSE)
irst=second=third=fourth=fifth=sixth=seventh=eighth=ninth=tenth-vector(length=nrow(
sent)
I put the length of the vector to 10 just to do a dummy problem.
Then do this:
for(j in 1:nrow(sent) {
sent[j,2:11]-strsplit(sent[j,1], )[[1]][1:10]
}
That will get you a result the crude brute force way.
try that.
Then you can learn sapply way. but first you need to learn R data
structures.
On Tue, Nov 2, 2010 at 1:47 PM, Matevž PavliÄ matevz.pav...@gi-zrmk.siwrote:
Hi Steven,
Thank you for the help. I get an error though when i do this :
lit-read.csv(litologija.csv, sep=;, dec=.)
sent -data.frame(sentence=lit$Opis,stringsAsFactors=FALSE)
str(sent)
sentV-rep(sent,10)
str(sentV)
first=second=third=fourth=fifth=sixth=seventh=eighth=ninth=tenth-vector(length=10)
DF
-data.frame(Sentence=sent,first,second,third,fourth,fifth,sixth,seventh,eighth,ninth,tenth,stringsAsFactors=FALSE)
»Error in data.frame(Sentence = sent, first, second, third, fourth, fifth,
:
arguments imply differing number of rows: 22928, 10«
What am I doing wrong?
Thnks, m
*From:* steven mosher [mailto:mosherste...@gmail.com]
*Sent:* Tuesday, November 02, 2010 8:45 PM
*To:* David Winsemius
*Cc:* Matevž PavliÄ; Gaj Vidmar; r-h...@stat.math.ethz.ch
*Subject:* Re: [R] spliting first 10 words in a string
Thanks david.
Matevz, maybe I can help explain by doing a very simple and brute force
approach
as opposed to the way david did it. But you should learn his methods.
I will just do a subset of your problem and if you understand how it works
then you should
be able to get something done and then make it more elegant.
First, I simplify the problem by separating out the sentence column.
You can do this with your data frame by simply doing this
MySentence -data.frame(sentence=yourbigDF$Opis,stringsAsFactors=FALSE)
so I take your original data.frame (yourbigDF) and I just create a copy of
that one column
$Opis
Later we can merge the two back together after I add 10 columns for the
words
Lets make some dummy data with just 10 rows
sentence- this is a sentence with ten words or maybe more than ten
words
sentV-rep(sentence,10)
# now I just made 10 rows of the same sentence
# NEXT because I am going to create 10 new colums of 10 rows I create
# 10 vectors each is named and each has 10 elements For the rows.
# they have NO DATA in them
first=second=third=fourth=fifth=sixth=seventh=eighth=ninth=tenth-vector(length=10)
#Next I create a dataframe with Sentence in the first column and 10 blank
colums.
# NOTE I use stringsAsFactors=False
DF
-data.frame(Sentence=sentence,first,second,third,fourth,fifth,sixth,seventh,eighth,ninth,tenth,stringsAsFactors=FALSE)
# This is what it would look like ( the first row)
DF[1,]
Sentence first second third fourth fifth sixth seventh eighth ninth tenth
1 this is a sentence with ten words or maybe more than ten words FALSE
FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
Next, I will show you how to assign the first ten words to the 10 blank
columns
DF[1,2:11]-strsplit(DF[1,1], )[[1]][1:10]
#DF[1,2:11] selects the columns 2-11 of the first row
#strsplit returns the first 10 words [1:10] and place them in the
columsn2-11
If you want to do this the slow way you can just loop through your
dataframe row by row
or you can probably use apply.
Make more sense?
DF[1,2:11]-strsplit(DF[1,1], )[[1]][1:10]
DF[1,]
Sentence first
second third fourth fifth sixth seventh eighth ninth tenth
1 this is a sentence with ten words or maybe more than ten words this
is a sentence with ten words or maybe more
DF[1,first]
[1] this
On Tue, Nov 2, 2010 at 12:22 PM, David Winsemius dwinsem...@comcast.net
wrote:
On Nov 2, 2010, at 3:01 PM, Matevž PavliÄ wrote:
Hi all,
Thanks for all the help. I managed to do it with what Gaj suggested (Excel
:().
The last solution from David is also freat i just don't undestand why R
put the words in 14 columns and thre rows?
Because the maximum number of words was 14 and the fill argument was TRUE.
There were three rows because there were three items in the supplied
character vector.
I would like it to put just the first 10 words in source field to 10
diefferent destiantion fields, but the same row. And so on...is that
possible?
I don't know what a destination field might be. Those are not R data types.
This would trim the extra columns (in this example set to those greater
than 8) by adding a lot of NULL's to the end of a colClasses specification
at the expense of a warning message which can be ignored:
read.table
Re: [R] splitting First 10 words in a string
Line should be:
first=second=third=fourth=fifth=sixth=seventh=eighth=ninth=tenth-vector(length=nrow(
sent))
sorry cut and past error
On Tue, Nov 2, 2010 at 3:32 PM, steven mosher mosherste...@gmail.comwrote:
That's easy you are confusing the dummy code I sent.
Do this:
lit-read.csv(litologija.csv, sep=;, dec=.)
sent -data.frame(sentence=lit$Opis,stringsAsFactors=FALSE)
first=second=third=fourth=fifth=sixth=seventh=eighth=ninth=tenth-vector(length=nrow(
sent)
I put the length of the vector to 10 just to do a dummy problem.
Then do this:
for(j in 1:nrow(sent) {
sent[j,2:11]-strsplit(sent[j,1], )[[1]][1:10]
}
That will get you a result the crude brute force way.
try that.
Then you can learn sapply way. but first you need to learn R data
structures.
On Tue, Nov 2, 2010 at 1:47 PM, Matevž PavliÄ
matevz.pav...@gi-zrmk.siwrote:
Hi Steven,
Thank you for the help. I get an error though when i do this :
lit-read.csv(litologija.csv, sep=;, dec=.)
sent -data.frame(sentence=lit$Opis,stringsAsFactors=FALSE)
str(sent)
sentV-rep(sent,10)
str(sentV)
first=second=third=fourth=fifth=sixth=seventh=eighth=ninth=tenth-vector(length=10)
DF
-data.frame(Sentence=sent,first,second,third,fourth,fifth,sixth,seventh,eighth,ninth,tenth,stringsAsFactors=FALSE)
»Error in data.frame(Sentence = sent, first, second, third, fourth,
fifth, :
arguments imply differing number of rows: 22928, 10«
What am I doing wrong?
Thnks, m
*From:* steven mosher [mailto:mosherste...@gmail.com]
*Sent:* Tuesday, November 02, 2010 8:45 PM
*To:* David Winsemius
*Cc:* Matevž PavliÄ; Gaj Vidmar; r-h...@stat.math.ethz.ch
*Subject:* Re: [R] spliting first 10 words in a string
Thanks david.
Matevz, maybe I can help explain by doing a very simple and brute force
approach
as opposed to the way david did it. But you should learn his methods.
I will just do a subset of your problem and if you understand how it works
then you should
be able to get something done and then make it more elegant.
First, I simplify the problem by separating out the sentence column.
You can do this with your data frame by simply doing this
MySentence -data.frame(sentence=yourbigDF$Opis,stringsAsFactors=FALSE)
so I take your original data.frame (yourbigDF) and I just create a copy of
that one column
$Opis
Later we can merge the two back together after I add 10 columns for the
words
Lets make some dummy data with just 10 rows
sentence- this is a sentence with ten words or maybe more than ten
words
sentV-rep(sentence,10)
# now I just made 10 rows of the same sentence
# NEXT because I am going to create 10 new colums of 10 rows I create
# 10 vectors each is named and each has 10 elements For the rows.
# they have NO DATA in them
first=second=third=fourth=fifth=sixth=seventh=eighth=ninth=tenth-vector(length=10)
#Next I create a dataframe with Sentence in the first column and 10 blank
colums.
# NOTE I use stringsAsFactors=False
DF
-data.frame(Sentence=sentence,first,second,third,fourth,fifth,sixth,seventh,eighth,ninth,tenth,stringsAsFactors=FALSE)
# This is what it would look like ( the first row)
DF[1,]
Sentence first second third fourth fifth sixth seventh eighth ninth tenth
1 this is a sentence with ten words or maybe more than ten words FALSE
FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
Next, I will show you how to assign the first ten words to the 10 blank
columns
DF[1,2:11]-strsplit(DF[1,1], )[[1]][1:10]
#DF[1,2:11] selects the columns 2-11 of the first row
#strsplit returns the first 10 words [1:10] and place them in the
columsn2-11
If you want to do this the slow way you can just loop through your
dataframe row by row
or you can probably use apply.
Make more sense?
DF[1,2:11]-strsplit(DF[1,1], )[[1]][1:10]
DF[1,]
Sentence first
second third fourth fifth sixth seventh eighth ninth tenth
1 this is a sentence with ten words or maybe more than ten words this
is a sentence with ten words or maybe more
DF[1,first]
[1] this
On Tue, Nov 2, 2010 at 12:22 PM, David Winsemius dwinsem...@comcast.net
wrote:
On Nov 2, 2010, at 3:01 PM, Matevž PavliÄ wrote:
Hi all,
Thanks for all the help. I managed to do it with what Gaj suggested (Excel
:().
The last solution from David is also freat i just don't undestand why R
put the words in 14 columns and thre rows?
Because the maximum number of words was 14 and the fill argument was TRUE.
There were three rows because there were three items in the supplied
character vector.
I would like it to put just the first 10 words in source field to 10
diefferent destiantion fields, but the same row. And so on...is that
possible?
I don't know what a destination field might be. Those are not R data
Re: [R] spliting first 10 words in a string
just merge the data.frames back together. use merge or cbind() cbind will be easier DF1 - data.frame(x,y,z) DF2 -data.frame(DF1$x) # copy a column then you added columns to DF2 just put them back together DF3 -cbind(DF2,DF1$y,DF$z) if you spend more time with R you will be able to do things like this elegantly, but for now This way will work and you will learn a bit about R. As for counting instances of a string, I might suggest looking at the table command k - c( all, but,all) table(k) k all but 2 1 So you can do a table for each column in your dataframe On Tue, Nov 2, 2010 at 12:53 PM, Matevž PavliÄ matevz.pav...@gi-zrmk.siwrote: Hi, Ok, i got this now. At least i think so. I got a data.frame with 15 fields, all other words have bee truncated. Which is what i want. But ia have that in a seperate data.frame from that one it was before (would be nice if it would be in the same ...) 'data.frame': 22801 obs. of 15 variables: $ V1 : chr HUMUS SLABO MALO SLABO ... $ V2 : chr IN GRANULIRAN PREPEREL VEZAN ... $ V3 : chr HUMUSNA PEÅ ÄEN MELJAST ,KONGLOMERAT, ... $ V4 : chr GLINA PROD PROD P0ROZEN, ... $ V5 : chr Z DO DO S ... $ V6 : chr MALO r r PLASTMI ... $ V7 : chr PODA, = = GFs, ... $ V8 : chr LAHKO 8Q 60mm, SIVORJAV ... $ V9 : chr GNETNA, mm, S ... $ V10: chr RJAVA S PRODNIKI, ... $ V11: chr PRODNIKI MALO ... $ V12: chr DO PEÅ ÄEN ... $ V13: chr R S ... $ V14: chr = TANKIMI ... Now, i have another problem. Is it possible to count which word occours most often each field (V1, V2, V3, ...) and which one is the second and so on. Ideally to create a table for each field (V1, V2, V3, ...) with the word and thenumber of occuraces in that field (column) . I suppose it could be done in SQL, but what since i saw what R can do i guess this can be done here to? Thanks, m -Original Message- From: David Winsemius [mailto:dwinsem...@comcast.net] Sent: Tuesday, November 02, 2010 8:23 PM To: Matevž PavliÄ Cc: Gaj Vidmar; r-h...@stat.math.ethz.ch Subject: Re: [R] spliting first 10 words in a string On Nov 2, 2010, at 3:01 PM, Matevž PavliÄ wrote: Hi all, Thanks for all the help. I managed to do it with what Gaj suggested (Excel :(). The last solution from David is also freat i just don't undestand why R put the words in 14 columns and thre rows? Because the maximum number of words was 14 and the fill argument was TRUE. There were three rows because there were three items in the supplied character vector. I would like it to put just the first 10 words in source field to 10 diefferent destiantion fields, but the same row. And so on...is that possible? I don't know what a destination field might be. Those are not R data types. This would trim the extra columns (in this example set to those greater than 8) by adding a lot of NULL's to the end of a colClasses specification at the expense of a warning message which can be ignored: read.table(textConnection(words), fill=T, colClasses = c(rep(character, 8), rep(NULL, 30) ) , stringsAsFactors=FALSE ) V1V2V3 V4V5V6V7 V8 1 I have a columnn with text that has 2 I would like to split these words in 3 but just first ten wordsin the string. Warning message: In read.table(textConnection(words), fill = T, colClasses = c(rep(character, : cols = 14 != length(data) = 38 If you want to assign the first column to a variable then just: first8 - read.table(textConnection(words), fill=T, colClasses = c(rep(character, 8), rep(NULL, 30) ) , stringsAsFactors=FALSE) var1 - first8[[1]] var1 [1] I I but -- David. Thank you, m -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org ] On Behalf Of David Winsemius Sent: Tuesday, November 02, 2010 3:47 PM To: Gaj Vidmar Cc: r-h...@stat.math.ethz.ch Subject: Re: [R] spliting first 10 words in a string On Nov 2, 2010, at 6:24 AM, Gaj Vidmar wrote: Though forbidden in this list, in Excel it's just (literally!) five clicks away! (with the column in question selected) Data - Text to Columns - Delimited - tick Space - Finish Pa je! (~Voila in Slovenian) (then import back to R, keeping only the first 10 columns if so desired) You could do the same thing without needing to leave R. Just read.table( textConnection(..), header=FALSE, fill=TRUE) read.table(textConnection(words), fill=T) V1V2V3 V4V5V6V7 V8 V9 V10 V11 V12 V13 V14 1 I have a columnn with text that hasquite a few words in it. 2 I would like to split these words in separate columns 3 but just first ten wordsin the string. Isthat possiblein R? Regards, Assist. Prof. Gaj Vidmar, PhD University Rehabilitattion Institute, Republic
[R] Strings from different locale
I'm doing some test processing of a cvs file that appears to use a different locale from my machine. I get the following warning: input string 1 is invalid in this locale My locale is US. Is this simply a matter of changing my locale to 'all; locales? I don't know what locale the string is in, is there a way to detect this or translate [[alternative HTML version deleted]] __ 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] doubt in climate variability analysis in R! - code
Ok I downloaded it and showed you how to get your data out. How to read it into a raster brick, how to plot the data, how to get the mean rainfall of every day.lots more you can do. there is a bad bit of data in the last time step. check my blog. In the future what you should do is write code to emulate your problem. for example, in your problem you had created a ncdf file with a 3D matrix of 65,69,2192. You should just do a subset of that, show the code to create a ncdf with random numbers in it. creating working code that emulates your problem is key if you want help. Off list for the rest. On Sun, Oct 31, 2010 at 10:21 AM, govin...@msu.edu wrote: I am sorry, i think the link was broken..! here is the correct one!!! http://www.4shared.com/file/4zV0g3JR/RF_80-85.html [[alternative HTML version deleted]] __ 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. [[alternative HTML version deleted]] __ 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] Reading in a tab delimitated file
if your data for the rest of the file looks like this then read.fwf will work. depending which vars you want to pull) widths= c(18,32,41) E-CBIL-28-raw-cel-1435145228.cel1 would pull 3 vars, E-CBIL-28-raw-cel-; 1435145228.cel;1 widths -c(32,41) E-CBIL-28-raw-cel-1435145228.cel;1 you can set it differently, assign colnames and column classes as well But the feilds must be fixed width. On Tue, Oct 26, 2010 at 5:35 AM, amindlessbrain jillianrowe91...@gmail.comwrote: Hi all, I have a total newbie question, but I could really use some help. I need to read in this file: SampleIDDisease E-CBIL-28-raw-cel-1435145228.cel1 E-CBIL-28-raw-cel-1435145451.cel2 E-CBIL-28-raw-cel-1435145479.cel2 E-CBIL-28-raw-cel-1435145132.cel3 E-CBIL-28-raw-cel-1435145417.cel3 E-CBIL-28-raw-cel-1435145301.cel2 E-CBIL-28-raw-cel-1435145558.cel1 E-CBIL-28-raw-cel-1435145073.cel3 E-CBIL-28-raw-cel-1435145196.cel2 E-CBIL-28-raw-cel-1435145511.cel1 E-CBIL-28-raw-cel-1435145336.cel3 E-CBIL-28-raw-cel-1435145260.cel2 E-CBIL-28-raw-cel-1435145167.cel2 E-CBIL-28-raw-cel-1435145387.cel3 E-CBIL-28-raw-cel-1435145099.cel3 (I'm not sure why the disease column isn't showing up as a tab here, but it is sep by \t in my file. I've tried several variations on these: pd - read.AnnotatedDataFrame (new_treat.txt , header = TRUE , sep=\t, row.names = SampleID, colClasses = c(Disease = character)) And I keep on getting this error: Error in read.table(filename, sep = sep, header = header, quote = quote, : more columns than column names Any help would be very very very appreciated! Thanks! -- View this message in context: http://r.789695.n4.nabble.com/Reading-in-a-tab-delimitated-file-tp3013620p3013620.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. [[alternative HTML version deleted]] __ 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] Best IDE for R
Thanks for the pointer, After looking at the many folders of R code I have I decided it was time to start working in an IDE and also getting my stuff under version control ( for my own sanity) I'll have a look at Geany.. for version control.. not so sure. On Wed, Oct 27, 2010 at 12:14 PM, Liviu Andronic landronim...@gmail.comwrote: On Wed, Oct 27, 2010 at 9:05 PM, Jonathan P Daily jda...@usgs.gov wrote: I can second using Geany as an IDE. Great, finally a soulmate! :) More seriously, I think Geany is under-appreciated and virtually unkonwn in the R community. Another large plus for it is that it is cross platform (I work in both Windows and Linux), cross environment (I also code in Python/Sage), very customizable, and even has a version on PortableApps for windows so you can take a customized version around on a USB stick with ease. One important feature that teh Windows version of Geany lacks is the integrated virtual terminal emulator. This is mainly because the VTE port to Windows was never finalised (although the patch is well in their bugtracker). One possibility is to use Geany in a VMware virtual Linux machine on Windows. Regards Liviu -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly From: Liviu Andronic landronim...@gmail.com To: Lee Hachadoorian lee.hachadooria...@gmail.comlee.hachadoorian%...@gmail.com Cc: r-h...@stat.math.ethz.ch Date: 10/27/2010 02:45 PM Subject: Re: [R] Best IDE for R Sent by: r-help-boun...@r-project.org On Wed, Oct 27, 2010 at 4:05 PM, Lee Hachadoorian lee.hachadooria...@gmail.com lee.hachadoorian%...@gmail.com wrote: For an R-enabled text editor, I would suggest Tinn-R for Windows or RGedit (a gedit plugin) for Linux/Gnome-desktop. Since both are just text editors, they will work with whatever version R you have installed (criteria 1). RGedit is pretty spare: basically just console integration and keyboard shortcuts to send code (current line, selection, defined blocks) to the console. Criteria 1 Y 2 basic 3 N 4 N For Linux and Mac, I usually suggest Geany [1] as an alternative to Gedit. Geany is an intuitive IDE that can send commands to rterm in the integrated virtual terminal emulator. It provides various features for project management, source highlighting, code folding, etc. Regards Liviu [1] http://www.r-bloggers.com/integrating-r-with-geany/ __ 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. -- Do you know how to read? http://www.alienetworks.com/srtest.cfm http://goodies.xfce.org/projects/applications/xfce4-dict#speed-reader Do you know how to write? http://garbl.home.comcast.net/~garbl/stylemanual/e.htm#e-mailhttp://garbl.home.comcast.net/%7Egarbl/stylemanual/e.htm#e-mail __ 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. [[alternative HTML version deleted]] __ 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] Overlaying two png?
I have a program that creates a Png file using Rgooglemap with an extent (lonmin,lonmax,latmin,latmax) I also have a contour plot of the same location, same extent, same sized (height/width) png file. I'm looking for a way to make the contour semi transparent and overlay it on the google map ( hybrid map) Since I have 7000 of these to do an automated process is desired ( grin) Any pointers in the right direction ? [[alternative HTML version deleted]] __ 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] Beginner question on bar plot
I've read a number of examples on doing a multiple bar plot, but cant seem to grasp how they work or how to get my data into the proper form. I have two variable holding the same factor The variables were created using a cut command, The following simulates that A - 1:100 B - 1:100 A[30:60] - 43 Acut - cut(A,breaks=c(0,10,45,120),labels=c(low,med,high)) Bcut - cut(B,breaks=c(0,10,45,120),labels=c(low,med,high)) What I want to do is create a barplot with 3 groups of side by side bars group 1, = low and the two bars would be the count for Acut, and the count for Bcut group 2 = med and the two bars again would be the counts for this factor level in Acut and Bcut group 3 = high and like the above two. [[alternative HTML version deleted]] __ 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] Read from a website
Hmm, RCurl might have something on this. otherwise pull you can figure out their scheme and just construct the url from scratch. when you finish filling in the form, look at the url they construct. do it a few times and you can just emulate that. I've done that in the past without problems. depends on the site. On Tue, Oct 12, 2010 at 2:32 AM, Santosh Srinivas santosh.srini...@gmail.com wrote: Something similar to this was discussed recently, but I'm unable to find the thread. I want to read from a site where I need to enter the date into a form before I am presented with the CSV link. E.g. like reading ticker data from yahoo (but assuming you HAVE to enter the dates and click on request). How do I simulate this from R? Thanks for the help. [[alternative HTML version deleted]] __ 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. [[alternative HTML version deleted]] __ 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] Loss of precision in read.csv.
Given a csv file from this location Airports-http://www.ourairports.com/data/airports.csv; download.file(Airports,basename(Airports)) airports -read.csv(airports.csv,encoding=UTF-8) airports[1,] id ident type name latitude_deg longitude_deg elevation_ft continent iso_country iso_region municipality scheduled_service 1 6523 00A heliport Total Rf Heliport *40.0708 -74.9336 * 11 NA US US-PA Bensalemno gps_code iata_code local_code home_link wikipedia_link keywords 1 00A 00A And the precision is lost which we can show by using readLines: fred-readLines(airports.csv) fred[2] [1] 6523,\00A\,\heliport\,\Total Rf Heliport\,* 40.07080078125,-74.9336013793945* ,11,\NA\,\US\,\US-PA\,\Bensalem\,\no\,\00A\,,\00A\,,, I tried various approaches, using colClasses, switching to read.tables, specifying dec=. I tested read.csv and it does preserve precision on my test case, but not on this data. Ideas? [[alternative HTML version deleted]] __ 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] Loss of precision in read.csv.
Ha Thanks, That was it. On Sat, Oct 9, 2010 at 2:38 PM, Joshua Wiley jwiley.ps...@gmail.com wrote: Hi Steven, As near as I can tell, no precision is lost. R is just being courteous and not excessively filling our consoles. Try: print(airports[1,latitude_deg], digits = 22) which is the most digits R will print (although internally it can store more I believe). Alternately, you can convert it to character class: as.character(airports[1, ]) So in short, this is just a cosmetic feature of presenting the data, not its actual storage. Cheers, Josh On Sat, Oct 9, 2010 at 1:33 PM, steven mosher mosherste...@gmail.com wrote: Given a csv file from this location Airports-http://www.ourairports.com/data/airports.csv; download.file(Airports,basename(Airports)) airports -read.csv(airports.csv,encoding=UTF-8) airports[1,] id ident type name latitude_deg longitude_deg elevation_ft continent iso_country iso_region municipality scheduled_service 1 6523 00A heliport Total Rf Heliport *40.0708 -74.9336 * 11 NA US US-PA Bensalemno gps_code iata_code local_code home_link wikipedia_link keywords 1 00A 00A And the precision is lost which we can show by using readLines: fred-readLines(airports.csv) fred[2] [1] 6523,\00A\,\heliport\,\Total Rf Heliport\,* 40.07080078125,-74.9336013793945* ,11,\NA\,\US\,\US-PA\,\Bensalem\,\no\,\00A\,,\00A\,,, I tried various approaches, using colClasses, switching to read.tables, specifying dec=. I tested read.csv and it does preserve precision on my test case, but not on this data. Ideas? [[alternative HTML version deleted]] __ 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. -- Joshua Wiley Ph.D. Student, Health Psychology University of California, Los Angeles http://www.joshuawiley.com/ [[alternative HTML version deleted]] __ 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] RE : R getting slower until it breaks...
I know its no consolation, but I have a similar issue with R on a MAC, also
ploting
out large numbers of raster layers. sometimes the problem lingers even
after I clear the workspace, do gc() etc. Almost as if R wont ask for
processor resources.
weird.
On Wed, Oct 6, 2010 at 12:06 PM, Bastien Ferland-Raymond
bastien.ferland-raymon...@ulaval.ca wrote:
Thanks a lot for your quick answer. Here is my answer to your questions:
Have you looked to see how fast your memory might be growing?
BFR- Yes I did, it's not to bad, it's starts around 60 000ko, rise up to
120 000 at the most, so not too scary.
Are you leaving around any large objects that should be removed?
BFR- I was carefull making sure the function doesn't create anything that
would be visible with objects(). Could it be creating other type (hidden)
objects? Maybe, but I'm not very familliar with that stuff.
Have you looked to see if you are paging?
BFR- I just red the wiki about paging, didn't know that term before. If I
look at perfmon, its looks like keeping steady at 6000 pages/s with rare
peaks as high as 900 000. Does it sounds normal? How can it affect R?
Is it your CPU time that is increasing, or your wall clock time?
BFR- If I go to the task manager - performance. R is initially using
around 40% of the processor (so around 80% of 1 core) but with (real) time
passing, it gets lower and lower to get as low as 6% (12% of one core). I
was surprized to see that as usually my simulation in R use one whole core.
It sounds like there might be some memory leak that might be causing your
process size to grow and possibly causing paging. You will need to gather
some of the performance data that perfmon can provide and look at the memory
usage, CPU time and I/O rates over time to see if there are any changes.
BFR- The term Memory leak feels right with my problem. Is there ways I
can control/detect/prevent this kind of problem in R. Also, how can I check
the I/O, i never looked at that before.
Thanks again
Bastien
On Wed, Oct 6, 2010 at 2:11 PM, Bastien Ferland-Raymond
bastien.ferland-raymon...@ulaval.ca wrote:
Hello R-users,
I'm currently facing a pretty hard problem which I'm hopping you'll be
able to help me with. I'm using R to create images. That alone is not the
problem, the problem is that I'm using R to create 168 000 images... My
code (which is given below) use different package (raster and rgdal) to
import a image (size 20gig) and divide it into 168 000 pictures that are 100
pixel x 100 pixel. The code works fine for making the images, but if I ask
it to run all 168 000, it always breaks around 15 000.
It starts with the code being able to make around 2 pictures per second,
but then it slows down and after around 2000 pictures it's only 1 picture
per second. Later on it's getting closer to 1 pictures every 3 seconds etc.
until it bugs. I have no error message, only Windows that tells me that R
encounter a problem and most be close... Initially I though it was a
Windows problem, that I couldn't put too many file into a folder and it was
slowering it down. Then I divided my batch process into smaller (5000
files) folder but it didn't help, still breaks at 15 000. I also try to do
gc() after each 5000 pictures to save memory but it didn't help either. I
removed every loops from the code because I thought it was the problem, but
it was just faster at bugging... After the bug, I need to restart the
computer if I want to go back to the initial speed.
I'm pretty much running out of options. It's there limitation in R as
the number of files it can create in one session? Is it a windows problem?
Is there better way to clear the memory than gc()? Any thought on that?
I'm using R 2.11.1, win XP, my hard drive is NTSF, computer: intel core2
duo E6750 32 bit with 2 gig of Ram.
Here is my code, but I doubt it would help much with my problem:
# It made of 4 functions (sorry, it's french):
##
##
### Ensemble des fonctions pour faire les images NDVI rouge et verte
###
##
## Bastien Ferland-Raymond, 5 oct 2010
#
##
## Simplement rouler le script au complet
### Library nécessaire:
library(raster)
library(rgdal)
library(shapefiles)
#
## Fonction 1 - NDVI a partir de coordonnee Pixel et largeur #
calculate_NDVI- function(Type, object, VALUE) {
redorgreen - ifelse(Type==red,2,3)
list1 - unstack(object)
rast1 - list1[[1]]
rast2 - list1[[redorgreen]]
NAvalue(rast1)-
Re: [R] RE : R getting slower until it breaks...
Thanks, haven't used valgrind in years, this should be fun. Steve On Wed, Oct 6, 2010 at 1:55 PM, Ben Bolker bbol...@gmail.com wrote: steven mosher moshersteven at gmail.com writes: I know its no consolation, but I have a similar issue with R on a MAC, also ploting out large numbers of raster layers. sometimes the problem lingers even after I clear the workspace, do gc() etc. Almost as if R wont ask for processor resources. If it is a memory leak, it might be worth reading up on the use of valgrind (section 4.3.2 in the 'R extensions' manual). The information provided by valgrind might not be immediately interpretable, but it could help others track down a problem ... __ 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. [[alternative HTML version deleted]] __ 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] Script auto-detecting its own path
in the package R.utils getAbsolutePath() or you can do a file.list(.. full.names=TRUE, recursive=TRUE,pattern=(.R)) the rest will require grep and pulling the file name and directory path apart If its not evident just ask and I'll write something for you. basically you want a call that returns the full path of a R script? On Mon, Oct 4, 2010 at 12:13 PM, Hadley Wickham had...@rice.edu wrote: I'm not sure this will solve the issue because if I move the script, I would still have to go into the script and edit the /path/to/my/script.r, or do I misunderstand your workaround? I'm looking for something like: file.path.is.here(myscript.r) and which would return something like: [1] c:/user/Desktop/ so that regardless of where the script is, as long as the accompanying scripts are in the same directory, they can be easily sourced with something like: dirX - file.path.is.here(MasterScript.r) source(paste(dirX, AuxillaryFile.r, sep=)) If you use relative paths like so: # master.r source(AuxillaryFile.r) Then source(path/to/master.r, chdir = T) will work. Mastering working directories is a much better idea than coming up with your own workarounds. Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ 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. [[alternative HTML version deleted]] __ 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] get absolute file path
The package R.utils has a function to get absolutepath On Sun, Sep 26, 2010 at 1:00 AM, Sebastian Gibb li...@sebastiangibb.dewrote: Hello, I get a value which stores a relative file name. (I get it from another function, which I don't want to change.) e.g. fileName - ../data/2010-08.csv; Is it possible to get the absolute file path out of this value? (e.g. /home/sebastian/documents/data/2010-08.csv) Kind regards, Sebastian __ 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. [[alternative HTML version deleted]] __ 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] diagnosing download.file() problems
I'm accessing around 95 tar files on an FTP server ranging in size between 10 and 40MB a piece. while certainly can click on them and download them outside of R, I'd like to have my script do it. Retrieving the ftp directory with RCurl works fine (about 90% of the time) but downloading the files by looping through all the files is a random process. I may get 1-8 files download and then it throws an error cannot open URL sometimes I only can get 1 file before this error. with tryCatch() I've been able to do some clean up after the crash, but automating this whole download process has turned into a bit of a circus. The parameters (url, destfile, mode) are all correct in the download.file call as the second attempt at a url will often succeed. Is there anyway to get a deeper look at the cause of the problem? I've tried closing all connections in between each download. any pointers would be welcomed. [[alternative HTML version deleted]] __ 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] diagnosing download.file() problems
That is what I feared. I know other people on slow connections have done
this without issue ( at least they didnt report an issue ) I had a similar
issue with geonames.org who at least published their terms
of service (requests per second or sumptin like that.. so could program
around it) I'll hunt around
on their ftp and then write the admin a note.. i really don't want to brute
force the matter
it's government data made available for the public so I expect the admin
will be helpful.
Thanks for confirming what I suspected, for a minute [ .ed: for two days] I
thought I had taken crazy pills.
i did note, however, some odd behavior with tryCatch, where statements
after the finally={} were executed. Not sure if that deserves a bug report.
On Tue, Sep 21, 2010 at 2:33 AM, Barry Rowlingson
b.rowling...@lancaster.ac.uk wrote:
On Tue, Sep 21, 2010 at 9:39 AM, steven mosher mosherste...@gmail.com
wrote:
I'm accessing around 95 tar files on an FTP server ranging in size
between
10 and 40MB a piece.
while certainly can click on them and download them outside of R, I'd
like
to have my script do it.
Retrieving the ftp directory with RCurl works fine (about 90% of the
time)
but downloading the files by looping through all the files is a random
process.
I may get 1-8 files download and then it throws an error
cannot open URL
sometimes I only can get 1 file before this error. with tryCatch() I've
been
able to do some clean up
after the crash, but automating this whole download process has turned
into
a bit of a circus.
The parameters (url, destfile, mode) are all correct in the download.file
call as the second attempt at a url will often succeed.
Is there anyway to get a deeper look at the cause of the problem? I've
tried
closing all connections
in between each download. any pointers would be welcomed.
Sounds to me like the FTP server is operating some kind of rate
limiting. Do you have access to the server log files, or the server
administrator, or perhaps the server's terms and conditions to see if
its so :)
Barry
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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.
Re: [R] Substitute NAs by zero
v-c(1,2,3,4,5,6,7,8,97,6,5,4,NA,NA) b-zoo(v) b 1 2 3 4 5 6 7 8 9 10 11 12 13 14 1 2 3 4 5 6 7 8 97 6 5 4 NA NA b[is.na(b)]-0 b 1 2 3 4 5 6 7 8 9 10 11 12 13 14 1 2 3 4 5 6 7 8 97 6 5 4 0 0 is.zoo(b) [1] TRUE On Mon, Sep 20, 2010 at 2:37 AM, skan juanp...@gmail.com wrote: Hello How can I substitute all NA values by zero in a R zoo series? I've been reading about na.locf and na.omit but I think none of them do what I need. thanks. -- View this message in context: http://r.789695.n4.nabble.com/Substitute-NAs-by-zero-tp2546715p2546715.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. [[alternative HTML version deleted]] __ 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] How to uncompress a gz file in R
you are welcome. Henrik's package is an great piece of work. It is worth the time to read through the whole thing and see how you can improve your programs by using other features as well. On Thu, Sep 16, 2010 at 2:16 AM, Wonsang You y...@ifn-magdeburg.de wrote: Dear Henrik and Steven, Thank you for your kind help and guidance even though it is a basic question. I misunderstood that gunzip is a part of not R.utils but utils. I could find out the function in R.utils. Then, it was successful to decompress any gz file as follows. library(R.utils) gunzip(foo.gz) Best Regards, Wonsang [[alternative HTML version deleted]] __ 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] How to uncompress a gz file in R
Wongsang, Just to be clear R.utils is different than utils As Henrik notes gunzip has been in R.utils ( see http://cran.r-project.org/) for some time. It works like a champ. R.utils is a great package. On Wed, Sep 15, 2010 at 9:30 AM, Wonsang You y...@ifn-magdeburg.de wrote: Dear Henrik, Thank you so much for your kind help. Unfortunately, I could not find out any function such as 'gunzip' in R.utils package. Instead, I could be successful by using the following command. system(gunzip filename) On the other hand, the function 'gzfile' supports the compression as gz format, but I still do not know how to decompress gz file by using the function 'gzfile'. Best Regards, Wonsang On 14 September 2010 15:23, Henrik Bengtsson h...@stat.berkeley.edu wrote: To uncompress an *.gz file into another file on disk, see also ?gunzip in the R.utils package. /Henrik 2010/9/14 Uwe Ligges lig...@statistik.tu-dortmund.de: See ?gzfile Uwe Ligges On 14.09.2010 11:02, Wonsang You wrote: Dear Fellows, I would like to know how to uncompress a gz file at the R console. I could not find out any help from the R-help archive. Thanks for your great help. Best Regards, Wonsang You - -- Wonsang You Special Lab Non-Invasive Brain Imaging Leibniz Institute for Neurobiology http://www.ifn-magdeburg.de __ 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. [[alternative HTML version deleted]] __ 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. [[alternative HTML version deleted]] __ 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] Get File Names in Folder, Read Files, Update, and Write
you are welcomed.
Steve
On Wed, Sep 15, 2010 at 6:11 PM, Suphajak Ngamlak
supha...@phatrasecurities.com wrote:
Thank you so much. It works well
Best Regards,
Suphajak Ngamlak
Equity and Derivatives Trading
Phatra Securities Public Company Limited
Tel: +662-305-9179
Email: supha...@phatrasecurities.com
*From:* steven mosher [mailto:mosherste...@gmail.com]
*Sent:* Thursday, September 16, 2010 2:29 AM
*To:* Suphajak Ngamlak
*Subject:* Re: [R] Get File Names in Folder, Read Files, Update, and Write
Import-C:/A0810.RSK
Table-read.table(file= Import, sep = ,, head=TRUE, na.strings = NA)
Table$VALUE -0
Export-C:/A_XVal0810.RSK
write.table(Table, file= Export, sep = ,, col.names = TRUE)
As uwe, suggests list.files() or you can use dir()
A robust way to do this would use R.utils package ( see Cran)
but this is only necessary if you want to move the folder and still
have the code work. it makes the code work regardless of your working
directory
assuming you know the name of the folder and its unique.
insertString - _XVal
targetFolder - yourfoldername
folderPath - getAbsolutePath(targetFolder) #see R.utils
outputFolder - folderpath # you could create a different output folder
name
# only grab the .RSK files using a regular expression
fullFilenames - list.files(path=folderPath,
full.names=TRUE,pattern=(.RSK))
# get only the file names for modification
filenames - list.files(path=folderPath,
full.names=FALSE,pattern=(.RSK))
for(filenumber in 1:length(fullFilenames)) {
Table-read.table(file= fullFilenames[filenumber], sep = ,,
head=TRUE, na.strings = NA)
Table$VALUE -0
outfileName - paste(substr(filenames[filenumber]1,1),
insertString,
substr(filenames[filenumber],2,nchar(filenames[filenumber]),
sep=)
outFilePath
-file.path(outputFolder,outfileName,fsep=.Platform$file.sep)
write.table(Table, file= outFilePath, sep = ,, col.names = TRUE)
}
On Wed, Sep 15, 2010 at 1:55 AM, Suphajak Ngamlak
supha...@phatrasecurities.com wrote:
Dear All,
Could you please recommend how I can do this?
I have several text files in one folder. Let's name them A0801.RSK,
A0802.RSK,
I would like R to
1) Know all file names in this folder
2) Update value in one column of these files
3) Write results in another text file with _xval in the file names
Below is R code for read, update, and write one file
Import-C:/A0810.RSK
Table-read.table(file= Import, sep = ,, head=TRUE, na.strings = NA)
Table$VALUE -0
Export-C:/A_XVal0810.RSK
write.table(Table, file= Export, sep = ,, col.names = TRUE)
Thank you
Best Regards,
Suphajak Ngamlak
Equity and Derivatives Trading
Phatra Securities Public Company Limited
Tel: +662-305-9179
Email: supha...@phatrasecurities.com
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and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] If then else with command for
not sure how you wanted sampling of x
R-142
color-rep(0,142)
for(i in 1:R){
y-sample(x,142,replace=FALSE)
onebit- as.numeric(3471 %in% y)
twobit-as.numeric(6720 %in% y)*2
fourbit-as.numeric(6263 %in% y)*4
colorbit-onebit+twobit+fourbit+1
color[i]-colorbit
}
On Tue, Sep 14, 2010 at 10:29 AM, Mestat mes...@pop.com.br wrote:
Hey listers,
I am trying to do something simple... Check the program below...
I would like to create a variable named COLOR according to the conditions
that I stablished... But the problem is that it seems that my variable
COLOR
is checking just on sample, may be last in the loop... Certainly, I am
missing something...
Thanks in advance,
Marcio
x-c(288,139,196,159,536,134,623,517,96,467,277,155,386,241,422,6263,612,532,250,412,339,55,290,249,164,97,74,144,1277,240,163,63,488,111,128,230,720,179,37,24,65,37,89,187,60,939,1008,81,310,58,169,38,68,190,78,807,220,226,69,179129,119,73,59,92,127,104,75,505,183,49,41,76,113,90,79,408,140,200,284,103,58,654,118,431,192,233,102,97,56,69,73,86,53,105,81,77,472,129,194,299,81,122,113,186,91,145,133,114,78,78,72,70,3471,641,275,815,149,185,172,240,67,526,122,229,298,317,179,233,66,129,87,82,63,65,72,6720,381,240,118,396,66,35,43,166,216,53,82,90,62,77,207,68,52,277,396,220,751,146,95,37,35,39,46,59,44,105,87,66,62,175,252,128,330,57,83,208,74,63,109,37,105,38,82,76,63,86,603,209,100,121,191,130,63,128,90,79,50,1025,121,87,309,75,189,36,82,84,60,132,46,965,155,132,219,112,53,90,66,100,77,52,60,100,153,418,392,76,130,197,262,49,105,87,70,147,720,342,233,203,249,92,134,231,782,184,182,432,49,63,94,124,69,53,91,451,53,21,42,50,40,32,58,26,28,61,60,35,764,105,592,55,28,46,34,123!
,4!
1,54,207,64,562,295,226,63,233)
R-142
color-rep(0,142)
for(i in 1:R){
x-sample(x,142,replace=FALSE)
if (!3471 %in% x !6263 %in% x !6720 %in% x){color[i]-1} else
if (3471 %in% x !6263 %in% x !6720 %in% x){color[i]-2} else
if (!3471 %in% x 6263 %in% x !6720 %in% x){color[i]-3} else
if (!3471 %in% x !6263 %in% x 6720 %in% x){color[i]-4} else
if (3471 %in% x 6263 %in% x !6720 %in% x){color[i]-5} else
if (3471 %in% x !6263 %in% x 6720 %in% x){color[i]-6} else
if (!3471 %in% x 6263 %in% x 6720 %in% x){color[i]-7} else
if (3471 %in% x 6263 %in% x 6720 %in% x){color[i]-8} else{color[i]-0}
}
--
View this message in context:
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and provide commented, minimal, self-contained, reproducible code.
[R] merging two maxtrices
j-matrix(nrow=10,ncol=10) k-matrix(seq(1:50), ncol=10) row.names(k) - seq(2,10,by=2) j [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [1,] NA NA NA NA NA NA NA NA NANA [2,] NA NA NA NA NA NA NA NA NANA [3,] NA NA NA NA NA NA NA NA NANA [4,] NA NA NA NA NA NA NA NA NANA [5,] NA NA NA NA NA NA NA NA NANA [6,] NA NA NA NA NA NA NA NA NANA [7,] NA NA NA NA NA NA NA NA NANA [8,] NA NA NA NA NA NA NA NA NANA [9,] NA NA NA NA NA NA NA NA NANA [10,] NA NA NA NA NA NA NA NA NANA k [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] 2 16 11 16 21 26 31 36 4146 4 27 12 17 22 27 32 37 4247 6 38 13 18 23 28 33 38 4348 8 49 14 19 24 29 34 39 4449 105 10 15 20 25 30 35 40 4550 is there a simple way to merge j and k By the row.names in k so that row named '2' is placed in the 2nd row of j.. and so forth through 4,6,8,10 the actual example has a sparse k.. not evenly spaced so this should also be mergeable row.names(k) - c(1,2,5,6,9) k [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] 116 11 16 21 26 31 36 4146 227 12 17 22 27 32 37 4247 538 13 18 23 28 33 38 4348 649 14 19 24 29 34 39 4449 95 10 15 20 25 30 35 40 4550 [[alternative HTML version deleted]] __ 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] merging two maxtrices
weird, I tried that but it didnt appear to work.. hmm. Thanks I try it again On Sun, Sep 5, 2010 at 12:21 AM, bill.venab...@csiro.au wrote: Is this all you want? j - matrix(nrow=10,ncol=10) k - matrix(seq(1:50), ncol=10) row.names(k) - seq(2,10,by=2) row.names(j) - 1:10 j[row.names(k), ] - k j [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] 1NA NA NA NA NA NA NA NA NANA 2 16 11 16 21 26 31 36 4146 3NA NA NA NA NA NA NA NA NANA 4 27 12 17 22 27 32 37 4247 5NA NA NA NA NA NA NA NA NANA 6 38 13 18 23 28 33 38 4348 7NA NA NA NA NA NA NA NA NANA 8 49 14 19 24 29 34 39 4449 9NA NA NA NA NA NA NA NA NANA 105 10 15 20 25 30 35 40 4550 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of steven mosher Sent: Sunday, 5 September 2010 5:10 PM To: r-help Subject: [R] merging two maxtrices j-matrix(nrow=10,ncol=10) k-matrix(seq(1:50), ncol=10) row.names(k) - seq(2,10,by=2) j [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [1,] NA NA NA NA NA NA NA NA NANA [2,] NA NA NA NA NA NA NA NA NANA [3,] NA NA NA NA NA NA NA NA NANA [4,] NA NA NA NA NA NA NA NA NANA [5,] NA NA NA NA NA NA NA NA NANA [6,] NA NA NA NA NA NA NA NA NANA [7,] NA NA NA NA NA NA NA NA NANA [8,] NA NA NA NA NA NA NA NA NANA [9,] NA NA NA NA NA NA NA NA NANA [10,] NA NA NA NA NA NA NA NA NANA k [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] 2 16 11 16 21 26 31 36 4146 4 27 12 17 22 27 32 37 4247 6 38 13 18 23 28 33 38 4348 8 49 14 19 24 29 34 39 4449 105 10 15 20 25 30 35 40 4550 is there a simple way to merge j and k By the row.names in k so that row named '2' is placed in the 2nd row of j.. and so forth through 4,6,8,10 the actual example has a sparse k.. not evenly spaced so this should also be mergeable row.names(k) - c(1,2,5,6,9) k [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] 116 11 16 21 26 31 36 4146 227 12 17 22 27 32 37 4247 538 13 18 23 28 33 38 4348 649 14 19 24 29 34 39 4449 95 10 15 20 25 30 35 40 4550 [[alternative HTML version deleted]] __ 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. [[alternative HTML version deleted]] __ 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] merging two maxtrices
ya, unfortunately k was actually a dataframe and not a matrix when it was returned from the function, which explains why I got unexpected results On Sun, Sep 5, 2010 at 12:21 AM, bill.venab...@csiro.au wrote: Is this all you want? j - matrix(nrow=10,ncol=10) k - matrix(seq(1:50), ncol=10) row.names(k) - seq(2,10,by=2) row.names(j) - 1:10 j[row.names(k), ] - k j [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] 1NA NA NA NA NA NA NA NA NANA 2 16 11 16 21 26 31 36 4146 3NA NA NA NA NA NA NA NA NANA 4 27 12 17 22 27 32 37 4247 5NA NA NA NA NA NA NA NA NANA 6 38 13 18 23 28 33 38 4348 7NA NA NA NA NA NA NA NA NANA 8 49 14 19 24 29 34 39 4449 9NA NA NA NA NA NA NA NA NANA 105 10 15 20 25 30 35 40 4550 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of steven mosher Sent: Sunday, 5 September 2010 5:10 PM To: r-help Subject: [R] merging two maxtrices j-matrix(nrow=10,ncol=10) k-matrix(seq(1:50), ncol=10) row.names(k) - seq(2,10,by=2) j [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [1,] NA NA NA NA NA NA NA NA NANA [2,] NA NA NA NA NA NA NA NA NANA [3,] NA NA NA NA NA NA NA NA NANA [4,] NA NA NA NA NA NA NA NA NANA [5,] NA NA NA NA NA NA NA NA NANA [6,] NA NA NA NA NA NA NA NA NANA [7,] NA NA NA NA NA NA NA NA NANA [8,] NA NA NA NA NA NA NA NA NANA [9,] NA NA NA NA NA NA NA NA NANA [10,] NA NA NA NA NA NA NA NA NANA k [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] 2 16 11 16 21 26 31 36 4146 4 27 12 17 22 27 32 37 4247 6 38 13 18 23 28 33 38 4348 8 49 14 19 24 29 34 39 4449 105 10 15 20 25 30 35 40 4550 is there a simple way to merge j and k By the row.names in k so that row named '2' is placed in the 2nd row of j.. and so forth through 4,6,8,10 the actual example has a sparse k.. not evenly spaced so this should also be mergeable row.names(k) - c(1,2,5,6,9) k [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] 116 11 16 21 26 31 36 4146 227 12 17 22 27 32 37 4247 538 13 18 23 28 33 38 4348 649 14 19 24 29 34 39 4449 95 10 15 20 25 30 35 40 4550 [[alternative HTML version deleted]] __ 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. [[alternative HTML version deleted]] __ 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] differecing a zoo series
A quick question x - as.yearmon(2000 + seq(0, 23)/12) x [1] Jan 2000 Feb 2000 Mar 2000 Apr 2000 May 2000 Jun 2000 Jul 2000 Aug 2000 Sep 2000 Oct 2000 Nov 2000 Dec 2000 Jan 2001 [14] Feb 2001 Mar 2001 Apr 2001 May 2001 Jun 2001 Jul 2001 Aug 2001 Sep 2001 Oct 2001 Nov 2001 Dec 2001 data-seq(1,24,by=1) testzoo-zoo(data,order.by=x) The operation I ant to perform on the zoo series is this. I will illustrate with a small example and formula: the coredata of the zoo series is 1,2,3,4,5,6,7,8) I want to calculate Result- zoo[x]-zoo[x-1] (NA,1,1,1,1,1...NA) The first element of course is undefined(NA). is there any method to do this elegantly, padding NAs at the start works but its ugly. if I get a simple function I can apply it to a matrix of zoo series [[alternative HTML version deleted]] __ 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] Trouble loading saved Rdata
The typos were just transcription errors I'' report out the session info On Sat, Aug 14, 2010 at 5:35 PM, Joshua Wiley jwiley.ps...@gmail.comwrote: That worked for me once I properly quoted test.RData on sessionInfo() R version 2.11.1 (2010-05-31) x86_64-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 If correcting the quoting does not help you, perhaps you can report the results of sessionInfo() Cheers, Josh On Sat, Aug 14, 2010 at 5:14 PM, steven mosher mosherste...@gmail.com wrote: In the particular application I have I save test.Rdata to a sub directory dir-Example dir.create(dir) test-data.frame(a=c(1,2,3),b=c(3,4,5) full-file.path(dir,test.Rdata,fsep=.Platform$file.sep) save(test,file=full) load(full) returns NULL it works fine when the object is saved to the working directory, but fails when saved to a sub directory. The Rdata is there. Bytes are in it. but loading it doesnt work. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Joshua Wiley Ph.D. Student, Health Psychology University of California, Los Angeles http://www.joshuawiley.com/ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Trouble loading saved Rdata
Did you exit R and then return? fname-test.Rdata full-file.path(Example,fname,fsep=.Platform$file.sep) full [1] Example/test.Rdata load(full) test NULL sessionInfo() R version 2.11.1 (2010-05-31) x86_64-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.11.1 On Sat, Aug 14, 2010 at 5:35 PM, Joshua Wiley jwiley.ps...@gmail.comwrote: That worked for me once I properly quoted test.RData on sessionInfo() R version 2.11.1 (2010-05-31) x86_64-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 If correcting the quoting does not help you, perhaps you can report the results of sessionInfo() Cheers, Josh On Sat, Aug 14, 2010 at 5:14 PM, steven mosher mosherste...@gmail.com wrote: In the particular application I have I save test.Rdata to a sub directory dir-Example dir.create(dir) test-data.frame(a=c(1,2,3),b=c(3,4,5) full-file.path(dir,test.Rdata,fsep=.Platform$file.sep) save(test,file=full) load(full) returns NULL it works fine when the object is saved to the working directory, but fails when saved to a sub directory. The Rdata is there. Bytes are in it. but loading it doesnt work. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Joshua Wiley Ph.D. Student, Health Psychology University of California, Los Angeles http://www.joshuawiley.com/ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Trouble loading saved Rdata
I think it came down to my actual program having a function that saved the objects it was passed with a .RData extension as opposed to .Rdata Rechecking the whole thing. On Sun, Aug 15, 2010 at 11:05 AM, Joshua Wiley jwiley.ps...@gmail.comwrote: Steven, I have exited my R session and restarted and I can load the file without issue. I have also tried loading the saved data on some older versions of R (2.10.1 and 2.11.0) and Windows (XP). Have you tried recreating the test object, ensuring that it is not NULL itself, resaving it, and then see if loading it works better? Josh On Sun, Aug 15, 2010 at 12:06 AM, steven mosher mosherste...@gmail.com wrote: Did you exit R and then return? fname-test.Rdata full-file.path(Example,fname,fsep=.Platform$file.sep) full [1] Example/test.Rdata load(full) test NULL sessionInfo() R version 2.11.1 (2010-05-31) x86_64-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.11.1 On Sat, Aug 14, 2010 at 5:35 PM, Joshua Wiley jwiley.ps...@gmail.com wrote: That worked for me once I properly quoted test.RData on sessionInfo() R version 2.11.1 (2010-05-31) x86_64-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 If correcting the quoting does not help you, perhaps you can report the results of sessionInfo() Cheers, Josh On Sat, Aug 14, 2010 at 5:14 PM, steven mosher mosherste...@gmail.com wrote: In the particular application I have I save test.Rdata to a sub directory dir-Example dir.create(dir) test-data.frame(a=c(1,2,3),b=c(3,4,5) full-file.path(dir,test.Rdata,fsep=.Platform$file.sep) save(test,file=full) load(full) returns NULL it works fine when the object is saved to the working directory, but fails when saved to a sub directory. The Rdata is there. Bytes are in it. but loading it doesnt work. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Joshua Wiley Ph.D. Student, Health Psychology University of California, Los Angeles http://www.joshuawiley.com/ -- Joshua Wiley Ph.D. Student, Health Psychology University of California, Los Angeles http://www.joshuawiley.com/ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Trouble loading saved Rdata
During my session I write several .Rdata objects to a variety of subdirectories so replicating the exact problem wasnt very easy. In the actual program all the files get written. all the files have sizes that fit the amount of data in them. It looks like the problem was naming the files .RData as opposed to .Rdata since there was one function that named all the files before saving, it kinda messed up the program and my ability to replicate the problem. Seems to be working now Thanks On Sun, Aug 15, 2010 at 6:44 AM, David Winsemius dwinsem...@comcast.netwrote: On Aug 15, 2010, at 3:06 AM, steven mosher wrote: Did you exit R and then return? fname-test.Rdata full-file.path(Example,fname,fsep=.Platform$file.sep) full [1] Example/test.Rdata load(full) test NULL I am unable to reproduce the problem (after correcting two different syntactic errors in the initial posting that should have thrown errors and prevented the creation of both test and full . I didn't exit my session and return but I did remove the test object after saving it. My guess is that the test object was not correctly formed at the time it was saved. test-data.frame(a=c(1,2,3),b=c(3,4,5)) save(test,file=full) test a b 1 1 3 2 2 4 3 3 5 full [1] Example/test.Rdata rm(test) load(file=full) test a b 1 1 3 2 2 4 3 3 5 (I pretty much have the same setup that is indicated below running on MacOS 10.5.8.) -- David. sessionInfo() R version 2.11.1 (2010-05-31) x86_64-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.11.1 On Sat, Aug 14, 2010 at 5:35 PM, Joshua Wiley jwiley.ps...@gmail.com wrote: That worked for me once I properly quoted test.RData on sessionInfo() R version 2.11.1 (2010-05-31) x86_64-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 If correcting the quoting does not help you, perhaps you can report the results of sessionInfo() Cheers, Josh On Sat, Aug 14, 2010 at 5:14 PM, steven mosher mosherste...@gmail.com wrote: In the particular application I have I save test.Rdata to a sub directory dir-Example dir.create(dir) test-data.frame(a=c(1,2,3),b=c(3,4,5) full-file.path(dir,test.Rdata,fsep=.Platform$file.sep) save(test,file=full) load(full) returns NULL it works fine when the object is saved to the working directory, but fails when saved to a sub directory. The Rdata is there. Bytes are in it. but loading it doesnt work. [[alternative HTML version deleted]] __ 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. -- Joshua Wiley Ph.D. Student, Health Psychology University of California, Los Angeles http://www.joshuawiley.com/ [[alternative HTML version deleted]] __ 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. David Winsemius, MD West Hartford, CT [[alternative HTML version deleted]] __ 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] Creating list from a long vector
Stupid question, but its been a long night. If I have a long vector how can I turn it into a list of the same length x-rep(seq(1,100,by=1),each=10) [[alternative HTML version deleted]] __ 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] Creating list from a long vector
Thx, I see my problem. more sleep required On Sat, Aug 14, 2010 at 9:25 AM, Romain Francois romain.franc...@dbmail.com wrote: Le 14/08/10 18:22, steven mosher a écrit : Stupid question, but its been a long night. If I have a long vector how can I turn it into a list of the same length x-rep(seq(1,100,by=1),each=10) Perhaps as.list ? -- Romain Francois Professional R Enthusiast +33(0) 6 28 91 30 30 http://romainfrancois.blog.free.fr |- http://bit.ly/bzoWrs : Rcpp svn revision 2000 |- http://bit.ly/b8VNE2 : Rcpp at LondonR, oct 5th `- http://bit.ly/aAyra4 : highlight 0.2-2 [[alternative HTML version deleted]] __ 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] Trouble loading saved Rdata
In the particular application I have I save test.Rdata to a sub directory dir-Example dir.create(dir) test-data.frame(a=c(1,2,3),b=c(3,4,5) full-file.path(dir,test.Rdata,fsep=.Platform$file.sep) save(test,file=full) load(full) returns NULL it works fine when the object is saved to the working directory, but fails when saved to a sub directory. The Rdata is there. Bytes are in it. but loading it doesnt work. [[alternative HTML version deleted]] __ 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] sweep and zoo objects
rc-list(c( 123,321,234,543,654,768,986,987,246,284),c(Jan,Feb,Mar,Apr,May,Jun,Jul,Aug,Sep,Oct,Nov,Dec)) # the matrix has rownames that are used as identifiers and columns # of time. 1 years worth of data. Thats the native format test-matrix(seq(1,120, by=1), nrow=10,dimnames=rc) test Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec 123 1 11 21 31 41 51 61 71 81 91 101 111 321 2 12 22 32 42 52 62 72 82 92 102 112 234 3 13 23 33 43 53 63 73 83 93 103 113 543 4 14 24 34 44 54 64 74 84 94 104 114 654 5 15 25 35 45 55 65 75 85 95 105 115 768 6 16 26 36 46 56 66 76 86 96 106 116 986 7 17 27 37 47 57 67 77 87 97 107 117 987 8 18 28 38 48 58 68 78 88 98 108 118 246 9 19 29 39 49 59 69 79 89 99 109 119 284 10 20 30 40 50 60 70 80 90 100 110 120 #The desired result would be a merged zoo object with the row names used as the colnames of the multiple zoo series test2-matrix(test,nrow=12, byrow=F) g-zoo(test2[,1],frequency=12) MYZOO -merge(g,test2[,2:10]) # the result MYZOO is a zoo object, but we've lost the row names in the transformation of the matrix #So colnames(MYZOO)-row.names(test) #Fixes that problem. Is there a more elegant way to do this??? # now this zoo object needs to be swept out of a much longer zoo object # with the same column names.. The 'sweep' function is - Sweep works normally by sweeping out a vector from an array (by column or by row sweep(x, MARGIN, STATS, FUN=-, check.margin=TRUE, ...) so in my example x would be a long yearmon zoo object with the same column names as MYZOO above, but decades of data. MARGIN would be rows and the STATS to sweep out would be the values in MYZOO. test3-matrix(seq(1,720, by=1), ncol=10) p-zoo(test3[,1], freq=12) longzoo-merge(p,test3[,2:10]) colnames(longzoo)-row.names(test) what we want to do is to sweep out MYZOO from longzoo. I could just repeat the data in MYZOO 6 times and then subtract MYZOO from longzoo, but thats a potential memory buster in this situation [[alternative HTML version deleted]] __ 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] Sweeping a zoo series
Given a long zoo matrix, the goal is to sweep out a statistic from the entire length of the sequences. longzoomatrix-zoo(matrix(rnorm(720),ncol=6),as.yearmon(outer(1900,seq(0,length=120)/12,+))) cnames-c(12345,23456,34567,45678,56789,67890) colnames(longzoomatrix)-cnames longzoomatrix[1:24,] 12345 23456 34567 45678 56789 67890 Jan 1900 -0.17123165 1.02087086 0.79514870 -0.54519494 -0.13025459 -0.009980402 Feb 1900 1.21729926 -0.74541038 -0.08138406 -2.01180775 0.19256998 0.551965871 Mar 1900 1.13222481 -1.25315703 0.01013473 0.08366155 -0.84246010 -1.405959298 Apr 1900 -0.02352559 -1.25001473 -1.53570550 -0.17945324 0.33368133 2.045125104 May 1900 2.08204920 1.28091067 -0.80888146 0.31796730 0.83248551 1.439049603 Jun 1900 0.62209570 -0.66189249 -0.57923119 -0.04346112 -2.71353384 -0.346826902 Jul 1900 -1.39758918 -0.54525469 -0.05230070 -0.36725079 1.28281798 1.391174712 Aug 1900 0.12594069 0.09303970 0.69916411 -1.01902352 -0.82720898 -0.208113626 Sep 1900 -0.34310543 0.41718435 0.79455765 1.13234707 0.14652667 -0.551426097 Oct 1900 1.70634123 -1.20073104 -1.08771551 -0.01715296 0.24931996 -0.753481196 Nov 1900 0.15224070 -0.05108370 -0.97410069 0.51130170 0.13880814 -2.160811186 Dec 1900 0.34726817 0.61830719 0.84429979 -0.26253635 0.95243068 -0.533562966 Jan 1901 0.28647563 -0.40650198 -1.19640622 0.70267162 0.18867804 0.098855045 Feb 1901 1.27269836 0.31797472 -1.13038040 1.33654480 0.08885501 -0.134690872 Mar 1901 -1.36934330 -0.17244539 0.81705554 -0.09113888 0.90241413 0.473939164 Apr 1901 -0.89768498 0.82497595 0.15684387 2.25294476 -1.72886103 -0.104769411 May 1901 -0.27898445 -1.24348285 1.36203180 0.02422083 -1.33745980 1.098856752 Jun 1901 -0.67968801 0.42082064 0.47056133 -0.12981223 0.19445803 -0.284638114 Jul 1901 0.03791761 -0.22118130 1.96044737 -1.18280989 0.90075205 0.055720535 Aug 1901 1.12904079 0.57177055 0.64300572 -0.16284983 0.07951656 -0.159396821 Sep 1901 -1.43513934 0.03036697 1.09039400 0.99201776 0.98744827 -0.057234838 Oct 1901 0.73828382 0.53967835 2.16608282 -0.82929778 -1.9987 0.352778450 Nov 1901 0.06561583 -1.20126258 0.67427027 0.15493106 0.08867697 1.223073528 Dec 1901 -1.23347027 -1.09699304 0.59398031 -0.22269292 -0.21569543 1.389667825 The statistic to be swept out is itself a zoo series with matching column names. There are twelve valies for each column representing an monthly average for that series. The average is to be subtracted sweepzoo-zoo(matrix(rnorm(72),ncol=6), frequency=12) colnames(sweepzoo)-cnames sweepzoo 12345 23456 34567 45678 56789 67890 1(1) -2.5569706 -0.4375741 -0.1803866 -0.6303760 -0.08995198 2.7293244 2(1) 1.4154202 0.2559212 0.2104513 0.7439446 0.84897905 -0.4144865 3(1) -1.3709275 1.0472759 1.5975148 0.3190503 1.10430959 -1.8285194 4(1) -1.1436430 2.2071763 -0.2637954 -0.4915366 -0.03925020 1.3311624 5(1) -0.8003656 1.6421541 -1.4603128 0.4493069 0.28194066 -0.4728086 6(1) 0.9236015 0.3780122 -1.3848196 0.4263684 0.99584590 -1.4536475 7(1) 0.8810281 0.0381152 0.3810457 -0.6884233 -0.11018089 0.4221188 8(1) 0.3819421 -0.8431364 1.9876901 0.7072257 0.45524929 2.7013515 9(1) -1.1247988 1.3083178 -0.3438442 0.3300832 0.67013503 1.2912443 10(1) -0.3643043 1.0756782 -1.2026318 0.4477054 0.54486700 -0.3369889 11(1) 0.8294049 1.8170357 0.5691249 1.9213791 -0.29295754 -0.2617228 12(1) -1.0085265 -0.7556545 -1.4033321 -0.4646647 -0.14984913 -0.4848657 A brute force way to do this is to repeat the 12 values for each column so that the number of rows in the sweepzoo is equal to the nmber of rows on the long zoo, object and then just subtract them. longzoomatrix-sweepzoo As a function sweep() wont work because it expects a vector whose dimensions matches the dimension of the MARGIN. Is there a elegant way to do this short of creating a sweep zoo that matches the row dimension of longzoo? ( would be a nice addition to sweep) [[alternative HTML version deleted]] __ 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] Sweeping a zoo series
The colMeans comes closest, for a single series the assume you have 100 years of monthly data. The mean you want to scale by is the mean for a restricted period in the center of the series.. say 1950-1960 for this period you have the average jan (1950-1960) average feb, ect. your final series would be jan 1900 - average jan(1950-60) feb 1990 - average feb jan 2000 - average jan(1950-60) Which gives you a scaling that is not relative to the mean of the whole, but relative to a base period which is selctable. BTW switching to zoo has greatly simplified the code. On Wed, Aug 11, 2010 at 11:21 AM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Wed, Aug 11, 2010 at 12:22 PM, steven mosher mosherste...@gmail.com wrote: Given a long zoo matrix, the goal is to sweep out a statistic from the entire length of the sequences. longzoomatrix-zoo(matrix(rnorm(720),ncol=6),as.yearmon(outer(1900,seq(0,length=120)/12,+))) cnames-c(12345,23456,34567,45678,56789,67890) colnames(longzoomatrix)-cnames longzoomatrix[1:24,] 12345 23456 34567 45678 56789 67890 Jan 1900 -0.17123165 1.02087086 0.79514870 -0.54519494 -0.13025459 -0.009980402 Feb 1900 1.21729926 -0.74541038 -0.08138406 -2.01180775 0.19256998 0.551965871 Mar 1900 1.13222481 -1.25315703 0.01013473 0.08366155 -0.84246010 -1.405959298 Apr 1900 -0.02352559 -1.25001473 -1.53570550 -0.17945324 0.33368133 2.045125104 May 1900 2.08204920 1.28091067 -0.80888146 0.31796730 0.83248551 1.439049603 Jun 1900 0.62209570 -0.66189249 -0.57923119 -0.04346112 -2.71353384 -0.346826902 Jul 1900 -1.39758918 -0.54525469 -0.05230070 -0.36725079 1.28281798 1.391174712 Aug 1900 0.12594069 0.09303970 0.69916411 -1.01902352 -0.82720898 -0.208113626 Sep 1900 -0.34310543 0.41718435 0.79455765 1.13234707 0.14652667 -0.551426097 Oct 1900 1.70634123 -1.20073104 -1.08771551 -0.01715296 0.24931996 -0.753481196 Nov 1900 0.15224070 -0.05108370 -0.97410069 0.51130170 0.13880814 -2.160811186 Dec 1900 0.34726817 0.61830719 0.84429979 -0.26253635 0.95243068 -0.533562966 Jan 1901 0.28647563 -0.40650198 -1.19640622 0.70267162 0.18867804 0.098855045 Feb 1901 1.27269836 0.31797472 -1.13038040 1.33654480 0.08885501 -0.134690872 Mar 1901 -1.36934330 -0.17244539 0.81705554 -0.09113888 0.90241413 0.473939164 Apr 1901 -0.89768498 0.82497595 0.15684387 2.25294476 -1.72886103 -0.104769411 May 1901 -0.27898445 -1.24348285 1.36203180 0.02422083 -1.33745980 1.098856752 Jun 1901 -0.67968801 0.42082064 0.47056133 -0.12981223 0.19445803 -0.284638114 Jul 1901 0.03791761 -0.22118130 1.96044737 -1.18280989 0.90075205 0.055720535 Aug 1901 1.12904079 0.57177055 0.64300572 -0.16284983 0.07951656 -0.159396821 Sep 1901 -1.43513934 0.03036697 1.09039400 0.99201776 0.98744827 -0.057234838 Oct 1901 0.73828382 0.53967835 2.16608282 -0.82929778 -1.9987 0.352778450 Nov 1901 0.06561583 -1.20126258 0.67427027 0.15493106 0.08867697 1.223073528 Dec 1901 -1.23347027 -1.09699304 0.59398031 -0.22269292 -0.21569543 1.389667825 The statistic to be swept out is itself a zoo series with matching column names. There are twelve valies for each column representing an monthly average for that series. The average is to be subtracted sweepzoo-zoo(matrix(rnorm(72),ncol=6), frequency=12) colnames(sweepzoo)-cnames sweepzoo 12345 23456 34567 45678 56789 67890 1(1) -2.5569706 -0.4375741 -0.1803866 -0.6303760 -0.08995198 2.7293244 2(1) 1.4154202 0.2559212 0.2104513 0.7439446 0.84897905 -0.4144865 3(1) -1.3709275 1.0472759 1.5975148 0.3190503 1.10430959 -1.8285194 4(1) -1.1436430 2.2071763 -0.2637954 -0.4915366 -0.03925020 1.3311624 5(1) -0.8003656 1.6421541 -1.4603128 0.4493069 0.28194066 -0.4728086 6(1) 0.9236015 0.3780122 -1.3848196 0.4263684 0.99584590 -1.4536475 7(1) 0.8810281 0.0381152 0.3810457 -0.6884233 -0.11018089 0.4221188 8(1) 0.3819421 -0.8431364 1.9876901 0.7072257 0.45524929 2.7013515 9(1) -1.1247988 1.3083178 -0.3438442 0.3300832 0.67013503 1.2912443 10(1) -0.3643043 1.0756782 -1.2026318 0.4477054 0.54486700 -0.3369889 11(1) 0.8294049 1.8170357 0.5691249 1.9213791 -0.29295754 -0.2617228 12(1) -1.0085265 -0.7556545 -1.4033321 -0.4646647 -0.14984913 -0.4848657 A brute force way to do this is to repeat the 12 values for each column so that the number of rows in the sweepzoo is equal to the nmber of rows on the long zoo, object and then just subtract them. longzoomatrix-sweepzoo As a function sweep() wont work because it expects a vector whose dimensions matches the dimension of the MARGIN. Is there a elegant way to do this short of creating a sweep zoo that matches the row dimension of longzoo? ( would be a nice addition
[R] nested 'by'
Assuming a data frame or matrix with two columns representing variable that you want to aggregate over. you want to calculate column means, by year, for each Id example-data.frame(id=c(rep(12345,5),rep(54321,6),rep(45678,7)),Year=rep(seq(1900,1902,by=1),6), x=seq(1,18,by=1),y=seq(18,1,by=-1)) example id Year x y 1 12345 1900 1 18 2 12345 1901 2 17 3 12345 1902 3 16 4 12345 1900 4 15 5 12345 1901 5 14 6 54321 1902 6 13 7 54321 1900 7 12 8 54321 1901 8 11 9 54321 1902 9 10 10 54321 1900 10 9 11 54321 1901 11 8 12 45678 1902 12 7 13 45678 1900 13 6 14 45678 1901 14 5 15 45678 1902 15 4 16 45678 1900 16 3 17 45678 1901 17 2 18 45678 1902 18 1 result-by(example[,3:4], example$id, by(example[,3:4], example$Year,colMeans, na.rm=T)) Error in FUN(X[[1L]], ...) : could not find function FUN desired result should look like: id Year meanx mean y 1 12345 1900 ...... 2 12345 1901 ... 3 12345 1902 ... 4 54321 1900 5 54321 1901 6 54321 1902 7 45678 1900 8 45678 1901 9 45678 1902 [[alternative HTML version deleted]] __ 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] nested 'by'
That works.
Thanks
On Mon, Aug 9, 2010 at 7:55 AM, Henrique Dallazuanna www...@gmail.comwrote:
Try this:
aggregate(example[c('x', 'y')], example[c('id', 'Year')], 'mean')
On Mon, Aug 9, 2010 at 11:46 AM, steven mosher mosherste...@gmail.comwrote:
Assuming a data frame or matrix with two columns representing variable
that
you want to aggregate over.
you want to calculate column means, by year, for each Id
example-data.frame(id=c(rep(12345,5),rep(54321,6),rep(45678,7)),Year=rep(seq(1900,1902,by=1),6),
x=seq(1,18,by=1),y=seq(18,1,by=-1))
example
id Year x y
1 12345 1900 1 18
2 12345 1901 2 17
3 12345 1902 3 16
4 12345 1900 4 15
5 12345 1901 5 14
6 54321 1902 6 13
7 54321 1900 7 12
8 54321 1901 8 11
9 54321 1902 9 10
10 54321 1900 10 9
11 54321 1901 11 8
12 45678 1902 12 7
13 45678 1900 13 6
14 45678 1901 14 5
15 45678 1902 15 4
16 45678 1900 16 3
17 45678 1901 17 2
18 45678 1902 18 1
result-by(example[,3:4], example$id, by(example[,3:4],
example$Year,colMeans, na.rm=T))
Error in FUN(X[[1L]], ...) : could not find function FUN
desired result should look like:
id Year meanx mean y
1 12345 1900 ......
2 12345 1901 ...
3 12345 1902 ...
4 54321 1900
5 54321 1901
6 54321 1902
7 45678 1900
8 45678 1901
9 45678 1902
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide
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and provide commented, minimal, self-contained, reproducible code.
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
[[alternative HTML version deleted]]
__
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.
