Nabble - R help

Re: Reading from Google Docs

2009-11-25T14:08:29Z

Oh OH! Could you please help with a problem that I never used to get.

library(RGoogleDocs)
ps <-readline(prompt="get the password in ")
sheets.con = getGoogleDocsConnection(getGoogleAuth("fjbuch@...", ps,
service ="wise"))
ts2=getWorksheets("OnCall",sheets.con)

Those opening lines of script used to work flawlesly. Now I get.
Error in getDocs(con) : problems connecting to get the list of documents

Yet I got it to work earlier while I had been toying with RGoogleData
package in another session. Could RGoogleData have opened something for
RGoogleDocs to use?

Farrel Buchinsky
Google Voice Tel: (412) 567-7870

Sent from Pittsburgh, Pennsylvania, United States

On Wed, Nov 25, 2009 at 16:34, Farrel Buchinsky <fjbuch@...> wrote:

> That was painless. I had already installed Rtools and had already put it on
> my path.
>
> Your line worked very well. [Thanks for telling me. However I did it last
> time was worse than sticking daggers in my eyes. ]
> install.packages( "RGoogleDocs", repos="http://www.omegahat.org/R", type="source"
> )
>
> I now have
> Package: RGoogleDocs
> Version: 0.4-0
> Title:....
> ....
> Maintainer: Duncan Temple Lang <duncan@...>
> Packaged: 2009-10-27 22:10:22 UTC; duncan
> Built: R 2.10.0; ; 2009-11-25 20:59:03 UTC; windows
>
> I am providing the following link to a copy of my RGoogleDocs zipped
> directory. It is for people who run R in windows and do not want to go
> through the pain of setting things up so that they can install source.
> http://dl.dropbox.com/u/23200/RGoogleDocs/RGoogleDocs.zip
>
> I BELIEVE that if one downloads the zip and extracts it to an empty
> directory called RGoogleDocs in one's Library directory then everything will
> work. Please let me know.
>
> Farrel Buchinsky
> Google Voice Tel: (412) 567-7870
>
>
>
> On Wed, Nov 25, 2009 at 15:15, Charlie Sharpsteen <chuck@...>wrote:
>
>> On Wed, Nov 25, 2009 at 12:02 PM, Farrel Buchinsky <fjbuch@...>
>> wrote:
>> > I reinstalled from a binary that Duncan Temple Lang placed in omegahat.
>> I
>> > see that omegahat has a subdirectory for each version of R. There is not
>> a
>> > directory for 2.10. I took the liberty of taking it from the 2.9
>> directory.
>>
>> That explains the warning message.
>>
>> > Who knows what crime I committed. Is that first or third degree murder.
>>
>> Well, it's just a warning-- so it shouldn't be a show-stopper. And
>> from what I see the warning is only referring to the package help
>> pages, which are available online. It looks like the functionality of
>> the package should still work just fine if you don't want to bother
>> with a reinstall.
>>
>> > I saw however that there is a far more recent version of RGoogleDocs
>> (Last
>> > Release: 0.4-0 (27 Oct 2009)). But it is in tar.gz. I assume that it is
>> in
>> > source. Once before I spent about 27000 hours getting a source to become
>> a
>> > binary. I don't know how I finally got it right and am reluctant to
>> wander
>> > into that swamp again.
>> > Farrel Buchinsky
>>
>> This shouldn't be extraordinarily difficult-- unfortunately Murphy's
>> Law does come into play sometimes. But it should just be a matter of:
>>
>> install.packages( "RGoogleDocs", repos="http://www.omegahat.org/R",
>> type="source" )
>>
>> And that's it for Linux, Mac OS or other UNIX-based system. With
>> Windows you will first have to install the toolset available at:
>>
>> http://www.murdoch-sutherland.com/Rtools/
>>
>> Grab the "Rtools210" installer as you are using R 2.10.x. Install
>> using the "Package Authoring" option and make sure you check any
>> options that ask about modifying your PATH.
>>
>> Good luck!
>>
>> -Charlie
>>
>
>

[[alternative HTML version deleted]]

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predict(): NoSuchMethodError

2009-11-25T14:05:30Z

I am currently working on a code which clusters attributes from a data set, then uses a linear regression model to predict NA values in the data set. The code works for almost all cases, but then errors out on a case that seems like it should work the same.

This is the line of code that is giving me the problem:

NewClusterData[j,att] <- predict(cl,newdata = ClusterData[j,],type="class")

Here is the code for the arguments:

algName <- "LinearRegression"
Formula <- as.formula(paste(as.name(att), " ~ ", paste(otherAtts, collapse= "+")))
myAlg <- get(algName)
cl <- myAlg(Formula, data = Data)

And this is the error I'm getting:

Error in .jnew("weka/core/Attribute", attname[i]) : java.lang.NoSuchMethodError: <init>

Here is the printout of the a working case:

cl = Linear Regression Model
petallength =
1.748 * sepallength +
-1.4174 * sepalwidth +
-2.1294

ClusterData[j,] = sepallength sepalwidth petallength petalwidth class
5.7 2.6 NA 1 1

petallength = 4.148813

And the non-working case:

cl = Linear Regression Model
petalwidth =
0.8948 * class +
0.3031
ClusterData[j,] = sepallength sepalwidth petallength petalwidth class
4.9 3 1.4 NA 0

Error in .jnew("weka/core/Attribute", attname[i]) :
java.lang.NoSuchMethodError: <init>

Thanks for any help that anyone can provide!

Re: R Packages Crack the 3,000 Mark!

2009-11-25T14:02:13Z

Hi Bob,

Muenchen, Robert A (Bob) wrote:
>
> Does anyone have a program that graphs the growth of R packages? I don't
> know if that historical data is around.

John Fox had a slide on this in his useR 2008 talk "The Social
Organization of the R Project" (page 7), with package counts up to March
2008. As "Source of Data" he gave https://svn.r-project.org/R/branches/.
I've been digging around in there but really have no idea how he found
the relevant data there.

I'd be quite interested in this, too, so if you find out anything please
drop me a line...

Best,
Stephan

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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Insert elements into a vector in a defined positions

2009-11-25T13:46:53Z

Dear R users,
I have a vector of length n and I want to insert some elements (in my case the NA string) into a defined positions. For example, my vector is z1 and I want to add NA's in positions 4, 6 y 7 so after that, my new vector, z2, should have a length of 10+3.

z1 <- 1:10
id <- c(4,6,7)

# And z2 should be:
z2 <- c(1,2,3,NA,4,5,NA,NA,6,7,8,9,10)

Anyone knows how can I do that?
Thank you.

Manuel Ramón Fernández
Group of Reproductive Biology (GBR)
University of Castilla-La Mancha (Spain)
mramon@...

Re: Feature request for as.Date() function

2009-11-25T13:42:22Z

hi,

it fails, when the NA is surrounded by double quotes, which is the
default way of quoting of the write.table command.

x <- read.csv(textConnection('date,value
+ + 2009-01-01,10
+ + 2009-02-01,1
+ + "NA", 3'), colClasses=c("Date", 'integer'))
Fehler in fromchar(x) :
character string is not in a standard unambiguous format

regards,
stefan

On Wed, Nov 25, 2009 at 02:56:56PM -0500, jim holtman wrote:

> Seems to work fine in my testing:
>
> > x <- read.csv(textConnection("date,value
> + 2009-01-01,10
> + 2009-02-01,1
> + 'NA', 3"), colClasses=c("Date", 'integer'))
> >
> > str(x)
> 'data.frame': 3 obs. of 2 variables:
> $ date :Class 'Date' num [1:3] 14245 14276 NA
> $ value: int 10 1 3
> > x <- read.csv(textConnection("date,value
> + 2009-01-01,10
> + 2009-02-01,1
> + NA, 3"), colClasses=c("Date", 'integer'))
> >
> > str(x)
> 'data.frame': 3 obs. of 2 variables:
> $ date :Class 'Date' num [1:3] 14245 14276 NA
> $ value: int 10 1 3
> >
>
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
> On Wed, Nov 25, 2009 at 12:38 PM,
> <nabble.30.miller_2555@...> wrote:
> > Hello -
> >
> > I have a csv file with a few date columns. Some of the records have an
> > "NA" character string instead of the date. When I attempt to use
> > read.csv() and typecast the columns using colClasses, I receive the
> > following error:
> > Error in charToDate(x) :
> > character string is not in a standard unambiguous format
> >
> > Similarly, the following command produces the same error:
> > as.Date("NA")
> >
> > However, as.Date(NA) performs as documented.
> >
> > Can we enhance the as.Date() function to convert "NA" strings into NA
> > value prior to type conversion?
> >
> > Thanks!
> >
> > ______________________________________________
> > R-help@... mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
>
>
> --
> Jim Holtman
> Cincinnati, OH
> +1 513 646 9390
>
> What is the problem that you are trying to solve?
>
> ______________________________________________
> R-help@... 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@... 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: Reading from Google Docs

2009-11-25T13:34:58Z

That was painless. I had already installed Rtools and had already put it on
my path.

Your line worked very well. [Thanks for telling me. However I did it last
time was worse than sticking daggers in my eyes. ]
install.packages( "RGoogleDocs", repos="http://www.omegahat.org/R",
type="source"
)

I now have
Package: RGoogleDocs
Version: 0.4-0
Title:....
....
Maintainer: Duncan Temple Lang <duncan@...>
Packaged: 2009-10-27 22:10:22 UTC; duncan
Built: R 2.10.0; ; 2009-11-25 20:59:03 UTC; windows

I am providing the following link to a copy of my RGoogleDocs zipped
directory. It is for people who run R in windows and do not want to go
through the pain of setting things up so that they can install source.
http://dl.dropbox.com/u/23200/RGoogleDocs/RGoogleDocs.zip

I BELIEVE that if one downloads the zip and extracts it to an empty
directory called RGoogleDocs in one's Library directory then everything will
work. Please let me know.

Farrel Buchinsky
Google Voice Tel: (412) 567-7870

On Wed, Nov 25, 2009 at 15:15, Charlie Sharpsteen <chuck@...>wrote:

> On Wed, Nov 25, 2009 at 12:02 PM, Farrel Buchinsky <fjbuch@...>
> wrote:
> > I reinstalled from a binary that Duncan Temple Lang placed in omegahat. I
> > see that omegahat has a subdirectory for each version of R. There is not
> a
> > directory for 2.10. I took the liberty of taking it from the 2.9
> directory.
>
> That explains the warning message.
>
> > Who knows what crime I committed. Is that first or third degree murder.
>
> Well, it's just a warning-- so it shouldn't be a show-stopper. And
> from what I see the warning is only referring to the package help
> pages, which are available online. It looks like the functionality of
> the package should still work just fine if you don't want to bother
> with a reinstall.
>
> > I saw however that there is a far more recent version of RGoogleDocs
> (Last
> > Release: 0.4-0 (27 Oct 2009)). But it is in tar.gz. I assume that it is
> in
> > source. Once before I spent about 27000 hours getting a source to become
> a
> > binary. I don't know how I finally got it right and am reluctant to
> wander
> > into that swamp again.
> > Farrel Buchinsky
>
> This shouldn't be extraordinarily difficult-- unfortunately Murphy's
> Law does come into play sometimes. But it should just be a matter of:
>
> install.packages( "RGoogleDocs", repos="http://www.omegahat.org/R",
> type="source" )
>
> And that's it for Linux, Mac OS or other UNIX-based system. With
> Windows you will first have to install the toolset available at:
>
> http://www.murdoch-sutherland.com/Rtools/
>
> Grab the "Rtools210" installer as you are using R 2.10.x. Install
> using the "Package Authoring" option and make sure you check any
> options that ask about modifying your PATH.
>
> Good luck!
>
> -Charlie
>

Re: order of panels in xyplots

2009-11-25T13:32:39Z

Titus Malsburg wrote:

> The documentation of xyplot could be improved here. It says:
>
> "If 'index.cond' is a list, it has to be as long as the number of conditioning
> variables, and the 'i'-th component has to be a valid indexing vector for the
> integer vector '1:nlevels(g_i)' (which can, among other things, repeat some
> of the levels or drop some altogether)."
>
> It should make explicit that nlevels is the number of levels actually
> used in the data and not length(levels(f)).
>

It does say "... _valid_ indexing vector ..." (my emphasis).
If nlevels(g) = 5, but you're only plotting 3 panels, it seems
to me that c(3,1,5) might be a valid indexing vector.

-Peter Ehlers

> Cheers,
>
> Titus
>
> ______________________________________________
> R-help@... 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 or C++ on FreeNX servers

2009-11-25T13:25:05Z

Hi Murray,

Murray Jorgensen wrote:

> I have just found out that the machine learning group in our Faculty has
> a lot of spare capacity on their FreeNX servers. I do not know a lot
> about these beasts but I understand that they are a free version of
> something produced by a firm called "NoMachine".
>
> They are designed for executing parallel algorithms and I thought that
> they might be of use in a project of mine comparing different
> model-fitting algorithms from the point of view of sensitivity to
> starting values.

As far as I know FreeNX is an implementation of a protocol that
allows to connect to remote X sessions (X being the standard
windowing system for *nix systems) in an optimized way.

There is (in my understanding) no relationship to parallel algorithm
execution. Using a NX client, you can connect to a remote (often
more powerful) machine (potentially making use of multiple cores on
that machine in a parallel way), but the FreeNX part of it is just
about having the remote machine's GUI forwarded such that you can
work "on the server" (in a window on) on your desktop machine.

HTH,
Tobias

> Anyway before revealing my near-total ignorance to my computer science
> colleagues I thought I would ask if any of my fellow R users have any
> experience with these things and possibly advice to offer. The CS people
> are probably using the servers in conjunction with Java or C++ and I
> could possibly use the latter of these. I wondered, though, if R could
> be used directly with such hardware and if so, how the parallelizing
> would be handled.
>
>
> Regards, Murray Jorgensen
>

Re: lattice: plotting in a loop

2009-11-25T13:18:22Z

Ah, it's a FAQ ... thought I'd looked hard enough. The ignominy, and for a
first post! Well, in any case, thanks a lot Baptiste.

2009/11/25 baptiste auguie <baptiste.auguie@...>

> Hi,
> it's a FAQ, you need to print() the plot,
>
>
> http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-do-lattice_002ftrellis-graphics-not-work_003f
>
> baptiste
>
> 2009/11/25 Ryan Archer <ra.lists.r@...>:
> > Hi,
> >
> > I'm having trouble seeing graphics output from lattice xyplot() when
> called
> > from inside a for loop:
> >
> > x <- 1:50
> > for ( i in 1:5 ) {
> > y <- rnorm(x)
> > xyplot(y~x) # no graphics when inside for-loop
> > # plot(x,y) # works fine
> > # Sys.sleep(0.5) # doesn't seem to help
> > }
> >
> > The xyplot() is fine outside the loop. Results are the same to X11
> device
> > and to file devices.
> >
> > I have noticed that there is a delay proportional to the size of the
> loop,
> > so presumably xyplot() is computing although the results aren't reaching
> the
> > graphics device.
> >
> > Can anyone suggest a cause or remedy?
> >
> > This is my first post to the list, although I've picked up a lot of
> useful
> > information reading here!
> >
> > -Ryan
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help@... 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: How to sum only a few elements in a line

2009-11-25T13:15:14Z

Marcio Resende wrote:

> Hello,
>
> I have a matrix with the numbers 0,1 and 9
> I would like to write a function that could sum each line skiping everytime
> a number 9 appears
> for example
> [0 1 0 1 1 9 1]
> the sum would be 4.
> However I cannot replace 9 by 0 otherwise after the sum is done I wouldnÂ´t
> be able to distiguish which ones were real zeros and which ones were nines
> replaced by zero just to sum.
> Thank you very much
>

In order to distinguish 'real' 0s from those resulting
from elimination of 9s (without going back to the original
matrix), you can do this:

f <- function(x){
Sum <- sum(x[x != 9])
has_9 <- 9 %in% x
c(Sum = Sum, has_9 = has_9)
}

# make a sample matrix
M <- matrix(sample(c(0,1,9), 30, TRUE), 6, 5)

# get sums and whether the row contained one or more 9s
t(apply(M, 1, f))

-Peter Ehlers

______________________________________________
R-help@... 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: lattice: plotting in a loop

2009-11-25T13:11:21Z

Hi,
it's a FAQ, you need to print() the plot,

http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-do-lattice_002ftrellis-graphics-not-work_003f

baptiste

2009/11/25 Ryan Archer <ra.lists.r@...>:

> Hi,
>
> I'm having trouble seeing graphics output from lattice xyplot() when called
> from inside a for loop:
>
> x <- 1:50
> for ( i in 1:5 ) {
> y <- rnorm(x)
> xyplot(y~x) # no graphics when inside for-loop
> # plot(x,y) # works fine
> # Sys.sleep(0.5) # doesn't seem to help
> }
>
> The xyplot() is fine outside the loop. Results are the same to X11 device
> and to file devices.
>
> I have noticed that there is a delay proportional to the size of the loop,
> so presumably xyplot() is computing although the results aren't reaching the
> graphics device.
>
> Can anyone suggest a cause or remedy?
>
> This is my first post to the list, although I've picked up a lot of useful
> information reading here!
>
> -Ryan
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help@... 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 or C++ on FreeNX servers

2009-11-25T13:09:04Z

All FreeNX allows you to do is access a regular linux machine using X
over SSH as opposed to ssh'ing in, redirecting the X-display back to
your local machine (running a xserver locally)..

You can install R on the machine(s) just as you would normally, and if
the machines are in some sort of clustered environment, you could setup
the packages specifically available on linux for R to do that (snow,
multicore, etc...)

Check out FreeNX here http://freenx.berlios.de/

hth
-c

Murray Jorgensen wrote:

> Hi all,
>
> I have just found out that the machine learning group in our Faculty has
> a lot of spare capacity on their FreeNX servers. I do not know a lot
> about these beasts but I understand that they are a free version of
> something produced by a firm called "NoMachine".
>
> They are designed for executing parallel algorithms and I thought that
> they might be of use in a project of mine comparing different
> model-fitting algorithms from the point of view of sensitivity to
> starting values.
>
> Anyway before revealing my near-total ignorance to my computer science
> colleagues I thought I would ask if any of my fellow R users have any
> experience with these things and possibly advice to offer. The CS people
> are probably using the servers in conjunction with Java or C++ and I
> could possibly use the latter of these. I wondered, though, if R could
> be used directly with such hardware and if so, how the parallelizing
> would be handled.
>
>
> Regards, Murray Jorgensen
>

lattice: plotting in a loop

2009-11-25T13:07:15Z

Hi,

I'm having trouble seeing graphics output from lattice xyplot() when called
from inside a for loop:

x <- 1:50
for ( i in 1:5 ) {
y <- rnorm(x)
xyplot(y~x) # no graphics when inside for-loop
# plot(x,y) # works fine
# Sys.sleep(0.5) # doesn't seem to help
}

The xyplot() is fine outside the loop. Results are the same to X11 device
and to file devices.

I have noticed that there is a delay proportional to the size of the loop,
so presumably xyplot() is computing although the results aren't reaching the
graphics device.

Can anyone suggest a cause or remedy?

This is my first post to the list, although I've picked up a lot of useful
information reading here!

-Ryan

[[alternative HTML version deleted]]

______________________________________________
R-help@... 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 or C++ on FreeNX servers

2009-11-25T13:03:40Z

Hi all,

I have just found out that the machine learning group in our Faculty has
a lot of spare capacity on their FreeNX servers. I do not know a lot
about these beasts but I understand that they are a free version of
something produced by a firm called "NoMachine".

They are designed for executing parallel algorithms and I thought that
they might be of use in a project of mine comparing different
model-fitting algorithms from the point of view of sensitivity to
starting values.

Anyway before revealing my near-total ignorance to my computer science
colleagues I thought I would ask if any of my fellow R users have any
experience with these things and possibly advice to offer. The CS people
are probably using the servers in conjunction with Java or C++ and I
could possibly use the latter of these. I wondered, though, if R could
be used directly with such hardware and if so, how the parallelizing
would be handled.

Regards, Murray Jorgensen

--
Dr Murray Jorgensen http://www.stats.waikato.ac.nz/Staff/maj.html
Department of Statistics, University of Waikato, Hamilton, New Zealand
Email: maj@... Fax 7 838 4155
Phone +64 7 838 4773 wk Home +64 7 825 0441 Mobile 021 0200 8350

______________________________________________
R-help@... 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: How to sum only a few elements in a line

2009-11-25T12:48:46Z

On Nov 25, 2009, at 3:27 PM, Marcio Resende wrote:

>
> Hello,
>
> I have a matrix with the numbers 0,1 and 9
> I would like to write a function that could sum each line skiping
> everytime
> a number 9 appears
> for example
> [0 1 0 1 1 9 1]

sum(x[x != 9])

> the sum would be 4.
> However I cannot replace 9 by 0 otherwise after the sum is done I
> wouldn´t
> be able to distiguish which ones were real zeros and which ones were
> nines
> replaced by zero just to sum.
> Thank you very much
>
> --

David Winsemius, MD
Heritage Laboratories
West Hartford, CT

______________________________________________
R-help@... 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: How to sum only a few elements in a line

2009-11-25T12:45:54Z

Tena koe Marcio

Try something like (untested)

apply(yourMatrix, 1, function(x) sum(x[x!=9]))

HTH ...

Peter Alspach

> -----Original Message-----
> From: r-help-bounces@...
> [mailto:r-help-bounces@...] On Behalf Of Marcio Resende
> Sent: Thursday, 26 November 2009 9:27 a.m.
> To: r-help@...
> Subject: [R] How to sum only a few elements in a line
>
>
> Hello,
>
> I have a matrix with the numbers 0,1 and 9 I would like to
> write a function that could sum each line skiping everytime a
> number 9 appears for example [0 1 0 1 1 9 1] the sum would be 4.
> However I cannot replace 9 by 0 otherwise after the sum is
> done I wouldn´t be able to distiguish which ones were real
> zeros and which ones were nines replaced by zero just to sum.
> Thank you very much
>
> --
> View this message in context:
> http://old.nabble.com/How-to-sum-only-a-few-elements-in-a-line
> -tp26519740p26519740.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help@... 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: How to sum only a few elements in a line

2009-11-25T12:45:44Z

> -----Original Message-----
> From: r-help-bounces@...
> [mailto:r-help-bounces@...] On Behalf Of Marcio Resende
> Sent: Wednesday, November 25, 2009 12:27 PM
> To: r-help@...
> Subject: [R] How to sum only a few elements in a line
>
>
> Hello,
>
> I have a matrix with the numbers 0,1 and 9
> I would like to write a function that could sum each line
> skiping everytime
> a number 9 appears
> for example
> [0 1 0 1 1 9 1]
> the sum would be 4.
> However I cannot replace 9 by 0 otherwise after the sum is
> done I wouldn´t
> be able to distiguish which ones were real zeros and which
> ones were nines
> replaced by zero just to sum.

One of the nice things about the S language is
that arguments functions are not altered by the
function. When the function appears to alter
an argument it is really altering a copy of it.
Thus you can write a function like
f <- function(matrix) {
matrix[matrix==9] <- 0
rowSums(matrix)
}
and use it as
> myMatrix <- rbind(c(0,1,0,1,1,9,1), c(9,9,9,9,9,17,9))
> f(myMatrix)
[1] 4 17
> myMatrix # not altered by running f over it
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 0 1 0 1 1 9 1
[2,] 9 9 9 9 9 17 9

By the way, it would help if you wrote your example data
as an S expression, e.g., rbind(c(...),c(...)), and not
as an expression in some other language, "[ 1 1 9 ]".

Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com

> Thank you very much
>
> --
> View this message in context:
> http://old.nabble.com/How-to-sum-only-a-few-elements-in-a-line
-tp26519740p26519740.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help@... 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@... 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: Grouped Barplot

2009-11-25T12:43:21Z

I'm able to add legend. ~Gary

On Wed, Nov 25, 2009 at 3:15 PM, Gary <mail2garymiller@...> wrote:

> Thanks David. I reduced the data set and its copied below (also attached to
> this email as text file). Now N=50, Only 2 years, Only 2 Cities. I tried:
>
> foo<-read.table("SampleData.txt", header=TRUE)
> boxplot(foo$admit ~ foo$city + foo$year, col=2:3)
>
> I need some help with:
> 1) Defining labels for x-axis (just "2000" and "2001").
> 2) Removing gap between cities boxplots (but leaving gap between years).
> 3) Adding "MEAN" to the boxplots.
>
>
> city year admit
> Asheville 2000 0
> Asheville 2000 0
> Asheville 2000 1
> Asheville 2000 2
> Asheville 2000 2
> Asheville 2000 0
> Asheville 2000 1
> Asheville 2000 0
> Asheville 2000 0
> Asheville 2000 0
> Asheville 2000 2
> Asheville 2000 3
> Asheville 2000 1
> Asheville 2000 2
> Asheville 2000 1
> Asheville 2000 1
> Asheville 2000 0
> Asheville 2000 0
> Asheville 2000 1
> Asheville 2001 1
> Asheville 2001 3
> Asheville 2001 0
> Asheville 2001 0
> Asheville 2001 2
> Asheville 2001 3
> Asheville 2001 3
> Charlotte 2000 5
> Charlotte 2000 1
> Charlotte 2000 0
> Charlotte 2000 4
> Charlotte 2000 1
> Charlotte 2000 3
> Charlotte 2000 0
> Charlotte 2000 3
> Charlotte 2000 3
> Charlotte 2000 3
> Charlotte 2000 2
> Charlotte 2000 1
> Charlotte 2000 1
> Charlotte 2000 3
> Charlotte 2001 1
> Charlotte 2001 4
> Charlotte 2001 2
> Charlotte 2001 4
> Charlotte 2001 3
> Charlotte 2001 3
> Charlotte 2001 1
> Charlotte 2001 7
> Charlotte 2001 4
> Charlotte 2001 1
>
> Sample: http://www.imachordata.com/wp-content/uploads/2009/09/boxplot.png
>
> Thanks!
>
>
> On Wed, Nov 25, 2009 at 2:45 PM, David Winsemius <dwinsemius@...>wrote:
>
>>
>> On Nov 25, 2009, at 1:48 PM, Gary wrote:
>>
>> Hi R Users,
>>>
>>> I tried plotting a similar boxplot as it is on the FOLLOWING LINK:
>>>
>>> http://www.imachordata.com/wp-content/uploads/2009/09/boxplot.png
>>>
>>
>> Looks like a product of a function from ggplot2. In fact trimming that URL
>> brings you to a page with the code that created it!
>>
>>>
>>> Sample data is attached --
>>>
>>
>> No, it's not. Read the Posting Guide for what file types are acceptable to
>> the server. I suspect you will get better success if the extension is
>> ".txt", even if it is comma separated.
>>
>> Or better yet follow the directions there for posting data in a form that
>> can be enclosed in your posting and copy-pasted into the console session.
>>
>>
>>
>> there are 9 years and 5 cities. In my case I'm
>>> looking to plot "Year" on x-axis and grouping boxplots by "City". I tried
>>> the following code.
>>>
>>> foo<-read.table("SampleData.csv", sep=",", header=TRUE)
>>> attach(foo)
>>> boxplot(Admit ~ City + Year, range=0.5, col=2:6) # its not solving the
>>> purpose
>>>
>>> I need some help with:
>>> 1) Plotting only 9 labels on x-axis (1996-2004).
>>> 2) For each "Year", I need to plot FIVE boxplots -- one for each "City".
>>> [so
>>> it will look like nine clusters with five boxplots each (with no gap
>>> between
>>> them, but with gaps between year labels].
>>> 3) Adding "MEAN" to the boxplots.
>>> 4) And, legend including "color" + "city name".
>>>
>>> Any help would be greatly appreciated!
>>>
>>>
>>
>> David Winsemius, MD
>> Heritage Laboratories
>> West Hartford, CT
>>
>>
>

Re: Mysterious R script behavior when called from webserver

2009-11-25T12:41:21Z

On Wednesday 25 November 2009, Barry Rowlingson wrote:

> On Wed, Nov 25, 2009 at 8:15 PM, Dylan Beaudette
>
> <debeaudette@...> wrote:
> > Hi,
> >
> > I am trying to transition a system based on dynamic image generation (via
> > R) from our development system to a production environment. Our R script
> > functions as expected when run by a regular user. However the script dies
> > when calling the png() function, when started by the webserver user.
> >
> > Here are some details
> >
> >>sessionInfo()
> >
> > R version 2.9.2 (2009-08-24)
> > i686-pc-linux-gnu
> > locale:
> > C
> > attached base packages:
> > [1] stats graphics grDevices utils datasets methods base
> >
> > The script gets to this line:
> >
> > png(file=filename, width=600, height=400)
> >
> > and then dies. It leaves an empty PNG file where it should be, however it
> > never finishes the file. If
> >
> > I replace png() with pdf() an output file is generated and closed by
> > dev.off() as expected.
> >
> > It seems like the environment is setup just as when started by a regular
> > user, specifically the LD_LIBRARY_PATH variable.
> >
> > This behavior suggests that R is encountering an error, and stopping.
> > However there is no reporting of the error. Is there any way to get more
> > verbose error reporting?
>
> How is R run from your web server? Does it start a new R process or
> is it an apache module thing with a dynamically linked R (if such a
> thing even exists)? Can't figure out how you could get more error
> reporting without knowing that - you need to see where stderr is
> going, possibly to the apache error.log file - have you looked there?
>
> Have you tried a trivial png generating example, just a three liner:
>
> png(file="/tmp/wherever/foo.png")
> plot(1:10)
> dev.off()
>
> just in case it's something else previous in your script that's
> breaking things.
>
> In the old days of R you needed an X11 display connection to do PNG
> graphics, but that was fixed before 2.9, I think. Try it interactively
> but unset the DISPLAY variable first:
>
> export -n DISPLAY
> R
>
> > png(... etc etc)
>
> Does that work?
>
> Barry

Hi Barry thanks for the tips. I was able to get more error reporting by
placing the png() function inside of try(). Turns out this was an X11 related
problem-- probably an unset DISPLAY variable for the www user.

For the record, R was being run by PHP. I just realized that R was not
compiled with Cairo support-- fixing this should make the problems go away...

Cheers,
Dylan

--
Dylan Beaudette
Soil Resource Laboratory
http://casoilresource.lawr.ucdavis.edu/
University of California at Davis
530.754.7341

______________________________________________
R-help@... 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: Mysterious R script behavior when called from webserver

2009-11-25T12:36:01Z

On Wed, Nov 25, 2009 at 8:15 PM, Dylan Beaudette
<debeaudette@...> wrote:

> Hi,
>
> I am trying to transition a system based on dynamic image generation (via R)
> from our development system to a production environment. Our R script
> functions as expected when run by a regular user. However the script dies
> when calling the png() function, when started by the webserver user.
>
> Here are some details
>
>>sessionInfo()
> R version 2.9.2 (2009-08-24)
> i686-pc-linux-gnu
> locale:
> C
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> The script gets to this line:
>
> png(file=filename, width=600, height=400)
>
> and then dies. It leaves an empty PNG file where it should be, however it
> never finishes the file. If
>
> I replace png() with pdf() an output file is generated and closed by dev.off()
> as expected.
>
> It seems like the environment is setup just as when started by a regular user,
> specifically the LD_LIBRARY_PATH variable.
>
> This behavior suggests that R is encountering an error, and stopping. However
> there is no reporting of the error. Is there any way to get more verbose
> error reporting?

How is R run from your web server? Does it start a new R process or
is it an apache module thing with a dynamically linked R (if such a
thing even exists)? Can't figure out how you could get more error
reporting without knowing that - you need to see where stderr is
going, possibly to the apache error.log file - have you looked there?

Have you tried a trivial png generating example, just a three liner:

png(file="/tmp/wherever/foo.png")
plot(1:10)
dev.off()

just in case it's something else previous in your script that's
breaking things.

In the old days of R you needed an X11 display connection to do PNG
graphics, but that was fixed before 2.9, I think. Try it interactively
but unset the DISPLAY variable first:

export -n DISPLAY
R
> png(... etc etc)

Does that work?

Barry

______________________________________________
R-help@... 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.

error with hmm()?

2009-11-25T12:29:10Z

Hello R users,

I am suing library(hmm.discnp)
I have a vector
y
".... 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0
[741] 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 2 2 1 0 0 0 0 0...."

So I did

y=y+1 (Otherwise R crahsed)

"... 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 6 1 1 1 1 1 1 1 1 1 1 1 1 1
[741] 1 1 1 1 1 1 1 1 1 6 1 1 1 1 1 1 1 3 3 2 1 1 ..."

I try to fit a hidden markov model with two states.
hmm(y,K=2)
and this is what I get

Error in FUN(X[[1L]], ...) : subscript out of bounds?

where is my error?
Thanks,
below is the system I use.

version.string R version 2.8.1 (2008-12-22)
platform i686-suse-linux-gnu

[[alternative HTML version deleted]]

______________________________________________
R-help@... 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.

Mysterious R script behavior when called from webserver

2009-11-25T12:15:42Z

Hi,

I am trying to transition a system based on dynamic image generation (via R)
from our development system to a production environment. Our R script
functions as expected when run by a regular user. However the script dies
when calling the png() function, when started by the webserver user.

Here are some details

>sessionInfo()
R version 2.9.2 (2009-08-24)
i686-pc-linux-gnu
locale:
C
attached base packages:
[1] stats graphics grDevices utils datasets methods base

The script gets to this line:

png(file=filename, width=600, height=400)

and then dies. It leaves an empty PNG file where it should be, however it
never finishes the file. If

I replace png() with pdf() an output file is generated and closed by dev.off()
as expected.

It seems like the environment is setup just as when started by a regular user,
specifically the LD_LIBRARY_PATH variable.

This behavior suggests that R is encountering an error, and stopping. However
there is no reporting of the error. Is there any way to get more verbose
error reporting?

Cheers,
Dylan

--
Dylan Beaudette
Soil Resource Laboratory
http://casoilresource.lawr.ucdavis.edu/
University of California at Davis
530.754.7341

______________________________________________
R-help@... 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: Reading from Google Docs

2009-11-25T12:15:28Z

On Wed, Nov 25, 2009 at 12:02 PM, Farrel Buchinsky <fjbuch@...> wrote:
> I reinstalled from a binary that Duncan Temple Lang placed in omegahat. I
> see that omegahat has a subdirectory for each version of R. There is not a
> directory for 2.10. I took the liberty of taking it from the 2.9 directory.

That explains the warning message.

> Who knows what crime I committed. Is that first or third degree murder.

Well, it's just a warning-- so it shouldn't be a show-stopper. And
from what I see the warning is only referring to the package help
pages, which are available online. It looks like the functionality of
the package should still work just fine if you don't want to bother
with a reinstall.

> I saw however that there is a far more recent version of RGoogleDocs (Last
> Release: 0.4-0 (27 Oct 2009)). But it is in tar.gz. I assume that it is in
> source. Once before I spent about 27000 hours getting a source to become a
> binary. I don't know how I finally got it right and am reluctant to wander
> into that swamp again.
> Farrel Buchinsky

This shouldn't be extraordinarily difficult-- unfortunately Murphy's
Law does come into play sometimes. But it should just be a matter of:

install.packages( "RGoogleDocs", repos="http://www.omegahat.org/R",
type="source" )

And that's it for Linux, Mac OS or other UNIX-based system. With
Windows you will first have to install the toolset available at:

http://www.murdoch-sutherland.com/Rtools/

Grab the "Rtools210" installer as you are using R 2.10.x. Install
using the "Package Authoring" option and make sure you check any
options that ask about modifying your PATH.

Good luck!

-Charlie

______________________________________________
R-help@... 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.

Charlie Sharpsteen
Undergraduate
Environmental Resources Engineering
Humboldt State University

Re: Grouped Barplot

2009-11-25T12:15:05Z

Thanks David. I reduced the data set and its copied below (also attached to
this email as text file). Now N=50, Only 2 years, Only 2 Cities. I tried:

foo<-read.table("SampleData.txt", header=TRUE)
boxplot(foo$admit ~ foo$city + foo$year, col=2:3)

I need some help with:
1) Defining labels for x-axis (just "2000" and "2001").
2) Removing gap between cities boxplots (but leaving gap between years).
3) Adding "MEAN" to the boxplots.
4) Adding legend including "color" + "city name".

city year admit
Asheville 2000 0
Asheville 2000 0
Asheville 2000 1
Asheville 2000 2
Asheville 2000 2
Asheville 2000 0
Asheville 2000 1
Asheville 2000 0
Asheville 2000 0
Asheville 2000 0
Asheville 2000 2
Asheville 2000 3
Asheville 2000 1
Asheville 2000 2
Asheville 2000 1
Asheville 2000 1
Asheville 2000 0
Asheville 2000 0
Asheville 2000 1
Asheville 2001 1
Asheville 2001 3
Asheville 2001 0
Asheville 2001 0
Asheville 2001 2
Asheville 2001 3
Asheville 2001 3
Charlotte 2000 5
Charlotte 2000 1
Charlotte 2000 0
Charlotte 2000 4
Charlotte 2000 1
Charlotte 2000 3
Charlotte 2000 0
Charlotte 2000 3
Charlotte 2000 3
Charlotte 2000 3
Charlotte 2000 2
Charlotte 2000 1
Charlotte 2000 1
Charlotte 2000 3
Charlotte 2001 1
Charlotte 2001 4
Charlotte 2001 2
Charlotte 2001 4
Charlotte 2001 3
Charlotte 2001 3
Charlotte 2001 1
Charlotte 2001 7
Charlotte 2001 4
Charlotte 2001 1

Sample: http://www.imachordata.com/wp-content/uploads/2009/09/boxplot.png

Thanks!

On Wed, Nov 25, 2009 at 2:45 PM, David Winsemius <dwinsemius@...>wrote:

>
> On Nov 25, 2009, at 1:48 PM, Gary wrote:
>
> Hi R Users,
>>
>> I tried plotting a similar boxplot as it is on the FOLLOWING LINK:
>>
>> http://www.imachordata.com/wp-content/uploads/2009/09/boxplot.png
>>
>
> Looks like a product of a function from ggplot2. In fact trimming that URL
> brings you to a page with the code that created it!
>
>>
>> Sample data is attached --
>>
>
> No, it's not. Read the Posting Guide for what file types are acceptable to
> the server. I suspect you will get better success if the extension is
> ".txt", even if it is comma separated.
>
> Or better yet follow the directions there for posting data in a form that
> can be enclosed in your posting and copy-pasted into the console session.
>
>
>
> there are 9 years and 5 cities. In my case I'm
>> looking to plot "Year" on x-axis and grouping boxplots by "City". I tried
>> the following code.
>>
>> foo<-read.table("SampleData.csv", sep=",", header=TRUE)
>> attach(foo)
>> boxplot(Admit ~ City + Year, range=0.5, col=2:6) # its not solving the
>> purpose
>>
>> I need some help with:
>> 1) Plotting only 9 labels on x-axis (1996-2004).
>> 2) For each "Year", I need to plot FIVE boxplots -- one for each "City".
>> [so
>> it will look like nine clusters with five boxplots each (with no gap
>> between
>> them, but with gaps between year labels].
>> 3) Adding "MEAN" to the boxplots.
>> 4) And, legend including "color" + "city name".
>>
>> Any help would be greatly appreciated!
>>
>>
>
> David Winsemius, MD
> Heritage Laboratories
> West Hartford, CT
>
>

city year admit
Asheville 2000 0
Asheville 2000 0
Asheville 2000 1
Asheville 2000 2
Asheville 2000 2
Asheville 2000 0
Asheville 2000 1
Asheville 2000 0
Asheville 2000 0
Asheville 2000 0
Asheville 2000 2
Asheville 2000 3
Asheville 2000 1
Asheville 2000 2
Asheville 2000 1
Asheville 2000 1
Asheville 2000 0
Asheville 2000 0
Asheville 2000 1
Asheville 2001 1
Asheville 2001 3
Asheville 2001 0
Asheville 2001 0
Asheville 2001 2
Asheville 2001 3
Asheville 2001 3
Charlotte 2000 5
Charlotte 2000 1
Charlotte 2000 0
Charlotte 2000 4
Charlotte 2000 1
Charlotte 2000 3
Charlotte 2000 0
Charlotte 2000 3
Charlotte 2000 3
Charlotte 2000 3
Charlotte 2000 2
Charlotte 2000 1
Charlotte 2000 1
Charlotte 2000 3
Charlotte 2001 1
Charlotte 2001 4
Charlotte 2001 2
Charlotte 2001 4
Charlotte 2001 3
Charlotte 2001 3
Charlotte 2001 1
Charlotte 2001 7
Charlotte 2001 4
Charlotte 2001 1

______________________________________________
R-help@... 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: Feature request for as.Date() function

2009-11-25T11:56:56Z

Seems to work fine in my testing:

> x <- read.csv(textConnection("date,value
+ 2009-01-01,10
+ 2009-02-01,1
+ 'NA', 3"), colClasses=c("Date", 'integer'))
>
> str(x)
'data.frame': 3 obs. of 2 variables:
$ date :Class 'Date' num [1:3] 14245 14276 NA
$ value: int 10 1 3
> x <- read.csv(textConnection("date,value
+ 2009-01-01,10
+ 2009-02-01,1
+ NA, 3"), colClasses=c("Date", 'integer'))
>
> str(x)
'data.frame': 3 obs. of 2 variables:
$ date :Class 'Date' num [1:3] 14245 14276 NA
$ value: int 10 1 3
>

PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

On Wed, Nov 25, 2009 at 12:38 PM,
<nabble.30.miller_2555@...> wrote:

> Hello -
>
> I have a csv file with a few date columns. Some of the records have an
> "NA" character string instead of the date. When I attempt to use
> read.csv() and typecast the columns using colClasses, I receive the
> following error:
> Error in charToDate(x) :
> character string is not in a standard unambiguous format
>
> Similarly, the following command produces the same error:
> as.Date("NA")
>
> However, as.Date(NA) performs as documented.
>
> Can we enhance the as.Date() function to convert "NA" strings into NA
> value prior to type conversion?
>
> Thanks!
>
> ______________________________________________
> R-help@... mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

--
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem that you are trying to solve?

______________________________________________
R-help@... 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: Grouped Barplot

2009-11-25T11:45:30Z

On Nov 25, 2009, at 1:48 PM, Gary wrote:

> Hi R Users,
>
> I tried plotting a similar boxplot as it is on the FOLLOWING LINK:
>
> http://www.imachordata.com/wp-content/uploads/2009/09/boxplot.png

Looks like a product of a function from ggplot2. In fact trimming that
URL brings you to a page with the code that created it!
>
> Sample data is attached --

No, it's not. Read the Posting Guide for what file types are
acceptable to the server. I suspect you will get better success if the
extension is ".txt", even if it is comma separated.

Or better yet follow the directions there for posting data in a form
that can be enclosed in your posting and copy-pasted into the console
session.

> there are 9 years and 5 cities. In my case I'm
> looking to plot "Year" on x-axis and grouping boxplots by "City". I
> tried
> the following code.
>
> foo<-read.table("SampleData.csv", sep=",", header=TRUE)
> attach(foo)
> boxplot(Admit ~ City + Year, range=0.5, col=2:6) # its not solving the
> purpose
>
> I need some help with:
> 1) Plotting only 9 labels on x-axis (1996-2004).
> 2) For each "Year", I need to plot FIVE boxplots -- one for each
> "City". [so
> it will look like nine clusters with five boxplots each (with no gap
> between
> them, but with gaps between year labels].
> 3) Adding "MEAN" to the boxplots.
> 4) And, legend including "color" + "city name".
>
> Any help would be greatly appreciated!
>

David Winsemius, MD
Heritage Laboratories
West Hartford, CT

______________________________________________
R-help@... 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: Reading from Google Docs

2009-11-25T11:44:44Z

On Wed, Nov 25, 2009 at 5:39 AM, Farrel Buchinsky <fjbuch@...> wrote:

> I recently installed R 2.10
>
> Now I get
>
>> library(RGoogleDocs)
> Loading required package: RCurl
> Loading required package: bitops
> Loading required package: XML
>
> Attaching package: 'RGoogleDocs'
>
>
> The following object(s) are masked from package:methods :
>
> getAccess
>
> Warning message:
> package 'RGoogleDocs' was built under R version 2.9.1 and help will not work
> correctly
> Please re-install it
>
> But alas reinstalling it does not take away the error message.
> Farrel Buchinsky

How did you try reinstalling it? It sounds like you are using a
binary distribution that was built under 2.9.1-- you probably have to
build and install from a source distribution of the package.

-Charlie

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Charlie Sharpsteen
Undergraduate
Environmental Resources Engineering
Humboldt State University

Re: help writing for loop

2009-11-25T11:40:07Z

Hi,

The great thing about the S language is that it is 'vectorized',
so you can do a lot of matrix manipulations without loops.

Here's a smaller example of what you describe.
matrix A with 3 columns and 10 rows (instead of 100)
matrix B with 3 columns and 15 rows (instead of 1500)

> set.seed(123)
> mA <- matrix(runif(30), ncol = 3)
> mA
[,1] [,2] [,3]
[1,] 0.2875775 0.95683335 0.8895393
[2,] 0.7883051 0.45333416 0.6928034
[3,] 0.4089769 0.67757064 0.6405068
[4,] 0.8830174 0.57263340 0.9942698
[5,] 0.9404673 0.10292468 0.6557058
[6,] 0.0455565 0.89982497 0.7085305
[7,] 0.5281055 0.24608773 0.5440660
[8,] 0.8924190 0.04205953 0.5941420
[9,] 0.5514350 0.32792072 0.2891597
[10,] 0.4566147 0.95450365 0.1471136

> x <- seq(15)
> mB <- cbind(1, x, x^2)
> mB
x
[1,] 1 1 1
[2,] 1 2 4
[3,] 1 3 9
[4,] 1 4 16
[5,] 1 5 25
[6,] 1 6 36
[7,] 1 7 49
[8,] 1 8 64
[9,] 1 9 81
[10,] 1 10 100
[11,] 1 11 121
[12,] 1 12 144
[13,] 1 13 169
[14,] 1 14 196
[15,] 1 15 225

> mR <- apply(mB, 1, function(x){mA %*% x})
> mR
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 2.133950 5.759401 11.163931 18.347540 27.310227 38.05199 50.57284
[2,] 1.934443 4.466187 8.383538 13.686496 20.375061 28.44923 37.90901
[3,] 1.727054 4.326145 8.206250 13.367368 19.809500 27.53265 36.53681
[4,] 2.449921 6.005363 11.549346 19.081867 28.602929 40.11253 53.61067
[5,] 1.699098 3.769140 7.150594 11.843459 17.847736 25.16342 33.79052
[6,] 1.653912 4.679328 9.121806 14.981344 22.257943 30.95160 41.06232
[7,] 1.318259 3.196545 6.162963 10.217513 15.360195 21.59101 28.90995
[8,] 1.528621 3.353106 6.365876 10.566930 15.956267 22.53389 30.29979
[9,] 1.168515 2.363915 4.137635 6.489674 9.420032 12.92871 17.01571
[10,] 1.558232 2.954077 4.644149 6.628448 8.906974 11.47973 14.34671
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 64.87276 80.95176 98.80984 118.44700 139.86324 163.05856 188.03295
[2,] 48.75440 60.98539 74.60199 89.60419 105.99201 123.76542 142.92445
[3,] 46.82198 58.38816 71.23536 85.36358 100.77281 117.46305 135.43430
[4,] 69.09735 86.57257 106.03633 127.48863 150.92947 176.35884 203.77676
[5,] 43.72904 54.97896 67.54029 81.41304 96.59720 113.09277 130.89975
[6,] 52.59011 65.53495 79.89685 95.67582 112.87184 131.48493 151.51508
[7,] 37.31703 46.81224 57.39559 69.06706 81.82667 95.67440 110.61027
[8,] 39.25398 49.39646 60.72722 73.24626 86.95358 101.84919 117.93309
[9,] 21.68102 26.92466 32.74662 39.14689 46.12549 53.68240 61.81763
[10,] 17.50792 20.96335 24.71302 28.75691 33.09502 37.72737 42.65394
[,15]
[1,] 214.78642
[2,] 163.46908
[3,] 154.68657
[4,] 233.18322
[5,] 150.01814
[6,] 172.96229
[7,] 126.63428
[8,] 135.20527
[9,] 70.53119
[10,] 47.87474
>

so the results matrix mR has one column for each element of x,
and the i-th row element is the solution for
y = a + bx + cx^2
for the i-th row of coefficients in the parameter estimates matrix mA

You can spot check with e.g.

> mA[1,] %*% mB[15,]
[,1]
[1,] 214.7864
> mA[1,] %*% mB[5,]
[,1]
[1,] 27.31023
> mA[1,]
[1] 0.2875775 0.9568333 0.8895393
> mB[5,]
x
1 5 25
>

HTH

Steven McKinney, Ph.D.

Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre

email: smckinney +at+ bccrc +dot+ ca

tel: 604-675-8000 x7561

BCCRC
Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C.
V5Z 1L3
Canada

________________________________________
From: r-help-bounces@... [r-help-bounces@...] On Behalf Of Jessica Schedlbauer [jschedlb@...]
Sent: November 25, 2009 10:43 AM
To: r-help@...
Subject: [R] help writing for loop

Hi,

I’d like to ask for some help in writing a loop. My situation is the following:

I have a matrix (matrix.A) containing 3 columns and 100 rows. The columns represent parameter estimates a, b, and c. The rows contain different values for these parameter estimates. Each row is unique.

I want to insert these parameter estimates into a model (say, y = a + bx + cx^2) and solve for y given a separate matrix (matrix.B) of x values (where x has a length of 1500).

I want to solve for y 100 times using each set of the parameter estimates in matrix.A once.

At present my code looks like this and it only performs the first iteration.

For (i in 1:length(matrix.A)) { y <- matrix.A$a[[i]] + matrixA$b[[i]] * matrix.B$x + matrixA$c[[i]] * matrix.B$x^2)

I have not been able to figure out how to loop through the rows of parameter estimates in matrix.A. I am new to writing loops, so any assistance would be much appreciated.

Regards,
Jessica Schedlbauer

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Re: Grouped Barplot

2009-11-25T11:23:53Z

On 11/25/2009 07:48 PM, Gary wrote:

> Hi R Users,
>
> I tried plotting a similar boxplot as it is on the FOLLOWING LINK:
>
> http://www.imachordata.com/wp-content/uploads/2009/09/boxplot.png
>
> Sample data is attached -- there are 9 years and 5 cities. In my case I'm
> looking to plot "Year" on x-axis and grouping boxplots by "City". I tried
> the following code.
>
> foo<-read.table("SampleData.csv", sep=",", header=TRUE)
> attach(foo)
> boxplot(Admit ~ City + Year, range=0.5, col=2:6) # its not solving the
> purpose
>
> I need some help with:
> 1) Plotting only 9 labels on x-axis (1996-2004).
> 2) For each "Year", I need to plot FIVE boxplots -- one for each "City". [so
> it will look like nine clusters with five boxplots each (with no gap between
> them, but with gaps between year labels].
> 3) Adding "MEAN" to the boxplots.
> 4) And, legend including "color" + "city name".
>
> Any help would be greatly appreciated!
>
> ~Gary
>
>
>
> ______________________________________________
> R-help@... 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.
>

Have a look at
https://stat.ethz.ch/pipermail/r-help/2000-November/009191.html. Might
be what you're looking for.

[[alternative HTML version deleted]]

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Re: predict: remove columns with new levels automatically

2009-11-25T11:20:30Z

Thank you all for the good advice.

Now i did a fast hack, which does want i was looking for, maybe anyone
else finds this usefull

set.seed(0)
x <- rnorm(9)
y <- x + rnorm(9)

training <- data.frame(x=x, y=y,
z1=c(rep("A", 3), rep("B", 3), rep("C", 3)),
z2=c(rep("F", 4), rep("G", 5)))
test <- data.frame(x=t<-rnorm(1), y=t+rnorm(1), z1="D", z2="F")

`predict.drop` <- function(f, dat, newdat)
{
datlev <- vector("list", ncol(dat))
newdatlev <- vector("list", ncol(newdat))

`filllevs` <- function(dat, veclev)
{
for (j in 1:ncol(dat))
{
if (is.factor(dat[,j]))
veclev[[j]] <- levels(dat[,j])
else
veclev[[j]] <- NULL
}

return(veclev)
}

datlev <- filllevs(dat, datlev)
newdatlev <- filllevs(newdat, newdatlev)

if (ncol(dat) == ncol(newdat))
{
drop <- logical(ncol(dat))
names(drop) <- colnames(dat)

for (j in 1:ncol(dat))
{
if (!is.null(datlev[[j]]))
{
if (!(newdatlev[[j]] %in% datlev[[j]]))
drop[j] <- TRUE
}
}
}
else
stop("dat and newdat must have the same column length!")

m <- lm(formula(f), data=dat[,(1:ncol(dat))[!drop]])
p <- predict(m, newdat)

return(list(drop=drop, p=p))
}

predict.drop(x ~ ., training, test)

best regards

Andreas

David Winsemius wrote:

>
> On Nov 25, 2009, at 1:48 AM, Andreas Wittmann wrote:
>
>> Sorry for my bad description, i don't want get a constructed
>> algorithm without own work. i only hoped to get some advice how to do
>> this. i don't want to predict any sort of data, i reference only to
>> newdata which variables are the same as in the model data. But if
>> factors in the data than i can by possibly that the newdata has a
>> level which doesn't exist in the original data.
>> So i have to compare each factor in the data and in the newdata and
>> if the newdata has a levels which is not in the original data and
>> drop this variable and do compute the model and prediction again.
>> I thought this problem is quite common and i can use an algorithm
>> somebody has already implemented.
>>
>> best regards
>>
>> Andreas
>>
> If you use str to look at the lm1 object you will find at the bottom a
> list called "x":
>
> lm1$x will show you the factors that were present in variables at the
> time of the model creation
> > lm1$x
> $z
> [1] "A" "B" "C"
>
> New testing scenario good level and bad level:
>
> test <- data.frame(x=t<-rnorm(2), y=t+rnorm(2), z=c("B", "D") )
> lm1 <- lm(x ~ ., data=training)
> predict(lm1, subset(test, z %in% lm1$x$z) ) # get prediction for
> good level only
> 1
> 0.4225204
>
>>
>>
>>
>> -------- Original-Nachricht --------
>>> Datum: Wed, 25 Nov 2009 00:48:59 -0500
>>> Von: David Winsemius <dwinsemius@...>
>>> An: Andreas Wittmann <andreas_wittmann@...>
>>> CC: r-help@...
>>> Betreff: Re: [R] predict: remove columns with new levels automatically
>>
>>>
>>> On Nov 24, 2009, at 2:24 PM, Andreas Wittmann wrote:
>>>
>>>> Dear R-users,
>>>>
>>>> in the follwing thread
>>>>
>>>> http://tolstoy.newcastle.edu.au/R/help/03b/3322.html
>>>>
>>>> the problem how to remove rows for predict that contain levels which
>>>> are not in the model.
>>>>
>>>> now i try to do this the other way round and want to remove columns
>>>> (variables) in the model which will be later problematic with new
>>>> levels for prediction.
>>>>
>>>> ## example:
>>>> set.seed(0)
>>>> x <- rnorm(9)
>>>> y <- x + rnorm(9)
>>>>
>>>> training <- data.frame(x=x, y=y, z=c(rep("A", 3), rep("B", 3),
>>>> rep("C", 3)))
>>>> test <- data.frame(x=t<-rnorm(1), y=t+rnorm(1), z="D")
>>>>
>>>> lm1 <- lm(x ~ ., data=training)
>>>> ## prediction does not work because the variable z has the new level
>>>> "D"
>>>> predict(lm1, test)
>>>>
>>>> ## solution: the variable z is removed from the model
>>>> ## the prediction happens without using the information of variable z
>>>> lm2 <- lm(x ~ y, data=training)
>>>> predict(lm2, test)
>>>>
>>>> How can i autmatically recognice this and calculate according to this?
>>>
>>> Let me get this straight. You want us to predict in advance (or more
>>> accurately design an algorithm that can see into the future and work
>>> around) any sort of newdata you might later construct????
>>>
>>> --
>>>
>>> David Winsemius, MD
>>> Heritage Laboratories
>>> West Hartford, CT
>>
>> --
>> Preisknaller: GMX DSL Flatrate für nur 16,99 Euro/mtl.!
>> http://portal.gmx.net/de/go/dsl02
>
> David Winsemius, MD
> Heritage Laboratories
> West Hartford, CT
>

Re: Is there a package for generating standardized R script command line options?

2009-11-25T11:04:00Z

> Hi,
>
> In python, there is a package that helps generating command line
> options. I am wondering if there is such a package in R that helps
> generating the command options for a R script?
>
> http://docs.python.org/library/optparse.html
>
> Regards,
> Peng

I recently put a package on CRAN that tries to implement much of the
functionality and approach of python's "optparse" library:

http://cran.r-project.org/web/packages/optparse/

It contains a package vignette (use vignette("optparse") after installing
the package) that illustrates an example program using optparse and trying
it with various options on the command line.

The "getopt" package or manually parsing the command line remain good
approaches too.

----------------------------------------------------------------------------
Trevor Davis
Research Assistant
Division of Research & Statistics
Federal Reserve Board of Governors

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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: order of panels in xyplots

2009-11-25T10:50:15Z

On 11/25/2009 07:33 PM, Titus Malsburg wrote:

> On Wed, Nov 25, 2009 at 7:03 PM, Titus Malsburg <malsburg@...> wrote:
>
>> I was expecting
>> that this should plot the panels in the order in which the levels
>> occur in the data frame:
>>
>> xyplot(dur~roi|trial, data, index.cond=unique(as.integer(data$trial)))
>>
> The answer is apparently:
>
> xyplot(dur~roi|trial, data, index.cond=rank(unique(data$trial)))
>
> (Strange phenomenon, that I very often find the solution myself
> minutes after posting to the mailing list.)
>
> Best,
> Titus
>
> ______________________________________________
> R-help@... 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.
>

An alternative could be to reorder the levels of "trial" prior to
calling xyplot or in the xyplot call itself (useful if you want to order
the levels on some other criterion like the mean or median of another
variable). See ?reorder

Just a thought

S

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Grouped Barplot

2009-11-25T10:48:23Z

Hi R Users,

I tried plotting a similar boxplot as it is on the FOLLOWING LINK:

http://www.imachordata.com/wp-content/uploads/2009/09/boxplot.png

Sample data is attached -- there are 9 years and 5 cities. In my case I'm
looking to plot "Year" on x-axis and grouping boxplots by "City". I tried
the following code.

foo<-read.table("SampleData.csv", sep=",", header=TRUE)
attach(foo)
boxplot(Admit ~ City + Year, range=0.5, col=2:6) # its not solving the
purpose

I need some help with:
1) Plotting only 9 labels on x-axis (1996-2004).
2) For each "Year", I need to plot FIVE boxplots -- one for each "City". [so
it will look like nine clusters with five boxplots each (with no gap between
them, but with gaps between year labels].
3) Adding "MEAN" to the boxplots.
4) And, legend including "color" + "city name".

Any help would be greatly appreciated!

~Gary

______________________________________________
R-help@... 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.

help writing for loop

2009-11-25T10:43:59Z

Hi,

I’d like to ask for some help in writing a loop. My situation is the following:

I have a matrix (matrix.A) containing 3 columns and 100 rows. The columns represent parameter estimates a, b, and c. The rows contain different values for these parameter estimates. Each row is unique.

I want to insert these parameter estimates into a model (say, y = a + bx + cx^2) and solve for y given a separate matrix (matrix.B) of x values (where x has a length of 1500).

I want to solve for y 100 times using each set of the parameter estimates in matrix.A once.

At present my code looks like this and it only performs the first iteration.

For (i in 1:length(matrix.A)) { y <- matrix.A$a[[i]] + matrixA$b[[i]] * matrix.B$x + matrixA$c[[i]] * matrix.B$x^2)

I have not been able to figure out how to loop through the rows of parameter estimates in matrix.A. I am new to writing loops, so any assistance would be much appreciated.

Regards,
Jessica Schedlbauer

______________________________________________
R-help@... 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: order of panels in xyplots

2009-11-25T10:39:26Z

The documentation of xyplot could be improved here. It says:

"If 'index.cond' is a list, it has to be as long as the number of conditioning
variables, and the 'i'-th component has to be a valid indexing vector for the
integer vector '1:nlevels(g_i)' (which can, among other things, repeat some
of the levels or drop some altogether)."

It should make explicit that nlevels is the number of levels actually
used in the data and not length(levels(f)).

Cheers,

Titus

______________________________________________
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and provide commented, minimal, self-contained, reproducible code.