From: <xz44_at_drexel.edu>

Date: Wed, 02 May 2007 21:39:39 -0400

R-help_at_stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Thu 03 May 2007 - 01:58:26 GMT

Date: Wed, 02 May 2007 21:39:39 -0400

On 5/2/07, r-help-request_at_stat.math.ethz.ch <
r-help-request_at_stat.math.ethz.ch> wrote:

*>
*

> Send R-help mailing list submissions to

*> r-help_at_stat.math.ethz.ch
**>
**> To subscribe or unsubscribe via the World Wide Web, visit
**> https://stat.ethz.ch/mailman/listinfo/r-help
**> or, via email, send a message with subject or body 'help' to
**> r-help-request_at_stat.math.ethz.ch
**>
**> You can reach the person managing the list at
**> r-help-owner_at_stat.math.ethz.ch
**>
**> When replying, please edit your Subject line so it is more specific
**> than "Re: Contents of R-help digest..."
**>
**>
**> Today's Topics:
**>
**> 1. Re: impossible to open SPSS file (Frank Thomas)
**> 2. Problem with the installation of "install R" on Sun Solaris
**> (Vipin Singhal)
**> 3. Re: Concepts question: environment, frame, search path
**> (Duncan Murdoch)
**> 4. adding column to a matrix (raymond chiruka)
**> 5. Re: intersect filled.contour and polygon (Roger Bivand)
**> 6. Re: to draw a smooth arc (Jim Lemon)
**> 7. Odp: adding column to a matrix (Petr PIKAL)
**> 8. Re: Problem with the installation of "install R" on Sun
**> Solaris (Prof Brian Ripley)
**> 9. Re: Problem with the installation of "install R" on Sun
**> Solaris (Peter Dalgaard)
**> 10. Re: to draw a smooth arc (Prof Brian Ripley)
**> 11. Re: Independent contrasts from lme with interactions (Kuhn, Max)
**> 12. Re: thousand separator (was RE: weight) (John Kane)
**> 13. Re: Problem with the installation of "install R" on Sun
**> Solaris (JONATHAN BUTCHAR)
**> 14. Re: to draw a smooth arc ( (Ted Harding))
**> 15. Polar graph of time and tide (Alan E. Davis)
**> 16. Re: to draw a smooth arc (Greg Snow)
**> 17. Re: Polar graph of time and tide (Earl F. Glynn)
**> 18. creating eps files (Tak Wing Chan)
**> 19. Re: to draw a smooth arc (Greg Snow)
**> 20. Re: creating eps files (Prof Brian Ripley)
**> 21. Re: Concepts question: environment, frame, search path
**> (Prof Brian Ripley)
**> 22. logrank test (raymond chiruka)
**> 23. Re: logrank test (Peter Dalgaard)
**> 24. Re: logrank test (Marc Schwartz)
**> 25. Re: logrank test (Roland Rau)
**> 26. Re: to draw a smooth arc (Prof Brian Ripley)
**> 27. linout=TRUE in nnet package ? (sj)
**> 28. Re: logrank test (Roland Rau)
**> 29. Matrix column name (alex lam (RI))
**> 30. Simulation using parts of density function (Th?r Brigitte)
**> 31. Simulation using parts of density function (Th?r Brigitte)
**> 32. Re: Matrix column name (Marc Schwartz)
**> 33. calculating area under the ROC curve (John Christie)
**> 34. Re: to draw a smooth arc (Paulo Barata)
**> 35. sorting in barplot (Romain.Mayor_at_ville-ge.ch)
**> 36. Re: sorting in barplot (Marc Schwartz)
**> 37. Re: Simulation using parts of density function ( (Ted Harding))
**> 38. Free Webinar: Vendor Neutral Intro to Data Mining for
**> Absolute Beginners, May 23, 2007 (Lisa Solomon)
**> 39. Re: to draw a smooth arc (Paul Murrell)
**> 40. Re: Matrix column name (Prof Brian Ripley)
**> 41. to calculate sums (Pedro Sobral)
**> 42. dlda{supclust} 's output (Weiwei Shi)
**> 43. Re: to draw a smooth arc (Paulo Barata)
**> 44. Re: to draw a smooth arc (Paul Murrell)
**> 45. Percentage area of a distribution (Alan Gibson)
**> 46. Re: Percentage area of a distribution (Alan Gibson)
**> 47. optimising fitted distributions (Floris Van Ogtrop)
**> 48. ED50 from logistic model with interactions (Kate Stark)
**> 49. Re: Concepts question: environment, frame, search path
**> (graham wideman)
**> 50. the Surv function (Jennifer Dillon)
**> 51. Re: the Surv function (Christos Hatzis)
**> 52. ? R 2.5.0 alpha bug (Inman, Brant A. M.D.)
**> 53. Warnings in package dependencies and /src contains object
**> files. (Steve Su)
**> 54. Re: ED50 from logistic model with interactions (Berwin A Turlach)
**> 55. Re: Simulation using parts of density function (Th?r Brigitte)
**> 56. Re: Simulation using parts of density function (Th?r Brigitte)
**> 57. Log-likelihood function (Doxastic)
**> 58. Get the difference of values to their own median value
**> (Felix Wave)
**> 59. Re: Simulation using parts of density function (Prof Brian Ripley)
**> 60. missing package (raymond chiruka)
**> 61. Re: Log-likelihood function (Prof Brian Ripley)
**> 62. Re: ? R 2.5.0 alpha bug (Stefan Grosse)
**> 63. Re: Simulation using parts of density function ( (Ted Harding))
**> 64. hello (elyakhlifi mustapha)
**> 65. Re: Log-likelihood function (Doxastic)
**> 66. Re: missing package (John Kane)
**> 67. missing values (elyakhlifi mustapha)
**> 68. Re: missing package (Petr Klasterecky)
**> 69. length of the object is not a multiple of... [was: Re: hello]
**> (Petr Klasterecky)
**>
**>
**> ----------------------------------------------------------------------
**>
**> Message: 1
**> Date: Tue, 01 May 2007 12:15:50 +0200
**> From: Frank Thomas <news.ftr_at_free.fr>
**> Subject: Re: [R] impossible to open SPSS file
**> To: "r-help_at_stat.math.ethz.ch" <r-help_at_stat.math.ethz.ch>
**> Message-ID: <46371356.5070802@free.fr>
**> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
**>
**> David Barron gave me a good tip that I had not seen:
**> > Have a look at FAQ 2.16 in the R for Windows FAQ.
**>
**>
**> Knut Krueger wrote:
**> > My workaround for that problem is to build the data sheet in Excel and
**> > import it to SPSS and R.
**> > Or to export the SPSS sheet to CSV (or maybe if it is possible to
**> > Excel) and import it to R
**> > SPSS does not externalize the data format :-(
**> > Regards Knut
**> >
**> We don't have SPSS so unfortunately this work around is not possible.
**>
**> Thank you both,
**> Frank
**>
**>
**> --
**> ..........................................
**> Dr. Frank Thomas
**> FTR Internet Research
**> 93110 Rosny-sous-Bois
**> France
**>
**>
**>
**> ------------------------------
**>
**> Message: 2
**> Date: Tue, 1 May 2007 16:39:00 +0530
**> From: "Vipin Singhal" <Vipin.Singhal_at_symphonysv.com>
**> Subject: [R] Problem with the installation of "install R" on Sun
**> Solaris
**> To: <R-help_at_stat.math.ethz.ch>
**> Message-ID:
**> <11E5F68D25F56948B8ADC29D0773DCC787B422@BLR2K3EXCL01.symphonysv.com
**> >
**> Content-Type: text/plain; charset="us-ascii"
**>
**> An embedded and charset-unspecified text was scrubbed...
**> Name: config.txt
**> Url:
**> https://stat.ethz.ch/pipermail/r-help/attachments/20070501/bdf55878/attachment-0001.txt
**>
**> ------------------------------
**>
**> Message: 3
**> Date: Tue, 01 May 2007 07:16:26 -0400
**> From: Duncan Murdoch <murdoch_at_stats.uwo.ca>
**> Subject: Re: [R] Concepts question: environment, frame, search path
**> To: Graham Wideman <gwlist_at_grahamwideman.com>
**> Cc: r-help_at_stat.math.ethz.ch
**> Message-ID: <4637218A.4090500@stats.uwo.ca>
**> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
**>
**> On 01/05/2007 12:29 AM, Graham Wideman wrote:
**> > Folks:
**> >
**> > I'd appreciate if someone could straighten me out on a few concepts
**> which
**> > are described a bit ambiguously in the docs.
**> >
**> > 1. data.frame:
**> > ----------------
**> > Refan p84: 'A data frame is a list of variables of the same length with
**> > unique row names, given class "data.frame".'
**> >
**> > I probably don't need to point out how opaque that is!
**>
**> Which manual are you looking at? The "reference index" (refman.pdf)? It
**> doesn't usually include statements like that; they are usually found in
**> the Introduction to R (R-intro.pdf) or the R Language Definition
**> (R-lang.pdf). But since the refman is just a collection of man pages,
**> it might be in there somewhere. And since the manuals do get updated,
**> that statement may not be present in the current release. (I did a
**> quick search of the source, and couldn't spot it, but my search might
**> have failed because of line breaks, strange formatting, or looking in
**> the wrong place.)
**>
**> By the way, it's generally best to cite the section name where you found
**> a quote, because the pagination varies from system to system. Even
**> better would be to give a URL to the online HTML version at
**> http://cran.r-project.org/manuals.html.
**>
**> For future reference, if you are suggesting a change, it's best to cite
**> the line number in the source at
**> https://svn.r-project.org/R/trunk/doc/manual in the *.texi files or
**> https://svn.r-project.org/R/trunk/src/library/*/man/*.Rd for man pages,
**> and send such suggestions to the R-devel list.
**>
**> > Anyhow, key question: Some places in the docs seem pretty firm that a
**> > data.frame is basically a 2-D array with:
**> > a) named rows and
**> > b) columns whose items within a column be of uniform data type.
**> >
**> > Elsewhere, it seems like a data.frame can be a collection of arbitrary
**> > variables.
**>
**> The former interpretation is correct. Since the variables all have the
**> same length, things like df[i, j] make sense: they choose the i'th
**> entry from the j'th variable (according to the "refan" definition), or
**> the i'th row, j'th column (according to the 2-D array interpretation.
**> >
**> > 2. environment
**> > ---------------
**> > Refman p122: "Environments consist of a frame, or collection of named
**> > objects, and a pointer to an enclosing environment."
**> >
**> > Is the "or" here explaining parenthetically that a frame is a collection
**> of
**> > named objects, or is separating too alternative structures for an
**> > environment?
**>
**> The former.
**> >
**> > If the former, does this imply that a frame can contain arbitrary
**> variables?
**>
**> Yes, but a frame isn't an R object, it's a concept that appears in
**> descriptions, e.g. part of an environment, or the local variables
**> created during function evaluation, etc.
**> >
**> > And "pointer"? Is that a type of thing in R?
**>
**> No, there are no pointers in R. There are a couple of tricks to fake
**> them (e.g. environment objects aren't copied when assigned, you just get
**> a new reference to the same environment; this allows you to construct
**> something like a pointer by wrapping an object in an environment), but I
**> don't recommend using these routinely.
**>
**> >
**> > 3. R search path; attach()
**> > ----------------------------
**> > The R search path appears to hold the list of "collections of data" (my
**> > term) that can be accessed by a users' commands. Refman p27 tells that
**> > search path can hold items that are data.frame, list, environment or R
**> data
**> > file (on disk). Yet R-intro p28 describes attach() as taking a
**> "directory
**> > name" argument. What is the concept "directory" in this context?
**>
**> I haven't read the preceding pages carefully, but that looks like an
**> error. The usual argument to attach is a package name, and what gets
**> attached is an environment holding the exports from the package.
**> Packages are stored in directories in the file system, so maybe that's
**> what the author of that line had in mind.
**>
**> Duncan Murdoch
**>
**>
**>
**> ------------------------------
**>
**> Message: 4
**> Date: Tue, 1 May 2007 04:25:18 -0700 (PDT)
**> From: raymond chiruka <rtchiruka_at_yahoo.com>
**> Subject: [R] adding column to a matrix
**> To: r <r-help_at_stat.math.ethz.ch>
**> Message-ID: <142954.90575.qm@web33005.mail.mud.yahoo.com>
**> Content-Type: text/plain
**>
**> l have the following dataset and would like to calculate the actual
**> survival time by
**> if censoring time > survival time then actual survival time =survival time
**> else its= censoring time.
**> treatmentgrp strata censoringTime survivalTime censoring
**> actualsurvivaltim
**> [1,] 1 1 1.012159 1137.80922
**> 0
**> [2,] 2 2 32.971439 247.21786
**> 0
**> [3,] 2 1 85.758253 797.04949
**> 0
**> [4,] 1 1 16.999171 78.92309
**> 0
**>
**> l used matrix to genarate the data
**> thanks in advance
**>
**>
**>
**> ---------------------------------
**>
**>
**> [[alternative HTML version deleted]]
**>
**>
**>
**> ------------------------------
**>
**> Message: 5
**> Date: Tue, 1 May 2007 13:39:37 +0200 (CEST)
**> From: Roger Bivand <Roger.Bivand_at_nhh.no>
**> Subject: Re: [R] intersect filled.contour and polygon
**> To: Pedro Mardones <mardones.p_at_gmail.com>
**> Cc: R-help_at_stat.math.ethz.ch
**> Message-ID: <Pine.LNX.4.44.0705011333180.20752-100000@reclus.nhh.no>
**> Content-Type: TEXT/PLAIN; charset=US-ASCII
**>
**> On Mon, 30 Apr 2007, Pedro Mardones wrote:
**>
**> > Dear R users;
**> >
**> > Is there any way to intersect a filled contour image and a polygon? My
**> > problem is that I want to create a kriging map and the boundaries of
**> > my map are given by the coordinates of the polygon.
**> >
**> > So far I can superompose the polygon in the filled.contour image but I
**> > don't know how to get rid of the contour image outside of the polygon
**> > boundaries.
**>
**> Two possibilities seem to be present: define your polygon as a hole inside
**> the bounding box of the image, with a link between the polygon and the
**> bounding box, and fill it; or, perhaps better, only make kriging
**> predictions for the polygon. Since you haven't given a code example, it
**> isn't obvious how you are making the kriging predictions, but the choice
**> of the newdata locations ought to decide - and they do not need to be a
**> full grid, or even a regular grid at all.
**>
**> If you need to follow this up, please consider using the R-sig-geo list.
**>
**> >
**> > Any hint will be appreciated
**> > PM
**> >
**> > ______________________________________________
**> > R-help_at_stat.math.ethz.ch mailing list
**> > https://stat.ethz.ch/mailman/listinfo/r-help
**> > PLEASE do read the posting guide
**> http://www.R-project.org/posting-guide.html
**> > and provide commented, minimal, self-contained, reproducible code.
**> >
**>
**> --
**> Roger Bivand
**> Economic Geography Section, Department of Economics, Norwegian School of
**> Economics and Business Administration, Helleveien 30, N-5045 Bergen,
**> Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
**> e-mail: Roger.Bivand_at_nhh.no
**>
**>
**>
**> ------------------------------
**>
**> Message: 6
**> Date: Tue, 01 May 2007 21:50:14 +1000
**> From: Jim Lemon <jim_at_bitwrit.com.au>
**> Subject: Re: [R] to draw a smooth arc
**> To: pbarata_at_infolink.com.br
**> Cc: r-help_at_stat.math.ethz.ch
**> Message-ID: <46372976.2040103@bitwrit.com.au>
**> Content-Type: text/plain; charset=us-ascii; format=flowed
**>
**> Paulo Barata wrote:
**> > Dear R-list members,
**> >
**> > I would like to draw a smooth arc. I can draw an arc
**> > parametrically, but this produces an arc too coarse,
**> > even allowing for different increments in sequence t
**> > in the example below. Function "symbols" (graphics) does
**> > produce a smooth circle, but it cannot produce an arc.
**> >
**> > Please see the following example, drawing complete circles:
**> >
**> > plot(-5:5,-5:5,type='n')
**> > ## draws circle with function symbols (package graphics)
**> > ## - inner circle is very smooth:
**> > symbols(0,0,circles=2,add=TRUE)
**> > ## draws circle parametrically - outer circle is too coarse:
**> > pi <- 4*atan(1)
**> > t <- seq(0,2*pi,0.02)
**> > lines(4*cos(t),4*sin(t))
**> >
**> > Package "plotrix" has a function "draw.arc", but arcs produced
**> > with this function are also either too coarse or too polygonal,
**> > depending on the number of polygons used to approximate the arc.
**> >
**> > Is there a way to harness the characteristics of function
**> > "symbols" (graphics) to draw a smooth arc, not just a complete
**> > circle?
**> >
**> Hi Paulo,
**> I may be misunderstanding you, but have you tried to increase the number
**> of segments in the arc using the "n" argument?
**>
**> draw.arc(1,1,1,n=100)
**>
**> Jim
**>
**>
**>
**> ------------------------------
**>
**> Message: 7
**> Date: Tue, 1 May 2007 13:50:30 +0200
**> From: Petr PIKAL <petr.pikal_at_precheza.cz>
**> Subject: [R] Odp: adding column to a matrix
**> To: raymond chiruka <rtchiruka_at_yahoo.com>
**> Cc: r <r-help_at_stat.math.ethz.ch>
**> Message-ID:
**> <
**> OF3C24AA82.42D08B37-ONC12572CE.0040EADC-C12572CE.00410C9B_at_precheza.cz>
**>
**> Content-Type: text/plain; charset="US-ASCII"
**>
**> Hi
**>
**> see ?ifelse
**>
**> ifelse(censoring>survival, survival, censoring)
**>
**> Regards
**>
**> Petr
**> petr.pikal_at_precheza.cz
**>
**> r-help-bounces_at_stat.math.ethz.ch napsal dne 01.05.2007 13:25:18:
**>
**> > l have the following dataset and would like to calculate the actual
**> survival time by
**> > if censoring time > survival time then actual survival time =survival
**> time
**> > else its= censoring time.
**> > treatmentgrp strata censoringTime survivalTime censoring
**>
**> > actualsurvivaltim
**> > [1,] 1 1 1.012159 1137.80922 0
**> > [2,] 2 2 32.971439 247.21786 0
**> > [3,] 2 1 85.758253 797.04949 0
**> > [4,] 1 1 16.999171 78.92309 0
**> >
**> > l used matrix to genarate the data
**> > thanks in advance
**> >
**> >
**> >
**> > ---------------------------------
**> >
**> >
**> > [[alternative HTML version deleted]]
**> >
**> > ______________________________________________
**> > R-help_at_stat.math.ethz.ch mailing list
**> > https://stat.ethz.ch/mailman/listinfo/r-help
**> > PLEASE do read the posting guide
**> http://www.R-project.org/posting-guide.html
**> > and provide commented, minimal, self-contained, reproducible code.
**>
**>
**>
**> ------------------------------
**>
**> Message: 8
**> Date: Tue, 1 May 2007 12:59:37 +0100 (BST)
**> From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
**> Subject: Re: [R] Problem with the installation of "install R" on Sun
**> Solaris
**> To: Vipin Singhal <Vipin.Singhal_at_symphonysv.com>
**> Cc: R-help_at_stat.math.ethz.ch
**> Message-ID: <Pine.LNX.4.64.0705011254340.20705@gannet.stats.ox.ac.uk>
**> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
**>
**> R has a file INSTALL which asks you to read R-admin.html if you have a
**> problem. That manual explains that you need a C (preferably C99) and a
**> Fortran compiler. This extensive posting merely says that you don't have
**> a C compiler in your path. That's not something we can help you with.
**> (Lots of other tools are missing as well.)
**>
**> On Tue, 1 May 2007, Vipin Singhal wrote:
**>
**> > This file contains any messages produced by compilers while
**> > running configure, to aid debugging if configure makes a mistake.
**> >
**> > It was created by R configure 2.4.1, which was
**> > generated by GNU Autoconf 2.59. Invocation command line was
**> >
**> > $ ./configure
**>
**> [...]
**>
**> > configure:4013: error: no acceptable C compiler found in $PATH
**>
**> --
**> Brian D. Ripley, ripley_at_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: 9
**> Date: Tue, 01 May 2007 14:13:22 +0200
**> From: Peter Dalgaard <p.dalgaard_at_biostat.ku.dk>
**> Subject: Re: [R] Problem with the installation of "install R" on Sun
**> Solaris
**> To: Vipin Singhal <Vipin.Singhal_at_symphonysv.com>
**> Cc: R-help_at_stat.math.ethz.ch
**> Message-ID: <46372EE2.6000700@biostat.ku.dk>
**> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
**>
**> Vipin Singhal wrote:
**>
**> (nothing, except for an attached file)
**>
**> configure:3749: checking for gcc
**> configure:3778: result: no
**> configure:3829: checking for cc
**> configure:3858: result: no
**> configure:3871: checking for cc
**> configure:3917: result: no
**> configure:3970: checking for cl
**> configure:3999: result: no
**> configure:4013: error: no acceptable C compiler found in $PATH
**> See `config.log' for more details.
**>
**> Which part of this is it that you have trouble understanding?
**>
**>
**>
**> ------------------------------
**>
**> Message: 10
**> Date: Tue, 1 May 2007 13:41:11 +0100 (BST)
**> From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
**> Subject: Re: [R] to draw a smooth arc
**> To: Jim Lemon <jim_at_bitwrit.com.au>
**> Cc: r-help_at_stat.math.ethz.ch, pbarata_at_infolink.com.br
**> Message-ID: <Pine.LNX.4.64.0705011337500.21493@gannet.stats.ox.ac.uk>
**> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
**>
**> On Tue, 1 May 2007, Jim Lemon wrote:
**>
**> > Paulo Barata wrote:
**> >> Dear R-list members,
**> >>
**> >> I would like to draw a smooth arc. I can draw an arc
**> >> parametrically, but this produces an arc too coarse,
**> >> even allowing for different increments in sequence t
**> >> in the example below. Function "symbols" (graphics) does
**> >> produce a smooth circle, but it cannot produce an arc.
**> >>
**> >> Please see the following example, drawing complete circles:
**> >>
**> >> plot(-5:5,-5:5,type='n')
**> >> ## draws circle with function symbols (package graphics)
**> >> ## - inner circle is very smooth:
**> >> symbols(0,0,circles=2,add=TRUE)
**> >> ## draws circle parametrically - outer circle is too coarse:
**> >> pi <- 4*atan(1)
**> >> t <- seq(0,2*pi,0.02)
**> >> lines(4*cos(t),4*sin(t))
**> >>
**> >> Package "plotrix" has a function "draw.arc", but arcs produced
**> >> with this function are also either too coarse or too polygonal,
**> >> depending on the number of polygons used to approximate the arc.
**> >>
**> >> Is there a way to harness the characteristics of function
**> >> "symbols" (graphics) to draw a smooth arc, not just a complete
**> >> circle?
**> >>
**> > Hi Paulo,
**> > I may be misunderstanding you, but have you tried to increase the number
**> > of segments in the arc using the "n" argument?
**> >
**> > draw.arc(1,1,1,n=100)
**>
**> Put it another way, drawing arcs is not a primitive in the R graphics
**> system but drawing circles is. So there is no low-level way to draw an
**> arc of a circle except via line segments. (Quite a few graphics devices
**> draw circles via line segments, but not all and vector-graphics systems
**> like postscript can often do better.)
**>
**>
**> --
**> Brian D. Ripley, ripley_at_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: 11
**> Date: Tue, 1 May 2007 08:44:59 -0400
**> From: "Kuhn, Max" <Max.Kuhn_at_pfizer.com>
**> Subject: Re: [R] Independent contrasts from lme with interactions
**> To: "Ken Nussear" <knussear_at_usgs.gov>, <r-help_at_stat.math.ethz.ch>
**> Message-ID:
**> <
**> 71257D09F114DA4A8E134DEAC70F25D3083B819A_at_groamrexm03.amer.pfizer.com>
**> Content-Type: text/plain; charset="us-ascii"
**>
**> Ken,
**>
**> Take a look at the just released contrast package.
**>
**> Max
**>
**>
**> -----Original Message-----
**> From: r-help-bounces_at_stat.math.ethz.ch
**> [mailto:r-help-bounces_at_stat.math.ethz.ch] On Behalf Of Ken Nussear
**> Sent: Monday, April 30, 2007 6:12 PM
**> To: r-help_at_stat.math.ethz.ch
**> Subject: [R] Independent contrasts from lme with interactions
**>
**> Hi All,
**>
**> I've been searching the help archives but haven't found a workable
**> solution to this problem.
**>
**> I'm running an lme model with the following call:
**>
**> >lme.fnl <- lme(Max ~ S + Tr + Yr + Tr:Yr, random = ~1 |TID)
**> > anova(lme.fnl)
**> numDF denDF F-value p-value
**> (Intercept) 1 168 19255.389 <.0001
**> S 1 168 5.912 0.0161
**> Tr 2 116 15.919 <.0001
**> Yr 1 168 77.837 <.0001
**> Tr:Yr 2 168 47.584 <.0001
**>
**>
**> >summary(lme.fnl)
**> Linear mixed-effects model fit by REML
**> Data: NULL
**> AIC BIC logLik
**> 580.6991 613.5399 -281.3496
**>
**> Random effects:
**> Formula: ~1 | TID
**> (Intercept) Residual
**> StdDev: 0.3697006 0.5316062
**>
**> Fixed effects: Max ~ S + Tr + Yr + Tr:Yr
**> Value Std.Error DF t-value p-value
**> (Intercept) -13.5681 113.2623 168 -0.119793 0.9048
**> SM 0.2187 0.0957 168 2.284605 0.0236
**> TrT97 1375.5897 164.0060 116 8.387434 0.0000
**> TrT98 2890.9462 455.3497 116 6.348848 0.0000
**> Yr 0.0099 0.0567 168 0.174005 0.8621
**> TrT97:Yr -0.6883 0.0821 168 -8.384798 0.0000
**> TrT98:Yr -1.4463 0.2279 168 -6.347310 0.0000
**> Correlation:
**> (Intr) SM TrT97 TrT98 Yr TT97:Y
**> SM 0.067
**> TrT97 -0.691 -0.049
**> TrT98 -0.248 -0.001 0.171
**> Yr -1.000 -0.067 0.691 0.248
**> TrT97:Yr 0.691 0.048 -1.000 -0.171 -0.691
**> TrT98:Yr 0.248 0.001 -0.171 -1.000 -0.248 0.171
**>
**> Standardized Within-Group Residuals:
**> Min Q1 Med Q3 Max
**> -2.19017911 -0.58108001 -0.04983642 0.57323031 2.39811353
**>
**> Number of Observations: 291
**> Number of Groups: 119
**>
**>
**>
**> I'm specifically interested in differences of in the differences
**> between my treatment groups (3) and Year (Yr), and importantly in the
**> interaction. Normally I'm used to running independent contrast
**> analysis to explore these differences, but I'm not sure how to
**> extract this information using lme. Can anyone point me in the right
**> direction?
**>
**> Thanks
**>
**> Ken
**>
**>
**>
**>
**>
**>
**> [[alternative HTML version deleted]]
**>
**> ______________________________________________
**> R-help_at_stat.math.ethz.ch mailing list
**> https://stat.ethz.ch/mailman/listinfo/r-help
**> PLEASE do read the posting guide
**> http://www.R-project.org/posting-guide.html
**> and provide commented, minimal, self-contained, reproducible code.
**>
**> ----------------------------------------------------------------------
**> LEGAL NOTICE\ Unless expressly stated otherwise, this messag...{{dropped}}
**>
**>
**>
**> ------------------------------
**>
**> Message: 12
**> Date: Tue, 1 May 2007 08:56:50 -0400 (EDT)
**> From: John Kane <jrkrideau_at_yahoo.ca>
**> Subject: Re: [R] thousand separator (was RE: weight)
**> To: "Liaw, Andy" <andy_liaw_at_merck.com>, Gabor Grothendieck
**> <ggrothendieck_at_gmail.com>
**> Cc: r-help_at_stat.math.ethz.ch
**> Message-ID: <323675.20228.qm@web32808.mail.mud.yahoo.com>
**> Content-Type: text/plain; charset=iso-8859-1
**>
**>
**> --- "Liaw, Andy" <andy_liaw_at_merck.com> wrote:
**>
**> > Looks very neat, Gabor!
**> >
**> > I just cannot fathom why anyone who want to write
**> > numerics with those
**> > separators in a flat file. That's usually not for
**> > human consumption,
**> > and computers don't need those separators!
**> >
**> > Andy
**>
**> It' often a case of taking what you can get. I've
**> seem myself taking formatted numbers from report
**> intended for reading and then cutting and pasting them
**> into a text editor.
**>
**> > From: Gabor Grothendieck
**> > >
**> > > That could be accomplished using a custom class
**> > like this:
**> > >
**> > > library(methods)
**> > > setClass("num.with.junk")
**> > > setAs("character", "num.with.junk",
**> > > function(from) as.numeric(gsub(",", "", from)))
**> > >
**> > >
**> > > ### test ###
**> > >
**> > > Input <- "A B
**> > > 1,000 1
**> > > 2,000 2
**> > > 3,000 3
**> > > "
**> > > DF <- read.table(textConnection(Input), header =
**> > TRUE,
**> > > colClasses = c("num.with.junk", "numeric"))
**> > > str(DF)
**> > >
**> > >
**> > >
**> > > On 4/30/07, Liaw, Andy <andy_liaw_at_merck.com>
**> > wrote:
**> > > > Still, though, it would be nice to have the data
**> > read in
**> > > correctly in
**> > > > the first place, instead of having to do this
**> > kind of
**> > > post-processing
**> > > > afterwards...
**> > > >
**> > > > Andy
**> > > >
**> > > > From: Bert Gunter
**> > > > >
**> > > > > Nothing! My mistake! gsub -- not sub -- is
**> > what you want to
**> > > > > get 'em all.
**> > > > >
**> > > > > -- Bert
**> > > > >
**> > > > >
**> > > > > Bert Gunter
**> > > > > Genentech Nonclinical Statistics
**> > > > >
**> > > > > -----Original Message-----
**> > > > > From: r-help-bounces_at_stat.math.ethz.ch
**> > > > > [mailto:r-help-bounces_at_stat.math.ethz.ch] On
**> > Behalf Of
**> > > Marc Schwartz
**> > > > > Sent: Monday, April 30, 2007 10:18 AM
**> > > > > To: Bert Gunter
**> > > > > Cc: r-help_at_stat.math.ethz.ch
**> > > > > Subject: Re: [R] thousand separator (was RE:
**> > weight)
**> > > > >
**> > > > > Bert,
**> > > > >
**> > > > > What am I missing?
**> > > > >
**> > > > > > print(as.numeric(gsub(",", "",
**> > "1,123,456.789")), 10)
**> > > > > [1] 1123456.789
**> > > > >
**> > > > >
**> > > > > FWIW, this is using:
**> > > > >
**> > > > > R version 2.5.0 Patched (2007-04-27 r41355)
**> > > > >
**> > > > > Marc
**> > > > >
**> > > > > On Mon, 2007-04-30 at 10:13 -0700, Bert Gunter
**> > wrote:
**> > > > > > Except this doesn't work for "1,123,456.789"
**> > Marc.
**> > > > > >
**> > > > > > I hesitate to suggest it, but gregexpr()
**> > will do it, as it
**> > > > > captures the
**> > > > > > position of **every** match to ",". This
**> > could be then used
**> > > > > to process the
**> > > > > > vector via some sort of loop/apply
**> > statement.
**> > > > > >
**> > > > > > But I think there **must** be a more elegant
**> > way using
**> > > > > regular expressions
**> > > > > > alone, so I, too, await a clever reply.
**> > > > > >
**> > > > > > -- Bert
**> > > > > >
**> > > > > >
**> > > > > > Bert Gunter
**> > > > > > Genentech Nonclinical Statistics
**> > > > > >
**> > > > > > -----Original Message-----
**> > > > > > From: r-help-bounces_at_stat.math.ethz.ch
**> > > > > > [mailto:r-help-bounces_at_stat.math.ethz.ch] On
**> > Behalf Of
**> > > Marc Schwartz
**> > > > > > Sent: Monday, April 30, 2007 10:02 AM
**> > > > > > To: Liaw, Andy
**> > > > > > Cc: r-help_at_stat.math.ethz.ch
**> > > > > > Subject: Re: [R] thousand separator (was RE:
**> > weight)
**> > > > > >
**> > > > > > One possibility would be to use something
**> > like the following
**> > > > > > post-import:
**> > > > > >
**> > > > > > > WTPP
**> > > > > > [1] 1,106.8250 1,336.5138
**> > > > > >
**> > > > > > > str(WTPP)
**> > > > > > Factor w/ 2 levels
**> > "1,106.8250","1,336.5138": 1 2
**> > > > > >
**> > > > > > > as.numeric(gsub(",", "", WTPP))
**> > > > > > [1] 1106.825 1336.514
**> > > > > >
**> > > > > >
**> > > > > > Essentially strip the ',' characters from
**> > the factors and
**> > > > > then coerce
**> > > > > > the resultant character vector to numeric.
**> > > > > >
**> > > > > > HTH,
**> > > > > >
**> > > > > > Marc Schwartz
**> > > > > >
**> > > > > >
**> > > > > > On Mon, 2007-04-30 at 12:26 -0400, Liaw,
**> > Andy wrote:
**> > > > > > > I've run into this occasionally. My
**> > current solution is
**> > > > > simply to read
**> > > > > > > it into Excel, re-format the offending
**> > column(s) by
**> > > unchecking the
**> > > > > > > "thousand separator" box, and write it
**> > back out. Not
**> > > > > exactly ideal to
**> > > > > > > say the least. If anyone can provide a
**> > better solution
**> > > > > in R, I'm all
**> > > > > > > ears...
**> > > > > > >
**> > > > > > > Andy
**> > > > > > >
**> > > > > > > From: Natalie O'Toole
**> > > > > > > >
**> > > > > > > > Hi,
**> > > > > > > >
**> > > > > > > > These are the variables in my file. I
**> > think the
**> > > > > variable i'm having
**> > > > > > > > problems with is WTPP which is of the
**> > Factor type. Does
**> > > > > > > > anyone know how to
**> > > > > > > > fix this, please?
**> > > > > > > >
**> > > > > > > > Thanks,
**> > > > > > > >
**> > > > > > > > Nat
**> > > > > > > >
**> > > > > > > > data.frame': 290 obs. of 5 variables:
**> > > > > > > > $ PROV : num 48 48 48 48 48 48 48 48
**> > 48 48 ...
**> > > > > > > > $ REGION: num 4 4 4 4 4 4 4 4 4 4 ...
**> > > > > > > > $ GRADE : num 7 7 7 7 7 7 7 7 7 7 ...
**> > > > > > > > $ Y_Q10A: num 1.1 1.1 1.1 1.1 1.1 1.1
**> > 1.1 1.1 1.1 1.1 ...
**> > > > > > > > $ WTPP : Factor w/ 1884 levels
**> > > > > > > > "1,106.8250","1,336.5138",..: 1544 67
**> > > > > > > > 1568 40 221 1702 1702 1434 310 310 ...
**> > > > > > > >
**> > > > > > > >
**> > > > > > > > __________________
**> > > > > > > >
**> > > > > > > >
**> > > > > > > >
**> > > > > > > > --- Douglas Bates <bates_at_stat.wisc.edu>
**> > wrote:
**> > > > > > > >
**> > > > > > > > > On 4/28/07, John Kane
**> > <jrkrideau_at_yahoo.ca> wrote:
**> >
**> === message truncated ===
**>
**>
**>
**> ------------------------------
**>
**> Message: 13
**> Date: Tue, 01 May 2007 08:57:21 -0400
**> From: JONATHAN BUTCHAR <butchar.2_at_osu.edu>
**> Subject: Re: [R] Problem with the installation of "install R" on Sun
**> Solaris
**> To: Vipin Singhal <Vipin.Singhal_at_symphonysv.com>
**> Cc: r-help_at_stat.math.ethz.ch
**> Message-ID: <e3cf8ae3bcd0.e3bcd0e3cf8a@osu.edu>
**> Content-Type: text/plain; charset="us-ascii"
**>
**> Greetings.
**>
**> It looks like your R config can't find your C compiler. Do you have /
**> usr/ccs/bin in your path? Or, if you installed Studio 11, do you have
**> /usr/ccs/bin and /opt/SUNWspro/bin in your path?
**>
**> Hope this helps,
**>
**> Jon
**> -------------- next part --------------
**> ______________________________________________
**> R-help_at_stat.math.ethz.ch mailing list
**> https://stat.ethz.ch/mailman/listinfo/r-help
**> PLEASE do read the posting guide
**> http://www.R-project.org/posting-guide.html
**> and provide commented, minimal, self-contained, reproducible code.
**>
**> ------------------------------
**>
**> Message: 14
**> Date: Tue, 01 May 2007 14:50:48 +0100 (BST)
**> From: (Ted Harding) <ted.harding_at_nessie.mcc.ac.uk>
**> Subject: Re: [R] to draw a smooth arc
**> To: r-help_at_stat.math.ethz.ch
**> Message-ID: <XFMail.070501145048.ted.harding@nessie.mcc.ac.uk>
**> Content-Type: text/plain; charset=iso-8859-1
**>
**> This thread prompts me to ask about something I've
**> been pondering for a while, as to whether there's an
**> implementation somewhere ticked away in the R resources.
**>
**> So far, people have been responding to the original query
**> in terms of increasing the numbers of points, and joining
**> these by lines.
**>
**> However, if you're using PostScript output, you can draw
**> really smooth curves by exploiting PS's "curveto" operator.
**> This draws a cubic-curve segment in the following way:
**>
**> The two points you want to join with a curve will be denoted
**> by (X0,Y0) and (X3,Y3) in the following (for reasons which
**> will appear). The PS command is of the form
**>
**> x1 y1 x2 y2 X3 Y3 curevto
**>
**> At (X0,Y0) the tangent to the curve (as it departs from (X0,Y0)
**> is in the direction of the directed line from (X0,Y0) to (x1,y1),
**> and at (X3,Y3) (as it arrives) the tangent to the curve is
**> in the direction of the directed line from (x2,y3) to (X3,Y3).
**>
**> The location of (X0,Y0) is not part of the command, since
**> it is implicit in the PS "currentpoint" which is the starting
**> point of the curve.
**>
**> The result is (in theory, and in practice to within the resolution
**> of the output device) a perfectly smooth curve, provided the
**> consecutive cubic segments have the same tangent at each of
**> the points being joined. This can be achieved by appropriate
**> choice of the "intermediate" points -- (x1,y2), (x2,y2) above.
**>
**> So far, when I've done this myself (including when using the
**> output from R to give the points being joined), I've done the
**> computation of the "intermediate" points "by hand". This basically
**> involves deciding, at each of the points being joined, what the
**> tangent to the smooth curve shouold be.
**>
**> Of course, there is an element of arbitrariness in this, unless
**> there is an analytic representation of the curve on which the
**> points lie (e.g. you're plotting sin(x)/x every pi/8, and
**> want to join them smoothly), when all you need is the derivatives
**> at the points.
**>
**> Crudely, you might evaluate the direction at a point in terms
**> os a weighted average of the directions to its two immediate
**> neighbours (the nearer meghbour ges the greater weight); less
**> crudely, you might fit a quadratic through the point and its
**> 2 neighbours and use the gradient at the middle point; and so on.
**>
**> Once you've decided on the tangent at each point, it's then
**> straightforward to compute suitable "intermediate points"
**> to serve as (x1,y2) and (x2,y2).
**>
**> (One application where this sort of approach is needed is in
**> joining computed points on iso-contours, where the individual
**> points have been determined by interpolation of spot-measurements
**> at nearby measuring stations).
**>
**> Anyway. The Question: is there a general function for the
**> above kind of smooth curve-drawing?
**>
**> With thanks,
**> Ted.
**>
**> --------------------------------------------------------------------
**> E-Mail: (Ted Harding) <ted.harding_at_nessie.mcc.ac.uk>
**> Fax-to-email: +44 (0)870 094 0861
**> Date: 01-May-07 Time: 14:50:38
**> ------------------------------ XFMail ------------------------------
**>
**>
**>
**> ------------------------------
**>
**> Message: 15
**> Date: Wed, 2 May 2007 00:04:50 +1000
**> From: "Alan E. Davis" <lngndvs_at_gmail.com>
**> Subject: [R] Polar graph of time and tide
**> To: r-help_at_stat.math.ethz.ch
**> Message-ID:
**> <7bef1f890705010704n491a34c6w91bd31ebe26bbdff@mail.gmail.com>
**> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
**>
**> I have been trying to visualize times of lowest tides, month by month.
**> I have tide predictions with times either in unix time or a text
**> format, and heights in feet or meters. I had been able to derive the
**> clock times of each prediction. I would now like to graph this data
**> with points showing heights as "r" and times as "theta", from 0000 to
**> 2355. There is a seasonal component: I am interested in displaying
**> times of lowest tides in particular.
**>
**> I am sure this is so simple as to burden those on the list; I however
**> have spent two evenings trying to figure out how to use polar.plot,
**> and I'm not sure that's the best way to do this. May I request some
**> advice? The docs with polar.plot are not complete, I fear.
**>
**> Thank you, begging for your indulgence,
**>
**> Alan
**>
**> --
**> Alan Davis, Kagman High School, Saipan lngndvs_at_gmail.com
**>
**>
**> Every great advance in natural knowledge has involved the absolute
**> rejection of authority. ----- Thomas H. Huxley
**>
**>
**>
**> ------------------------------
**>
**> Message: 16
**> Date: Tue, 1 May 2007 08:53:54 -0600
**> From: "Greg Snow" <Greg.Snow_at_intermountainmail.org>
**> Subject: Re: [R] to draw a smooth arc
**> To: ted.harding_at_manchester.ac.uk, r-help_at_stat.math.ethz.ch
**> Message-ID:
**> <07E228A5BE53C24CAD490193A7381BBB9727A3@LP-EXCHVS07.CO.IHC.COM>
**> Content-Type: text/plain; charset=us-ascii
**>
**> There is the grid.xspline function in the grid package that allows for
**> things like this (the control points, though more general than what you
**> state). I don't know if it uses the postscript curveto, or approximates
**> using line segments.
**>
**> You can also use the xfig device, then use xfig, winfig, or jfig to
**> explicitly convert any polylines to xslpines, adjust any parameters of
**> the spline that you want, then export to other formats.
**>
**> Hope this helps,
**>
**> --
**> Gregory (Greg) L. Snow Ph.D.
**> Statistical Data Center
**> Intermountain Healthcare
**> greg.snow_at_intermountainmail.org
**> (801) 408-8111
**>
**>
**>
**> > -----Original Message-----
**> > From: r-help-bounces_at_stat.math.ethz.ch
**> > [mailto:r-help-bounces_at_stat.math.ethz.ch] On Behalf Of
**> > ted.harding_at_nessie.mcc.ac.uk
**> > Sent: Tuesday, May 01, 2007 7:51 AM
**> > To: r-help_at_stat.math.ethz.ch
**> > Subject: Re: [R] to draw a smooth arc
**> >
**> > This thread prompts me to ask about something I've been
**> > pondering for a while, as to whether there's an
**> > implementation somewhere ticked away in the R resources.
**> >
**> > So far, people have been responding to the original query in
**> > terms of increasing the numbers of points, and joining these by lines.
**> >
**> > However, if you're using PostScript output, you can draw
**> > really smooth curves by exploiting PS's "curveto" operator.
**> > This draws a cubic-curve segment in the following way:
**> >
**> > The two points you want to join with a curve will be denoted
**> > by (X0,Y0) and (X3,Y3) in the following (for reasons which
**> > will appear). The PS command is of the form
**> >
**> > x1 y1 x2 y2 X3 Y3 curevto
**> >
**> > At (X0,Y0) the tangent to the curve (as it departs from
**> > (X0,Y0) is in the direction of the directed line from (X0,Y0)
**> > to (x1,y1), and at (X3,Y3) (as it arrives) the tangent to the
**> > curve is in the direction of the directed line from (x2,y3)
**> > to (X3,Y3).
**> >
**> > The location of (X0,Y0) is not part of the command, since it
**> > is implicit in the PS "currentpoint" which is the starting
**> > point of the curve.
**> >
**> > The result is (in theory, and in practice to within the
**> > resolution of the output device) a perfectly smooth curve,
**> > provided the consecutive cubic segments have the same tangent
**> > at each of the points being joined. This can be achieved by
**> > appropriate choice of the "intermediate" points -- (x1,y2),
**> > (x2,y2) above.
**> >
**> > So far, when I've done this myself (including when using the
**> > output from R to give the points being joined), I've done the
**> > computation of the "intermediate" points "by hand". This
**> > basically involves deciding, at each of the points being
**> > joined, what the tangent to the smooth curve shouold be.
**> >
**> > Of course, there is an element of arbitrariness in this,
**> > unless there is an analytic representation of the curve on
**> > which the points lie (e.g. you're plotting sin(x)/x every
**> > pi/8, and want to join them smoothly), when all you need is
**> > the derivatives at the points.
**> >
**> > Crudely, you might evaluate the direction at a point in terms
**> > os a weighted average of the directions to its two immediate
**> > neighbours (the nearer meghbour ges the greater weight); less
**> > crudely, you might fit a quadratic through the point and its
**> > 2 neighbours and use the gradient at the middle point; and so on.
**> >
**> > Once you've decided on the tangent at each point, it's then
**> > straightforward to compute suitable "intermediate points"
**> > to serve as (x1,y2) and (x2,y2).
**> >
**> > (One application where this sort of approach is needed is in
**> > joining computed points on iso-contours, where the individual
**> > points have been determined by interpolation of
**> > spot-measurements at nearby measuring stations).
**> >
**> > Anyway. The Question: is there a general function for the
**> > above kind of smooth curve-drawing?
**> >
**> > With thanks,
**> > Ted.
**> >
**> > --------------------------------------------------------------------
**> > E-Mail: (Ted Harding) <ted.harding_at_nessie.mcc.ac.uk>
**> > Fax-to-email: +44 (0)870 094 0861
**> > Date: 01-May-07 Time: 14:50:38
**> > ------------------------------ XFMail ------------------------------
**> >
**> > ______________________________________________
**> > R-help_at_stat.math.ethz.ch mailing list
**> > https://stat.ethz.ch/mailman/listinfo/r-help
**> > PLEASE do read the posting guide
**> > http://www.R-project.org/posting-guide.html
**> > and provide commented, minimal, self-contained, reproducible code.
**> >
**>
**>
**>
**> ------------------------------
**>
**> Message: 17
**> Date: Tue, 1 May 2007 10:02:38 -0500
**> From: "Earl F. Glynn" <efg_at_stowers-institute.org>
**> Subject: Re: [R] Polar graph of time and tide
**> To: r-help_at_stat.math.ethz.ch
**> Message-ID: <f17kqh$j90$1@sea.gmane.org>
**>
**> "Alan E. Davis" <lngndvs_at_gmail.com> wrote in message
**> news:7bef1f890705010704n491a34c6w91bd31ebe26bbdff_at_mail.gmail.com...
**> >I have been trying to visualize times of lowest tides, month by month.
**> > I have tide predictions with times either in unix time or a text
**> > format, and heights in feet or meters. I had been able to derive the
**> > clock times of each prediction. I would now like to graph this data
**> > with points showing heights as "r" and times as "theta", from 0000 to
**> > 2355. There is a seasonal component: I am interested in displaying
**> > times of lowest tides in particular.
**>
**> Does this get you started?
**>
**>
**> library(plotrix)
**>
**> theta <- seq(0, 23.5, by=0.5)
**> r <- runif(length(theta), 5, 10)
**>
**> clock24.plot(r, theta, main="Polar Plot")
**>
**> or
**>
**> clock24.plot(r, theta, main="Polar Plot", rp.type="p")
**>
**>
**> efg
**> Stowers Institute for Medical Research
**>
**>
**>
**> ------------------------------
**>
**> Message: 18
**> Date: Tue, 1 May 2007 16:06:01 +0100
**> From: Tak Wing Chan <tw.chan_at_sociology.ox.ac.uk>
**> Subject: [R] creating eps files
**> To: r-help_at_stat.math.ethz.ch
**> Message-ID: <6945da33a4ea4243a1dbe43085b75ac9@sociology.ox.ac.uk>
**> Content-Type: text/plain; charset=US-ASCII; format=flowed
**>
**> Hello,
**>
**> For a long time, I have been creating eps files from R using the
**> following command:
**>
**> dev.copy2eps(file="my.eps")
**>
**> This has worked very well. But recently, the compositor of a journal is
**> complaining that
**>
**> "The eps files would be useable except that they have not converted the
**> type to outlines"
**>
**> Sorry for being vague, but I have no idea what this compositor is
**> talking about. Do people have similar experience? And is there an
**> option in the dev.copy2eps() that I could use to fix this problem?
**>
**> Many thanks for any suggestion.
**>
**> Best, Wing
**>
**>
**>
**>
**> dept addr: Department of Sociology, University of Oxford, Manor Road,
**> Oxford OX1 3UQ, UK
**> college addr: New College, Holywell Street, Oxford OX1 3BN, UK
**> dept tel: +44 (1865) 286176; college tel: +44 (1865) 279593
**> http://users.ox.ac.uk/~sfos0006
**>
**>
**>
**> ------------------------------
**>
**> Message: 19
**> Date: Tue, 1 May 2007 09:26:09 -0600
**> From: "Greg Snow" <Greg.Snow_at_intermountainmail.org>
**> Subject: Re: [R] to draw a smooth arc
**> To: pbarata_at_infolink.com.br, r-help_at_stat.math.ethz.ch
**> Message-ID:
**> <07E228A5BE53C24CAD490193A7381BBB9727C1@LP-EXCHVS07.CO.IHC.COM>
**> Content-Type: text/plain; charset=us-ascii
**>
**> Here is an approach that clips the circle you like from symbols down to
**> an arc (this will work as long as the arc is less than half a circle,
**> for arcs greater than half a circle, you could draw the whole circle
**> then use this to draw an arc of the bacground color over the section you
**> don't want):
**>
**> library(TeachingDemos)
**> plot(-5:5, -5:5, type='n')
**> clipplot( symbols(0,0,circles=2, add=TRUE), c(0,5), c(0,5) )
**>
**> Hope this helps,
**>
**> --
**> Gregory (Greg) L. Snow Ph.D.
**> Statistical Data Center
**> Intermountain Healthcare
**> greg.snow_at_intermountainmail.org
**> (801) 408-8111
**>
**>
**>
**> > -----Original Message-----
**> > From: r-help-bounces_at_stat.math.ethz.ch
**> > [mailto:r-help-bounces_at_stat.math.ethz.ch] On Behalf Of Paulo Barata
**> > Sent: Monday, April 30, 2007 8:17 PM
**> > To: r-help_at_stat.math.ethz.ch
**> > Subject: [R] to draw a smooth arc
**> >
**> >
**> > Dear R-list members,
**> >
**> > I would like to draw a smooth arc. I can draw an arc
**> > parametrically, but this produces an arc too coarse, even
**> > allowing for different increments in sequence t in the
**> > example below. Function "symbols" (graphics) does produce a
**> > smooth circle, but it cannot produce an arc.
**> >
**> > Please see the following example, drawing complete circles:
**> >
**> > plot(-5:5,-5:5,type='n')
**> > ## draws circle with function symbols (package graphics) ## -
**> > inner circle is very smooth:
**> > symbols(0,0,circles=2,add=TRUE)
**> > ## draws circle parametrically - outer circle is too coarse:
**> > pi <- 4*atan(1)
**> > t <- seq(0,2*pi,0.02)
**> > lines(4*cos(t),4*sin(t))
**> >
**> > Package "plotrix" has a function "draw.arc", but arcs
**> > produced with this function are also either too coarse or too
**> > polygonal, depending on the number of polygons used to
**> > approximate the arc.
**> >
**> > Is there a way to harness the characteristics of function
**> > "symbols" (graphics) to draw a smooth arc, not just a complete circle?
**> >
**> > I am using R 2.5.0, running under Windows XP.
**> >
**> > Thank you very much.
**> >
**> > Paulo Barata
**> >
**> > -----------------------------------------------------------------
**> > Paulo Barata
**> > Fundacao Oswaldo Cruz (Oswaldo Cruz Foundation) Rua Leopoldo
**> > Bulhoes 1480 - 8A 21041-210 Rio de Janeiro - RJ Brazil
**> > E-mail: pbarata_at_infolink.com.br
**> >
**> > ______________________________________________
**> > R-help_at_stat.math.ethz.ch mailing list
**> > https://stat.ethz.ch/mailman/listinfo/r-help
**> > PLEASE do read the posting guide
**> > http://www.R-project.org/posting-guide.html
**> > and provide commented, minimal, self-contained, reproducible code.
**> >
**>
**>
**>
**> ------------------------------
**>
**> Message: 20
**> Date: Tue, 1 May 2007 16:27:32 +0100 (BST)
**> From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
**> Subject: Re: [R] creating eps files
**> To: Tak Wing Chan <tw.chan_at_sociology.ox.ac.uk>
**> Cc: r-help_at_stat.math.ethz.ch
**> Message-ID: <Pine.LNX.4.64.0705011621480.27865@gannet.stats.ox.ac.uk>
**> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
**>
**> On Tue, 1 May 2007, Tak Wing Chan wrote:
**>
**> > Hello,
**> >
**> > For a long time, I have been creating eps files from R using the
**> > following command:
**> >
**> > dev.copy2eps(file="my.eps")
**> >
**> > This has worked very well. But recently, the compositor of a journal is
**> > complaining that
**> >
**> > "The eps files would be useable except that they have not converted the
**> > type to outlines"
**> >
**> > Sorry for being vague, but I have no idea what this compositor is
**> > talking about. Do people have similar experience? And is there an
**> > option in the dev.copy2eps() that I could use to fix this problem?
**>
**> I suspect he means that he wants the fonts embedded, which is not what eps
**> requires. See the article in R-News about doing that:
**>
**> http://cran.r-project.org/doc/Rnews/Rnews_2006-2.pdf
**>
**>
**> --
**> Brian D. Ripley, ripley_at_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: 21
**> Date: Tue, 1 May 2007 16:34:23 +0100 (BST)
**> From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
**> Subject: Re: [R] Concepts question: environment, frame, search path
**> To: Duncan Murdoch <murdoch_at_stats.uwo.ca>
**> Cc: r-help_at_stat.math.ethz.ch, Graham Wideman
**> <gwlist_at_grahamwideman.com>
**> Message-ID: <Pine.LNX.4.64.0705011627590.27865@gannet.stats.ox.ac.uk>
**> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
**>
**> On Tue, 1 May 2007, Duncan Murdoch wrote:
**>
**> > On 01/05/2007 12:29 AM, Graham Wideman wrote:
**> >> Folks:
**> >>
**> >> I'd appreciate if someone could straighten me out on a few concepts
**> which
**> >> are described a bit ambiguously in the docs.
**> >>
**> >> 1. data.frame:
**> >> ----------------
**> >> Refan p84: 'A data frame is a list of variables of the same length with
**> >> unique row names, given class "data.frame".'
**> >>
**> >> I probably don't need to point out how opaque that is!
**> >
**> > Which manual are you looking at? The "reference index" (refman.pdf)? It
**> > doesn't usually include statements like that; they are usually found in
**> > the Introduction to R (R-intro.pdf) or the R Language Definition
**> > (R-lang.pdf). But since the refman is just a collection of man pages,
**> > it might be in there somewhere. And since the manuals do get updated,
**> > that statement may not be present in the current release. (I did a
**> > quick search of the source, and couldn't spot it, but my search might
**> > have failed because of line breaks, strange formatting, or looking in
**> > the wrong place.)
**> >
**> > By the way, it's generally best to cite the section name where you found
**> > a quote, because the pagination varies from system to system. Even
**> > better would be to give a URL to the online HTML version at
**> > http://cran.r-project.org/manuals.html.
**> >
**> > For future reference, if you are suggesting a change, it's best to cite
**> > the line number in the source at
**> > https://svn.r-project.org/R/trunk/doc/manual in the *.texi files or
**> > https://svn.r-project.org/R/trunk/src/library/*/man/*.Rd for man pages,
**> > and send such suggestions to the R-devel list.
**> >
**> >> Anyhow, key question: Some places in the docs seem pretty firm that a
**> >> data.frame is basically a 2-D array with:
**> >> a) named rows and
**> >> b) columns whose items within a column be of uniform data type.
**> >>
**> >> Elsewhere, it seems like a data.frame can be a collection of arbitrary
**> >> variables.
**> >
**> > The former interpretation is correct. Since the variables all have the
**> > same length, things like df[i, j] make sense: they choose the i'th
**> > entry from the j'th variable (according to the "refan" definition), or
**> > the i'th row, j'th column (according to the 2-D array interpretation.
**> >>
**> >> 2. environment
**> >> ---------------
**> >> Refman p122: "Environments consist of a frame, or collection of named
**> >> objects, and a pointer to an enclosing environment."
**> >>
**> >> Is the "or" here explaining parenthetically that a frame is a
**> collection of
**> >> named objects, or is separating too alternative structures for an
**> >> environment?
**> >
**> > The former.
**> >>
**> >> If the former, does this imply that a frame can contain arbitrary
**> variables?
**> >
**> > Yes, but a frame isn't an R object, it's a concept that appears in
**> > descriptions, e.g. part of an environment, or the local variables
**> > created during function evaluation, etc.
**> >>
**> >> And "pointer"? Is that a type of thing in R?
**> >
**> > No, there are no pointers in R. There are a couple of tricks to fake
**> > them (e.g. environment objects aren't copied when assigned, you just get
**> > a new reference to the same environment; this allows you to construct
**> > something like a pointer by wrapping an object in an environment), but I
**> > don't recommend using these routinely.
**>
**> Nevertheless, the statement is true. R is implemented using pointers.
**>
**>
**> >> 3. R search path; attach()
**> >> ----------------------------
**> >> The R search path appears to hold the list of "collections of data" (my
**> >> term) that can be accessed by a users' commands. Refman p27 tells that
**> >> search path can hold items that are data.frame, list, environment or R
**> data
**> >> file (on disk). Yet R-intro p28 describes attach() as taking a
**> "directory
**> >> name" argument. What is the concept "directory" in this context?
**> >
**> > I haven't read the preceding pages carefully, but that looks like an
**> > error. The usual argument to attach is a package name, and what gets
**> > attached is an environment holding the exports from the package.
**> > Packages are stored in directories in the file system, so maybe that's
**> > what the author of that line had in mind.
**>
**> For the record, it is old S terminology: that document was converted from
**> notes for S. What S(-PLUS) now calls 'chapters' it used to call
**> directories.
**>
**> Also for the record, these documents do not have page numbers: their
**> layout depends on the version of R, paper size and the tools used to
**> prepare them.
**>
**> --
**> Brian D. Ripley, ripley_at_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: 22
**> Date: Tue, 1 May 2007 08:34:57 -0700 (PDT)
**> From: raymond chiruka <rtchiruka_at_yahoo.com>
**> Subject: [R] logrank test
**> To: r <r-help_at_stat.math.ethz.ch>
**> Message-ID: <94689.23988.qm@web33006.mail.mud.yahoo.com>
**> Content-Type: text/plain
**>
**> how do l programme the logrank test. l am trying to compare 2 survival
**> curves
**>
**>
**>
**> ---------------------------------
**>
**>
**> [[alternative HTML version deleted]]
**>
**>
**>
**> ------------------------------
**>
**> Message: 23
**> Date: Tue, 01 May 2007 18:01:38 +0200
**> From: Peter Dalgaard <p.dalgaard_at_biostat.ku.dk>
**> Subject: Re: [R] logrank test
**> To: raymond chiruka <rtchiruka_at_yahoo.com>
**> Cc: r <r-help_at_stat.math.ethz.ch>
**> Message-ID: <46376462.70607@biostat.ku.dk>
**> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
**>
**> raymond chiruka wrote:
**> > how do l programme the logrank test. l am trying to compare 2 survival
**> curves
**> >
**> >
**> >
**> library(survival)
**> ?survdiff
**>
**>
**>
**> ------------------------------
**>
**> Message: 24
**> Date: Tue, 01 May 2007 11:01:47 -0500
**> From: Marc Schwartz <marc_schwartz_at_comcast.net>
**> Subject: Re: [R] logrank test
**> To: raymond chiruka <rtchiruka_at_yahoo.com>
**> Cc: r <r-help_at_stat.math.ethz.ch>
**> Message-ID: <1178035307.5009.1.camel@localhost.localdomain>
**> Content-Type: text/plain
**>
**> On Tue, 2007-05-01 at 08:34 -0700, raymond chiruka wrote:
**> > how do l programme the logrank test. l am trying to compare 2 survival
**> curves
**>
**>
**> See:
**>
**> library(survival)
**> ?survdiff
**>
**> and take note of the 'rho' argument, which when set to 0 is the logrank
**> test.
**>
**> HTH,
**>
**> Marc Schwartz
**>
**>
**>
**> ------------------------------
**>
**> Message: 25
**> Date: Tue, 1 May 2007 12:03:27 -0400
**> From: "Roland Rau" <roland.rproject_at_gmail.com>
**> Subject: Re: [R] logrank test
**> To: "raymond chiruka" <rtchiruka_at_yahoo.com>
**> Cc: r <r-help_at_stat.math.ethz.ch>
**> Message-ID:
**> <47c7c59e0705010903t72c2bb35oee6971bb1f08d0a9@mail.gmail.com>
**> Content-Type: text/plain
**>
**> Hi,
**>
**> On 5/1/07, raymond chiruka <rtchiruka_at_yahoo.com> wrote:
**> >
**> > how do l programme the logrank test. l am trying to compare 2 survival
**> > curves
**>
**>
**> if you simply want to use the logrank test, have a look at the first
**> example
**> of the function survdiff in the survival package. If you read the help
**> page
**> there, it says that the default setting of rho=0 is the log rank test.
**> library(survival)
**> survdiff(Surv(futime, fustat) ~ rx,data=ovarian)
**> survdiff(Surv(futime, fustat) ~ rx,data=ovarian, rho=0)
**>
**> I hope this helps?
**>
**> Best,
**> Roland
**>
**> [[alternative HTML version deleted]]
**>
**>
**>
**> ------------------------------
**>
**> Message: 26
**> Date: Tue, 1 May 2007 17:04:50 +0100 (BST)
**> From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
**> Subject: Re: [R] to draw a smooth arc
**> To: Greg Snow <Greg.Snow_at_intermountainmail.org>
**> Cc: r-help_at_stat.math.ethz.ch, pbarata_at_infolink.com.br
**> Message-ID: <Pine.LNX.4.64.0705011656260.28173@gannet.stats.ox.ac.uk>
**> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
**>
**> On Tue, 1 May 2007, Greg Snow wrote:
**>
**> > Here is an approach that clips the circle you like from symbols down to
**> > an arc (this will work as long as the arc is less than half a circle,
**> > for arcs greater than half a circle, you could draw the whole circle
**> > then use this to draw an arc of the bacground color over the section you
**> > don't want):
**> >
**> > library(TeachingDemos)
**> > plot(-5:5, -5:5, type='n')
**> > clipplot( symbols(0,0,circles=2, add=TRUE), c(0,5), c(0,5) )
**>
**> I had considered this approach: clipping a circle to a rectangle isn't
**> strictly an arc, as will be clear if the line width is large.
**> Consider
**>
**> clipplot(symbols(0, 0 ,circles=2, add=TRUE, lwd=5), c(-1,5), c(-1,5))
**>
**> Note too that what happens with clipping is device-dependent. If R's
**> internal clipping is used, the part-circle is converted to a polygon.
**>
**>
**> --
**> Brian D. Ripley, ripley_at_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: 27
**> Date: Tue, 1 May 2007 10:07:38 -0600
**> From: sj <ssj1364_at_gmail.com>
**> Subject: [R] linout=TRUE in nnet package ?
**> To: r-help <r-help_at_stat.math.ethz.ch>
**> Message-ID:
**> <1c6126db0705010907rfba9d00n22ac108e0c697917@mail.gmail.com>
**> Content-Type: text/plain
**>
**> Hello,
**>
**> I am trying to figure out what nnet does when you select nnet =TRUE, I
**> understand that it provides you with linear outputs, but I don't
**> understand
**> how it arrives at those linear outputs. I assume that nnet still applies
**> the
**> logistic function as the activation function for the nodes in the hidden
**> layer, but I also assume another activation function must be applied at
**> the
**> output layer in order to return the predictions to the linear scale. I am
**> not able to figure out what is happening from the documentation, could
**> anyone provide more details about what nnet does at the output layer?
**>
**> best,
**>
**> Spencer
**>
**> [[alternative HTML version deleted]]
**>
**>
**>
**> ------------------------------
**>
**> Message: 28
**> Date: Tue, 1 May 2007 12:09:12 -0400
**> From: "Roland Rau" <roland.rproject_at_gmail.com>
**> Subject: Re: [R] logrank test
**> To: "raymond chiruka" <rtchiruka_at_yahoo.com>
**> Cc: r <r-help_at_stat.math.ethz.ch>
**> Message-ID:
**> <47c7c59e0705010909p1174447bn65504bb98182d083@mail.gmail.com>
**> Content-Type: text/plain
**>
**> And since Peter Dalgaard also just answered (without advertising his
**> book):
**> if you (or your library) happen to have 'Introductory Statistics with R'
**> by
**> Peter Dalgaard, have a look at section 12.4.
**>
**> Best,
**> Roland
**>
**> On 5/1/07, raymond chiruka <rtchiruka_at_yahoo.com> wrote:
**> >
**> > how do l programme the logrank test. l am trying to compare 2 survival
**> > curves
**> >
**> >
**> >
**> > ---------------------------------
**> >
**> >
**> > [[alternative HTML version deleted]]
**> >
**> > ______________________________________________
**> > R-help_at_stat.math.ethz.ch mailing list
**> > https://stat.ethz.ch/mailman/listinfo/r-help
**> > PLEASE do read the posting guide
**> > http://www.R-project.org/posting-guide.html
**> > and provide commented, minimal, self-contained, reproducible code.
**> >
**>
**> [[alternative HTML version deleted]]
**>
**>
**>
**> ------------------------------
**>
**> Message: 29
**> Date: Tue, 1 May 2007 18:03:04 +0100
**> From: "alex lam \(RI\)" <alex.lam_at_bbsrc.ac.uk>
**> Subject: [R] Matrix column name
**> To: <r-help_at_stat.math.ethz.ch>
**> Message-ID:
**> <84DA9D8AC9B05F4B889E7C70238CB45105C8FCD6@rie2ksrv1.ri.bbsrc.ac.uk>
**> Content-Type: text/plain; charset="us-ascii"
**>
**> Dear R users,
**>
**> Having searched the mail archive I think the conclusion was that it is
**> not possible to have a column name when there is only one column in the
**> matrix. But I thought I'd check with the more experienced users.
**>
**> What I tried to do was: in a loop I pick a column, record the column
**> name and remove the column from the matrix. But when there were 2
**> columns left, after one column was removed, the last column name
**> disappeared by default. It means that I always miss out the last column.
**>
**> I tried this by hand:
**>
**> > matrix.a
**> 801 802 803
**> [1,] -0.0906346 0.0906346 0.0906346
**> [2,] -0.0804911 0.0804911 0.0804911
**> [3,] -0.0703796 0.0703796 0.0703796
**> > matrix.a<-as.matrix(matrix.a[,-1])
**> > matrix.a
**> 802 803
**> [1,] 0.0906346 0.0906346
**> [2,] 0.0804911 0.0804911
**> [3,] 0.0703796 0.0703796
**> > matrix.a<-as.matrix(matrix.a[,-1])
**> > matrix.a
**> [,1]
**> [1,] 0.0906346
**> [2,] 0.0804911
**> [3,] 0.0703796
**>
**> Is there a way to force the column name to remain in such a case?
**>
**> Thanks,
**> Alex
**>
**> > sessionInfo()
**> R version 2.4.1 (2006-12-18)
**> i386-pc-mingw32
**>
**> 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
**>
**> attached base packages:
**> [1] "stats" "graphics" "grDevices" "utils" "datasets"
**> "methods"
**> [7] "base"
**> >
**>
**> ------------------------------------
**> Alex Lam
**> PhD student
**> Department of Genetics and Genomics
**> Roslin Institute (Edinburgh)
**> Roslin
**> Midlothian EH25 9PS
**> Great Britain
**>
**> Phone +44 131 5274471
**> Web http://www.roslin.ac.uk
**>
**> Roslin Institute is a company limited by guarantee, registered in
**> Scotland (registered number SC157100) and a Scottish Charity (registered
**> number SC023592). Our registered office is at Roslin, Midlothian, EH25
**> 9PS. VAT registration number 847380013.
**>
**> The information contained in this e-mail (including any attachments) is
**> confidential and is intended for the use of the addressee only. The
**> opinions expressed within this e-mail (including any attachments) are
**> the opinions of the sender and do not necessarily constitute those of
**> Roslin Institute (Edinburgh) ("the Institute") unless specifically
**> stated by a sender who is duly authorised to do so on behalf of the
**> Institute
**>
**>
**>
**> ------------------------------
**>
**> Message: 30
**> Date: Tue, 1 May 2007 19:03:46 +0200
**> From: Th?r Brigitte <Brigitte.Thuer_at_swica.ch>
**> Subject: [R] Simulation using parts of density function
**> To: <r-help_at_stat.math.ethz.ch>
**> Cc: <r-help_at_stat.math.ethz.ch>
**> Message-ID:
**> <486F261AFF288E498FD724CD4A289DD8AFE49B@msxwtgd02.internal.loc>
**> Content-Type: text/plain
**>
**>
**> Hi
**>
**> My simulation with the followin R code works perfectly:
**> sim <- replicate(999, sum(exp(rgamma(rpois(1,2000), scale = 0.5, shape =
**> 12))))
**>
**> But now I do not want to have values in object "sim" exceeding 5'000'000,
**> that means that I am just using the beginning of densitiy function gamma x <
**> 15.4. Is there a possibility to modify my code in an easy way?
**>
**> Thanks for any help!
**>
**> Regards, Brigitte
**>
**>
**>
**>
**>
**>
**>
**> [[alternative HTML version deleted]]
**>
**>
**>
**> ------------------------------
**>
**> Message: 31
**> Date: Tue, 1 May 2007 19:03:46 +0200
**> From: Th?r Brigitte <Brigitte.Thuer_at_swica.ch>
**> Subject: [R] Simulation using parts of density function
**> To: <r-help_at_stat.math.ethz.ch>
**> Cc: <r-help_at_stat.math.ethz.ch>
**> Message-ID:
**> <486F261AFF288E498FD724CD4A289DD8AFE49B@msxwtgd02.internal.loc>
**> Content-Type: text/plain
**>
**>
**> Hi
**>
**> My simulation with the followin R code works perfectly:
**> sim <- replicate(999, sum(exp(rgamma(rpois(1,2000), scale = 0.5, shape =
**> 12))))
**>
**> But now I do not want to have values in object "sim" exceeding 5'000'000,
**> that means that I am just using the beginning of densitiy function gamma x <
**> 15.4. Is there a possibility to modify my code in an easy way?
**>
**> Thanks for any help!
**>
**> Regards, Brigitte
**>
**>
**>
**>
**>
**>
**>
**> [[alternative HTML version deleted]]
**>
**>
**>
**> ------------------------------
**>
**> Message: 32
**> Date: Tue, 01 May 2007 12:14:07 -0500
**> From: Marc Schwartz <marc_schwartz_at_comcast.net>
**> Subject: Re: [R] Matrix column name
**> To: "alex lam (RI)" <alex.lam_at_bbsrc.ac.uk>
**> Cc: r-help_at_stat.math.ethz.ch
**> Message-ID: <1178039647.5009.14.camel@localhost.localdomain>
**> Content-Type: text/plain
**>
**> On Tue, 2007-05-01 at 18:03 +0100, alex lam (RI) wrote:
**> > Dear R users,
**> >
**> > Having searched the mail archive I think the conclusion was that it is
**> > not possible to have a column name when there is only one column in the
**> > matrix. But I thought I'd check with the more experienced users.
**> >
**> > What I tried to do was: in a loop I pick a column, record the column
**> > name and remove the column from the matrix. But when there were 2
**> > columns left, after one column was removed, the last column name
**> > disappeared by default. It means that I always miss out the last column.
**>
**> See R FAQ 7.5 Why do my matrices lose dimensions:
**>
**>
**> http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-do-my-matrices-lose-dimensions_003f
**>
**> which has some examples, along with ?Extract
**>
**> To wit:
**>
**> MAT <- matrix(1:12, ncol = 3)
**>
**> colnames(MAT) <- LETTERS[1:3]
**>
**> > MAT
**> A B C
**> [1,] 1 5 9
**> [2,] 2 6 10
**> [3,] 3 7 11
**> [4,] 4 8 12
**>
**>
**> > MAT[, 1]
**> [1] 1 2 3 4
**>
**>
**> > MAT[, 1, drop = FALSE]
**> A
**> [1,] 1
**> [2,] 2
**> [3,] 3
**> [4,] 4
**>
**>
**> HTH,
**>
**> Marc Schwartz
**>
**>
**>
**> ------------------------------
**>
**> Message: 33
**> Date: Tue, 1 May 2007 13:18:36 -0400
**> From: John Christie <jc_at_or.psychology.dal.ca>
**> Subject: [R] calculating area under the ROC curve
**> To: R-help_at_stat.math.ethz.ch
**> Message-ID:
**> <2CEA8F03-C473-43A3-BD60-89187821290B@or.psychology.dal.ca>
**> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
**>
**> Hi,
**> I recently did a study where we gathered decisions and confidence
**> ratings. My understanding is that I can convert this to a ROC curve
**> by getting hits and false alarms at the various confidence ratings.
**> I figured out that part of the problem. I noticed a few functions
**> for calculating AUC. Are there any preferred ones for this
**> particular kind of design?
**>
**>
**>
**> ------------------------------
**>
**> Message: 34
**> Date: Tue, 01 May 2007 14:29:53 -0300
**> From: Paulo Barata <pbarata_at_infolink.com.br>
**> Subject: Re: [R] to draw a smooth arc
**> To: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
**> Cc: r-help_at_stat.math.ethz.ch, Greg Snow
**> <Greg.Snow_at_intermountainmail.org>
**> Message-ID: <46377911.9000404@infolink.com.br>
**> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
**>
**>
**> Dr. Snow and Prof. Ripley,
**>
**> Dr. Snow's suggestion, using clipplot (package TeachingDemos),
**> is maybe a partial solution to the problem of drawing an arc of
**> a circle (as long as the line width of the arc is not that large,
**> as pointed out by Prof. Ripley). If the arc is symmetrical around
**> a vertical line, then it is not so difficult to draw it that way.
**> But an arc that does not have this kind of symmetry would possibly
**> require some geometrical computations to find the proper rectangle
**> to be used for clipping.
**>
**> I would like to suggest that in a future version of R some function
**> be included in the graphics package to draw smooth arcs with
**> given center, radius, initial and final angles. I suppose
**> that the basic ingredients are available in function "symbols"
**> (graphics).
**>
**> Thank you very much.
**>
**> Paulo Barata
**> (Rio de Janeiro - Brazil)
**>
**> -----------------------------------------------------------------------
**> Prof Brian Ripley wrote:
**> > On Tue, 1 May 2007, Greg Snow wrote:
**> >
**> >> Here is an approach that clips the circle you like from symbols down to
**> >> an arc (this will work as long as the arc is less than half a circle,
**> >> for arcs greater than half a circle, you could draw the whole circle
**> >> then use this to draw an arc of the bacground color over the section
**> you
**> >> don't want):
**> >>
**> >> library(TeachingDemos)
**> >> plot(-5:5, -5:5, type='n')
**> >> clipplot( symbols(0,0,circles=2, add=TRUE), c(0,5), c(0,5) )
**> >
**> > I had considered this approach: clipping a circle to a rectangle isn't
**> > strictly an arc, as will be clear if the line width is large.
**> > Consider
**> >
**> > clipplot(symbols(0, 0 ,circles=2, add=TRUE, lwd=5), c(-1,5), c(-1,5))
**> >
**> > Note too that what happens with clipping is device-dependent. If R's
**> > internal clipping is used, the part-circle is converted to a polygon.
**> >
**> >
**>
**>
**>
**> ------------------------------
**>
**> Message: 35
**> Date: Tue, 1 May 2007 19:33:58 +0200
**> From: Romain.Mayor_at_ville-ge.ch
**> Subject: [R] sorting in barplot
**> To: r-help_at_stat.math.ethz.ch
**> Message-ID:
**> <
**> OF0EB452E4.9B269070-ONC12572CE.005FE2DA-C12572CE.00607EC2_at_ville-ge.ch>
**>
**> Content-Type: text/plain; charset=US-ASCII
**>
**>
**> Hello,
**>
**> I'm trying to sort my bargraph.CI plot (function like barplot in the
**> SCIPLOT package) by the mean of the response variable.
**>
**> Does somebody have a trick for it.
**>
**> Thank you.
**>
**> Romain Mayor, PHD student.
**>
**>
**>
**> ------------------------------
**>
**> Message: 36
**> Date: Tue, 01 May 2007 12:49:17 -0500
**> From: Marc Schwartz <marc_schwartz_at_comcast.net>
**> Subject: Re: [R] sorting in barplot
**> To: Romain.Mayor_at_ville-ge.ch
**> Cc: r-help_at_stat.math.ethz.ch
**> Message-ID: <1178041757.5009.19.camel@localhost.localdomain>
**> Content-Type: text/plain
**>
**> On Tue, 2007-05-01 at 19:33 +0200, Romain.Mayor_at_ville-ge.ch wrote:
**> > Hello,
**> >
**> > I'm trying to sort my bargraph.CI plot (function like barplot in the
**> > SCIPLOT package) by the mean of the response variable.
**> >
**> > Does somebody have a trick for it.
**> >
**> > Thank you.
**> >
**> > Romain Mayor, PHD student.
**>
**> If it is built on top of barplot(), then by default, the factor levels
**> of your response variable will determine the order of the bars in the
**> plot.
**>
**> See ?reorder.factor for more details relative to defining the order
**> based upon the mean of the variable. There is an example there of using
**> the median.
**>
**> HTH,
**>
**> Marc Schwartz
**>
**>
**>
**> ------------------------------
**>
**> Message: 37
**> Date: Tue, 01 May 2007 19:18:07 +0100 (BST)
**> From: (Ted Harding) <ted.harding_at_nessie.mcc.ac.uk>
**> Subject: Re: [R] Simulation using parts of density function
**> To: Th?r Brigitte <Brigitte.Thuer_at_swica.ch>
**> Cc: r-help_at_stat.math.ethz.ch
**> Message-ID: <XFMail.070501191807.ted.harding@nessie.mcc.ac.uk>
**> Content-Type: text/plain; charset=iso-8859-1
**>
**> On 01-May-07 17:03:46, Th?r Brigitte wrote:
**> >
**> > Hi
**> >
**> > My simulation with the followin R code works perfectly:
**> > sim <- replicate(999, sum(exp(rgamma(rpois(1,2000),
**> > scale = 0.5, shape = 12))))
**> >
**> > But now I do not want to have values in object "sim" exceeding
**> > 5'000'000, that means that I am just using the beginning of
**> > densitiy function gamma x < 15.4. Is there a possibility to
**> > modify my code in an easy way?
**> >
**> > Thanks for any help!
**> >
**> > Regards, Brigitte
**>
**> A somewhat extreme problem!
**>
**> The easiest way to modify the code is as below -- certiainly easier
**> than writing a special function to draw random samples from the
**> truncated gamma distribution.
**>
**> A bit of experimentation shows that, from your code above, about
**> 10% of the results are <= 5000000. So:
**>
**> sim<-NULL
**> remain <- 999
**> while(remain>0){
**> sim0<-replicate(10*remain,
**> sum(exp(rgamma(rpois(1,2000), scale = 0.5, shape = 12)))
**> )
**> sim<-c(sim,sim0[sim0<=5000000])
**> remain<-(999 - length(sim))
**> }
**> sim<-sim[1:999]
**>
**> Results of a run:
**>
**> sum(sim>5000000)
**> [1] 0
**>
**> max(sim)
**> [1] 4999696
**>
**> length(sim)
**> [1] 999
**>
**> It may be on the slow side (though not hugely -- on a quite slow
**> machine the above run was completed in 2min 5sec, while the
**> 999-replicate in your original took 15sec. So about 8 times as long.
**> Most of this, of course, is taken up with the first round.
**>
**> Hoping this helps,
**> Ted.
**>
**> --------------------------------------------------------------------
**> E-Mail: (Ted Harding) <ted.harding_at_nessie.mcc.ac.uk>
**> Fax-to-email: +44 (0)870 094 0861
**> Date: 01-May-07 Time: 19:18:01
**> ------------------------------ XFMail ------------------------------
**>
**>
**>
**> ------------------------------
**>
**> Message: 38
**> Date: Tue, 1 May 2007 11:46:18 -0700
**> From: Lisa Solomon <lisas_at_salford-systems.com>
**> Subject: [R] Free Webinar: Vendor Neutral Intro to Data Mining for
**> Absolute Beginners, May 23, 2007
**> To: r-help <r-help_at_stat.math.ethz.ch>
**> Message-ID: <Q0s4QVhWUiVaLjJQIC8pODkzNjY5Mzc@sspc-lisa>
**> Content-Type: text/plain
**>
**> ONLINE VENDOR NEUTRAL INTRO TO DATA MINING FOR ABSOLUTE BEGINNERS
**> (no charge)
**>
**> A non-technical data mining introduction for absolute beginners
**> May 23, 2007, 10AM - 11AM PST
**> Future Sessions (June 14, Sept 7)
**>
**> To register for the webinar
**> -------------------------------------------------------
**> 1. Go to https://salford.webex.com/salford/onstage/g.php?d=928318845&t=a
**> 2. Click "Enroll".
**> 3. On the registration form, enter your information and then click
**> "Submit".
**>
**> Once you have registered, you will receive a confirmation email message
**> with instructions on how to join the event, as well as audio and system
**> requirements. Please read this confirmation email carefully!
**>
**> This one-hour webinar is a perfect place to start if you are new to data
**> mining and have little-to-no background in statistics or machine learning.
**>
**> In one hour, we will discuss:
**>
**> **Data basics: what kind of data is required for data mining and
**> predictive analytics; In what format must the data be; what steps are
**> necessary to prepare data appropriately
**>
**> **What kinds of questions can we answer with data mining
**>
**> **How data mining models work: the inputs, the outputs, and the nature of
**> the predictive mechanism
**>
**> **Evaluation criteria: how predictive models can be assessed and their
**> value measured
**>
**> **Specific background knowledge to prepare you to begin a data mining
**> project.
**>
**> Please do not hesitate to contact me if you have any questions.
**>
**> Sincerely,
**> Lisa Solomon
**> lisas_at_salford-systems.com
**>
**>
**>
**> ------------------------------
**>
**> Message: 39
**> Date: Wed, 02 May 2007 08:44:07 +1200
**> From: Paul Murrell <p.murrell_at_auckland.ac.nz>
**> Subject: Re: [R] to draw a smooth arc
**> To: pbarata_at_infolink.com.br
**> Cc: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>, Greg Snow
**> <Greg.Snow_at_intermountainmail.org>, r-help_at_stat.math.ethz.ch
**> Message-ID: <4637A697.8090400@stat.auckland.ac.nz>
**> Content-Type: text/plain; charset=ISO-8859-1
**>
**> Hi
**>
**>
**> Paulo Barata wrote:
**> > Dr. Snow and Prof. Ripley,
**> >
**> > Dr. Snow's suggestion, using clipplot (package TeachingDemos),
**> > is maybe a partial solution to the problem of drawing an arc of
**> > a circle (as long as the line width of the arc is not that large,
**> > as pointed out by Prof. Ripley). If the arc is symmetrical around
**> > a vertical line, then it is not so difficult to draw it that way.
**> > But an arc that does not have this kind of symmetry would possibly
**> > require some geometrical computations to find the proper rectangle
**> > to be used for clipping.
**> >
**> > I would like to suggest that in a future version of R some function
**> > be included in the graphics package to draw smooth arcs with
**> > given center, radius, initial and final angles. I suppose
**> > that the basic ingredients are available in function "symbols"
**> > (graphics).
**>
**>
**> Just to back up a few previous posts ...
**>
**> There is something like this facility already available via the
**> grid.xspline() function in the grid package. This provides very
**> flexible curve drawing (including curves very close to Bezier curves)
**> based on the X-Splines implemented in xfig. The grid.curve() function
**> provides a convenience layer that allows for at least certain
**> parameterisations of arcs (you specify the arc end points and the angle).
**>
**> These functions are built on functionality within the core graphics
**> engine, so exposing a similar interface (e.g., an xspline() function)
**> within "traditional" graphics would be relatively straightforward.
**>
**> The core functionality draws the curves as line segments (but
**> automatically figures out how many segments to use so that the curve
**> looks smooth); it does NOT call curve-drawing primitives in the
**> graphics device (like PostScript's curveto).
**>
**> In summary: there is some support for smooth curves, but we could still
**> benefit from a specific arc() function with the standard
**> centre-radius-angle parameterisation and we could also benefit from
**> exposing the native strengths of different graphics devices (rather than
**> the current lowest-common-denominator approach).
**>
**> Paul
**>
**>
**> > Thank you very much.
**> >
**> > Paulo Barata
**> > (Rio de Janeiro - Brazil)
**> >
**> > -----------------------------------------------------------------------
**> > Prof Brian Ripley wrote:
**> >> On Tue, 1 May 2007, Greg Snow wrote:
**> >>
**> >>> Here is an approach that clips the circle you like from symbols down
**> to
**> >>> an arc (this will work as long as the arc is less than half a circle,
**> >>> for arcs greater than half a circle, you could draw the whole circle
**> >>> then use this to draw an arc of the bacground color over the section
**> you
**> >>> don't want):
**> >>>
**> >>> library(TeachingDemos)
**> >>> plot(-5:5, -5:5, type='n')
**> >>> clipplot( symbols(0,0,circles=2, add=TRUE), c(0,5), c(0,5) )
**> >> I had considered this approach: clipping a circle to a rectangle isn't
**> >> strictly an arc, as will be clear if the line width is large.
**> >> Consider
**> >>
**> >> clipplot(symbols(0, 0 ,circles=2, add=TRUE, lwd=5), c(-1,5), c(-1,5))
**> >>
**> >> Note too that what happens with clipping is device-dependent. If R's
**> >> internal clipping is used, the part-circle is converted to a polygon.
**> >>
**> >>
**> >
**> > ______________________________________________
**> > R-help_at_stat.math.ethz.ch mailing list
**> > https://stat.ethz.ch/mailman/listinfo/r-help
**> > PLEASE do read the posting guide
**> http://www.R-project.org/posting-guide.html
**> > and provide commented, minimal, self-contained, reproducible code.
**>
**> --
**> Dr Paul Murrell
**> Department of Statistics
**> The University of Auckland
**> Private Bag 92019
**> Auckland
**> New Zealand
**> 64 9 3737599 x85392
**> paul_at_stat.auckland.ac.nz
**> http://www.stat.auckland.ac.nz/~paul/
**>
**>
**>
**> ------------------------------
**>
**> Message: 40
**> Date: Tue, 1 May 2007 22:14:01 +0100 (BST)
**> From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
**> Subject: Re: [R] Matrix column name
**> To: "alex lam (RI)" <alex.lam_at_bbsrc.ac.uk>
**> Cc: r-help_at_stat.math.ethz.ch
**> Message-ID: <Pine.LNX.4.64.0705012212390.20822@gannet.stats.ox.ac.uk>
**> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
**>
**> You seem to be looking for matrix.a[,-1, drop = TRUE]
**>
**> On Tue, 1 May 2007, alex lam (RI) wrote:
**>
**> > Dear R users,
**> >
**> > Having searched the mail archive I think the conclusion was that it is
**> > not possible to have a column name when there is only one column in the
**> > matrix. But I thought I'd check with the more experienced users.
**> >
**> > What I tried to do was: in a loop I pick a column, record the column
**> > name and remove the column from the matrix. But when there were 2
**> > columns left, after one column was removed, the last column name
**> > disappeared by default. It means that I always miss out the last column.
**>
**> And the matrix became a vector.
**>
**> >
**> > I tried this by hand:
**> >
**> >> matrix.a
**> > 801 802 803
**> > [1,] -0.0906346 0.0906346 0.0906346
**> > [2,] -0.0804911 0.0804911 0.0804911
**> > [3,] -0.0703796 0.0703796 0.0703796
**> >> matrix.a<-as.matrix(matrix.a[,-1])
**> >> matrix.a
**> > 802 803
**> > [1,] 0.0906346 0.0906346
**> > [2,] 0.0804911 0.0804911
**> > [3,] 0.0703796 0.0703796
**> >> matrix.a<-as.matrix(matrix.a[,-1])
**> >> matrix.a
**> > [,1]
**> > [1,] 0.0906346
**> > [2,] 0.0804911
**> > [3,] 0.0703796
**> >
**> > Is there a way to force the column name to remain in such a case?
**> >
**> > Thanks,
**> > Alex
**> >
**> >> sessionInfo()
**> > R version 2.4.1 (2006-12-18)
**> > i386-pc-mingw32
**> >
**> > 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
**> >
**> > attached base packages:
**> > [1] "stats" "graphics" "grDevices" "utils" "datasets"
**> > "methods"
**> > [7] "base"
**> >>
**> >
**> > ------------------------------------
**> > Alex Lam
**> > PhD student
**> > Department of Genetics and Genomics
**> > Roslin Institute (Edinburgh)
**> > Roslin
**> > Midlothian EH25 9PS
**> > Great Britain
**> >
**> > Phone +44 131 5274471
**> > Web http://www.roslin.ac.uk
**>
**>
**> --
**> Brian D. Ripley, ripley_at_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: 41
**> Date: Tue, 1 May 2007 22:37:29 +0100
**> From: "Pedro Sobral" <sobralix_at_gmail.com>
**> Subject: [R] to calculate sums
**> To: r-help_at_stat.math.ethz.ch
**> Message-ID:
**> <855386b70705011437j63d5260bnb811d014bea44259@mail.gmail.com>
**> Content-Type: text/plain; charset="iso-8859-1"
**>
**> Dear R-users,
**>
**> I am trying to use R to calculate sums like the ones in the file attached.
**> Would you please provide some help? At the moment I have no clue about how
**> to due...
**>
**> Thank you in advance,
**>
**> Kind regards,
**> Pedro
**>
**> ------------------------------
**>
**> Message: 42
**> Date: Tue, 1 May 2007 17:50:01 -0400
**> From: "Weiwei Shi" <helprhelp_at_gmail.com>
**> Subject: [R] dlda{supclust} 's output
**> To: "R Help" <R-help_at_stat.math.ethz.ch>
**> Cc: dettling_at_stat.math.ethz.ch
**> Message-ID:
**> <cdf817830705011450m51381074s82e3d5d4f42c1c61@mail.gmail.com>
**> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
**>
**> Hi,
**>
**> I am using dlda algorithm from supclust package and I am wondering if
**> the output can be a continuous probability instead of discrete class
**> label (zero or one) since it puts some restriction on convariance
**> matrix, compared with lda, while the latter can.
**>
**> thanks,
**>
**> --
**> Weiwei Shi, Ph.D
**> Research Scientist
**> GeneGO, Inc.
**>
**> "Did you always know?"
**> "No, I did not. But I believed..."
**> ---Matrix III
**>
**>
**>
**> ------------------------------
**>
**> Message: 43
**> Date: Tue, 01 May 2007 18:57:10 -0300
**> From: Paulo Barata <pbarata_at_infolink.com.br>
**> Subject: Re: [R] to draw a smooth arc
**> To: Paul Murrell <p.murrell_at_auckland.ac.nz>
**> Cc: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>, Greg Snow
**> <Greg.Snow_at_intermountainmail.org>, r-help_at_stat.math.ethz.ch
**> Message-ID: <4637B7B6.7000303@infolink.com.br>
**> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
**>
**>
**> Dr. Murrell and all,
**>
**> One final suggestion: a future function arc() in package graphics,
**> with centre-radius-angle parameterisation, could also include an
**> option to draw arrows at either end of the arc, as one can find
**> in function arrows().
**>
**> Thank you.
**>
**> Paulo Barata
**>
**> -----------------------------------------------------------------------
**> Paul Murrell wrote:
**> > Hi
**> >
**> >
**> > Paulo Barata wrote:
**> >> Dr. Snow and Prof. Ripley,
**> >>
**> >> Dr. Snow's suggestion, using clipplot (package TeachingDemos),
**> >> is maybe a partial solution to the problem of drawing an arc of
**> >> a circle (as long as the line width of the arc is not that large,
**> >> as pointed out by Prof. Ripley). If the arc is symmetrical around
**> >> a vertical line, then it is not so difficult to draw it that way.
**> >> But an arc that does not have this kind of symmetry would possibly
**> >> require some geometrical computations to find the proper rectangle
**> >> to be used for clipping.
**> >>
**> >> I would like to suggest that in a future version of R some function
**> >> be included in the graphics package to draw smooth arcs with
**> >> given center, radius, initial and final angles. I suppose
**> >> that the basic ingredients are available in function "symbols"
**> >> (graphics).
**> >
**> >
**> > Just to back up a few previous posts ...
**> >
**> > There is something like this facility already available via the
**> > grid.xspline() function in the grid package. This provides very
**> > flexible curve drawing (including curves very close to Bezier curves)
**> > based on the X-Splines implemented in xfig. The grid.curve() function
**> > provides a convenience layer that allows for at least certain
**> > parameterisations of arcs (you specify the arc end points and the
**> angle).
**> >
**> > These functions are built on functionality within the core graphics
**> > engine, so exposing a similar interface (e.g., an xspline() function)
**> > within "traditional" graphics would be relatively straightforward.
**> >
**> > The core functionality draws the curves as line segments (but
**> > automatically figures out how many segments to use so that the curve
**> > looks smooth); it does NOT call curve-drawing primitives in the
**> > graphics device (like PostScript's curveto).
**> >
**> > In summary: there is some support for smooth curves, but we could still
**> > benefit from a specific arc() function with the standard
**> > centre-radius-angle parameterisation and we could also benefit from
**> > exposing the native strengths of different graphics devices (rather than
**> > the current lowest-common-denominator approach).
**> >
**> > Paul
**> >
**> >
**> >> Thank you very much.
**> >>
**> >> Paulo Barata
**> >> (Rio de Janeiro - Brazil)
**> >>
**> >> -----------------------------------------------------------------------
**> >> Prof Brian Ripley wrote:
**> >>> On Tue, 1 May 2007, Greg Snow wrote:
**> >>>
**> >>>> Here is an approach that clips the circle you like from symbols down
**> to
**> >>>> an arc (this will work as long as the arc is less than half a circle,
**> >>>> for arcs greater than half a circle, you could draw the whole circle
**> >>>> then use this to draw an arc of the bacground color over the section
**> you
**> >>>> don't want):
**> >>>>
**> >>>> library(TeachingDemos)
**> >>>> plot(-5:5, -5:5, type='n')
**> >>>> clipplot( symbols(0,0,circles=2, add=TRUE), c(0,5), c(0,5) )
**> >>> I had considered this approach: clipping a circle to a rectangle isn't
**> >>> strictly an arc, as will be clear if the line width is large.
**> >>> Consider
**> >>>
**> >>> clipplot(symbols(0, 0 ,circles=2, add=TRUE, lwd=5), c(-1,5), c(-1,5))
**> >>>
**> >>> Note too that what happens with clipping is device-dependent. If R's
**> >>> internal clipping is used, the part-circle is converted to a polygon.
**> >>>
**> >>>
**> >> ______________________________________________
**> >> R-help_at_stat.math.ethz.ch mailing list
**> >> https://stat.ethz.ch/mailman/listinfo/r-help
**> >> PLEASE do read the posting guide
**> http://www.R-project.org/posting-guide.html
**> >> and provide commented, minimal, self-contained, reproducible code.
**> >
**>
**>
**>
**> ------------------------------
**>
**> Message: 44
**> Date: Wed, 02 May 2007 11:03:45 +1200
**> From: Paul Murrell <p.murrell_at_auckland.ac.nz>
**> Subject: Re: [R] to draw a smooth arc
**> To: pbarata_at_infolink.com.br
**> Cc: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>, Greg Snow
**> <Greg.Snow_at_intermountainmail.org>, r-help_at_stat.math.ethz.ch
**> Message-ID: <4637C751.4080502@stat.auckland.ac.nz>
**> Content-Type: text/plain; charset=ISO-8859-1
**>
**> Hi
**>
**>
**> Paulo Barata wrote:
**> > Dr. Murrell and all,
**> >
**> > One final suggestion: a future function arc() in package graphics,
**> > with centre-radius-angle parameterisation, could also include an
**> > option to draw arrows at either end of the arc, as one can find
**> > in function arrows().
**>
**>
**> ... and in grid.xspline() and grid.curve().
**>
**> Paul
**>
**>
**> > Thank you.
**> >
**> > Paulo Barata
**> >
**> > -----------------------------------------------------------------------
**> > Paul Murrell wrote:
**> >> Hi
**> >>
**> >>
**> >> Paulo Barata wrote:
**> >>> Dr. Snow and Prof. Ripley,
**> >>>
**> >>> Dr. Snow's suggestion, using clipplot (package TeachingDemos),
**> >>> is maybe a partial solution to the problem of drawing an arc of
**> >>> a circle (as long as the line width of the arc is not that large,
**> >>> as pointed out by Prof. Ripley). If the arc is symmetrical around
**> >>> a vertical line, then it is not so difficult to draw it that way.
**> >>> But an arc that does not have this kind of symmetry would possibly
**> >>> require some geometrical computations to find the proper rectangle
**> >>> to be used for clipping.
**> >>>
**> >>> I would like to suggest that in a future version of R some function
**> >>> be included in the graphics package to draw smooth arcs with
**> >>> given center, radius, initial and final angles. I suppose
**> >>> that the basic ingredients are available in function "symbols"
**> >>> (graphics).
**> >>
**> >> Just to back up a few previous posts ...
**> >>
**> >> There is something like this facility already available via the
**> >> grid.xspline() function in the grid package. This provides very
**> >> flexible curve drawing (including curves very close to Bezier curves)
**> >> based on the X-Splines implemented in xfig. The grid.curve() function
**> >> provides a convenience layer that allows for at least certain
**> >> parameterisations of arcs (you specify the arc end points and the
**> angle).
**> >>
**> >> These functions are built on functionality within the core graphics
**> >> engine, so exposing a similar interface (e.g., an xspline() function)
**> >> within "traditional" graphics would be relatively straightforward.
**> >>
**> >> The core functionality draws the curves as line segments (but
**> >> automatically figures out how many segments to use so that the curve
**> >> looks smooth); it does NOT call curve-drawing primitives in the
**> >> graphics device (like PostScript's curveto).
**> >>
**> >> In summary: there is some support for smooth curves, but we could
**> still
**> >> benefit from a specific arc() function with the standard
**> >> centre-radius-angle parameterisation and we could also benefit from
**> >> exposing the native strengths of different graphics devices (rather
**> than
**> >> the current lowest-common-denominator approach).
**> >>
**> >> Paul
**> >>
**> >>
**> >>> Thank you very much.
**> >>>
**> >>> Paulo Barata
**> >>> (Rio de Janeiro - Brazil)
**> >>>
**> >>>
**> -----------------------------------------------------------------------
**> >>> Prof Brian Ripley wrote:
**> >>>> On Tue, 1 May 2007, Greg Snow wrote:
**> >>>>
**> >>>>> Here is an approach that clips the circle you like from symbols down
**> to
**> >>>>> an arc (this will work as long as the arc is less than half a
**> circle,
**> >>>>> for arcs greater than half a circle, you could draw the whole circle
**> >>>>> then use this to draw an arc of the bacground color over the section
**> you
**> >>>>> don't want):
**> >>>>>
**> >>>>> library(TeachingDemos)
**> >>>>> plot(-5:5, -5:5, type='n')
**> >>>>> clipplot( symbols(0,0,circles=2, add=TRUE), c(0,5), c(0,5) )
**> >>>> I had considered this approach: clipping a circle to a rectangle
**> isn't
**> >>>> strictly an arc, as will be clear if the line width is large.
**> >>>> Consider
**> >>>>
**> >>>> clipplot(symbols(0, 0 ,circles=2, add=TRUE, lwd=5), c(-1,5), c(-1,5))
**> >>>>
**> >>>> Note too that what happens with clipping is device-dependent. If R's
**> >>>> internal clipping is used, the part-circle is converted to a polygon.
**> >>>>
**> >>>>
**> >>> ______________________________________________
**> >>> R-help_at_stat.math.ethz.ch mailing list
**> >>> https://stat.ethz.ch/mailman/listinfo/r-help
**> >>> PLEASE do read the posting guide
**> http://www.R-project.org/posting-guide.html
**> >>> and provide commented, minimal, self-contained, reproducible code.
**>
**> --
**> Dr Paul Murrell
**> Department of Statistics
**> The University of Auckland
**> Private Bag 92019
**> Auckland
**> New Zealand
**> 64 9 3737599 x85392
**> paul_at_stat.auckland.ac.nz
**> http://www.stat.auckland.ac.nz/~paul/
**>
**>
**>
**> ------------------------------
**>
**> Message: 45
**> Date: Tue, 1 May 2007 17:01:52 -0700
**> From: "Alan Gibson" <alan.gibson_at_gmail.com>
**> Subject: [R] Percentage area of a distribution
**> To: R-help_at_stat.math.ethz.ch
**> Message-ID:
**> <a2f3b2d90705011701x34810e88wd03c3a9d597f1f7a@mail.gmail.com>
**> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
**>
**> It seems like this should be pretty straight forward, but for some
**> reason the answer escapes me.
**>
**> I have a normal distribution S made up of two normal distributions C
**> and C-bar. I need to find the percentage of the area of S that both C
**> and C-bar occupy.
**>
**> Any suggestions?
**>
**> Thanks in advance,
**> Alan Gibson
**>
**>
**>
**> ------------------------------
**>
**> Message: 46
**> Date: Tue, 1 May 2007 17:38:44 -0700
**> From: "Alan Gibson" <alan.gibson_at_gmail.com>
**> Subject: Re: [R] Percentage area of a distribution
**> To: R-help_at_stat.math.ethz.ch
**> Cc: "Leeds, Mark \(IED\)" <Mark.Leeds_at_morganstanley.com>
**> Message-ID:
**> <a2f3b2d90705011738p4c4650cfh1414b6cd297f45ef@mail.gmail.com>
**> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
**>
**> let me amend my previous message to remove a silly mistake:
**>
**> I have a (non-normal) distribution S that is a mixture of two normal
**> distributions C and C-bar. I need to find the percentage of the area
**> of S that both C and C-bar occupy.
**>
**> Thanks again,
**> Alan Gibson
**>
**> On 5/1/07, Leeds, Mark (IED) <Mark.Leeds_at_morganstanley.com> wrote:
**> > What do you mean by a normal distribution made up of to normal
**> > distributions ? A mixture of two
**> > Normals with different variances doesn't result in a normal distribution
**> > so I'm not sure what you
**> > Nean but maybe someone else does. No offense intended but, if noone
**> > replies,
**> > That means that noone else understood either.
**> >
**> >
**> > -----Original Message-----
**> > From: r-help-bounces_at_stat.math.ethz.ch
**> > [mailto:r-help-bounces_at_stat.math.ethz.ch] On Behalf Of Alan Gibson
**> > Sent: Tuesday, May 01, 2007 8:02 PM
**> > To: R-help_at_stat.math.ethz.ch
**> > Subject: [R] Percentage area of a distribution
**> >
**> > It seems like this should be pretty straight forward, but for some
**> > reason the answer escapes me.
**> >
**> > I have a normal distribution S made up of two normal distributions C and
**> > C-bar. I need to find the percentage of the area of S that both C and
**> > C-bar occupy.
**> >
**> > Any suggestions?
**> >
**> > Thanks in advance,
**> > Alan Gibson
**> >
**> > ______________________________________________
**> > R-help_at_stat.math.ethz.ch mailing list
**> > https://stat.ethz.ch/mailman/listinfo/r-help
**> > PLEASE do read the posting guide
**> > http://www.R-project.org/posting-guide.html
**> > and provide commented, minimal, self-contained, reproducible code.
**> > --------------------------------------------------------
**> >
**> > This is not an offer (or solicitation of an offer) to buy/sell the
**> securities/instruments mentioned or an official confirmation. Morgan
**> Stanley may deal as principal in or own or act as market maker for
**> securities/instruments mentioned or may advise the issuers. This is not
**> research and is not from MS Research but it may refer to a research
**> analyst/research report. Unless indicated, these views are the author's and
**> may differ from those of Morgan Stanley research or others in the Firm. We
**> do not represent this is accurate or complete and we may not update
**> this. Past performance is not indicative of future returns. For additional
**> information, research reports and important disclosures, contact me or see
**> https://secure.ms.com/servlet/cls. You should not use e-mail to request,
**> authorize or effect the purchase or sale of any security or instrument, to
**> send transfer instructions, or to effect any other transactions. We cannot
**> guarantee that any such requests received vi!
**> a e-mail will be processed in a timely manner. This communication is
**> solely for the addressee(s) and may contain confidential information. We do
**> not waive confidentiality by mistransmission. Contact me if you do not wish
**> to receive these communications. In the UK, this communication is directed
**> in the UK to those persons who are market counterparties or intermediate
**> customers (as defined in the UK Financial Services Authority's rules).
**> >
**>
**>
**>
**> ------------------------------
**>
**> Message: 47
**> Date: Wed, 2 May 2007 10:47:20 +1000
**> From: "Floris Van Ogtrop" <f.vanogtrop_at_usyd.edu.au>
**> Subject: [R] optimising fitted distributions
**> To: <r-help_at_stat.math.ethz.ch>
**> Message-ID:
**> <3518808712EC8A459CC1FEDAD446449F404432@MAIL1.mcs.usyd.edu.au>
**> Content-Type: text/plain
**>
**> Dear R experts,
**>
**>
**>
**> I am relatively new to R and am interested in whether there is a package
**> which will fit data with a swag of distributions and determine the
**> optimal fit such as stat::fit from technical software solutions?
**>
**> As is discussed in the following r-help posting goodfit in vcd seems to
**> do this for three of the distribution
**>
**> http://finzi.psych.upenn.edu/R/Rhelp02a/archive/37053.html, have there
**> been any further developments for extending this to other distributions?
**>
**>
**>
**> Thanks in advanced
**>
**>
**>
**> Floris
**>
**>
**>
**> Floris van Ogtrop
**>
**> University of Sydney
**>
**> Dept. Food Agriculture and Natural Resources
**>
**> Australia
**>
**>
**> [[alternative HTML version deleted]]
**>
**>
**>
**> ------------------------------
**>
**> Message: 48
**> Date: Wed, 02 May 2007 11:37:22 +1000
**> From: Kate Stark <lhodgson_at_postoffice.utas.edu.au>
**> Subject: [R] ED50 from logistic model with interactions
**> To: r-help_at_stat.math.ethz.ch
**> Message-ID: <200705020137.l421bMJX011553@corinna.its.utas.edu.au>
**> Content-Type: text/plain
**>
**>
**> Hi,
**>
**> I was wondering if someone could please help me. I am doing a logistic
**> regression to compare size at maturity between 3 seasons. My model is:
**>
**> fit <- glm(Mature ~ Season * Size - 1, family = binomial, data=dat)
**>
**> where Mature is a binary response, 0 for immature, 1 for mature. There
**> are 3 Seasons.
**>
**> The Season * Size interaction is significant. I would like to compare the
**> size at 50% maturity between Seasons, which I have calculated as:
**>
**> Mat50_S1 <- -fit$coef[1]/fit$coef[4]
**> Mat50_S2 <- -fit$coef[2]/(fit$coef[4] + fit$coef[5])
**> Mat50_S3 <- -fit$coef[3]/(fit$coef[4] + fit$coef[6])
**>
**> But I am not sure how to calculate the standard error around each of
**> these estimates. The p.dose function from the MASS package does this
**> automatically, but it doesn�t seem to allow interaction terms.
**>
**> In Faraway(2006) he has an example using the delta method to calculate
**> the StdErr, but again without any interactions. I can apply this for the
**> first Season, as there is just one intercept and one slope coefficient,
**> but for the other 2 Seasons, the slope is a combination of the Size
**> coefficient and the Size*Season coefficient, and I am not sure how to use
**> the covariance matrix in the delta calculation.
**>
**> I could divide the data and do 3 different logistic regressions, one for
**> each season, but while the Mat50 (i.e. mean Size at 50% maturity) is the
**> same as that calculated by the separate lines regression, Im not sure how
**> this may change the StdErr?
**>
**> Regards,
**>
**> Kate
**>
**>
**> Kate Stark | PhD Candidate
**> Institute of Antarctic & Southern Ocean Studies &
**> Tasmanian Aquaculture & Fisheries Institute
**> University of Tasmania
**> Email: kate.stark at utas.edu.au
**>
**>
**>
**> ------------------------------
**>
**> Message: 49
**> Date: Tue, 01 May 2007 19:12:32 -0700
**> From: graham wideman <gwa_at_grahamwideman.com>
**> Subject: Re: [R] Concepts question: environment, frame, search path
**> To: r-help_at_stat.math.ethz.ch
**> Message-ID: <4.1.20070501175311.016b3160@grahamwideman.com>
**> Content-Type: text/plain; charset="us-ascii"
**>
**> Duncan:
**>
**> Thanks for taking a stab at my questions -- in following up I discovered
**> the root of my difficulties -- I had not noticed document R-lang.pdf ("R
**> Language Definition"). This clarifies a great deal.
**>
**> FWIW, it seems to me that a number of things I was hung up on (and which
**> you discussed) revolved around:
**>
**> 1. Confusion between "frame" and "data.frame". R-lang.pdf has several
**> sections that touch on each of these, from which it's more clear (though not
**> explicit) that these are not the same things. (Problematic: frame is
**> mentioned first, is a more fundamental concept, yet has no entry in the
**> Table of Contents, while data.frame does have an entry). (And the converse
**> is true of the index!).
**>
**> 2. Ambiguity in the docs regarding environment, frame (and also regarding
**> closely-related concepts closure and enclosure).
**>
**> Anyhow, I'm now in a much happier state :-).
**>
**> Regarding your questions:
**>
**> >> 1. data.frame:
**> >> Ref[m]an p84: 'A data frame is a list of variables of the same length
**> with
**> >> unique row names, given class "data.frame".'
**>
**> >Which manual are you looking at? The "reference index" (refman.pdf)?
**> >[...] that statement may not be present in the current release
**>
**> Yes, the doc titled "R: A Language and Environment for Statistical
**> Computing Reference Index". This is in section I "The base package",
**> subsection "data.frame", which was on page 84 of refman.pdf (which I
**> downloaded yesterday, but now don't know where from) or on page 86 of
**> fullrefman.pdf (downloaded today -- ie: current release).
**>
**> (And point understood on the suggestions about reporting doc issues --
**> though tracking them down to line numbers in the SVN is a bit optimistic,
**> not to mention a moving target :-)
**>
**> -----------
**>
**> Anyhow, thanks again for the response.
**>
**> Graham
**>
**> ---------------------------------------------------
**> Graham Wideman
**> Resources for programmable diagramming at:
**> http://www.diagramantics.com
**>
**> Brain-related resources:
**> http://wideman-one.com
**>
**>
**>
**> ------------------------------
**>
**> Message: 50
**> Date: Tue, 1 May 2007 23:16:18 -0400
**> From: "Jennifer Dillon" <jdillon_at_hsph.harvard.edu>
**> Subject: [R] the Surv function
**> To: r-help_at_stat.math.ethz.ch
**> Message-ID:
**> <7c0535c00705012016h79203c4byc33d9af211515046@mail.gmail.com>
**> Content-Type: text/plain
**>
**> Hi,
**>
**> I'm trying to do a simple survival analysis on some data, and I'm having
**> the
**> following problem (here's my code and the error message):
**>
**> out <- Surv(fup,event=status)
**> Error in Surv(fup, event = status) : argument "time2" is missing, with no
**> default
**>
**> >From reading the documentation, it seems that I should be able to simply
**> write: Surv(time1, event) if my data is right-censored, which it is.
**> Help!
**>
**> Thanks a million,
**>
**> Jen
**>
**>
**>
**> --
**> Jennifer Dillon
**> Doctoral Student
**> Harvard Biostatistics
**> Room 414B, Building 1
**>
**> [[alternative HTML version deleted]]
**>
**>
**>
**> ------------------------------
**>
**> Message: 51
**> Date: Tue, 1 May 2007 23:42:24 -0400
**> From: "Christos Hatzis" <christos_at_nuverabio.com>
**> Subject: Re: [R] the Surv function
**> To: "'Jennifer Dillon'" <jdillon_at_hsph.harvard.edu>,
**> <r-help_at_stat.math.ethz.ch>
**> Message-ID:
**> <002f01c78c6b$e67fe840$0202a8c0@headquarters.silicoinsights>
**> Content-Type: text/plain; charset="us-ascii"
**>
**> Try using the following (without naming the arguments) - it should work.
**>
**> Surv(fup, status)
**>
**> I think what is happening is that if you use one or two arguments
**> (unnamed),
**> Surv assumes that you have right-censored data, with the first argument
**> being time and the second being status. By specifying 'event' as you did,
**> Surv assumes that you have 3 arguments of "type"=counting and it is
**> looking
**> for the ending time required by the counting data format and this is why
**> you
**> got the error.
**>
**> If you are not afraid of R code, type Surv (without the parentheses) to
**> see
**> the code behind the function.
**>
**> -Christos
**>
**> Christos Hatzis, Ph.D.
**> Nuvera Biosciences, Inc.
**> 400 West Cummings Park
**> Suite 5350
**> Woburn, MA 01801
**> Tel: 781-938-3830
**> www.nuverabio.com
**>
**>
**> > -----Original Message-----
**> > From: r-help-bounces_at_stat.math.ethz.ch
**> > [mai...
**>
**> [Message clipped]
*

[[alternative HTML version deleted]]

R-help_at_stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Thu 03 May 2007 - 01:58:26 GMT

Archive maintained by Robert King, hosted by
the discipline of
statistics at the
University of Newcastle,
Australia.

Archive generated by hypermail 2.2.0, at Thu 03 May 2007 - 02:31:36 GMT.

*
Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help.
Please read the posting
guide before posting to the list.
*