Hi,

I am a new user of R 2.8.1. I use Tinn-R for code editing.  I use a windows
2003 system with  1 GB RAM.

I am interested to generate  dashboard and reports based on data from  MS
Access.  These reports need to be posted on a weekly basis to the web. The
reporting interface should provide facilities for "what if" scenarios.

Is it possible to interface R analysis results to good open source reporting
tools like Jasper Reports. what is the appropriate system requirements for
carrying out real time reporting using R.

any help in this regard is highly  appreciated,

thanks in advance,

regards,
srinivas
statistical analyst.



On Sun, Jan 11, 2009 at 4:30 PM, <r-help-request@r-project.org> wrote:

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> Today's Topics:
>
>   1. Re: Help needed for Loading "tm" package (Prof Brian Ripley)
>   2. Re: rpart with interval censored data crashes R (David Winsemius)
>   3.  AT&T Researchers and the New York Times (Alan Zaslavsky)
>   4. Re: The R Inferno (Tom Backer Johnsen)
>   5. Re: The R Inferno (Jason Morgan)
>   6. Re: Ashlee Vance's article on R in the New York Times
>      (Stavros Macrakis)
>   7. Print specific matrix value??? (Nidhi Kohli)
>   8. Fitting pareto to some data (Borja Soto Varela)
>   9. Print specific matrix value??? (Nidhi Kohli)
>  10. Re: The R Inferno (Ajay ohri)
>  11. Re: Plot link points (Roy Mendelssohn)
>  12. Re: Print specific matrix value??? (Stephan Kolassa)
>  13. Re: Fw: Re:  R Stacked Histogram (hadley wickham)
>  14. Re: R in the NY Times (Tony Breyal)
>  15. Arguments for Rcmd BATCH (Andrew Hicks)
>  16. Calling C from FORTRAN and vice versa (Michael H?hle)
>  17. R version requires Bioconductor 2.3 version (Andreas Scherer)
>  18.  JGR editor setting problem (tedzzx)
>  19. Setting a contingency table (Bhargab Chattopadhyay)
>  20. Applying 'lm' in each group (Bhargab Chattopadhyay)
>  21. Re: R in the NY Times (Florian Lengyel)
>  22. Re: Arguments for Rcmd BATCH (Prof Brian Ripley)
>  23. Re: R in the NY Times (Barry Rowlingson)
>  24. Re: R in the NY Times (Ajay ohri)
>  25. Re: Print specific matrix value??? (Uwe Ligges)
>  26. Re: R version requires Bioconductor 2.3 version (Uwe Ligges)
>  27. Re: bug in R2WinBUGS (Uwe Ligges)
>  28. Re: R in the NY Times (Bert Gunter)
>  29. Re: Applying 'lm' in each group (David Winsemius)
>  30. Re: Applying 'lm' in each group (Ben Bolker)
>  31. Re: Applying 'lm' in each group (Chuck Cleland)
>  32. Re: R in the NY Times (Kingsford Jones)
>  33. install.views() (oscar linares)
>  34. Re: install.views() (Kingsford Jones)
>  35. Re: Setting a contingency table (David Winsemius)
>  36. Re: install.views() (David Winsemius)
>  37. Hmisc-xtable label (Felipe Carrillo)
>  38. Re: R in the NY Times (Johannes Huesing)
>  39. Re: R in the NY Times (Gabor Grothendieck)
>  40. Re: Hmisc-xtable label (Solved) (Felipe Carrillo)
>  41. how to get the signed distance in SVM? (Qing Li)
>  42. Problem with compiling shared C/C++ library for loading into
>      R (Linux) (Samsiddhi Bhattacharjee)
>  43. Problem with compiling shared C/C++ library for loading into
>      R (Linux) (Samsiddhi Bhattacharjee)
>  44. Rserve/RandomForest does not work with a CSV?
>      (anthony@resolution.com)
>  45. Re: The R Inferno (milton ruser)
>  46. Re: Arguments for Rcmd BATCH (Prof Brian Ripley)
>  47. Re: Zipf fitting using R (Stefan Evert)
>  48. Re: Arguments for Rcmd BATCH (Andrew Hicks)
>  49. temporal join (mckenzig)
>  50. problems installing package XML to a computer without an
>      internet connection (Bob Green)
>  51. Re: problems installing package XML to a computer without an
>      internet connection (Gabor Grothendieck)
>  52.  I'm looking for a book about spatial point patterns (Diggle,
>      2003) (Unangu)
>  53. Re: install.views() (oscar linares)
>  54. Convert date/time string to date (Heston Capital)
>  55. Re: problems installing package XML to a computer without an
>      internet connection (Bob Green)
>  56.  How to get solution of following polynomial? (RON70)
>  57. Re: problems installing package XML to a computer without an
>      internet connection (Prof Brian Ripley)
>  58. Re: Convert date/time string to date (Prof Brian Ripley)
>  59. Re: ftp connections for uploading files (Prof Brian Ripley)
>  60. Re: Extracting File Basename without Extension (Wacek Kusnierczyk)
>  61. Re: Extracting File Basename without Extension (Wacek Kusnierczyk)
>  62. PAW Update: Predictive analytics workshops and more case
>      studies (EliseJ)
>  63. Re: Arguments for Rcmd BATCH (Andrew Hicks)
>  64.  PHP and R (Applejus)
>  65. Re: PHP and R (Prof Brian Ripley)
>  66. upgrade R version (ms.com)
>  67. Strange behaviour of paste (Oliver Bandel)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 10 Jan 2009 11:06:47 +0000 (GMT)
> From: Prof Brian Ripley <ripley@stats.ox.ac.uk>
> Subject: Re: [R] Help needed for Loading "tm" package
> To: Kum-Hoe Hwang <phdhwang@gmail.com>
> Cc: R Help mail address <r-help@stat.math.ethz.ch>
> Message-ID: <alpine.OSX.1.00.0901101102390.91535@tystie.local>
> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>
> On Sat, 10 Jan 2009, Kum-Hoe Hwang wrote:
>
> > Howdy Gurus again
> >
> > Thanks to  Tony.Breyal, I was able to writing the following script for
> > analyzing a text document.
> > But I got an error with "tm' package. I don't why I got the error from
> the R
> > script below. I think I followed proccess of R tm manual.
>
> Please do read the messages you got.  I see
>
> > Error in .jinit(system.file("jar", c("weka.jar", "RWeka.jar"), package =
> > pkgname,  :
> >  Cannot create Java virtual machine (-1)
>
> so the problem is with your Java installation and RWeka, not 'tm'.
>
> First make sure you have a working installation of RWeka -- I suspect
> you do not even have Java installed, but it could be a version or path
> issue (but very unlikely to be an R issue).
>
> >
> > I use R v2.8.1. and tm_0.3-3.zip under Win XP.
> >
> > Thanks in advance,
> >
> > Kum Hwang
> >
> >> # setting directory
> >> my.path <-'C:\\_work\\Daddy"s\\myProjects\\2009
> > defaultProject\\R\\textfile\\'
> >>
> >> # text miner pakacge
> >> library(tm)
> > Loading required package: Snowball
> > Loading required package: RWeka
> > ---------------------------------------------------------
> > Error in .jinit(system.file("jar", c("weka.jar", "RWeka.jar"), package =
> > pkgname,  :
> >  Cannot create Java virtual machine (-1)
> > Error : .onLoad failed in 'loadNamespace' for 'RWeka'
> > Error: package 'RWeka' could not be loaded
> >> my.corpurs <-Corpus(DirSource(my.path), readerControl =
> > list(reader=readPlain))
> > Error: could not find function "Corpus"
> >> my.tdm <- TermDocMatrix(my.corpus)
> > Error: could not find function "TermDocMatrix"
> >> my.tdm[1,]
> > Error: object "my.tdm" not found
> >
> >
> > --
> > Kum-Hoe Hwang, Ph.D.
> >
> > Phone : 82-31-250-3516
> > Email : phdhwang@gmail.com
> >
> >       [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
> --
> Brian D. Ripley,                  ripley@stats.ox.ac.uk
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> University of Oxford,             Tel:  +44 1865 272861 (self)
> 1 South Parks Road,                     +44 1865 272866 (PA)
> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
>
>
>
> ------------------------------
>
> Message: 2
> Date: Sat, 10 Jan 2009 08:42:46 -0500
> From: David Winsemius <dwinsemius@comcast.net>
> Subject: Re: [R] rpart with interval censored data crashes R
> To: "Keith Jewell" <k.jewell@campden.co.uk>
> Cc: r-help@stat.math.ethz.ch
> Message-ID: <5467EAED-927D-4C5C-A656-FB1D510C63BC@comcast.net>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
> On a Leopard Mac with the Urbanek compiled 64 bit R, one sees this:
>
>  > library(rpart)
>  > library(survival)
> Loading required package: splines
>  > fit<-rpart(Surv(N,Y,type="interval2")~Salt+pH+Temp, data=myD)
>
>  *** caught segfault ***
> address 0x0, cause 'memory not mapped'
>
> Traceback:
>  1: .C(C_rpartexp2, as.integer(length(dtimes)),
> as.double(dtimes),     as.double(.Machine$double.eps), keep =
> integer(length(dtimes)))
>  2: (get(paste("rpart", method, sep = ".")))(Y, offset, , wt)
>  3: rpart(Surv(N, Y, type = "interval2") ~ Salt + pH + Temp, data =
> myD)
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
>
> Choosing "4" does save the workspace.
> --
> David Winsemius
>
> On Jan 9, 2009, at 9:04 AM, Keith Jewell wrote:
>
> > Hi Everyone,
> >
> > This example code results in R 'crashing'; that is the R application
> > closes
> > with no warnings or error messages.
> > #-----------------------
> > myD <- read.table(stdin(), header=TRUE, nrows=20)
> > Broth Salt   pH Temp    N  Y Growth
> > 1        310    9.0 2.92      10 90.0 NA            0
> > 2        615    6.0 7.82      30  1.0  2            1
> > 3        217    2.0 7.34      10  7.0  8            1
> > 4        338   10.0 4.44      10 90.0 NA            0
> > 5        240    4.0 7.33      10 20.0 21            1
> > 6        336   10.0 3.90      10 90.0 NA            0
> > 7        279    7.0 6.73      10 90.0 NA            0
> > 8       1021    9.0 5.03      45  8.0  9            1
> > 9        974    7.0 4.01      45 90.0 NA            0
> > 10       265    7.0 2.93      10 90.0 NA            0
> > 11       934    4.0 5.28      45  0.1  1            1
> > 12       669    9.0 5.03      30 90.0 NA            0
> > 13       875   10.0 6.24      37  1.0  2            1
> > 14       385    2.0 5.84      20  1.0  2            1
> > 15       562    2.0 5.84      30  0.1  1            1
> > 16       718    0.5 5.54      37  0.1  1            1
> > 17       845    9.0 5.03      37  3.0  6            1
> > 18       913    2.0 5.84      45  0.1  1            1
> > 19       577    4.0 4.10      30 90.0 NA            0
> > 20        20    0.5 7.44       8 24.0 27            1
> >
> > library(rpart)
> > library(survival)
> > fit<-rpart(Surv(N,Y,type="interval2")~Salt+pH+Temp, data=myD)
> > #---------------------
> >
> > Professor Ripley helpfully pointed out that the documentation does
> > not say
> > that interval censoring is supported, and indeed this seems only to
> > happen
> > with interval censored data.
> >
> > ?rpart indicates that the dependent variable may be a survival object.
> > Neither ?rpart nor "An Introduction to Recursive Partitioning Using
> > the
> > RPART Routines" (Therneau et al 1997) suggest that the dependent
> > variable
> > may contain interval censored data, but neither do they suggest it
> > shouldn't; i.e. as far as I'm aware (!) this restriction is not
> > documented.
> >
> > This post has three purposes:
> >
> > 1) Bring this behaviour - especially the crash in response to 'bad'
> > data -
> > to the attention of the authors.
> >
> > 2) Seek an explanation of the restriction (if intentional). In my
> > simplicity, it seems that interval censored data should be easier to
> > handle
> > than left or right censored - after all the information content is
> > greater.
> >
> > 3) Seek guidance on how to work around the problem. I'm minded to
> > replace
> > the interval censored data by the mid points of the intervals. Does
> > anyone
> > have any comments on such an approach?
> >
> > Any comments gratefully received.
> >
> > Keith Jewell
> > ==========================================
> > Version:
> > platform = i386-pc-mingw32
> > arch = i386
> > os = mingw32
> > system = i386, mingw32
> > status = Patched
> > major = 2
> > minor = 8.1
> > year = 2009
> > month = 01
> > day = 07
> > svn rev = 47502
> > language = R
> > version.string = R version 2.8.1 Patched (2009-01-07 r47502)
> >
> > Windows Server 2003 x64 (build 3790) Service Pack 2
> >
> > Locale:
> > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
> > Kingdom.1252;LC_MONETARY=English_United
> > Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
> >
> > Search Path:
> > .GlobalEnv, package:stats, package:graphics, package:grDevices,
> > package:utils, package:datasets, package:methods, Autoloads,
> > package:base
> >
> > ______________________________________________
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
> > and provide commented, minimal, self-contained, reproducible code.
>
>
>
> ------------------------------
>
> Message: 3
> Date: Sat, 10 Jan 2009 09:38:07 -0500 (EST)
> From: Alan Zaslavsky <zaslavsk@hcp.med.harvard.edu>
> Subject: [R]  AT&T Researchers and the New York Times
> To: r-help@r-project.org
> Message-ID:
>        <Pine.GSO.4.60.0901100935550.21550@mikado.hcp.med.harvard.edu>
> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>
>
> I've submitted a posting to the NY Times blog mentioned by David Smith,
> specifically mentioning John, Rick and Allan.  (Now awaiting moderation.)
> Of course there are many others deserving credit but far to numerous to
> list so I didn't get started.
>
> On Thu, Jan 8, 2009 at 5:58 PM, Robert Wilkins <irishhacker@gmail.com
> >wrote:
> > Is anyone in the leadership of the R-project going to contact the New
> > York Times and clarify that the article gave remarkably short shrift
> > to the people who designed the user interface for R, to a large extent
> > AT&T researchers from an earlier generation? It would be the
> > appropriate thing to do.
>
>
>
> ------------------------------
>
> Message: 4
> Date: Sat, 10 Jan 2009 16:26:40 +0100
> From: Tom Backer Johnsen <backer@psych.uib.no>
> Subject: Re: [R] The R Inferno
> To: Patrick Burns <pburns@pburns.seanet.com>
> Cc: "r-help@stat.math.ethz.ch" <r-help@stat.math.ethz.ch>
> Message-ID: <4968BE30.9020408@psych.uib.no>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Extremely nice.  Tons of useful information presented in a very
> entertaining way.  Thanks!
>
> Tom
>
> Patrick Burns wrote:
> > "The R Inferno" is now on the Burns Statistics website at
> >
> > http://www.burns-stat.com/pages/Tutor/R_inferno.pdf
> >
> > Abstract: If you are using R and you think you're in hell,
> > this is a map for you.
> >
> > Also, I've expanded the outline concerning R on the
> > Burns Statistics 'Links' page. Suggestions (off-list) for
> > additional items are encouraged.
> >
> >
> > Patrick Burns
> > patrick@burns-stat.com
> > +44 (0)20 8525 0696
> > http://www.burns-stat.com
> > (home of "The R Inferno" and "A Guide for the Unwilling S User")
> >
> > ______________________________________________
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
> > and provide commented, minimal, self-contained, reproducible code.
>
>
> --
> +----------------------------------------------------------------+
> | Tom Backer Johnsen, Psychometrics Unit,  Faculty of Psychology |
> | University of Bergen, Christies gt. 12, N-5015 Bergen,  NORWAY |
> | Tel : +47-5558-9185                        Fax : +47-5558-9879 |
> | Email : backer@psych.uib.no    URL : http://www.galton.uib.no/ |
> +----------------------------------------------------------------+
>
>
>
> ------------------------------
>
> Message: 5
> Date: Sat, 10 Jan 2009 11:03:40 -0500
> From: Jason Morgan <jwm-r-help@skepsi.net>
> Subject: Re: [R] The R Inferno
> To: "r-help\@stat\.math\.ethz\.ch" <r-help@stat.math.ethz.ch>
> Message-ID: <20090110160340.GC6775@skepsi.net>
> Content-Type: text/plain; charset=utf-8
>
> Excellent read, Patrick. A very useful and clear guide.
>
> On 2009.01.09 16:14:49, Patrick Burns wrote:
> > "The R Inferno" is now on the Burns Statistics website at
> >
> > http://www.burns-stat.com/pages/Tutor/R_inferno.pdf
> >
> > Abstract: If you are using R and you think you're in hell,
> > this is a map for you.
> >
> > Also, I've expanded the outline concerning R on the
> > Burns Statistics 'Links' page. Suggestions (off-list) for
> > additional items are encouraged.
> >
> >
> > Patrick Burns
> > patrick@burns-stat.com
> > +44 (0)20 8525 0696
> > http://www.burns-stat.com
> > (home of "The R Inferno" and "A Guide for the Unwilling S User")
> >
> > ______________________________________________
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
> > and provide commented, minimal, self-contained, reproducible code.
>
> --
> ~ Jason Morgan
>
>
>
> ------------------------------
>
> Message: 6
> Date: Sat, 10 Jan 2009 11:03:50 -0500
> From: "Stavros Macrakis" <macrakis@alum.mit.edu>
> Subject: Re: [R] Ashlee Vance's article on R in the New York Times
> To: "Robert Wilkins" <irishhacker@gmail.com>
> Cc: r-help@r-project.org
> Message-ID:
>        <8b356f880901100803rd5e0f17he36778ae37be2d17@mail.gmail.com>
> Content-Type: text/plain
>
> On Thu, Jan 8, 2009 at 1:26 AM, Robert Wilkins <irishhacker@gmail.com
> >wrote:
>
> > ...The user interface for R, otherwise known as the S programming
> language
> > has the same origins as C and Unix....
>
>
> We could take this one step further, and note that C's design (its "user
> interface"?) was based on BCPL, which was developed at Cambridge University
> and MIT (which was in turn loosely based on CPL).  But BCPL declined into
> obscurity, while we're still stuck witxxx benefitting from C.
>
> As for Unix, most of its ideas came from Multics (developed mostly at MIT,
> but with Bell Labs and GE). And some of the core ideas and utilities of
> Multics came from CTSS (also MIT) -- Unix roff/nroff/troff was a knock-off
> of CTSS's runoff, for example.  But Multics failed and Unix succeeded.
>
> Fast forward a few years, and Unix itself was (alas) fading into
> marginality
> until GNU/Linux* came around. (I had a front-row seat at this decline as a
> staffer at OSF.) As with R/S, the specification was of course important,
> but
> the dynamics were completely changed by the development of a free and open
> version.  The NYT reporter correctly focussed on the success of R.
>
> I do agree that the core of R could use renewal and rethinking, and that
> many free/open projects have been reimplementations of existing designs.
> But
> there is also innovation within the framework of R, such as Hadley
> Wickham's
> ggplot2.
>
> Is it enough?  It never is....
>
>            -s
>
> * Speaking of giving credit where credit is due, Stallman is absolutely
> right when he insists on recognition for the huge contribution of the GNU
> project to GNU/Linux, though it's no doubt to late to insist on the full
> name....
>
>        [[alternative HTML version deleted]]
>
>
>
> ------------------------------
>
> Message: 7
> Date: Sat, 10 Jan 2009 11:15:00 -0500 (EST)
> From: Nidhi Kohli <nidhik@umd.edu>
> Subject: [R] Print specific matrix value???
> To: r-help@r-project.org
> Message-ID: <20090110111500.BIN51794@po3.mail.umd.edu>
> Content-Type: text/plain; charset=us-ascii
>
> Hello All,
>
> I'm trying to print specific row and column for Observed_Scores matrix,
> however, when I execute the command "Observed_Scores[1,1]", I get the
> message "Error in Observed_Scores[1, 1] : incorrect number of dimensions".
> Could you please help and let me know where is the mistake? Here is my
> program:
>
>
> library(ltm)
> library(psych)
>
> # Settting the working directory path to C:/NCME
>
> path="C:/NCME"
> setwd(path)
>
> #IRT Data Simulation Routine#
>
> n.exams = 500   #Sets number of examinees to be generated#
> n.items = 20     #Sets number of items to be generated#
>
> #The following intialize empty (NA) vectors or matrices#
> beta.values = rep(NA,n.items)
> resp.prob = matrix(rep(NA,n.exams*n.items),nrow=n.exams,ncol=n.items)
> Observed_Scores = matrix(rep(NA,n.exams*n.items),nrow=n.exams,ncol=n.items)
>
>
> #filling item parameters into beta.values
> beta.values = runif(n.items,-2,2)
>
> #Calculating Threshold
> thresh.values = .5 * beta.values
>
>
> #for (i in 1:10)
> #{
>
> #Using the function to generate the data
> GenData <- congeneric.sim(N=500, loads = rep(.5,20), err=NULL, short =
> FALSE)
> Observed_Scores = GenData[1]
>
> Regards
> Nidhi Kohli
>
>
>
> ------------------------------
>
> Message: 8
> Date: Sat, 10 Jan 2009 17:16:15 +0100
> From: "Borja Soto Varela" <borja.soto@gmail.com>
> Subject: [R] Fitting pareto to some data
> To: r-help@r-project.org
> Message-ID:
>        <c23bd7a0901100816p4c1d2e42i591f95f30dd5d77c@mail.gmail.com>
> Content-Type: text/plain
>
> Dear R-users,
>
> I am trying to fit pareto distribution to some data but i've one problem.
> Using optim to calculate the maximum of the likelihood function of the
> pareto I use as start parameters the moments method(using the distribution
> function in the package actuar):
>
> media=mean(x)
> var=mean(x^2)-media^2
> scale=2*var/(var-media^2)
> shape=(scale-1)*media
>
> fitdistr(x,dpareto,list(shape=shape,scale=scale))
>
> The problem is how to initialize the shape and scale parameters when
> "var<=media^2" . When "var<=media^2" scale and shape parameters are
> negative
> using moments method.
> Does anyone know how to initialize the paramaters when "var<=media^2"?
>
> Thanks
> Borja
>
>        [[alternative HTML version deleted]]
>
>
>
> ------------------------------
>
> Message: 9
> Date: Sat, 10 Jan 2009 11:21:05 -0500 (EST)
> From: Nidhi Kohli <nidhik@umd.edu>
> Subject: [R] Print specific matrix value???
> To: r-help@r-project.org
> Cc: r-help@stat.math.ethz.ch
> Message-ID: <20090110112105.BIN51911@po3.mail.umd.edu>
> Content-Type: text/plain; charset=us-ascii
>
> Hello All,
>
> I'm trying to print specific row and column for Observed_Scores matrix,
> however, when I execute the command "Observed_Scores[1,1]", I get the
> message "Error in Observed_Scores[1, 1] : incorrect number of dimensions".
> Could you please help and let me know where is the mistake? Here is my
> program:
>
>
> library(ltm)
> library(psych)
>
> # Settting the working directory path to C:/NCME
>
> path="C:/NCME"
> setwd(path)
>
> #IRT Data Simulation Routine#
>
> n.exams = 500   #Sets number of examinees to be generated#
> n.items = 20     #Sets number of items to be generated#
>
> #The following intialize empty (NA) vectors or matrices#
> beta.values = rep(NA,n.items)
> resp.prob = matrix(rep(NA,n.exams*n.items),nrow=n.exams,ncol=n.items)
> Observed_Scores = matrix(rep(NA,n.exams*n.items),nrow=n.exams,ncol=n.items)
>
>
> #filling item parameters into beta.values
> beta.values = runif(n.items,-2,2)
>
> #Calculating Threshold
> thresh.values = .5 * beta.values
>
>
> #for (i in 1:10)
> #{
>
> #Using the function to generate the data
> GenData <- congeneric.sim(N=500, loads = rep(.5,20), err=NULL, short =
> FALSE)
> Observed_Scores = GenData[1]
>
> Regards
> Nidhi Kohli
>
>
>
> ------------------------------
>
> Message: 10
> Date: Sat, 10 Jan 2009 22:01:52 +0530
> From: Ajay ohri <ohri2007@gmail.com>
> Subject: Re: [R] The R Inferno
> To: Jason Morgan <jwm-r-help@skepsi.net>
> Cc: "r-help@stat.math.ethz.ch" <r-help@stat.math.ethz.ch>
> Message-ID:
>        <4bc14e460901100831u66e3233cyee1481ea44c7ec26@mail.gmail.com>
> Content-Type: text/plain
>
> Hi ,
> I have been trying to convince Pat to come up with a book on this.
>
> He can add in the chapters on *Purgatorio*
> (Purgatory<http://en.wikipedia.org/wiki/Purgatory>),
> and *Paradiso* (Paradise <http://en.wikipedia.org/wiki/Heaven>)
>
>
> Regards,
>
> Ajay
>
> On Sat, Jan 10, 2009 at 9:33 PM, Jason Morgan <jwm-r-help@skepsi.net>
> wrote:
>
> > Excellent read, Patrick. A very useful and clear guide.
> >
> > On 2009.01.09 16:14:49, Patrick Burns wrote:
> > > "The R Inferno" is now on the Burns Statistics website at
> > >
> > > http://www.burns-stat.com/pages/Tutor/R_inferno.pdf
> > >
> > > Abstract: If you are using R and you think you're in hell,
> > > this is a map for you.
> > >
> > > Also, I've expanded the outline concerning R on the
> > > Burns Statistics 'Links' page. Suggestions (off-list) for
> > > additional items are encouraged.
> > >
> > >
> > > Patrick Burns
> > > patrick@burns-stat.com
> > > +44 (0)20 8525 0696
> > > http://www.burns-stat.com
> > > (home of "The R Inferno" and "A Guide for the Unwilling S User")
> > >
> > > ______________________________________________
> > > R-help@r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
> > > and provide commented, minimal, self-contained, reproducible code.
> >
> > --
> > ~ Jason Morgan
> >
> > ______________________________________________
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
>        [[alternative HTML version deleted]]
>
>
>
> ------------------------------
>
> Message: 11
> Date: Sat, 10 Jan 2009 08:48:59 -0800
> From: Roy Mendelssohn <Roy.Mendelssohn@noaa.gov>
> Subject: Re: [R] Plot link points
> To: Jim Lemon <jim@bitwrit.com.au>
> Cc: r-help@stat.math.ethz.ch, lee.kitty@yahoo.com
> Message-ID: <8D0FD9CD-6D0B-43F5-836E-F963D3932222@noaa.gov>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
> Look at:
>
> http://geography.uoregon.edu/geogr/topics/maps.htm
>
> -Roy
>
> On Jan 10, 2009, at 1:48 AM, Jim Lemon wrote:
>
> > Kitty Lee wrote:
> >> Hi. This may be a straight-forward question...
> >>
> >> I have a time series from 1950 to 2000 (by year) with missing values.
> >> Sometimes only a year has value and the adjacent years have missing
> >> data, e.g.
> >>
> >> 1950 2.7
> >> 1951 1952
> >> 1953 3.4
> >> 1954
> >> 1955
> >> 1956 2.9
> >> 1957 3.6
> >> 1958 2.7
> >>
> >>
> >> When I use plot (type='l'), the line can't connect the 'stand-
> >> alone' years. Is there a way I have have R to skip over the NA and
> >> draw a line with the points available?
> >>
> >>
> > Hi Kitty,
> > Assuming that the above is a data frame with two columns, the second
> > of which is named "value":
> >
> > plot(my.data.frame[!is.na(my.data.frame$value),],type="l")
> >
> > 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<http://www.r-project.org/posting-guide.html>
> > and provide commented, minimal, self-contained, reproducible code.
>
> **********************
> "The contents of this message do not reflect any position of the U.S.
> Government or NOAA."
> **********************
> Roy Mendelssohn
> Supervisory Operations Research Analyst
> NOAA/NMFS
> Environmental Research Division
> Southwest Fisheries Science Center
> 1352 Lighthouse Avenue
> Pacific Grove, CA 93950-2097
>
> e-mail: Roy.Mendelssohn@noaa.gov (Note new e-mail address)
> voice: (831)-648-9029
> fax: (831)-648-8440
> www: http://www.pfeg.noaa.gov/
>
> "Old age and treachery will overcome youth and skill."
> "From those who have been given much, much will be expected"
>
>
>
> ------------------------------
>
> Message: 12
> Date: Sat, 10 Jan 2009 18:16:53 +0100
> From: Stephan Kolassa <Stephan.Kolassa@gmx.de>
> Subject: Re: [R] Print specific matrix value???
> To: Nidhi Kohli <nidhik@umd.edu>
> Cc: r-help@r-project.org
> Message-ID: <4968D805.10202@gmx.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Nidhi,
>
> in your very last line, you set
> Observed_Scores = GenData[1]
>
> After that, Observed_Scores is not a matrix any more, but a list with a
> single entry Observed_Scores$model, which is in fact a data.frame, but
> with different dimensions than you initially set Observed_Scores to.
>
> HTH,
> Stephan
>
>
> Nidhi Kohli schrieb:
> > Hello All,
> >
> > I'm trying to print specific row and column for Observed_Scores matrix,
> however, when I execute the command "Observed_Scores[1,1]", I get the
> message "Error in Observed_Scores[1, 1] : incorrect number of dimensions".
> Could you please help and let me know where is the mistake? Here is my
> program:
> >
> >
> > library(ltm)
> > library(psych)
> >
> > # Settting the working directory path to C:/NCME
> >
> > path="C:/NCME"
> > setwd(path)
> >
> > #IRT Data Simulation Routine#
> >
> > n.exams = 500   #Sets number of examinees to be generated#
> > n.items = 20     #Sets number of items to be generated#
> >
> > #The following intialize empty (NA) vectors or matrices#
> > beta.values = rep(NA,n.items)
> > resp.prob = matrix(rep(NA,n.exams*n.items),nrow=n.exams,ncol=n.items)
> > Observed_Scores =
> matrix(rep(NA,n.exams*n.items),nrow=n.exams,ncol=n.items)
> >
> >
> > #filling item parameters into beta.values
> > beta.values = runif(n.items,-2,2)
> >
> > #Calculating Threshold
> > thresh.values = .5 * beta.values
> >
> >
> > #for (i in 1:10)
> > #{
> >
> > #Using the function to generate the data
> > GenData <- congeneric.sim(N=500, loads = rep(.5,20), err=NULL, short =
> FALSE)
> > Observed_Scores = GenData[1]
> >
> > Regards
> > Nidhi Kohli
> >
> > ______________________________________________
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
>
>
> ------------------------------
>
> Message: 13
> Date: Sat, 10 Jan 2009 11:33:44 -0600
> From: "hadley wickham" <h.wickham@gmail.com>
> Subject: Re: [R] Fw: Re:  R Stacked Histogram
> To: jasonkrupert@yahoo.com
> Cc: R-help <R-help@r-project.org>
> Message-ID:
>        <f8e6ff050901100933l17459de9n75f2c1ff3328a098@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Jason,
>
> You can do:
>
> qplot(mpg, wt, data = mtcars, colour = factor(cyl)) +
> opts(legend.position = c(0.5, 0.5))
>
> Hadley
>
> On Thu, Jan 8, 2009 at 3:04 PM, Jason Rupert <jasonkrupert@yahoo.com>
> wrote:
> > Thank you again for your response.
> >
> > This worked great.
> >
> > Quick question about the legend for qplot.  Instead of being outside the
> > plot, is it possible to move the location of the legend to the upper left
> or
> > right corner of the plot?  Could you possibly provide an example.
> >
> > Thank you again for your feedback and insights.
> >
> > --- On Wed, 1/7/09, hadley wickham <h.wickham@gmail.com> wrote:
> >
> > From: hadley wickham <h.wickham@gmail.com>
> > Subject: Re: Fw: Re: [R] R Stacked Histogram
> > To: jasonkrupert@yahoo.com, "R-help" <R-help@r-project.org>
> > Date: Wednesday, January 7, 2009, 12:17 PM
> >
> > Hi Jason,
> >
> >> Well, one last questions about stack plot (please forgive the lame
> example
> >> below).  I thought the below allow me to resize the the "title"
> > of the
> >> stacked histogram, but no luck.  Any suggestions as to the modificaiton
> >> necessary to get it to work?  Right now the title is obscured by the
> plot
> >> and my boss will be none too happy.  Thanks again.
> >
> > Yes, that's a really stupid bug that I accidentally introduced in the
> > latest version.  You can fix it with:
> >
> > qplot(mpg, wt, data = mtcars, main = "My title") + opts(plot.title =
> > theme_text(vjust = 0, size = 16))
> >
> > or by adding a new line to the end of the title:
> >
> > qplot(mpg, wt, data = mtcars, main = "My title\n")
> >
> > Regards,
> >
> > Hadley
> > --
> > http://had.co.nz/
> >
> >
>
>
>
> --
> http://had.co.nz/
>
>
>
> ------------------------------
>
> Message: 14
> Date: Sat, 10 Jan 2009 05:11:52 -0800 (PST)
> From: Tony Breyal <tony.breyal@googlemail.com>
> Subject: Re: [R] R in the NY Times
> To: r-help@r-project.org
> Message-ID:
>        <762dbc5f-58ee-4a0c-8a88-c0baccfc00fa@d36g2000prf.googlegroups.com>
> Content-Type: text/plain; charset=windows-1252
>
> ?We have customers who build engines for aircraft. I am happy they are
> not using freeware when I get on a jet.?
>
> The lady who made this comment, Anne H. Milley, director of technology
> product marketing at SAS, has written a response to try and clarify
> what she meant (funilly enough, i got this link from a SAS mate of
> mine who is now going to have a look into R for the first time):
>
>
> http://blogs.sas.com/sascom/index.php?/archives/434-This-post-is-rated-R.html
>
>
> [quote]
> "As for open source and my airplane quote ?
>
> My remark reflects a key difference between R and SAS, that of
> support, reliability, and validation. Customers value SAS for many
> things, including our extensive testing, documentation, 24/7 support,
> and training. In contrast, the quality of proliferating R packages is
> varied and uneven, especially in complex analytical modules. Mistakes
> in these packages can lead to misleading results, even for experienced
> users.
>
> The airplane comment was meant to point out this key difference. Not
> to condemn open source. In fact, SAS values open-source software. Our
> software runs on Linux. We use some open-source tools in development.
> And we plan to embrace open source further in the future.
>
> The world has many complex problems. We advocate approaches based on
> science, on analysis to address these problems. Making more analytic
> methods readily available is a good thing. From SAS; from R; from the
> resourceful individuals who innovate with their tools of choice,
> regardless of the source."
> [end quote]
>
>
>
> On 7 Jan, 14:50, Marc Schwartz <marc_schwa...@comcast.net> wrote:
> > on 01/07/2009 08:44 AM Kevin E. Thorpe wrote:
> >
> >
> >
> > > Zaslavsky, Alan M. wrote:
> > >> This article is accompanied by nice pictures of Robert and Ross.
> >
> > >> Data Analysts Captivated by Power of R
> > >>http://www.nytimes.com/2009/01/07/technology/business-computing/07pro.
> ..
> >
> > >> January 7, 2009 Data Analysts Captivated by R?s Power By ASHLEE VANCE
> >
> > >> SAS says it has noticed R?s rising popularity at universities,
> > >> despite educational discounts on its own software, but it dismisses
> > >> the technology as being of interest to a limited set of people
> > >> working on very hard tasks.
> >
> > >> ?I think it addresses a niche market for high-end data analysts that
> > >> want free, readily available code," said Anne H. Milley, director of
> > >> technology product marketing at SAS. She adds, ?We have customers who
> > >> build engines for aircraft. I am happy they are not using freeware
> > >> when I get on a jet.?
> >
> > > Thanks for posting. ?Does anyone else find the statement by SAS to be
> > > humourous yet arrogant and short-sighted?
> >
> > > Kevin
> >
> > It is an ignorant comment by a marketing person who has been spoon fed
> > her lines...it is also a comment being made from a very defensive and
> > insecure posture.
> >
> > Congrats to R Core and the R Community. This is yet another sign of R's
> > growth and maturity.
> >
> > Regards,
> >
> > Marc Schwartz
> >
> > ______________________________________________
> > R-h...@r-project.org mailing listhttps://
> stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guidehttp://
> www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
> > and provide commented, minimal, self-contained, reproducible code.
>
>
>
> ------------------------------
>
> Message: 15
> Date: Sat, 10 Jan 2009 13:12:11 -0000
> From: "Andrew Hicks" <andrew@quanttoolbox.com>
> Subject: [R] Arguments for Rcmd BATCH
> To: <r-help@R-project.org>
> Cc: 'Andrew Hicks' <andrew@quanttoolbox.com>
> Message-ID: <007301c97325$0e1cea50$2a56bef0$@com>
> Content-Type: text/plain; charset="us-ascii"
>
> Sorry to bother you and I hope this will be easy to solve.
>
>
>
> I am trying to run R scripts in batch, called from another programme, under
> Windows XP. I have R 2.4.1
>
>
>
> I need to be able to pass a list of numeric arguments to the script as
> well.
>
>
>
> The Rscript and its input data file are attached.
>
>
>
> I have been trying the syntax below but it doesn't work:
>
>
>
> Rcmd BATCH -no-save -no-restore -args parms=c(1,2,3) test01b.R
>
>
>
> (each of these BATCH options is preceded by 2 - characters, but my Outlook
> is munging them together here)
>
>
>
> The script then accesses (or tries to) the variables as parms[1], parms[2],
> etc.
>
>
>
> I get the respose "unable to open input file" at the command line and no
> other diagnostic output.
>
>
>
> I got this syntax from p85 of the R-Intro doc and from the website
> http://quantitative-ecology.blogspot.com/search/label/scripts. I could not
> find any other illustrations or instructions of how to use args with BATCH.
>
>
>
> Without using any parameter args it otherwise runs fine.
>
>
>
> Please can you advise what am I doing wrong and how should this command be
> structured? Do I also need to change the way the script is accessing the
> arguments?
>
>
>
> Many thanks,
>
>
>
> Andrew Hicks
>
>
> ------------------------------
>
> Message: 16
> Date: Sat, 10 Jan 2009 16:09:12 +0100
> From: Michael H?hle  <Michael.Hoehle@stat.uni-muenchen.de>
> Subject: [R] Calling C from FORTRAN and vice versa
> To: r-help@stat.math.ethz.ch
> Message-ID: <4968BA18.3050105@stat.uni-muenchen.de>
> Content-Type: text/plain; charset=ISO-8859-1
>
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> Dear R-Help,
>
> as I am not sure where to put this suggestion for improving the
> documentation in "Writing R extensions" Section 6.6 (Calling C from
> FORTRAN and vice versa) I send it to R-Help as suggested by the R Bug
> Report page.
>
> In Sect 6.6 an example is given on how to create .f and .c file in order
> to call C from Fortran and vice versa. For better readability and for
> preventing ppl calling the .c and the .f file the same base name
> (causing "multiple definitions of symbol") I suggest that the docu
> should provide file names for the two example programs, e.g.:
>
> frand.f:
>
>      subroutine testit()
>      double precision normrnd, x
>      call rndstart()
>      x = normrnd()
>      call dblepr("X was", 5, x, 1)
>      call rndend()
>      end
>
> frand-helper.c:
>
> #include <R.h>
>
> /* Fortran */
> void F77_SUB(rndstart)(void) { GetRNGstate(); }
> void F77_SUB(rndend)(void) { PutRNGstate(); }
> double F77_SUB(normrnd)(void) { return norm_rand(); }
>
> As a further suggestion, it would also be nice to provide the call for
> generating the dynamic library at this point:
> R CMD SHLIB frand.f frand-helper.c .
>
> At least this would have helped me in trying to get things to work, but
> again - its just a suggestion.
>
> Best regards,
>
> Michael
>
>
> - --
>
> Michael H?hle, Ph.D.
> Department of Statistics
> University of Munich
> Ludwigstrasse 33
> 80539 Munich
> Germany
>
> Phone:    +49 89 2180 6404
> Fax:      +49 89 2180 5040
>
> Email: hoehle@stat.uni-muenchen.de
> Homepage: http://www.stat.uni-muenchen.de/~hoehle
> PGP public key id: 0xA9589121
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.4.6 (Darwin)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>
> iD8DBQFJaLoYJenxFqlYkSERAgMeAKCtuX+SByQR4Eo1/xJj8Pg073jM8ACfa56t
> 7xnDhLzuS4q75ownnESyqek=
> =yYKr
> -----END PGP SIGNATURE-----
>
>
>
> ------------------------------
>
> Message: 17
> Date: Sat, 10 Jan 2009 19:21:16 +0200
> From: Andreas Scherer <Andreas.Scherer@Spheromics.com>
> Subject: [R] R version requires Bioconductor 2.3 version
> To: r-help@r-project.org
> Message-ID: <4968D90C.9090404@Spheromics.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Dear support,
>
> I am new to R. I installed R 2.8.1 under Windows, and upon starting it I
> get the message that it requires Bioconductor version 2.3.
> I thought this was kind of installed in parallel or so. Where can I
> upgrade it ?
>
> Best regards,
> Andreas
>
> --
> Andreas Scherer, PhD,APM
> CEO
> Spheromics
> Pajutie 3A
> 81100 Kontiolahti
> Finland
>
> Phone   +358 (0)400 138 510
> FAX     +358 (0)13 731 431
> Skype   Andreas1.Scherer
>
> www.Spheromics.com <http://www.spheromics.com/>
>
>
>
> ------------------------------
>
> Message: 18
> Date: Sat, 10 Jan 2009 08:16:21 -0800 (PST)
> From: tedzzx <zengzhenxing@gmail.com>
> Subject: [R]  JGR editor setting problem
> To: r-help@r-project.org
> Message-ID: <21389631.post@talk.nabble.com>
> Content-Type: text/plain; charset=us-ascii
>
>
> Hi all,
>
> I am using the JGR (Java GUI for R ) and I am facing some problem.
> I want to use the help agent in the editor. I try to change the setting in
> the
> preference to use the help agent in editor, but it does not work. Though I
> have
> apply and save this seting ,it will return to the default seting that only
> use
> the help agent in the console. Will you help me? Thanks
>
> R version: 2.7.2
> JGR:1.6-2
>
>
> Ted
>
> --
> View this message in context:
> http://www.nabble.com/JGR-editor-setting-problem-tp21389631p21389631.html
> Sent from the R help mailing list archive at Nabble.com.
>
>
>
> ------------------------------
>
> Message: 19
> Date: Sat, 10 Jan 2009 08:32:07 -0800 (PST)
> From: Bhargab Chattopadhyay <bhargab_1@yahoo.com>
> Subject: [R] Setting a contingency table
> To: r-help@r-project.org
> Cc: swati84patel@gmail.com
> Message-ID: <255638.44310.qm@web59413.mail.ac4.yahoo.com>
> Content-Type: text/plain
>
> Hi,
>
> I want to set a make a contingency table which will look like this.. The
> problem is that I can't  set the table like the following.
>
>
>                      col1     col2       Total
>     row1              a         b         n10
>                      rp1       rp2        100
>                      cp1       cp2       rtp1
>   ---------------------------------------------
>     row2             c         d         n20
>                      rp3       rp4       100
>                      cp3       cp4       rtp2
>   ---------------------------------------------
>     Total            n01       n02         n
>                      ctp1      ctp2       100
>                      100       100        100
>
>
> Suppose
>
> a<-67; b<-10; c<-79; d<-67;
> n<-a+b+c+d;
>   n10<-a+b;
>   n01<-a+c;
>   n20<-n-n10;
>   n02<-n-n01;
>   rp1<-(a/n10)*100;
>   rp2<-100-rp1;
>   rp3<-(c/n20)*100;
>   rp4<-100-rp3;
>   cp1<-(a/n01)*100;
>   cp2<-100-cp1;
>   cp3<-(c/n02)*100;
>   cp4<-100-cp3;
>   rtp1<-(n10/n)*100;
>   rtp2<-100-rtp1;
>   ctp1<-(n01/n)*100;
>   ctp2<-100-ctp1;
>
> After this I can't procced in a meaningful way. Can anyone help me out?
> Thanks in advance.
>
> Bhargab
>
>
>
>        [[alternative HTML version deleted]]
>
>
>
> ------------------------------
>
> Message: 20
> Date: Sat, 10 Jan 2009 09:55:01 -0800 (PST)
> From: Bhargab Chattopadhyay <bhargab_1@yahoo.com>
> Subject: [R] Applying 'lm' in each group
> To: r-help@r-project.org
> Message-ID: <318792.36066.qm@web59402.mail.ac4.yahoo.com>
> Content-Type: text/plain
>
> Hi,
>
>
>  I want to do regression in each group. I made the group the following way.
> Now I want to run regression in each of the three groups..
> Suppose ,
>
> x<-c(0.5578196,6.5411662,13.2728619,2.0217271,6.7216176,3.37220617,2.5773252,7.2600583,15.3731026,3.4140288,8.1335874,
>
> 15..6476637,4.3014084,9.1224379,18.5605355,4.7448394,11.9296663,18.5866354,12.3797674,18.7572812,2.70433816,2.88924220,
>     2.94688208,3.37154364,2.26311786,3.31002593)
>
>
> y<-c(18.63654,233.55387,152.61107,103.49646,234.55054,14.2767453,160.78742,150.35391,223.89225,168.55567,190.51031,
>     227.68339,152.42658,208.70115, 223.91982, 221.70702,
> 213.71135,168.0199, 222.69040,228.49353, 164.95750,243.18828,
>     229.94688,313.37154364,202.263786,139.31002593)
>
> n<-length(x)
> m<-3;
> r<-8;
> c<-r*(m-1);
> g1<-rep(1:(m-1),each=r);
> g<-c(g1,rep(m,n-c))
> xg<-split(x,g);
> yg<-split(y,g);
>
> Now if I write lm(yg~xg) then it won't work. Please advice how to proceed.
>
> Thanks in advance.
>
> Bhargab
>
>
>
>
>        [[alternative HTML version deleted]]
>
>
>
> ------------------------------
>
> Message: 21
> Date: Sat, 10 Jan 2009 13:16:59 -0500
> From: "Florian Lengyel" <florian.lengyel@gmail.com>
> Subject: Re: [R] R in the NY Times
> To: "Tony Breyal" <tony.breyal@googlemail.com>
> Cc: r-help@r-project.org
> Message-ID:
>        <80e171fe0901101016r4365d7d3x5ec610cacd8e74d@mail.gmail.com>
> Content-Type: text/plain; charset=WINDOWS-1252
>
> On Sat, Jan 10, 2009 at 8:11 AM, Tony Breyal <tony.breyal@googlemail.com>
> wrote:
> > "We have customers who build engines for aircraft. I am happy they are
> > not using freeware when I get on a jet."
> >
> > The lady who made this comment, Anne H. Milley, director of technology
> > product marketing at SAS, has written a response to try and clarify
> > what she meant (funilly enough, i got this link from a SAS mate of
> > mine who is now going to have a look into R for the first time):
> >
> >
> http://blogs.sas.com/sascom/index.php?/archives/434-This-post-is-rated-R.html
> >
> >
> > [quote]
> > "As for open source and my airplane quote ?
> >
> > My remark reflects a key difference between R and SAS, that of
> > support, reliability, and validation. Customers value SAS for many
> > things, including our extensive testing, documentation, 24/7 support,
> > and training. In contrast, the quality of proliferating R packages is
> > varied and uneven, especially in complex analytical modules. Mistakes
> > in these packages can lead to misleading results, even for experienced
> > users.
> >
> > The airplane comment was meant to point out this key difference. Not
> > to condemn open source. In fact, SAS values open-source software. Our
> > software runs on Linux. We use some open-source tools in development.
> > And we plan to embrace open source further in the future.
> >
> > The world has many complex problems. We advocate approaches based on
> > science, on analysis to address these problems. Making more analytic
> > methods readily available is a good thing. From SAS; from R; from the
> > resourceful individuals who innovate with their tools of choice,
> > regardless of the source."
> > [end quote]
> >
>
>
> Ms. Milley mischaracterizes her remark about the relative
> unreliability of "freeware"
> as if she had employed the term"open source."
>
> David A. Wheeler's "Why Open Source Software / Free Software (OSS/FS,
> FLOSS, or FOSS)? Look at the Numbers!" provides quantitative measures
> for evaluating open source software, including
> market share, reliability, performance, scalability, security, and
> total cost of ownership. With respect to
> the reliability of open source software, Wheeler writes, "There are a
> lot of anecdotal stories that OSS/FS is more reliable, but finally
> there is quantitative data confirming that mature OSS/FS programs are
> often more reliable [than equivalent proprietary software programs]."
> Wheeler lists among his sources the Fuzz Report
> http://pages.cs.wisc.edu/~bart/fuzz/fuzz.html .
>
>
>
> ------------------------------
>
> Message: 22
> Date: Sat, 10 Jan 2009 18:18:16 +0000 (GMT)
> From: Prof Brian Ripley <ripley@stats.ox.ac.uk>
> Subject: Re: [R] Arguments for Rcmd BATCH
> To: Andrew Hicks <andrew@quanttoolbox.com>
> Cc: r-help@r-project.org
> Message-ID: <alpine.OSX.1.00.0901101813100.86500@tystie.local>
> Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII
>
> Your R is far too old, and in particular too old for the example you
> are trying.
>
> Please do you as asked in the posting guide to do before posting, and
> upgrade.  Then you will have Rscript, as described in the current 'An
> Introduction to R' manual for this purpose (with examples).
>
> On Sat, 10 Jan 2009, Andrew Hicks wrote:
>
> > Sorry to bother you and I hope this will be easy to solve.
> >
> >
> > I am trying to run R scripts in batch, called from another programme,
> under
> > Windows XP. I have R 2.4.1
> >
> >
> >
> > I need to be able to pass a list of numeric arguments to the script as
> well.
> >
> >
> >
> > The Rscript and its input data file are attached.
> >
> >
> >
> > I have been trying the syntax below but it doesn't work:
> >
> >
> >
> > Rcmd BATCH -no-save -no-restore -args parms=c(1,2,3) test01b.R
> >
> >
> >
> > (each of these BATCH options is preceded by 2 - characters, but my
> Outlook
> > is munging them together here)
> >
> >
> >
> > The script then accesses (or tries to) the variables as parms[1],
> parms[2],
> > etc.
> >
> >
> >
> > I get the respose "unable to open input file" at the command line and no
> > other diagnostic output.
> >
> >
> >
> > I got this syntax from p85 of the R-Intro doc and from the website
> > http://quantitative-ecology.blogspot.com/search/label/scripts. I could
> not
> > find any other illustrations or instructions of how to use args with
> BATCH.
> >
> >
> >
> > Without using any parameter args it otherwise runs fine.
> >
> >
> >
> > Please can you advise what am I doing wrong and how should this command
> be
> > structured? Do I also need to change the way the script is accessing the
> > arguments?
> >
> >
> >
> > Many thanks,
> >
> >
> >
> > Andrew Hicks
> >
> >
>
> --
> Brian D. Ripley,                  ripley@stats.ox.ac.uk
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> University of Oxford,             Tel:  +44 1865 272861 (self)
> 1 South Parks Road,                     +44 1865 272866 (PA)
> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
>
>
>
> ------------------------------
>
> Message: 23
> Date: Sat, 10 Jan 2009 18:31:39 +0000
> From: "Barry Rowlingson" <b.rowlingson@lancaster.ac.uk>
> Subject: Re: [R] R in the NY Times
> To: "Tony Breyal" <tony.breyal@googlemail.com>
> Cc: r-help@r-project.org
> Message-ID:
>        <d8ad40b50901101031k2b1ffa8es2a8cd33caf804f2d@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> 2009/1/10 Tony Breyal <tony.breyal@googlemail.com>:
>
> > [SAS marketroid quote]
> > "In fact, SAS values open-source software."
>
>  But clearly not enough to open-source SAS itself. It would seem that
> SAS values _other_people's_ open source.
>
>  If SAS was open source and free, then SAS would collect on all the
> other things "Customers value SAS for" - support, testing, training,
> docs, etc etc. And there would be a lot more people using it.
>
>  Another quote: "We advocate approaches based on science" - closed
> source is closed knowledge and is nearer alchemy than science. I may
> use proprietary software for video editing or music production, but
> when it comes to science, it's got to be open.
>
> Barru
>
>
>
> ------------------------------
>
> Message: 24
> Date: Sun, 11 Jan 2009 00:22:29 +0530
> From: Ajay ohri <ohri2007@gmail.com>
> Subject: Re: [R] R in the NY Times
> To: Barry Rowlingson <b.rowlingson@lancaster.ac.uk>
> Cc: r-help@r-project.org, Tony Breyal <tony.breyal@googlemail.com>
> Message-ID:
>        <4bc14e460901101052o16d95fcen60993d203c79d57e@mail.gmail.com>
> Content-Type: text/plain
>
> more on the reasons R is bad for you
> http://www.decisionstats.com/2009/01/top-ten-rrreasons-r-is-bad-for-you/
>
>
> On Sun, Jan 11, 2009 at 12:01 AM, Barry Rowlingson <
> b.rowlingson@lancaster.ac.uk> wrote:
>
> > 2009/1/10 Tony Breyal <tony.breyal@googlemail.com>:
> >
> > > [SAS marketroid quote]
> > > "In fact, SAS values open-source software."
> >
> >  But clearly not enough to open-source SAS itself. It would seem that
> > SAS values _other_people's_ open source.
> >
> >  If SAS was open source and free, then SAS would collect on all the
> > other things "Customers value SAS for" - support, testing, training,
> > docs, etc etc. And there would be a lot more people using it.
> >
> >  Another quote: "We advocate approaches based on science" - closed
> > source is closed knowledge and is nearer alchemy than science. I may
> > use proprietary software for video editing or music production, but
> > when it comes to science, it's got to be open.
> >
> > Barru
> >
> > ______________________________________________
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
>        [[alternative HTML version deleted]]
>
>
>
> ------------------------------
>
> Message: 25
> Date: Sat, 10 Jan 2009 19:53:32 +0100
> From: Uwe Ligges <ligges@statistik.tu-dortmund.de>
> Subject: Re: [R] Print specific matrix value???
> To: Nidhi Kohli <nidhik@umd.edu>
> Cc: r-help@r-project.org
> Message-ID: <4968EEAC.4050304@statistik.tu-dortmund.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Nidhi Kohli wrote:
> > Hello All,
> >
> > I'm trying to print specific row and column for Observed_Scores matrix,
> however, when I execute the command "Observed_Scores[1,1]", I get the
> message "Error in Observed_Scores[1, 1] : incorrect number of dimensions".
> Could you please help and let me know where is the mistake? Here is my
> program:
> >
> >
> > library(ltm)
> > library(psych)
> >
> > # Settting the working directory path to C:/NCME
> >
> > path="C:/NCME"
> > setwd(path)
> >
> > #IRT Data Simulation Routine#
> >
> > n.exams = 500   #Sets number of examinees to be generated#
> > n.items = 20     #Sets number of items to be generated#
> >
> > #The following intialize empty (NA) vectors or matrices#
> > beta.values = rep(NA,n.items)
> > resp.prob = matrix(rep(NA,n.exams*n.items),nrow=n.exams,ncol=n.items)
> > Observed_Scores =
> matrix(rep(NA,n.exams*n.items),nrow=n.exams,ncol=n.items)
> >
> >
> > #filling item parameters into beta.values
> > beta.values = runif(n.items,-2,2)
> >
> > #Calculating Threshold
> > thresh.values = .5 * beta.values
> >
> >
> > #for (i in 1:10)
> > #{
> >
> > #Using the function to generate the data
> > GenData <- congeneric.sim(N=500, loads = rep(.5,20), err=NULL, short =
> FALSE)
> > Observed_Scores = GenData[1]
>
>
>
>
> Say
>
>   str(Observed_Scores)
>
> and find that Observed_Scores is not a matrix but a list!
> If you want to extract the matrix (first element of GenData), then use
>   Observed_Scores = GenData[[1]]
>
> Uwe Ligges
>
>
>
> > Regards
> > Nidhi Kohli
> >
> > ______________________________________________
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
> > and provide commented, minimal, self-contained, reproducible code.
>
>
>
> ------------------------------
>
> Message: 26
> Date: Sat, 10 Jan 2009 19:57:44 +0100
> From: Uwe Ligges <ligges@statistik.tu-dortmund.de>
> Subject: Re: [R] R version requires Bioconductor 2.3 version
> To: Andreas.Scherer@Spheromics.com
> Cc: r-help@r-project.org
> Message-ID: <4968EFA8.5050509@statistik.tu-dortmund.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Andreas Scherer wrote:
> > Dear support,
>
> This is not "support", but the R-help mailing list.
> Please do read docuemntation on how to upgrade R and contributed
> packages such as those from the Bioconductor project.
>
>
> > I am new to R. I installed R 2.8.1 under Windows, and upon starting it I
> > get the message that it requires Bioconductor version 2.3.
>
> So you installed by overwriting some older version?
> Anyway, for the Bioconductor project, see
> http://www.Bioconductor.org <http://www.bioconductor.org/>
> which has its own mailing list.
>
> You can choose the BioC Repositories from your R GUI and run, for example,
>
> update.packages(checkBuilt=TRUE)
>
> afterwards, which will upgrade your outdated CRAN and BioC packages.
>
> Uwe Ligges
>
>
>
> > I thought this was kind of installed in parallel or so. Where can I
> > upgrade it ?
> >
> > Best regards,
> > Andreas
> >
>
>
>
> ------------------------------
>
> Message: 27
> Date: Sat, 10 Jan 2009 20:03:20 +0100
> From: Uwe Ligges <ligges@statistik.tu-dortmund.de>
> Subject: Re: [R] bug in R2WinBUGS
> To: John Smith <zmring@gmail.com>
> Cc: "r-help@stat.math.ethz.ch" <r-help@stat.math.ethz.ch>
> Message-ID: <4968F0F8.5090209@statistik.tu-dortmund.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> John Smith wrote:
> > In newest version of R2WinBUGS, the default directory is changed to
> > working.directory, but never changed back once finished bugs call.
>
>
> Thank you for the report!
> I will see what happened and release a fixed version tomorrow.
>
> Best wishes,
> Uwe
>
>
>
>
> >       [[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<http://www.r-project.org/posting-guide.html>
> > and provide commented, minimal, self-contained, reproducible code.
>
>
>
> ------------------------------
>
> Message: 28
> Date: Sat, 10 Jan 2009 11:31:03 -0800
> From: Bert Gunter <gunter.berton@gene.com>
> Subject: Re: [R] R in the NY Times
> To: "'Barry Rowlingson'" <b.rowlingson@lancaster.ac.uk>,        "'Tony
>        Breyal'" <tony.breyal@googlemail.com>
> Cc: r-help@stat.math.ethz.ch
> Message-ID: <000001c97359$f9c15390$6701a8c0@gne.windows.gene.com>
> Content-Type: text/plain;       charset="us-ascii"
>
>
> I think the substance of the issue is that the more eyes on code, the fewer
> the bugs (assuming a well-designed examination and debugging process is in
> place, as is typical for large open source projects like R). By this
> (obvious?)criterion, both the remarks about the dangers of proprietary code
> and the greater unreliability of R's lesser-used specialty packages, which
> by their nature tend to be less carefully perused, are valid.
>
> Perhaps an argument is that certain code might not get written at all if it
> were not proprietary. Device drivers might be an example. But possibly
> other
> than that, it does seem like SAS needs to reconsider their marketing
> strategy and advertising claims.
>
> Anecdotal remark: I orginally moved from S-Plus to R because R provided
> **better** documentation, support, and had fewer bugs, which were more
> rapidly fixed when found. One of my smarter "investment" choices.
>
> Cheers to all,
> Bert Gunter
>
>
>
>
>
>
>
> -----Original Message-----
> From: r-help-bounces@r-project.org [mailto:r-help-bounces@r-project.org]
> On
> Behalf Of Barry Rowlingson
> Sent: Saturday, January 10, 2009 10:32 AM
> To: Tony Breyal
> Cc: r-help@r-project.org
> Subject: Re: [R] R in the NY Times
>
> 2009/1/10 Tony Breyal <tony.breyal@googlemail.com>:
>
> > [SAS marketroid quote]
> > "In fact, SAS values open-source software."
>
>  But clearly not enough to open-source SAS itself. It would seem that
> SAS values _other_people's_ open source.
>
>  If SAS was open source and free, then SAS would collect on all the
> other things "Customers value SAS for" - support, testing, training,
> docs, etc etc. And there would be a lot more people using it.
>
>  Another quote: "We advocate approaches based on science" - closed
> source is closed knowledge and is nearer alchemy than science. I may
> use proprietary software for video editing or music production, but
> when it comes to science, it's got to be open.
>
> Barru
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
> and provide commented, minimal, self-contained, reproducible code.
>
>
>
> ------------------------------
>
> Message: 29
> Date: Sat, 10 Jan 2009 14:32:19 -0500
> From: David Winsemius <dwinsemius@comcast.net>
> Subject: Re: [R] Applying 'lm' in each group
> To: Bhargab Chattopadhyay <bhargab_1@yahoo.com>
> Cc: r-help@r-project.org
> Message-ID: <796167B3-2B9D-4C9C-A354-22F4F9EC55D1@comcast.net>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
> Did you read the error message? Generally saying "doesn't work" will
> elicit undesirable responses.
>
> Now would be a good time to read the Posting Guide:
>
> http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
>
> Including:
> "Say exactly what happened, including any error messages you received. "
>
>  > lm(yg~xg)
> Error in model.frame.default(formula = yg ~ xg, drop.unused.levels =
> TRUE) :
>   invalid type (list) for variable 'yg'
>
> You need to offer lm an object that it can use. You actually shot
> yourself in the foot by turning your data into a list. It's not clear
> what you actually want, but perhaps this will move you a bit further
> along:
>
>  dfg <- data.frame(y=unlist(yg), x=unlist(xg), g=g)
>  lm(y ~ x | g, data= dfg)
>
> Which would also be the same result as the following (without the
> detour to the yg and xg lists.)
>
> lm(y ~ x + g)
>
> It's also possible that what you really wanted was:
>
> lm(y ~ x + as.factor(g)) # which estimates mean differences of grp=2
> and grp=3 from grp=1 with a common estimated slope of y on x.
>
> Or even lm(y ~ x * as.factor(g)) which gives you separate slopes and
> mean differences from those estimated for group 1 for groups 2 and 3
> and is most consistent with the phrase "separate regressions in each
> of three groups".
>
> --
> David Winsemius
> Heritage Laboratories
>
> On Jan 10, 2009, at 12:55 PM, Bhargab Chattopadhyay wrote:
>
> > Hi,
> >
> >
> >  I want to do regression in each group. I made the group the
> > following way. Now I want to run regression in each of the three
> > groups..
> > Suppose ,
> > x<-
> > c
> >
> (0.5578196,6.5411662,13.2728619,2.0217271,6.7216176,3.37220617,2.5773252,7.2600583,15.3731026,3.4140288,8.1335874
> > ,
> >
> > 15
> > ..
> >
> 6476637,4.3014084,9.1224379,18.5605355,4.7448394,11.9296663,18.5866354,12.3797674,18.7572812,2.70433816,2.88924220
> > ,
> >     2.94688208,3.37154364,2.26311786,3.31002593)
> >
> > y<-
> > c
> >
> (18.63654,233.55387,152.61107,103.49646,234.55054,14.2767453,160.78742,150.35391,223.89225,168.55567,190.51031
> > ,
> >     227.68339,152.42658,208.70115, 223.91982, 221.70702,
> > 213.71135,168.0199, 222.69040,228.49353, 164.95750,243.18828,
> >     229.94688,313.37154364,202.263786,139.31002593)
> >
> > n<-length(x)
> > m<-3;
> > r<-8;
> > c<-r*(m-1);
> > g1<-rep(1:(m-1),each=r);
> > g<-c(g1,rep(m,n-c))
> > xg<-split(x,g);
> > yg<-split(y,g);
> >
> > Now if I write lm(yg~xg) then it won't work. Please advice how to
> > proceed.
> >
> > Thanks in advance.
> >
> > Bhargab
> >
> >
> >
> >
> >       [[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<http://www.r-project.org/posting-guide.html>
> > and provide commented, minimal, self-contained, reproducible code.
>
>
>
> ------------------------------
>
> Message: 30
> Date: Sat, 10 Jan 2009 19:34:05 +0000 (UTC)
> From: Ben Bolker <bolker@ufl.edu>
> Subject: Re: [R] Applying 'lm' in each group
> To: r-help@stat.math.ethz.ch
> Message-ID: <loom.20090110T192806-24@post.gmane.org>
> Content-Type: text/plain; charset=utf-8
>
> Bhargab Chattopadhyay <bhargab_1 <at> yahoo.com> writes:
>
> >
> > Hi,
> >
> > ?I want to?do regression?in each group. I made the group the following
> way.
> Now I want to run regression
> > in each of the three groups..
> > Suppose ,
> > w
> >
> > Now if I write lm(yg~xg) then it won't work. Please advice how to
> proceed.
> >
> > Thanks in advance.
> >
>
>  The one-liner is
>
>
> mapply(function(x,y) lm(y~x,data=data.frame(x,y)),xg,yg,
>       SIMPLIFY=FALSE)
>
> Perhaps easier to understand:
>
> results <- list()
> for (i in seq(along=xg)) {
>  results[[i]] <- lm(yg[[i]]~xg[[i]])
> }
>
>  Ben Bolker
>
>
>
> ------------------------------
>
> Message: 31
> Date: Sat, 10 Jan 2009 14:37:53 -0500
> From: Chuck Cleland <ccleland@optonline.net>
> Subject: Re: [R] Applying 'lm' in each group
> To: Bhargab Chattopadhyay <bhargab_1@yahoo.com>
> Cc: r-help@r-project.org
> Message-ID: <4968F911.7060606@optonline.net>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On 1/10/2009 12:55 PM, Bhargab Chattopadhyay wrote:
> > Hi,
> >
> >
> >  I want to do regression in each group. I made the group the following
> way. Now I want to run regression in each of the three groups..
> > Suppose ,
> >
> x<-c(0.5578196,6.5411662,13.2728619,2.0217271,6.7216176,3.37220617,2.5773252,7.2600583,15.3731026,3.4140288,8.1335874,
> >
> 15..6476637,4.3014084,9.1224379,18.5605355,4.7448394,11.9296663,18.5866354,12.3797674,18.7572812,2.70433816,2.88924220,
> >     2.94688208,3.37154364,2.26311786,3.31002593)
> >
> >
> y<-c(18.63654,233.55387,152.61107,103.49646,234.55054,14.2767453,160.78742,150.35391,223.89225,168.55567,190.51031,
> >     227.68339,152.42658,208.70115, 223.91982, 221.70702,
> 213.71135,168.0199, 222.69040,228.49353, 164.95750,243.18828,
> >     229.94688,313.37154364,202.263786,139.31002593)
> >
> > n<-length(x)
> > m<-3;
> > r<-8;
> > c<-r*(m-1);
> > g1<-rep(1:(m-1),each=r);
> > g<-c(g1,rep(m,n-c))
> > xg<-split(x,g);
> > yg<-split(y,g);
> >
> > Now if I write lm(yg~xg) then it won't work. Please advice how to
> proceed.
>
> mdf <- data.frame(y,x,g)
>
> lapply(split(mdf, g), function(X){lm(y ~ x, data = X)})
> $`1`
>
> Call:
> lm(formula = y ~ x, data = X)
>
> Coefficients:
> (Intercept)            x
>      76.11        10.85
>
>
> $`2`
>
> Call:
> lm(formula = y ~ x, data = X)
>
> Coefficients:
> (Intercept)            x
>    166.693        3.580
>
>
> $`3`
>
> Call:
> lm(formula = y ~ x, data = X)
>
> Coefficients:
> (Intercept)            x
>    218.412       -0.735
>
> > Thanks in advance.
> >
> > Bhargab
> >
> >
> >
> >
> >       [[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<http://www.r-project.org/posting-guide.html>
> > and provide commented, minimal, self-contained, reproducible code.
>
> --
> Chuck Cleland, Ph.D.
> NDRI, Inc. (www.ndri.org)
> 71 West 23rd Street, 8th floor
> New York, NY 10010
> tel: (212) 845-4495 (Tu, Th)
> tel: (732) 512-0171 (M, W, F)
> fax: (917) 438-0894
>
>
>
> ------------------------------
>
> Message: 32
> Date: Sat, 10 Jan 2009 12:50:36 -0700
> From: "Kingsford Jones" <kingsfordjones@gmail.com>
> Subject: Re: [R] R in the NY Times
> To: "Tony Breyal" <tony.breyal@googlemail.com>
> Cc: r-help@r-project.org
> Message-ID:
>        <2ad0cc110901101150t191458f7j9d16eb076f42e30d@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> The reactions to the NYT article have certainly made for some
> interesting reading.
>
> Here are some of the links:
>
> http://overdetermined.net/site/content/new-york-times-article-r
>
> http://jackman.stanford.edu/blog/?p=1053
>
> http://ggorjan.blogspot.com/2009/01/new-york-times-on-r.html
>
> several posts on Andrew Gelman's blog:
> http://www.stat.columbia.edu/~gelman/blog/
>
>
> http://www.reddit.com/r/programming/comments/7nwgq/the_new_york_times_notices_the_r_programming/
>
> comments here: http://bits.blogs.nytimes.com/2009/01/08/r-you-ready-for-r/
>
>
> It's too bad that SAS has reacted to the negative reactions to their
> NYT quote with more FUD.  The quote that Tony posted is just a
> thinly-veiled jab at R (veiled by a disingenuous "we value open
> source" veneer).  Perhaps SAS is shooting themselves in the foot with
> their reactions; aren't they making it harder if they should ever
> decide the best thing to do is to embrace R and the philosophies
> behind it?  Four years ago, Marc Schwartz posted interesting comments
> realted to this:
>
> http://tolstoy.newcastle.edu.au/R/help/04/12/9497.html
>
>
> On another note, I wonder why in the various conversations there seems
> to be pervasive views that a) the FDA won't accept work done in R, and
> b) SAS is the only way to effectively handle data?
>
>
> best,
>
> Kingsford Jones
>
>
>
>
> >
> >
> >
> > On 7 Jan, 14:50, Marc Schwartz <marc_schwa...@comcast.net> wrote:
> >> on 01/07/2009 08:44 AM Kevin E. Thorpe wrote:
> >>
> >>
> >>
> >> > Zaslavsky, Alan M. wrote:
> >> >> This article is accompanied by nice pictures of Robert and Ross.
> >>
> >> >> Data Analysts Captivated by Power of R
> >> >>
> http://www.nytimes.com/2009/01/07/technology/business-computing/07pro...
> >>
> >> >> January 7, 2009 Data Analysts Captivated by R's Power By ASHLEE VANCE
> >>
> >> >> SAS says it has noticed R's rising popularity at universities,
> >> >> despite educational discounts on its own software, but it dismisses
> >> >> the technology as being of interest to a limited set of people
> >> >> working on very hard tasks.
> >>
> >> >> "I think it addresses a niche market for high-end data analysts that
> >> >> want free, readily available code," said Anne H. Milley, director of
> >> >> technology product marketing at SAS. She adds, "We have customers who
> >> >> build engines for aircraft. I am happy they are not using freeware
> >> >> when I get on a jet."
> >>
> >> > Thanks for posting.  Does anyone else find the statement by SAS to be
> >> > humourous yet arrogant and short-sighted?
> >>
> >> > Kevin
> >>
> >> It is an ignorant comment by a marketing person who has been spoon fed
> >> her lines...it is also a comment being made from a very defensive and
> >> insecure posture.
> >>
> >> Congrats to R Core and the R Community. This is yet another sign of R's
> >> growth and maturity.
> >>
> >> Regards,
> >>
> >> Marc Schwartz
> >>
> >> ______________________________________________
> >> R-h...@r-project.org mailing listhttps://
> stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guidehttp://
> www.R-project.org/posting-guide.html<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<http://www.r-project.org/posting-guide.html>
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
>
>
> ------------------------------
>
> Message: 33
> Date: Sat, 10 Jan 2009 15:00:42 -0500
> From: "oscar linares" <winsaam@gmail.com>
> Subject: [R] install.views()
> To: r-help@r-project.org
> Message-ID:
>        <7f3f57470901101200i18b5109ei99655d56de0092eb@mail.gmail.com>
> Content-Type: text/plain
>
> Dear Rxperts,
>
> Using R 2.8.1 and trying
>
> install.views("Cluster")
>
> getting error
>
> Error: could not find function "install.views"
>
>
> Please help:-(
>
>
> --
> Oscar
> Oscar A. Linares
> Molecular Medicine Unit
> Bolles Harbor
> Monroe, Michigan
>
>        [[alternative HTML version deleted]]
>
>
>
> ------------------------------
>
> Message: 34
> Date: Sat, 10 Jan 2009 13:09:07 -0700
> From: "Kingsford Jones" <kingsfordjones@gmail.com>
> Subject: Re: [R] install.views()
> To: "oscar linares" <winsaam@gmail.com>
> Cc: r-help@r-project.org
> Message-ID:
>        <2ad0cc110901101209j1448d4a3k31748f06466b96a3@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> did you install and load the 'ctv' package?
>
> install.packages('ctv')
> library('ctv')
>
> then try your code...
>
>
>
>
> Kingsford Jones
>
> On Sat, Jan 10, 2009 at 1:00 PM, oscar linares <winsaam@gmail.com> wrote:
> > Dear Rxperts,
> >
> > Using R 2.8.1 and trying
> >
> > install.views("Cluster")
> >
> > getting error
> >
> > Error: could not find function "install.views"
> >
> >
> > Please help:-(
> >
> >
> > --
> > Oscar
> > Oscar A. Linares
> > Molecular Medicine Unit
> > Bolles Harbor
> > Monroe, Michigan
> >
> >        [[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<http://www.r-project.org/posting-guide.html>
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
>
>
> ------------------------------
>
> Message: 35
> Date: Sat, 10 Jan 2009 15:27:59 -0500
> From: David Winsemius <dwinsemius@comcast.net>
> Subject: Re: [R] Setting a contingency table
> To: Bhargab Chattopadhyay <bhargab_1@yahoo.com>
> Cc: r-help@r-project.org, swati84patel@gmail.com
> Message-ID: <ADE81433-0B02-48B7-820C-283C4E03F034@comcast.net>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
>  library(gmodels)
>  ?CrossTable        # by Marc Schwartz
>
> > a<-67; b<-10; c<-79; d<-67;
>
>  > dft<- with(as.data.frame.table(as.table(c(a=77,b=10,c=79,d=67))),
> data.frame(Var1 = rep(Var1,Freq)) )
>
> There are probably more efficient ways to replicate entries. I am just
> drawing a blank right now.
>
>  > dft$Rw <- with(dft, ifelse((Var1 == "a" | Var1 == "c"), 1, 2))
>  > dft$Cl <- with(dft, ifelse((Var1 == "a" | Var1 == "b"), 1, 2))
>
>
>  > table(dft$Rw, dft$Cl)
>
>      1  2
>   1 77 10
>   2 79 67
>
>  > CrossTable(dft$Rw,dft$Cl, prop.chisq=FALSE)
>
>
>    Cell Contents
> |-------------------------|
> |                       N |
> |           N / Row Total |
> |           N / Col Total |
> |         N / Table Total |
> |-------------------------|
>
>
> Total Observations in Table:  233
>
>
>              | dft$Cl
>       dft$Rw |         1 |         2 | Row Total |
> -------------|-----------|-----------|-----------|
>            1 |        77 |        10 |        87 |
>              |     0.885 |     0.115 |     0.373 |
>              |     0.494 |     0.130 |           |
>              |     0.330 |     0.043 |           |
> -------------|-----------|-----------|-----------|
>            2 |        79 |        67 |       146 |
>              |     0.541 |     0.459 |     0.627 |
>              |     0.506 |     0.870 |           |
>              |     0.339 |     0.288 |           |
> -------------|-----------|-----------|-----------|
> Column Total |       156 |        77 |       233 |
>              |     0.670 |     0.330 |           |
> -------------|-----------|-----------|-----------|
>
>
>
> --
> David Winsemius
> On Jan 10, 2009, at 11:32 AM, Bhargab Chattopadhyay wrote:
>
> > Hi,
> >
> > I want to set a make a contingency table which will look like this..
> > The problem is that I can't  set the table like the following.
> >
> >
> >                      col1     col2       Total
> >     row1              a         b         n10
> >                      rp1       rp2        100
> >                      cp1       cp2       rtp1
> >   ---------------------------------------------
> >     row2             c         d         n20
> >                      rp3       rp4       100
> >                      cp3       cp4       rtp2
> >   ---------------------------------------------
> >     Total            n01       n02         n
> >                      ctp1      ctp2       100
> >                      100       100        100
> >
> >
> > Suppose
> >
> > a<-67; b<-10; c<-79; d<-67;
> > n<-a+b+c+d;
> >   n10<-a+b;
> >   n01<-a+c;
> >   n20<-n-n10;
> >   n02<-n-n01;
> >   rp1<-(a/n10)*100;
> >   rp2<-100-rp1;
> >   rp3<-(c/n20)*100;
> >   rp4<-100-rp3;
> >   cp1<-(a/n01)*100;
> >   cp2<-100-cp1;
> >   cp3<-(c/n02)*100;
> >   cp4<-100-cp3;
> >   rtp1<-(n10/n)*100;
> >   rtp2<-100-rtp1;
> >   ctp1<-(n01/n)*100;
> >   ctp2<-100-ctp1;
> >
> > After this I can't procced in a meaningful way. Can anyone help me
> > out?
> > Thanks in advance.
> >
> > Bhargab
> >
> >
> >
> >       [[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<http://www.r-project.org/posting-guide.html>
> > and provide commented, minimal, self-contained, reproducible code.
>
>
>
> ------------------------------
>
> Message: 36
> Date: Sat, 10 Jan 2009 15:38:45 -0500
> From: David Winsemius <dwinsemius@comcast.net>
> Subject: Re: [R] install.views()
> To: "oscar linares" <winsaam@gmail.com>
> Cc: r-help@r-project.org
> Message-ID: <59FC7A0A-A1AD-4FEE-BE23-36EBB7080272@comcast.net>
> Content-Type: text/plain; charset=US-ASCII; format=flowed
>
> Does your session info show that you have ctv installed?
>
>  > sessionInfo()
> R version 2.8.0 Patched (2008-11-14 r46932)
> i386-apple-darwin9.5.0
>
> locale:
> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] ctv_0.4-7      gmodels_2.14.1
>
> loaded via a namespace (and not attached):
> [1] MASS_7.2-45  gdata_2.4.2  gtools_2.5.0 tools_2.8.0
>
>
> --
> David Winsemius
> On Jan 10, 2009, at 3:00 PM, oscar linares wrote:
>
> > Dear Rxperts,
> >
> > Using R 2.8.1 and trying
> >
> > install.views("Cluster")
> >
> > getting error
> >
> > Error: could not find function "install.views"
> >
> >
> > Please help:-(
> >
> >
> > --
> > Oscar
> > Oscar A. Linares
> > Molecular Medicine Unit
> > Bolles Harbor
> > Monroe, Michigan
> >
> >       [[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<http://www.r-project.org/posting-guide.html>
> > and provide commented, minimal, self-contained, reproducible code.
>
>
>
> ------------------------------
>
> Message: 37
> Date: Sat, 10 Jan 2009 13:36:30 -0800 (PST)
> From: Felipe Carrillo <mazatlanmexico@yahoo.com>
> Subject: [R] Hmisc-xtable label
> To: r-help@stat.math.ethz.ch
> Message-ID: <324412.14653.qm@web56606.mail.re3.yahoo.com>
> Content-Type: text/plain; charset=us-ascii
>
> Dear all:
> Does anybody know about label conflicts between xtable and Hmisc? I found a
> couple of e-mails similar to this problem but is not clear to me how to get
> around the label problem.
> The first table(longtable below) is generated with the latex function from
> Hmisc but for some reason when I try to hyperlink to it,it takes me to the
> top of the document. The second table created with the xtable package(bottom
> of document)hyperlinks OK, but if I would create the bottom table first
> using xtable and then create the longtable using Hmisc then the hyperlink
> works OK on the longtable but not on the other one.  Thanks
> I'am using Sweave and Miktex, windows XP,R-2.8.1 to generate the document
> below:
>
>
>
> \documentclass[11pt]{article}
>
> \usepackage{amsmath}
> \usepackage{floatflt,graphicx,times}
> \usepackage[usenames,dvipsnames]{color}
> \usepackage{longtable,pdflscape}
> \usepackage{rotating}
> \usepackage{verbatim}
> \usepackage[ps2pdf,
> bookmarks=true,
> bookmarksnumbered=false,
> bookmarksopen=false,
> colorlinks=true,
> linkcolor=webblue]{hyperref}
>
> \definecolor{webgreen}{rgb}{0, 0.5, 0} % less intense green
> \definecolor{webblue}{rgb}{0, 0, 0.5} % less intense blue
> \definecolor{webred}{rgb}{0.5, 0, 0} % less intense red
>
> \usepackage[all]{hypcap}
> \pdfbookmark[1]{Contents}{table}
> \title{BROOD-YEAR 2007 WINTER CHINOOK JUVENILE PRODUCTION}
> \author{Felipe D. Carrillo}
> \date{January 5, 2009}
> \pagestyle{headings}
> \parskip 7.2pt
> \begin{document}
> \setkeys{Gin}{width=1.1\textwidth}
> \maketitle
>
> \tableofcontents
> The hyperlink of table 1 doesn't work!!!! but the hyperlink of table 2
> works OK
> \newpage
> \listoftables
> \listoffigures
> \section{Introduction}
> \label{sec:introduction}
> Winter-run Chinook salmon is one of four distinct "runs" of Chinook salmon
> (Oncorhynchus tshawytscha)....
> \section{Study Area}
> The Sacramento River is the largest river system in California, flowing
> south through 600 kilometers (km)...
> \section{Methods}
> \subsection{Sampling gear}
> Sampling was conducted along a transect using four 2.4 m diameter
> rotary-screw traps.........
> \subsection{Sampling regimes}
> In general, rotary traps sampled continuously throughout 24-hour periods
> and were serviced once daily.
> \subsection{Data collection}
> All fish captured were anesthetized, identified to species......
>
> The first table(longtable below) is generated with the latex function from
> Hmisc but for some reason when I try to hyperlink to it
> takes me to the top of the document. The second table created with the
> xtable package(bottom of document)hyperlinks OK, but
>  If I would create the bottom table first using xtable and then create the
> longtable using Hmisc then the hyperlink works OK on the
>  longtable but not on the other one. Does anybody know about conflicts
> between these two packages? I found a couple of e-mails similar to
>  this problem but is not clear to me how to get around the label problem.
> Thanks
> \newpage
> <<tab.R,echo=FALSE,results=tex>>=
> library(Hmisc)
> x <- matrix(rnorm(1000), ncol = 10)
> x.big <- data.frame(x)
> latex(x.big,"",label="tab:nice",file="",longtable=TRUE,
> dec=2,landscape=TRUE,
> caption='longtable generated with Hmisc.')
> @
>
> \section{Results}
> \subsection{Sampling effort}
> Weekly sampling effort throughout the 2006 brood-year emigration period was
> highly variable and ranged
> from 0.21 to 1.00 (0 = 0.74, N = 52 weeks; Table 1).  Weekly sampling
> effort ranged from 0.21 to 1.00 (0 = 0.73, N = 26 weeks)
> between July and December, the period of greatest juvenile winter Chinook
> emigration, and 0.21 to 1.00 (0 = 0.75, N = 26 weeks)
> during the latter half of the emigration period (Table 1).\\
> \subsection{Trap efficiency trials}
> Eight mark-recapture trials were conducted using naturally produced fall
> run fry sized Chinook
>
> <<tab.RR,echo=F,results=tex>>=
> library(xtable)
> x <- matrix(rnorm(100), ncol = 10)
> ci.table <- data.frame(x)
> ci.table <- xtable(x,label='tab:mytable',align="ccccccccccc",caption='Table
> created with xtable',digits=0)
>
> print(ci.table,tabular.environment='longtable',include.rownames=FALSE,floating=FALSE)
> @
> \end{document}
>
>
> Felipe D. Carrillo
> Supervisory Fishery Biologist
> Department of the Interior
> US Fish & Wildlife Service
> California, USA
>
>
>
> ------------------------------
>
> Message: 38
> Date: Sat, 10 Jan 2009 22:43:45 +0100
> From: Johannes Huesing <johannes@huesing.name>
> Subject: Re: [R] R in the NY Times
> To: r-help@r-project.org
> Message-ID: <20090110214345.GA13841@huesing.name>
> Content-Type: text/plain; charset=utf-8
>
> Bert Gunter <gunter.berton@gene.com> [Sat, Jan 10, 2009 at 08:31:03PM
> CET]:
> [...]
> > Perhaps an argument is that certain code might not get written at all if
> it
> > were not proprietary. Device drivers might be an example.
>
> Device drivers are not an example. Linux is ubiquitous _despite_ device
> manufacturers being secretive about their protocols and interfaces. There's
> a whole lot of people out there who seem to take pride, if not joy, in
> reengineering. At the moment I am profiting immensely from the gpsbabel
> tool, which translates readily between all different GPS-related formats,
> closed or documented.
>
> --
> Johannes H?sing               There is something fascinating about science.
>                              One gets such wholesale returns of conjecture
> mailto:johannes@huesing.name  from such a trifling investment of fact.
> http://derwisch.wikidot.com         (Mark Twain, "Life on the
> Mississippi")
>
>
>
> ------------------------------
>
> Message: 39
> Date: Sat, 10 Jan 2009 17:04:49 -0500
> From: "Gabor Grothendieck" <ggrothendieck@gmail.com>
> Subject: Re: [R] R in the NY Times
> To: "Bert Gunter" <gunter.berton@gene.com>
> Cc: r-help@stat.math.ethz.ch
> Message-ID:
>        <971536df0901101404k457ef561kd02363539510fa5e@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> There do exist device manufacturers who GPL their device drivers, e.g.
>
> http://freshmeat.net/projects/wanpipe/?branch_id=73783&release_id=290741
>
> On Sat, Jan 10, 2009 at 2:31 PM, Bert Gunter <gunter.berton@gene.com>
> wrote:
> >
> > I think the substance of the issue is that the more eyes on code, the
> fewer
> > the bugs (assuming a well-designed examination and debugging process is
> in
> > place, as is typical for large open source projects like R). By this
> > (obvious?)criterion, both the remarks about the dangers of proprietary
> code
> > and the greater unreliability of R's lesser-used specialty packages,
> which
> > by their nature tend to be less carefully perused, are valid.
> >
> > Perhaps an argument is that certain code might not get written at all if
> it
> > were not proprietary. Device drivers might be an example. But possibly
> other
> > than that, it does seem like SAS needs to reconsider their marketing
> > strategy and advertising claims.
> >
> > Anecdotal remark: I orginally moved from S-Plus to R because R provided
> > **better** documentation, support, and had fewer bugs, which were more
> > rapidly fixed when found. One of my smarter "investment" choices.
> >
> > Cheers to all,
> > Bert Gunter
> >
> >
> >
> >
> >
> >
> >
> > -----Original Message-----
> > From: r-help-bounces@r-project.org [mailto:r-help-bounces@r-project.org]
> On
> > Behalf Of Barry Rowlingson
> > Sent: Saturday, January 10, 2009 10:32 AM
> > To: Tony Breyal
> > Cc: r-help@r-project.org
> > Subject: Re: [R] R in the NY Times
> >
> > 2009/1/10 Tony Breyal <tony.breyal@googlemail.com>:
> >
> >> [SAS marketroid quote]
> >> "In fact, SAS values open-source software."
> >
> >  But clearly not enough to open-source SAS itself. It would seem that
> > SAS values _other_people's_ open source.
> >
> >  If SAS was open source and free, then SAS would collect on all the
> > other things "Customers value SAS for" - support, testing, training,
> > docs, etc etc. And there would be a lot more people using it.
> >
> >  Another quote: "We advocate approaches based on science" - closed
> > source is closed knowledge and is nearer alchemy than science. I may
> > use proprietary software for video editing or music production, but
> > when it comes to science, it's got to be open.
> >
> > Barru
> >
> > ______________________________________________
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
> > and provide commented, minimal, self-contained, reproducible code.
> >
> > ______________________________________________
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
>
>
> ------------------------------
>
> Message: 40
> Date: Sat, 10 Jan 2009 14:09:05 -0800 (PST)
> From: Felipe Carrillo <mazatlanmexico@yahoo.com>
> Subject: Re: [R] Hmisc-xtable label (Solved)
> To: r-help@stat.math.ethz.ch
> Message-ID: <158786.31640.qm@web56602.mail.re3.yahoo.com>
> Content-Type: text/plain; charset=us-ascii
>
> As soon as I sent the e-mail I found a solution to the hyperlink problem.
> I removed the squared brackets and the number 1 from the line below. I
> don't know why I had the number there in the first place.
> \pdfbookmark[1]{Contents}{table}
>
> --- On Sat, 1/10/09, Felipe Carrillo <mazatlanmexico@yahoo.com> wrote:
>
> > From: Felipe Carrillo <mazatlanmexico@yahoo.com>
> > Subject: [R] Hmisc-xtable label
> > To: r-help@stat.math.ethz.ch
> > Date: Saturday, January 10, 2009, 1:36 PM
> > Dear all:
> > Does anybody know about label conflicts between xtable and
> > Hmisc? I found a couple of e-mails similar to this problem
> > but is not clear to me how to get around the label problem.
> > The first table(longtable below) is generated with the
> > latex function from Hmisc but for some reason when I try to
> > hyperlink to it,it takes me to the top of the document. The
> > second table created with the xtable package(bottom of
> > document)hyperlinks OK, but if I would create the bottom
> > table first using xtable and then create the longtable using
> > Hmisc then the hyperlink works OK on the longtable but not
> > on the other one.  Thanks
> > I'am using Sweave and Miktex, windows XP,R-2.8.1 to
> > generate the document below:
> >
> >
> >
> > \documentclass[11pt]{article}
> >
> > \usepackage{amsmath}
> > \usepackage{floatflt,graphicx,times}
> > \usepackage[usenames,dvipsnames]{color}
> > \usepackage{longtable,pdflscape}
> > \usepackage{rotating}
> > \usepackage{verbatim}
> > \usepackage[ps2pdf,
> > bookmarks=true,
> > bookmarksnumbered=false,
> > bookmarksopen=false,
> > colorlinks=true,
> > linkcolor=webblue]{hyperref}
> >
> > \definecolor{webgreen}{rgb}{0, 0.5, 0} % less intense
> > green
> > \definecolor{webblue}{rgb}{0, 0, 0.5} % less intense
> > blue
> > \definecolor{webred}{rgb}{0.5, 0, 0} % less intense red
> >
> > \usepackage[all]{hypcap}
> > \pdfbookmark[1]{Contents}{table}
> > \title{BROOD-YEAR 2007 WINTER CHINOOK JUVENILE
> > PRODUCTION}
> > \author{Felipe D. Carrillo}
> > \date{January 5, 2009}
> > \pagestyle{headings}
> > \parskip 7.2pt
> > \begin{document}
> > \setkeys{Gin}{width=1.1\textwidth}
> > \maketitle
> >
> > \tableofcontents
> > The hyperlink of table 1 doesn't work!!!! but the
> > hyperlink of table 2 works OK
> > \newpage
> > \listoftables
> > \listoffigures
> > \section{Introduction}
> > \label{sec:introduction}
> > Winter-run Chinook salmon is one of four distinct
> > "runs" of Chinook salmon (Oncorhynchus
> > tshawytscha)....
> > \section{Study Area}
> > The Sacramento River is the largest river system in
> > California, flowing south through 600 kilometers (km)...
> > \section{Methods}
> > \subsection{Sampling gear}
> > Sampling was conducted along a transect using four 2.4 m
> > diameter rotary-screw traps.........
> > \subsection{Sampling regimes}
> > In general, rotary traps sampled continuously throughout
> > 24-hour periods and were serviced once daily.
> > \subsection{Data collection}
> > All fish captured were anesthetized, identified to
> > species......
> >
> > The first table(longtable below) is generated with the
> > latex function from Hmisc but for some reason when I try to
> > hyperlink to it
> > takes me to the top of the document. The second table
> > created with the xtable package(bottom of
> > document)hyperlinks OK, but
> >  If I would create the bottom table first using xtable and
> > then create the longtable using Hmisc then the hyperlink
> > works OK on the
> >  longtable but not on the other one. Does anybody know
> > about conflicts between these two packages? I found a couple
> > of e-mails similar to
> >  this problem but is not clear to me how to get around the
> > label problem. Thanks
> > \newpage
> > <<tab.R,echo=FALSE,results=tex>>=
> > library(Hmisc)
> > x <- matrix(rnorm(1000), ncol = 10)
> > x.big <- data.frame(x)
> > latex(x.big,"",label="tab:nice",file="",longtable=TRUE,
> > dec=2,landscape=TRUE,
> > caption='longtable generated with Hmisc.')
> > @
> >
> > \section{Results}
> > \subsection{Sampling effort}
> > Weekly sampling effort throughout the 2006 brood-year
> > emigration period was highly variable and ranged
> > from 0.21 to 1.00 (0 = 0.74, N = 52 weeks; Table 1).
> > Weekly sampling effort ranged from 0.21 to 1.00 (0 = 0.73, N
> > = 26 weeks)
> > between July and December, the period of greatest juvenile
> > winter Chinook emigration, and 0.21 to 1.00 (0 = 0.75, N =
> > 26 weeks)
> > during the latter half of the emigration period (Table
> > 1).\\
> > \subsection{Trap efficiency trials}
> > Eight mark-recapture trials were conducted using naturally
> > produced fall run fry sized Chinook
> >
> > <<tab.RR,echo=F,results=tex>>=
> > library(xtable)
> > x <- matrix(rnorm(100), ncol = 10)
> > ci.table <- data.frame(x)
> > ci.table <-
> > xtable(x,label='tab:mytable',align="ccccccccccc",caption='Table
> > created with xtable',digits=0)
> >
> print(ci.table,tabular.environment='longtable',include.rownames=FALSE,floating=FALSE)
> > @
> > \end{document}
> >
> >
> > Felipe D. Carrillo
> > Supervisory Fishery Biologist
> > Department of the Interior
> > US Fish & Wildlife Service
> > California, 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<http://www.r-project.org/posting-guide.html>
> > and provide commented, minimal, self-contained,
> > reproducible code.
>
>
>
> ------------------------------
>
> Message: 41
> Date: Sat, 10 Jan 2009 16:36:50 -0600
> From: Qing Li <shunqinature@gmail.com>
> Subject: [R] how to get the signed distance in SVM?
> To: r-help@r-project.org
> Message-ID: <49692302.7030408@math.wustl.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Dear all,
>
> In the svm() function in the package e1071, is there anyway to get the
> signed distance of a sample point to the separating hyperplane in the
> feature space? Namely, if the separating hyperplane is given by f(x) =
> h(x)^T * w - rho, is there any way to get f(x)?
>
> Also, in the returned values of the function svm(), what does "$coefs"
> mean? It is said to be the "corresponding coefficients times the
> training labels", but I don't know what is that "corresponding
> coefficients" denoting?
>
> Thank you very much!
>
> Best,
> Qing
>
>
>
> ------------------------------
>
> Message: 42
> Date: Sat, 10 Jan 2009 17:52:54 -0500
> From: Samsiddhi Bhattacharjee <samsiddhi.bhattacharjee@gmail.com>
> Subject: [R] Problem with compiling shared C/C++ library for loading
>        into R  (Linux)
> To: r-help@r-project.org
> Message-ID:
>        <2c0ef9870901101452t70264745xddc6964a758d67cf@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> I am using the .Call interface to call c++ code from R. For that, I am
> trying to create a dynamic library (mylib.so)
> using "R CMD SHLIB" by linking my own c++ code and an external c++
> library (blitz++).
>
> The makefile works fine on my Mac, produces mylib.so and I am able to
> call .Call() from R,  but on a linux
> server (I think Debian),  I got the following error:
>
> ----------
> /usr/bin/ld: /somepath/blitz/lib/libblitz.a(globals.o):
> relocation R_X86_64_32 against `a local symbol' can not be used when
> making a shared object; recompile with -fPIC
> /somepath/blitz/lib/libblitz.a: could not read symbols: Bad value
> collect2: ld returned 1 exit status
> ----------
>
> I tried recompiling the blitz++ library with the -fPIC flag, and then
> linking using -fPIC, it went thorugh without error
> producing a "mylib.so" file.  But when I tried "dyn.load(mylib.so)"
> from R, I got the error:
>
> ----------
> Error in dyn.load("mylib.so") :
>  unable to load shared library '/somepath/mylib.so':
>  /somepath/mylib.so: undefined symbol: _ZSt4cerr
> ---------
>
> I will really appreciate any help or advice on this problem.
>
> --Samsiddhi
>
>
>
> ------------------------------
>
> Message: 43
> Date: Sat, 10 Jan 2009 18:40:14 -0500
> From: Samsiddhi Bhattacharjee <samsiddhi.bhattacharjee@gmail.com>
> Subject: [R] Problem with compiling shared C/C++ library for loading
>        into R  (Linux)
> To: r-devel@r-project.org
> Cc: r-help@r-project.org
> Message-ID:
>        <2c0ef9870901101540l1adfcba8x31058f5643c69882@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear all,
>   Sorry about posting this to R-help by mistake. I just realized it
> belongs to the r-devel list.
> So I am reposting it there.
> ---------
>
> I am using the .Call interface to call c++ code from R. For that, I am
> trying to create a dynamic library (mylib.so)
> using "R CMD SHLIB" by linking my own c++ code and an external c++
> library (blitz++).
>
> The makefile works fine on my Mac, produces mylib.so and I am able to
> call .Call() from R,  but on a linux
> server (I think Debian),  I got the following error:
>
> ----------
> /usr/bin/ld: /somepath/blitz/lib/libblitz.a(globals.o):
> relocation R_X86_64_32 against `a local symbol' can not be used when
> making a shared object; recompile with -fPIC
> /somepath/blitz/lib/libblitz.a: could not read symbols: Bad value
> collect2: ld returned 1 exit status
> ----------
>
> I tried recompiling the blitz++ library with the -fPIC flag, and then
> linking using -fPIC, it went thorugh without error
> producing a "mylib.so" file.  But when I tried "dyn.load(mylib.so)"
> from R, I got the error:
>
> ----------
> Error in dyn.load("mylib.so") :
>  unable to load shared library '/somepath/mylib.so':
>  /somepath/mylib.so: undefined symbol: _ZSt4cerr
> ---------
>
> I will really appreciate any help or advice on this problem.
>
> --Samsiddhi
>
>
>
> ------------------------------
>
> Message: 44
> Date: Sat, 10 Jan 2009 17:45:59 -0600 (CST)
> From: anthony@resolution.com
> Subject: [R] Rserve/RandomForest does not work with a CSV?
> To: r-help@r-project.org
> Message-ID:
>        <be951d84bc3753e7d58525ca05177f8a.squirrel@webmail.resolution.com>
> Content-Type: text/plain;charset=iso-8859-1
>
> Hi all,
>
> We're using Rserve and RandomForest to do classification from within a
> Java program.  The total is about 4 lines of R code:
>
> library('randomForest')
> x
> y
> future
> fit<-randomForest(x,y,no.action=na.roughfix,importance=T,proximity=T)
> p<-predict(fit, future)
>
> What is very frustrating is that we have tried this two different ways
> (both work in R):
>
> 1.  Load x, y, and future from a CSV.  If I do this, Rserve throws an
> error when randomForest() is called.
>
> 2.  Load x, y, and future by using arrays, and manually building them.  If
> I do this, randomForest() works fine.
>
> Either way can be done inside of R, and they work great.
>
> Rserve is running as root, and our Java application is running inside of
> Tomcat, and is also running as root.
>
> The actual code looks something like:
>
> RConnection conn = new RConnection("127.0.0.1");
> conn.voidEval("library('randomForest')");
> conn.voidEval("train<-read.csv(\"" + (outfile.getAbsolutePath()) +
> "\",header=FALSE)");
> conn.voidEval("x<-train[1:" + totalTrainData + ",1:11]");
> conn.voidEval("y<-as.factor(train[1:" + totalTrainData + ",12])");
> conn.voidEval("future<-train[" + (totalTrainData + 1) + ":" +
> (totalTrainData + totalPredictions) + ",1:11]");
>
> conn.voidEval("fit<-randomForest(x,y,no.action=na.roughfix,importance=T,proximity=T)");
> conn.voidEval("p<-predict(fit, future)");
> conn.voidEval("write.csv(p, file=\"" + (filename.getAbsolutePath()) +
> "\")");
>
> Every time we use this, it errors on the randomForest() call.
>
> (If I run this in R, it works perfectly fine).
>
> Any ideas why I cannot call randomForest() this way, but if instead, the x
> / y / future values are built using the array command, it works fine?
>
> As a secondary question, is it faster/slower to do it this way?  Certainly
> is pretty convenient to use the CSV's.
>
> This one is driving us bonkers!
>
>
> --
> Anthony
>
>
>
> ------------------------------
>
> Message: 45
> Date: Sat, 10 Jan 2009 21:02:49 -0300
> From: "milton ruser" <milton.ruser@gmail.com>
> Subject: Re: [R] The R Inferno
> To: "Ajay ohri" <ohri2007@gmail.com>
> Cc: "r-help@stat.math.ethz.ch" <r-help@stat.math.ethz.ch>
> Message-ID:
>        <3aaf1a030901101602r4328e7c7p1ba68bae72d8ef74@mail.gmail.com>
> Content-Type: text/plain
>
> Hi Pat & R-list,
> Congratulation for this very informative and funny reading!
> I enjoyed so much.
>
> Best wishes,
>
> miltinho astronauta
> brazil
>
> On Sat, Jan 10, 2009 at 1:31 PM, Ajay ohri <ohri2007@gmail.com> wrote:
>
> > Hi ,
> > I have been trying to convince Pat to come up with a book on this.
> >
> > He can add in the chapters on *Purgatorio*
> > (Purgatory<http://en.wikipedia.org/wiki/Purgatory>),
> > and *Paradiso* (Paradise <http://en.wikipedia.org/wiki/Heaven>)
> >
> >
> > Regards,
> >
> > Ajay
> >
> > On Sat, Jan 10, 2009 at 9:33 PM, Jason Morgan <jwm-r-help@skepsi.net>
> > wrote:
> >
> > > Excellent read, Patrick. A very useful and clear guide.
> > >
> > > On 2009.01.09 16:14:49, Patrick Burns wrote:
> > > > "The R Inferno" is now on the Burns Statistics website at
> > > >
> > > > http://www.burns-stat.com/pages/Tutor/R_inferno.pdf
> > > >
> > > > Abstract: If you are using R and you think you're in hell,
> > > > this is a map for you.
> > > >
> > > > Also, I've expanded the outline concerning R on the
> > > > Burns Statistics 'Links' page. Suggestions (off-list) for
> > > > additional items are encouraged.
> > > >
> > > >
> > > > Patrick Burns
> > > > patrick@burns-stat.com
> > > > +44 (0)20 8525 0696
> > > > http://www.burns-stat.com
> > > > (home of "The R Inferno" and "A Guide for the Unwilling S User")
> > > >
> > > > ______________________________________________
> > > > R-help@r-project.org mailing list
> > > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > > PLEASE do read the posting guide
> > > http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
> > > > and provide commented, minimal, self-contained, reproducible code.
> > >
> > > --
> > > ~ Jason Morgan
> > >
> > > ______________________________________________
> > > R-help@r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide
> > > http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
> > > and provide commented, minimal, self-contained, reproducible code.
> > >
> >
> >         [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
>        [[alternative HTML version deleted]]
>
>
>
> ------------------------------
>
> Message: 46
> Date: Sun, 11 Jan 2009 01:23:04 +0000 (GMT)
> From: Prof Brian Ripley <ripley@stats.ox.ac.uk>
> Subject: Re: [R] Arguments for Rcmd BATCH
> To: Andrew Hicks <andrew@quanttoolbox.com>
> Cc: r-help@r-project.org
> Message-ID: <alpine.LFD.2.00.0901110116380.32590@auk.stats.ox.ac.uk>
> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>
> I suggested you use Rscript, please do.
>
> R CMD BATCH is the Unix-alike notation.  Rcmd BATCH is the recommended
> way on Windows, but R CMD BATCH is also accepted.
>
> There is nothing to reproduce here, so here is a simple example.
>
> tystie% cat foo.R
> args <- commandArgs(TRUE)
> print(args)
>
> tystie% Rscript foo.R parms=1:33
> [1] "parms=1:33"
>
> You can redirect the output as you wish.
>
> On Sun, 11 Jan 2009, Andrew Hicks wrote:
>
> > Dear Professor Ripley,
> >
> > Firstly, thank you very much for your advice. I was not aware my R was so
> > old. Sorry I must have missed the instruction on reading the posting
> > guidelines.
> >
> > I have updated it and it now runs again. This is a big step forward.
> However
> > it is not running properly (or I am doing something wrong).
> >
> > There are still two problems may I ask for your help with please?
> >
> > 1. When I call the script it fails with the following message in the
> output
> > file:
> >
> >> ##First read in the arguments listed at the command line
> >> args <- commandArgs(TRUE)
> > Error in commandArgs(TRUE) : unused argument(s) (TRUE)
> > Execution halted
> >
> > 2. The diagnostic details (that should be going to test01b.ROUT are now
> > going to strange places, overwriting the test01b.R file if I do not
> include
> > the < and > redirectors.
> >
> > I am now using the following syntax, from the manual:
> >
> > Rcmd BATCH --no-save --no-restore --args parms=c(1,2,3) < test01b.R >
> > test01b.ROUT
>
> That's nothing like what is documented.
>
> > Currently it is writing the output to "parms=c(1,2,3).ROUT"
> >
> > This is attached but says "fatal error cannot open file "--args"
> >
> > The file test01b.ROUT is created but empty.
> >
> > I get the same results if I start it with R CMD BATCH ...
> >
> > Is the a difference between R CMD... and Rcmd... please? The manual is
> not
> > very clear on this.
> >
> > I am sorry to impose on you but guess I am still doing something wrong. I
> > have looked through the documentation but cannot find much on this or
> many
> > examples.
> >
> > Many thanks,
> >
> > Andrew Hicks
> >
> >
> > -----Original Message-----
> > From: Prof Brian Ripley [mailto:ripley@stats.ox.ac.uk]
> > Sent: 10 January 2009 18:18
> > To: Andrew Hicks
> > Cc: r-help@r-project.org
> > Subject: Re: [R] Arguments for Rcmd BATCH
> >
> > Your R is far too old, and in particular too old for the example you
> > are trying.
> >
> > Please do you as asked in the posting guide to do before posting, and
> > upgrade.  Then you will have Rscript, as described in the current 'An
> > Introduction to R' manual for this purpose (with examples).
> >
> > On Sat, 10 Jan 2009, Andrew Hicks wrote:
> >
> >> Sorry to bother you and I hope this will be easy to solve.
> >>
> >>
> >> I am trying to run R scripts in batch, called from another programme,
> > under
> >> Windows XP. I have R 2.4.1
> >>
> >>
> >>
> >> I need to be able to pass a list of numeric arguments to the script as
> > well.
> >>
> >>
> >>
> >> The Rscript and its input data file are attached.
> >>
> >>
> >>
> >> I have been trying the syntax below but it doesn't work:
> >>
> >>
> >>
> >> Rcmd BATCH -no-save -no-restore -args parms=c(1,2,3) test01b.R
> >>
> >>
> >>
> >> (each of these BATCH options is preceded by 2 - characters, but my
> Outlook
> >> is munging them together here)
> >>
> >>
> >>
> >> The script then accesses (or tries to) the variables as parms[1],
> > parms[2],
> >> etc.
> >>
> >>
> >>
> >> I get the respose "unable to open input file" at the command line and no
> >> other diagnostic output.
> >>
> >>
> >>
> >> I got this syntax from p85 of the R-Intro doc and from the website
> >> http://quantitative-ecology.blogspot.com/search/label/scripts. I could
> not
> >> find any other illustrations or instructions of how to use args with
> > BATCH.
> >>
> >>
> >>
> >> Without using any parameter args it otherwise runs fine.
> >>
> >>
> >>
> >> Please can you advise what am I doing wrong and how should this command
> be
> >> structured? Do I also need to change the way the script is accessing the
> >> arguments?
> >>
> >>
> >>
> >> Many thanks,
> >>
> >>
> >>
> >> Andrew Hicks
> >>
> >>
> >
> > --
> > Brian D. Ripley,                  ripley@stats.ox.ac.uk
> > Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> > University of Oxford,             Tel:  +44 1865 272861 (self)
> > 1 South Parks Road,                     +44 1865 272866 (PA)
> > Oxford OX1 3TG, UK                Fax:  +44 1865 272595
> >
>
> --
> Brian D. Ripley,                  ripley@stats.ox.ac.uk
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> University of Oxford,             Tel:  +44 1865 272861 (self)
> 1 South Parks Road,                     +44 1865 272866 (PA)
> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
>
>
>
> ------------------------------
>
> Message: 47
> Date: Sun, 11 Jan 2009 02:49:56 +0100
> From: Stefan Evert <stefan.evert@uos.de>
> Subject: Re: [R] Zipf fitting using R
> To: Epithemeus <epithemeus.afterthought@googlemail.com>
> Cc: r-help@r-project.org
> Message-ID: <975BA0A9-0784-432D-999F-D6E884F1F553@uos.de>
> Content-Type: text/plain
>
> Hi there,
>
> I haven't seen any answers to your question on the list, so here's a
> rather late response.
>
> I'm not familiar with the VGAM package, but if you just want to fit
> Zipf's law (did you mean Zipf's law or an actual probability
> distribution?) to some data, why not do this directly with nls() or
> optim()?  If you pass the Zipf equation to those functions, they
> should give you estimates for the parameters you're interested in.
>
> If you're particularly interested in low-frequency data (i.e. the long
> tail of the Zipf ranking) and actual probability distributions, you
> could try our "zipfR" package available from CRAN.  The tutorial and
> background materials at
>
>        http://zipfR.R-Forge.R-project.org/<http://zipfr.r-forge.r-project.org/>
>
> should help you to get started and will also explain how to calculate
> the coefficients of Zipf's law from estimates of the model parameters.
>
>
> Best regards,
> Stefan Evert
>
> [ s...
>
> [Message clipped]

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