[R] Best settings for RStudio video recording?
Folks: I was wondering if you all would suggest some helpful RStudio configurations that make recording a session via e.g. zoom the most useful for students doing remote learning. Thoughts? --j -- Jonathan A. Greenberg, PhD Randall Endowed Professor and Associate Professor of Remote Sensing Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Natural Resources & Environmental Science University of Nevada, Reno 1664 N Virginia St MS/0186 Reno, NV 89557 Phone: 415-763-5476 https://www.gearslab.org/ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] Checking for a proper "stop" statement...
Folks:
Consider the following two use cases:
goodfunction <- function()
{
stop("Something went wrong..."
}
# vs.
badfunction <- function()
{
notgood()
}
Is there a way for me to test if the functions make use of a stop()
statement WITHOUT modifying the stop() output (assume I can't mod the
function containing the stop() statement itself)? For "goodfunction" the
answer is TRUE, for "badfunction" the answer is FALSE. Both return an
error, but only one does it "safely".
I thought the answer might lie in a tryCatch statement but I'm having a
hard time figuring out how to do this test.
--j
--
--
Jonathan A. Greenberg, PhD
Randall Endowed Professor and Associate Professor of Remote Sensing
Global Environmental Analysis and Remote Sensing (GEARS) Laboratory
Natural Resources & Environmental Science
University of Nevada, Reno
1664 N Virginia St MS/0186
Reno, NV 89557
Phone: 415-763-5476
http://www.unr.edu/nres
Gchat: jgrn...@gmail.com, Skype: jgrn3007
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[R] R command to open a file browser on Windows and Mac?
Folks: Is there an easy function to open a finder window (on mac) or windows explorer window (on windows) given an input folder? A lot of times I want to be able to see via a file browser my working directory. Is there a good R hack to do this? --j [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] table over a matrix dimension...
R-helpers:
I'm trying to determine the frequency of characters for a matrix
applied to a single dimension, and generate a matrix as an output.
I've come up with a solution, but it appears inelegant -- I was
wondering if there is an easier way to accomplish this task:
# Create a matrix of factors (characters):
random_characters=matrix(sample(letters[1:4],1000,replace=TRUE),100,10)
# Applying with the table() function doesn't work properly, because not all rows
# have ALL of the factors, so I get a list output:
apply(random_characters,1,table)
# Hacked solution:
unique_values = letters[1:4]
countsmatrix - t(apply(random_characters,1,function(x,unique_values)
{
counts=vector(length=length(unique_values))
for(i in seq(unique_values))
{
counts[i] = sum(x==unique_values[i])
}
return(counts)
},
unique_values=unique_values
))
# Gets me the output I want but requires two nested loops (apply and
for() ), so
# not efficient for very large datasets.
###
Is there a more elegant solution to this?
--j
--
Jonathan A. Greenberg, PhD
Assistant Professor
Global Environmental Analysis and Remote Sensing (GEARS) Laboratory
Department of Geography and Geographic Information Science
University of Illinois at Urbana-Champaign
259 Computing Applications Building, MC-150
605 East Springfield Avenue
Champaign, IL 61820-6371
Phone: 217-300-1924
http://www.geog.illinois.edu/~jgrn/
AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007
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[R] StatET and R 3.1.0
R-helpers: I posted a message to the statet listserv, but I thought I'd ask here as well since it is one of the major R developer environments-- has anyone gotten the StatET plugin for Eclipse working with R 3.1.0 yet? Any tricks? I did manage to get rj updated to 2.0 via: install.packages(c(rj, rj.gd), repos=http://download.walware.de/rj-2.0,type=source;) But the plugin is throwing an error (using the last maintenance update at http://download.walware.de/eclipse-4.3/testing): Launching the R Console was cancelled, because it seems starting the R engine failed. Please make sure that R package 'rj' (1.1 or compatible) is installed and that the R library paths are set correctly for the R environment configuration 'R'. --j -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 259 Computing Applications Building, MC-150 605 East Springfield Avenue Champaign, IL 61820-6371 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 __ 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] Ignore escape characters in a string...
Thanks all, I'll try some of these suggestions out but it seems like a raw string ability could come in helpful -- there aren't any packages out there that have this capability? --j On Tue, Apr 8, 2014 at 1:23 PM, Jeff Newmiller jdnew...@dcn.davis.ca.us wrote: What is wrong with winpath - readLines(clipboard ) ? If you want to show that as a literal in your code, then don't bother assigning it to a variable, but let it echo to output and copy THAT and put it in your source code. There is also file.choose()... --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. On April 8, 2014 8:00:03 AM PDT, Jonathan Greenberg j...@illinois.edu wrote: R-helpers: One of the minor irritations I have is copying paths from Windows explorer, which look like: C:\Program Files\R\R-3.0.3 and using them in a setwd() statement, since the \ is, of course, interpreted as an escape character. I have to, at present, manually add in the double slashes or reverse them. So, I'd like to write a quick function that takes this path: winpath - C:\Program Files\R\R-3.0.3 and converts it to a ready-to-go R path -- is there a way to have R IGNORE escape characters in a character vector? Alternatively, is there some trick to using a copy/paste from Windows explorer I'm not aware of? --j -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 259 Computing Applications Building, MC-150 605 East Springfield Avenue Champaign, IL 61820-6371 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 __ 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] Ignore escape characters in a string...
R-helpers: One of the minor irritations I have is copying paths from Windows explorer, which look like: C:\Program Files\R\R-3.0.3 and using them in a setwd() statement, since the \ is, of course, interpreted as an escape character. I have to, at present, manually add in the double slashes or reverse them. So, I'd like to write a quick function that takes this path: winpath - C:\Program Files\R\R-3.0.3 and converts it to a ready-to-go R path -- is there a way to have R IGNORE escape characters in a character vector? Alternatively, is there some trick to using a copy/paste from Windows explorer I'm not aware of? --j -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 259 Computing Applications Building, MC-150 605 East Springfield Avenue Champaign, IL 61820-6371 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 __ 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] numeric to factor via lookup table
R-helpers: Hopefully this is an easy one. Given a lookup table: mylevels - data.frame(ID=1:10,code=letters[1:10]) And a set of values (note these do not completely cover the mylevels range): values - c(1,2,5,5,10) How do I convert values to a factor object, using the mylevels to define the correct levels (ID matches the values), and code is the label? --j -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 259 Computing Applications Building, MC-150 605 East Springfield Avenue Champaign, IL 61820-6371 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 __ 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] Overriding predict based on newdata...
David: Thanks! Is it generally frowned upon (if I'm Incorporating this into a package) to override a generic function like predict, even if I plan on making it a pass-through function (same parameters, and if the data type doesn't match my weird data type, it will simply pass the parameters through to the generic S3 predict)? --j On Mon, Mar 17, 2014 at 4:08 AM, David Winsemius dwinsem...@comcast.net wrote: S3 classes only dispatch on the basis of the first parameter class. That was one of the reasons for the development of S4-classed objects. You say you have the expectation that the object is of a class that has an ordinary `predict` method presumably S3 in character, so you probably need to write a function that will mask the existing method. You would rewrite the existing test for the existence of 'newdata' and the the definition of the new function would persist through the rest of the session and could be source()-ed in further sessions. -- David. On Mar 16, 2014, at 2:09 PM, Jonathan Greenberg wrote: R-helpers: I'm having some trouble with this one -- I figure because I'm a bit of a noob with S3 classes... Here's my challenge: I want to write a custom predict statement that is triggered based on the presence and class of a *newdata* parameter (not the object parameter). The reason is I am trying to write a custom function based on an oddly formatted dataset that has been assigned an R class. If the predict function detects it (class(newdata) == myweirdformat) it does a conversion of the newdata to what most predict statements expect (e.g. a dataframe) and then passes the converted dataset along to the generic predict statement. If newdata is missing or is not of the odd class it should just pass everything along to the generic predict as usual. What would be the best way to approach this problem? Since (my understanding) is that predict is dispatched based on the object parameter, this is causing me confusion -- my object should still remain the model, I'm just allowing a new data type to be fed into the predict model(s). Cheers! --j -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 259 Computing Applications Building, MC-150 605 East Springfield Avenue Champaign, IL 61820-6371 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 __ 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 Alameda, CA, USA -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 259 Computing Applications Building, MC-150 605 East Springfield Avenue Champaign, IL 61820-6371 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 __ 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] Overriding predict based on newdata...
R-helpers: I'm having some trouble with this one -- I figure because I'm a bit of a noob with S3 classes... Here's my challenge: I want to write a custom predict statement that is triggered based on the presence and class of a *newdata* parameter (not the object parameter). The reason is I am trying to write a custom function based on an oddly formatted dataset that has been assigned an R class. If the predict function detects it (class(newdata) == myweirdformat) it does a conversion of the newdata to what most predict statements expect (e.g. a dataframe) and then passes the converted dataset along to the generic predict statement. If newdata is missing or is not of the odd class it should just pass everything along to the generic predict as usual. What would be the best way to approach this problem? Since (my understanding) is that predict is dispatched based on the object parameter, this is causing me confusion -- my object should still remain the model, I'm just allowing a new data type to be fed into the predict model(s). Cheers! --j -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 259 Computing Applications Building, MC-150 605 East Springfield Avenue Champaign, IL 61820-6371 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 __ 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] install packages from R-forge SVN
R-helpers: I was curious if anyone developed a package/approach to installing packages directly from the R-forge SVN subsystem (rather than waiting for it to build)? I can, of course, SVN it command line but I was hoping for an install.packages(svn://) sort of approach. Cheers! --j -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 259 Computing Applications Building, MC-150 605 East Springfield Avenue Champaign, IL 61820-6371 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 __ 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] Checking for and adding ... arguments to a function...
R-helpers:
I'm guessing this is an easy one for some of you, but I'm a bit
stumped. Given some arbitrary function (doesn't matter what it does):
myfunction - function(a,b,c)
{
return(a+b+c)
}
I want to test this function for the presence of the ellipses (...)
and, if they are missing, create a new function that has them:
myfunction - function(a,b,c,...)
{
return(a+b+c)
}
So, 1) how do I test for whether a function has an ellipses argument
and, 2) how do I append the ellipses to the argument list if they do
exist?
Note that the test/modification should be done without invoking the
function, e.g. I'm not asking how to test for this WITHIN the
function, I'm asking how to test myfunction directly as an R object.
Thanks!
--j
--
Jonathan A. Greenberg, PhD
Assistant Professor
Global Environmental Analysis and Remote Sensing (GEARS) Laboratory
Department of Geography and Geographic Information Science
University of Illinois at Urbana-Champaign
259 Computing Applications Building, MC-150
605 East Springfield Avenue
Champaign, IL 61820-6371
Phone: 217-300-1924
http://www.geog.illinois.edu/~jgrn/
AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007
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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] Official way to set/retrieve options in packages?
Wanted to re-start this thread a bit, since I'm still not exactly sure
the best approach to my problem -- basically, the parameters I'm try
to make persistent are installation locations of a particular command
line program that is not installed along with an R package I'm working
on (GDAL, for those of you who are interested in the specifics). The
function tries to dummy-proof this process by doing a (mostly)
brute-force search of the user's drive for the program location the
first time it executes, and then stores this information (the path to
a given executable) in an option for use with other functions. This
search process can take some time, so I'd prefer to have this option
set in a semi-permanent way (so it persists between sessions).
Now, Brian Ripley suggested modifying the .Rprofile, but Bert Guntner
suggested this might not be a welcome behavior. Given that, on an
operating system level, there are often per-program directories for
preferences, would it follow that it might make sense to store
package-options in some standardized location? If so, where might
this be? Would it make sense to drop then in the package directory?
Is this a discussion that should move over to r-developers?
--j
On Sat, Jun 1, 2013 at 4:57 PM, Prof Brian Ripley rip...@stats.ox.ac.uk wrote:
On 01/06/2013 22:44, Anthony Damico wrote:
hope this helps.. :)
# define an object `x`
x - list( any value here , 10 )
# set `myoption` to that object
options( myoption = x )
# retrieve it later (perhaps within a function elsewhere in the package)
( y - getOption( myoption ) )
it's nice to name your options `mypackage.myoption` so users know what
package the option is associated with in case they type `options()`
here's the `.onLoad` function in the R survey package. notice how the
options are only set *if* they don't already exist--
But a nicer convention is that used by most packages in R itself: if the
option is not set, the function using it assumes a suitable default.
That would make sense for all the FALSE defaults below.
Note though that this is not 'persistent': users have to set options in
their startup files (see ?Startup). There is no official location to
store package configurations. Users generally dislike software saving
settings in their own file space so it seems very much preferable to use
the standard R mechanisms (.Rprofile etc).
survey:::.onLoad
function (...)
{
if (is.null(getOption(survey.lonely.psu)))
options(survey.lonely.psu = fail)
if (is.null(getOption(survey.ultimate.cluster)))
options(survey.ultimate.cluster = FALSE)
if (is.null(getOption(survey.want.obsolete)))
options(survey.want.obsolete = FALSE)
if (is.null(getOption(survey.adjust.domain.lonely)))
options(survey.adjust.domain.lonely = FALSE)
if (is.null(getOption(survey.drop.replicates)))
options(survey.drop.replicates = TRUE)
if (is.null(getOption(survey.multicore)))
options(survey.multicore = FALSE)
if (is.null(getOption(survey.replicates.mse)))
options(survey.replicates.mse = FALSE)
}
environment: namespace:survey
On Sat, Jun 1, 2013 at 4:01 PM, Jonathan Greenberg j...@illinois.eduwrote:
R-helpers:
Say I'm developing a package that has a set of user-definable options that
I would like to be persistent across R-invocations (they are saved
someplace). Of course, I can create a little text file to be written/read,
but I was wondering if there is an officially sanctioned way to do this?
I see there is an options() and getOptions() function, but I'm unclear how
I would use this in my own package to create/save new options for my
particular package. Cheers!
--j
--
Jonathan A. Greenberg, PhD
Assistant Professor
Global Environmental Analysis and Remote Sensing (GEARS) Laboratory
Department of Geography and Geographic Information Science
University of Illinois at Urbana-Champaign
607 South Mathews Avenue, MC 150
Urbana, IL 61801
Phone: 217-300-1924
http://www.geog.illinois.edu/~jgrn/
AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007
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and provide commented, minimal, self-contained, reproducible code.
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--
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
Re: [R] Error: C stack usage is too close to the limit when using list.files()
Thanks all -- ok, so the symbolic link issue is a distinct possibility, but fundamentally doesn't solve the issue since most users will have symbolic links on their machines SOMEPLACE, so a full drive scan will run into these issues -- is list.files calling find, or is it using a different algorithm? This seems like a shortcoming in the list.files algorithm -- is there a better solution (short of a System call, which I'm still not sure will work on Macs without Xcode -- a colleague of mine did NOT have Xcode, and reported not being able to run find from the command line) -- perhaps a different package? --j On Fri, Sep 27, 2013 at 3:08 PM, William Dunlap wdun...@tibco.com wrote: Toss a couple of extra files in there and you will see the output grow exponentially. % touch dir/IMPORTANT_1 dir/subdir/IMPORTANT_2 and in R those two new files cause 82 more strings to appear in list.file's output: nchar(list.files(dir, recursive=TRUE)) [1] 11 18 33 40 55 62 77 84 99 106 121 128 143 150 165 172 187 194 209 [20] 216 231 238 253 260 275 282 297 304 319 326 341 348 363 370 385 392 407 414 [39] 429 436 451 458 473 480 495 502 517 524 539 546 561 568 583 590 605 612 627 [58] 634 649 656 671 678 693 700 715 722 737 744 759 766 781 788 803 810 825 832 [77] 847 854 869 876 891 898 901 'find', by default, does not following symbolic links. % find dir dir dir/subdir dir/subdir/IMPORTANT_2 dir/subdir/linkToUpperDir dir/IMPORTANT_1 The -L option makes it follow them, but it won't follow loops: % find -L dir dir dir/subdir dir/subdir/IMPORTANT_2 find: File system loop detected; `dir/subdir/linkToUpperDir' is part of the same file system loop as `dir'. dir/IMPORTANT_1 Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of William Dunlap Sent: Friday, September 27, 2013 12:56 PM To: Jonathan Greenberg; r-help Subject: Re: [R] Error: C stack usage is too close to the limit when using list.files() Do you have some symbolic links that make loops in your file system? list.files() has problems with such loops and find does not. E.g., on a Linux box: % cd /tmp % mkdir dir dir/subdir % cd dir/subdir % ln -s ../../dir linkToUpperDir % cd /tmp % R --quiet list.files(dir, recursive=TRUE, full=TRUE) [1] dir/subdir/linkToUpperDir/subdir/linkToUpperDir/subdir/linkToUpperDir/subdir/linkToU pperDir/subdir/linkToUpperDir/subdir/linkToUpperDir/subdir/linkToUpperDir/subdir/linkT oUpperDir/subdir/linkToUpperDir/subdir/linkToUpperDir/subdir/linkToUpperDir/subdir/li nkToUpperDir/subdir/linkToUpperDir/subdir/linkToUpperDir/subdir/linkToUpperDir/subdi r/linkToUpperDir/subdir/linkToUpperDir/subdir/linkToUpperDir/subdir/linkToUpperDir/su bdir/linkToUpperDir/subdir/linkToUpperDir/subdir/linkToUpperDir/subdir/linkToUpperDir /subdir/linkToUpperDir/subdir/linkToUpperDir/subdir/linkToUpperDir/subdir/linkToUpper Dir/subdir/linkToUpperDir/subdir/linkToUpperDir/subdir/linkToUpperDir/subdir/linkToUp perDir/subdir/linkToUpperDir/subdir/linkToUpperDir/subdir/linkToUpperDir/subdir/linkTo UpperDir/subdir/linkToUpperDir/subdir/linkToUpperDir/subdir/linkToUpperDir/subdir/lin kToUpperDir/subdir/linkToUpperDir/subdir/linkToUpperDir system(find dir) dir dir/subdir dir/subdir/linkToUpperDir Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Jonathan Greenberg Sent: Friday, September 27, 2013 12:13 PM To: r-help Subject: [R] Error: C stack usage is too close to the limit when using list.files() R-helpers: I'm running a file search on my entire drive (Mac OS X) using: files_found - list.files(dir=/,pattern=somepattern,recursive=TRUE,full.names=TRUE) where somepattern is a search pattern (which I have confirmed via a unix find / -name somepattern only returns ~ 3 results). I keep getting an error: Error: C stack usage is too close to the limit when running this command. Any ideas on 1) how to fix this or 2) if there is an alternative to using list.files() to accomplish this search without resorting to an external package? Cheers! --jonathan -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 259 Computing Applications Building, MC-150 605 East Springfield Avenue Champaign, IL 61820-6371 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide
[R] Error: C stack usage is too close to the limit when using list.files()
R-helpers: I'm running a file search on my entire drive (Mac OS X) using: files_found - list.files(dir=/,pattern=somepattern,recursive=TRUE,full.names=TRUE) where somepattern is a search pattern (which I have confirmed via a unix find / -name somepattern only returns ~ 3 results). I keep getting an error: Error: C stack usage is too close to the limit when running this command. Any ideas on 1) how to fix this or 2) if there is an alternative to using list.files() to accomplish this search without resorting to an external package? Cheers! --jonathan -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 259 Computing Applications Building, MC-150 605 East Springfield Avenue Champaign, IL 61820-6371 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 __ 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] Error: C stack usage is too close to the limit when using list.files()
Ben: I'd like to avoid using that (previous version of my code solved it in that way) -- I would like cross-platform compatibility and I am pretty sure, along with Windows, vanilla Macs don't come with find either unless XCode has been installed. Is the list.files() code itself recursive when using recursive=TRUE (so it has one recursion per bottom-folder)? --j P.S. I recognized that in my initial post I indicated using dir as the parameter -- it should have been path (the error occurred through the correct usage of list.files(path=/,...) That'll teach me not to copy/paste from my code... On Fri, Sep 27, 2013 at 2:36 PM, Ben Bolker bbol...@gmail.com wrote: Jonathan Greenberg jgrn at illinois.edu writes: R-helpers: I'm running a file search on my entire drive (Mac OS X) using: files_found - list.files(dir=/,pattern=somepattern,recursive=TRUE,full.names=TRUE) where somepattern is a search pattern (which I have confirmed via a unix find / -name somepattern only returns ~ 3 results). I keep getting an error: Error: C stack usage is too close to the limit when running this command. Any ideas on 1) how to fix this or 2) if there is an alternative to using list.files() to accomplish this search without resorting to an external package? I assuming that using system(find / -name somepattern) (possibly with intern=TRUE) isn't allowed? (I don't know what you're trying to do, but if you don't need it to work on Windows-without-cygwin, this should work across most Unix variants (although a -print might be required) __ 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 Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 259 Computing Applications Building, MC-150 605 East Springfield Avenue Champaign, IL 61820-6371 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 __ 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] library() and install.packages() no longer working (Access is denied error)
In the last week, SOMETHING on my system must have changed because when trying to library() or install.packages() on R 3.0.1 x64 on a Windows 2008 R2 server: library(raster) Error in normalizePath(path.expand(path), winslash, mustWork) : path[1]=D:/Users/[UID]/Documents/R/win-library/3.0: Access is denied install.packages(raster) Installing package into ‘D:/Users/[UID]/Documents/R/win-library/3.0’ (as ‘lib’ is unspecified) trying URL 'http://ftp.osuosl.org/pub/cran/bin/windows/contrib/3.0/raster_2.1-49.zip' Content type 'application/zip' length 2363295 bytes (2.3 Mb) opened URL downloaded 2.3 Mb Error in normalizePath(path.expand(path), winslash, mustWork) : path[1]=D:\Users\[UID]\Documents\R\win-library\3.0: Access is denied In addition: Warning message: In normalizePath(path.expand(path), winslash, mustWork) : path[1]=D:/Users/[UID]/Documents/R/win-library/3.0: Access is denied The permissions on that directory APPEAR to be correct (I can add files/folders, rename them, delete them), but alas R continues to give me these errors. Both the users and the sysadmin claim nothing was changed, but clearly something did. As a heads up, I did try removing PATHTO/win-library/3.0, and re-ran the install.packages(raster), at which point R asked me Would you like to use a personal directory instead?. I clicked yes. It then asks me Would you like to create a personal library 'D:/Users/[UID]/Documents/R/win-library/3.0' to install packages into? I clicked yes. The Mirror browser shows up, I select a mirror. A 3.0 directory is created, but I got the same error, and when examining the (new) 3.0 directory, nothing is created inside of it. Any ideas what this could be caused by? --j -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 607 South Mathews Avenue, MC 150 Urbana, IL 61801 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 __ 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] ifelse question (I'm not sure why this is working)...
R-helpers:
One of my intrepid students came up with a solution to a problem where
they need to write a function that takes a vector x and a scalar d,
and return the indices of the vector x where x %% d is equal to 0 (x
is evenly divisible by d). I thought I had a good handle on the
potential solutions, but one of my students sent me a function that
WORKS, but for the life of me I can't figure out WHY. Here is the
solution:
remainderFunction-function(x,d)
{
ifelse(x%%d==0,yes=return(which(x%%d==0)),no=return(NULL))
}
remainderFunction(x=c(23:47),d=3)
I've never seen an ifelse statement used that way, and I was fully
expecting that to NOT work, or to place the output of which(x%%d==0)
in each location where the statement x%%d==0 was true.
Any ideas on deconstructing this?
--j
--
Jonathan A. Greenberg, PhD
Assistant Professor
Global Environmental Analysis and Remote Sensing (GEARS) Laboratory
Department of Geography and Geographic Information Science
University of Illinois at Urbana-Champaign
607 South Mathews Avenue, MC 150
Urbana, IL 61801
Phone: 217-300-1924
http://www.geog.illinois.edu/~jgrn/
AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007
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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] Vectorized version of colMeans/rowMeans for higher dimension arrays?
For matrices, colMeans/rowMeans are quick, vectorized functions. But say I have a higher dimensional array: moo - array(runif(400*9*3),dim=c(400,9,3)) And I want to get the mean along the 2nd dimension. I can, of course, use apply: moo1 - apply(moo,c(1,3),mean) But this is not a vectorized operation (so it doesn't execute as quickly). How would one vectorize this operation (if possible)? Is there an array equivalent of colMeans/rowMeans? --j -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 607 South Mathews Avenue, MC 150 Urbana, IL 61801 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 __ 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] Determining the maximum memory usage of a function
Folks: I apologize for the cross-posting between r-help and r-sig-hpc, but I figured this question was relevant to both lists. I'm writing a function to be applied to an input dataset that will be broken up into chunks for memory management reasons and for parallel execution. I am trying to determine, for a given function, what the *maximum* memory usage during its execution is (which may not be the beginning or the end of the function, but somewhere in the middle), so I can plan for the chunk size (e.g. have a table of chunk size vs. max memory usage). Is there a trick for determining this? --j -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 607 South Mathews Avenue, MC 150 Urbana, IL 61801 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 __ 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] Determining the maximum memory usage of a function
Jim: Thanks, but I'm looking for something that can be used somewhat automatically -- the function in question would be user-provided and passed to my chunking algorithm, so in this case it would be the end-user (not me) who would have to embed these -- would Rprof(memory.profiling=TRUE) # my function Rprof(NULL) ... and then taking the max of the tseries output be a reasonable approach? If so, which of the three outputs (vsize.small vsize.large nodes) would be best compared against the available memory? Cheers! --j On Thu, Jun 20, 2013 at 10:07 AM, jim holtman jholt...@gmail.com wrote: What I would do is to use memory.size() to get the amount of memory being used. Do a call at the beginning of the function to determine the base, and then at other points in the code to see what the difference from the base is and keep track of the maximum difference. I am not sure if just getting the memory usage at the end would be sufficient since there may be some garbage collection in between, or you might be creating some large objects and then deleting/reusing them. So keep track after large chunks of code to see what is happening. On Thu, Jun 20, 2013 at 10:45 AM, Jonathan Greenberg j...@illinois.edu wrote: Folks: I apologize for the cross-posting between r-help and r-sig-hpc, but I figured this question was relevant to both lists. I'm writing a function to be applied to an input dataset that will be broken up into chunks for memory management reasons and for parallel execution. I am trying to determine, for a given function, what the *maximum* memory usage during its execution is (which may not be the beginning or the end of the function, but somewhere in the middle), so I can plan for the chunk size (e.g. have a table of chunk size vs. max memory usage). Is there a trick for determining this? --j -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 607 South Mathews Avenue, MC 150 Urbana, IL 61801 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Data Munger Guru What is the problem that you are trying to solve? Tell me what you want to do, not how you want to do it. -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 607 South Mathews Avenue, MC 150 Urbana, IL 61801 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 __ 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] Official way to set/retrieve options in packages?
What would be an example of setting, saving, and re-loading an option to a
user's .Rprofile -- and would this be a no-no in a CRAN package?
--j
On Sat, Jun 1, 2013 at 4:57 PM, Prof Brian Ripley rip...@stats.ox.ac.ukwrote:
On 01/06/2013 22:44, Anthony Damico wrote:
hope this helps.. :)
# define an object `x`
x - list( any value here , 10 )
# set `myoption` to that object
options( myoption = x )
# retrieve it later (perhaps within a function elsewhere in the
package)
( y - getOption( myoption ) )
it's nice to name your options `mypackage.myoption` so users know what
package the option is associated with in case they type `options()`
here's the `.onLoad` function in the R survey package. notice how the
options are only set *if* they don't already exist--
But a nicer convention is that used by most packages in R itself: if the
option is not set, the function using it assumes a suitable default.
That would make sense for all the FALSE defaults below.
Note though that this is not 'persistent': users have to set options in
their startup files (see ?Startup). There is no official location to
store package configurations. Users generally dislike software saving
settings in their own file space so it seems very much preferable to use
the standard R mechanisms (.Rprofile etc).
survey:::.onLoad
function (...)
{
if (is.null(getOption(survey.lonely.psu)))
options(survey.lonely.psu = fail)
if (is.null(getOption(survey.ultimate.cluster)))
options(survey.ultimate.cluster = FALSE)
if (is.null(getOption(survey.want.obsolete)))
options(survey.want.obsolete = FALSE)
if (is.null(getOption(survey.adjust.domain.lonely)))
options(survey.adjust.domain.lonely = FALSE)
if (is.null(getOption(survey.drop.replicates)))
options(survey.drop.replicates = TRUE)
if (is.null(getOption(survey.multicore)))
options(survey.multicore = FALSE)
if (is.null(getOption(survey.replicates.mse)))
options(survey.replicates.mse = FALSE)
}
environment: namespace:survey
On Sat, Jun 1, 2013 at 4:01 PM, Jonathan Greenberg j...@illinois.edu
wrote:
R-helpers:
Say I'm developing a package that has a set of user-definable options
that
I would like to be persistent across R-invocations (they are saved
someplace). Of course, I can create a little text file to be
written/read,
but I was wondering if there is an officially sanctioned way to do
this?
I see there is an options() and getOptions() function, but I'm
unclear how
I would use this in my own package to create/save new options for my
particular package. Cheers!
--j
--
Jonathan A. Greenberg, PhD
Assistant Professor
Global Environmental Analysis and Remote Sensing (GEARS) Laboratory
Department of Geography and Geographic Information Science
University of Illinois at Urbana-Champaign
607 South Mathews Avenue, MC 150
Urbana, IL 61801
Phone: 217-300-1924
http://www.geog.illinois.edu/~jgrn/
AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007
[[alternative HTML version deleted]]
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http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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__
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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.
--
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
--
Jonathan A. Greenberg, PhD
Assistant Professor
Global Environmental Analysis and Remote Sensing (GEARS) Laboratory
Department of Geography and Geographic Information Science
University of Illinois at Urbana-Champaign
607 South Mathews Avenue, MC 150
Urbana, IL 61801
Phone: 217-300-1924
http://www.geog.illinois.edu/~jgrn/
AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007
[[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.
[R] Official way to set/retrieve options in packages?
R-helpers: Say I'm developing a package that has a set of user-definable options that I would like to be persistent across R-invocations (they are saved someplace). Of course, I can create a little text file to be written/read, but I was wondering if there is an officially sanctioned way to do this? I see there is an options() and getOptions() function, but I'm unclear how I would use this in my own package to create/save new options for my particular package. Cheers! --j -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 607 South Mathews Avenue, MC 150 Urbana, IL 61801 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 [[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] RCurl: using ls instead of NLST
R-helpers: I'm trying to retrieve the contents of a directory from an ftp site (ideally, the file/folder names as a character vector): ftp://e4ftl01.cr.usgs.gov/MOTA/MCD12C1.005/; # (MODIS data) Where I get the following error via RCurl: require(RCurl) url - ftp://e4ftl01.cr.usgs.gov/MOTA/MCD12C1.005/; filenames = getURL(url,ftp.use.epsv=FALSE,ftplistonly=TRUE) Error in function (type, msg, asError = TRUE) : RETR response: 550 Through some sleuthing, it turns out the ftp site does not support NLST (which RCurl is using), but will use ls to list the directory contents -- is there any way to use ls remotely on this site? Thanks! --j -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 607 South Mathews Avenue, MC 150 Urbana, IL 61801 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 [[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] Singular design matrix in rq
Roger: Doh! Just realized I had that error in the code -- raw_data is the same as mydata, so it should be: mydata - read.csv(singular.csv) plot(mydata$predictor,mydata$response) # A big cloud of points, nothing too weird summary(mydata) # No NAs: # Xresponse predictor # Min. :1 Min. :0.0 Min. : 0.000 # 1st Qu.:12726 1st Qu.: 851.2 1st Qu.: 0.000 # Median :25452 Median : 2737.0 Median : 0.000 # Mean :25452 Mean : 3478.0 Mean : 5.532 # 3rd Qu.:38178 3rd Qu.: 5111.6 3rd Qu.: 5.652 # Max. :50903 Max. :26677.8 Max. :69.342 fit_spl - rq(response ~ bs(predictor,df=15),tau=1,data=mydata) # Error in rq.fit.br(x, y, tau = tau, ...) : Singular design matrix --j On Fri, Apr 19, 2013 at 8:15 AM, Koenker, Roger W rkoen...@illinois.eduwrote: Jonathan, This is not what we call a reproducible example... what is raw_data? Does it have something to do with mydata? what is i? Roger url:www.econ.uiuc.edu/~rogerRoger Koenker emailrkoen...@uiuc.eduDepartment of Economics vox: 217-333-4558University of Illinois fax: 217-244-6678Urbana, IL 61801 On Apr 16, 2013, at 2:58 PM, Greenberg, Jonathan wrote: Quantreggers: I'm trying to run rq() on a dataset I posted at: https://docs.google.com/file/d/0B8Kij67bij_ASUpfcmJ4LTFEUUk/edit?usp=sharing (it's a 1500kb csv file named singular.csv) and am getting the following error: mydata - read.csv(singular.csv) fit_spl - rq(raw_data[,1] ~ bs(raw_data[,i],df=15),tau=1) Error in rq.fit.br(x, y, tau = tau, ...) : Singular design matrix Any ideas what might be causing this or, more importantly, suggestions for how to solve this? I'm just trying to fit a smoothed hull to the top of the data cloud (hence the large df). Thanks! --jonathan -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 607 South Mathews Avenue, MC 150 Urbana, IL 61801 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 607 South Mathews Avenue, MC 150 Urbana, IL 61801 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 [[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] Singular design matrix in rq
Quantreggers: I'm trying to run rq() on a dataset I posted at: https://docs.google.com/file/d/0B8Kij67bij_ASUpfcmJ4LTFEUUk/edit?usp=sharing (it's a 1500kb csv file named singular.csv) and am getting the following error: mydata - read.csv(singular.csv) fit_spl - rq(raw_data[,1] ~ bs(raw_data[,i],df=15),tau=1) Error in rq.fit.br(x, y, tau = tau, ...) : Singular design matrix Any ideas what might be causing this or, more importantly, suggestions for how to solve this? I'm just trying to fit a smoothed hull to the top of the data cloud (hence the large df). Thanks! --jonathan -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 607 South Mathews Avenue, MC 150 Urbana, IL 61801 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 [[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] Check if a character vector can be coerced to numeric?
Given an arbitrary set of character vectors: myvect1 - c(abc,3,4) myvect2 - c(2,3,4) I would like to develop a function that will convert any vectors that can be PROPERLY converted to a numeric (myvect2) into a numeric, but leaves character vectors which cannot be converted (myvect1) alone. Is there any simple way to do this (e.g. some function that tests if a vector is coercible to a numeric before doing so)? --j -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 607 South Mathews Avenue, MC 150 Urbana, IL 61801 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 [[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] Check if a character vector can be coerced to numeric?
Yep, type.convert was exactly what I was looking for (with as.is=TRUE). Thanks! On Thu, Mar 21, 2013 at 1:31 PM, Prof Brian Ripley rip...@stats.ox.ac.ukwrote: On 21/03/2013 18:20, Jonathan Greenberg wrote: Given an arbitrary set of character vectors: myvect1 - c(abc,3,4) myvect2 - c(2,3,4) I would like to develop a function that will convert any vectors that can be PROPERLY converted to a numeric (myvect2) into a numeric, but leaves character vectors which cannot be converted (myvect1) alone. Is there any simple way to do this (e.g. some function that tests if a vector is coercible to a numeric before doing so)? --j ?type.convert It does depend what you mean by 'properly'. Can 123.456789012344567890123455 be converted 'properly'? [See the NEWS for R-devel.] -- 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. -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 607 South Mathews Avenue, MC 150 Urbana, IL 61801 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 [[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] Loading a list into the environment
Thanks all! list2env was exactly what I was looking for. As an FYI (and
please correct me if I'm wrong), if you want to load a list into the
current environment, use:
myvariables - list(a=1:10,b=20)
loadenv - list2env(myvariables ,envir=environment())
a
b
--j
On Fri, Feb 1, 2013 at 5:49 PM, Rui Barradas ruipbarra...@sapo.pt wrote:
Hello,
Something like this?
myfun - function(x, envir = .GlobalEnv){
nm - names(x)
for(i in seq_along(nm))
assign(nm[i], x[[i]], envir)
}
myvariables - list(a=1:10,b=20)
myfun(myvariables)
a
b
Hope this helps,
Rui Barradas
Em 01-02-2013 22:24, Jonathan Greenberg escreveu:
R-helpers:
Say I have a list:
myvariables - list(a=1:10,b=20)
Is there a way to load the list components into the environment as
variables based on the component names? i.e. by applying this theoretical
function to myvariables I would have the variables a and b loaded into the
environment without having to explicitly define them.
--j
--
Jonathan A. Greenberg, PhD
Assistant Professor
Global Environmental Analysis and Remote Sensing (GEARS) Laboratory
Department of Geography and Geographic Information Science
University of Illinois at Urbana-Champaign
607 South Mathews Avenue, MC 150
Urbana, IL 61801
Phone: 217-300-1924
http://www.geog.illinois.edu/~jgrn/
AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007
[[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.
[R] Loading a list into the environment
R-helpers: Say I have a list: myvariables - list(a=1:10,b=20) Is there a way to load the list components into the environment as variables based on the component names? i.e. by applying this theoretical function to myvariables I would have the variables a and b loaded into the environment without having to explicitly define them. --j -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 607 South Mathews Avenue, MC 150 Urbana, IL 61801 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 [[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] Adding a line to barchart
Great! This really helped! One quick follow-up -- is there a trick to
placing a label wherever the line intersects the x-axis (either above or
below the plot)?
On Tue, Jan 22, 2013 at 11:49 PM, PIKAL Petr petr.pi...@precheza.cz wrote:
Hi
This function adds line to each panel
addLine - function (a = NULL, b = NULL, v = NULL, h = NULL, ..., once = F)
{
tcL - trellis.currentLayout()
k - 0
for (i in 1:nrow(tcL)) for (j in 1:ncol(tcL)) if (tcL[i,
j] 0) {
k - k + 1
trellis.focus(panel, j, i, highlight = FALSE)
if (once)
panel.abline(a = a[k], b = b[k], v = v[k], h = h[k],
...)
else panel.abline(a = a, b = b, v = v, h = h, ...)
trellis.unfocus()
}
}
addLine(v=2, col=2, lty=3)
Petr
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
project.org] On Behalf Of Jonathan Greenberg
Sent: Tuesday, January 22, 2013 11:42 PM
To: r-help
Subject: [R] Adding a line to barchart
R-helpers:
I need a quick help with the following graph (I'm a lattice newbie):
require(lattice)
npp=1:5
names(npp)=c(A,B,C,D,E)
barchart(npp,origin=0,box.width=1)
# What I want to do, is add a single vertical line positioned at x = 2
that lays over the bars (say, using a dotted line). How do I go about
doing this?
--j
--
Jonathan A. Greenberg, PhD
Assistant Professor
Global Environmental Analysis and Remote Sensing (GEARS) Laboratory
Department of Geography and Geographic Information Science University
of Illinois at Urbana-Champaign
607 South Mathews Avenue, MC 150
Urbana, IL 61801
Phone: 217-300-1924
http://www.geog.illinois.edu/~jgrn/
AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007
[[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.
--
Jonathan A. Greenberg, PhD
Assistant Professor
Global Environmental Analysis and Remote Sensing (GEARS) Laboratory
Department of Geography and Geographic Information Science
University of Illinois at Urbana-Champaign
607 South Mathews Avenue, MC 150
Urbana, IL 61801
Phone: 217-300-1924
http://www.geog.illinois.edu/~jgrn/
AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007
[[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] Adding a line to barchart
R-helpers: I need a quick help with the following graph (I'm a lattice newbie): require(lattice) npp=1:5 names(npp)=c(A,B,C,D,E) barchart(npp,origin=0,box.width=1) # What I want to do, is add a single vertical line positioned at x = 2 that lays over the bars (say, using a dotted line). How do I go about doing this? --j -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 607 South Mathews Avenue, MC 150 Urbana, IL 61801 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 [[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] Best way to coerce numerical data to a predetermined histogram bin?
Folks: Say I have a set of histogram breaks: breaks=c(1:10,15) # With bin ids: bin_ids=1:(length(breaks)-1) # and some data (note that some of it falls outside the breaks: data=runif(min=1,max=20,n=100) *** What is the MOST EFFICIENT way to classify data into the histogram bins (return the bin_ids) and, say, return NA if the value falls outside of the bins. By classify, I mean if the data value is greater than one break, and less than or equal to the next break, it gets assigned that bin's ID (note that length(breaks) = length(bin_ids)+1) Also note that, as per this example, the bins are not necessarily equal widths. I can, of course, cycle through each element of data, and then move through breaks, stopping when it finds the correct bin, but I feel like there is probably a faster (and more elegant) approach to this. Thoughts? --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: 217-300-1924 AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 [[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] Best R textbook for undergraduates
R-helpers: I'm sure this question has been asked and answered through the ages, but given there are some new textbooks out there, I wanted to re-pose it. For a course that will cover the application of R for general computing and spatial modeling, what textbook would be best to introduce computing with R to *undergrads*? I understand Bivand and Pebesma's book is fine for spatial work, but it appears to be for more advanced users -- I'd like a companion textbook that is better for complete beginners to ALL forms of programming (e.g. they don't know what an object is, a loop is, an if-then statement, etc). Suggestions? In particular, I'd like to hear from those of you who have TAUGHT classes using R. Thanks! --jonathan -- 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: 217-300-1924 AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 [[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] Completely ignoring an error in a function...
The code base is a bit too complicated to paste in here, but the gist of my
question is this: given I have a function
myfunction - function(x)
{
# Do something A
# Do something B
# Do something C
}
Say #Do something B returns this error:
Error in cat(list(...), file, sep, fill, labels, append) :
argument 2 (type 'list') cannot be handled by 'cat'
A standard function would stop here. HOWEVER, I want, in this odd case, to
say keep going to my function and have it proceeed to # Do something C.
How do I accomplish this? I thought suppressWarnings() would do it but it
doesn't appear to.
Assume that debugging Do something B is out of the question. Why am I
doing this? Because in my odd case, Do something B actually does what I
needed it to, but returned an error that is irrelevant to my special case
(it creates two files, failing on the second of the two files -- but the
first file it creates is what I wanted and there is no current way to
create that single file on its own without a lot of additional coding).
--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: 217-300-1924
AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007
[[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] [R-sig-hpc] Quickest way to make a large empty file on disk?
Rui:
Quick follow-up -- it looks like seek does do what I want (I see Simon
suggested it some time ago) -- what do mean by trash your disk? What I'm
trying to accomplish is getting parallel, asynchronous writes to a large
binary image (just a binary file) working. Each node writes to a different
sector of the file via mmap, filling in the values as the process runs,
but the file needs to be pre-created before I can mmap it. Running a
writeBin with a bunch of 0s would mean I'd basically have to write the file
twice, but the seek/ff trick seems to be much faster.
Do I risk doing some damage to my filesystem if I use seek? I see there is
a strongly worded warning in the help for ?seek:
Use of seek on Windows is discouraged. We have found so many errors in the
Windows implementation of file positioning that users are advised to use it
only at their own risk, and asked not to waste the *R* developers' time
with bug reports on Windows' deficiencies. -- there's no detail here on
which errors people have experienced, so I'm not sure if doing something as
simple as just creating a file using seek falls under the discouraging
category.
As a note, we are trying to work this up on both Windows and *nix systems,
hence our wanting to have a single approach that works on both OSs.
--j
On Thu, Sep 27, 2012 at 3:49 PM, Rui Barradas ruipbarra...@sapo.pt wrote:
Hello,
If you really need to trash your disk, why not use seek()?
fl - file(Test.txt, open = wb)
seek(fl, where = 1024, origin = start, rw = write)
[1] 0
writeChar(character(1), fl, nchars = 1, useBytes = TRUE)
Warning message:
In writeChar(character(1), fl, nchars = 1, useBytes = TRUE) :
writeChar: more characters requested than are in the string - will
zero-pad
close(fl)
File Test.txt is now 1Kb in size.
Hope this helps,
Rui Barradas
Em 27-09-2012 20:17, Jonathan Greenberg escreveu:
Folks:
Asked this question some time ago, and found what appeared (at first) to be
the best solution, but I'm now finding a new problem. First off, it seemed
like ff as Jens suggested worked:
# outdata_ncells = the number of rows * number of columns * number of bands
in an image:
out-ff(vmode=double,length=outdata_ncells,filename=filename)
finalizer(out) - close
close(out)
This was working fine until I attempted to set length to a VERY large
number: outdata_ncells = 17711913600. This would create a file that is
131.964GB. Big, but not obscenely so (and certainly not larger than the
filesystem can handle). However, length appears to be restricted
by .Machine$integer.max (I'm on a 64-bit windows box):
.Machine$integer.max
[1] 2147483647
Any suggestions on how to solve this problem for much larger file sizes?
--j
On Thu, May 3, 2012 at 10:44 AM, Jonathan Greenberg j...@illinois.edu
j...@illinois.eduwrote:
Thanks, all! I'll try these out. I'm trying to work up something that is
platform independent (if possible) for use with mmap. I'll do some tests
on these suggestions and see which works best. I'll try to report back in a
few days. Cheers!
--j
2012/5/3 Jens Oehlschlägel jens.oehlschlae...@truecluster.com
jens.oehlschlae...@truecluster.com
Jonathan,
On some filesystems (e.g. NTFS, see below) it is possible to create
'sparse' memory-mapped files, i.e. reserving the space without the cost of
actually writing initial values.
Package 'ff' does this automatically and also allows to access the file
in parallel. Check the example below and see how big file creation is
immediate.
Jens Oehlschlägel
library(ff)
library(snowfall)
ncpus - 2
n - 1e8
system.time(
+ x - ff(vmode=double, length=n, filename=c:/Temp/x.ff)
+ )
User System verstrichen
0.010.000.02
# check finalizer, with an explicit filename we should have a 'close'
finalizer
finalizer(x)
[1] close
# if not, set it to 'close' inorder to not let slaves delete x on slave
shutdown
finalizer(x) - close
sfInit(parallel=TRUE, cpus=ncpus, type=SOCK)
R Version: R version 2.15.0 (2012-03-30)
snowfall 1.84 initialized (using snow 0.3-9): parallel execution on 2
CPUs.
sfLibrary(ff)
Library ff loaded.
Library ff loaded in cluster.
Warnmeldung:
In library(package = ff, character.only = TRUE, pos = 2, warn.conflicts
= TRUE, :
'keep.source' is deprecated and will be ignored
sfExport(x) # note: do not export the same ff multiple times
# explicitely opening avoids a gc problem
sfClusterEval(open(x, caching=mmeachflush)) # opening with
'mmeachflush' inststead of 'mmnoflush' is a bit slower but prevents OS
write storms when the file is larger than RAM
[[1]]
[1] TRUE
[[2]]
[1] TRUE
system.time(
+ sfLapply( chunk(x, length=ncpus), function(i){
+ x[i] - runif(sum(i))
+ invisible()
+ })
+ )
User System verstrichen
0.000.00 30.78
system.time(
+ s - sfLapply( chunk(x, length=ncpus), function(i
Re: [R] [R-sig-hpc] Quickest way to make a large empty file on disk?
Folks:
Asked this question some time ago, and found what appeared (at first) to be
the best solution, but I'm now finding a new problem. First off, it seemed
like ff as Jens suggested worked:
# outdata_ncells = the number of rows * number of columns * number of bands
in an image:
out-ff(vmode=double,length=outdata_ncells,filename=filename)
finalizer(out) - close
close(out)
This was working fine until I attempted to set length to a VERY large
number: outdata_ncells = 17711913600. This would create a file that is
131.964GB. Big, but not obscenely so (and certainly not larger than the
filesystem can handle). However, length appears to be restricted
by .Machine$integer.max (I'm on a 64-bit windows box):
.Machine$integer.max
[1] 2147483647
Any suggestions on how to solve this problem for much larger file sizes?
--j
On Thu, May 3, 2012 at 10:44 AM, Jonathan Greenberg j...@illinois.eduwrote:
Thanks, all! I'll try these out. I'm trying to work up something that is
platform independent (if possible) for use with mmap. I'll do some tests
on these suggestions and see which works best. I'll try to report back in a
few days. Cheers!
--j
2012/5/3 Jens Oehlschlägel jens.oehlschlae...@truecluster.com
Jonathan,
On some filesystems (e.g. NTFS, see below) it is possible to create
'sparse' memory-mapped files, i.e. reserving the space without the cost of
actually writing initial values.
Package 'ff' does this automatically and also allows to access the file
in parallel. Check the example below and see how big file creation is
immediate.
Jens Oehlschlägel
library(ff)
library(snowfall)
ncpus - 2
n - 1e8
system.time(
+ x - ff(vmode=double, length=n, filename=c:/Temp/x.ff)
+ )
User System verstrichen
0.010.000.02
# check finalizer, with an explicit filename we should have a 'close'
finalizer
finalizer(x)
[1] close
# if not, set it to 'close' inorder to not let slaves delete x on slave
shutdown
finalizer(x) - close
sfInit(parallel=TRUE, cpus=ncpus, type=SOCK)
R Version: R version 2.15.0 (2012-03-30)
snowfall 1.84 initialized (using snow 0.3-9): parallel execution on 2
CPUs.
sfLibrary(ff)
Library ff loaded.
Library ff loaded in cluster.
Warnmeldung:
In library(package = ff, character.only = TRUE, pos = 2, warn.conflicts
= TRUE, :
'keep.source' is deprecated and will be ignored
sfExport(x) # note: do not export the same ff multiple times
# explicitely opening avoids a gc problem
sfClusterEval(open(x, caching=mmeachflush)) # opening with
'mmeachflush' inststead of 'mmnoflush' is a bit slower but prevents OS
write storms when the file is larger than RAM
[[1]]
[1] TRUE
[[2]]
[1] TRUE
system.time(
+ sfLapply( chunk(x, length=ncpus), function(i){
+ x[i] - runif(sum(i))
+ invisible()
+ })
+ )
User System verstrichen
0.000.00 30.78
system.time(
+ s - sfLapply( chunk(x, length=ncpus), function(i) quantile(x[i],
c(0.05, 0.95)) )
+ )
User System verstrichen
0.000.004.38
# for completeness
sfClusterEval(close(x))
[[1]]
[1] TRUE
[[2]]
[1] TRUE
csummary(s)
5% 95%
Min.0.04998 0.95
1st Qu. 0.04999 0.95
Median 0.05001 0.95
Mean0.05001 0.95
3rd Qu. 0.05002 0.95
Max.0.05003 0.95
# stop slaves
sfStop()
Stopping cluster
# with the close finalizer we are responsible for deleting the file
explicitely (unless we want to keep it)
delete(x)
[1] TRUE
# remove r-side metadata
rm(x)
# truly free memory
gc()
*Gesendet:* Donnerstag, 03. Mai 2012 um 00:23 Uhr
*Von:* Jonathan Greenberg j...@illinois.edu
*An:* r-help r-help@r-project.org, r-sig-...@r-project.org
*Betreff:* [R-sig-hpc] Quickest way to make a large empty file on
disk?
R-helpers:
What would be the absolute fastest way to make a large empty file (e.g.
filled with all zeroes) on disk, given a byte size and a given number
number of empty values. I know I can use writeBin, but the object in
this case may be far too large to store in main memory. I'm asking because
I'm going to use this file in conjunction with mmap to do parallel writes
to this file. Say, I want to create a blank file of 10,000 floating point
numbers.
Thanks!
--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
[[alternative HTML version deleted]]
___
R-sig-hpc mailing list
r-sig-...@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-hpc
--
Jonathan A. Greenberg, PhD
Assistant Professor
Department of Geography and Geographic Information Science
University
[R] Dummies guide to getting HPC working on R
R-folks: Sorry for the cross-posting, but I wanted to share a link to a (fairly long) blog post I created which tries to take the mystery out of getting R setup for doing high performance/parallel computing if you have to compile R from scratch: http://lostingeospace.blogspot.com/2012/06/r-and-hpc-blas-mpi-in-linux-environment.html Let me know if you have any comments/corrections on it. Cheers! --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.
[R] Dummies guide to getting HPC working on R
R-folks. Sorry for the cross-posting, but I wanted to share a link to a (fairly long) blog post I created which tries to take the mystery out of getting R setup for doing high performance/parallel computing if you have to compile R from scratch: http://lostingeospace.blogspot.com/2012/06/r-and-hpc-blas-mpi-in-linux-environment.html Let me know if you have any comments/corrections on it. Cheers! --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.
Re: [R] [R-sig-hpc] Quickest way to make a large empty file on disk?
Thanks, all! I'll try these out. I'm trying to work up something that is
platform independent (if possible) for use with mmap. I'll do some tests
on these suggestions and see which works best. I'll try to report back in a
few days. Cheers!
--j
2012/5/3 Jens Oehlschlägel jens.oehlschlae...@truecluster.com
Jonathan,
On some filesystems (e.g. NTFS, see below) it is possible to create
'sparse' memory-mapped files, i.e. reserving the space without the cost of
actually writing initial values.
Package 'ff' does this automatically and also allows to access the file in
parallel. Check the example below and see how big file creation is
immediate.
Jens Oehlschlägel
library(ff)
library(snowfall)
ncpus - 2
n - 1e8
system.time(
+ x - ff(vmode=double, length=n, filename=c:/Temp/x.ff)
+ )
User System verstrichen
0.010.000.02
# check finalizer, with an explicit filename we should have a 'close'
finalizer
finalizer(x)
[1] close
# if not, set it to 'close' inorder to not let slaves delete x on slave
shutdown
finalizer(x) - close
sfInit(parallel=TRUE, cpus=ncpus, type=SOCK)
R Version: R version 2.15.0 (2012-03-30)
snowfall 1.84 initialized (using snow 0.3-9): parallel execution on 2 CPUs.
sfLibrary(ff)
Library ff loaded.
Library ff loaded in cluster.
Warnmeldung:
In library(package = ff, character.only = TRUE, pos = 2, warn.conflicts
= TRUE, :
'keep.source' is deprecated and will be ignored
sfExport(x) # note: do not export the same ff multiple times
# explicitely opening avoids a gc problem
sfClusterEval(open(x, caching=mmeachflush)) # opening with
'mmeachflush' inststead of 'mmnoflush' is a bit slower but prevents OS
write storms when the file is larger than RAM
[[1]]
[1] TRUE
[[2]]
[1] TRUE
system.time(
+ sfLapply( chunk(x, length=ncpus), function(i){
+ x[i] - runif(sum(i))
+ invisible()
+ })
+ )
User System verstrichen
0.000.00 30.78
system.time(
+ s - sfLapply( chunk(x, length=ncpus), function(i) quantile(x[i],
c(0.05, 0.95)) )
+ )
User System verstrichen
0.000.004.38
# for completeness
sfClusterEval(close(x))
[[1]]
[1] TRUE
[[2]]
[1] TRUE
csummary(s)
5% 95%
Min.0.04998 0.95
1st Qu. 0.04999 0.95
Median 0.05001 0.95
Mean0.05001 0.95
3rd Qu. 0.05002 0.95
Max.0.05003 0.95
# stop slaves
sfStop()
Stopping cluster
# with the close finalizer we are responsible for deleting the file
explicitely (unless we want to keep it)
delete(x)
[1] TRUE
# remove r-side metadata
rm(x)
# truly free memory
gc()
*Gesendet:* Donnerstag, 03. Mai 2012 um 00:23 Uhr
*Von:* Jonathan Greenberg j...@illinois.edu
*An:* r-help r-help@r-project.org, r-sig-...@r-project.org
*Betreff:* [R-sig-hpc] Quickest way to make a large empty file on disk?
R-helpers:
What would be the absolute fastest way to make a large empty file (e.g.
filled with all zeroes) on disk, given a byte size and a given number
number of empty values. I know I can use writeBin, but the object in
this case may be far too large to store in main memory. I'm asking because
I'm going to use this file in conjunction with mmap to do parallel writes
to this file. Say, I want to create a blank file of 10,000 floating point
numbers.
Thanks!
--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
[[alternative HTML version deleted]]
___
R-sig-hpc mailing list
r-sig-...@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-hpc
--
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.
[R] Quickest way to make a large empty file on disk?
R-helpers: What would be the absolute fastest way to make a large empty file (e.g. filled with all zeroes) on disk, given a byte size and a given number number of empty values. I know I can use writeBin, but the object in this case may be far too large to store in main memory. I'm asking because I'm going to use this file in conjunction with mmap to do parallel writes to this file. Say, I want to create a blank file of 10,000 floating point numbers. Thanks! --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 [[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] Solve an ordinary or generalized eigenvalue problem in R?
Building in Berend's suggestions I think this function should work for most
people (I'm going to wrap it into a package but figured people may want to
grab this directly):
# Please see http://www.netlib.org/lapack/double/dggev.f for a description
of inputs and outputs.
Rdggev - function(A,B,JOBVL=FALSE,JOBVR=TRUE)
{
# R implementation of the DGGEV LAPACK function (with generalized
eigenvalue computation)
# See http://www.netlib.org/lapack/double/dggev.f
# coded by Jonathan A. Greenberg i...@estarcion.net
# Contributions from Berend Hasselman.
if( .Platform$OS.type == windows ) {
Lapack.so -
file.path(R.home(bin),paste(Rlapack,.Platform$dynlib.ext,sep=))
} else {
Lapack.so -
file.path(R.home(modules),paste(lapack,.Platform$dynlib.ext,sep=))
}
dyn.load(Lapack.so)
if(JOBVL)
{
JOBVL=V
} else
{
JOBVL=N
}
if(JOBVR)
{
JOBVR=V
} else
{
JOBVR=N
}
if(!is.matrix(A)) stop(Argument A should be a matrix)
if(!is.matrix(B)) stop(Argument B should be a matrix)
dimA - dim(A)
if(dimA[1]!=dimA[2]) stop(A must be a square matrix)
dimB - dim(B)
if(dimB[1]!=dimB[2]) stop(B must be a square matrix)
if(dimA[1]!=dimB[1]) stop(A and B must have the same dimensions)
if( is.complex(A) ) stop(A may not be complex)
if( is.complex(B) ) stop(B may not be complex)
# Input parameters
N=dim(A)[[1]]
LDA=N
LDB=N
LDVL=N
LDVR=N
LWORK=as.integer(max(1,8*N))
Rdggev_out - .Fortran(dggev, JOBVL, JOBVR, N, A, LDA, B, LDB,
double(N), double(N), double(N),
array(data=0,dim=c(LDVL,N)), LDVL, array(data=0,dim=c(LDVR,N)), LDVR,
double(max(1,LWORK)), LWORK, integer(1))
names(Rdggev_out)=c(JOBVL,JOBVR,N,A,LDA,B,LDB,ALPHAR,ALPHAI,
BETA,VL,LDVL,VR,LDVR,WORK,LWORK,INFO)
# simplistic calculation of eigenvalues (see caveat in
http://www.netlib.org/lapack/double/dggev.f)
if( all(Rdggev_out$ALPHAI==0) )
Rdggev_out$GENEIGENVALUES - Rdggev_out$ALPHAR/Rdggev_out$BETA
else
Rdggev_out$GENEIGENVALUES - complex(real=Rdggev_out$ALPHAR,
imaginary=Rdggev_out$ALPHAI)/Rdggev_out$BETA
return(Rdggev_out)
}
Thanks!
--j
On Sun, Apr 22, 2012 at 2:27 PM, Berend Hasselman b...@xs4all.nl wrote:
On 22-04-2012, at 21:08, Jonathan Greenberg wrote:
Thanks all (particularly to you, Berend) -- I'll push forward with these
solutions and integrate them into my code. I did come across geigen while
rooting around in the CCA code but its not formally documented (it just
says for internal use or something along those lines) and as you found
out above, it does not produce the same solution as the dggev. It would be
nice to have a more complete set of formal packages for doing LA in R
(rather than having to hand-write .Fortran calls) but I'll leave that to
someone with more expertise in linear algebra than me. Something that
perhaps matches the SciPy set of functions (both in terms of input and
output):
http://docs.scipy.org/doc/scipy/reference/linalg.html
Some of these are already implemented, but clearly not all of them.
Package CCA has package fda as dependency.
And package fda defines a function geigen.
The first 14 lines of this function are
geigen - function(Amat, Bmat, Cmat)
{
# solve the generalized eigenanalysis problem
#
#max {tr L'AM / sqrt[tr L'BL tr M'CM] w.r.t. L and M
#
# Arguments:
# AMAT ... p by q matrix
# BMAT ... order p symmetric positive definite matrix
# CMAT ... order q symmetric positive definite matrix
# Returns:
# VALUES ... vector of length s = min(p,q) of eigenvalues
# LMAT ... p by s matrix L
# MMAT ... q by s matrix M
It's not clear to me how it is used and exactly what it is doing and how
that compares with Lapack.
Berend
--
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
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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] Solve an ordinary or generalized eigenvalue problem in R?
Thanks all (particularly to you, Berend) -- I'll push forward with these solutions and integrate them into my code. I did come across geigen while rooting around in the CCA code but its not formally documented (it just says for internal use or something along those lines) and as you found out above, it does not produce the same solution as the dggev. It would be nice to have a more complete set of formal packages for doing LA in R (rather than having to hand-write .Fortran calls) but I'll leave that to someone with more expertise in linear algebra than me. Something that perhaps matches the SciPy set of functions (both in terms of input and output): http://docs.scipy.org/doc/scipy/reference/linalg.html Some of these are already implemented, but clearly not all of them. --j On Sat, Apr 21, 2012 at 1:31 PM, Berend Hasselman b...@xs4all.nl wrote: On 21-04-2012, at 20:20, peter dalgaard wrote: The eigenvalues are identical upto the printed 9 digits but the eigenvectors appear to be quite different. Maybe this is what Luke meant. Berend They look quite similar to me: ev - eigen(solve(B,A) )$vectors ge - geigen(A, B, TRUE , TRUE) ev / ge$vl [,1] [,2] [,3] [1,] 0.9324603 0.813422 -0.7423694 [2,] 0.9324603 0.813422 -0.7423694 [3,] 0.9324603 0.813422 -0.7423694 ev / ge$vr [,1] [,2] [,3] [1,] 0.9324603 0.813422 -0.7423694 [2,] 0.9324603 0.813422 -0.7423694 [3,] 0.9324603 0.813422 -0.7423694 (and of course, eigenvectors of any sort are only defined up to a constant multiplier) Correct. I should have checked your way and not optically. Berend __ 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] Solve an ordinary or generalized eigenvalue problem in R?
So I am a complete noob at doing this type of linking. When I write this statement (all the input values are assigned, but I have to confess I don't know what to do with the output variables -- in this call they are all assigned NA): .Call(La_dgeev, JOBVL, JOBVR, N, A, LDA, B, LDB, ALPHAR=NA, ALPHAI=NA, BETA=NA, + VL=NA, LDVL, VR=NA, LDVR, WORK=NA, LWORK, INFO=NA, PACKAGE=base) I get: Error in .Call(La_dgeev, JOBVL, JOBVR, N, A, LDA, B, LDB, ALPHAR = NA, : C symbol name La_dgeev not in DLL for package base I'm running this on Windows 7 x64 version of R 2.14.2. The R_ext/Lapack.h file states: /* DGEEV - compute for an N-by-N real nonsymmetric matrix A, the */ /* eigenvalues and, optionally, the left and/or right eigenvectors */ La_extern void F77_NAME(dgeev)(const char* jobvl, const char* jobvr, const int* n, double* a, const int* lda, double* wr, double* wi, double* vl, const int* ldvl, double* vr, const int* ldvr, double* work, const int* lwork, int* info); Any ideas? --j On Fri, Apr 20, 2012 at 1:37 AM, Berend Hasselman b...@xs4all.nl wrote: On 19-04-2012, at 20:50, Jonathan Greenberg wrote: Folks: I'm trying to port some code from python over to R, and I'm running into a wall finding R code that can solve a generalized eigenvalue problem following this function model: http://docs.scipy.org/doc/scipy/reference/generated/scipy.linalg.eig.html Any ideas? I don't want to call python from within R for various reasons, I'd prefer a native R solution if one exists. Thanks! An old thread is here: http://tolstoy.newcastle.edu.au/R/help/05/06/6802.html R does provide eigen(). R has the Lapack routines dggev and dgges in its library. You'd have to write your own .Fortran interface to those routines. Berend -- 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] Solve an ordinary or generalized eigenvalue problem in R?
Incidentally, if you want to test this out: A [,1] [,2] [,3] [1,] 1457.738 1053.181 1256.953 [2,] 1053.181 1213.728 1302.838 [3,] 1256.953 1302.838 1428.269 B [,1] [,2] [,3] [1,] 4806.033 1767.480 2622.744 [2,] 1767.480 3353.603 3259.680 [3,] 2622.744 3259.680 3476.790 I THINK this is correct for the other parameters: JOBVL=N JOBVR=N N=dim(A)[[1]] LDA=N LDB=N LDVL=N LDVR=N LWORK=max(1,8*N) .Call(La_dgeev, JOBVL, JOBVR, N, A, LDA, B, LDB, ALPHAR=NA, ALPHAI=NA, BETA=NA, VL=NA, LDVL, VR=NA, LDVR, WORK=NA, LWORK, INFO=NA, PACKAGE=base) LAPACK's documentation is: http://www.netlib.org/lapack/double/dggev.f --j On Fri, Apr 20, 2012 at 11:58 AM, Jonathan Greenberg j...@illinois.eduwrote: So I am a complete noob at doing this type of linking. When I write this statement (all the input values are assigned, but I have to confess I don't know what to do with the output variables -- in this call they are all assigned NA): .Call(La_dgeev, JOBVL, JOBVR, N, A, LDA, B, LDB, ALPHAR=NA, ALPHAI=NA, BETA=NA, + VL=NA, LDVL, VR=NA, LDVR, WORK=NA, LWORK, INFO=NA, PACKAGE=base) I get: Error in .Call(La_dgeev, JOBVL, JOBVR, N, A, LDA, B, LDB, ALPHAR = NA, : C symbol name La_dgeev not in DLL for package base I'm running this on Windows 7 x64 version of R 2.14.2. The R_ext/Lapack.h file states: /* DGEEV - compute for an N-by-N real nonsymmetric matrix A, the */ /* eigenvalues and, optionally, the left and/or right eigenvectors */ La_extern void F77_NAME(dgeev)(const char* jobvl, const char* jobvr, const int* n, double* a, const int* lda, double* wr, double* wi, double* vl, const int* ldvl, double* vr, const int* ldvr, double* work, const int* lwork, int* info); Any ideas? --j On Fri, Apr 20, 2012 at 1:37 AM, Berend Hasselman b...@xs4all.nl wrote: On 19-04-2012, at 20:50, Jonathan Greenberg wrote: Folks: I'm trying to port some code from python over to R, and I'm running into a wall finding R code that can solve a generalized eigenvalue problem following this function model: http://docs.scipy.org/doc/scipy/reference/generated/scipy.linalg.eig.html Any ideas? I don't want to call python from within R for various reasons, I'd prefer a native R solution if one exists. Thanks! An old thread is here: http://tolstoy.newcastle.edu.au/R/help/05/06/6802.html R does provide eigen(). R has the Lapack routines dggev and dgges in its library. You'd have to write your own .Fortran interface to those routines. Berend -- 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 -- 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] Solve an ordinary or generalized eigenvalue problem in R?
Ok, I figured out a solution and I'd like to get some feedback on this from
the R-helpers as to how I could modify the following to be package
friendly -- the main thing I'm worried about is how to dynamically set the
dyn.load statement below correctly (obviously, its hard coded to my
particular install, and would only work with windows since I'm using a
.dll):
Rdggev - function(JOBVL=F,JOBVR=T,A,B)
{
# R implementation of the DGGEV LAPACK function (with generalized
eigenvalue computation)
# See http://www.netlib.org/lapack/double/dggev.f
# coded by Jonathan A. Greenberg j...@illinois.edu
dyn.load(C:\\Program Files\\R\\R-2.14.2\\bin\\x64\\Rlapack.dll)
if(JOBVL)
{
JOBVL=V
} else
{
JOBVL=N
}
if(JOBVR)
{
JOBVR=V
} else
{
JOBVR=N
}
# Note, no error checking is performed.
# Input parameters
N=dim(A)[[1]]
LDA=N
LDB=N
LDVL=N
LDVR=N
LWORK=as.integer(max(1,8*N))
Rdggev_out - .Fortran(dggev, JOBVL, JOBVR, N, A, LDA, B, LDB,
double(N), double(N), double(N),
array(data=0,dim=c(LDVL,N)), LDVL, array(data=0,dim=c(LDVR,N)), LDVR,
double(max(1,LWORK)), LWORK, integer(1))
names(Rdggev_out)=c(JOBVL,JOBVR,N,A,LDA,B,LDB,ALPHAR,ALPHAI,
BETA,VL,LDVL,VR,LDVR,WORK,LWORK,INFO)
Rdggev_out$GENEIGENVALUES=(Rdggev_out$ALPHAR+Rdggev_out$ALPHAI)/Rdggev_out$BETA
return(Rdggev_out)
}
On Fri, Apr 20, 2012 at 12:01 PM, Jonathan Greenberg j...@illinois.eduwrote:
Incidentally, if you want to test this out:
A
[,1] [,2] [,3]
[1,] 1457.738 1053.181 1256.953
[2,] 1053.181 1213.728 1302.838
[3,] 1256.953 1302.838 1428.269
B
[,1] [,2] [,3]
[1,] 4806.033 1767.480 2622.744
[2,] 1767.480 3353.603 3259.680
[3,] 2622.744 3259.680 3476.790
I THINK this is correct for the other parameters:
JOBVL=N
JOBVR=N
N=dim(A)[[1]]
LDA=N
LDB=N
LDVL=N
LDVR=N
LWORK=max(1,8*N)
.Call(La_dgeev, JOBVL, JOBVR, N, A, LDA, B, LDB, ALPHAR=NA, ALPHAI=NA,
BETA=NA,
VL=NA, LDVL, VR=NA, LDVR, WORK=NA, LWORK, INFO=NA, PACKAGE=base)
LAPACK's documentation is:
http://www.netlib.org/lapack/double/dggev.f
--j
On Fri, Apr 20, 2012 at 11:58 AM, Jonathan Greenberg j...@illinois.eduwrote:
So I am a complete noob at doing this type of linking. When I write this
statement (all the input values are assigned, but I have to confess I don't
know what to do with the output variables -- in this call they are all
assigned NA):
.Call(La_dgeev, JOBVL, JOBVR, N, A, LDA, B, LDB, ALPHAR=NA, ALPHAI=NA,
BETA=NA,
+ VL=NA, LDVL, VR=NA, LDVR, WORK=NA, LWORK, INFO=NA, PACKAGE=base)
I get:
Error in .Call(La_dgeev, JOBVL, JOBVR, N, A, LDA, B, LDB, ALPHAR = NA,
:
C symbol name La_dgeev not in DLL for package base
I'm running this on Windows 7 x64 version of R 2.14.2. The
R_ext/Lapack.h file states:
/* DGEEV - compute for an N-by-N real nonsymmetric matrix A, the */
/* eigenvalues and, optionally, the left and/or right eigenvectors */
La_extern void
F77_NAME(dgeev)(const char* jobvl, const char* jobvr,
const int* n, double* a, const int* lda,
double* wr, double* wi, double* vl, const int* ldvl,
double* vr, const int* ldvr,
double* work, const int* lwork, int* info);
Any ideas?
--j
On Fri, Apr 20, 2012 at 1:37 AM, Berend Hasselman b...@xs4all.nl wrote:
On 19-04-2012, at 20:50, Jonathan Greenberg wrote:
Folks:
I'm trying to port some code from python over to R, and I'm running
into a
wall finding R code that can solve a generalized eigenvalue problem
following this function model:
http://docs.scipy.org/doc/scipy/reference/generated/scipy.linalg.eig.html
Any ideas? I don't want to call python from within R for various
reasons,
I'd prefer a native R solution if one exists. Thanks!
An old thread is here:
http://tolstoy.newcastle.edu.au/R/help/05/06/6802.html
R does provide eigen().
R has the Lapack routines dggev and dgges in its library.
You'd have to write your own .Fortran interface to those routines.
Berend
--
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
--
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
--
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
Re: [R] Solve an ordinary or generalized eigenvalue problem in R?
My apologies: When reviewing my initial email I made a typo -- what I needed was dggev, not dgeev. I have confirmed that my function reproduces the scipy outputs I mentioned in my first email. The function is part of lapack. I'm not an R noob, I just haven't dealt with external Fortran or C calls before. The reason I need it is that I am trying to port an existing python/IDL algorithm to R (iMad/RADCAL, located at http://mcanty.homepage.t-online.de/software.html). The algorithm is fairly complex so I'm trying to reproduce it line-by-line as closely as possible before going back and improving its efficiency using various R functions (checking the inputs and the outputs between R and the python code each step). This algorithm does a weighted canonical correlation analysis which does not apparently exist in other CCA R packages. So, my main question at this point is given I can call dggev via .Fortran() and get the outputs I want, what is the best way to package this up with a dyn.load() statement that would work on any R install that has the lapack libraries available to it? --j Yes. Stop this. You are completely on the wrong track and getting yourself into a real muddle. 1. you are mixing up dgeev and dggev. You are using the dggev arguments to call dgeev. Even if you got it all correct this would result in nasty errors. 2. La_dgeev doesn't exist in the R sources (nor does it exist in Lapack) and you don't need to use dgeev. See below. Since you are a noob I would advise you to not try and interface with Fortran or C at this moment. It is possible to interface with dggev for generalized eigenvalues but it is not a straightforward and easy job to do. I've had a look at the R and C code used in the R sources to interface with dgeev. It would need a lot of TLC. As I told you before: R provides a function eigen for calculating normal eigenvalues end eigenvectors. It's probably a good idea to explain why you need generalized eigenvalues. Then someone may be able to come up with suggestions and/or alternatives. Berend -- 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.
[R] Solve an ordinary or generalized eigenvalue problem in R?
Folks: I'm trying to port some code from python over to R, and I'm running into a wall finding R code that can solve a generalized eigenvalue problem following this function model: http://docs.scipy.org/doc/scipy/reference/generated/scipy.linalg.eig.html Any ideas? I don't want to call python from within R for various reasons, I'd prefer a native R solution if one exists. Thanks! --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 [[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] Listing the contents of an FTP directory via R?
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.
Re: [R] Listing the contents of an FTP directory via R?
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 __ 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?
It seems to be choking on NLST: require(RCurl) getURL(ftp://e4ftl01.cr.usgs.gov/MOTA/MCD15A3.005/,verbose=TRUE,ftp.use.epsv=TRUE, dirlistonly = TRUE) ... 230 Guest login ok, access restrictions apply. PWD 257 / is current directory. * Entry path is '/' CWD MOTA 250 CWD command successful. CWD MCD15A3.005 250 CWD command successful. EPSV * Connect data stream passively 500 'EPSV': command not understood. * disabling EPSV usage PASV 227 Entering Passive Mode (152,61,133,5,177,17) * Trying 152.61.133.5... * connected * Connecting to 152.61.133.5 (152.61.133.5) port 45329 TYPE A 200 Type set to A. NLST 550 No files found. * RETR response: 550 * Remembering we are in dir MOTA/MCD15A3.005/ * Connection #0 to host e4ftl01.cr.usgs.gov left intact Error in function (type, msg, asError = TRUE) : RETR response: 550 Thanks for looking into this! --j On Mon, Apr 9, 2012 at 1:45 PM, steven mosher mosherste...@gmail.com wrote: 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.edu wrote: 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 -- 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.
[R] Best way to search r- functions and mailing list?
R-helpers: It looks like http://finzi.psych.upenn.edu/search.html has stopped spidering the mailing lists -- this used to be my go-to site for searching for R solutions. Are there any good replacements for this? I want to be able to search both functions and mailing lists at the same time. Cheers! --j -- Jonathan A. Greenberg, PhD Assistant Professor Department of Geography 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.
[R] Parallel writes in R
R-helpers: I'm curious what support R has for parallel writes to a binary file? If I want to use snow to have each node write different rows of a flat binary file (possibly out of sequence), are there any tricks/issues I should be aware of? --j -- Jonathan A. Greenberg, PhD Assistant Professor Department of Geography 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.
[R] Ignoring version numbers when installing packages...
R-helpers: I'm trying to install a package from r-forge, and I'm wondering if there is a way to force R to install a package, even if the package requires a certain version of R (short of modifying the DESCRIPTION file)? Cheers! --j -- Jonathan A. Greenberg, PhD Assistant Professor Department of Geography 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.
Re: [R] Ignoring version numbers when installing packages...
Follow-up: r-forge seems to have some weirdnesses with version numbers, and since this is an incubation site, there are occasions where the version numbers were put in based on whatever the programmer was using at a time (e.g. other versions were simply not tested, so they erred on the safe side). I understand that the internals may have changed, but I would argue that 9/10 times if something is working on R 2.14.1 but not 2.14.2 it has nothing to do with some incompatibility, just that the package hasn't been updated in some time and tested against the new version. So, to follow-up, the only way to override the version installation check is to modify the DESCRIPTION file? There's no flag either in install.packages() or R CMD INSTALL that will force the installation even if the version check fails? --j On Fri, Mar 30, 2012 at 11:41 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 30/03/2012 12:05 PM, Jonathan Greenberg wrote: R-helpers: I'm trying to install a package from r-forge, and I'm wondering if there is a way to force R to install a package, even if the package requires a certain version of R (short of modifying the DESCRIPTION file)? Cheers! You don't give details, so the explanation is uncertain, but the answer is clear: don't do that. If you are trying to install a binary build, don't do that. It might appear to work but fail in messy ways if you use it in the wrong version of R. Some packages link to R internals, and those might have changed. If you are trying to install from source, but the author said you need a particular version of R, then you could modify the DESCRIPTION file: but presumably the author had a reason to ask for a particular version, so don't do that either. Duncan Murdoch -- Jonathan A. Greenberg, PhD Assistant Professor Department of Geography 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.
[R] Creating a list from all combinations of two lists
R-helpers: Say I have two lists of arbitrary elements, e.g.: list1=list(c(1:3),R is fun!,c(3:6)) list2=list(c(10:5),c(5:3),c(13,5),I am so confused) I would like to produce a single new list that is composed of all combinations of the top level of list1 and list2, e.g.: listcombo=list(list(list1[[1]],list2[[1]]),list(list1[[1]],list2[[2]] ),...,list(list1[[length(list1)]],list2[[length(list2]])) What is the most efficient way to do this? Thanks! --j -- Jonathan A. Greenberg, PhD Assistant Professor Department of Geography 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.
[R] How do I query ... in a function call?
This is probably a very noobish question, but if I want to create a
function that allows an undetermined number of, say, numeric vectors to be
fed to it, I would use:
myfunction = function(...)
{
# Do something
}
Right? If so, how do I a) count the number of vectors fed to the
function, and b) how do I treat those vectors as variables, e.g. for the
call:
myfunction(c(1:10),c(2:11),c(3:13))
Thanks!
--j
--
Jonathan A. Greenberg, PhD
Assistant Professor
Department of Geography
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]]
__
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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.
[R] Setting hostname in the .Renvironment
This is a follow-up to a question I asked a few years back. We have a pair of computers that share a common home directory (and therefor a common .Renviron) with identical hardware, but very different sets of libraries such that using a shared R_LIBS between two computers does not work. They both use this as the default library for user installations: '~/R/x86_64-pc-linux-gnu-library/2.13' I would like to mod the .Renviron in such a way so '~/R/hostname-1/x86_64-pc-linux-gnu-library/2.13' '~/R/hostname-2/x86_64-pc-linux-gnu-library/2.13' How can I modify my R_LIBS_USER in the .Renviron to match this? The hostname would need to be dynamically set based on which computer I log into, but I tried something like this: R_LIBS_USER=~/lib/R/library/$HOSTNAME_%p_%a_%o_R%V and R did not resolve the $HOSTNAME environment variable even though I can (from bash) echo $HOSTNAME and it return the correct name. Thoughts? Thanks! --j -- Jonathan A. Greenberg, PhD Assistant Professor Department of Geography 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.
[R] setMethods/setGeneric problem when R CMD CHECK'ing a package
R-helpers:
I'm trying to build a package, but I'm a bit new to the whole S3/S4
methods concept. I'm trying to add a new definition of the zoo
function as.yearmon, but I'm getting the following error when it
gets to this point during a package install:
***
R CMD INSTALL STARStools
* installing to library
‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library’
WARNING: omitting pointless dependence on 'R' without a version requirement
* installing *source* package ‘STARStools’ ...
** R
** inst
** preparing package for lazy loading
Loading required package: sp
raster version 1.9-5 (28-July-2011)
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 1.8.0, released 2011/01/12
Path to GDAL shared files:
/Library/Frameworks/GDAL.framework/Versions/1.8/Resources/gdal
Loaded PROJ.4 runtime: Rel. 4.7.1, 23 September 2009
Path to PROJ.4 shared files: (autodetected)
Attaching package: 'zoo'
The following object(s) are masked from 'package:base':
as.Date
Creating a new generic function for as.Date in STARStools
Creating a new generic function for as.list in STARStools
Error in setGeneric(f, where = where) :
must supply a function skeleton, explicitly or via an existing function
Error : unable to load R code in package 'STARStools'
ERROR: lazy loading failed for package ‘STARStools’
* removing
‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library/STARStools’
* restoring previous
‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library/STARStools’
***
# Note that these require statements do not appear in the code, but
appear in the DESCRIPTION file:
require(sp)
require(zoo)
# Here are the class definitions (filename AAAclassdefinitions.R):
setClass(SpatialPointsDataFrameList,representation(list=list),contains=c(SpatialPointsDataFrame))
setClass(SpatialPointsDataFrameListZoo,contains=c(SpatialPointsDataFrameList))
# And here is where it is getting hung up. filename
as.yearmon.SpatialPointsDataFrameListZoo_SpatialPointsDataFrameListZoo.R
setMethod(as.yearmon,
signature(x = SpatialPointsDataFrameListZoo),
as.yearmon.SpatialPointsDataFrameListZoo
)
# Filename as.yearmon.SpatialPointsDataFrameListZoo.R
as.yearmon.SpatialPointsDataFrameListZoo=function(x,...)
{
newlist=mapply(zoo:::as.yearmon,x@list,MoreArgs=list(...),simplify=FALSE)
x@list=newlist
return(x)
}
Thoughts?
--j
--
Jonathan A. Greenberg, PhD
Assistant Project Scientist
Center for Spatial Technologies and Remote Sensing (CSTARS)
Department of Land, Air and Water Resources
University of California, Davis
One Shields Avenue
Davis, CA 95616
Phone: 415-763-5476
AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307
__
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] Easier ways to create .Rd files?
Thanks Kevin! Got started with roxygen tonight! Cheers! On Tue, Aug 23, 2011 at 6:28 PM, Kevin Wright kw.s...@gmail.com wrote: I like the roxygen2 package for combining code and documentation. If you use Emacs + ESS, it will even create much of the roxygen code for you (and auto-revise it if you change the function arguments). Kevin Wright On Tue, Aug 23, 2011 at 6:55 PM, Jonathan Greenberg greenb...@ucdavis.edu wrote: R-helpers: Are there any ways to auto-generate R-friendly (e.g. will pass a compilation check) .Rd files given a set of .R code? How about GUIs that help properly format the .Rd files? Thanks! I want a basic set of .Rd files that I can update as I go, but as with most things my documentation typically lags behind my coding by a few days. --j -- Jonathan A. Greenberg, PhD Assistant Project Scientist Center for Spatial Technologies and Remote Sensing (CSTARS) Department of Land, Air and Water Resources University of California, Davis One Shields Avenue Davis, CA 95616 Phone: 415-763-5476 AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307 __ 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 Project Scientist Center for Spatial Technologies and Remote Sensing (CSTARS) Department of Land, Air and Water Resources University of California, Davis One Shields Avenue Davis, CA 95616 Phone: 415-763-5476 AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307 __ 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] setMethods/setGeneric problem when R CMD CHECK'ing a package
Hmm, so I moved the function call to the same file as the methods
call, and placed it above the method in the file -- but I'm getting
the same error. Is there something odd about as.yearmon in the zoo
package that it might not be getting defined as a generic function?
If so, how would I go about creating a generic?
setGeneric(as.yearmon) doesn't seem to cut it.
Here's the new file contents:
as.yearmon.SpatialPointsDataFrameListZoo=function(x,...)
{
newlist=mapply(zoo:::as.yearmon,x@list,MoreArgs=list(...),simplify=FALSE)
x@list=newlist
return(x)
}
setMethod(as.yearmon,
signature(x = SpatialPointsDataFrameListZoo),
as.yearmon.SpatialPointsDataFrameListZoo
)
--j
2011/8/24 Uwe Ligges lig...@statistik.tu-dortmund.de:
On 24.08.2011 10:30, Jonathan Greenberg wrote:
R-helpers:
I'm trying to build a package, but I'm a bit new to the whole S3/S4
methods concept. I'm trying to add a new definition of the zoo
function as.yearmon, but I'm getting the following error when it
gets to this point during a package install:
Thhis seesm more appropiate for the R-devel rather than the R-help list.
Anyway, see below.
***
R CMD INSTALL STARStools
* installing to library
‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library’
WARNING: omitting pointless dependence on 'R' without a version
requirement
* installing *source* package ‘STARStools’ ...
** R
** inst
** preparing package for lazy loading
Loading required package: sp
raster version 1.9-5 (28-July-2011)
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 1.8.0, released 2011/01/12
Path to GDAL shared files:
/Library/Frameworks/GDAL.framework/Versions/1.8/Resources/gdal
Loaded PROJ.4 runtime: Rel. 4.7.1, 23 September 2009
Path to PROJ.4 shared files: (autodetected)
Attaching package: 'zoo'
The following object(s) are masked from 'package:base':
as.Date
Creating a new generic function for as.Date in STARStools
Creating a new generic function for as.list in STARStools
Error in setGeneric(f, where = where) :
must supply a function skeleton, explicitly or via an existing function
Error : unable to load R code in package 'STARStools'
ERROR: lazy loading failed for package ‘STARStools’
* removing
‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library/STARStools’
* restoring previous
‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library/STARStools’
***
# Note that these require statements do not appear in the code, but
appear in the DESCRIPTION file:
require(sp)
require(zoo)
??? Not valid in the DESCRIPTION file. Either use this in your code or
import from the corresponding Namespaces which you will have to do anyway
for the next R release.
# Here are the class definitions (filename AAAclassdefinitions.R):
setClass(SpatialPointsDataFrameList,representation(list=list),contains=c(SpatialPointsDataFrame))
setClass(SpatialPointsDataFrameListZoo,contains=c(SpatialPointsDataFrameList))
# And here is where it is getting hung up. filename
as.yearmon.SpatialPointsDataFrameListZoo_SpatialPointsDataFrameListZoo.R
setMethod(as.yearmon,
signature(x = SpatialPointsDataFrameListZoo),
as.yearmon.SpatialPointsDataFrameListZoo
)
You try to register the method pointing to a function definition that does
not exist at this point (since you define it below). Just move the
definition up.
Uwe Ligges
# Filename as.yearmon.SpatialPointsDataFrameListZoo.R
as.yearmon.SpatialPointsDataFrameListZoo=function(x,...)
{
newlist=mapply(zoo:::as.yearmon,x@list,MoreArgs=list(...),simplify=FALSE)
x@list=newlist
return(x)
}
Thoughts?
--j
--
Jonathan A. Greenberg, PhD
Assistant Project Scientist
Center for Spatial Technologies and Remote Sensing (CSTARS)
Department of Land, Air and Water Resources
University of California, Davis
One Shields Avenue
Davis, CA 95616
Phone: 415-763-5476
AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307
__
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] Easier ways to create .Rd files?
R-helpers: Are there any ways to auto-generate R-friendly (e.g. will pass a compilation check) .Rd files given a set of .R code? How about GUIs that help properly format the .Rd files? Thanks! I want a basic set of .Rd files that I can update as I go, but as with most things my documentation typically lags behind my coding by a few days. --j -- Jonathan A. Greenberg, PhD Assistant Project Scientist Center for Spatial Technologies and Remote Sensing (CSTARS) Department of Land, Air and Water Resources University of California, Davis One Shields Avenue Davis, CA 95616 Phone: 415-763-5476 AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307 __ 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] Best way to setClass and setMethod for an R package?
Folks: I'm putting together an R package, and I was wondering where, specifically, I put both class definitions (via setClass) as well as setMethod calls? Is there a particular file name I need to use? Thanks! --j -- Jonathan A. Greenberg, PhD Assistant Project Scientist Center for Spatial Technologies and Remote Sensing (CSTARS) Department of Land, Air and Water Resources University of California, Davis One Shields Avenue Davis, CA 95616 Phone: 415-763-5476 AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307 __ 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] Data frame to list?
Answered my own question. ?split Never mind! --j On Wed, Aug 10, 2011 at 7:35 PM, Jonathan Greenberg greenb...@ucdavis.edu wrote: R-helpers: Is there an easy way to transfer a data frame to a list, where each list element is a dataframe containing a single row from the original data frame? --j -- Jonathan A. Greenberg, PhD Assistant Project Scientist Center for Spatial Technologies and Remote Sensing (CSTARS) Department of Land, Air and Water Resources University of California, Davis One Shields Avenue Davis, CA 95616 Phone: 415-763-5476 AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307 -- Jonathan A. Greenberg, PhD Assistant Project Scientist Center for Spatial Technologies and Remote Sensing (CSTARS) Department of Land, Air and Water Resources University of California, Davis One Shields Avenue Davis, CA 95616 Phone: 415-763-5476 AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307 __ 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] Data frame to list?
R-helpers: Is there an easy way to transfer a data frame to a list, where each list element is a dataframe containing a single row from the original data frame? --j -- Jonathan A. Greenberg, PhD Assistant Project Scientist Center for Spatial Technologies and Remote Sensing (CSTARS) Department of Land, Air and Water Resources University of California, Davis One Shields Avenue Davis, CA 95616 Phone: 415-763-5476 AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307 __ 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] Data frame to list
I'm hoping this is an easy problem that I'm missing something obvious. Given:
x=c(1,1,1,2,2,3,3,3)
y=c(1:length(x))
dataframe=data.frame(x,y)
I would like to convert this to a list for use with certain functions,
where each entry of the list is a subsetted dataframe based on
dataframe$x
I can do this brute force by a for-next loop:
unique_x=unique(dataframe$x)
unique_x_N=length(unique_x)
dataframe_to_list=vector(mode=list,length=unique_x_N)
for(i in 1:unique_x_N)
{
dataframe_to_list[[i]]=subset(dataframe,x==unique_x[i])
}
My R-gut is telling me there's a much more efficient way of doing this
-- is it right?
--j
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Data frame to list
Yep, my R-gut was right! Thanks Jean and Greg!
--j
On Thu, Jul 28, 2011 at 1:29 PM, Jean V Adams jvad...@usgs.gov wrote:
Try this:
split(dataframe, dataframe$x)
Jean
`·.,, (((º `·.,, (((º `·.,, (((º
Jean V. Adams
Statistician
U.S. Geological Survey
Great Lakes Science Center
223 East Steinfest Road
Antigo, WI 54409 USA
From: Jonathan Greenberg j...@illinois.edu To: r-help
r-help@r-project.org Date: 07/28/2011 03:22 PM Subject:
[R] Data frame to list
Sent by: r-help-boun...@r-project.org
--
I'm hoping this is an easy problem that I'm missing something obvious.
Given:
x=c(1,1,1,2,2,3,3,3)
y=c(1:length(x))
dataframe=data.frame(x,y)
I would like to convert this to a list for use with certain functions,
where each entry of the list is a subsetted dataframe based on
dataframe$x
I can do this brute force by a for-next loop:
unique_x=unique(dataframe$x)
unique_x_N=length(unique_x)
dataframe_to_list=vector(mode=list,length=unique_x_N)
for(i in 1:unique_x_N)
{
dataframe_to_list[[i]]=subset(dataframe,x==unique_x[i])
}
My R-gut is telling me there's a much more efficient way of doing this
-- is it right?
--j
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http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Querying the path separator?
Unfortunately, no. .Platform$file.sep on a windows box is the /. For this DOS program it needs to be the classic backslash. Ok, we'll hack this a bit (query the platform and test if it is windows), but now I'm running into escape character problems. Given: files1=*.las files1_formatted=file.path(getwd(),files1) files1_formatted [1] X:/pathto/*.las I want files1_formatted to read: X:\pathto\*.las Using: sub(/,\,files1_formatted) Doesn't work (in fact, its not a complete statement -- I assume since its waiting for something to follow the / ). What's the trick with this? --j On Tue, Jun 28, 2011 at 11:05 PM, Berend Hasselman b...@xs4all.nl wrote: Jonathan Greenberg wrote: The problem is that I'm trying to create a path to use with a system() call, and the command window will not work with the forward slash, only with the standard backslash. I do understand that within R it will work with either way, but not via the system call. I'm trying to create a generic system() call that will work with an external executable that is available on both windows and unix machines. Would .Platform$file.sep help you? I can't test this. Berend -- View this message in context: http://r.789695.n4.nabble.com/Querying-the-path-separator-tp3631806p3632161.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. -- Jonathan A. Greenberg, PhD Assistant Project Scientist Center for Spatial Technologies and Remote Sensing (CSTARS) Department of Land, Air and Water Resources University of California, Davis One Shields Avenue Davis, CA 95616 Phone: 415-763-5476 AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307 __ 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] Querying the path separator?
Hopefully this is a pretty easy fix -- I need to have R query the path separator for some code I'm trying to write (it involves using a system() call) -- the call requires a path and a wildcard, e.g.: command=mycommand /path/to/*.files in the case of unix or, command=mycommand.exe C:\\path\\to\\*.files on a windows box System.which is working correctly, so the mycommand vs mycommand.exe part is working fine. The issue is that the /path/to should be set to getwd(), but this strips the trailing path separator. How do I go about querying the correct path separator for the system, so I can include it in a paste command (via sep=)? Thanks! --j -- Jonathan A. Greenberg, PhD Assistant Project Scientist Center for Spatial Technologies and Remote Sensing (CSTARS) Department of Land, Air and Water Resources University of California, Davis One Shields Avenue Davis, CA 95616 Phone: 415-763-5476 AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307 __ 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] Querying the path separator?
Thanks Henrik, but as the help for this function states: Note The components are separated by / (not \) on Windows. , the slashes it uses are incorrect for use in a CMD window on a Windows box (they need to be \ but file.path uses /). I suppose I can do a query as to whether the platform is Windows (in which case use \) or other (in which case use /) -- there isn't a more clever way of doing this? --j On Tue, Jun 28, 2011 at 7:10 PM, Henrik Bengtsson h...@biostat.ucsf.edu wrote: See file.path(). /Henrik On Tue, Jun 28, 2011 at 6:59 PM, Jonathan Greenberg greenb...@ucdavis.edu wrote: Hopefully this is a pretty easy fix -- I need to have R query the path separator for some code I'm trying to write (it involves using a system() call) -- the call requires a path and a wildcard, e.g.: command=mycommand /path/to/*.files in the case of unix or, command=mycommand.exe C:\\path\\to\\*.files on a windows box System.which is working correctly, so the mycommand vs mycommand.exe part is working fine. The issue is that the /path/to should be set to getwd(), but this strips the trailing path separator. How do I go about querying the correct path separator for the system, so I can include it in a paste command (via sep=)? Thanks! --j -- Jonathan A. Greenberg, PhD Assistant Project Scientist Center for Spatial Technologies and Remote Sensing (CSTARS) Department of Land, Air and Water Resources University of California, Davis One Shields Avenue Davis, CA 95616 Phone: 415-763-5476 AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307 __ 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 Project Scientist Center for Spatial Technologies and Remote Sensing (CSTARS) Department of Land, Air and Water Resources University of California, Davis One Shields Avenue Davis, CA 95616 Phone: 415-763-5476 AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307 __ 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] Querying the path separator?
The problem is that I'm trying to create a path to use with a system() call, and the command window will not work with the forward slash, only with the standard backslash. I do understand that within R it will work with either way, but not via the system call. I'm trying to create a generic system() call that will work with an external executable that is available on both windows and unix machines. --j On Tue, Jun 28, 2011 at 10:02 PM, Jeff Newmiller jdnew...@dcn.davis.ca.us wrote: Windows will work with either separator. --- Jeff Newmiller The . . Go Live... DCN:jdnew...@dcn.davis.ca.us Basics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/Batteries O.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. Jonathan Greenberg greenb...@ucdavis.edu wrote: Thanks Henrik, but as the help for this function states: Note The components are separated by / (not \) on Windows. , the slashes it uses are incorrect for use in a CMD window on a Windows box (they need to be \ but file.path uses /). I suppose I can do a query as to whether the platform is Windows (in which case use \) or other (in which case use /) -- there isn't a more clever way of doing this? --j On Tue, Jun 28, 2011 at 7:10 PM, Henrik Bengtsson h...@biostat.ucsf.edu wrote: See file.path(). /Henrik On Tue, Jun 28, 2011 at 6:59 PM, Jonathan Greenberg greenb...@ucdavis.edu wrote: Hopefully this is a pretty easy fix -- I need to have R query the path separator for some code I'm trying to write (it involves using a system() call) -- the call requires a path and a wildcard, e.g.: command=mycommand /path/to/*.files in the case of unix or, command=mycommand.exe C:\\path\\to\\*.files on a windows box System.which is working correctly, so the mycommand vs mycommand.exe part is working fine. The issue is that the /path/to should be set to getwd(), but this strips the trailing path separator. How do I go about querying the correct path separator for the system, so I can include it in a paste command (via sep=)? Thanks! --j -- Jonathan A. Greenberg, PhD Assistant Project Scientist Center for Spatial Technologies and Remote Sensing (CSTARS) Department of Land, Air and Water Resources University of California, Davis One S hields Avenue Davis, CA 95616 Phone: 415-763-5476 AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307 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 Project Scientist Center for Spatial Technologies and Remote Sensing (CSTARS) Department of Land, Air and Water Resources University of California, Davis One Shields Avenue Davis, CA 95616 Phone: 415-763-5476 AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307 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 Project Scientist Center for Spatial Technologies and Remote Sensing (CSTARS) Department of Land, Air and Water Resources University of California, Davis One Shields Avenue Davis, CA 95616 Phone: 415-763-5476 AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307 __ 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] Passing a function as a parameter...
R-helpers:
If I want to pass a character name of a function TO a function, and then
have that function executed, how would I do this? I want
an arbitrary version of the following, where any function can be used (e.g.
I don't want the if-then statement here):
apply_some_function - function(data,function_name)
{
if(function_name==mean)
{
return(mean(data))
}
if(function_name==min)
{
return(min(data))
}
}
apply_some_function(1:10,mean)
apply_some_function(1:10,min)
Basically, I want the character name of the function used to actually
execute that function. Thanks!
--j
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Re: [R] Removing inter-bar spaces in barchart
Oops, small typo, should be: barchart_test_heights=sin(c(1:100)) barchart_test_bins=c(c(1:50),c(1:50)) groups=c(rep(1,50),rep(2,50)) # Wish below didn't have spaces! barchart(barchart_test_bins~barchart_test_heights,groups=groups) On Wed, Aug 25, 2010 at 4:46 PM, Jonathan Greenberg greenb...@ucdavis.edu wrote: I apologize, let me add some data to play with: barchart_test_heights=sin(c(1:100)) barchart_test_bins=c(1:100) groups=c(rep(1,50),rep(2,50)) I have pre-calculated histogram data and the bins they belong to. I would like to plot the two histograms superimposed on one-another, having group 1 bars for a given bin be next to group 2 bars, something along the lines of: barchart(barchart_test_bins~barchart_test_heights,groups=groups) except with no space between the bars (and a key for the groups). --j P.S. And yes I was talking about barchart() from lattice -- however, I am happy to use another function if that makes this easier. On Wed, Aug 25, 2010 at 1:55 PM, David Winsemius dwinsem...@comcast.net wrote: On Aug 24, 2010, at 10:20 PM, Jonathan Greenberg wrote: Rhelpers: I'm trying to make a barchart of a 2-group dataset (barchart(x~y,data=data,groups=z,horizontal=FALSE)). My problem is that I can't, for the life of me, seem to get rid of the inter-bar space -- box.ratio set to 1 doesn't do much. Any ideas? I'd ideally want zero space between the bars. Thanks! You didn't provide any data (nor did you illustrate with one of the available datasets that are used in examples.) Compare these two outputs: barchart(yield ~ year, data = barley, groups = variety, ylab = Barley Yield (bushels/acre), ) barchart(yield ~ variety, data = barley, groups = year, ylab = Barley Yield (bushels/acre), ) ... and notice that the variables in the group have no separation of their bars whereas the rhs variables do. This is the opposite of what I expected, so perhaps you think as I did and reversing the roles ofy and z might help? -- David Winsemius, MD West Hartford, CT -- Jonathan A. Greenberg, PhD Assistant Project Scientist Center for Spatial Technologies and Remote Sensing (CSTARS) Department of Land, Air and Water Resources University of California, Davis One Shields Avenue Davis, CA 95616 Phone: 415-763-5476 AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307 -- Jonathan A. Greenberg, PhD Assistant Project Scientist Center for Spatial Technologies and Remote Sensing (CSTARS) Department of Land, Air and Water Resources University of California, Davis One Shields Avenue Davis, CA 95616 Phone: 415-763-5476 AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307 __ 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] Removing inter-bar spaces in barchart
I apologize, let me add some data to play with: barchart_test_heights=sin(c(1:100)) barchart_test_bins=c(1:100) groups=c(rep(1,50),rep(2,50)) I have pre-calculated histogram data and the bins they belong to. I would like to plot the two histograms superimposed on one-another, having group 1 bars for a given bin be next to group 2 bars, something along the lines of: barchart(barchart_test_bins~barchart_test_heights,groups=groups) except with no space between the bars (and a key for the groups). --j P.S. And yes I was talking about barchart() from lattice -- however, I am happy to use another function if that makes this easier. On Wed, Aug 25, 2010 at 1:55 PM, David Winsemius dwinsem...@comcast.net wrote: On Aug 24, 2010, at 10:20 PM, Jonathan Greenberg wrote: Rhelpers: I'm trying to make a barchart of a 2-group dataset (barchart(x~y,data=data,groups=z,horizontal=FALSE)). My problem is that I can't, for the life of me, seem to get rid of the inter-bar space -- box.ratio set to 1 doesn't do much. Any ideas? I'd ideally want zero space between the bars. Thanks! You didn't provide any data (nor did you illustrate with one of the available datasets that are used in examples.) Compare these two outputs: barchart(yield ~ year, data = barley, groups = variety, ylab = Barley Yield (bushels/acre), ) barchart(yield ~ variety, data = barley, groups = year, ylab = Barley Yield (bushels/acre), ) ... and notice that the variables in the group have no separation of their bars whereas the rhs variables do. This is the opposite of what I expected, so perhaps you think as I did and reversing the roles ofy and z might help? -- David Winsemius, MD West Hartford, CT -- Jonathan A. Greenberg, PhD Assistant Project Scientist Center for Spatial Technologies and Remote Sensing (CSTARS) Department of Land, Air and Water Resources University of California, Davis One Shields Avenue Davis, CA 95616 Phone: 415-763-5476 AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307 __ 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] Removing inter-bar spaces in barchart
Rhelpers: I'm trying to make a barchart of a 2-group dataset (barchart(x~y,data=data,groups=z,horizontal=FALSE)). My problem is that I can't, for the life of me, seem to get rid of the inter-bar space -- box.ratio set to 1 doesn't do much. Any ideas? I'd ideally want zero space between the bars. Thanks! --j -- Jonathan A. Greenberg, PhD Assistant Project Scientist Center for Spatial Technologies and Remote Sensing (CSTARS) Department of Land, Air and Water Resources University of California, Davis One Shields Avenue Davis, CA 95616 Phone: 415-763-5476 AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307 __ 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] Evaluating a string
Rhelpers: How do I get R to evaluate a string, as if it was an R statement, e.g.: a=3 b=2 operator=- statement_string=paste(a,operator,b,sep=) --j __ 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] using zoo() to coerce time series to a different reference frame
Folks: I have two sets of dates, and one set of data: *** require(chron) require(zoo) reference_dates=seq.dates(01/01/92, 12/31/92, by = months) data_dates=seq.dates(01/15/91, 12/15/93, by = months) data=1:length(data_dates) reference_zoo=zoo(order.by=reference_dates) data_zoo=zoo(data,data_dates) *** What I would like is to have a zoo object that uses the index from reference_dates, but grabs the data for each of the dates (using a spline interpolation) from data_zoo object. I feel like my solution is a bit slow, can someone let me know if there is a quicker way to do this? Thanks: *** reference_data_zoo_merge=merge(reference_zoo,data_zoo) reference_data_zoo_data=na.spline(reference_data_zoo_merge) reference_data_zoo_data=merge(reference_zoo,reference_data_zoo_data,all=FALSE) *** --j __ 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] seq.dates in reverse?
Pardon the barrage of time series related questions, but another issue I'm trying to solve is how to determine a sequence of dates a la seq.dates() except going BACKWARDS in time, e.g. if seq.dates() allowed for the to variables to be set alone, rather than the from=. Ultimately, I'd like to have a set of dates preceding a given date in predefined intervals (the same ones seq.dates() uses would be fine). Thoughts? Would there be an easy way to reverse engineer a starting date given the by= variable and the length=? With the exception of using by=days, I'm a bit unfamiliar with how to easily determine what date was, say, 4 months ago without doing a lot of string hacking (seq.dates() conveniently keeps the days of the month constant when generate date sequences, which is what I'd like). --j __ 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] exists() and functions
Always nice to answer my own question 3 minutes later. The missing()
function does what I want. Still, why DOES this exists() statement
fail? Do functions auto create the variables once they are called,
regardless of whether or not they are assigned?
--j
On Fri, Jun 25, 2010 at 1:05 PM, Jonathan Greenberg
greenb...@ucdavis.edu wrote:
I'm a bit confused about how exists() work within a function -- I want
to test for unassigned variables, but I'm doing tests in the main
environment to figure out the function, so the variables DO exist in
the parent environment of a function call.
Why does:
myfunction - function(variable_outside_function)
{
print(exists(variable_outside_function,inherit=FALSE))
print(exists(another_variable_outside_function,inherit=FALSE))
}
myfunction()
Return:
[1] TRUE
[1] FALSE
I didn't assign anything to variable_outside_function, so I'm unclear
why it thinks it exists...
--j
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and provide commented, minimal, self-contained, reproducible code.
[R] exists() and functions
I'm a bit confused about how exists() work within a function -- I want
to test for unassigned variables, but I'm doing tests in the main
environment to figure out the function, so the variables DO exist in
the parent environment of a function call.
Why does:
myfunction - function(variable_outside_function)
{
print(exists(variable_outside_function,inherit=FALSE))
print(exists(another_variable_outside_function,inherit=FALSE))
}
myfunction()
Return:
[1] TRUE
[1] FALSE
I didn't assign anything to variable_outside_function, so I'm unclear
why it thinks it exists...
--j
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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] RSQLite and fetching rows from multiple tables
I'm trying to use RSQLite statement to cycle through a large database
in chunks via the fetch(...,n=2). As far as I can tell,
however, it keeps re-fetching the same beginning set of rows -- any
ideas what might be wrong with the following code? The select
statement is pulling from multiple tables. I apologize in advance --
the DB is about 4gb so I can't make it easily available, but I'm
guessing someone can tell what I'm doing wrong just from the example
code below:
climate_query=dbSendQuery(con,SELECT
PPT_PRISM.data_vector,TMIN_PRISM.data_vector,TMAX_PRISM.data_vector,RAD_RSUN.data_vector,DEM_25M.data_vector,UWIND_NARR.data_vector,VWIND_NARR.data_vector,PPT_PRISM.date_vector,TMIN_PRISM.date_vector,TMAX_PRISM.date_vector,RAD_RSUN.date_vector,DEM_25M.date_vector,UWIND_NARR.date_vector,VWIND_NARR.date_vector
FROM PPT_PRISM,TMIN_PRISM,TMAX_PRISM,RAD_RSUN,DEM_25M,UWIND_NARR,VWIND_NARR)
while(!dbHasCompleted(climate_query)){
climate_data_fetch - fetch(climate_query, n = db_fetch_n)
print(climate_data_fetch[1,1]
print(dbGetRowCount(climate_query))
# I want to do something with the climate_data_fetch
chunk here, write out the results to a new table, and go to the next
set of rows.
}
dbClearResult(climate_query)
The first print statement shows the same thing over and over again,
and the second print statement (dbGetRowCount) eventually exceeds the
total number of rows in each of the tables.
Is the issue that I'm selecting from multiple tables at once (they all
have the same length)? If so, what would be a better approach to
doing this? Is there a way to control fetch so it pulls a range of
rows?
--j
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and provide commented, minimal, self-contained, reproducible code.
[R] Fastest way to merge matrix columns into a comma delimited string?
Folks: Say I have a matrix: test=matrix(c(1,2,3),nrow=10,ncol=3) I would like to have an output character vector where each line is row's values delimited by commas, e.g.: 1,2,3 2,3,1 3,1,2 ... 1,2,3 What is the fastest way of doing this? I can paste() row-by-row but this seems an inefficient approach to doing this. Thanks! I'm not asking how to write a CSV file, mind you, I want the array as an R data.frame or vector. --j __ 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] Matrix to database -- best practices/efficiency?
Its a race! I decided to go ahead and time everyone's results, and
all of the method's (except mine) are around the same speed. I ran
them a few times and Gabor's application of melt() tends to be a tad
bit faster than the other two, although that is far from conclusive --
do these methods share code in common? Should I expect one to of
these to have a smaller during-processing footprint than the others?
Thanks again!
--j
# My terrible approach:
my_matrix=matrix(c(1:60),nrow=600,ncol=100)
id_m=seq(10,6000,by=10)
id_n=seq(100,1,by=100)
system.time(
for (a in 1:length(id_m))
{
for (b in 1:length(id_n))
{
if ((a==1) (b==1))
{
my_database=c(id_m[a],id_n[b],my_matrix[a,b])
} else
{
my_database=rbind(my_database,c(id_m[a],id_n[b],my_matrix[a,b]))
}
}
}
)
user system elapsed
173.601 10.288 202.433
# Gabor's method with reshape
library(reshape)
my_matrix =
matrix(c(1:60),nrow=600,ncol=100,dimnames=list(seq(10,6000,by=10),seq(100,1,by=100)))
system.time(
my_database - melt(my_matrix)
)
user system elapsed
0.006 0.006 0.014
# Jorge's method with as.data.frame.table
my_matrix =
matrix(c(1:60),nrow=600,ncol=100,dimnames=list(seq(10,6000,by=10),seq(100,1,by=100)))
system.time(
my_database - as.data.frame.table(my_matrix)
)
user system elapsed
0.027 0.005 0.036
# Bill's method with expand.grid
my_matrix=matrix(c(1:60),nrow=600,ncol=100)
id_m=seq(10,6000,by=10)
id_n=seq(100,1,by=100)
system.time(
my_database - cbind(
expand.grid(id_m = id_m, id_n = id_n),
mat = as.vector(my_matrix)
)
)
user system elapsed
0.007 0.006 0.020
On Mon, Jun 7, 2010 at 9:30 PM, bill.venab...@csiro.au wrote:
I think what you are groping for is something like this
my_matrix - matrix(1:60, nrow = 6)
id_a - seq(10,60,by=10)
id_b - seq(100,1000,by=100)
my_database - cbind(
expand.grid(id_a = id_a, id_b = id_b),
mat = as.vector(my_matrix)
)
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Jonathan Greenberg
Sent: Tuesday, 8 June 2010 12:34 PM
To: r-help
Subject: [R] Matrix to database -- best practices/efficiency?
I have a matrix of, say, M and N dimensions:
my_matrix=matrix(c(1:60),nrow=6,ncol=10)
I have two id vectors corresponding to the rows and columns, e.g.:
id_m=seq(10,60,by=10)
id_n=seq(100,1000,by=100)
I would like to create a proper database (let's say a data.frame for
this example -- i'm going to be loading these into an SQLite database,
but we'll leave that complication out of this discussion for now) of m
x n rows, and 3 columns, where the 3 columns relate to the values from
m, n, and my_matrix respectively, e.g. a single row follows the form:
c(id_m[a],id_n[b],my_matrix[a,b])
I can, of course, for-loop this thing with an if-then, e.g.:
***
for (a in 1:length(id_m))
{
for (b in 1:length(id_n))
{
if ((a==1) (b==1))
{
my_database=c(id_m[a],id_n[b],my_matrix[a,b])
} else
{
my_database=rbind(my_database,c(id_m[a],id_n[b],my_matrix[a,b]))
}
}
}
***
But my gut is telling me this is an incredibly inefficient way of
doing this -- is there a faster approach to doing this same process?
Thanks!
--j
__
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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@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] Matrix to database -- best practices/efficiency?
I have a matrix of, say, M and N dimensions:
my_matrix=matrix(c(1:60),nrow=6,ncol=10)
I have two id vectors corresponding to the rows and columns, e.g.:
id_m=seq(10,60,by=10)
id_n=seq(100,1000,by=100)
I would like to create a proper database (let's say a data.frame for
this example -- i'm going to be loading these into an SQLite database,
but we'll leave that complication out of this discussion for now) of m
x n rows, and 3 columns, where the 3 columns relate to the values from
m, n, and my_matrix respectively, e.g. a single row follows the form:
c(id_m[a],id_n[b],my_matrix[a,b])
I can, of course, for-loop this thing with an if-then, e.g.:
***
for (a in 1:length(id_m))
{
for (b in 1:length(id_n))
{
if ((a==1) (b==1))
{
my_database=c(id_m[a],id_n[b],my_matrix[a,b])
} else
{
my_database=rbind(my_database,c(id_m[a],id_n[b],my_matrix[a,b]))
}
}
}
***
But my gut is telling me this is an incredibly inefficient way of
doing this -- is there a faster approach to doing this same process?
Thanks!
--j
__
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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.
Re: [R] R and ATLAS
Peter and Dirk: Thanks for the quick response -- I'm trying to get multiple CPU responses as Peter indicated should happen, but those R commands only illicit a single CPU response. When I check the libraries: ldd /usr/lib/R/bin/exec/R linux-vdso.so.1 = (0x7fffd05ff000) libR.so = /usr/lib/R/lib/libR.so (0x7f5f3b667000) libc.so.6 = /lib/libc.so.6 (0x7f5f3b313000) libblas.so.3gf = /usr/lib/libblas.so.3gf (0x7f5f3a7fe000) libgfortran.so.3 = /usr/lib/libgfortran.so.3 (0x7f5f3a512000) libm.so.6 = /lib/libm.so.6 (0x7f5f3a29) libreadline.so.6 = /lib/libreadline.so.6 (0x7f5f3a04b000) libpcre.so.3 = /lib/libpcre.so.3 (0x7f5f39e1c000) libbz2.so.1.0 = /lib/libbz2.so.1.0 (0x7f5f39c0c000) libz.so.1 = /usr/lib/libz.so.1 (0x7f5f399f4000) libdl.so.2 = /lib/libdl.so.2 (0x7f5f397f) /lib64/ld-linux-x86-64.so.2 (0x7f5f3bbec000) libgcc_s.so.1 = /lib/libgcc_s.so.1 (0x7f5f395da000) libpthread.so.0 = /lib/libpthread.so.0 (0x7f5f393bd000) libncurses.so.5 = /lib/libncurses.so.5 (0x7f5f39177000) Following /usr/lib/libblas.so.3gf : ls -l /usr/lib/libblas.so.3gf /usr/lib/libblas.so.3gf - /etc/alternatives/libblas.so.3gf And again following this: ls -l /etc/alternatives/libblas.so.3gf /etc/alternatives/libblas.so.3gf - /usr/lib/atlas-base/atlas/libblas.so.3gf So it appears to be properly linked to Atlas. Note that I got this same response from both the binary install of r-base (apt-get install r-base) and the source build of r-base-dev (apt-get source -b r-base-dev). Also, I did a tuned install of ATLAS 3.8.3 using: apt-get source atlas -t unstable cd atlas-3.8.3 DEFAULTS=n fakeroot debian/rules custom I did notice during the VERY long compilation that it seemed to correctly identify that I have 4 CPUs. Can someone confirm that the test: a = matrix(rnorm(5000*5000), 5000, 5000) b = matrix(rnorm(5000*5000), 5000, 5000) c = a%*%b Should illicit a multi-CPU response with R/ATLAS? If so, any suggestions on how to tweak my install to get it working? Thanks! --j On Wed, May 26, 2010 at 3:17 PM, Peter Langfelder peter.langfel...@gmail.com wrote: If you didn't specify an external BLAS when you ran R configure script, you are not using ATLAS. If you're not sure and you still have the output of the configure script, at the end it'll say whether it uses an external BLAS. Alternatively, you may also want to generate two random 5000x5000 matrices and do their multiplication a = matrix(rnorm(5000*5000), 5000, 5000) b = matrix(rnorm(5000*5000), 5000, 5000) c = a%*%b While the calculation is running, in a separate terminal, run top and watch how much CPU R takes. AFAIK standard installation of R is single threaded and will only use one CPU (up to 100%). ATLAS is multithreaded and (unless you configured it otherwise) it will use all available processors, so if you have a 4-core machine, you will see CPU usage of nearly 400%. Note though that this will not discriminate ATLAS from other multi-threaded BLASes. HTH, Peter On Wed, May 26, 2010 at 2:16 PM, Jonathan Greenberg greenb...@ucdavis.edu wrote: Rhelpers: I recently installed the 64-bit version of R on my Debian system, and afterwards was asked if it was compiled using ATLAS. Is there a way to test to see if R is using ATLAS? --j __ 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. __ 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] R and ATLAS
Rhelpers: I recently installed the 64-bit version of R on my Debian system, and afterwards was asked if it was compiled using ATLAS. Is there a way to test to see if R is using ATLAS? --j __ 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] Comparing histograms?
Rhelpers: I'm curious what the appropriate analysis to use for testing the hypothesis that two histograms are statistically different from one another? Thanks! --j __ 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] RSQLite equivalent of .schema?
Rhelpers: (Thanks for the previous help with getting a where statement working). Now on to my next question -- our database guru has asked me to run .schema on an sqlite database, and I was wondering if there is an equivalent in R to do this? Thanks! --j __ 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] dbSendQuery with R variables
Rhelpers: I'd like to modify this RSQLite statement: rs_stations-dbSendQuery(con_stations, select * from stations) so that stations is actually an R variable, e.g.: stations=c(stationA,stationB) How would I modify the above statement to query from stations[[1]] (aka stationA)? --j __ 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] R and screen (UNIX question)
I'm having a mixed experience with using R and UNIX's screen function -- sometimes when I close a connection that used screen, the R process is killed (which, in theory, it shouldn't be -- it should be running in the background). Does anyone have any ideas on how well (or not) R behaves with screen, and if there any tricks to using R and SOME type of background program that doesn't require permanent connection? --j __ 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] Using auto.key with two variable plots
Rhelpers: Having a problem solving this. I have an xyplot call that looks like this: print(xyplot(temp_species_EAM_Pred_Pop$x+temp_species_NULL_Pred_Pop$x~temp_species_EAM_Pred_Pop$Action,main=current_species, xlab=Action,ylab=Predicted Pop, xlim=c(xmin,xmax),ylim=c(ymin,ymax), auto.key=list(corner=c(1,1 This is just a scatterplot with two response variables sharing the same predictor variable (temp_species_EAM_Pred_Pop$Action). Right now, the key has the words temp_species_EAM_Pred_Pop$x and temp_species_NULL_Pred_Pop$x next to their symbols. I would like to rename these in the key, say EAM and NULL -- using the group= command doesn't work (since these aren't really different groups). What is the right way to rename these variables in the key? Is using auto.key the right approach? Thanks! --j -- Jonathan A. Greenberg, PhD Postdoctoral Scholar Center for Spatial Technologies and Remote Sensing (CSTARS) University of California, Davis One Shields Avenue The Barn, Room 250N Davis, CA 95616 Phone: 415-763-5476 AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307 __ 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] Data frame of different sized lists in a function call
I'm hoping to get some best practice feedback for constructing a
function call which takes an undefined set of DIFFERENT length vectors
-- e.g. say we have two lists:
list1=c(1:10)
list2=c(2:4)
lists = data.frame(list1,list2) coerces those two to be the same length
(recycling list2 to fill in the missing rows) -- what is a quick way of
having each of those lists retain their original lengths? my function
ultimately should look like:
myfunction = function(lists) {
...
}
I'm hoping this can be done with a single line, so the user doesn't have
to pre-construct the data.frame before running the function, if at all
possible.
Thanks!
--j
--
Jonathan A. Greenberg, PhD
Postdoctoral Scholar
Center for Spatial Technologies and Remote Sensing (CSTARS)
University of California, Davis
One Shields Avenue
The Barn, Room 250N
Davis, CA 95616
Phone: 415-763-5476
AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307
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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] x,y plot question (two sets of labels)
I'm trying to figure out the best way to do a scatterplot using the following data as an example: plothelp_x=1:10 plothelp_A1=sin(plothelp_x) plothelp_A2=tan(plothelp_x) plothelp_B=c(A,B,C,A,B,C,A,B,C,A) (note that all 4 of these vectors have 10 entries each) What I would like is to have two plots on the same graph: 1) plothelp_A1 vs. plothelp_x 2) plothelp_A2 vs. plothelp_x I want plot #1 to have a set symbol SHAPE (say, crosses) and plot #2 a different symbol shape (say, dots). On top of that, I want all points to be color coded based on plothelp_B, e.g. all As are black, all Bs are red, all Cs are blue; e.g a sin point with the letter A should be a black cross, a tan point with the letter C should be a red dot. Finally, I'd like two have TWO keys in the graph showing a) what the symbol shapes represent (e.g. cross=sin, dot=tan), and b) what the colors mean. Thanks for any help you can give me! --j -- Jonathan A. Greenberg, PhD Postdoctoral Scholar Center for Spatial Technologies and Remote Sensing (CSTARS) University of California, Davis One Shields Avenue The Barn, Room 250N Davis, CA 95616 Phone: 415-763-5476 AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307 __ 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] Finally, the first R spam!
I got that same email from Steve Blum: Hi folks, Which is the best statistical package out there. I am out of work and looking to get the best buck for my money. Tx - ed --j Max Kuhn wrote: ... and this one I received this morning: Hi folks, Which is the best statistical package out there. I am out of work and looking to get the best buck for my money. Thanks, Mike. I guess this is still better than those AOL disks. On Thu, Jan 7, 2010 at 3:49 AM, Liviu Andronic landronim...@gmail.com wrote: On 1/7/10, David Croll david.cr...@gmx.ch wrote: Just for fun (or concern): I received a R spam mail. Perhaps the first in history... No, not quite first. There was one before on Inference with R, at least. Liviu __ 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.
[R] Safe way to automatically install required packages...
R-helpers:
I'm working on an r-package that I want to make as easy-to-use as
possible for a novice R-user, which includes automatically installing
required packages. I, myself, am a novice R-packager, so the solution
I came up with was to embed:
print(Loading required packages...)
if (!require(reshape)) { install.packages(reshape) }
if (!require(reshape)) {
print(Could not install package 'reshape', please contact your
sysadmin.)
return()
}
in the code proper, and put together the package using
package.skeleton() and R CMD build.
I'm guessing there's a better way to do this -- any suggestions?
--j
--
Jonathan A. Greenberg, PhD
Postdoctoral Scholar
Center for Spatial Technologies and Remote Sensing (CSTARS)
University of California, Davis
One Shields Avenue
The Barn, Room 250N
Davis, CA 95616
Phone: 415-763-5476
AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307
__
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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] Aggregate and cross tabulation
R-helpers:
I have a data frame containing 4 factor variables (let's say A,B,C,
and D) and 1 numerical variable (N). I would like to produce a
cross-tabulated data frame in which A,B,C are individual columns, each
factor of D is its own column, and the field is calculated as a given
function of N (I would like to have two output data frames, one with the
mean(N) and one with the sum(N), e.g.:
A,B,C,D1,D2,
...,DM
A1 B1 C1 mean(N{A1,B1,C1,D1)}) mean(N{A1,B1,C1,D2)})
mean(N{A1,B1,C1,DM)})
A2 B1 C1 mean(N{A2,B1,C1,D1)}) mean(N{A2,B1,C1,D2)})
mean(N{A2,B1,C1,DM)})
etc...
I can mostly do this with aggregate, e.g.
output = aggregate(N,list(A,B,C,D),mean), but I can't get that last step
of cross-tabulating the Ds to column headers. table() and xtabs()
appear to just count, rather than giving me access to sum() and mean().
Any ideas? Ideally I'd like to do this in a single step, as the
aggregate output (above) produces a much larger data frame than a
cross-tabulated output would (in my particular case).
--j
--
Jonathan A. Greenberg, PhD
Postdoctoral Scholar
Center for Spatial Technologies and Remote Sensing (CSTARS)
University of California, Davis
One Shields Avenue
The Barn, Room 250N
Davis, CA 95616
Phone: 415-763-5476
AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307
__
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] splitting a vector of strings...
Quick question -- if I have a vector of strings that I'd like to split into two new vectors based on a substring that is inside of each string, what is the most efficient way to do this? The substring that I want to split on is multiple characters, if that matters, and it is contained in every element of the character vector. --j -- Jonathan A. Greenberg, PhD Postdoctoral Scholar Center for Spatial Technologies and Remote Sensing (CSTARS) University of California, Davis One Shields Avenue The Barn, Room 250N Davis, CA 95616 Phone: 415-763-5476 AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307 __ 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] splitting a vector of strings...
William et al:
Thanks! I think I have a somewhat more complicated issue due to the
type of string I'm using -- the split is | (space pipe space) -- how
do I code that based on your sub code below? Using | * doesn't seem
to be working. Thanks!
--j
William Dunlap wrote:
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Jonathan Greenberg
Sent: Thursday, October 22, 2009 7:35 PM
To: r-help
Subject: [R] splitting a vector of strings...
Quick question -- if I have a vector of strings that I'd like
to split
into two new vectors based on a substring that is inside of
each string,
what is the most efficient way to do this? The substring
that I want to
split on is multiple characters, if that matters, and it is
contained in
every element of the character vector.
strsplit and sub can both be used for this. If you know
the string will be split into 2 parts then 2 calls to sub
with slightly different patterns will do it. strsplit requires
less fiddling with the pattern and is handier when the number
of parts is variable or large. strsplit's output often needs to
be rearranged for convenient use.
E.g., I made 100,000 strings with a 'qaz' in their middles with
x-paste(X,sample(1e5),sep=)
y-sub(X,Y,x)
xy-paste(x,y,sep=qaz)
and split them by the 'qaz' in two ways:
system.time(ret1-list(x=sub(qaz.*,,xy),y=sub(.*qaz,,xy)))
# user system elapsed
# 0.220.000.21
system.time({tmp-strsplit(xy,qaz);ret2-list(x=unlist(lapply(tmp,`[`,
1)),y=unlist(lapply(tmp,`[`,2)))})
user system elapsed
# 2.420.002.20
identical(ret1,ret2)
#[1] TRUE
identical(ret1$x,x) identical(ret1$y,y)
#[1] TRUE
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
--j
--
Jonathan A. Greenberg, PhD
Postdoctoral Scholar
Center for Spatial Technologies and Remote Sensing (CSTARS)
University of California, Davis
One Shields Avenue
The Barn, Room 250N
Davis, CA 95616
Phone: 415-763-5476
AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307
__
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
Postdoctoral Scholar
Center for Spatial Technologies and Remote Sensing (CSTARS)
University of California, Davis
One Shields Avenue
The Barn, Room 250N
Davis, CA 95616
Phone: 415-763-5476
AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307
__
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] Stochastic (transition) matrices: how to determine distributions and variance?
(apologies for the cross-posting, and for this being a more general stats question rather than a specific-to-R one. I assure you I will be doing the actual analysis in R :) I am trying to determine the distribution and variance for a classic stochastic (transition) matrix problem such that: let x(t) be an initial state vector consisting of counts of classes A, B and C: x(t) = [A(t),B(t),C(t)] T is the stochastic (transition) matrix for these classes consisting of the transition probabilities between each combination of A,B and C: pAA pBA pCA T= pAB pBB pCB pAC pBC pCC By doing matrix multiplication of Tx(t) we can determine the *mean* counts of these classes at t+1 such that: x mean (t+1) = Tx(t) = [A mean (t+1),B mean (t+1),C mean (t+1)] What I want to know is what is a) what is the *distribution* of A(t+1),B(t+1) and C(t+1), and what is the variance around these mean values? Since pXY are stochastic probabilities, it seems that the distribution and variance should be calculable. Thanks! --j -- Jonathan A. Greenberg, PhD Postdoctoral Scholar Center for Spatial Technologies and Remote Sensing (CSTARS) University of California, Davis One Shields Avenue The Barn, Room 250N Davis, CA 95616 Cell: 415-794-5043 AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307 __ 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] Best R text editors?
Quick informal poll: what is everyone's favorite text editor for working with R? I'd like to hear from people who are using editors that have some level of direct R interface (e.g. Tinn-R, Komodo+SciViews). Thanks! --j -- Jonathan A. Greenberg, PhD Postdoctoral Scholar Center for Spatial Technologies and Remote Sensing (CSTARS) University of California, Davis One Shields Avenue The Barn, Room 250N Davis, CA 95616 Cell: 415-794-5043 AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307 __ 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.
