[R] Error while installing 'netmodels'
Dear all ,
I am trying to install a package by name 'netmodels' keep
on getting the following error :
> install.packages("netmodels")
Warning in install.packages("netmodels") :
argument 'lib' is missing: using '/usr/lib64/R/library'
also installing the dependency VGAM
trying URL 'http://cran.stat.ucla.edu/src/contrib/VGAM_0.7-10.tar.gz'
Content type 'application/x-tar' length 1608488 bytes (1.5 Mb)
opened URL
==
downloaded 1.5 Mb
trying URL 'http://cran.stat.ucla.edu/src/contrib/netmodels_0.2.tar.gz'
Content type 'application/x-tar' length 20049 bytes (19 Kb)
opened URL
==
downloaded 19 Kb
* Installing *source* package VGAM ...
** libs
gfortran -fpic -O2 -g -c cqof.f -o cqof.o
gfortran: error trying to exec 'f951': execvp: No such file or directory
make: *** [cqof.o] Error 1
ERROR: compilation failed for package VGAM
* Removing /usr/lib64/R/library/VGAM
* Installing *source* package netmodels ...
** R
** data
** preparing package for lazy loading
Error : package 'VGAM' required by 'netmodels' could not be found
ERROR: lazy loading failed for package netmodels
* Removing /usr/lib64/R/library/netmodels
The downloaded packages are in
/tmp/RtmpnUr2jb/downloaded_packages
Updating HTML index of packages in '.Library'
Warning messages:
1: In install.packages("netmodels") :
installation of package 'VGAM' had non-zero exit status
2: In install.packages("netmodels") :
installation of package 'netmodels' had non-zero exit status
Here's my sessionInfo(). Can anyone help me out with this ?
> sessionInfo()
R version 2.9.0 (2009-04-17)
x86_64-redhat-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tcltk_2.9.0 tools_2.9.0
> Detecting remotely related proteins by their
Error: unexpected symbol in "Detecting remotely"
> interactions and sequence similarity
Error: unexpected symbol in "interactions and"
Regards,
Anupam Sinha
[[alternative HTML version deleted]]
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Re: [R] sql query variable
RagingJim wrote: > > This is the very last thing I need to make everything work properly. My > query: > sqlQuery(conn, "select to_char(lsd,'-mm') as yr,ttl_mo_prcp from > mo_rains where stn_num=023000") > > Is there a way to may the stn_num in the query variable, ie make it so > that whenever my script is run, the user must choose and input the station > number? > You could use tclTk to input the stn_num, and generate the query string with paste() Dieter -- View this message in context: http://n4.nabble.com/sql-query-variable-tp1558189p1558308.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to compute heteroskedasticity-robust LM statistic?
Anyone using Wooldrige's Introductory Econometrics: A Modern Approach?
In the 3rd edition example 8.3, I use the following method to compute
heteroskedasticity-robust LM statistic
library(car)
linear.hypothesis(model,c("avgsen=0","I(avgsen^2)=0")
,test="Chisq",vcov=hccm(model,type="hc0"))
The result is different from the one introduced in the text. The p-value is
also differ greatly from using heteroskedasticity-robust F statistic.
Any thought on this?
--
View this message in context:
http://n4.nabble.com/How-to-compute-heteroskedasticity-robust-LM-statistic-tp1558305p1558305.html
Sent from the R help mailing list archive at Nabble.com.
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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] error message when downloading packages using the OS X shell
Thank you all for your help thus far. I have taken care of the destdir
issue (you do need to specify a destdir, something I never had to do
with OS X 10.4). However, a delightful new message has popped up. Has
anyone seen this one before? I've tried both an R CMD INSTALL command
from the shell and the download.packages() command within the R
environment but neither works. In the terminal I get this error:
$ R CMD INSTALL genetics_1.3.4.tgz
Warning: invalid package ‘genetics_1.3.4.tgz’
while in R I get this error:
> download.packages(genetics,destdir=.libPaths())
Error in unique(pkgs) : object 'genetics' not found
The errors are not worded the same but they appear to be suggesting
the same issue. I've tried the names of 6 or so different packages
just to see what would happen but it's always the same message. And,
in answer to Ista, I am using download.packages() instead of
install.packages() because they are both giving me the same error
message but at least download.packages() gives me some response by
loading a Tcl/Tk interface to select my CRAN mirror so I at least know
it's working.
Thank you all!
Jessica
On Mon, Feb 15, 2010 at 11:11 PM, Ista Zahn wrote:
>
> Hi Jessica,
> As far as I know that's the expected behavior (at least it's not OS
> X-specific: I get the same on OpenSuse 11.2). What happens if you do
>
> download.packages("ape", destdir = "~/Desktop/")
>
> ?
>
> Also, out of curiosity, why are you using download.packages() instead
> of install.packages()?
>
> Best,
> Ista
>
> On Mon, Feb 15, 2010 at 10:51 PM, Jessica Joganic wrote:
> > I apologize for not including my entire script. What I typed into the shell
> > was:
> >
> > *download.packages(ape)*
> >
> > to which R responded with a Tcl/Tk interface allowing me to set my CRAN.
> > After I did so it proceeded to spit out the following error:
> >
> > *Loading Tcl/Tk interface ... done*
> > Error in **file.info* *(x) : argument "destdir" is
> > missing, with no default*
> >
> > Let me know if that doesn't clarify my query. If this ends up being a
> > product of my preferring the terminal over the R.app then I'll post to the
> > Mac people and see what they have to say.
> >
> > Jessica
> > **
> >
> > On Mon, Feb 15, 2010 at 9:06 PM, David Winsemius
> > wrote:
> >
> >>
> >> On Feb 15, 2010, at 8:58 PM, Jessica Joganic wrote:
> >>
> >> Hi Fellow R Users,
> >>> I recently upgraded to Mac OS X 10.5 (Snow Leopard) and had some issues
> >>> downloading and running R 2.10.1. I fixed the tcl/tk problem I was
> >>> originally having but it was replaced with another. I run R out of the
> >>> shell
> >>> (terminal) and when I ask it to download.packages() it gives me the
> >>> following message:
> >>>
> >>> *Loading Tcl/Tk interface ... done*
> >>> *Error in file.info(x) : argument "destdir" is missing, with no default*
> >>> *
> >>> *
> >>>
> >>
> >> I am a bit puzzled by that function call. I would have expected there to be
> >> some arguments in the call. What were you expecting to be the results?
> >> After I run that function, I get a window of CRAN sites to choose and
> >> after
> >> choosing the CMU site I get:
> >>
> >> > download.packages()
> >> --- Please select a CRAN mirror for use in this session ---
> >>
> >> Loading Tcl/Tk interface ... done
> >> Error in file.info(x) : argument "destdir" is missing, with no default
> >>
> >> I searched around on the help archives and various online message boards
> >>> and
> >>> the most I could discern was that the directory where the library is
> >>> located
> >>> isn't being recognized by R (it should recognize it by default). I tried
> >>> setting the "destdir" argument manually to no avail. I am able to
> >>> successfully download and install packages with no problem if I run the
> >>> actual R program out of the Applications folder,
> >>>
> >>
> >> Heh, the thing you are calling the "actual R program" is probably the
> >> R-GUI, typically named R.app or R64.app, and it is a front-end to the R
> >> executable.
> >>
> >>
> >> however I prefer to use the
> >>> shell. I did find one mention of a recognized issue with OS X 10.5 and R
> >>> 2.10.1 conflicting when trying to download packages, which results in the
> >>> library pathway being broken. The only problem is the fix for this problem
> >>>
> >>
> >> given in the R manual doesn't work. Has anyone had a similar problem or
> >>> have
> >>> any ideas as to how to solve this?
> >>>
> >>
> >> It happens for me as well, but I guess I don't see it as a problem, since I
> >> did not offer a sensible set of arguments to the function. (Plus, I always
> >> use the GUI despite Rolf Turner's efforts to shame me into being a terminal
> >> dude.) You may want to post follow-ups to the Mac-SIG mailing list where
> >> this would be amore appropriate question:
> >>
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >>
> >>>
> >>> --
> >>
> >> David Winsemius, MD
> >> Heritage Laboratories
> >> West Hartford, CT
> >>
> >>
> >
>
Re: [R] Bivariate Uniform distribution
> -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] > On Behalf Of li li > Sent: Tuesday, February 16, 2010 6:46 PM > To: r-help > Subject: [R] Bivariate Uniform distribution > > Hi all, >Is there a function in R to calculate the probability, or quantile, or > generate random numbers, and so on for > bivariate uniform distribution, like for the bivariate normal > distribution? >Thanks! > Hannah > Hannah, It might help to know what you are trying to do, so that better advice can be given. A bivariate uniform distribution is simply pairs of uniform random numbers. The density is constant, so it is easy to get to the other quantities that you want based on that. So what is it that you are actually wanting to do? Dan Daniel Nordlund Bothell, WA USA __ 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] Using text put into a dialog box
Thanks mate, awesome :) Everything is now working as ordered. Thanks to everyone who has chipped in and helped out this past week, much appreciated!!! -- View this message in context: http://n4.nabble.com/Using-text-put-into-a-dialog-box-tp1555761p1558278.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Using text put into a dialog box
This function will pop up the window, get the number, and return it:
tmpfun <- function() {
tt <- tktoplevel()
Name <- tclVar("")
entry.Name <-tkentry(tt,width="20",textvariable=Name)
tkgrid(tklabel(tt,text="Please enter site number."))
tkgrid(entry.Name)
OnOK <- function()
{
NameVal <- tclvalue(Name)
use.this=NameVal
tkdestroy(tt)
}
OK.but <-tkbutton(tt,text=" OK ",command=OnOK)
tkbind(entry.Name, "",OnOK)
tkgrid(OK.but)
tkwait.window(tt)
return(as.numeric(tclvalue(Name)))
}
Run it like:
> tmp <- tmpfun()
And after clicking on OK tmp will have the number in it.
The database experts will need to tell you how to include that into your query
(either using the above function, or putting the query in place of the return
and returning the result).
Hope this helps,
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111
> -Original Message-
> From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
> project.org] On Behalf Of RagingJim
> Sent: Tuesday, February 16, 2010 5:31 PM
> To: r-help@r-project.org
> Subject: Re: [R] Using text put into a dialog box
>
>
> Thanks Greg, the problem is I have no idea how to return and use what I
> have
> typed into the pop up. Add to that the complication that with this
> query
>
> x<-sqlQuery(conn, "select to_char(lsd,'-mm') as yr,ttl_mo_prcp from
> mo_rains where stn_num=23090")
>
> if I put anything other than a number into stn_num=... then it does not
> run.
> eg if I just do sn=23090 and then use that in the query
>
> sqlQuery(conn, "select to_char(lsd,'-mm') as yr,ttl_mo_prcp from
> mo_rains where stn_num=sn")
>
> I get the following error.
>
> [1] "[RODBC] ERROR: Could not SQLExecDirect"
> [2] "42S22 904 [Oracle][ODBC][Ora]ORA-00904: \"SN\": invalid
> identifier\n"
>
> So my question is in two parts. Firstly, how do I return the number
> written
> in the popup, and then secondly how do I actually put it into the
> query?
>
> Thanks again
> --
> View this message in context: http://n4.nabble.com/Using-text-put-into-
> a-dialog-box-tp1555761p1558124.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.
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Re: [R] converting character vector "hh:mm" to chron or strptime 24 clock time vectors
Try this (and note that times must be less than 24 hours): > Lines <- "LogData date time + 177.16 2008/04/24 02:00 + 261.78 2008/04/24 04:00 + 375.44 2008/04/24 06:00 + 489.43 2008/04/24 08:00 + 595.83 2008/04/24 10:00 + 696.88 2008/04/24 24:00" > > DF <- read.table(textConnection(Lines)) > > library(chron) > DF2 <- transform(DF, + chron = as.chron(paste(date, time)), + POSIXct = as.POSIXct(paste(date, time))) > DF2 LogData date time chron POSIXct 1 77.16 2008/04/24 02:00 (04/24/08 02:00:00) 2008-04-24 02:00:00 2 61.78 2008/04/24 04:00 (04/24/08 04:00:00) 2008-04-24 04:00:00 3 75.44 2008/04/24 06:00 (04/24/08 06:00:00) 2008-04-24 06:00:00 4 89.43 2008/04/24 08:00 (04/24/08 08:00:00) 2008-04-24 08:00:00 5 95.83 2008/04/24 10:00 (04/24/08 10:00:00) 2008-04-24 10:00:00 6 96.88 2008/04/24 24:00 (NA NA) On Tue, Feb 16, 2010 at 5:47 AM, Alex Anderson wrote: > Hi All, > I am attempting to work with some data from loggers. I have read in a .csv > exported from MS Access that already has my dates and times (in 24 clock > format), (with StringsAsFactors=FALSE). > >> head(tdata) > > LogData date time > 1 77.16 2008/04/24 02:00 > 2 61.78 2008/04/24 04:00 > 3 75.44 2008/04/24 06:00 > 4 89.43 2008/04/24 08:00 > 5 95.83 2008/04/24 10:00 > 6 96.88 2008/04/24 24:00 > > I wish to be able to summarise the data using the character vectors $data > and $time (daily, monthly averages, maxima of my $LogData for example) so I > am trying to get R to recognise the $date and $time columns as valid dates > and times. Using... > >> tdata$date2 = as.Date(as.character(tdata$date)) > > I can get a new column of valid dates, but neither: > >> tdata$time2= strptime(tdata$time,"%k") > > Error in `$<-.data.frame`(`*tmp*`, "time2", value = list(sec = c(0, 0, : > replacement has 9 rows, data has 10 > > nor trying: > >> tdata$time2=chron(times=as.character(tdata$time, format= "hh:mm")) > > In addition: Warning messages: > 1: In unpaste(times, sep = fmt$sep, fnames = fmt$periods, nfields = 3) : > wrong number of fields in entry(ies) 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 > 2: In convert.times(times., fmt) : NAs introduced by coercion > 3: In convert.times(times., fmt) : NAs introduced by coercion > 4: In convert.times(times., fmt) : NAs introduced by coercion > > gives me any valid times from my time vector. the Chron documentation > doesn't mention 24 clocks, strptime neither, and the Rnews issue 1/4 with an > article about time is no help... Any thoughts would be much appreciated. > regards > > Alex Anderson > James Cook University > Townsville, Australia > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Keyboard
Steven Martin wrote: All, I installed R-2.10.1 with Readline=no. Now for some reason R does not recognize some key strokes like the directional arrows. I am not sure if Readline is the problem or not. What particular OS are you using? In many cases, there is a preconfigured package available to save you from compiling it yourself. __ 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] [Reminder] R/Finance 2010: Applied Finance with R
[ Registration for R/Finance 2010 is going strong: after only ten days of registrations one tutorial is already at 65% of capacity, and two others are approaching the 50% mark. Tutorials are capped at fourty participants each, the conference itself may be capped at three hundred registrations. Conference details are provided below. ] R/Finance 2010: Applied Finance with R April 16 & 17, Chicago, IL, USA The second annual R/Finance conference for applied finance using R, the premier free software system for statistical computation and graphics, will be held this spring in Chicago, IL, USA on Friday April 16 and Saturday April 17, 2010. The two-day conference will cover portfolio management, time series analysis, advanced risk tools, high-performance computing, econometrics and more. All will be discussed within the context of using R as a primary tool for financial risk management, analysis and trading. The 2010 conference will build upon the success of last year's event. It will include traditional keynotes from leading names in the R and finance community, presentations of contributed papers, short "lightning-style" presentations as well as the chance to meet and discuss colloboratively the future of the R in Finance community. R/Finance 2010 is organized by a local group of R package authors and community contributors, hosted by the International Center for Futures and Derivatives [ICFD] at the University of Illinois at Chicago and made possible via sponsorship support from ICFD, REvolution Computing, OneMarketData and Insight Algorithmics. The conference will feature invited keynote lectures by: * Bernhard Pfaff, Author, Analysis of Integrated and Co-integrated Time Series with R * Ralph Vince, Author, Leverage Space Portfolio Model * Marc Wildi, Author, Signal Extraction. ZHAW, Zurich, Switzerland * Achim Zeileis, Author, Applied Econometrics with R. Universitaet Innsbruck, Austria Plus additional talks over two days from: Maria Belianina, Kris Boudt, Josh Buckner, Peter Carl, Jon Cornelissen, Dirk Eddelbuettel, Robert Grossman, Saptarshi Guha, Mike Kane, Ruud Koning, Bryan Lewis, Wei-han Liu, James "JD" Long, Brian Peterson, Soren MacBeth, Khanh Nguyen, Michael North, Stefan Theussl, Josh Ulrich, Tony Plate, Jeff Ryan, Mark Seligman, David Smith, and Eric Zivot. Also offered are four optional pre-conference tutorials: Josh Buckner & Mark Seligman GPU Programming with R - An Introduction To GPU Programming with R Peter Carl & Brian Peterson Complex Portfolio Optimization with Generalized Business Objectives Dirk Eddelbuettel Rcpp / RInside - Extending and Embedding R with C++ for Fun and Profit Jeff Ryan Trading with R - Idea to Execution in 50 Minutes with IBrokers and R More details and registration information can be found at the website at http://www.RinFinance.com For the program committee: Gib Bassett, Peter Carl, Dirk Eddelbuettel, John Miller, Brian Peterson, Dale Rosenthal, Jeffrey Ryan -- Registration is open for the 2nd International conference R / Finance 2010 See http://www.RinFinance.com for details, and see you in Chicago in April! __ 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] Interactive plot (histogram) in R..........possible?
This can be done fairly simply using the tkexamp function from the
TeachingDemos package.
Here are some examples:
library(TeachingDemos)
histfunc <- function(n, mu=0, sigma=1) {
x <- rnorm(n, mu, sigma)
hist(x)
}
hist.list1 <- list( n=list('slider', from=10, to=1, resolution=10),
mu=list('numentry', init=0), sigma=list('numentry', init=1) )
tkexamp( histfunc, hist.list1 )
### maybe better
hist.list2 <- list( n=list('spinbox', values=c(10,50,100,500,1000,5000,1),
init=10, from=10, to=1))
tkexamp( histfunc, hist.list2 )
# another variation
x <- rnorm(1)
histfunc2 <- function(n) {
hist(x[seq_len(n)])
}
tkexamp( histfunc2,
list( n=list('slider', from=10, to=1, resolution=10) ) )
You may want to set some of the other arguments as well.
Hope this helps,
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111
> -Original Message-
> From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
> project.org] On Behalf Of Megh
> Sent: Tuesday, February 16, 2010 2:44 PM
> To: r-help@r-project.org
> Subject: [R] Interactive plot (histogram) in R..possible?
>
>
> Dear all,
>
> I am looking for some kind of interactive plot to draw a histogram for
> a
> normal distribution with different sample size. In that plot there
> would be
> some sort of "scroll-bar" which will take min value 10 and maximum
> value of
> 10,000 as sample size (n) from a standard normal distribution.
>
> In that case user will scroll in that scroll bar and histogram with
> different sample numbers will be drawn in the same plot.
>
> Is there any function/package in R to do that? Your help will be highly
> appreciated.
>
> Thanks,
> --
> View this message in context: http://n4.nabble.com/Interactive-plot-
> histogram-in-R-possible-tp1557984p1557984.html
> Sent from the R help mailing list archive at Nabble.com.
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-
> guide.html
> and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
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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] converting character vector "hh:mm" to chron or strptime 24 clock time vectors
... If it gets too confusing, just coerce your POSIXlt objects to POSIXct objects which don't have issues with odd lengths. Thanks to Mark and Charlie, your messages have enlightened me and hopefully provided a solution for Alex, who was the one with the problem. tdata$datetime<-as.POSIXct(strptime(paste(tdata$date,tdata$time,sep="-"), "%Y/%m/%d-%H:%M")) Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] converting character vector "hh:mm" to chron or strptime 24 clock time vectors
Jim Lemon wrote: > > On 02/16/2010 09:47 PM, Alex Anderson wrote: >> ... > This is the problem >> 6 96.88 2008/04/24 24:00 >> >> Error in `$<-.data.frame`(`*tmp*`, "time2", value = list(sec = c(0, 0, : >> replacement has 9 rows, data has 10 > > Hi Alex, > You have a problem with an invalid time. The line should read: > > 6 96.88 2008/05/24 00:00 > > However, there is something else going on here that puzzles me. When I > tried this with your sample data: > > tdata$datetime<-strptime(paste(tdata$date,tdata$time,sep="-"),"%Y/%m/%d-%H:%M") > Error in `$<-.data.frame`(`*tmp*`, "datetime", value = list(sec = c(0, : >replacement has 9 rows, data has 6 > > Yet: > > datetime<-strptime(paste(tdata$date,tdata$time,sep="-"), > "%Y/%m/%d-%H:%M") > datetime > [1] "2008-04-24 02:00:00" "2008-04-24 04:00:00" "2008-04-24 06:00:00" > [4] "2008-04-24 08:00:00" "2008-04-24 10:00:00" "2008-05-24 00:00:00" > length(datetime) > [1] 9 > > This is the first time I have encountered a discrepancy between "length" > and the printed extent of an object, and I can't work out what is going > on. > > Jim > This is because you are working with a POSIXlt object which has 9 components and therefore always has a length of 9. That second part has always struck me as an odd design decision-- but one which we will have to live with. The important detail is that each component of POSIXlt, such as "min", are the length you would expect them to be. I.E. if you have a POSIXlt object storing 15 timestamps: length( object ) = 9 <- not what you expect length( object$min ) = 15 <- what you expect If it gets too confusing, just coerce your POSIXlt objects to POSIXct objects which don't have issues with odd lengths. Hope this helps! -Charlie -- View this message in context: http://n4.nabble.com/converting-character-vector-hh-mm-to-chron-or-strptime-24-clock-time-vectors-tp1557308p1558213.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] converting character vector "hh:mm" to chron or strptime 24 clock time vectors
On 02/16/2010 09:47 PM, Alex Anderson wrote: ... This is the problem 6 96.88 2008/04/24 24:00 Error in `$<-.data.frame`(`*tmp*`, "time2", value = list(sec = c(0, 0, : replacement has 9 rows, data has 10 Hi Alex, You have a problem with an invalid time. The line should read: 6 96.88 2008/05/24 00:00 However, there is something else going on here that puzzles me. When I tried this with your sample data: tdata$datetime<-strptime(paste(tdata$date,tdata$time,sep="-"),"%Y/%m/%d-%H:%M") Error in `$<-.data.frame`(`*tmp*`, "datetime", value = list(sec = c(0, : replacement has 9 rows, data has 6 Yet: datetime<-strptime(paste(tdata$date,tdata$time,sep="-"), "%Y/%m/%d-%H:%M") datetime [1] "2008-04-24 02:00:00" "2008-04-24 04:00:00" "2008-04-24 06:00:00" [4] "2008-04-24 08:00:00" "2008-04-24 10:00:00" "2008-05-24 00:00:00" length(datetime) [1] 9 This is the first time I have encountered a discrepancy between "length" and the printed extent of an object, and I can't work out what is going on. Jim __ 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] extract the data that match
Roslina Zakaria wrote: > > Hi r-users, > > I would like to extract the data that match. > I'm interested in matchind the value in column 'intg' with value in column > 'rand_no' > Match how? Rows where intg equals rand_no at the same position? The rows of intg that are present somewhere in rand_no regardless of position? You need to be more specific. Roslina Zakaria wrote: > > Attached is my data: > >> cbind(z=z,intg=dd,rand_no = rr) > z intg rand_no > [1,] 0.00 0.000 0.001 > [2,] 0.01 0.000 0.002 > > > Thank you for your help. > This isn't a good way to provide tabular data-- people that want to help you can't just paste it into R and start working. They will have to reprocess the columns so that they can be read in by a function like read.table or read.csv. This will take some time and most won't bother-- they will just ignore your question. The best way to provide tabulated R data is to run your data frame through the dput() function and post that output. It won't look as nice, but any list user will be able to paste the code into their console and regenerate your table. -Charlie -- View this message in context: http://n4.nabble.com/extract-the-data-that-match-tp1558193p1558200.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] extract the data that match
Tena koe Roslina It is not entirely clear to me what you want to do, but have you looked at match or %in%? Or do you simply want yourData[yourData[,2]==yourData[,3],]? Also, you might need to bear in mind issues with floating point arithmetic which is a frequent question on this list. HTH . Peter Alspach > -Original Message- > From: r-help-boun...@r-project.org > [mailto:r-help-boun...@r-project.org] On Behalf Of Roslina Zakaria > Sent: Wednesday, 17 February 2010 3:39 p.m. > To: r-help@r-project.org > Subject: [R] extract the data that match > > Hi r-users, > > I would like to extract the data that match. Attached is my data: > I'm interested in matchind the value in column 'intg' with > value in column 'rand_no' > > cbind(z=z,intg=dd,rand_no = rr) > z intg rand_no > [1,] 0.00 0.000 0.001 > [2,] 0.01 0.000 0.002 > [3,] 0.02 0.000 0.002 > [4,] 0.03 0.000 0.003 > [5,] 0.04 0.000 0.003 > [6,] 0.05 0.000 0.004 > [7,] 0.06 0.000 0.004 > [8,] 0.07 0.000 0.004 > [9,] 0.08 0.000 0.004 > [10,] 0.09 0.000 0.008 > [11,] 0.10 0.000 0.008 > [12,] 0.11 0.000 0.008 > [13,] 0.12 0.000 0.009 > [14,] 0.13 0.000 0.009 > [15,] 0.14 0.000 0.010 > [16,] 0.15 0.000 0.010 > [17,] 0.16 0.001 0.010 > [18,] 0.17 0.001 0.011 > [19,] 0.18 0.001 0.012 > [20,] 0.19 0.001 0.012 > [21,] 0.20 0.001 0.012 > [22,] 0.21 0.001 0.012 > [23,] 0.22 0.002 0.013 > [24,] 0.23 0.002 0.014 > [25,] 0.24 0.002 0.014 > [26,] 0.25 0.002 0.014 > [27,] 0.26 0.003 0.015 > [28,] 0.27 0.003 0.016 > [29,] 0.28 0.003 0.016 > [30,] 0.29 0.004 0.017 > [31,] 0.30 0.004 0.017 > [32,] 0.31 0.005 0.018 > [33,] 0.32 0.005 0.019 > [34,] 0.33 0.005 0.020 > [35,] 0.34 0.006 0.020 > [36,] 0.35 0.006 0.020 > [37,] 0.36 0.007 0.021 > [38,] 0.37 0.007 0.024 > [39,] 0.38 0.008 0.025 > [40,] 0.39 0.008 0.025 > [41,] 0.40 0.009 0.026 > [42,] 0.41 0.010 0.027 > [43,] 0.42 0.010 0.028 > [44,] 0.43 0.011 0.030 > [45,] 0.44 0.011 0.030 > [46,] 0.45 0.012 0.031 > [47,] 0.46 0.013 0.031 > [48,] 0.47 0.014 0.032 > [49,] 0.48 0.014 0.033 > [50,] 0.49 0.015 0.033 > [51,] 0.50 0.016 0.033 > [52,] 0.51 0.017 0.034 > [53,] 0.52 0.017 0.037 > [54,] 0.53 0.018 0.039 > [55,] 0.54 0.019 0.039 > [56,] 0.55 0.020 0.040 > [57,] 0.56 0.021 0.040 > [58,] 0.57 0.022 0.040 > [59,] 0.58 0.022 0.041 > [60,] 0.59 0.023 0.042 > [61,] 0.60 0.024 0.042 > [62,] 0.61 0.025 0.043 > [63,] 0.62 0.026 0.045 > [64,] 0.63 0.027 0.046 > [65,] 0.64 0.028 0.046 > [66,] 0.65 0.029 0.047 > [67,] 0.66 0.030 0.047 > [68,] 0.67 0.031 0.047 > [69,] 0.68 0.032 0.048 > [70,] 0.69 0.033 0.051 > [71,] 0.70 0.034 0.051 > [72,] 0.71 0.036 0.051 > [73,] 0.72 0.037 0.052 > [74,] 0.73 0.038 0.052 > [75,] 0.74 0.039 0.052 > [76,] 0.75 0.040 0.052 > [77,] 0.76 0.041 0.052 > [78,] 0.77 0.042 0.053 > [79,] 0.78 0.044 0.053 > [80,] 0.79 0.045 0.053 > [81,] 0.80 0.046 0.054 > [82,] 0.81 0.047 0.054 > [83,] 0.82 0.048 0.055 > [84,] 0.83 0.050 0.055 > [85,] 0.84 0.051 0.055 > [86,] 0.85 0.052 0.057 > [87,] 0.86 0.054 0.060 > [88,] 0.87 0.055 0.062 > [89,] 0.88 0.056 0.063 > [90,] 0.89 0.057 0.064 > [91,] 0.90 0.059 0.064 > [92,] 0.91 0.060 0.064 > [93,] 0.92 0.062 0.066 > [94,] 0.93 0.063 0.067 > [95,] 0.94 0.064 0.067 > [96,] 0.95 0.066 0.068 > [97,] 0.96 0.067 0.068 > [98,] 0.97 0.068 0.069 > [99,] 0.98 0.070 0.071 > [100,] 0.99 0.071 0.071 > [101,] 1.00 0.073 0.071 > [102,] 1.01 0.074 0.071 > [103,] 1.02 0.076 0.072 > [104,] 1.03 0.077 0.072 > [105,] 1.04 0.079 0.075 > [106,] 1.05 0.080 0.075 > [107,] 1.06 0.082 0.076 > [108,] 1.07 0.083 0.076 > [109,] 1.08 0.085 0.078 > [110,] 1.09 0.086 0.078 > [111,] 1.10 0.088 0.078 > [112,] 1.11 0.089 0.079 > [113,] 1.12 0.091 0.080 > [114,] 1.13 0.092 0.080 > [115,] 1.14 0.094 0.081 > [116,] 1.15 0.095 0.081 > [117,] 1.16 0.097 0.081 > [118,] 1.17 0.099 0.084 > [119,] 1.18 0.100 0.086 > [120,] 1.19 0.102 0.086 > [121,] 1.20 0.103 0.086 > [122,] 1.21 0.105 0.087 > [123,] 1.22 0.107 0.087 > [124,] 1.23 0.108 0.088 > [125,] 1.24 0.110 0.088 > [126,] 1.25 0.111 0.089 > [127,] 1.26 0.113 0.090 > [128,] 1.27 0.115 0.090 > [129,] 1.28 0.116 0.093 > [130,] 1.29 0.118 0.094 > [131,] 1.30 0.120 0.094 > [132,] 1.31 0.121 0.096 > [133,] 1.32 0.123 0.097 > [134,] 1.33 0.125 0.097 > [135,] 1.34 0.127 0.100 > [136,] 1.35 0.128 0.100 > [137,] 1.36 0.130 0.100 > [138,] 1.37 0.132 0.100 > [139,] 1.38 0.133 0.101 > [140,] 1
[R] Building R from source
I found the problem but not a solution. It turns out if I add the following lines to dqrdc2.f I get the error: write(*,300) ldx,n,p 300 format(3i4) I don't get a compile error but I get the seemingly unrelated error in linking R.DLL I guess the question now is, "How do I add a simple print statement?". Or, what is wrong with the above print statement? Thank you. Kevin __ 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] Bivariate Uniform distribution
Hi all, Is there a function in R to calculate the probability, or quantile, or generate random numbers, and so on for bivariate uniform distribution, like for the bivariate normal distribution? Thanks! Hannah [[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] extract the data that match
Hi r-users, I would like to extract the data that match. Attached is my data: I'm interested in matchind the value in column 'intg' with value in column 'rand_no' > cbind(z=z,intg=dd,rand_no = rr) z intg rand_no [1,] 0.00 0.000 0.001 [2,] 0.01 0.000 0.002 [3,] 0.02 0.000 0.002 [4,] 0.03 0.000 0.003 [5,] 0.04 0.000 0.003 [6,] 0.05 0.000 0.004 [7,] 0.06 0.000 0.004 [8,] 0.07 0.000 0.004 [9,] 0.08 0.000 0.004 [10,] 0.09 0.000 0.008 [11,] 0.10 0.000 0.008 [12,] 0.11 0.000 0.008 [13,] 0.12 0.000 0.009 [14,] 0.13 0.000 0.009 [15,] 0.14 0.000 0.010 [16,] 0.15 0.000 0.010 [17,] 0.16 0.001 0.010 [18,] 0.17 0.001 0.011 [19,] 0.18 0.001 0.012 [20,] 0.19 0.001 0.012 [21,] 0.20 0.001 0.012 [22,] 0.21 0.001 0.012 [23,] 0.22 0.002 0.013 [24,] 0.23 0.002 0.014 [25,] 0.24 0.002 0.014 [26,] 0.25 0.002 0.014 [27,] 0.26 0.003 0.015 [28,] 0.27 0.003 0.016 [29,] 0.28 0.003 0.016 [30,] 0.29 0.004 0.017 [31,] 0.30 0.004 0.017 [32,] 0.31 0.005 0.018 [33,] 0.32 0.005 0.019 [34,] 0.33 0.005 0.020 [35,] 0.34 0.006 0.020 [36,] 0.35 0.006 0.020 [37,] 0.36 0.007 0.021 [38,] 0.37 0.007 0.024 [39,] 0.38 0.008 0.025 [40,] 0.39 0.008 0.025 [41,] 0.40 0.009 0.026 [42,] 0.41 0.010 0.027 [43,] 0.42 0.010 0.028 [44,] 0.43 0.011 0.030 [45,] 0.44 0.011 0.030 [46,] 0.45 0.012 0.031 [47,] 0.46 0.013 0.031 [48,] 0.47 0.014 0.032 [49,] 0.48 0.014 0.033 [50,] 0.49 0.015 0.033 [51,] 0.50 0.016 0.033 [52,] 0.51 0.017 0.034 [53,] 0.52 0.017 0.037 [54,] 0.53 0.018 0.039 [55,] 0.54 0.019 0.039 [56,] 0.55 0.020 0.040 [57,] 0.56 0.021 0.040 [58,] 0.57 0.022 0.040 [59,] 0.58 0.022 0.041 [60,] 0.59 0.023 0.042 [61,] 0.60 0.024 0.042 [62,] 0.61 0.025 0.043 [63,] 0.62 0.026 0.045 [64,] 0.63 0.027 0.046 [65,] 0.64 0.028 0.046 [66,] 0.65 0.029 0.047 [67,] 0.66 0.030 0.047 [68,] 0.67 0.031 0.047 [69,] 0.68 0.032 0.048 [70,] 0.69 0.033 0.051 [71,] 0.70 0.034 0.051 [72,] 0.71 0.036 0.051 [73,] 0.72 0.037 0.052 [74,] 0.73 0.038 0.052 [75,] 0.74 0.039 0.052 [76,] 0.75 0.040 0.052 [77,] 0.76 0.041 0.052 [78,] 0.77 0.042 0.053 [79,] 0.78 0.044 0.053 [80,] 0.79 0.045 0.053 [81,] 0.80 0.046 0.054 [82,] 0.81 0.047 0.054 [83,] 0.82 0.048 0.055 [84,] 0.83 0.050 0.055 [85,] 0.84 0.051 0.055 [86,] 0.85 0.052 0.057 [87,] 0.86 0.054 0.060 [88,] 0.87 0.055 0.062 [89,] 0.88 0.056 0.063 [90,] 0.89 0.057 0.064 [91,] 0.90 0.059 0.064 [92,] 0.91 0.060 0.064 [93,] 0.92 0.062 0.066 [94,] 0.93 0.063 0.067 [95,] 0.94 0.064 0.067 [96,] 0.95 0.066 0.068 [97,] 0.96 0.067 0.068 [98,] 0.97 0.068 0.069 [99,] 0.98 0.070 0.071 [100,] 0.99 0.071 0.071 [101,] 1.00 0.073 0.071 [102,] 1.01 0.074 0.071 [103,] 1.02 0.076 0.072 [104,] 1.03 0.077 0.072 [105,] 1.04 0.079 0.075 [106,] 1.05 0.080 0.075 [107,] 1.06 0.082 0.076 [108,] 1.07 0.083 0.076 [109,] 1.08 0.085 0.078 [110,] 1.09 0.086 0.078 [111,] 1.10 0.088 0.078 [112,] 1.11 0.089 0.079 [113,] 1.12 0.091 0.080 [114,] 1.13 0.092 0.080 [115,] 1.14 0.094 0.081 [116,] 1.15 0.095 0.081 [117,] 1.16 0.097 0.081 [118,] 1.17 0.099 0.084 [119,] 1.18 0.100 0.086 [120,] 1.19 0.102 0.086 [121,] 1.20 0.103 0.086 [122,] 1.21 0.105 0.087 [123,] 1.22 0.107 0.087 [124,] 1.23 0.108 0.088 [125,] 1.24 0.110 0.088 [126,] 1.25 0.111 0.089 [127,] 1.26 0.113 0.090 [128,] 1.27 0.115 0.090 [129,] 1.28 0.116 0.093 [130,] 1.29 0.118 0.094 [131,] 1.30 0.120 0.094 [132,] 1.31 0.121 0.096 [133,] 1.32 0.123 0.097 [134,] 1.33 0.125 0.097 [135,] 1.34 0.127 0.100 [136,] 1.35 0.128 0.100 [137,] 1.36 0.130 0.100 [138,] 1.37 0.132 0.100 [139,] 1.38 0.133 0.101 [140,] 1.39 0.135 0.102 [141,] 1.40 0.137 0.102 [142,] 1.41 0.139 0.103 [143,] 1.42 0.140 0.103 [144,] 1.43 0.142 0.105 [145,] 1.44 0.144 0.105 [146,] 1.45 0.146 0.107 [147,] 1.46 0.147 0.107 [148,] 1.47 0.149 0.107 [149,] 1.48 0.151 0.109 [150,] 1.49 0.153 0.110 [151,] 1.50 0.154 0.111 [152,] 1.51 0.156 0.111 [153,] 1.52 0.158 0.111 [154,] 1.53 0.160 0.112 [155,] 1.54 0.161 0.112 [156,] 1.55 0.163 0.114 [157,] 1.56 0.165 0.114 [158,] 1.57 0.167 0.114 [159,] 1.58 0.169 0.114 [160,] 1.59 0.170 0.115 [161,] 1.60 0.172 0.115 [162,] 1.61 0.174 0.116 [163,] 1.62 0.176 0.116 [164,] 1.63 0.178 0.117 [165,] 1.64 0.180 0.117 [166,] 1.65 0.181 0.119 [167,] 1.66 0.183 0.120 [168,] 1.67 0.185 0.121 [169,] 1.68 0.187 0.121 [170,] 1.69 0.189 0.122 [171,] 1
[R] sql query variable
This is the very last thing I need to make everything work properly. My query: sqlQuery(conn, "select to_char(lsd,'-mm') as yr,ttl_mo_prcp from mo_rains where stn_num=023000") Is there a way to may the stn_num in the query variable, ie make it so that whenever my script is run, the user must choose and input the station number? Cheers. -- View this message in context: http://n4.nabble.com/sql-query-variable-tp1558189p1558189.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Keyboard
Steven Martin wrote: > > All, > > I installed R-2.10.1 with Readline=no. Now for some reason R does not > recognize some key strokes like the directional arrows. > I am not sure if Readline is the problem or not. > Yes-- readline supplies functionality such as command history. Steven Martin wrote: > > I have tried .Cofigure with Readline = yes but it doesn't fix the problem > nor do I really know if readline is the problem to start with. > > Has anybody else run into similar problems? > > Thanks, > Steve > Did you try: make distclean ./configure make make install ? If that doesn't work, try: which R To see if the version of R being run is the one that you just compiled/installed. Good luck! -Charlie -- View this message in context: http://n4.nabble.com/Keyboard-tp1558126p1558185.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] side-effects in functions that replace object values andattributes
> -Original Message-
> From: r-help-boun...@r-project.org
> [mailto:r-help-boun...@r-project.org] On Behalf Of Stephen Tucker
> Sent: Tuesday, February 16, 2010 5:32 PM
> To: r-help@r-project.org
> Subject: [R] side-effects in functions that replace object
> values andattributes
>
> Hello list,
>
> I encountered some surprising behavior in R and wanted to
> check to see if I was imagining things. Previously, I thought
> that replacement/setter operators in prefix notation (e.g.,
> `[<-`(x,1,y) rather than x[1] <- y) did not produce side
> effects (i.e., left 'x' unchanged), but just realized that
> this is not the case anymore (or has it always been this way?
> - I don't have access to old R distributions at the moment,
> but using R 2.10.1 on Ubuntu and OS X)? I went through the
> NEWS file but did not see a change documented if there was
> one, but just going by my recollection...
>
> In any case, my understanding was that when modifying a value
> or attribute of an object, R reassigned the modified object
> to the original symbol. For instance, the help file for
> `name<-`() says that
>
> > names(z)[3] <- "c2"
>
> is evaluated as
>
> > z <- "names<-"(z, "[<-"(names(z), 3, "c2"))
>
> But the final (re)assignment (`<-`) seems redundant as
>
> > invisible("names<-"(z, "[<-"(names(z), 3, "c2")))
>
> does the same thing.
>
> In this case, I wonder if there is a preferred way to use the
> replacement/setter operators in prefix notation without
> producing such side effects
I would never recommend using replacement operators
this way. In part this is because S+ doesn't like it:
S+> x<-1:10
S+> `[<-`(x, 1, value=66.6)
[1] 66.6 2.0 3.0 4.0 5.0 6.0 7.0 8.0 9.0 10.0
Warning messages:
looks like the internal reference count was not updated in: x[1] <-
66.6
S+> x
[1] 1 2 3 4 5 6 7 8 9 10
in part because it is ugly, but mostly it is because
forcing the program to accept such usage closes off,
or at least restricts, an avenue for saving memory when
doing replacement operations.
If you have a replacement function that you are tempted
to use in this way, I recommend that you write a wrapper
function for it. E.g., instead of using
namedX <- `names<-`(x, value=as.character(x))
write
setNames <- function(x, names) {
names(x) <- names
x
}
and use it as
namesX <- setNames(x, as.character(x))
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
> (replace() exists for `[<-`() and
> `[[<-`(), but perhaps something more general). For instance,
> if I did not desire the following modification in x:
>
> > x <- c("1","2")
> > y <- `names<-`(x,c("a","b"))
> > y
> a b
> "1" "2"
> > x
> a b
> "1" "2"
> >
>
> I might take advantage of R's lazy evaluation and use create
> a copy in the local function environment and allow that copy
> to be modified:
>
> > x <- c("1","2")
> > y <- `names<-`(`<-`(x,x),c("a","b"))
> > y
> a b
> "1" "2"
> > x
> [1] "1" "2"
>
> The interesting thing is that `mode<-`(), while also a
> "setter" function in that it sets an object attribute, does
> not behave as `names<-`():
>
> > x <- c("1","2")
> > y <- `mode<-`(x,"integer")
> > y
> [1] 1 2
> > x
> [1] "1" "2"
> > mode(x)
> [1] "character"
>
> So another question that naturally arises is whether there a
> general rule by which we can predict the behavior of these
> types of operators (whether they produce side effects or not)?
>
> Thanks,
>
> Stephen
>
> __
> 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.
>
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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] strangeness in Predict() {rms}
Both plyr and rms contain an object called ".".
In plyr it is a "closure" (the common kind of
function) and in rms is is NA. If plyr is attached
in front of rms then you get your problem with
Predict().
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
> bill.venab...@csiro.au
> Sent: Tuesday, February 16, 2010 4:21 PM
> To: dylan.beaude...@gmail.com; r-help@r-project.org
> Subject: Re: [R] strangeness in Predict() {rms}
>
> This works without a glitch on my linux system (info below).
> You might try upgrading your R to 2.10.1, perhaps.
>
> > sessionInfo()
> R version 2.10.1 (2009-12-14)
> x86_64-unknown-linux-gnu
>
> locale:
> [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_AU.UTF-8LC_COLLATE=en_AU.UTF-8
> [5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8
> [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] splines grid stats graphics grDevices utils
> datasets
> [8] methods base
>
> other attached packages:
> [1] rms_2.1-0 plyr_0.1.9 Design_2.3-0Hmisc_3.7-0
> [5] survival_2.35-9
>
> loaded via a namespace (and not attached):
> [1] ASOR_0.1 cluster_1.12.1 lattice_0.18-3 tcltk_2.10.1
> tools_2.10.1
> >
>
>
> Bill Venables
> CSIRO/CMIS Cleveland Laboratories
>
>
> -Original Message-
> From: r-help-boun...@r-project.org
> [mailto:r-help-boun...@r-project.org] On Behalf Of Dylan Beaudette
> Sent: Wednesday, 17 February 2010 10:05 AM
> To: r-help@r-project.org
> Subject: [R] strangeness in Predict() {rms}
>
> Hi,
>
> Running the following example from ?Predict() throws an error
> I have never
> seen before:
>
> set.seed(1)
> x1 <- runif(300)
> x2 <- runif(300)
> ddist <- datadist(x1,x2); options(datadist='ddist')
> y <- exp(x1+ x2 - 1 + rnorm(300))
> f <- ols(log(y) ~ pol(x1,2) + x2)
> p1 <- Predict(f, x1=., conf.type='mean')
>
> Error in paste(nmc[i], "=", if (is.numeric(x)) format(x) else
> x, sep = "") :
> cannot coerce type 'closure' to vector of type 'character'
> In addition: Warning message:
> In is.na(v) : is.na() applied to non-(list or vector) of type
> 'closure'
>
> Here is the output from sessionInfo()
>
> R version 2.9.0 (2009-04-17)
> i686-pc-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLA
> TE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=
> en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREME
> NT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] grid splines stats graphics grDevices utils
> datasets
> [8] methods base
>
> other attached packages:
> [1] plyr_0.1.9 mgcv_1.5-5 RColorBrewer_1.0-2
> nlme_3.1-94
> [5] rms_2.1-0 Hmisc_3.7-0survival_2.35-6
> lattice_0.17-25
>
> loaded via a namespace (and not attached):
> [1] cluster_1.12.0
>
>
> Any ideas?
> Thanks!
>
> Dylan
>
>
> --
> Dylan Beaudette
> Soil Resource Laboratory
> http://casoilresource.lawr.ucdavis.edu/
> University of California at Davis
> 530.754.7341
>
> __
> 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
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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] side-effects in functions that replace object values and attributes
Hello list,
I encountered some surprising behavior in R and wanted to check to see if I was
imagining things. Previously, I thought that replacement/setter operators in
prefix notation (e.g., `[<-`(x,1,y) rather than x[1] <- y) did not produce side
effects (i.e., left 'x' unchanged), but just realized that this is not the case
anymore (or has it always been this way? - I don't have access to old R
distributions at the moment, but using R 2.10.1 on Ubuntu and OS X)? I went
through the NEWS file but did not see a change documented if there was one, but
just going by my recollection...
In any case, my understanding was that when modifying a value or attribute of
an object, R reassigned the modified object to the original symbol. For
instance, the help file for `name<-`() says that
> names(z)[3] <- "c2"
is evaluated as
> z <- "names<-"(z, "[<-"(names(z), 3, "c2"))
But the final (re)assignment (`<-`) seems redundant as
> invisible("names<-"(z, "[<-"(names(z), 3, "c2")))
does the same thing.
In this case, I wonder if there is a preferred way to use the
replacement/setter operators in prefix notation without producing such side
effects (replace() exists for `[<-`() and `[[<-`(), but perhaps something more
general). For instance, if I did not desire the following modification in x:
> x <- c("1","2")
> y <- `names<-`(x,c("a","b"))
> y
a b
"1" "2"
> x
a b
"1" "2"
>
I might take advantage of R's lazy evaluation and use create a copy in the
local function environment and allow that copy to be modified:
> x <- c("1","2")
> y <- `names<-`(`<-`(x,x),c("a","b"))
> y
a b
"1" "2"
> x
[1] "1" "2"
The interesting thing is that `mode<-`(), while also a "setter" function in
that it sets an object attribute, does not behave as `names<-`():
> x <- c("1","2")
> y <- `mode<-`(x,"integer")
> y
[1] 1 2
> x
[1] "1" "2"
> mode(x)
[1] "character"
So another question that naturally arises is whether there a general rule by
which we can predict the behavior of these types of operators (whether they
produce side effects or not)?
Thanks,
Stephen
__
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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] Keyboard
All, I installed R-2.10.1 with Readline=no. Now for some reason R does not recognize some key strokes like the directional arrows. I am not sure if Readline is the problem or not. I have tried .Cofigure with Readline = yes but it doesn't fix the problem nor do I really know if readline is the problem to start with. Has anybody else run into similar problems? Thanks, Steve [[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] Using text put into a dialog box
Thanks Greg, the problem is I have no idea how to return and use what I have typed into the pop up. Add to that the complication that with this query x<-sqlQuery(conn, "select to_char(lsd,'-mm') as yr,ttl_mo_prcp from mo_rains where stn_num=23090") if I put anything other than a number into stn_num=... then it does not run. eg if I just do sn=23090 and then use that in the query sqlQuery(conn, "select to_char(lsd,'-mm') as yr,ttl_mo_prcp from mo_rains where stn_num=sn") I get the following error. [1] "[RODBC] ERROR: Could not SQLExecDirect" [2] "42S22 904 [Oracle][ODBC][Ora]ORA-00904: \"SN\": invalid identifier\n" So my question is in two parts. Firstly, how do I return the number written in the popup, and then secondly how do I actually put it into the query? Thanks again -- View this message in context: http://n4.nabble.com/Using-text-put-into-a-dialog-box-tp1555761p1558124.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Separating columns, and sorting by rows
Thanks for the help guys. This worked: x<-sqlQuery(conn, "select to_char(lsd,'-mm') as yr,ttl_mo_prcp from mo_rains where stn_num=23090") myDF=x myDF[,1]=as.yearmon(myDF[,1]) myDF$R=myDF$TTL_MO_PRCP myDF[,-2] myDF$<-substr(myDF$YR,5,8) myDF$mm<-substr(myDF$YR,1,4) myDF<-subset(myDF, select=c(,mm,R)) myDF.reshape<-reshape(myDF,v.names="R",idvar="",timevar="mm",direction="wide") myDF.reshape kent=myDF.reshape library(zoo) rows=nrow(myDF.reshape) kent[,1]=as.numeric(as.character(kent[,1])) ann=c(kent1[,2]+kent1[,3]+kent1[,4]+kent1[,5]+kent1[,6]+kent1[,7]+kent1[,8]+kent1[,9]+kent1[,10]+kent1[,11]+kent1[,12]+kent1[,13]) kent1=cbind(kent$,kent$R.Jan,kent$R.Feb,kent$R.Mar,kent$R.Apr,kent$R.May,kent$R.Jun,kent$R.Jul,kent$R.Aug,kent$R.Sep,kent$R.Oct,kent$R.Nov,kent$R.Dec,ann) Still some cleaning up to do, but it now works as promised :) All I ahve to figure out now is how to fix have a pop up for people to write in a station number, and that station number then gets input into the query. x<-sqlQuery(conn, "select to_char(lsd,'-mm') as yr,ttl_mo_prcp from mo_rains where stn_num=23090") Any ideas at all? Cheers again! -- View this message in context: http://n4.nabble.com/Separating-columns-and-sorting-by-rows-tp1555806p1558118.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] strangeness in Predict() {rms}
This works without a glitch on my linux system (info below). You might try
upgrading your R to 2.10.1, perhaps.
> sessionInfo()
R version 2.10.1 (2009-12-14)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_AU.UTF-8LC_COLLATE=en_AU.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8
[7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] splines grid stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] rms_2.1-0 plyr_0.1.9 Design_2.3-0Hmisc_3.7-0
[5] survival_2.35-9
loaded via a namespace (and not attached):
[1] ASOR_0.1 cluster_1.12.1 lattice_0.18-3 tcltk_2.10.1 tools_2.10.1
>
Bill Venables
CSIRO/CMIS Cleveland Laboratories
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Dylan Beaudette
Sent: Wednesday, 17 February 2010 10:05 AM
To: r-help@r-project.org
Subject: [R] strangeness in Predict() {rms}
Hi,
Running the following example from ?Predict() throws an error I have never
seen before:
set.seed(1)
x1 <- runif(300)
x2 <- runif(300)
ddist <- datadist(x1,x2); options(datadist='ddist')
y <- exp(x1+ x2 - 1 + rnorm(300))
f <- ols(log(y) ~ pol(x1,2) + x2)
p1 <- Predict(f, x1=., conf.type='mean')
Error in paste(nmc[i], "=", if (is.numeric(x)) format(x) else x, sep = "") :
cannot coerce type 'closure' to vector of type 'character'
In addition: Warning message:
In is.na(v) : is.na() applied to non-(list or vector) of type 'closure'
Here is the output from sessionInfo()
R version 2.9.0 (2009-04-17)
i686-pc-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] grid splines stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] plyr_0.1.9 mgcv_1.5-5 RColorBrewer_1.0-2 nlme_3.1-94
[5] rms_2.1-0 Hmisc_3.7-0survival_2.35-6lattice_0.17-25
loaded via a namespace (and not attached):
[1] cluster_1.12.0
Any ideas?
Thanks!
Dylan
--
Dylan Beaudette
Soil Resource Laboratory
http://casoilresource.lawr.ucdavis.edu/
University of California at Davis
530.754.7341
__
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.
__
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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] strangeness in Predict() {rms}
Hi, Running the following example from ?Predict() throws an error I have never seen before: set.seed(1) x1 <- runif(300) x2 <- runif(300) ddist <- datadist(x1,x2); options(datadist='ddist') y <- exp(x1+ x2 - 1 + rnorm(300)) f <- ols(log(y) ~ pol(x1,2) + x2) p1 <- Predict(f, x1=., conf.type='mean') Error in paste(nmc[i], "=", if (is.numeric(x)) format(x) else x, sep = "") : cannot coerce type 'closure' to vector of type 'character' In addition: Warning message: In is.na(v) : is.na() applied to non-(list or vector) of type 'closure' Here is the output from sessionInfo() R version 2.9.0 (2009-04-17) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] grid splines stats graphics grDevices utils datasets [8] methods base other attached packages: [1] plyr_0.1.9 mgcv_1.5-5 RColorBrewer_1.0-2 nlme_3.1-94 [5] rms_2.1-0 Hmisc_3.7-0survival_2.35-6lattice_0.17-25 loaded via a namespace (and not attached): [1] cluster_1.12.0 Any ideas? Thanks! Dylan -- Dylan Beaudette Soil Resource Laboratory http://casoilresource.lawr.ucdavis.edu/ University of California at Davis 530.754.7341 __ 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] RODBC missing values in integer columns
It turns out that in the sqlQuery I must set rows_at_time =0 to get rid of
this problem.
Does anyone have any idea why this might be?
On Tue, Feb 16, 2010 at 12:52 PM, Rob Forler wrote:
> some more info
> > t(t(odbcGetInfo(connection)))
> [,1]
> DBMS_Name"Adaptive Server Anywhere"
> DBMS_Ver "12.70."
> Driver_ODBC_Ver "03.51"
> Data_Source_Name "dbname"
> Driver_Name "Adaptive Server Anywhere"
> Driver_Ver "09.00.0001"
> ODBC_Ver "03.52."
> Server_Name "dbname"
>
>
>
>
> On Tue, Feb 16, 2010 at 11:39 AM, Rob Forler wrote:
>
>> Hello,
>>
>> We are having some strange issues with RODBC related to integer columns.
>> Whenever we do a sql query the data in a integer column is 150 actual data
>> points then 150 0's then 150 actual data points then 150 0's. However, our
>> database actually has numbers where the 0's are filled in. Furthermore,
>> other datatypes do not have this problem: double and varchar are correct and
>> do not alternate to null. Also, if we increase the rows_at_time to 1024
>> there are larger gaps between the 0's and actual data. The server is a
>> sybase IQ database. We have tested it on a different database sybase ASE and
>> we still get this issue.
>>
>> For example :
>>
>> We have the following query
>>
>> sqlString = "Select ActionID, Velocity from ActionDataTable"
>>
>> #where ActionID is of integer type and Velocity is of double type.
>> connection = odbcConnect("IQDatabase"); #this database is a sybase IQ
>> database
>> sqlData = sqlQuery(connection, sqlString);
>>
>>
>> sqlData$ActionID might be 1,2,3,4,5,6,150, 0,0,0,0,0,0,0,,0,0,0,
>> 301,302,303,304,.448,449,500,0,0,0...,0,0
>>
>> and Velocity will have data values along the whole column without these
>> big areas of 0's.
>>
>> Thanks for the help,
>> Robert Forler
>>
>
>
[[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] nls.lm & AIC
I will consider putting methods for AIC and logLik into the next version
of minpack.lm (contributions welcome).
For now, the following should work for logLik, where 'object' is the
return value of nls.lm.
logLik.nls.lm <- function(object, REML = FALSE, ...)
{
res <- object$fvec
N <- length(res)
val <- -N * (log(2 * pi) + 1 - log(N) + log(sum(res^2)))/2
## the formula here corresponds to estimating sigma^2.
attr(val, "df") <- 1L + length(coef(object))
attr(val, "nobs") <- attr(val, "nall") <- N
class(val) <- "logLik"
val
}
On Tue, 16 Feb 2010, Baudron, Alan Ronan wrote:
> Hi there,
>
> I'm a PhD student investigating growth patterns in fish. I've been using
> the minpack.lm package to fit extended von Bertalanffy growth models
> that include explanatory covariates (temperature and density). I found
> the nls.lm comand a powerful tool to fit models with a lot of
> parameters. However, in order to select the best model over the possible
> candidates (without covariates, with both covariates, or with only one
> of them) I'd like to compare them based on their AIC criterion. However,
> it seems that the nls.lm comand doesn't return an AIC, or a Log
> Likelihood. Does someone have any idea of how I could proceed to get
> such informations about my models?
>
> Thanks for your help. Best regards,
>
> Alan Baudron
>
>
> The University of Aberdeen is a charity registered in Scotland, No SC013683.
>
> [[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.
>
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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] Problems building from sources
I am trying to build R-2.9.2 from source on a Windows 7 machine. I have installed all of the requisite software and followed the instructions. I also could have sworn that I had a successful build. But now I get the following error. gcc -std=gnu99 -shared -s -mwindows -o R.dll R.def console.o dataentry.o dynload .o edit.o editor.o embeddedR.o extra.o opt.o pager.o preferences.o psignal.o rho me.o rt_complete.o rui.o run.o shext.o sys-win32.o system.o dos_wglob.o e_pow.o malloc.o ../main/libmain.a ../appl/libappl.a ../nmath/libnmath.a getline/gl.a .. /extra/xdr/libxdr.a ../extra/pcre/libpcre.a ../extra/bzip2/libbz2.a ../extra/int l/libintl.a ../extra/trio/libtrio.a ../extra/tzone/libtz.a dllversion.o -L. -lgf ortran -lRblas -L../../bin -lRzlib -lRgraphapp -lRiconv -lcomctl32 -lversion c:/rtools/mingw/bin/../lib/gcc/mingw32/4.2.1-sjlj/../../../libmingwex.a(mingw_sn printf.o):mingw_snprintf.c:(.text+0x1970): multiple definition of `snprintf' ../extra/trio/libtrio.a(compat.o):compat.c:(.text+0x30): first defined here c:/rtools/mingw/bin/../lib/gcc/mingw32/4.2.1-sjlj/../../../libmingwex.a(mingw_sn printf.o):mingw_snprintf.c:(.text+0x170): multiple definition of `vsnprintf' ../extra/trio/libtrio.a(compat.o):compat.c:(.text+0x20): first defined here collect2: ld returned 1 exit status make[3]: *** [R.dll] Error 1 make[2]: *** [../../bin/R.dll] Error 2 make[1]: *** [rbuild] Error 2 make: *** [all] Error 2 It seems like vsnprint and snprintf are multiply defined. Any ideas? Kevin Dimitri Shvorob wrote: > > Now that we have a reproducible example... ;) > -- > View this message in context: > http://n4.nabble.com/Problems-with-boxplot-in-ggplot2-qplot-tp1555338p1557994.html > Sent from the R help mailing list archive at Nabble.com. > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problems with boxplot in ggplot2:qplot
Now that we have a reproducible example... ;) -- View this message in context: http://n4.nabble.com/Problems-with-boxplot-in-ggplot2-qplot-tp1555338p1557994.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Interactive plot (histogram) in R..........possible?
On Feb 16, 2010, at 4:44 PM, Megh wrote: Dear all, I am looking for some kind of interactive plot to draw a histogram for a normal distribution with different sample size. In that plot there would be some sort of "scroll-bar" which will take min value 10 and maximum value of 10,000 as sample size (n) from a standard normal distribution. In that case user will scroll in that scroll bar and histogram with different sample numbers will be drawn in the same plot. Is there any function/package in R to do that? Your help will be highly appreciated. Have you looked at TeachingDemos? It has a bunch of "tk" interactive stuff like that. Thanks, -- View this message in context: http://n4.nabble.com/Interactive-plot-histogram-in-R-possible-tp1557984p1557984.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. David Winsemius, MD Heritage Laboratories West Hartford, CT __ 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] Math.factor error message
On Feb 16, 2010, at 4:40 PM, David Winsemius wrote:
On Feb 16, 2010, at 2:25 PM, Hichem Ben Khedhiri wrote:
Dear R-helpers,
I am using a vrtest on time series data. My commands are as follows;
read.table("B.txt",sep="\t",fill=TRUE, na.strings = "NA")
require(vrtest)
rm(list=ls(all=TRUE))
datamat <- read.table("B.txt",sep="\t",fill=TRUE, na.strings = "NA")
column <- 1
nob <- nrow(datamat)
y <- log(datamat[2:nob,column])-log(datamat[1:(nob-1),column])
After, the use of last command, I get the following message;
in Math.factor(c(37L, 36L, 42L, 41L, 44L, 38L, 31L, 61L, 66L, 91L, :
log not meaningful for factors
My data is composed of one column.
It appears that you may need to apply as.numeric(as.character( )) to
that column after input (See the FAQ if you don't know why you need
both functions.) You seem to have created a factor in datamat. You
can prevent factor-formation with stringsAsFactors or colClasses
arguments to read.table.
OOOPs. I did not notice that you had attached the file. It's not a tab
separated file and so both of your columns get read in as one
character variable. (or maybe they are commas as decimal points in
which case see below.) You also did not tell read.table() that you
had a header and furthermore to completely complicate things, you
enclosed the two columns within paired double-quotes.
Get rid of the enclosing quotes and read back in with correct
arguments, perhaps sep="," unless you are in a locale that uses commas
as decimal points, in which case you only need read.csv2(). The
fill=TRUE appears superfluous.
I would appreciate, if any one could provide me with some hints to
get
around the problem.
Best regards,
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
__
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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.
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problems with boxplot in ggplot2:qplot
On 2/15/2010 2:41 PM, Dimitri Shvorob wrote:
> library(sqldf)
> library(ggplot2)
>
> t = data.frame(t = seq.Date(as.Date("2009-01-01"), to =
> as.Date("2009-12-01"), by = "month"))
> x = data.frame(x = rnorm(5))
> df = sqldf("select * from t, x")
A simpler way to get random data that doesn't involve the sqldf package, and
gets different x values for each date:
df <- data.frame(t = seq.Date(as.Date("2009-01-01"), to=as.Date("2009-12-01"),
by="month"), x=rnorm(60))
> qplot(factor(df$t), df$x, geom = "boxplot") + theme_bw()
You are converting your dates to a factor, so they are no longer dates. I'm
guessing you did this to get a separate boxplot for each date, but that is not
the right way to do that. Use the "group" aesthetic to make different groups.
qplot(df$t, df$x, geom = "boxplot", group=df$t) + theme_bw()
> qplot(factor(df$t), df$x, geom = "boxplot") + theme_bw() +
> scale_x_date(major = "months", minor = "weeks", format = "%b")
qplot(df$t, df$x, geom = "boxplot", group=df$t) + theme_bw() +
scale_x_date(major = "months", minor = "weeks", format = "%b")
> qplot(factor(df$t), df$x, geom = "boxplot") + theme_bw() +
> scale_x_date(format = "%b")
qplot(df$t, df$x, geom = "boxplot", group=df$t) + theme_bw() +
scale_x_date(format = "%b")
--
Brian Diggs, Ph.D.
Senior Research Associate, Department of Surgery, Oregon Health & Science
University
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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[R] Interactive plot (histogram) in R..........possible?
Dear all, I am looking for some kind of interactive plot to draw a histogram for a normal distribution with different sample size. In that plot there would be some sort of "scroll-bar" which will take min value 10 and maximum value of 10,000 as sample size (n) from a standard normal distribution. In that case user will scroll in that scroll bar and histogram with different sample numbers will be drawn in the same plot. Is there any function/package in R to do that? Your help will be highly appreciated. Thanks, -- View this message in context: http://n4.nabble.com/Interactive-plot-histogram-in-R-possible-tp1557984p1557984.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Math.factor error message
On Feb 16, 2010, at 2:25 PM, Hichem Ben Khedhiri wrote:
Dear R-helpers,
I am using a vrtest on time series data. My commands are as follows;
read.table("B.txt",sep="\t",fill=TRUE, na.strings = "NA")
require(vrtest)
rm(list=ls(all=TRUE))
datamat <- read.table("B.txt",sep="\t",fill=TRUE, na.strings = "NA")
column <- 1
nob <- nrow(datamat)
y <- log(datamat[2:nob,column])-log(datamat[1:(nob-1),column])
After, the use of last command, I get the following message;
in Math.factor(c(37L, 36L, 42L, 41L, 44L, 38L, 31L, 61L, 66L, 91L, :
log not meaningful for factors
My data is composed of one column.
It appears that you may need to apply as.numeric(as.character( )) to
that column after input (See the FAQ if you don't know why you need
both functions.) You seem to have created a factor in datamat. You can
prevent factor-formation with stringsAsFactors or colClasses arguments
to read.table.
I would appreciate, if any one could provide me with some hints to get
around the problem.
Best regards,
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
__
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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] igraph
Hi gabrielap wrote: Hello... I am a system engeenering student and I am using R for first time for Graph Theory. I would like to know if there is anyway you can plot an ghaph (igraph library) and obtain a graph whose vertices dont appear identified with number, instead I would like the vertices to be identified with letters or words, names... is there anyway I can do this? You can set the "label" attribute for the graph vertices, for example, ... g <- graph.ring(10) plot(g) g <- set.vertex.attribute(g, "label", value=letters[1:10]) plot(g) Paul Thanks in Advance for your Help. Sincerly. Gabriela Prasad P.D. Sorry for my not at all perfect english. I am from a Spanish Country. -- Dr Paul Murrell Department of Statistics The University of Auckland Private Bag 92019 Auckland New Zealand 64 9 3737599 x85392 p...@stat.auckland.ac.nz http://www.stat.auckland.ac.nz/~paul/ __ 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 on MAC OS X
On Feb 16, 2010, at 2:23 PM, Mestat wrote:
Hi listers,
I just got a MAC, so I am trying to use the command READ.TABLE but I
am
getting a error that is probably caused by the wrong path that I am
using...
The command is the following...
file<-read.table("/Users/Márcio/UdeM/Travail Dirigé/Data/MU284
Population.txt",header=T,skip=24)
And I am getting the following error...
Erro em file(file, "rt") : não é possível abrir a conexão
Além disso: Warning message:
In file(file, "rt") :
cannot open file
'/User/Márcio/UdeM/Travail_Dirigé/Data/MU284_Population.txt': No
such file
or directory
I checked already the messages but I didn't find what could be my
mistake...
Any suggestions???
1) Post on the correct list:
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
2a) Include sessionInfo()
2b) if not, then at least tell us whether you are running as a
terminal session or with the GUI.
3a) use file.choose() as your file argument ... or
3b) click-hold-drag the file icon onto the console ... this should
create a correct folder/file designation suitable for enclosure within
quotes.
4) do not spell R functions with all caps.
--
David.
--
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
__
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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] odfTable: table width and alignment
Aleksey,
Go ahead and send me a test file.
Also: what version of OO are you using (or are you using something else)?
Thanks,
Max
On Tue, Feb 16, 2010 at 3:40 PM, Aleksey Naumov wrote:
> Max,
>
> Thank you for your help. Please see my responses below.
>
>
> On Tue, Feb 9, 2010 at 8:20 PM, Max Kuhn wrote:
>>
>> > I am trying to figure out how to control table width and alignment on
>> > the
>> > page for a table generated by odfTable. Based on reading odfWeave
>> > documentation (including formattingOut.odt), here is how I manipulate
>> > the
>> > styles:
>> >
>> st = getStyleDefs()
>> # modify the table style
>> tab = getStyles()$table
>> st[[tab]]$align = "center" # seems to have no effect
>> st[[tab]]$marginLeft = "2.0 in" # seems to have no effect
>> setStyleDefs(st)
>> >
>> > My table always ends up fully justified (taking all page width). When I
>> > check Table Format in the output .odf, Alignment is always "Automatic".
>> > When
>> > doing Column/Optimal Width on the table, the table shrinks but becomes
>> > left
>> > aligned, not centered.
>>
>> It's hard to tell without an actual file to test with (and what
>> versions of R and odfWeave, and what platform etc)
>
> I am working with R 2.10.1 om Windows XP Professional 2002, SP 3. My package
> versions are listed below:
>> pkgVersions(type = "matrix")
> [,1] [,2] [,3]
> [,4]
> [1,] "base (2.10.1)" "grDevices (2.10.1)" "MASS (7.3-4)" "stats
> (2.10.1)"
> [2,] "datasets (2.10.1)" "grid (2.10.1)" "methods (2.10.1)" "utils
> (2.10.1)"
> [3,] "graphics (2.10.1)" "lattice (0.17-26)" "odfWeave (0.7.10)" "XML
> (2.6-0)"
>
> Would it help if I send you a small ODT file which concisely shows what I am
> trying to do?
>
>>
>> Did you read the example files in the examples directory of the
>> package? There are examples of what you are doing there and they seem
>> to work (last time I checked at least).
>>
>> Can you you reproduce those example tables?
>
> Yes, I looked into these examples, they are nice, thank you. I am able to
> run (odfWeave) 3 out of 4: "examples.odt", "simple.odt" and "testCases.odt",
> but they do not make use of the table style "align" or "margin" properties,
> so all tables are fully justified per default (except for the case where a
> code chuck lives in a small 1x1 table, which effectively restricts the
> output width -- in fact, this is a partial alternative to manipulating table
> margins).
>
> I cannot run odfWeave on "formatting.odt". The initial error message has to
> do with the fact that I do not have the "RTable2" style, which is referenced
> in chunk:
>
> 13 : echo term verbatim(label=showTableStyles)
>
> Error: chunk 13 (label=showTableStyles)
> Error in names(x) <- value :
> 'names' attribute [1] must be the same length as the vector [0]
>
> However, once I comment out styleDetails("RTable2") from this chunk I get a
> different error, here is the full output:
>
>> odfWeave("formatting.odt", "[AN]_formatting_out.odt")
> Copying formatting.odt
> Setting wd to
> C:\DOCUME~1\anaumov\LOCALS~1\Temp\RtmplqVqs5/odfWeave16142147610
> Unzipping ODF file using unzip -o "formatting.odt"
> Archive: formatting.odt
> extracting: mimetype
> creating: Configurations2/statusbar/
> inflating: Configurations2/accelerator/current.xml
> creating: Configurations2/floater/
> creating: Configurations2/popupmenu/
> creating: Configurations2/progressbar/
> creating: Configurations2/menubar/
> creating: Configurations2/toolbar/
> creating: Configurations2/images/Bitmaps/
> extracting: Pictures/121301899B642BA5.png
> extracting: Pictures/10EA01757E0E322B.png
> extracting: Pictures/1211018638600D3B.png
> inflating: layout-cache
> inflating: content.xml
> inflating: styles.xml
> extracting: meta.xml
> inflating: Thumbnails/thumbnail.png
> inflating: settings.xml
> inflating: META-INF/manifest.xml
>
> Removing formatting.odt
>
> Pre-processing the contents
> Error: cc$parentId == parentId is not TRUE
> In addition: Warning message:
> In function (name, .state) : found start of code chunk in a code chunk
>
> Surprisingly, even if I remove the comment I still get the same message as
> above ("found start of code chunk ...") which is very puzzling. Is
> formatting.odt working for you with the latest R and package versions?
>
>
>> The table style is understood by odfWeave -- here is the output I get
>> after
>> sourcing my style definition file:
>>
>>> getStyles()$table
>> [1] "RTable1"
>>> getStyleDefs()[[getStyles()$table]]
>> $type
>> [1] "Table"
>>
>> $marginLeft
>> [1] "2.0 in"
>>
>> $marginRight
>> [1] "0.05in"
>>
>> $marginTop
>> [1] "0.05in"
>>
>> $marginBottom
>> [1] "0.05in"
>>
>> $align
>> [1] "center"
>>
>> I am not sure why these style options do not seem to have effect on the
>> output. My specific questions are:
>>
>> (1) How do I get table alignment to work?
>>
>>
Re: [R] READ.TABLE for Mac
Mestat wrote:
>
> Hi listers,
> I just got a MAC, so I am trying to use the command READ.TABLE but I am
> getting a error that is probably caused by the wrong path that I am
> using...
> The command is the following...
>
> file<-read.table("/Users/Márcio/UdeM/Travail Dirigé/Data/MU284
> Population.txt",header=T,skip=24)
>
> And I am getting the following error...
>
> Erro em file(file, "rt") : não é possível abrir a conexão
> Além disso: Warning message:
> In file(file, "rt") :
> cannot open file
> '/User/Márcio/UdeM/Travail_Dirigé/Data/MU284_Population.txt': No such file
> or directory
>
> I checked already the messages but I didn't find what could be my
> mistake... Any suggestions???
> Thanks in advance,
> Marcio
>
Well there are a couple inconsistencies between the example command you give
and the error message you are reporting:
1. The root path '/Users' is '/User' in the error message.
2. The file name 'MU284 Population.txt' is 'MU284_Population.txt' in the
error message. The same thing has happened to the directory name "Travail
Dirigé"
I also use R on OS X and have never observed it alter or sanitize my file
names-- I suspect you may have mistyped the path. If this is the case, use
the TAB key to help you autofill the path rather then trying to type it all
out correctly yourself. Just type the first few letters of a folder or file
name and push TAB to have the rest autocompleted.
Good luck!
-Charlie
--
View this message in context:
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Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
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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 on MAC OS X
Hi listers,
I just got a MAC, so I am trying to use the command READ.TABLE but I am
getting a error that is probably caused by the wrong path that I am using...
The command is the following...
file<-read.table("/Users/Márcio/UdeM/Travail Dirigé/Data/MU284
Population.txt",header=T,skip=24)
And I am getting the following error...
Erro em file(file, "rt") : não é possível abrir a conexão
Além disso: Warning message:
In file(file, "rt") :
cannot open file
'/User/Márcio/UdeM/Travail_Dirigé/Data/MU284_Population.txt': No such file
or directory
I checked already the messages but I didn't find what could be my mistake...
Any suggestions???
Thanks in advance,
Marcio
--
View this message in context:
http://n4.nabble.com/R-on-MAC-OS-X-tp802729p1557818.html
Sent from the R help mailing list archive at Nabble.com.
__
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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] Analyzing event times with densityplot
Dear useRs,
I have a file with a sequence of event timestamps, for instance the
times at which someone visits a website:
02.02.2010 09:00:00
02.02.2010 09:00:00
02.02.2010 09:00:00
02.02.2010 09:00:01
02.02.2010 09:00:03
02.02.2010 09:00:05
02.02.2010 09:00:06
02.02.2010 09:00:06
02.02.2010 09:00:09
02.02.2010 09:00:11
02.02.2010 09:00:11
02.02.2010 09:00:11
etc, for several thousand rows.
I'd like to get an idea how the web hits are distributed over time,
over the week etc. I extract the data to a dataframe and I tried
plotting densityplots:
library(lattice)
data <- as.POSIXct(scan("data.txt",
what=character(0),
sep="\n"),
format="%d.%m.%Y %T")
data.lt <- as.POSIXlt(data)
data.df <- data.frame(time=data,
sec=jitter(data.lt$sec, amount=.5),
min=data.lt$min,
hour=data.lt$hour,
wday=weekdays(data))
densityplot(~(sec+60*min+3600*hour)|wday,
data.df,
plot.points=FALSE)
1) Is a densityplot the most appropriate way to analyze this kind of data?
2) The densityplot yields a pdf, but I'd rather see the number of
visits per second on the y-axis. How can I do that?
3) I've found that the shape of the plot depends heavily on the chosen
bandwidth. Ideally I'd like to identify spikes when several visitors
come to the site at the "same" time (say, within 5 seconds of each
others). How should I choose the bandwidth (and kernel for that
matter)?
Your help would be much, much appreciated.
--
David Lindelöf, Ph.D.
+41 (0)79 415 66 41 or skype:david.lindelof
Better Software for Tomorrow's Cities:
http://computersandbuildings.com
Follow me on Twitter:
http://twitter.com/dlindelof
__
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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] Math.factor error message
Dear R-helpers,
I am using a vrtest on time series data. My commands are as follows;
read.table("B.txt",sep="\t",fill=TRUE, na.strings = "NA")
require(vrtest)
rm(list=ls(all=TRUE))
datamat <- read.table("B.txt",sep="\t",fill=TRUE, na.strings = "NA")
column <- 1
nob <- nrow(datamat)
y <- log(datamat[2:nob,column])-log(datamat[1:(nob-1),column])
After, the use of last command, I get the following message;
in Math.factor(c(37L, 36L, 42L, 41L, 44L, 38L, 31L, 61L, 66L, 91L, :
log not meaningful for factors
My data is composed of one column.
I would appreciate, if any one could provide me with some hints to get
around the problem.
Best regards,
Ben
BNS CER
"11,14"
"11,11"
"11,25"
"11,22"
"11,31"
"11,15"
"11,00"
"11,88"
"11,94"
"12,44"
"12,90"
"12,94"
"12,97"
"12,80"
"12,78"
"13,14"
"13,72"
"13,12"
"12,93"
"12,62"
"12,62"
"12,22"
"12,30"
"12,12"
"12,16"
"11,89"
"12,30"
"12,37"
"12,50"
"12,50"
"12,41"
"12,72"
"12,54"
"12,44"
"12,73"
"12,94"
"13,04"
"13,16"
"13,60"
"13,58"
"13,65"
"13,67"
"13,80"
"13,87"
"13,33"
"13,32"
"13,42"
"13,51"
"13,63"
"13,90"
"13,68"
"13,57"
"13,43"
"13,61"
"13,84"
"13,48"
"13,39"
"12,83"
"12,54"
"12,59"
"12,57"
"12,15"
"11,93"
"11,98"
"12,09"
"11,91"
"12,27"
"12,12"
"12,00"
"12,35"
"12,69"
"12,83"
"12,59"
"12,64"
"12,88"
"12,90"
"12,37"
"12,97"
"13,37"
"13,41"
"13,56"
"13,59"
"13,52"
"13,53"
"13,33"
"13,22"
"13,36"
"13,43"
"13,40"
"13,45"
"13,43"
"13,36"
"13,38"
"13,27"
"13,10"
"13,02"
"12,81"
"12,70"
"12,69"
"12,66"
"12,60"
"12,64"
"12,67"
"12,67"
"12,69"
"12,81"
"12,67"
"12,36"
"12,40"
"12,39"
"12,64"
"12,87"
"12,85"
"12,85"
"12,87"
"12,92"
"12,90"
"12,88"
"13,01"
"12,70"
"12,32"
"12,53"
"12,19"
"11,98"
"11,94"
"12,00"
"11,80"
"11,92"
"11,88"
"12,00"
"11,80"
"12,09"
"11,80"
"11,82"
"11,65"
"11,42"
"11,16"
"11,40"
"11,03"
"11,04"
"11,10"
"10,61"
"11,10"
"11,50"
"11,45"
"11,35"
"11,50"
"12,03"
"12,20"
"12,13"
"12,65"
"12,79"
"12,52"
"12,79"
"12,79"
"12,56"
"12,58"
"12,33"
"12,10"
"12,55"
"12,00"
"11,74"
"11,76"
"11,85"
"12,03"
"12,27"
"12,81"
"12,47"
"12,06"
"11,92"
"11,59"
"11,80"
"11,47"
"11,59"
"11,50"
"11,61"
"11,63"
"11,35"
"11,14"
"11,00"
"10,88"
"11,00"
"11,01"
"10,90"
"10,89"
"10,74"
"10,45"
"10,30"
"10,56"
"10,85"
"10,60"
"10,83"
"10,45"
"10,29"
"10,30"
"9,75"
"9,55"
"10,23"
"10,72"
"10,22"
"10,77"
"11,25"
"11,74"
"11,43"
"11,20"
"10,83"
"10,78"
"11,00"
"10,63"
"10,15"
"10,80"
"10,78"
"10,16"
"9,45"
"9,50"
"9,91"
"9,25"
"8,68"
"8,94"
"9,30"
"9,75"
"9,10"
"8,28"
"7,95"
"8,26"
"7,60"
"7,96"
"8,78"
"9,64"
"9,60"
"9,61"
"9,76"
"10,00"
"10,34"
"10,60"
"10,54"
"10,61"
"10,53"
"10,73"
"10,43"
"10,63"
"10,51"
"10,39"
"10,46"
"11,30"
"12,21"
"12,06"
"12,33"
"12,58"
"12,68"
"12,80"
"13,53"
"13,55"
"13,30"
"13,25"
"13,53"
"13,40"
"13,06"
"13,01"
"12,83"
"12,91"
"13,07"
"13,09"
"13,90"
"13,43"
"13,61"
"13,22"
"13,36"
"13,23"
"13,38"
"13,28"
"13,18"
"13,90"
"14,31"
"14,34"
"14,58"
"14,08"
"14,45"
"14,18"
"14,15"
"14,35"
"13,90"
"13,66"
"15,13"
"15,15"
"15,55"
"15,89"
"16,08"
"15,74"
"15,63"
"15,69"
"15,66"
"15,28"
"15,22"
"15,44"
"15,08"
"15,02"
"15,23"
"15,50"
"15,25"
"15,17"
"16,20"
"16,95"
"16,65"
"18,05"
"18,65"
"18,93"
"18,98"
"19,85"
"20,26"
"19,65"
"19,08"
"19,78"
"18,83"
"18,55"
"18,38"
"18,80"
"19,57"
"18,88"
"18,65"
"18,88"
"19,83"
"19,43"
"19,56"
"20,15"
"20,18"
"20,18"
"19,25"
"18,98"
"18,90"
"19,10"
"19,59"
"18,83"
"18,85"
"19,13"
"20,05"
"20,31"
"20,65"
"20,25"
"20,45"
"20,80"
"20,90"
"20,63"
"20,65"
"20,30"
"20,10"
"20,05"
"20,25"
"20,00"
"19,98"
"19,90"
"19,60"
"19,74"
"19,83"
__
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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] Random center effect
Hello R users, I'm trying to take into acount the center effect in a clinical study comparing 3 treatments (data from the book Applied Mixed Models in Medicine Statistics by Helen Brown and Robin Prescott): - dbp: diastolic blood pressure at 8 weeks - dbp0: diastolic blood pressure at inclusion - treat: three treatments A, B and C - centre: centres of the study First, I have fitted a marginal model with gls (nlme package), with a compound symmetry structure: require(nlme) gls1 <- gls(dbp ~ factor(centre) + treat + dbp0, data = tension1, correlation = corCompSymm(form = ~ 1 | centre)) summary(gls1) anova(gls1) Denom. DF: 224 numDF F-value p-value (Intercept)1 33349.45 <.0001 factor(centre)28 2.38 0.0003 treat 2 1.79 0.1700 dbp0 1 2.61 0.1075 Second, I tried to fit a random effect model with lme: lme1 <- lme(dbp ~ factor(centre) + treat + dbp0, random = ~ 1 | centre, data = tension1) anova(lme1) numDF denDF F-value p-value (Intercept)1 224 3753.228 <.0001 factor(centre)28 00.335 NaN treat 2 2241.786 0.1700 dbp0 1 2242.612 0.1075 Message d'avis : In pf(q, df1, df2, lower.tail, log.p) : production de NaN I thought this two models equivalent, and I don't understand why the fixed center effect produced NaN in lme model. I also tried with lmer (from lme4 package): require(lme4) lmer1 <- lmer(dbp ~ factor(centre) + treat + dbp0 + (1 | centre), data = tension1) anova(lmer1) Analysis of Variance Table Df Sum Sq Mean Sq F value factor(centre) 28 1214.42 43.372 0.7026 treat 2 220.52 110.262 1.7862 dbp01 161.23 161.231 2.6118 F values for centre effect are very different in the 3 models. It is surely a naive question, but does someone could to me explain what happens here? Thank you very much in advance. Here the data : tension1 <- structure(list(patient = c(1L, 3L, 4L, 5L, 7L, 8L, 9L, 10L, 11L, 13L, 14L, 15L, 18L, 19L, 23L, 24L, 25L, 28L, 30L, 31L, 32L, 34L, 35L, 36L, 37L, 38L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 52L, 53L, 54L, 55L, 56L, 57L, 58L, 60L, 63L, 64L, 70L, 71L, 72L, 73L, 74L, 80L, 81L, 82L, 84L, 92L, 93L, 94L, 95L, 96L, 97L, 98L, 99L, 100L, 101L, 102L, 103L, 104L, 105L, 106L, 107L, 108L, 109L, 110L, 111L, 112L, 113L, 114L, 116L, 117L, 118L, 119L, 120L, 122L, 124L, 125L, 127L, 128L, 129L, 130L, 131L, 132L, 133L, 134L, 135L, 136L, 137L, 139L, 140L, 141L, 142L, 143L, 144L, 145L, 146L, 147L, 150L, 157L, 158L, 160L, 161L, 162L, 165L, 166L, 167L, 169L, 170L, 171L, 172L, 173L, 174L, 175L, 176L, 177L, 178L, 180L, 181L, 182L, 183L, 185L, 186L, 187L, 189L, 190L, 191L, 192L, 199L, 200L, 201L, 202L, 203L, 204L, 205L, 206L, 207L, 208L, 212L, 213L, 214L, 216L, 217L, 218L, 219L, 220L, 221L, 223L, 224L, 225L, 226L, 227L, 228L, 229L, 230L, 237L, 241L, 242L, 243L, 244L, 245L, 246L, 247L, 248L, 249L, 250L, 251L, 252L, 255L, 256L, 258L, 260L, 261L, 262L, 263L, 264L, 265L, 266L, 267L, 268L, 269L, 270L, 271L, 272L, 273L, 274L, 275L, 279L, 280L, 281L, 282L, 283L, 284L, 285L, 286L, 287L, 290L, 291L, 292L, 293L, 294L, 301L, 302L, 303L, 304L, 305L, 306L, 307L, 308L, 309L, 310L, 311L, 312L, 319L, 320L, 322L, 323L, 324L, 325L, 326L, 327L, 328L, 329L, 330L, 332L, 333L, 334L, 335L, 337L, 338L, 339L, 340L, 341L, 342L, 343L, 344L, 345L, 346L, 347L, 348L, 350L, 352L, 355L, 357L, 361L, 362L, 363L, 364L, 365L, 366L), centre = c(29L, 5L, 5L, 29L, 3L, 3L, 3L, 3L, 3L, 36L, 36L, 36L, 36L, 5L, 5L, 5L, 15L, 15L, 15L, 4L, 4L, 4L, 4L, 4L, 23L, 23L, 7L, 7L, 7L, 7L, 7L, 7L, 30L, 30L, 30L, 30L, 30L, 18L, 18L, 18L, 18L, 18L, 24L, 23L, 35L, 35L, 35L, 27L, 27L, 1L, 1L, 1L, 1L, 26L, 26L, 26L, 26L, 26L, 14L, 14L, 14L, 14L, 14L, 14L, 11L, 11L, 11L, 11L, 11L, 11L, 7L, 7L, 7L, 7L, 7L, 7L, 6L, 6L, 6L, 6L, 6L, 32L, 32L, 32L, 25L, 25L, 25L, 25L, 25L, 25L, 31L, 31L, 31L, 31L, 31L, 14L, 14L, 14L, 14L, 14L, 14L, 37L, 37L, 37L, 37L, 31L, 31L, 31L, 31L, 31L, 13L, 13L, 13L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 9L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 31L, 31L, 31L, 31L, 31L, 31L, 8L, 8L, 8L, 8L, 11L, 11L, 11L, 11L, 12L, 12L, 12L, 12L, 12L, 36L, 36L, 36L, 36L, 36L, 36L, 40L, 40L, 41L, 14L, 14L, 14L, 14L, 14L, 14L, 4L, 4L, 4L, 4L, 4L, 4L, 36L, 36L, 36L, 1L, 1L, 1L, 1L, 1L, 7L, 7L, 7L, 7L, 7L, 7L, 1L, 1L, 1L, 1L, 1L, 5L, 5L, 5L, 5L, 25L, 26L, 26L, 26L, 26L, 12L, 12L, 12L, 12L, 12L, 15L, 15L, 15L, 15L, 15L, 15L, 1L, 1L, 1L, 1L, 1L, 1L, 36L, 36L, 36L, 36L, 36L, 31L, 31L, 31L, 31L, 31L, 31L, 1L, 1L, 1L, 1L, 14L, 14L, 14L, 14L, 14L, 14L, 31L, 31L, 31L, 31L, 31L, 31L, 1L, 1L, 36L, 36L, 31L, 31L, 31L, 31L, 31L, 31L), treat = structure(c(3L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 3L, 2L, 1L, 3L, 1L, 2L, 1L, 3L, 3L, 2L, 2L, 2L, 3L, 2L, 1L, 3L, 3L, 3L, 2L, 1L, 1L, 3L, 3L, 2L, 2L, 3L, 3L, 2L, 1L, 2L, 1L, 3L, 3L, 2L, 3L, 1L, 3L, 2L, 1L, 2L, 3L, 2L, 3L, 1L, 3L, 3L, 1L, 1L, 2L, 3L, 2L, 1L, 1L, 3L, 2L, 3L, 3L, 2L, 3L, 2L, 1L, 1L, 3L, 2L, 1L, 3L, 1L, 2L, 3L, 1L, 3L, 2L, 1L, 1L,
Re: [R] odfTable: table width and alignment
Max,
Thank you for your help. Please see my responses below.
On Tue, Feb 9, 2010 at 8:20 PM, Max Kuhn wrote:
> > I am trying to figure out how to control table width and alignment on the
> > page for a table generated by odfTable. Based on reading odfWeave
> > documentation (including formattingOut.odt), here is how I manipulate the
> > styles:
> >
> st = getStyleDefs()
> # modify the table style
> tab = getStyles()$table
> st[[tab]]$align = "center"# seems to have no effect
> st[[tab]]$marginLeft = "2.0 in" # seems to have no effect
> setStyleDefs(st)
> >
> > My table always ends up fully justified (taking all page width). When I
> > check Table Format in the output .odf, Alignment is always "Automatic".
> When
> > doing Column/Optimal Width on the table, the table shrinks but becomes
> left
> > aligned, not centered.
>
> It's hard to tell without an actual file to test with (and what
> versions of R and odfWeave, and what platform etc)
>
I am working with R 2.10.1 om Windows XP Professional 2002, SP 3. My package
versions are listed below:
> pkgVersions(type = "matrix")
[,1][,2] [,3]
[,4]
[1,] "base (2.10.1)" "grDevices (2.10.1)" "MASS (7.3-4)" "stats
(2.10.1)"
[2,] "datasets (2.10.1)" "grid (2.10.1)" "methods (2.10.1)" "utils
(2.10.1)"
[3,] "graphics (2.10.1)" "lattice (0.17-26)" "odfWeave (0.7.10)" "XML
(2.6-0)"
Would it help if I send you a small ODT file which concisely shows what I am
trying to do?
> Did you read the example files in the examples directory of the
> package? There are examples of what you are doing there and they seem
> to work (last time I checked at least).
>
> Can you you reproduce those example tables?
>
Yes, I looked into these examples, they are nice, thank you. I am able to
run (odfWeave) 3 out of 4: "examples.odt", "simple.odt" and "testCases.odt",
but they do not make use of the table style "align" or "margin" properties,
so all tables are fully justified per default (except for the case where a
code chuck lives in a small 1x1 table, which effectively restricts the
output width -- in fact, this is a partial alternative to manipulating table
margins).
I cannot run odfWeave on "formatting.odt". The initial error message has to
do with the fact that I do not have the "RTable2" style, which is referenced
in chunk:
13 : echo term verbatim(label=showTableStyles)
Error: chunk 13 (label=showTableStyles)
Error in names(x) <- value :
'names' attribute [1] must be the same length as the vector [0]
However, once I comment out styleDetails("RTable2") from this chunk I get a
different error, here is the full output:
> odfWeave("formatting.odt", "[AN]_formatting_out.odt")
Copying formatting.odt
Setting wd to
C:\DOCUME~1\anaumov\LOCALS~1\Temp\RtmplqVqs5/odfWeave16142147610
Unzipping ODF file using unzip -o "formatting.odt"
Archive: formatting.odt
extracting: mimetype
creating: Configurations2/statusbar/
inflating: Configurations2/accelerator/current.xml
creating: Configurations2/floater/
creating: Configurations2/popupmenu/
creating: Configurations2/progressbar/
creating: Configurations2/menubar/
creating: Configurations2/toolbar/
creating: Configurations2/images/Bitmaps/
extracting: Pictures/121301899B642BA5.png
extracting: Pictures/10EA01757E0E322B.png
extracting: Pictures/1211018638600D3B.png
inflating: layout-cache
inflating: content.xml
inflating: styles.xml
extracting: meta.xml
inflating: Thumbnails/thumbnail.png
inflating: settings.xml
inflating: META-INF/manifest.xml
Removing formatting.odt
Pre-processing the contents
Error: cc$parentId == parentId is not TRUE
In addition: Warning message:
In function (name, .state) : found start of code chunk in a code chunk
Surprisingly, even if I remove the comment I still get the same message as
above ("found start of code chunk ...") which is very puzzling. Is
formatting.odt working for you with the latest R and package versions?
> The table style is understood by odfWeave -- here is the output I get
after
> sourcing my style definition file:
>
>> getStyles()$table
> [1] "RTable1"
>> getStyleDefs()[[getStyles()$table]]
> $type
> [1] "Table"
>
> $marginLeft
> [1] "2.0 in"
>
> $marginRight
> [1] "0.05in"
>
> $marginTop
> [1] "0.05in"
>
> $marginBottom
> [1] "0.05in"
>
> $align
> [1] "center"
>
> I am not sure why these style options do not seem to have effect on the
> output. My specific questions are:
>
> (1) How do I get table alignment to work?
>
> (2) Is the only way to control table width via setting the margins in the
> $table style? What am I doing wrong in the above style code?
At present, yes.
>
Ok, thank you, As I found out by looking at testCases.odt, another way which
may work for simple tables is to embed a chuck into a 1x1 table with
specified dimensions, even though this approach is not flexible (no way to
control table dimensions at
[R] General JRI questions
Hi all, I recently started to work with JRI/rJava and have already run R statements from Java. Since I have larger units encapsulated in R scripts, I would like to run those from Java directly. I was not able to answer the following questions and would appreciate your help on this: How do I run entire R scripts from Java using JRI? (scripts are located in the same folder) How do I pass data from java to these scripts? How can I return results from these scripts back to Java? Ralf __ 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] False convergence of a glmer model
On Tue, Feb 16, 2010 at 9:38 AM, Shige Song wrote: > Hi Doug, > > Thanks. Next time I will post it to the R-SIG0-mixed-models mailing > list, as you suggested. I have added R-SIG-mixed-models to the cc: list. I suggest we drop the cc: to R-help after this message. > With respect to your question, the answer is no, these parameters do > not make sense. Here is the Stata output from "exactly" the same > model: > . xi:xtlogit inftmort i.cohort, i(code) > i.cohort _Icohort_1-3 (naturally coded; _Icohort_1 omitted) > > Fitting comparison model: > > Iteration 0: log likelihood = -1754.4476 > Iteration 1: log likelihood = -1749.3366 > Iteration 2: log likelihood = -1749.2491 > Iteration 3: log likelihood = -1749.2491 > > Fitting full model: > > tau = 0.0 log likelihood = -1749.2491 > tau = 0.1 log likelihood = -1743.8418 > tau = 0.2 log likelihood = -1739.0769 > tau = 0.3 log likelihood = -1736.4914 > tau = 0.4 log likelihood = -1739.5415 > > Iteration 0: log likelihood = -1736.4914 > Iteration 1: log likelihood = -1722.6629 > Iteration 2: log likelihood = -1694.9114 > Iteration 3: log likelihood = -1694.6509 > Iteration 4: log likelihood = -1694.649 > Iteration 5: log likelihood = -1694.649 > > Random-effects logistic regression Number of obs = 21694 > Group variable: code Number of groups = 10789 > > Random effects u_i ~ Gaussian Obs per group: min = 1 > avg = 2.0 > max = 9 > > Wald chi2(2) = 8.05 > Log likelihood = -1694.649 Prob > chi2 = 0.0178 Well, the quantities being displayed in the iteration output from glmer are the deviance and the parameter values. This stata log-likelihood corresponds to a deviance of 3389.3. It is possible that glmer and stata don't measure the log-likelihood on the same scale but, if not, then the estimates where glmer gets stalled are producing a lower deviance of 2837.49. The reason that glmer is getting stalled is because of the coefficient of -7.45883 for the intercept. This corresponds to a mean success probability of 0.0005 for cohort 1. The stata coefficient estimate of -5.214642 corresponds to a mean success probability of 0.0055 for cohort 1, which is still very, very small. The success probabilities for the other cohorts are going to be even smaller. What is the overall proportion of zeros in the response? The optimization to determine the maximum likelihood estimates of the coefficients is being done on the scale of the linear predictor. When the values of the linear predictor become very small or very large, the fitted values become insensitive to the coefficients. The fact the one program converges and another one doesn't may have more to do with the convergence criterion than with the quality of the fit. > -- > inftmort | Coef. Std. Err. z P>|z| [95% Conf. Interval] > -+ > _Icohort_2 | -.5246846 .1850328 -2.84 0.005 -.8873422 -.1620269 > _Icohort_3 | -.1424331 .140369 -1.01 0.310 -.4175513 .132685 > _cons | -5.214642 .1839703 -28.35 0.000 -5.575217 -4.854067 > -+ > /lnsig2u | .9232684 .1416214 .6456956 1.200841 > -+ > sigma_u | 1.586665 .1123528 1.381055 1.822885 > rho | .4335015 .0347791 .3669899 .5024984 > -- > Likelihood-ratio test of rho=0: chibar2(01) = 109.20 Prob >= chibar2 = 0.000 > > The difference is quite huge, and Stata did not have any difficulties > estimating this model, which makes feel that I might get some very > basic specification wrong in my R model... > > Best, > Shige > > On Tue, Feb 16, 2010 at 10:29 AM, Douglas Bates wrote: >> On Tue, Feb 16, 2010 at 9:05 AM, Shige Song wrote: >>> Dear All, >> >>> I am trying to fit a 2-level random intercept logistic regression on a >>> data set of 20,000 cases. The model is specified as the following: >> >>> m1 <- glmer(inftmort ~ as.factor(cohort) + (1|code), family=binomial, >>> data=d) >> >>> I got "Warning message: In mer_finalize(ans) : false convergence (8)" >> >> That message means that the optimizer function, nlminb, got stalled. >> It has converged but the point at which is has converged is not >> clearly the optimum. In many cases this just indicates that the >> optim
Re: [R] Legend Text Font Size
On 16.02.2010 19:59, Rob Helpert wrote: Hi. I have a plot containing a large number of lines. I have placed a legend in the plot, but with so many lines, the legend takes up a lot of space. I have tried to reduce the spacing between the lines using the legend parameter x.intersp=0.7, but this does not compress the legend enough. Is there some way to make the text font size smaller in "legend"? Use argument cex, as usual in plot functions: plot(1) legend(1,1,legend="a very long text - some very small font size", pch=1, cex=0.5) Uwe Ligges Thanks, RH. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] lmer - error asMethod(object) : matrix is not symmetric
On Tue, Feb 16, 2010 at 10:54 AM, Luisa Carvalheiro wrote: > Dear Douglas, > > Thank you for your reply. > Just some extra info on the dataset: In my case Number of obs is 33, > and number of groups of factor(Farm_code) is 12. > This is the information on iterations I get: > > summary(lmer(round(SR_SUN)~Dist_NV + (1|factor(Farm_code)) , > family=poisson, verbose =TRUE)) > 0: 60.054531: 1.06363 2.14672 -0.000683051 > 1: 60.054531: 1.06363 2.14672 -0.000683051 > Error in asMethod(object) : matrix is not symmetric [1,2] > In addition: Warning message: > In mer_finalize(ans) : singular convergence (7) > When I run a similar model (exp variable Dist_hives) the number of > iterations is 11: > summary(lmer(round(SR_SUN)~Dist_hives + (1|factor(Farm_code)) , > family=poisson, verbose =TRUE)) > 0: 61.745238: 0.984732 1.63769 0.000126484 > 1: 61.648229: 0.984731 1.63769 -2.08637e-05 > 2: 61.498777: 0.984598 1.63769 4.11867e-05 > 3: 47.960908: 0.381062 1.63585 6.77029e-05 > 4: 46.223789: 0.250732 1.66727 8.31854e-05 > 5: 46.23: 0.250732 1.66727 6.97790e-05 > 6: 46.216710: 0.250730 1.66727 7.60560e-05 > 7: 46.168835: 0.230386 1.64883 9.16430e-05 > 8: 46.165955: 0.228062 1.65658 8.70694e-05 > 9: 46.165883: 0.228815 1.65737 8.63400e-05 > 10: 46.165883: 0.228772 1.65734 8.63698e-05 > 11: 46.165883: 0.228772 1.65734 8.63701e-05 > I am very confused with the fact that it runs with Dist_hives and not > with Dist_NV. Both variables are distance values, the first having no > obvious relation with the response variable and the second (Dist_NV) > seems to have a negative effect on SR_SUN. As you say, Dist_hives has very little relationship to the response variable. The two fixed-effects coefficients are the last two parameters in the iteration output (the first parameter is the standard deviation of the random effects). So the slope with respect to Dist_hives for the linear predictor is 0.863. Either you have very large magnitudes of Dist_hives or that variable does not have much predictive power. For the second (Dist_NV) variable, the optimization algorithm is not able to make progress from the starting estimates. This may be an indication that the problem is badly scaled. Are the values of Dist_NV very large? If so, you may want to change the unit (say from meters to kilometers) so the values are much smaller. It may also help to use a starting estimate for the standard deviation of the random effects derived from the other model. That is, include start = 0.22 in the call to lmer. > Does this information helps identifying the problem with my data/analysis? > > Thank you, > > Luisa > > > > > On Tue, Feb 16, 2010 at 5:35 PM, Douglas Bates wrote: >> This is similar to another question on the list today. >> >> On Tue, Feb 16, 2010 at 4:39 AM, Luisa Carvalheiro >> wrote: >>> Dear R users, >>> >>> I am having problems using package lme4. >>> >>> I am trying to analyse the effect of a continuous variable (Dist_NV) >>> on a count data response variable (SR_SUN) using Poisson error >>> distribution. However, when I run the model: >>> >>> summary(lmer((SR_SUN)~Dist_NV + (1|factor(Farm_code)) , >>> family=poisson, REML=FALSE)) >>> >>> 1 error message and 1 warning message show up: >>> >>> in asMethod(object) : matrix is not symmetric [1,2] >>> In addition: Warning message: >>> In mer_finalize(ans) : singular convergence (7) >> >> So the first thing to do is to include the optional argument verbose = >> TRUE in the call to lmer. (Also, REML = FALSE is ignored for >> Generalized Linear Mixed Models and can be omitted. although there is >> no harm in including it.) >> >> You need to know where the optimizer is taking the parameter values >> before you can decide why. >> >> P.S. Questions like this will probably be more readily answered on the >> R-SIG-Mixed-Models mailing list. >> >>> A model including Dist_NV together with other variables runs with no >>> problems. >>> What am I doing wrong? >>> >>> Thank you, >>> >>> Luisa >>> >>> >>> -- >>> Luisa Carvalheiro, PhD >>> Southern African Biodiversity Institute, Kirstenbosch Research Center, >>> Claremont >>> & University of Pretoria >>> Postal address - SAWC Pbag X3015 Hoedspruit 1380, South Africa >>> telephone - +27 (0) 790250944 >>> carvalhe...@sanbi.org >>> lgcarvalhe...@gmail.com >>> >>> __ >>> R-help@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-help >>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >>> and provide commented, minimal, self-contained, reproducible code. >>> >> > > > > -- > Luisa Carvalheiro, PhD > Southern African Biodiversity Institute, Kirstenbosch Research Center, > Claremont > & University of Pretoria > Postal address - SAWC Pbag X3015 Hoedspruit 1380, South Africa > telephone - +27 (0) 790250944 > carvalhe...@sanbi.org > lgcarvalhe...@gmail.com > ___
Re: [R] Reading sas7bdat files directly
If you don't have SAS and still need to read or write sas7bdat files: there is the "World Programming System" (WPS) (commercial software). http://www.teamwpc.co.uk/home/ -- View this message in context: http://n4.nabble.com/Reading-sas7bdat-files-directly-tp1469515p1557807.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] delete repeated values - not unique...
rle() is cool. - PhD Candidate in Statistics Dept. of Mathematics & Statistics University of New Hampshire Durham, NH 03824 USA -- View this message in context: http://n4.nabble.com/delete-repeated-values-not-unique-tp1557625p1557728.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Legend Text Font Size
Hi. I have a plot containing a large number of lines. I have placed a legend in the plot, but with so many lines, the legend takes up a lot of space. I have tried to reduce the spacing between the lines using the legend parameter x.intersp=0.7, but this does not compress the legend enough. Is there some way to make the text font size smaller in "legend"? Thanks, RH. __ 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] Double Integral Minimization Problem
Hi, I am using v1.0-4 of adapt and v2.10.1 of R. Thank you, M. -- View this message in context: http://n4.nabble.com/Double-Integral-Minimization-Problem-tp1475150p155.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] SVM e1071
Dear R-users, Does anyone know how to get margins' information using SVM under package e1071? I have a two class classification problem and I'd like to have, for each input example, the distance of this example to the margin just like it's possible to obtain using C-based SVM-light, for instance. Thanks in advance, -- Anderson [[elided Yahoo spam]] __ 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] RODBC missing values in integer columns
some more info
> t(t(odbcGetInfo(connection)))
[,1]
DBMS_Name"Adaptive Server Anywhere"
DBMS_Ver "12.70."
Driver_ODBC_Ver "03.51"
Data_Source_Name "dbname"
Driver_Name "Adaptive Server Anywhere"
Driver_Ver "09.00.0001"
ODBC_Ver "03.52."
Server_Name "dbname"
On Tue, Feb 16, 2010 at 11:39 AM, Rob Forler wrote:
> Hello,
>
> We are having some strange issues with RODBC related to integer columns.
> Whenever we do a sql query the data in a integer column is 150 actual data
> points then 150 0's then 150 actual data points then 150 0's. However, our
> database actually has numbers where the 0's are filled in. Furthermore,
> other datatypes do not have this problem: double and varchar are correct and
> do not alternate to null. Also, if we increase the rows_at_time to 1024
> there are larger gaps between the 0's and actual data. The server is a
> sybase IQ database. We have tested it on a different database sybase ASE and
> we still get this issue.
>
> For example :
>
> We have the following query
>
> sqlString = "Select ActionID, Velocity from ActionDataTable"
>
> #where ActionID is of integer type and Velocity is of double type.
> connection = odbcConnect("IQDatabase"); #this database is a sybase IQ
> database
> sqlData = sqlQuery(connection, sqlString);
>
>
> sqlData$ActionID might be 1,2,3,4,5,6,150, 0,0,0,0,0,0,0,,0,0,0,
> 301,302,303,304,.448,449,500,0,0,0...,0,0
>
> and Velocity will have data values along the whole column without these big
> areas of 0's.
>
> Thanks for the help,
> Robert Forler
>
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[R] replicating aov results with lmer
I am trying to replicate the results of an aov command with lmer, to understand
the syntax, but I can't quite figure it out. I have a dataset from Montgomery
p. 520 with a nested and factorial layout. There are 3 fixtures, 2 layouts (the
treatments) in a factorial design, but the operators who perform the runs are
nest in layouts (4 operators per layout=8 different operators). Thus, each
operator tries each fixture twice, but only 1 layout. Everything is balanced so
I know what the results should be. I give a dump of the data at the bottom of
the email.
If I use the aov command, I get exactly what I would expect:
> ass.aov<-aov(Time~Fixture*Layout+Error(Operator/Layout),data=ass)
> summary(ass.aov)
Error: Operator
Df Sum Sq Mean Sq F value Pr(>F)
Layout 1 4.083 4.0833 0.3407 0.5807
Residuals 6 71.917 11.9861
Error: Within
Df Sum Sq Mean Sq F valuePr(>F)
Fixture 2 82.792 41.396 12.2319 8.842e-05 ***
Fixture:Layout 2 19.042 9.521 2.8133 0.07325 .
Residuals 36 121.833 3.384
If I use the lmer command, the layout SS is NOT what I would expect from the
aov (and my calculations). However, the estimates of variance components (not
shown here) are exactly the same. Note, I have coded Operator as 1-8 (not 1-4),
so if understand lmer correctly I can just add a (1|Operator) term into the
model and the nesting is taken care of.
If I try to add a Operator:Fixture interaction (as done in Montgomery) I also
do not get agreement with my manual calculations (which are the same as in the
Montgomery book). Can I recreate the standard anova table broken into the
correct strata using lmer?
Thanks,
Elizabeth
> ass.lmer2<-lmer(Time~Layout*Fixture+(1|Operator),data=ass)
> anova(ass.lmer2)
Analysis of Variance Table
Df Sum Sq Mean Sq F value
Layout 1 1.153 1.153 0.3406
Fixture 2 82.792 41.396 12.2319
Layout:Fixture 2 19.042 9.521 2.8133
> summary(ass.lmer2)
Linear mixed model fit by REML
Formula: Time ~ Layout + (1 | Operator) + Fixture + Layout:Fixture
Data: ass
AIC BIC logLik deviance REMLdev
215 230 -99.5198.4 199
Random effects:
Groups NameVariance Std.Dev.
Operator (Intercept) 1.4336 1.1973
Residual 3.3843 1.8396
Number of obs: 48, groups: Operator, 8
Fixed effects:
Estimate Std. Error t value
(Intercept) 26.0833 0.4997 52.20
Layout1 -0.2917 0.4997 -0.58
Fixture1 -0.8333 0.3755 -2.22
Fixture2 1.8542 0.37554.94
Layout1:Fixture1 -0.2083 0.3755 -0.55
Layout1:Fixture2 0.8542 0.37552.27
Correlation of Fixed Effects:
(Intr) Layot1 Fixtr1 Fixtr2 Ly1:F1
Layout1 0.000
Fixture1 0.000 0.000
Fixture2 0.000 0.000 -0.500
Layt1:Fxtr1 0.000 0.000 0.000 0.000
Layt1:Fxtr2 0.000 0.000 0.000 0.000 -0.500
ass <-
structure(list(Time = c(22, 24, 30, 27, 25, 21, 23, 24, 29, 28,
24, 22, 28, 29, 30, 32, 27, 25, 25, 23, 27, 25, 26, 23, 26, 28,
29, 28, 27, 25, 27, 25, 30, 27, 26, 24, 28, 25, 24, 23, 24, 27,
24, 23, 28, 30, 28, 27), Operator = structure(c(1L, 1L, 1L, 1L,
1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L,
4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 6L, 6L, 6L, 6L, 6L, 6L,
7L, 7L, 7L, 7L, 7L, 7L, 8L, 8L, 8L, 8L, 8L, 8L), .Label = c("1",
"2", "3", "4", "5", "6", "7", "8"), class = "factor"), Layout = structure(c(1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c("1",
"2"), class = "factor"), Fixture = structure(c(1L, 1L, 2L, 2L,
3L, 3L, 1L, 1L, 2L, 2L, 3L, 3L, 1L, 1L, 2L, 2L, 3L, 3L, 1L, 1L,
2L, 2L, 3L, 3L, 1L, 1L, 2L, 2L, 3L, 3L, 1L, 1L, 2L, 2L, 3L, 3L,
1L, 1L, 2L, 2L, 3L, 3L, 1L, 1L, 2L, 2L, 3L, 3L), .Label = c("1",
"2", "3"), class = "factor"), opF = structure(c(1L, 1L, 9L, 9L,
17L, 17L, 2L, 2L, 10L, 10L, 18L, 18L, 3L, 3L, 11L, 11L, 19L,
19L, 4L, 4L, 12L, 12L, 20L, 20L, 5L, 5L, 13L, 13L, 21L, 21L,
6L, 6L, 14L, 14L, 22L, 22L, 7L, 7L, 15L, 15L, 23L, 23L, 8L, 8L,
16L, 16L, 24L, 24L), .Label = c("1:1", "1:2", "1:3", "1:4", "1:5",
"1:6", "1:7", "1:8", "2:1", "2:2", "2:3", "2:4", "2:5", "2:6",
"2:7", "2:8", "3:1", "3:2", "3:3", "3:4", "3:5", "3:6", "3:7",
"3:8"), class = "factor"), LF = structure(c(1L, 1L, 3L, 3L, 5L,
5L, 1L, 1L, 3L, 3L, 5L, 5L, 1L, 1L, 3L, 3L, 5L, 5L, 1L, 1L, 3L,
3L, 5L, 5L, 2L, 2L, 4L, 4L, 6L, 6L, 2L, 2L, 4L, 4L, 6L, 6L, 2L,
2L, 4L, 4L, 6L, 6L, 2L, 2L, 4L, 4L, 6L, 6L), .Label = c("1:1",
"1:2", "2:1", "2:2", "3:1", "3:2"), class = "factor")), .Names = c("Time",
"Operator", "Layout", "Fixture", "opF", "LF"), row.names = c(NA,
-48L), class = "data.frame")
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Re: [R] suppress printing within a function
On Feb 16, 2010, at 1:31 PM, Jarrett Byrnes wrote: I'm working with a few functions (e.g. do.base.descriptions in the netstat package) that, in addition to returning an object with variables I want to extract, also print output. There is no way to turn this default printing behavior off in many of the functions. Is there a blanket way to suppress such printing, say, within a loop or a ddply statement? ?capture.output ?sink Thanks! -Jarrett David Winsemius, MD Heritage Laboratories West Hartford, CT __ 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] Random Forest
From: Dror
>
> Hi,
> i'm using randomForest package and i have 2 questions:
> 1. Can i drop one tree from an RF object?
Yes.
> 2. i have a 300 trees forest, but when i use the predict
> function on new
> data (with predict.all=TRUE) i get only 270 votes. did i do
> something wrong?
Try to follow the posting guide (link in the footer of the message) and
you may just get the help you're looking for. Please help us to help
you!
Andy
> Thanks
>
> --
> View this message in context:
> http://n4.nabble.com/Random-Forest-tp1557464p1557464.html
> Sent from the R help mailing list archive at Nabble.com.
>
> [[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.
>
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[R] suppress printing within a function
I'm working with a few functions (e.g. do.base.descriptions in the netstat package) that, in addition to returning an object with variables I want to extract, also print output. There is no way to turn this default printing behavior off in many of the functions. Is there a blanket way to suppress such printing, say, within a loop or a ddply statement? Thanks! -Jarrett Jarrett Byrnes Postdoctoral Associate, Santa Barbara Coastal LTER Marine Science Institute University of California Santa Barbara Santa Barbara, CA 93106-6150 http://www.lifesci.ucsb.edu/eemb/labs/cardinale/people/byrnes/index.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] Triangular filled contour plot
Johannes,
Some months ago it was posted on R-help a list of packages that handle with
ternaryplots, altough none of them can handle surfaceplots, just
scatterplots, on a triangular area. The packages were
plot.acomp in compositions
tri in cwhmisc.cwhtool
triax in plotrix
ternary in StatDA
ternaryplot in vcd
ternaryplot in Zelig
See http://n4.nabble.com/triangular-plot-td893434.html#a893435
Due my needs I implemented something a little bit useful (at least to me) to
make a prediction surface triangle plot using Lattice package. My
reproducible code is the following:
paint <- data.frame(mono=c(17.5, 10, 15, 25, 5, 5, 11.25, 5, 18.13, 8.13,
25, 15, 10, 5),
cross=c(32.5, 40, 25, 25, 25, 32.5, 32.5, 40, 28.75,
28.75, 25, 25, 40, 25),
resin=c(50, 50, 60, 50, 70, 62.5, 56.25, 55, 53.13,
63.13, 50, 60, 50, 70),
hardness=c(29, 26, 17, 28, 35, 31, 21, 20, 29, 25, 19,
14, 30, 23))
pseudo <- with(paint, data.frame(mono=(mono-5)/(25-5),
resin=(resin-50)/(70-50)))
pseudo$cross <- with(pseudo, 1-mono-resin)
pseudo$hardness <- paint$hardness
m1 <- lm(hardness~(mono+cross+resin)^2-mono, data=pseudo)
trian <- expand.grid(base=seq(0,1,l=100*2), high=seq(0,sin(pi/3),l=87*2))
trian <- subset(trian, (base*sin(pi/3)*2)>high)
trian <- subset(trian, ((1-base)*sin(pi/3)*2)>high)
new2 <- data.frame(cross=trian$high*2/sqrt(3))
new2$resin <- trian$base-trian$high/sqrt(3)
new2$mono <- 1-new2$resin-new2$cross
trian$yhat <- predict(m1, newdata=new2)
grade.trellis <- function(from=0.2, to=0.8, step=0.2, col=1, lty=2,
lwd=0.5){
x1 <- seq(from, to, step)
x2 <- x1/2
y2 <- x1*sqrt(3)/2
x3 <- (1-x1)*0.5+x1
y3 <- sqrt(3)/2-x1*sqrt(3)/2
panel.segments(x1, 0, x2, y2, col=col, lty=lty, lwd=lwd)
panel.text(x1, 0, label=x1, pos=1)
panel.segments(x1, 0, x3, y3, col=col, lty=lty, lwd=lwd)
panel.text(x2, y2, label=rev(x1), pos=2)
panel.segments(x2, y2, 1-x2, y2, col=col, lty=lty, lwd=lwd)
panel.text(x3, y3, label=rev(x1), pos=4)
}
levelplot(yhat~base*high, trian, aspect="iso", xlim=c(-0.1,1.1),
ylim=c(-0.1,0.96),
xlab=NULL, ylab=NULL, contour=TRUE,
par.settings=list(axis.line=list(col=NA), axis.text=list(col=NA)),
panel=function(..., at, contour=TRUE, labels=NULL){
panel.levelplot(..., at=at, contour=contour, #labels=labels,
lty=3, lwd=0.5, col=1)
})
trellis.focus("panel", 1, 1, highlight=FALSE)
panel.segments(c(0,0,0.5), c(0,0,sqrt(3)/2), c(1,1/2,1), c(0,sqrt(3)/2,0))
grade.trellis()
panel.text(0, 0, label="mono", pos=2)
panel.text(1/2, sqrt(3)/2, label="cross", pos=3)
panel.text(1, 0, label="resin", pos=4)
trellis.unfocus()
http://n4.nabble.com/file/n1557735/one.png
I think (and hope :-) ) Deepayan Sarkar will implement this on Lattice soon
because R doesn't have this kind of graphic yet. My code isn't perfect so I
expect suggestions.
Walmes Zeviani, Brasil.
-
..ooo0
...
..()... 0ooo... Walmes Zeviani
...\..(.(.)... Master in Statistics and Agricultural
Experimentation
\_). )../ walmeszevi...@hotmail.com, Lavras - MG, Brasil
(_/
--
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Re: [R] delete repeated values - not unique...
Ah, the request was 'hidden' in the subject of the message, apologies! Erik Iverson wrote: Well, can you algorithmically describe what you are trying to do? Your example is not sufficient to determine it. For instance, are you trying to: 1) remove repeated elements of a vector and concatenate the first element at the end? 2) remove repeated elements of a vector and concatenate the minimum element at the end? 3) always return the vector c(4, 5, 6, 4) ? 4) something else? jorgusch wrote: Hello, I must be blind not to see it, but I have the following vector: 4 4 5 6 6 4 What I would like to have as a result is: 4 5 6 4 All repeated values are gone. I cannot use unique for this, as the second 4 would disappear. Is there another fast function for this problem? Thanks in advance! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] delete repeated values - not unique...
On Feb 16, 2010, at 12:01 PM, jorgusch wrote: Hello, I must be blind not to see it, but I have the following vector: 4 4 5 6 6 4 What I would like to have as a result is: 4 5 6 4 ?diff > vec <- c(4,4,5,6,6,4) > vec[ c(1, diff(vec)) != 0 ] [1] 4 5 6 4 All repeated values are gone. I cannot use unique for this, as the second 4 would disappear. Is there another fast function for this problem? Thanks in advance! -- View this message in context: http://n4.nabble.com/delete-repeated-values-not-unique-tp1557625p1557625.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. David Winsemius, MD Heritage Laboratories West Hartford, CT __ 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] delete repeated values - not unique...
> -Original Message- > From: r-help-boun...@r-project.org > [mailto:r-help-boun...@r-project.org] On Behalf Of jorgusch > Sent: Tuesday, February 16, 2010 9:01 AM > To: r-help@r-project.org > Subject: [R] delete repeated values - not unique... > > > Hello, > > I must be blind not to see it, but I have the following vector: > > 4 > 4 > 5 > 6 > 6 > 4 > > What I would like to have as a result is: > > 4 > 5 > 6 > 4 > > All repeated values are gone. I cannot use unique for this, > as the second 4 > would disappear. Is there another fast function for this problem? Is this what you want? It keeps only those values which are the not the same as the previous value in the vector. > isFirstInRun <- function(x) c(TRUE, x[-1]!=x[-length(x)]) > data <- c(4, 4, 5, 6, 6, 4) > data[isFirstInRun(data)] [1] 4 5 6 4 Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com > > Thanks in advance! > > -- > View this message in context: > http://n4.nabble.com/delete-repeated-values-not-unique-tp15576 25p1557625.html > Sent from the R help mailing list archive at Nabble.com. > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] delete repeated values - not unique...
Well, can you algorithmically describe what you are trying to do? Your example is not sufficient to determine it. For instance, are you trying to: 1) remove repeated elements of a vector and concatenate the first element at the end? 2) remove repeated elements of a vector and concatenate the minimum element at the end? 3) always return the vector c(4, 5, 6, 4) ? 4) something else? jorgusch wrote: Hello, I must be blind not to see it, but I have the following vector: 4 4 5 6 6 4 What I would like to have as a result is: 4 5 6 4 All repeated values are gone. I cannot use unique for this, as the second 4 would disappear. Is there another fast function for this problem? Thanks in advance! __ 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] delete repeated values - not unique...
On Feb 16, 2010, at 11:01 AM, jorgusch wrote: > > Hello, > > I must be blind not to see it, but I have the following vector: > > 4 > 4 > 5 > 6 > 6 > 4 > > What I would like to have as a result is: > > 4 > 5 > 6 > 4 > > All repeated values are gone. I cannot use unique for this, as the second 4 > would disappear. Is there another fast function for this problem? > > Thanks in advance! See ?rle x <- c(4, 4, 5, 6, 6, 4) > rle(x)$values [1] 4 5 6 4 HTH, Marc Schwartz __ 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] lint for R? and debugging
On 16-Feb-10 09:03, Karl Ove Hufthammer wrote: On Tue, 16 Feb 2010 08:00:09 -0500 Esmail wrote: And along the same lines, any type of interactive debugging utility for R? See this article in R News: 'Debugging Without (Too Many) Tears' http://cran.r-project.org/doc/Rnews/Rnews_2003-3.pdf#page=29 Thanks for the pointer, that looks very interesting. Any lint-like utilities out there? I miss a lot of the development tools I have available for Python or Java with R, esp once the code starts to grow beyond a few hundred lines. Esmail __ 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] delete repeated values - not unique...
Hello, I must be blind not to see it, but I have the following vector: 4 4 5 6 6 4 What I would like to have as a result is: 4 5 6 4 All repeated values are gone. I cannot use unique for this, as the second 4 would disappear. Is there another fast function for this problem? Thanks in advance! -- View this message in context: http://n4.nabble.com/delete-repeated-values-not-unique-tp1557625p1557625.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] combining dataframes with different row lenght
If you can specify the questions in more details, that would be more helpful. -- View this message in context: http://n4.nabble.com/combining-dataframes-with-different-row-lenght-tp1557569p1557610.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] margin text warning message NAs coercion
I have a question for you. What's your purpose to put "additional text" in the margin? In your code, the first expression(A[1]~B[2]) corresponds to text. If you wanna "additional text" together with expression(A[1]~B[2]), you should use paste. If you can clarify what kind of margin you want, that would be better to clear your confusions. By the way, you forgot a right ")" after ylab= statement. -- View this message in context: http://n4.nabble.com/margin-text-warning-message-NAs-coercion-tp1557567p1557591.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] argh .. if/else .. why?
On Feb 16, 2010, at 12:15 PM, William Dunlap wrote: -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Peter Dalgaard Sent: Tuesday, February 16, 2010 1:33 AM To: Gabor Grothendieck Cc: r-help@r-project.org Subject: Re: [R] argh .. if/else .. why? Gabor Grothendieck wrote: On Mon, Feb 15, 2010 at 11:24 AM, David Winsemius wrote: On Feb 15, 2010, at 11:01 AM, hadley wickham wrote: I, personally, utilize the ifelse(test,statement,statement) function when possible over the methodology outlined. if + else and ifelse perform quite different tasks, and in general can not (and should not) be exchanged. In particular, note that for ifelse, "the class attribute of the result is taken from 'test' and may be inappropriate for the values selected from 'yes' and 'no'". I have always been puzzled by that bit of advice/knowledge on the help page. "test" will of necessity be of class "logical", and yet I regularly succeed in producing numeric and character vectors with ifelse. In fact ifelse would be rather limited in utility if it only returned logical vectors. I think it had intended to refer to oldClass rather than class. oldClass(TRUE) NULL oldClass(ifelse(TRUE, 1, 2)) NULL Well, it does date back to S v.3, but the docs do say class _attribute_ and "logical" & friends aren't. It happens with all attributes, and I suspect that the original intention was for things like this to work ifelse(matrix(c(T,T,F,F),2),1,2) [,1] [,2] [1,]12 [2,]12 I can't think of a situation where it is actually useful to copy the class attribute from the condition to the result. The container-related attributes of ifelse's first argument can be profitably copied to the output. E.g., for classes "matrix" and "ts", which can contain a variety of primitive data types, we get: m<-matrix(1:12,3,4) ifelse(m>5, TRUE, FALSE) # return a matrix the shape of m [,1] [,2] [,3] [,4] [1,] FALSE FALSE TRUE TRUE [2,] FALSE FALSE TRUE TRUE [3,] FALSE TRUE TRUE TRUE t <- ts(1:5, start=2010, freq=12) ifelse(t>3, TRUE, FALSE) # return a ts like t Jan Feb Mar Apr May 2010 FALSE FALSE FALSE TRUE TRUE Thanks, Bill that is very helpful. It's possible that the same notion was expressed earlier but I didn't "get it" until your version. The message I take away is that as long as the functional evaluation (of for example ">") produces a "vectorish" arrangement of logicals having some additional structure, that structure is being preserved by the indexing within ifelse. Looking at the code of ifelse is helpful in this regard, and it also answers my question about the evaluation/ performance issues. Whenever the antecedents are a mixture of T and F, then _all_ of the positive and negative consequents will be evaluated before they are then selectively transferred to the result. -- David Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com Presumably, the idea is that of the three possibilities, only the condition attributes are unambiguous (think if(cond, A, B) vs. if(!cond, B, A)), so if any set of attributes should be copied, those are the ones. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K David Winsemius, MD Heritage Laboratories West Hartford, CT __ 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] Triangular filled contour plot
hello,
maybe this code can be useful for you.
cleber
---
trimage <- function(f){
x = y = seq( 1, 0, l=181 )
t1 = length(x)
im = aux = numeric(0)
for( i in seq( 1, t1, by = 2 ) ){
#idx = seq( t1**2, i*t1, by = -t1 ) - ((t1 - i):0)
idx = seq( i*t1, t1**2, by = t1 ) - (i-1)
im = c(im, aux, idx, aux )
aux = c(aux, NA)
}
z = outer(X=x, Y=y, FUN=f)
return( matrix(z[im],nr=t1) )
}
### for chemical mixtures
### restriction: sum( x[i]==1 ) and 0 < x[i] < 1
### naive example
f <- function(x1,x2) { x3=1-x2-x1; -100*x1 + 0*x2 + 100*x3 }
windows(w=4.5, h=4.5, restoreConsole = TRUE )
par(mar=c(0,0,0,0), pty='s', xaxt='n', yaxt='n', bty='n' )
trimat <- trimage( f )
image( trimat )
contour( trimat, add=T)
Em 16/2/2010 11:25, kajo escreveu:
Hi all,
I am working on a filled contour plot which shows a triangular matrix data
set (as shown below). Is there a possibilty to draw a triangular filled
contour in a equilateral triangle (like a ternary plot)?
Thanks in advance
Johannes
http://n4.nabble.com/file/n1557386/Bild3.png
--
O bom senso é a coisa do mundo mais bem distribuída:
Todos pensamos tê-lo em tal medida que até os mais difíceis
de contentar nas outras coisas não costumam desejar mais bom senso do que
aquele que têm.
[René Descartes]
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[R] RODBC missing values in integer columns
Hello,
We are having some strange issues with RODBC related to integer columns.
Whenever we do a sql query the data in a integer column is 150 actual data
points then 150 0's then 150 actual data points then 150 0's. However, our
database actually has numbers where the 0's are filled in. Furthermore,
other datatypes do not have this problem: double and varchar are correct and
do not alternate to null. Also, if we increase the rows_at_time to 1024
there are larger gaps between the 0's and actual data. The server is a
sybase IQ database. We have tested it on a different database sybase ASE and
we still get this issue.
For example :
We have the following query
sqlString = "Select ActionID, Velocity from ActionDataTable"
#where ActionID is of integer type and Velocity is of double type.
connection = odbcConnect("IQDatabase"); #this database is a sybase IQ
database
sqlData = sqlQuery(connection, sqlString);
sqlData$ActionID might be 1,2,3,4,5,6,150, 0,0,0,0,0,0,0,,0,0,0,
301,302,303,304,.448,449,500,0,0,0...,0,0
and Velocity will have data values along the whole column without these big
areas of 0's.
Thanks for the help,
Robert Forler
[[alternative HTML version deleted]]
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Re: [R] margin text warning message NAs coercion
On Feb 16, 2010, at 12:18 PM, e-letter wrote: On 16/02/2010, Peter Ehlers wrote: On 2010-02-16 9:21, e-letter wrote: Readers, I tried to the following commands: plot(y~x,ylab=expression(A[1]~B[2],xlab=expression(C~D)) mtext(expression(A[1]~B[2]),"additional text",side=3,line=1) Your plot() call is not reproducible. Anyway, try mtext(expression(A[1]~B[2]~~"additional text"),side=3,line=1) Thank you. I had seen the command (~~) in the help guide for the package plotmath(grdevices), but there is no statement that this command can be used to join the expression to literal text. It's not a "command", it's one of the available separators (or connectors depending on how you think about them) for expressions. If you wanted no separation between adjacent terms, you would use a "*" (asterisk). You cannot use "," because it creates a separate element in the expression vector: plot(1,1) mtext(expression(A[1]~B[2],"additional text", "more text"),side=3,line=1:3) (Which results in the reverse order of what this newbie expected.) -- David Winsemius, MD Heritage Laboratories West Hartford, CT __ 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] margin text warning message NAs coercion
On 2010-02-16 10:18, e-letter wrote: On 16/02/2010, Peter Ehlers wrote: On 2010-02-16 9:21, e-letter wrote: Readers, I tried to the following commands: plot(y~x,ylab=expression(A[1]~B[2],xlab=expression(C~D)) mtext(expression(A[1]~B[2]),"additional text",side=3,line=1) Your plot() call is not reproducible. Anyway, try mtext(expression(A[1]~B[2]~~"additional text"),side=3,line=1) Thank you. I had seen the command (~~) in the help guide for the package plotmath(grdevices), but there is no statement that this command can be used to join the expression to literal text. It's a hard space, borrowed from TeX. ?plotmath has this x ~~ y put extra space between x and y Try also x ~ y. -Peter Ehlers __ 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] argh .. if/else .. why?
> -Original Message- > From: r-help-boun...@r-project.org > [mailto:r-help-boun...@r-project.org] On Behalf Of Peter Dalgaard > Sent: Tuesday, February 16, 2010 1:33 AM > To: Gabor Grothendieck > Cc: r-help@r-project.org > Subject: Re: [R] argh .. if/else .. why? > > Gabor Grothendieck wrote: > > On Mon, Feb 15, 2010 at 11:24 AM, David Winsemius > > wrote: > >> On Feb 15, 2010, at 11:01 AM, hadley wickham wrote: > >> > I, personally, utilize the > ifelse(test,statement,statement) function when > possible over the methodology outlined. > >>> if + else and ifelse perform quite different tasks, and > in general can > >>> not (and should not) be exchanged. In particular, note that for > >>> ifelse, "the class attribute of the result is taken from > 'test' and > >>> may be inappropriate for the values selected from 'yes' > and 'no'". > >> I have always been puzzled by that bit of advice/knowledge > on the help page. > >> "test" will of necessity be of class "logical", and yet I > regularly succeed > >> in producing numeric and character vectors with ifelse. In > fact ifelse would > >> be rather limited in utility if it only returned logical vectors. > >> > > > > I think it had intended to refer to oldClass rather than class. > > > >> oldClass(TRUE) > > NULL > >> oldClass(ifelse(TRUE, 1, 2)) > > NULL > > Well, it does date back to S v.3, but the docs do say class > _attribute_ > and "logical" & friends aren't. It happens with all attributes, and I > suspect that the original intention was for things like this to work > > > ifelse(matrix(c(T,T,F,F),2),1,2) > [,1] [,2] > [1,]12 > [2,]12 > > I can't think of a situation where it is actually useful to copy the > class attribute from the condition to the result. The container-related attributes of ifelse's first argument can be profitably copied to the output. E.g., for classes "matrix" and "ts", which can contain a variety of primitive data types, we get: > m<-matrix(1:12,3,4) > ifelse(m>5, TRUE, FALSE) # return a matrix the shape of m [,1] [,2] [,3] [,4] [1,] FALSE FALSE TRUE TRUE [2,] FALSE FALSE TRUE TRUE [3,] FALSE TRUE TRUE TRUE > t <- ts(1:5, start=2010, freq=12) > ifelse(t>3, TRUE, FALSE) # return a ts like t Jan Feb Mar Apr May 2010 FALSE FALSE FALSE TRUE TRUE Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com > Presumably, the idea > is that of the three possibilities, only the condition attributes are > unambiguous (think if(cond, A, B) vs. if(!cond, B, A)), so if > any set of > attributes should be copied, those are the ones. > > -- >O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B > c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K > (*) \(*) -- University of Copenhagen Denmark Ph: > (+45) 35327918 > ~~ - (p.dalga...@biostat.ku.dk) FAX: > (+45) 35327907 > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] margin text warning message NAs coercion
On 16/02/2010, Peter Ehlers wrote: > On 2010-02-16 9:21, e-letter wrote: >> Readers, >> >> I tried to the following commands: >> >> plot(y~x,ylab=expression(A[1]~B[2],xlab=expression(C~D)) >> mtext(expression(A[1]~B[2]),"additional text",side=3,line=1) > > Your plot() call is not reproducible. > > Anyway, try > > mtext(expression(A[1]~B[2]~~"additional text"),side=3,line=1) > Thank you. I had seen the command (~~) in the help guide for the package plotmath(grdevices), but there is no statement that this command can be used to join the expression to literal text. __ 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] popbio and stochastic lambda calculation
Hello R users,
I am trying to calculate the stochastic lambda for a published matrix
population model using the popbio package.
Unfortunately, I have been unable to match the published results. Can
anyone tell me whether this is due to slightly different methods being
used, or have I gone wrong somewhere in my code?
Could the answer be as simple as comparing deterministic lambdas to
stochastic lambdas? My stoch. lambda is lower (as expected) however the
CI is substantially larger than published. The authors of the published
example used a different method to calculate the CIs around lambda, but
I would have expected the results of the vitalsim to be closer. (The
authors used the 'delta' method from Caswell (2001)).
My main questions are:
1. Have I correctly calculated stochastic lambda and its 95% CIs?
2. Why am I unable to use any distributions other than beta? What can I
do about that?
Thank you,
Shawn Morrison
#
#My example:
rm(list = ls())
objects()
library(popbio)
# Vital rate means and variances, and 'types' for the vrtypes argument
in vitalsim
# 'names' is not used, but indicates what the vital
# rates represent: Sad = adult survival, Scub = cub survival
# Syrl = yearling survival, Ssub - subadult survival
# mx = number of female offspring per year
names = c("Sad", "Scub", "Syrl", "Ssub", "mx") # vital rate names, not used
mean = c(0.835, 0.640, 0.670, 0.765, 0.467) # vital rate means
var = c(0.213, 0.252, 0.241, 0.133, 0.0405) #variances of means
var.se = c(0.106, 0.107, 0.142, 0.149, 0.09) #standard errors of means
types = c(1,1,1,1,1) #for vrtypes argument
ex.vrs = data.frame(cbind(mean, var, var.se, types))
attach(ex.vrs)
## Define the matrix
ex.mxdef= function (vrs)
{
matrix(c(0,0, 0, 0,
vrs[5]*vrs[1],
vrs[2], 0, 0,
0, 0,
0, vrs[3], 0,
0, 0,
0,0, vrs[4],
0,0,
0,0, 0,
vrs[4], vrs[1]),
nrow = 5, byrow = TRUE)
}
ex.mxdef(ex.vrs$mean)
# Matrix in published article is:
# 0, 0, 0, 0, 0.390,
# 0.640, 0, 0, 0,0,
# 0, 0.67, 0, 0,0, # 0,0, 0.765, 0,0,
# 0,0, 0, 0.765, 0.835
# "My' result matches this.
### TRIAL 1
### Using variances estimated from published paper returns an error
(ex.var$var), perhaps because variances are too large?
## run no.corr model
no.corr<-vitalsim(ex.vrs$mean, ex.vrs$var, diag(5),
diag(5), ex.mxdef, vrtypes=ex.vrs$types,
n0=c(200,130,90,80,490), yrspan=20 , runs=200)
### TRIAL 2
### Using standard error instead of variances (ex.var$var.se)
### This also produces an error when 'types' is set to anything but 1
(betas).
## run no.corr model
no.corr<-vitalsim(ex.vrs$mean, ex.vrs$var.se, diag(5),
diag(5), ex.mxdef, vrtypes=ex.vrs$types,
n0=c(200,130,90,80,490), yrspan=20 , runs=200)
## deterministic lambda
no.corr[1:2] # The published deterministic lambda is 0.953 so this
appear to be working correctly
?popbio
# stochastic lambda
no.corr[2]
# The paper reports a 95% CI of 0.79 - 1.10
# "My" reproduced result for the CIs is much larger, especially on the
upper end. Why would this be?
# The authors report using the 'delta' method (Caswell, 2001) to
calculate the CI in which the
# sensitivities were used to weight the variances.
## log stochastic lambda
log(no.corr$stochLambda)
sd(no.corr$logLambdas)
se=function(x) sqrt(var(x)/length(x))
se(no.corr$logLambdas) # The published article reports deterministic
lambda ± SE to be 0.953 ± 0.079
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] margin text warning message NAs coercion
On 2010-02-16 9:21, e-letter wrote: Readers, I tried to the following commands: plot(y~x,ylab=expression(A[1]~B[2],xlab=expression(C~D)) mtext(expression(A[1]~B[2]),"additional text",side=3,line=1) Your plot() call is not reproducible. Anyway, try mtext(expression(A[1]~B[2]~~"additional text"),side=3,line=1) -Peter Ehlers I receive the text that I want, but the command terminal shows the following response: Warning message: NAs introduced by coercion in: mtext(expression(A[1]~B[2]),"additional text", side = 3, What is my mistake please? Yours, r251 rhelpatconference.jabber.org __ 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. -- Peter Ehlers University of Calgary 403.202.3921 __ 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] OT: computing percentage changes with negative and zero values?
Dear all I need to compute percentage changes of my data, but unfortunately they contain both negative and zero values, and I am quite confused on how to proceed. Searching the internet I found that many people ran into similar issues, with no obvious solution available. The last couple of weeks I've been playing with all the data transformations that I could think of. Below I will expose on a dummy example the issues encountered: > x$var [1] 0.43 -0.79 0.69 0.76 0.00 -1.51 -0.71 0.80 1.17 1.58 1.48 -1.83 -0.88 1.44 -0.72 -0.22 1.89 -1.27 -0.76 [20] 1.33 - raw data: percentage variations of the original data---containing negative and zero values---get messed up when passing from a negative to a positive value, and around the value 0. > x[, "raw"] <- c(NA, diff(x$var) / x[1:19,"var"]) - raw data with abs denominator: compared to the above improves the handling of the signs, but still fails around zero, and in some cases gives unexpected results (see [1]). > x[, "raw abs"] <- c(NA, diff(x$var) / abs(x[1:19,"var"])) - raw data + constant: add a constant to the data to transform them to strictly positive, then compute the deltas. This solves the negative and zero value problems, but I am not sure if this introduces some bias along the way. > x[, "raw +cst"] <- c(NA, diff((2 + x$var)) / (2 + x[1:19,"var"])) - log, car::box.cox.powers: both transformations involve adding a constant to the original data. > x[, "log"] <- c(NA, diff(log(2 + x$var)) / log(2 + x[1:19,"var"])) > require(car) > x1 <- box.cox.powers(2 + x$var); x1$lambda > x[, "box cox"] <- c(NA, diff(box.cox(2 + x$var, x1$lambda)) / box.cox(2 + > x[1:19,"var"], x1$lambda)) - sqrt: very similar to the above, but the results are a bit different (and apparently better). > x[, "sqrt"] <- c(NA, diff(sqrt(2 + x$var)) / sqrt(2 + x[1:19,"var"])) - exp: the exponential transformation introduces too much, and unevenly distributed variability (my actual data contain values bigger than "5"), and the variations can quickly get to astronomical levels. > x[, "exp"] <- c(NA, diff(exp(x$var)) / exp(x[1:19,"var"])) - atan transformation: this is an in-house bred solution, which insures that values from -Inf to +Inf are stacked between 0 and pi. Again, not sure what bias this might introduce. > mytan <- function(x) .5*pi + atan(x) > x[, "mytan"] <- c(NA, diff(mytan(x$var)) / mytan(x[1:19,"var"])) The resulting data frame: > round(x, 3) varraw raw abs raw +cstlog sqrt box coxexp mytan 1 0.43 NA NA NA NA NA NA NA NA 2 -0.79 -2.837 -2.837 -0.502 -0.785 -0.294 -0.840 -0.705 -0.544 3 0.69 -1.873 1.8731.223 4.191 0.491 6.289 3.393 1.411 4 0.76 0.101 0.1010.026 0.026 0.013 0.038 0.073 0.021 5 0.00 -1.000 -1.000 -0.275 -0.317 -0.149 -0.407 -0.532 -0.293 6 -1.51 -Inf-Inf -0.755 -2.029 -0.505 -1.591 -0.779 -0.628 7 -0.71 -0.530 0.5301.633 -1.357 0.623 -1.517 1.226 0.630 8 0.80 -2.127 2.1271.171 3.043 0.473 4.631 3.527 1.355 9 1.17 0.462 0.4620.132 0.121 0.064 0.185 0.448 0.084 10 1.58 0.350 0.3500.129 0.105 0.063 0.169 0.507 0.059 11 1.48 -0.063 -0.063 -0.028 -0.022 -0.014 -0.035 -0.095 -0.012 12 -1.83 -2.236 -2.236 -0.951 -2.421 -0.779 -1.450 -0.963 -0.804 13 -0.88 -0.519 0.5195.588 -1.064 1.567 -1.124 1.586 0.698 14 1.44 -2.636 2.6362.071 9.902 0.753 16.643 9.176 1.985 15 -0.72 -1.500 -1.500 -0.628 -0.800 -0.390 -0.870 -0.885 -0.626 16 -0.22 -0.694 0.6940.391 1.336 0.179 1.679 0.649 0.430 17 1.89 -9.591 9.5911.185 1.356 0.478 2.333 7.248 0.960 18 -1.27 -1.672 -1.672 -0.812 -1.232 -0.567 -1.115 -0.958 -0.749 19 -0.76 -0.402 0.4020.699 -1.684 0.303 -1.841 0.665 0.381 20 1.33 -2.750 2.7501.685 4.592 0.639 7.559 7.085 1.711 As you have noticed, I'm quite unsure on how to proceed. My actual data represents financial EPS (earnings per share) forecasts, ranging from -1 to 5. So, it has a "natural zero point" (see David Winsemius' comments in [2]). However, I need to compute percentage variations since I am primarily interested in the evolution of the forecasts (for a given company), while EPS data between two companies are not necessarily comparable. The percentage data would subsequently be used in performing statistical analyses (regression, etc.). Please advise Liviu [1] http://sci.tech-archive.net/Archive/sci.stat.math/2006-04/msg00544.html [2] http://sci.tech-archive.net/Archive/sci.stat.math/2006-04/msg00548.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] reading quattro pro spreadsheet .qpw into R
On Feb 16, 2010, at 10:35 AM, Barry Rowlingson wrote: > On Tue, Feb 16, 2010 at 4:12 PM, stephen sefick wrote: >> I have many quattro pro spreadsheets and no quattro pro. Is there a >> way to access the data using R, or any other solution that anyone can >> think of? > > OpenOffice claims it can read Quattro Pro 6.0 'wb2' files, but maybe > they are different to .qpw files. MS Excel claims some Quattro Pro > readability - I've just read something about wb1 files. Maybe Gnumeric > can read them? What have you tried? > > Perhaps if you put a representative file somewhere we can download and try? > > Barry Gnumeric comes with the ssconvert utility, but that does not appear to support .QPW files: http://projects.gnome.org/gnumeric/doc/file-format-qpro.shtml I don't see any indication that Excel or OO.org's Calc support the .QPW format either. It would appear that you can download a trial of Corel's WordPerfect Office suite, within which Quattro is bundled. You should be able to open the files in that application and then save them to .XLS formats: http://www.corel.com/servlet/Satellite/ca/en/Content/1152796555406 HTH, Marc Schwartz __ 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] Sampling from Bivariate Uniform Distribution
The correlation will not be exactly 0, but will represent a draw from an independent population. There may be something in the copulas package to allow for more independence (but that about exhausts my knowledge of that package). -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 > -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- > project.org] On Behalf Of Haneef_An > Sent: Monday, February 15, 2010 11:53 AM > To: r-help@r-project.org > Subject: Re: [R] Sampling from Bivariate Uniform Distribution > > > When I wrap those values in to a matrix will it be still independent ? > ( non > zero correlation). > > Can I do this for any multivariate distribution which has the > univariate > form? > > Thank you for the response. > > Haneef > -- > View this message in context: http://n4.nabble.com/Sampling-from- > Bivariate-Uniform-Distribution-tp1476485p1556481.html > Sent from the R help mailing list archive at Nabble.com. > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting- > guide.html > and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] lmer - error asMethod(object) : matrix is not symmetric
Dear Douglas, Thank you for your reply. Just some extra info on the dataset: In my case Number of obs is 33, and number of groups of factor(Farm_code) is 12. This is the information on iterations I get: summary(lmer(round(SR_SUN)~Dist_NV + (1|factor(Farm_code)) , family=poisson, verbose =TRUE)) 0: 60.054531: 1.06363 2.14672 -0.000683051 1: 60.054531: 1.06363 2.14672 -0.000683051 Error in asMethod(object) : matrix is not symmetric [1,2] In addition: Warning message: In mer_finalize(ans) : singular convergence (7) When I run a similar model (exp variable Dist_hives) the number of iterations is 11: summary(lmer(round(SR_SUN)~Dist_hives + (1|factor(Farm_code)) , family=poisson, verbose =TRUE)) 0: 61.745238: 0.984732 1.63769 0.000126484 1: 61.648229: 0.984731 1.63769 -2.08637e-05 2: 61.498777: 0.984598 1.63769 4.11867e-05 3: 47.960908: 0.381062 1.63585 6.77029e-05 4: 46.223789: 0.250732 1.66727 8.31854e-05 5: 46.23: 0.250732 1.66727 6.97790e-05 6: 46.216710: 0.250730 1.66727 7.60560e-05 7: 46.168835: 0.230386 1.64883 9.16430e-05 8: 46.165955: 0.228062 1.65658 8.70694e-05 9: 46.165883: 0.228815 1.65737 8.63400e-05 10: 46.165883: 0.228772 1.65734 8.63698e-05 11: 46.165883: 0.228772 1.65734 8.63701e-05 I am very confused with the fact that it runs with Dist_hives and not with Dist_NV. Both variables are distance values, the first having no obvious relation with the response variable and the second (Dist_NV) seems to have a negative effect on SR_SUN. Does this information helps identifying the problem with my data/analysis? Thank you, Luisa On Tue, Feb 16, 2010 at 5:35 PM, Douglas Bates wrote: > This is similar to another question on the list today. > > On Tue, Feb 16, 2010 at 4:39 AM, Luisa Carvalheiro > wrote: >> Dear R users, >> >> I am having problems using package lme4. >> >> I am trying to analyse the effect of a continuous variable (Dist_NV) >> on a count data response variable (SR_SUN) using Poisson error >> distribution. However, when I run the model: >> >> summary(lmer((SR_SUN)~Dist_NV + (1|factor(Farm_code)) , >> family=poisson, REML=FALSE)) >> >> 1 error message and 1 warning message show up: >> >> in asMethod(object) : matrix is not symmetric [1,2] >> In addition: Warning message: >> In mer_finalize(ans) : singular convergence (7) > > So the first thing to do is to include the optional argument verbose = > TRUE in the call to lmer. (Also, REML = FALSE is ignored for > Generalized Linear Mixed Models and can be omitted. although there is > no harm in including it.) > > You need to know where the optimizer is taking the parameter values > before you can decide why. > > P.S. Questions like this will probably be more readily answered on the > R-SIG-Mixed-Models mailing list. > >> A model including Dist_NV together with other variables runs with no >> problems. >> What am I doing wrong? >> >> Thank you, >> >> Luisa >> >> >> -- >> Luisa Carvalheiro, PhD >> Southern African Biodiversity Institute, Kirstenbosch Research Center, >> Claremont >> & University of Pretoria >> Postal address - SAWC Pbag X3015 Hoedspruit 1380, South Africa >> telephone - +27 (0) 790250944 >> carvalhe...@sanbi.org >> lgcarvalhe...@gmail.com >> >> __ >> R-help@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. >> > -- Luisa Carvalheiro, PhD Southern African Biodiversity Institute, Kirstenbosch Research Center, Claremont & University of Pretoria Postal address - SAWC Pbag X3015 Hoedspruit 1380, South Africa telephone - +27 (0) 790250944 carvalhe...@sanbi.org lgcarvalhe...@gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] multiple-test correlation
?p.adjust
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111
> -Original Message-
> From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
> project.org] On Behalf Of Manuel Jesús López Rodríguez
> Sent: Sunday, February 14, 2010 5:35 AM
> To: r-help@r-project.org
> Subject: [R] multiple-test correlation
>
> Dear all,
> I am trying to study the correlation between one "independent" variable
> ("V1") and several others dependent among them ("V2","V3","V4" and
> "V5"). For doing so, I would like to analyze my data by multiple-test
> (applying the Bonferroni´s correction or other similar), but I do not
> find the proper command in R. What I want to do is to calculate
> Kendall´s correlation between "V1" and the others variables (i.e. "V1"
> vs "V2", "V1" vs "V3", etc.) and to correct the p values by Bonferroni
> or other. I have found "outlier.test", but I do not know if this is
> what I need (also, I would prefer to use a less conservative method
> than Bonferroni´s, if possible).
> Thank you very much in advance!
>
>
> __
> 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.
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Re: [R] Does the R "statistical language includes modules/packagesto carry out nonlinear optimization similar to the SAS NLINand NLP procedures?
Randall:
Are you familiar with R's Search facilities? If not, don't you think you
should be? If so, why don't you try using them BEFORE posting on this list.
?help
?help.search
help.search("optimization") ##gives several alternatives
Bert Gunter
Genentech Nonclinical Biostatistics
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of David Winsemius
Sent: Tuesday, February 16, 2010 8:31 AM
To: Powers, Randall - BLS
Cc: r-help@r-project.org
Subject: Re: [R] Does the R "statistical language includes
modules/packagesto carry out nonlinear optimization similar to the SAS
NLINand NLP procedures?
On Feb 16, 2010, at 11:09 AM, Powers, Randall - BLS wrote:
> Hello R folks,
>
> I'm hoping the answer to the question in the subject line.
>
> I have in the past used SAS PROC NLIN and PROC NLP to carry out
> nonlinear optimizations. I'm wondering if there is analogous ways for
> doing this using R. If so, could someone please point me to some
> literature that would help me examine this further?
The CRAN Task Views are a good place to start any such search:
http://cran.r-project.org/web/views/
There is one for Optimization:
http://cran.r-project.org/web/views/Optimization.html
--
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
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Re: [R] reading quattro pro spreadsheet .qpw into R
stephen sefick wrote: I have many quattro pro spreadsheets and no quattro pro. Is there a way to access the data using R, or any other solution that anyone can think of? thanks, One possibility is to download the trial version of Corel Office and use that to convert the files to something more common, er even a simple .csv file, which is way easy to read into R. Tom __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] reading quattro pro spreadsheet .qpw into R
On Tue, Feb 16, 2010 at 4:12 PM, stephen sefick wrote: > I have many quattro pro spreadsheets and no quattro pro. Is there a > way to access the data using R, or any other solution that anyone can > think of? OpenOffice claims it can read Quattro Pro 6.0 'wb2' files, but maybe they are different to .qpw files. MS Excel claims some Quattro Pro readability - I've just read something about wb1 files. Maybe Gnumeric can read them? What have you tried? Perhaps if you put a representative file somewhere we can download and try? Barry __ 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] Reminder: ASA Stat Comp/Graph Chambers Award Competition Deadline 2/22
Just a gentle reminder that the deadline for submission to the Chambers Award Competition is fast approaching. All application materials must be received by 5:00pm EST, Monday, February 22, 2010. For submission guidelines, please visit http://stat-computing.org/awards/jmc/announcement.html _ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/201469229/direct/01/ [[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] Does the R "statistical language includes modules/packages to carry out nonlinear optimization similar to the SAS NLIN and NLP procedures?
On Feb 16, 2010, at 11:09 AM, Powers, Randall - BLS wrote: Hello R folks, I'm hoping the answer to the question in the subject line. I have in the past used SAS PROC NLIN and PROC NLP to carry out nonlinear optimizations. I'm wondering if there is analogous ways for doing this using R. If so, could someone please point me to some literature that would help me examine this further? The CRAN Task Views are a good place to start any such search: http://cran.r-project.org/web/views/ There is one for Optimization: http://cran.r-project.org/web/views/Optimization.html -- David Winsemius, MD Heritage Laboratories West Hartford, CT __ 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] for loop Vs apply function Vs foreach (REvolution enhancement)
Hi,
> 2. foreach (REvolution enhancement)
>
>seems the rationale of this function is to facilitate the use of
>multithreading to enhance the for loop speed. Given a moderate time
>sensitivity (process must run fast but a gain of 10-20% speed seen as probably
>not justifying the additional learning + dependence from yet another package),
>is it really worth going down that route?
>
> Has anyone extensive experience with this matter (using foreach to boost for
> loop running time)? any feedback welcome.
I'm not sure what you mean by "moderate time sensitivity" notion, but
you should definitely use foreach if you have a block of code that you
are iterating over that (i) takes a moderately long time to execute;
(ii) is independent of the code that runs before/after it in the loop;
and (tangentially but not really pertinent) (iii) running a linux/os x
machine so you can use the multicore package.
There isn't much learning involved since parallelizing over the cpu's
of a single machine is pretty much painless as long as you satisfy
(iii) above. This is only because the last I heard the "multicore"
package (which foreach/doMC depends on) doesn't really work on
windows. For instance, instead of something like:
results <- lapply(1:100, function(x) doSomethingWith(x))
or:
results <- list()
for (x in 1:100) {
results[[x]] <- doSomethingWith(x)
}
You do:
results <- foreach(x=1:100) %dopar% {
doSomethingWith(x)
}
That having been said, I wouldn't use foreach all the time as a
"default" replacement for the normal/sequential "for" loop, because
there is some rigging involved in using it, and it might not be worth
it if the code you are iterating over isn't too heavy.
Another nice thing is that the foreach process "degrades" gracefully.
For instance, if you are running on a machine that doesn't have any
foreach backend packages installed/enabled (the backend package
determines the "parallelization strategy", eg: "doMC" is a foreach
backend that parallelizes over the cpus/cores of 1 machine, others
parallelize over different machines in a cluster), then it will just
run the code in the %dopar% block sequentially.
Hope that helps,
-steve
--
Steve Lianoglou
Graduate Student: Computational Systems Biology
| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
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and provide commented, minimal, self-contained, reproducible code.
[R] Build failure on Solaris 10 (SPARC)
I'm trying to build R 2.10.1 on a Sun Blade 1000 running Solaris 10 (03/05 release). I've installed iconv 1.13.1 and used: CPPFLAGS="-I /export/home/drkirkby/sage-4.3.3.alpha0/local/include" (which is where iconv is) LDFLAGS= -R/export/home/drkirkby/sage-4.3.3.alpha0/local/lib -L/export/home/drkirkby/sage-4.3.3.alpha0/local/lib The build of R fails as below. gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include -I /export/home/drkirkby/sage-4.3.3.alpha0/local/include -DHAVE_CONFIG_H-g -O2 -c unique.c -o unique.o gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include -I /export/home/drkirkby/sage-4.3.3.alpha0/local/include -DHAVE_CONFIG_H-g -O2 -c util.c -o util.o util.c: In function 'Rf_Scollate': util.c:1679: warning: implicit declaration of function 'uiter_setUTF8' util.c:1681: warning: implicit declaration of function 'ucol_strcollIter' gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include -I /export/home/drkirkby/sage-4.3.3.alpha0/local/include -DHAVE_CONFIG_H-g -O2 -c version.c -o version.o gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include -I /export/home/drkirkby/sage-4.3.3.alpha0/local/include -DHAVE_CONFIG_H-g -O2 -c vfonts.c -o vfonts.o gfortran -g -O2 -c xxxpr.f -o xxxpr.o gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include -I /export/home/drkirkby/sage-4.3.3.alpha0/local/include -DHAVE_CONFIG_H-g -O2 -c mkdtemp.c -o mkdtemp.o ar cr libR.a CConverters.o CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o apply.o arithmetic.o array.o attrib.o base.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cov.o cum.o dcf.o datetime.o debug.o deparse.o deriv.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o engine.o envir.o errors.o eval.o format.o fourier.o gevents.o gram.o gram-ex.o gramRd.o graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o model.o names.o objects.o optim.o optimize.o options.o par.o paste.o pcre.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o random.o raw.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o size.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o unique.o util.o version.o vfonts.o xxxpr.o mkdtemp.o libs/*o ranlib libR.a gcc -std=gnu99 -R/export/home/drkirkby/sage-4.3.3.alpha0/local/lib -L/export/home/drkirkby/sage-4.3.3.alpha0/local/lib -o R.bin Rmain.o libR.a -L../../lib -lRblas -R/export/home/drkirkby/sage-4.3.3.alpha0/local/lib -lgfortran -lm-lreadline -ltermcap -lnsl -lsocket -ldl -lm -liconv -licuuc -licui18n Undefined first referenced symbol in file uiter_setUTF8 libR.a(util.o) ucol_strcollIterlibR.a(util.o) ld: fatal: Symbol referencing errors. No output written to R.bin collect2: ld returned 1 exit status note the two earlier lines: util.c:1679: warning: implicit declaration of function 'uiter_setUTF8' util.c:1681: warning: implicit declaration of function 'ucol_strcollIter' Any ideas how I might solve this? I'm using gcc 4.4.3. Dave __ 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] line options on read.spss
Hi, I am a newbie here. I like the ability to read SPSS file since it comes with other info. My problem with it is that it seems that I have to read the whole file into the memory. For the csv file, I can read part of it and dump them into the database so that even though I don't have a powerful system, I can work with a big data file as long as I only extract the part I need from the database at a time. I think can be a useful addition to the project. Thanks. Duncan [[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] Does the R "statistical language includes modules/packages to carry out nonlinear optimization similar to the SAS NLIN and NLP procedures?
Hello R folks, I'm hoping the answer to the question in the subject line. I have in the past used SAS PROC NLIN and PROC NLP to carry out nonlinear optimizations. I'm wondering if there is analogous ways for doing this using R. If so, could someone please point me to some literature that would help me examine this further? Thanks very much. [[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] combining dataframes with different row lenght
Hello list, I want to combine dataframes from tsv files which have different row lenght. I tryed cbind but doesn't work. Is there an easy way to fill with NAs till a common point of rows for all the dataframes and then merge them? Any other idea? Thanks a lot, Juan [[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] margin text warning message NAs coercion
Readers, I tried to the following commands: plot(y~x,ylab=expression(A[1]~B[2],xlab=expression(C~D)) mtext(expression(A[1]~B[2]),"additional text",side=3,line=1) I receive the text that I want, but the command terminal shows the following response: Warning message: NAs introduced by coercion in: mtext(expression(A[1]~B[2]),"additional text", side = 3, What is my mistake please? Yours, r251 rhelpatconference.jabber.org __ 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] reading quattro pro spreadsheet .qpw into R
I have many quattro pro spreadsheets and no quattro pro. Is there a way to access the data using R, or any other solution that anyone can think of? thanks, -- Stephen Sefick Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ 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] Odp: error : unused argument(s) when boxplot
Hi r-help-boun...@r-project.org napsal dne 16.02.2010 15:18:21: > Dear all, > > I am a total beginner in R, so sorry if this is the wrong place. I am using R > 2.10.1 on a Mac (Mac OS 10.6.2). > I have this small dataset : > growth sugar > 75 C > 72 C > 73 C > 61 F > 67 F > 64 F > 62 S > 63 S > I have no problem reading the table, or getting the summary, but if I try > boxplot(growth~sugar, ylab="growth", xlab="sugar", data=Dataset), I have the > following error : ERROR: unused argument(s) (sugar). > > Any suggestions ? What does str(Dataset) tell you about your data? Petr > > Thanks a lot, > > PH > __ > 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] Random Forest
Hi, i'm using randomForest package and i have 2 questions: 1. Can i drop one tree from an RF object? 2. i have a 300 trees forest, but when i use the predict function on new data (with predict.all=TRUE) i get only 270 votes. did i do something wrong? Thanks -- View this message in context: http://n4.nabble.com/Random-Forest-tp1557464p1557464.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Total and heading of portfoilo table
Hi
r-help-boun...@r-project.org napsal dne 16.02.2010 08:05:08:
> Hi!
>
> I am not expert in R, but perhaps you can try the following -
>
> X = as.numeric(read.csv('quantity.csv'))
> Y = read.csv('equity_price.csv')
> Y = Y[, -1]
>
> Z = X*Y
>
> port_val = NULL
>
> for(i in 1 : nrow(Z))
> {
>
> port_val[i] = sum(Z[i,])
>
> }
If I am not mistaken and if you ensure that column positions in both data
frames are the same.
rowSums(mapply("*", Y, X))
Shall do the trick
Regards
Petr
>
> write.csv(data.frame(Z, port_val = port_val), 'PORTFOLIO.csv', row.names
= FALSE)
>
>
> I am sure the experts will have much simpler way to address this
problem.
>
> Regards
>
> Madhavi
>
> --- On Mon, 15/2/10, Sarah Sanchez wrote:
>
>
> From: Sarah Sanchez
> Subject: [R] Total and heading of portfoilo table
> To: r-help@r-project.org
> Date: Monday, 15 February, 2010, 10:08 PM
>
>
> Dear R helpers,
>
> I have two input files as 'quantity.csv' and 'equity_price.csv' as (for
> example) given below.
>
> 'quantity.csv'
> GOOG YHOO
> 1000 100
>
>
> 'equity_price.csv'
> sr_no GOOG_price YHOO_price
> 115.22 536.40
> 215.07 532.97
> 315.19 534.05
> 415.16 531.86
> 515.11 532.11
>
> My problem is to calculate the portfolio value for each of these 5 days
> (actually my portfolio
> consists of 47 comanies and prices taken are for last 1 year).
>
> I had defined
>
> X = read.csv('quantity.csv')
> Y = read.csv('equity_price.csv')
>
> I have tried the loop
>
> Z = array()
>
> for (i in 1:2)
> {
> Z[i] = (X[[i]]*Y[i])
> }
>
> # When I write this dataframe as
>
> write.csv(data.frame(Z), 'Z.csv', row.names = FALSE)
>
> When I open 'Z.csv' file, I get
>
> c.2500L..3300L..4500L..1000L..4400L.
c.14000L..45000L..48000L..26000L..15000L.
> 250014000
> 330045000
> 450048000
> 100026000
> 440015000
>
> My requirement is to have the column heads and the portfolio total as
> GOOGYHOO Total
> 2500 14000 16500
> 3300 45000 48300
> 4500 48000 52500
> 1000 26000 27000
> 4400 15000 19400
>
>
> Please guide
>
> Regards
>
> Sarah
>
>
>
>
>
> [[alternative HTML version deleted]]
>
>
> -Inline Attachment Follows-
>
>
> __
> 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.
>
>
>
>
> tp://downloads.yahoo.com/in/internetexplorer/
>[[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.
__
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