date:20100316

See:
https://stat.ethz.ch/pipermail/r-help/2005-April/070581.html

On Mon, Mar 15, 2010 at 11:16 PM, statmobile statmob...@gmail.com wrote:
 Hey Gabor,

 Thanks, I tried that, although I can't compile it directly.  Do you know
 where I can get the R LaTeX definitions in order to compile that?

 Thanks!

 Gabor Grothendieck wrote:

 Try:

 R CMD Rdconv --type=latex myfile.Rd


 On Mon, Mar 15, 2010 at 8:46 PM, statmobile statmob...@gmail.com wrote:

 Hey Everyone,

 I wrote up a library for my dissertation work, and I'd love to include it
 as
 an appendix.  I have found ways to export the Rd files as html, txt and
 pdf/ps, but not a raw tex export.  I've had to resort to dumping it into
 text files, and just using verbatim in my LaTeX code.  Does anybody have
 any
 recommendations or experiences with dealing with this?

 Please CC me on any response, as I only get summary emails from the list.

 Thanks in advance!
 Brian

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[R] Ensembles in cforest

2010-03-16 Thread Philip Whittall

Dear List,

I'm trying to find a way to extract the individual conditional inference
trees from cforest ( a modelling function in the party package) in a
manner analogous to 
getTree in randomForest and I'm struggling. I can see that the
information is held within the ensemble list, but haven't been able to
work out how this sequence
of nested lists is structured or if any of the items are named. Any help
would be appreciated.

I'm running R2.10.0 on windows XP.

Kind Regards,

Philip


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[R] How to parse a string (by a new markup) with R ?

Hello all,

For some work I am doing on RNA, I want to use R to do string parsing that
(I think) is like a simplistic HTML parsing.


For example, let's say we have the following two variables:

Seq -
GCCTCGATAGCTCAGTTGGGAGAGCGTACGACTGAAGATCGTAAGGtCACCAGTTCGATCCTGGTTCCA
Str -
...

Say that I want to parse Seq According to Str, by using the legend here

Seq: GCCTCGATAGCTCAGTTGGGAGAGCGTACGACTGAAGATCGTAAGGtCACCAGTTCGATCCTGGTTCCA
Str: ...

 | |  |  | |   | |   || |

 +-+  +--+ +---+ +---++-+

|Stem 1Stem 2 Stem 3 |

||

++

Stem 0

Assume that we always have 4 stems (0 to 3), but that the length of letters
before and after each of them can very.

The output should be something like the following list structure:


list(
 Stem 0 opening = GCCTCGA,
 before Stem 1 = TA,
 Stem 1 = list(opening = GCTC,
 inside = AGTTGGGA,
 closing = GAGC
 ),
 between Stem 1 and 2 = G,
 Stem 2 = list(opening = TACGA,
 inside = CTGAAGA,
 closing = TCGTA
 ),
 between Stem 2 and 3 = AGGtC,
 Stem 3 = list(opening = ACCAG,
 inside = TTCGATC,
 closing = CTGGT
 ),
 After Stem 3 = ,
 Stem 0 closing = TCC
)


I don't have any experience with programming a parser, and would like
advices as to what strategy to use when programming something like this (and
any recommended R commands to use).


What I was thinking of is to first get rid of the Stem 0, then go through
the inner string with a recursive function (let's call it seperate.stem)
that each time will split the string into:
1. before stem
2. opening stem
3. inside stem
4. closing stem
5. after stem

Where the after stem will then be recursively entered into the same
function (seperate.stem)

The thing is that I am not sure how to try and do this coding without using
a loop.

Any advices will be most welcomed.


Contact
Details:---
Contact me: tal.gal...@gmail.com |  972-52-7275845
Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
www.r-statistics.com (English)
--

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Re: [R] C# DLL Library

2010-03-16 Thread Jeremie Smaga

Hello Richard,

Thanks for the tips.

I was aware of the R(D)COM. In the last public version, there is now splash
screen appearing which is kind of boring so I think I need to buy it or
something.

Anyway, I think the idea was to create a common CORE library that can be
used from C# and from R. So I think I'll have a look at RCPP which looks to
be the best solution.

Have you tried it already? Do you know any good tutorial for this package?

Thanks,

Jeremie


On Tue, Mar 16, 2010 at 5:23 PM, richard.cot...@hsl.gov.uk wrote:


  I would like to develop a core library which I will be using both from R
 and
  from C#.

  - Writing the DLL freely in C# and then create a wrapper?
  - Writing it in C++
  - Writing it in C, the other options are really not good ideas.

 As far as I know, there currently is no way to call .NET code from R.  If
 you want a library that can be called from both a .NET environment and from
 R, then writing it in C or C++ is likely your best bet.  Alternatively, you
 can run R code from within .NET using the rcom package.  There's an example
 in F# here (what's true for F# is true for C#).


 http://cs.hubfs.net/blogs/thepopeofthehub/archive/2007/11/06/FSharpWithR.aspx

 See ?.C for calling C code, and the rcpp package for an interface to C++
 code.  Choosing between those two languages mostly depends on whether on not
 your library is especially suited to object oriented programming or not.

 Regards,
 Richie.

 Mathematical Sciences Unit*
 **HSL* http://www.hsl.gov.uk/contact-us.htm


 r-help-boun...@r-project.org wrote on 16/03/2010 09:04:54:


  Good afternoon everybody,
 
  I am sorry, this question might look trivial to some of you, but I read
  quite a lot of stuff about package creation and I would like a bit of you
  advices.
 

 
  I read that it was possible to import DLL to R.
 
  The thing is, I am not sure that the DLL created with C# will be
 compatible.
  I still have not implemented anything, so if it is only a matter of
 method
  signatures, I can make sure everything fits.
 
  Otherwise, I could use a C++ DLL, but I don't know if it is really
  recommended. (In fact, I would love to be able to develop it in Visual
  Studio because it is where I developed the rest of my platform).
 
  So, what would you advise?
 

 
  Thanks,
 
  --
  Jeremie Smaga

 
 [[alternative HTML version deleted]]
 
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  PLEASE do read the posting guide
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and provide commented, minimal, self-contained, reproducible code.

Re: [R] C# DLL Library

2010-03-16 Thread Romain Francois


Hello,

disclaimer: I don't know C# at all and how it might connect to c++, etc ...

For an introductory ride about Rcpp, you can consult the 
Rcpp-introduction vignette which you can download from the cran page of 
Rcpp or if you have it installed, you can just do:


 vignette( Rcpp-introduction, package = Rcpp )

For semi-self-explanatory code examples, you can consult our unit tests:

 system.file( unitTests, package = Rcpp )

For more questions, we have a dedicated mailing list: 
https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel


Romain


Le 16/03/10 11:43, Jeremie Smaga a écrit :


Hello Richard,

Thanks for the tips.

I was aware of the R(D)COM. In the last public version, there is now splash
screen appearing which is kind of boring so I think I need to buy it or
something.

Anyway, I think the idea was to create a common CORE library that can be
used from C# and from R. So I think I'll have a look at RCPP which looks to
be the best solution.

Have you tried it already? Do you know any good tutorial for this package?

Thanks,

Jeremie


On Tue, Mar 16, 2010 at 5:23 PM,richard.cot...@hsl.gov.uk  wrote:




I would like to develop a core library which I will be using both from R

and

from C#.



- Writing the DLL freely in C# and then create a wrapper?
- Writing it in C++
- Writing it in C, the other options are really not good ideas.


As far as I know, there currently is no way to call .NET code from R.  If
you want a library that can be called from both a .NET environment and from
R, then writing it in C or C++ is likely your best bet.  Alternatively, you
can run R code from within .NET using the rcom package.  There's an example
in F# here (what's true for F# is true for C#).


http://cs.hubfs.net/blogs/thepopeofthehub/archive/2007/11/06/FSharpWithR.aspx

See ?.C for calling C code, and the rcpp package for an interface to C++
code.  Choosing between those two languages mostly depends on whether on not
your library is especially suited to object oriented programming or not.

Regards,
Richie.

Mathematical Sciences Unit*
**HSL*http://www.hsl.gov.uk/contact-us.htm


r-help-boun...@r-project.org wrote on 16/03/2010 09:04:54:



Good afternoon everybody,

I am sorry, this question might look trivial to some of you, but I read
quite a lot of stuff about package creation and I would like a bit of you
advices.





I read that it was possible to import DLL to R.

The thing is, I am not sure that the DLL created with C# will be

compatible.

I still have not implemented anything, so if it is only a matter of

method

signatures, I can make sure everything fits.

Otherwise, I could use a C++ DLL, but I don't know if it is really
recommended. (In fact, I would love to be able to develop it in Visual
Studio because it is where I developed the rest of my platform).

So, what would you advise?





Thanks,

--
Jeremie Smaga




--
Romain Francois
Professional R Enthusiast
+33(0) 6 28 91 30 30
http://romainfrancois.blog.free.fr
|- http://tr.im/OIXN : raster images and RImageJ
|- http://tr.im/OcQe : Rcpp 0.7.7
`- http://tr.im/O1wO : highlight 0.1-5

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

[R] Fwd: Cumulative normal distr

2010-03-16 Thread Антон Морковин


   Hi,
   How to fit data to cumulative normal distribution?
   I tried such way:
   library(MASS)
   ed-c(1:10)
   cnd-function(mn,sdd){pnorm(c(1:10),mn,sdd)}
   fitdistr(ed,cnd,start=list(mn=mean(ed),sdd=sd(ed)))

   ..but an error occured:


   Error in solve.default(res$hessian) :
   function Lapack 'dgesv': system are exactly singular
   Thank you for help
   Antony
   --
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Re: [R] kknn and logistic regression: how to cross-validate binary prediction

2010-03-16 Thread Max Kuhn


Take a look at the caret package

http://cran.r-project.org/web/packages/caret/index.html

and the package vignettes, especially the one labeled as model  
builing.


Max



On Mar 15, 2010, at 6:11 PM, noclue_ tim@netzero.net wrote:



I am comparing kknn and logistic regression for binary outcome  
prediction -


For kknn, I can do -

kknn_-kknn(out_come ~ age + gender , learn_, valid_)
fit-fitted(kknn_)
table(valid_$out_come, fit)

to get validation results in cross-tabulation.

-

For logistic, how can I do the equivalent cross-validation?

logit_-glm(out_come ~ age + gender, data=learn_, family=binomial)
...
...
then how could I fit the logistic regression on validation data (ie.  
valid_)

to get predicted outcome?

Thanks!
--
View this message in context: 
http://n4.nabble.com/kknn-and-logistic-regression-how-to-cross-validate-binary-prediction-tp1594107p1594107.html
Sent from the R help mailing list archive at Nabble.com.

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[R] interactive 3d plot (identifying datapoint when clicked or mouse-overed)

2010-03-16 Thread June Kim

Is there a package that provides interactive 3d scatter plot with the
functionality of identifying the datapoint when clicked or
mouse-overed? Or, if not, which package is the best alternative (with
some modification) to produce the similar effect?

If there is a rotation feature, it is +1.

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

Re: [R] interactive 3d plot (identifying datapoint when clicked or mouse-overed)

2010-03-16 Thread John Fox

Dear June Kim,

The scatter3d function in the Rcmdr package, or in the development version
of the car package on R-Forge, can do interactive point identification. (For
the version in car, set id.method=identify.)

Regards,
 John


John Fox
Senator William McMaster 
  Professor of Social Statistics
Department of Sociology
McMaster University
Hamilton, Ontario, Canada
web: socserv.mcmaster.ca/jfox


 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On
 Behalf Of June Kim
 Sent: March-16-10 7:20 AM
 To: r-help@r-project.org
 Subject: [R] interactive 3d plot (identifying datapoint when clicked or
 mouse-overed)
 
 Is there a package that provides interactive 3d scatter plot with the
 functionality of identifying the datapoint when clicked or
 mouse-overed? Or, if not, which package is the best alternative (with
 some modification) to produce the similar effect?
 
 If there is a rotation feature, it is +1.
 
 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.

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

Re: [R] map2poly - map lat/long cannot be unconstrained?

2010-03-16 Thread Roger Bivand


An ideal question for R-sig-geo.

Firstly, consider using sp classes, which try to help more in plotting
correctly specified spatial data, and note that Map2poly has not only been
deprecated for a long time, but was recently removed from the namespace of
the maptools package.

Secondly, consider that the aspect of spatial data should not in general be
manipulable, meters should stay meters on both axes. 

Thrirdly, if you want to overplot points, do use points(), not plot(). Using
methods for sp classes would handle this directly, where plot(..., add=TRUE)
assumes that a previous plot() call has set the plotting window and axes.

Hope this helps,

Roger


Euan Reavie wrote:
 
 Using the maptools function map2poly I have created a map/polylist
 object
 - a map of the Great Lakes. My goal is to passively plot additional data
 on
 this map. Unfortunately I am not able to change (distort) the relative
 scale
 of the axes for the map, and so the sample points do not line up correctly
 on the map.
 
 In the code below, notice that I have set the same axis ranges on each
 plot
 for x (longitude) and y (latitude), and yet it has no effect on the map
 plot. For example, if I stretch the plot window vertically, the y data
 spread out accordingly, but the map remains undistorted. No matter how
 much
 I try to stretch the y axis, the y:x ratio scale remains 1:1. How do I
 force
 the map to fit the ranges that I set like I can for the data plot?
 
 *# make the map object lakes
 tmp - read.shape('D:/R/great lakes map/grtlakes/grtlakes')
 lakes - Map2poly(tmp)
 
 # read sample location data to be plotted on map
 locs - read.table(locs.csv, header=TRUE, sep=,, na.strings=NA,
 dec=., strip.white=TRUE)
 
 # plot map, then sample locations
 plot(lakes,xlim=range(-76,-93), ylim=range(40,50))
 par(new=TRUE) # put next plot on same graph
 plot(LATITUDE~LONGITUDE, data=locs,xlim=range(-76,-93),ylim=range(40,50))
 box()*
 
 
 Thank you for any help - Euan.
 
 Euan D. Reavie
 
 Center for Water and the Environment
 
 Natural Resources Research Institute
 
 University of Minnesota Duluth
 
 1900 East Camp Street, Ely, MN 55731
 
 email ereavie *at sign* nrri.umn.edu
 
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 PLEASE do read the posting guide
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 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

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Re: [R] How to parse a string (by a new markup) with R ?

2010-03-16 Thread jim holtman

How are you supposed to interprete the string that is doing the parsing?
Does each sequence have the same number of  for the opening sequence
as it does for  on the ending sequence?  That what it appears to be
looking at the way stem 3 is parsed.  You will have to provide a little more
insight on how to interprete the  symbols.  Does the parsing always start
with a partial stem 0 as your example shows?  Is there a way of making sure
you have the right sequences when you start?  Is there a chance of error in
the middle of the string that you have to restart from?  How long are these
strings that you want to parse?  Is each one a self contained sequence like
you show in your example, or do they go on for thousands of characters?  Is
there always at least one '.' between stems?  A full set of rules as to how
the parsing should be done would be useful.  Do you have the BNF syntax for
parsing?

On Tue, Mar 16, 2010 at 6:10 AM, Tal Galili tal.gal...@gmail.com wrote:

 Hello all,

 For some work I am doing on RNA, I want to use R to do string parsing that
 (I think) is like a simplistic HTML parsing.


 For example, let's say we have the following two variables:

Seq -
 GCCTCGATAGCTCAGTTGGGAGAGCGTACGACTGAAGATCGTAAGGtCACCAGTTCGATCCTGGTTCCA
Str -
 ...

 Say that I want to parse Seq According to Str, by using the legend here

 Seq:
 GCCTCGATAGCTCAGTTGGGAGAGCGTACGACTGAAGATCGTAAGGtCACCAGTTCGATCCTGGTTCCA
 Str:
 ...

 | |  |  | |   | |   ||
 |

 +-+  +--+ +---+
 +---++-+

|Stem 1Stem 2 Stem 3 |

||

++

Stem 0

 Assume that we always have 4 stems (0 to 3), but that the length of letters
 before and after each of them can very.

 The output should be something like the following list structure:


list(
 Stem 0 opening = GCCTCGA,
 before Stem 1 = TA,
 Stem 1 = list(opening = GCTC,
 inside = AGTTGGGA,
 closing = GAGC
 ),
 between Stem 1 and 2 = G,
 Stem 2 = list(opening = TACGA,
 inside = CTGAAGA,
 closing = TCGTA
 ),
 between Stem 2 and 3 = AGGtC,
 Stem 3 = list(opening = ACCAG,
 inside = TTCGATC,
 closing = CTGGT
 ),
 After Stem 3 = ,
 Stem 0 closing = TCC
)


 I don't have any experience with programming a parser, and would like
 advices as to what strategy to use when programming something like this
 (and
 any recommended R commands to use).


 What I was thinking of is to first get rid of the Stem 0, then go through
 the inner string with a recursive function (let's call it seperate.stem)
 that each time will split the string into:
 1. before stem
 2. opening stem
 3. inside stem
 4. closing stem
 5. after stem

 Where the after stem will then be recursively entered into the same
 function (seperate.stem)

 The thing is that I am not sure how to try and do this coding without using
 a loop.

 Any advices will be most welcomed.


 Contact
 Details:---
 Contact me: tal.gal...@gmail.com |  972-52-7275845
 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
 www.r-statistics.com (English)

 --

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




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

What is the problem that you are trying to solve?

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[R] function arguments: name of an object vs. call producing the object?

2010-03-16 Thread Michael Friendly

In a function, say foo.glm for glm objects I want to use the name of the 
object as a label for some output,
but *only* if a glm object was passed as an argument, not a call to 
glm() producing that object.

How can I distinguish these two cases?

For example, I can use the following to get the name of the argument:

foo.glm - function(object) {
   oname - as.character(sys.call())[2]
   oname
}

 indep - glm(Freq ~ mental + ses, family = poisson, data = Mental)
 foo.glm(indep)
[1] indep

But in foo.glm() I want to avoid using this as oname:
 foo.glm(glm(formula = Freq ~ mental + ses, family = poisson, data = 
Mental))

[1] glm(formula = Freq ~ mental + ses, family = poisson, data = Mental)

Here is Mental, if it matters.

dput(Mental)
structure(list(ses = structure(c(1L, 1L, 1L, 1L, 2L, 2L, 2L,
2L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 6L, 6L, 6L,
6L), .Label = c(1, 2, 3, 4, 5, 6), class = c(ordered,
factor)), mental = structure(c(1L, 2L, 3L, 4L, 1L, 2L, 3L,
4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L,
4L), .Label = c(Well, Mild, Moderate, Impaired), class = 
c(ordered,

factor)), Freq = c(64L, 94L, 58L, 46L, 57L, 94L, 54L, 40L,
57L, 105L, 65L, 60L, 72L, 141L, 77L, 94L, 36L, 97L, 54L, 78L,
21L, 71L, 54L, 71L)), .Names = c(ses, mental, Freq), row.names = 
c(NA,

-24L), class = data.frame)

--
Michael Friendly Email: friendly AT yorku DOT ca 
Professor, Psychology Dept.

York University  Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Streethttp://www.math.yorku.ca/SCS/friendly.html
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Re: [R] R on Linux - a primer

2010-03-16 Thread Kevin E. Thorpe


Axel Urbiz wrote:

Hi,

I'm looking to move from Windows into a 64-bit Linux environment. Which is
the best Linux Flavor to use within R? To install R on this environment, do
I need to do any compiling?

Thanks all!

Axel.



You have received a number of useful replies.  I will add my 2 cents as 
well.


First, make sure the distribution you choose does have a 64 bit version, 
since that is what you are looking for.  That said, allow me to share my 
Linux philosophy.


There are many distributions out there, each with their pluses and 
minuses.  For example, I used SuSE and OpenSuSE for awhile.  It was good 
in that things worked out of the box, and it has (had?) a good 
sysadmin tool.  The problem was, if I needed to compile stuff, the tools 
for development were not included in the default install, so I had to 
search for them (a full install may have fixed this, but the full 
install was really bloated).


Most of the popular distributions come with some kind of sysadmin tool. 
 This is a useful thing for someone totally new to Linux.  It can be 
frustrating if you decide on a new distribution, since the sysadmin 
stuff will look different.


I eventually moved away from OpenSuSE because the life cycle of 
supported versions was quite short.  I don't like being forced to 
re-install a new OS just to get the latest patches.  So, I moved to 
Slackware (they have a 64 bit version now BTW).  I love it, but it's not 
for everybody.  The biggest obstacle to most people is that it has no 
sysadmin tool.  It is your responsibility to edit the config files in a 
text editor, if you want to fine-tune or customize things.  It is your 
responsibility to do dependency checking when installing packages (this 
is a plus in that when you install something and something breaks, you 
know what to blame).  This means you need to invest some time and learn 
a little more Linux than other distributions forces you to learn.  The 
full install is not bloated and comes with all the development tools 
needed.  I always compile R from source and it is easy.


./configure
make
su
make install

In closing (congratulations if you've read this far), there is probably 
not a wrong choice of Linux to run R on.  Choose a flavour of Linux that 
you like.  Many distributions have Live versions.  These are versions 
that boot and run from your DVD drive.  It's a good way to get a feeling 
for a particular distribution without installing anything.


--
Kevin E. Thorpe
Biostatistician/Trialist, Knowledge Translation Program
Assistant Professor, Dalla Lana School of Public Health
University of Toronto
email: kevin.tho...@utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016

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Re: [R] function arguments: name of an object vs. call producing the object?

2010-03-16 Thread Duncan Murdoch


On 16/03/2010 8:26 AM, Michael Friendly wrote:
In a function, say foo.glm for glm objects I want to use the name of the 
object as a label for some output,
but *only* if a glm object was passed as an argument, not a call to 
glm() producing that object.

How can I distinguish these two cases?


Look at typeof(substitute(object)).  For example,

 f - function(object) typeof(substitute(object))
 f(aname)
[1] symbol
 f(aname+1)
[1] language

That will tell you if an object was passed by name, or if you got an 
expression to produce the object.


One problem with this approach is that it only looks at the direct call 
to f, for example


 g - function(x) f(x)
 g(aname + 1)
[1] symbol

because substitute looks at the f(x) call, not the g(aname + 1) call.

Duncan Murdoch




For example, I can use the following to get the name of the argument:

foo.glm - function(object) {
oname - as.character(sys.call())[2]
oname
}

  indep - glm(Freq ~ mental + ses, family = poisson, data = Mental)
  foo.glm(indep)
[1] indep

But in foo.glm() I want to avoid using this as oname:
  foo.glm(glm(formula = Freq ~ mental + ses, family = poisson, data = 
Mental))

[1] glm(formula = Freq ~ mental + ses, family = poisson, data = Mental)

Here is Mental, if it matters.

 dput(Mental)
structure(list(ses = structure(c(1L, 1L, 1L, 1L, 2L, 2L, 2L,
2L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 6L, 6L, 6L,
6L), .Label = c(1, 2, 3, 4, 5, 6), class = c(ordered,
factor)), mental = structure(c(1L, 2L, 3L, 4L, 1L, 2L, 3L,
4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L,
4L), .Label = c(Well, Mild, Moderate, Impaired), class = 
c(ordered,

factor)), Freq = c(64L, 94L, 58L, 46L, 57L, 94L, 54L, 40L,
57L, 105L, 65L, 60L, 72L, 141L, 77L, 94L, 36L, 97L, 54L, 78L,
21L, 71L, 54L, 71L)), .Names = c(ses, mental, Freq), row.names = 
c(NA,

-24L), class = data.frame)



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[R] How can I calculate the error of a fit parameter, when the data set has an error itself?

2010-03-16 Thread Markus Schmotz


Hi out there,

imagine you have a dataset (x,y) with errors f,
so that each y_i is y_i +- f_i. This is the normal case for almost all 
measurements, that one quantity y can only be measured with a certain 
accuracy.


 x-c(1,2,3)
 y-c(1.1,0.8,1.3)
 f-c(0.2,0.2,0.2)
 plot(x,y) #whereas every y has the uncertainty of f

If I now perform a nls-fit (and force the data through (0,0) to have 
only one fitting parameter)


 n-nls(y~a*x,start=list(a=1))
 summary(n)

I end up with an estimate of a of 1.4 +- 0.06 as standard error of the fit.
In this case the error gives only the accuracy of the fit itself, but 
does not include the measurement errors in y: f (error bars).
How is it possible to take them into account? I know that there is the 
chi-squared test, where the goodness of the fit is calculated, but again 
this does not include the errors itself.
There should be an easy solution, since this is a common problem in 
science, which I haven't found yet.


Any suggestions or solutions?
Thanks in advance!

-- Markus

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[R] R-Documentation including an image?

2010-03-16 Thread Roth, Thomas

Dear List Members,

I was wondering if there's a way to include an image in a .Rd file,
something like \img{}

In http://cran.r-project.org/doc/manuals/R-exts.html#Documenting-packages
nothing's mentioned regarding images (besides the image of the workspace)

Is there a way to include an image?

Thanks in advance,

Thomas



-- 
Dipl.-Ing. Thomas Roth (geb. Kaliwe)
Technische Universitaet Berlin
Institut für Werkzeugmaschinen und Fabrikbetrieb (IWF)
Fachgebiet Qualitaetswissenschaft
Pascalstr. 8-9

10587 Berlin

Tel:+49 (0) 30 / 314 23 565

e-mail:   thomas.r...@tu-berlin.de
Web:  www.qualitaetswissenschaft.de

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Re: [R] unknown compression

2010-03-16 Thread R Heberto Ghezzo, Dr

Thanks to Uwe Ligges, simply putting
library(xxx)
dump(ls(pos=2)),file=xxx.r)
gives a file with all the 'pure R' function in a package
This just solved my problem, as an added curiosity or just for completion sake, 
if the package 'xxx'
has some C/Fortran code , ie an /lib/xxx.dll in Windows, will Rcmd INSTALL xxx 
work when xxx has
a R; man and lib subfolders? not a src subfolder since I have the dll not the 
original C/for
Thanks 
Heberto Ghezzo



From: Uwe Ligges [lig...@statistik.tu-dortmund.de]
Sent: Sunday, March 14, 2010 2:04 PM
To: R Heberto Ghezzo, Dr
Subject: Re: [R] unknown compression

On 13.03.2010 22:33, R Heberto Ghezzo, Dr wrote:
 Hello Uwe / Rohlf
 Yes I know that, the problem here is that I have a package, old, it says 
 Built: R 2.0.0; ; 2004-11-15 14:58:41; windows
   it is not in CRAN the author and manteiner can not be reached, so I have no 
 way of obtaining the source tarball. The only solution is to decompress the 
 pair .rdb .rdx if it is possible?

In that case you can load the package and save all functions from that
environment into a new package.

The tool to load the serialized databases is lazyLoad() - or more low
level lazyLoadDBfetch(), both not intended to be called by a user.

Best wishes,
Uwe



 Thanks for any help
 Heberto Ghezzo

 
 From: Uwe Ligges [lig...@statistik.tu-dortmund.de]
 Sent: Saturday, March 13, 2010 3:37 PM
 To: R Heberto Ghezzo, Dr
 Cc: r-help@r-project.org
 Subject: Re: [R] unknown compression

 On 12.03.2010 21:34, R Heberto Ghezzo, Dr wrote:
 Hello, I am trying to modify some functions in an existing package. I can 
 get a function by just typing the name in the console, but how can I get all 
 the functions in a package? the ./R/ subdirectory has files xx.rdb and 
 xx.rdx which I can not decompress with 7-zip or with unzip, unrar etc. The 
 help files are compressed with gzip in the ./man/ folder and can be unzipped 
 easily.

 You are looking in a binary package.

 Instead of that, just download a source package (i.e. a not yet compiled
 one) from CRAN where you find the sources in plain text.

 Uwe Ligges

 Thanks for your help
 heberto.ghe...@mcgill.ca
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[R] G-test : log-likelihood ratio test

2010-03-16 Thread Gubelmann Carine

Dear Peter,

I am running your g.test() with the william's correction but I have a question 
about the input numbers. These are my data:

Our data are consistent with those obtained using microarray comparative 
genome hybridization in that we found significantly fewer variants per Mb on 
the X compared to the autosomal chromosomes (152 versus 336 respectively, G = 
93.4, P  2e-16, df = 1), and in exons (including UTRs) compared to non-exonic 
regions (69 versus 392 respectively, G = 14,226, P  2e-16, df = 1).

How do I have to write the input? Should I have to include any total number (in 
this case Mb) minus the variants?

g.test(rbind(c(152,(999848)),c(336,(999664))), correct = williams) or 
g.test(rbind(c(152,336)), correct = williams) ?

Thanks a lot for your help,
Carine


Carine Gubelmann, PhD student
EPFL, Institute of Bioengineering
Bldg. AI 1351
Station 15
CH-1015 Lausanne
Phone: + 41 (0) 21 693 09 59
Fax: + 41 (0) 21 693 09 80


[[alternative HTML version deleted]]

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Re: [R] G-test : log-likelihood ratio test

2010-03-16 Thread Gubelmann Carine

Can you please, do not write my question on the internet server,
Thanks

De : Gubelmann Carine
Envoyé : mardi, 16. mars 2010 13:36
À : 'r-h...@stat.math.ethz.ch'
Objet : [R] G-test : log-likelihood ratio test

Dear Peter,

I am running your g.test() with the william's correction but I have a question 
about the input numbers. These are my data:

Our data are consistent with those obtained using microarray comparative 
genome hybridization in that we found significantly fewer variants per Mb on 
the X compared to the autosomal chromosomes (152 versus 336 respectively, G = 
93.4, P  2e-16, df = 1), and in exons (including UTRs) compared to non-exonic 
regions (69 versus 392 respectively, G = 14,226, P  2e-16, df = 1).

How do I have to write the input? Should I have to include any total number (in 
this case Mb) minus the variants?

g.test(rbind(c(152,(999848)),c(336,(999664))), correct = williams) or 
g.test(rbind(c(152,336)), correct = williams) ?

Thanks a lot for your help,
Carine


[[alternative HTML version deleted]]

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[R] R Training

2010-03-16 Thread Sarah Lewis

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Bellinger Close
Chippenham
Wilts
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[R] boxplot, vertical position of x-axis labels

2010-03-16 Thread Kay Cichini


hello,

i can't figure out how to change the vertical position of my x axis labels..

boxplot(c(1:12)~c(rep(1,6),rep(2,6)),at=c(1,2),
col=c(0,grey),las=1,xaxt=n)

### i put paragraphs in the x-labels because of limited horizontal space

axis(1,at=c(1,2),adj=1,labels=c(Salix
Scrub,Tall
Forb))

...the labels are one line above usual position and cross the tickmarks and
i don't know how to get around this.

can anyone help with this?
thanks in advance. 

kay
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Re: [R] R-Documentation including an image?

2010-03-16 Thread Dieter Menne



Roth, Thomas wrote:
 
 
 I was wondering if there's a way to include an image in a .Rd file,
 something like \img{}
 
 

Not yet, but it has been on the top wish list since years now, and there is
hope. 

Dieter

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Re: [R] R-Documentation including an image?

2010-03-16 Thread Duncan Murdoch


On 16/03/2010 9:26 AM, Roth, Thomas wrote:

Dear List Members,

I was wondering if there's a way to include an image in a .Rd file,
something like \img{}

In http://cran.r-project.org/doc/manuals/R-exts.html#Documenting-packages
nothing's mentioned regarding images (besides the image of the workspace)

Is there a way to include an image?


Not currently.  That's an improvement that may eventually come, but it 
won't make 2.11.x.


Duncan Murdoch

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Re: [R] How to parse a string (by a new markup) with R ?

Hi Jim,
Thanks for the questions, here are my answers:

*Q: Does each sequence have the same number of for the opening
sequence as it does for on the ending sequence? *
A: Yes

*Q: Does the parsing always start with a partial stem 0 as your example
shows? *
A: No. Sometimes it will start with a few .

*Q: Is there a way of making sure you have the right sequences when you
start? *
A: I am not sure I understand what you mean.

*Q: Is there a chance of error in the middle of the string that you have to
restart from?*
A: Sadly, yes. In which case, I'll need to ignore one of the inner stems...

*Q: How long are these strings that you want to parse? *
A: Each string has between 60 to 150 characters (and I have tens
of thousands of them...)

*Q: Is each one a self contained sequence like you show in your example, or
do they go on for thousands of characters? *
A: each sequence is self contained.

*Q: Is there always at least one '.' between stems? *
A: No.

*Q: A full set of rules as to how the parsing should be done would be
useful.*
A: I agree. But since I don't have even a basic idea on how to start coding
this, I thought first to have some help on the beginning and try to tweak
with the other cases that will come up before turning back for help.

*Q: Do you have the BNF syntax for parsing?*
A: No. Your e-mail is the first time I came across it (
http://en.wikipedia.org/wiki/BackusNaur_Formhttp://en.wikipedia.org/wiki/Backus%E2%80%93Naur_Form
).

Thanks for the help,
Tal

Contact
Details:---
Contact me: tal.gal...@gmail.com | 972-52-7275845
Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
www.r-statistics.com (English)
--

On Tue, Mar 16, 2010 at 1:59 PM, jim holtman jholt...@gmail.com wrote:

How are you supposed to interprete the string that is doing the parsing?
Does each sequence have the same number of for the opening sequence
as it does for on the ending sequence? That what it appears to be
looking at the way stem 3 is parsed. You will have to provide a little more
insight on how to interprete the symbols. Does the parsing always start
with a partial stem 0 as your example shows? Is there a way of making sure
you have the right sequences when you start? Is there a chance of error in
the middle of the string that you have to restart from? How long are these
strings that you want to parse? Is each one a self contained sequence like
you show in your example, or do they go on for thousands of characters? Is
there always at least one '.' between stems? A full set of rules as to how
the parsing should be done would be useful. Do you have the BNF syntax for
parsing?

On Tue, Mar 16, 2010 at 6:10 AM, Tal Galili tal.gal...@gmail.com wrote:

Hello all,

For some work I am doing on RNA, I want to use R to do string parsing that
(I think) is like a simplistic HTML parsing.

For example, let's say we have the following two variables:

Seq -

GCCTCGATAGCTCAGTTGGGAGAGCGTACGACTGAAGATCGTAAGGtCACCAGTTCGATCCTGGTTCCA
Str -

...

Say that I want to parse Seq According to Str, by using the legend
here

Seq:
GCCTCGATAGCTCAGTTGGGAGAGCGTACGACTGAAGATCGTAAGGtCACCAGTTCGATCCTGGTTCCA
Str:
...

| | | | | | | ||
|

+-+ +--+ +---+
+---++-+

|Stem 1Stem 2 Stem 3 |

Stem 0

Assume that we always have 4 stems (0 to 3), but that the length of
letters
before and after each of them can very.

The output should be something like the following list structure:

list(
Stem 0 opening = GCCTCGA,
before Stem 1 = TA,
Stem 1 = list(opening = GCTC,
inside = AGTTGGGA,
closing = GAGC
),
between Stem 1 and 2 = G,
Stem 2 = list(opening = TACGA,
inside = CTGAAGA,
closing = TCGTA
),
between Stem 2 and 3 = AGGtC,
Stem 3 = list(opening = ACCAG,
inside = TTCGATC,
closing = CTGGT
),
After Stem 3 = ,
Stem 0 closing = TCC
)

I don't have any experience with programming a parser, and would like
advices as to what strategy to use when programming something like this
(and
any recommended R commands to use).

What I was thinking of is to first get rid of the Stem 0, then go
through
the inner string with a recursive function (let's call it seperate.stem)
that each time will split the string into:
1. before stem
2. opening stem
3. inside stem
4. closing stem
5. after stem

Where the after stem will then be

[R] passing columns of tables as a variable to functions

2010-03-16 Thread Sacha Viquerat


hello! ive come across the following problem:
im writing a function to ease the production of maps. as my tables have 
headers, id like to include an option in my function header to pass 
these columns to use them inside the evaluation block. the function 
looks as follows:


# maptable #the name of the table containing coordinates and columns for 
measured values

# value: which column of my table to use (e.g. Alt, slope, us, etc...
# labels(maptable)
# [1] pos.e pos.n Alt slope us uus lc

make.map-function (maptable,value)
{
pos.e-maptable$pos.e #calling the column directly works
pos.n-maptable$pos.n #calling the column directly works
key-maptable$value #this doesnt work. output: NULL
... rest of function, irrelevant to my question
}

for example, i call the function by:

make.map(elevation,Alt,Altitude,Sightings)

and my interp from akima package denies work, since key is NULL

interp(pos.e,pos.n,key,...)

have i just missed something? ive browsed the help pages and the 
archive, looked into crawleys R book but didnt find any solution, though 
im pretty sure this should be achievable!


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Re: [R] Loading workspaces from the command line

2010-03-16 Thread Wincent

It is a promising solution. Yet, there is room for improvement. I
revise the if condition so it won't throw an error during ordinary
startup.

.First - function() {
  if (length(commandArgs(T))0  commandArgs(T)[1] == ld){
load(commandArgs(T)[-1], .GlobalEnv)
  }
}

For the Rload script, it should be:
gnome-terminal --command R --args ld '$1'

Note the single quotation of $1. Without it, it does not work if the
file name contains space.

HTH
Best
Ronggui

On 12 January 2009 23:45, Zhou Fang zhou.zf...@gmail.com wrote:
 Well, that isn't ideal for my purposes. (A little context - basically
 I have a script that I'm running for a lot of simulations, which is
 kinda buggy, and what I'm doing is I'm having the script periodically
 save whatever it has done so far to an automatically named file. Then
 if something odd happens in between two saves, I can run forward from
 a previously saved point to find the problem and figure out why it
 happened, and also I won't risk losing everything if something
 catastrophic happens.)

 Anyways, if anyone's interested, in .Rprofile

 .First - function(){
  if (rev(commandArgs())[2] == ld){
    load(rev(commandArgs())[1], .GlobalEnv)
  }
 }

 Then e.g.

 alias Rload='R --arg ld'

 or make a bash script with

 gnome-terminal --command R --args ld $1

 and set some Open With options, and you'll be about to open R
 workspaces from Nautilus etc by point and click.

 Zhou


 On Mon, Jan 12, 2009 at 3:14 PM, Gabor Grothendieck
 ggrothendi...@gmail.com wrote:
 Another possibility is to have a separate directory
 for each project and place an .RData file in each.
 Now just cd to whatever directory corresponds to the
 project you wish to work on and start R normally.
 No code is needed.

 On Mon, Jan 12, 2009 at 10:04 AM, Zhou Fang zhou.zf...@gmail.com wrote:
 Ok, looks like I can do what I want with --args, commandArgs() and an
 appropiate .First.

 Thanks,

 Zhou

 On Mon, Jan 12, 2009 at 2:27 PM, David Winsemius dwinsem...@comcast.net 
 wrote:
 See if this material is helpful:

 http://cran.r-project.org/doc/manuals/R-intro.html#Invoking-R-from-the-command-line

 -- David Winsemius

 On Jan 12, 2009, at 7:24 AM, Zhou Fang wrote:

 That's not really what I meant by 'command line'. I meant, well,
 loading from e.g. a bash shell, not from within an interactive R
 session itself.

 Thanks anyways,

 Zhou

 (Possibly this email was sent twice. Apologies)

 On Mon, Jan 12, 2009 at 12:15 PM, Henrique Dallazuanna www...@gmail.com
 wrote:

 See ?load

 On Mon, Jan 12, 2009 at 10:12 AM, Zhou Fang zhou.zf...@gmail.com wrote:

 Hi,

 Is there any way to load workspaces (e.g. stuff from save.image) from
 the command line? I'm on Linux, and would find this very helpful.

 I'm guessing this functionality can be duplicated with a skillful bash
 script to rename the particular file to .RData (and then back once R
 terminates), but I'm wondering if there's a better way.

 Zhou Fang

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-- 
Wincent Ronggui HUANG
Doctoral Candidate
Dept of Public and Social Administration
City University of Hong Kong
http://asrr.r-forge.r-project.org/rghuang.html

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Re: [R] How to parse a string (by a new markup) with R ?

We show how to use the gsubfn package to parse this.

The rules are not entirely clear so we will assume the following:

- there is a fixed template for the output which is the same as your
output but possibly with different character strings filled in.  This
implies, for example, that there are exactly Stem0, Stem1, Stem2 and
Stem3 and no fewer or more stems.

- the sequence always starts with the open of Stem0, at least one dot
and the open of Stem1.  There are no dots prior to the open of Stem0.
This seems to be implicit in your sample output since there is no zero
length string in your sample output corresponding to dots prior to
Stem0.

- Stem0 closes with the same number of  as there are  to open it

You can modify this yourself to take into account the actual rules
whatever they are.

We first calculate, k, the number of leading 's using strapply.

Then we replace the leading k 's with }'s and the trailing k 's with
{'s giving us Str3:

 }}}..{{{.

We again use strapply, this time to get the lengths of the runs.  Note that
zero length runs are possible so we cannot, for example, use rle for this.  For
example there is a zero length run of dots between the last  and the first {.
read.fwf is used to actually parse out the strings using the lengths we just
calculated.

Finally we fill in the template using relist.

# inputs

Seq -
GCCTCGATAGCTCAGTTGGGAGAGCGTACGACTGAAGATCGTAAGGtCACCAGTTCGATCCTGGTTCCA
Str -
...
template -
  list(
Stem 0 opening = ,
before Stem 1 = ,
Stem 1 = list(opening = ,
inside = ,
closing = 
),
between Stem 1 and 2 = ,
Stem 2 = list(opening = ,
inside = ,
closing = 
),
between Stem 2 and 3 = ,
Stem 3 = list(opening = ,
inside = ,
closing = 
),
After Stem 3 = ,
Stem 0 closing = 
   )

# processing

# create string made by repeating string s k times followed by more
reps - function(s, k, more = ) {
paste(paste(rep(s, k), collapse = ), more, sep = )
}

library(gsubfn)
k - nchar(strapply(Str, ^+, c)[[1]])
Str2 - sub(^+, reps(}, k), Str)
Str3 - sub(reps(, k, ([^]*)$), reps({, k, \\1), Str2)

pat -
^(}*)([.]*)(*)([.]*)(*)([.]*)(*)([.]*)(*)([.]*)(*)([.]*)(*)([.]*)({*)([.]*)$
lens - sapply(strapply(Str3, pat, c)[[1]], nchar)
tokens - unlist(read.fwf(textConnection(Seq), lens, as.is = TRUE))
closeAllConnections()
tokens[is.na(tokens)] - 
out - relist(tokens, template)
out


Here is the str of the output for your sample input:

 str(out)
List of 9
 $ Stem 0 opening  : chr GCCTCGA
 $ before Stem 1   : chr TA
 $ Stem 1  :List of 3
  ..$ opening: chr GCTC
  ..$ inside : chr AGTTGGGA
  ..$ closing: chr GAGC
 $ between Stem 1 and 2: chr G
 $ Stem 2  :List of 3
  ..$ opening: chr TACGA
  ..$ inside : chr CTGAAGA
  ..$ closing: chr TCGTA
 $ between Stem 2 and 3: chr AGGtC
 $ Stem 3  :List of 3
  ..$ opening: chr ACCAG
  ..$ inside : chr TTCGATC
  ..$ closing: chr CTGGT
 $ After Stem 3: chr 
 $ Stem 0 closing  : chr TCC



On Tue, Mar 16, 2010 at 6:10 AM, Tal Galili tal.gal...@gmail.com wrote:
 Hello all,

 For some work I am doing on RNA, I want to use R to do string parsing that
 (I think) is like a simplistic HTML parsing.


 For example, let's say we have the following two variables:

    Seq -
 GCCTCGATAGCTCAGTTGGGAGAGCGTACGACTGAAGATCGTAAGGtCACCAGTTCGATCCTGGTTCCA
    Str -
 ...

 Say that I want to parse Seq According to Str, by using the legend here

 Seq: GCCTCGATAGCTCAGTTGGGAGAGCGTACGACTGAAGATCGTAAGGtCACCAGTTCGATCCTGGTTCCA
 Str: ...

     |     |  |              | |               |     |               ||     |

     +-+  +--+ +---+     +---++-+

        |        Stem 1            Stem 2                 Stem 3         |

        |                                                                |

        ++

                                Stem 0

 Assume that we always have 4 stems (0 to 3), but that the length of letters
 before and after each of them can very.

 The output should be something like the following list structure:


    list(
     Stem 0 opening = GCCTCGA,
     before Stem 1 = TA,
     Stem 1 = list(opening = GCTC,
     inside = AGTTGGGA,
     closing = GAGC
     ),
     between Stem 1 and 2 = G,
     Stem 2 = list(opening = TACGA,
     inside = CTGAAGA,
     closing = TCGTA
     ),
     between Stem 2 and 3 = AGGtC,
     Stem 3 = list(opening = ACCAG,
     inside = TTCGATC,
     closing = CTGGT
     ),
     After Stem 3 = ,
     Stem 0 closing = TCC
    )


 I don't have any experience with programming a parser, and would like
 advices as to what strategy to use when programming something like this (and
 any recommended R commands to use).


 What I was thinking of is to first get rid of the Stem 0,

Re: [R] boxplot, vertical position of x-axis labels



On Mar 16, 2010, at 9:37 AM, Kay Cichini wrote:



hello,

i can't figure out how to change the vertical position of my x axis  
labels..


boxplot(c(1:12)~c(rep(1,6),rep(2,6)),at=c(1,2),
col=c(0,grey),las=1,xaxt=n)

### i put paragraphs in the x-labels because of limited horizontal  
space



?axis

Try using the padj argument (and it bothered me to use the cr's  
rather than \n, so I modified the labels argument as well):


axis(1,at=c(1,2),adj=1,padj=0.5,labels=c(Salix\nScrub,Tall\nForb))




...the labels are one line above usual position and cross the  
tickmarks and

i don't know how to get around this.

can anyone help with this?
thanks in advance.

--

David Winsemius, MD
West Hartford, CT

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[R] Odp: boxplot, vertical position of x-axis labels

2010-03-16 Thread Petr PIKAL

Hi

r-help-boun...@r-project.org napsal dne 16.03.2010 14:37:01:

 
 hello,
 
 i can't figure out how to change the vertical position of my x axis 
labels..
 
 boxplot(c(1:12)~c(rep(1,6),rep(2,6)),at=c(1,2),
 col=c(0,grey),las=1,xaxt=n)
 
 ### i put paragraphs in the x-labels because of limited horizontal space
 
 axis(1,at=c(1,2),adj=1,labels=c(Salix
 Scrub,Tall
 Forb))
 
 ...the labels are one line above usual position and cross the tickmarks 
and
 i don't know how to get around this.
 

Not sure if it is the only way but

# first put only labels
axis(1,at=c(1,2),adj=1, tick=F, line=2,labels=c(Salix 
Scrub,Tall 
Forb))

# add axis without labels
axis(1,at=c(1,2),adj=1, tick=T,labels=c(NA, NA))

Regards
Petr


 can anyone help with this?
 thanks in advance. 
 
 kay
 -- 
 View this message in context: 
http://n4.nabble.com/boxplot-vertical-position-
 of-x-axis-labels-tp1594857p1594857.html
 Sent from the R help mailing list archive at Nabble.com.
 
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[R] remove substring from each string vector component

2010-03-16 Thread arnaud chozo

Hi all,

I have a string vector like that: x=c(1\t\t, 2, 3\t\t\t)
I need to remove all the occurrences of \t, in order to obtain: x = 1
2   3

I'm trying to use the function substring2, and it works for each component,
for example:
substring2(x[1], \t) =
gives x = 1   23\t\t\t

I'd like to apply this function to each component and I tried the following:

myfun = function(x, i) {
  substring2(x[i], \t) = 
}

lapply(x, myfun)

which gives x=  

I know that I'm wrong somewhere using lapply, but I can't fix it.

Thanks in advance,
Arnaud Chozo

[[alternative HTML version deleted]]

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Re: [R] Problem in installing ncdf package




On 16.03.2010 07:06, BabyL BabyK wrote:

Dear R communities

Could you please help me with the problem I encounter while trying to install 
the ncdf package?

download.packages(ncdf, /home/user/soft/R/library/)
cd /home/user/soft/R/library
R CMD INSTALL ncdf_1.6.tar.gz # fail
sudo R CMD INSTALL ncdf_1.6.tar.gz # fail

cd /home/user/soft/
# download http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-4.0.1.tar.gz
tar -xzvf netcdf-4.0.1.tar.gz

R CMD INSTALL 
--configure-args=-with-netcdf_incdir=/home/user/soft/netcdf-4.0.1/libsrc 
-with-netcdf_libdir=/home/user/soft/netcdf-4.0.1/libsrc/ ncdf_1.6.tar.gz  # Error: 
user specified netCDF library directory does not have libnetcdf.a !



You need to install netcdf first, then specify the include and libdir 
(the later will contain the lib afterwards).


Uwe Ligges




Thank you very much for your kind help.




[[alternative HTML version deleted]]

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Re: [R] passing columns of tables as a variable to functions

2010-03-16 Thread Phil Spector


Sacha -
   The $ notation can only be used when you literally use
the name of the column you want.  If the name of the column
is stored in a variable, you should use this notation:

  maptable[,value]

to refer to the column whose name is stored in value.


- Phil Spector
 Statistical Computing Facility
 Department of Statistics
 UC Berkeley
 spec...@stat.berkeley.edu


On Tue, 16 Mar 2010, Sacha Viquerat wrote:


hello! ive come across the following problem:
im writing a function to ease the production of maps. as my tables have 
headers, id like to include an option in my function header to pass these 
columns to use them inside the evaluation block. the function looks as 
follows:


# maptable #the name of the table containing coordinates and columns for 
measured values

# value: which column of my table to use (e.g. Alt, slope, us, etc...
# labels(maptable)
# [1] pos.e pos.n Alt slope us uus lc

make.map-function (maptable,value)
{
pos.e-maptable$pos.e #calling the column directly works
pos.n-maptable$pos.n #calling the column directly works
key-maptable$value #this doesnt work. output: NULL
... rest of function, irrelevant to my question
}

for example, i call the function by:

make.map(elevation,Alt,Altitude,Sightings)

and my interp from akima package denies work, since key is NULL

interp(pos.e,pos.n,key,...)

have i just missed something? ive browsed the help pages and the archive, 
looked into crawleys R book but didnt find any solution, though im pretty 
sure this should be achievable!


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Re: [R] remove substring from each string vector component

2010-03-16 Thread Eik Vettorazzi


Hi Arnaud,
how about this:

x=c(1\t\t, 2, 3\t\t\t)

gsub(\t,,x)

hth.

arnaud chozo schrieb:

Hi all,

I have a string vector like that: x=c(1\t\t, 2, 3\t\t\t)
I need to remove all the occurrences of \t, in order to obtain: x = 1
2   3

I'm trying to use the function substring2, and it works for each component,
for example:
substring2(x[1], \t) =
gives x = 1   23\t\t\t

I'd like to apply this function to each component and I tried the following:

myfun = function(x, i) {
  substring2(x[i], \t) = 
}

lapply(x, myfun)

which gives x=  

I know that I'm wrong somewhere using lapply, but I can't fix it.

Thanks in advance,
Arnaud Chozo

[[alternative HTML version deleted]]

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--
Eik Vettorazzi
Institut für Medizinische Biometrie und Epidemiologie
Universitätsklinikum Hamburg-Eppendorf

Martinistr. 52
20246 Hamburg

T ++49/40/7410-58243
F ++49/40/7410-57790

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[R] heatmap.2 - ColSideColors question

2010-03-16 Thread Tim Smith

Hi,

I wanted to make more than one side color bar. For example, I can make one side 
color bar (col1) with the following code:
---
library(gplots)

mat - matrix(sample(1:100,40),nrow=5)
class1 - c(rep(0,4),rep(1,4))
col1 - ifelse(class1 == 0,blue,red)
class2 - c(rep(1,3),rep(2,5))
col2 - ifelse(class2 == 0,yellow,green)

heatmap.2(mat,col=greenred(75),ColSideColors=col1,trace=none,
  dendrogram = column,labCol = NULL)


---
How can I modify the code so that both col1  col2 are displayed in the 
heatmap? 
thanks!


  
[[alternative HTML version deleted]]

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[R] Save variable in the file

2010-03-16 Thread rizesimoes


 Hi user's

 I'm learning how to use R and I have a problem with the format file. How
 do I to write in a file? I have some variables which I would like to write
 in a file.

 Â

 Att.

 Marize SimÃµes
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Re: [R] heatmap.2 - ColSideColors question

2010-03-16 Thread Rainer Machne

On 03/16/2010 04:06 PM, Tim Smith wrote:
 Hi,
 
 I wanted to make more than one side color bar. 

The function heatmap.plus (library: heatmap.plus) can do that, just
combine the different color vectors with cbind(col1,col2). Unfortunately
the arguments required for heatmap, heatmap.2 and heatmap.plus are
slightly different.

r




For example, I can make one side color bar (col1) with the following code:
 ---
 library(gplots)
 
 mat - matrix(sample(1:100,40),nrow=5)
 class1 - c(rep(0,4),rep(1,4))
 col1 - ifelse(class1 == 0,blue,red)
 class2 - c(rep(1,3),rep(2,5))
 col2 - ifelse(class2 == 0,yellow,green)
 
 heatmap.2(mat,col=greenred(75),ColSideColors=col1,trace=none,
   dendrogram = column,labCol = NULL)
 
 
 ---
 How can I modify the code so that both col1  col2 are displayed in the 
 heatmap? 
 thanks!
 
 
   
   [[alternative HTML version deleted]]
 
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Re: [R] remove substring from each string vector component

2010-03-16 Thread Miguel Porto

Hi!
It's just this easy:

x=gsub(\t,,x)

For more complex things, it's worth learning some regular expressions
syntax.
Miguel


On Tue, Mar 16, 2010 at 2:50 PM, arnaud chozo arnaud.ch...@gmail.comwrote:

 Hi all,

 I have a string vector like that: x=c(1\t\t, 2, 3\t\t\t)
 I need to remove all the occurrences of \t, in order to obtain: x = 1
 2   3

 I'm trying to use the function substring2, and it works for each component,
 for example:
 substring2(x[1], \t) =
 gives x = 1   23\t\t\t

 I'd like to apply this function to each component and I tried the
 following:

 myfun = function(x, i) {
  substring2(x[i], \t) = 
 }

 lapply(x, myfun)

 which gives x=  

 I know that I'm wrong somewhere using lapply, but I can't fix it.

 Thanks in advance,
 Arnaud Chozo

[[alternative HTML version deleted]]

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[[alternative HTML version deleted]]

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Re: [R] Save variable in the file

2010-03-16 Thread Joshua Wiley

Dear Marize,

It depends a bit on what format you would like to write your data as
and what your goals are.  Try looking at

?save
?write.table

save() will save objects as an R data file, write.table() will write
tables to a file, you can specify the delimiter (e.g., , for commas,
\t for tab, etc.).

What kind of file are you hoping to write to?

Best regards,


Josh

On Tue, Mar 16, 2010 at 8:15 AM, rizesimoes rizesim...@uol.com.br wrote:

     Hi user's

     I'm learning how to use R and I have a problem with the format file. How
     do I to write in a file? I have some variables which I would like to write
     in a file.

     Â

     Att.

     Marize SimÃµes
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-- 
Joshua Wiley
Senior in Psychology
University of California, Riverside
http://www.joshuawiley.com/

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Re: [R] aggregate without removing empty subset

2010-03-16 Thread Christophe Genolini

As I told you in private, thanks, it works perfectly.

More precisely, I am working with 3D array. Your code works well (both 
on matrix or on array).
But when part is a factor with only one value, the result has not a 
correct dimension (vector if m is a matrix, a matrix if m is an array).
Any way to fix that ?

m1 - matrix(1:12,4)
m2 - array(1:24,dim=c(4,3,2))
part1 - factor(c(A,B,A,B),levels=c(A,B,C))
part2 - factor(c(A,A,A,A),levels=c(A))


apply(m1, 2, tapply, part1, mean) ##Perfect (dim=c(3,3))
apply(m1, 2, tapply, part2, mean) ## dim=NULL...

apply(m2, c(2,3), tapply, part1, mean) ## Perfect (dim=c(3,3,2))
apply(m2, c(2,3), tapply, part2, mean) ## dim=c(3,2)


Christophe

 Try this:

 apply(m, 2, tapply, part, mean)

 On Mon, Mar 15, 2010 at 2:10 PM, Christophe Genolini
 cgeno...@u-paris10.fr wrote:
   
 Hi the list,

 As it is say in its doc, the aggregate function remove empty subsets. Is it
 possible to NOT remove empty subset ?
 --- 8 ---
 m - matrix(1:12,4)
 part - factor(c(A,B,A,B),levels=c(A,B,C))
 aggregate(m,list(part),mean)

 ### I get:
 #   Group.1 V1 V2 V3
 # 1   A  2  6 10
 # 2   B  3  7 11
 #
 ### I would like:
 #   Group.1 V1 V2 V3
 # 1   A  2  6 10
 # 2   B  3  7 11
 # 3   C NA NA NA
 --- 8 --


 Thanks
 Christophe

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Re: [R] remove substring from each string vector component

2010-03-16 Thread Marc Schwartz

On Mar 16, 2010, at 9:50 AM, arnaud chozo wrote:

 Hi all,
 
 I have a string vector like that: x=c(1\t\t, 2, 3\t\t\t)
 I need to remove all the occurrences of \t, in order to obtain: x = 1
 2   3
 
 I'm trying to use the function substring2, and it works for each component,
 for example:
 substring2(x[1], \t) =
 gives x = 1   23\t\t\t
 
 I'd like to apply this function to each component and I tried the following:
 
 myfun = function(x, i) {
  substring2(x[i], \t) = 
 }
 
 lapply(x, myfun)
 
 which gives x=  
 
 I know that I'm wrong somewhere using lapply, but I can't fix it.
 
 Thanks in advance,
 Arnaud Chozo


This is a place to use regular expressions with gsub():

x - c(1\t\t, 2, 3\t\t\t)

 gsub(\\t, , x)
[1] 1 2 3

See ?regex and ?gsub

Note that you have to double the backslashes in the regex.

HTH,

Marc Schwartz

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Re: [R] How to parse a string (by a new markup) with R ?

Gabor,
Thank you very very much!
Your code consists of so many commands I never played with, both helpful and
educational.

Thanks!
Tal

Contact
Details:---
Contact me: tal.gal...@gmail.com |  972-52-7275845
Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
www.r-statistics.com (English)
--




On Tue, Mar 16, 2010 at 4:24 PM, Gabor Grothendieck ggrothendi...@gmail.com
 wrote:

 We show how to use the gsubfn package to parse this.

 The rules are not entirely clear so we will assume the following:

 - there is a fixed template for the output which is the same as your
 output but possibly with different character strings filled in.  This
 implies, for example, that there are exactly Stem0, Stem1, Stem2 and
 Stem3 and no fewer or more stems.

 - the sequence always starts with the open of Stem0, at least one dot
 and the open of Stem1.  There are no dots prior to the open of Stem0.
 This seems to be implicit in your sample output since there is no zero
 length string in your sample output corresponding to dots prior to
 Stem0.

 - Stem0 closes with the same number of  as there are  to open it

 You can modify this yourself to take into account the actual rules
 whatever they are.

 We first calculate, k, the number of leading 's using strapply.

 Then we replace the leading k 's with }'s and the trailing k 's with
 {'s giving us Str3:


  }}}..{{{.

 We again use strapply, this time to get the lengths of the runs.  Note that
 zero length runs are possible so we cannot, for example, use rle for this.
  For
 example there is a zero length run of dots between the last  and the first
 {.
 read.fwf is used to actually parse out the strings using the lengths we
 just
 calculated.

 Finally we fill in the template using relist.

 # inputs

 Seq -
 GCCTCGATAGCTCAGTTGGGAGAGCGTACGACTGAAGATCGTAAGGtCACCAGTTCGATCCTGGTTCCA
 Str -
 ...
 template -
  list(
Stem 0 opening = ,
before Stem 1 = ,
Stem 1 = list(opening = ,
inside = ,
closing = 
),
between Stem 1 and 2 = ,
Stem 2 = list(opening = ,
inside = ,
closing = 
),
between Stem 2 and 3 = ,
Stem 3 = list(opening = ,
inside = ,
closing = 
 ),
After Stem 3 = ,
Stem 0 closing = 
)

 # processing

 # create string made by repeating string s k times followed by more
 reps - function(s, k, more = ) {
paste(paste(rep(s, k), collapse = ), more, sep = )
 }

 library(gsubfn)
 k - nchar(strapply(Str, ^+, c)[[1]])
 Str2 - sub(^+, reps(}, k), Str)
 Str3 - sub(reps(, k, ([^]*)$), reps({, k, \\1), Str2)

 pat -

 ^(}*)([.]*)(*)([.]*)(*)([.]*)(*)([.]*)(*)([.]*)(*)([.]*)(*)([.]*)({*)([.]*)$
 lens - sapply(strapply(Str3, pat, c)[[1]], nchar)
 tokens - unlist(read.fwf(textConnection(Seq), lens, as.is = TRUE))
 closeAllConnections()
 tokens[is.na(tokens)] - 
 out - relist(tokens, template)
 out


 Here is the str of the output for your sample input:

  str(out)
 List of 9
  $ Stem 0 opening  : chr GCCTCGA
  $ before Stem 1   : chr TA
  $ Stem 1  :List of 3
  ..$ opening: chr GCTC
  ..$ inside : chr AGTTGGGA
  ..$ closing: chr GAGC
  $ between Stem 1 and 2: chr G
  $ Stem 2  :List of 3
  ..$ opening: chr TACGA
  ..$ inside : chr CTGAAGA
  ..$ closing: chr TCGTA
  $ between Stem 2 and 3: chr AGGtC
  $ Stem 3  :List of 3
  ..$ opening: chr ACCAG
  ..$ inside : chr TTCGATC
  ..$ closing: chr CTGGT
  $ After Stem 3: chr 
  $ Stem 0 closing  : chr TCC



 On Tue, Mar 16, 2010 at 6:10 AM, Tal Galili tal.gal...@gmail.com wrote:
  Hello all,
 
  For some work I am doing on RNA, I want to use R to do string parsing
 that
  (I think) is like a simplistic HTML parsing.
 
 
  For example, let's say we have the following two variables:
 
 Seq -
 
 GCCTCGATAGCTCAGTTGGGAGAGCGTACGACTGAAGATCGTAAGGtCACCAGTTCGATCCTGGTTCCA
 Str -
 
 ...
 
  Say that I want to parse Seq According to Str, by using the legend
 here
 
  Seq:
 GCCTCGATAGCTCAGTTGGGAGAGCGTACGACTGAAGATCGTAAGGtCACCAGTTCGATCCTGGTTCCA
  Str:
 ...
 
  | |  |  | |   | |   ||
   |
 
  +-+  +--+ +---+
 +---++-+
 
 |Stem 1Stem 2 Stem 3 |
 
 ||
 
 ++
 
 Stem 0
 
  Assume that we always have 4 stems (0 to 3), but that the length of
 letters
  before and after each of them can very.
 
  The output should be something like the following list structure:
 
 
 list(
  Stem 0 opening =

Re: [R] R-Documentation including an image?

2010-03-16 Thread Thomas Roth

Thank you for the info, I couldn't find anything in the documentation and
wasn't sure ut now I know for sure.

-Ursprüngliche Nachricht-
Von: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Im
Auftrag von Dieter Menne
Gesendet: Dienstag, 16. März 2010 14:36
An: r-help@r-project.org
Betreff: Re: [R] R-Documentation including an image?



Roth, Thomas wrote:
 
 
 I was wondering if there's a way to include an image in a .Rd file,
 something like \img{}
 
 

Not yet, but it has been on the top wish list since years now, and there is
hope. 

Dieter

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[R] memory failure in adonis function (permanova)

2010-03-16 Thread Paloma Ruiz

Dear all,

I am trying to get a PERMANOVA with quite large data set. I am reading a lot
about this question, but I do not get the answer about it. Although I know
that the R function is adonis () (vegan package), it does not work:

adonis(Pha.env~SPha, data=Pha, permutations=10)

The error message:
 Error: cannot allocate vector of size 334.2 Mb
In addition: Warning messages:
1: In vegdist(lhs, method = method, ...) :
  Reached total allocation of 1535Mb: see help(memory.size)
2: In vegdist(lhs, method = method, ...) :
  Reached total allocation of 1535Mb: see help(memory.size)
3: In vegdist(lhs, method = method, ...) :
  Reached total allocation of 1535Mb: see help(memory.size)
4: In vegdist(lhs, method = method, ...) :
  Reached total allocation of 1535Mb: see help(memory.size)

When I have received this message from R usually it is due to an incorrect
introduction of the function elements (i.e., memory message errors).
However, I've just checked my matrix (Pha.env is a data.frame with num or
int variables, and, Pha is a data.frame with factor variables) and the
length of matrices is the same. I know that I'm wrong somewhere specifying
the matrices in adonis(), but I can't fix it.

Thanks in advance,

Paloma

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Re: [R] function arguments: name of an object vs. call producing the object?

2010-03-16 Thread Michael Friendly


Thanks, Duncan

In my context, the following gives me what I want:

 foo.glm - function(object) {
+ if (typeof(substitute(object))==symbol)
+ oname - as.character(sys.call())[2]
+ else oname - NULL
+ oname
+ }



 indep - glm(Freq ~ mental + ses, family = poisson, data = Mental)
 foo.glm(indep)
[1] indep

 foo.glm(glm(formula = Freq ~ mental + ses, family = poisson, data = 
Mental))

NULL



Duncan Murdoch wrote:

On 16/03/2010 8:26 AM, Michael Friendly wrote:
In a function, say foo.glm for glm objects I want to use the name of 
the object as a label for some output,
but *only* if a glm object was passed as an argument, not a call to 
glm() producing that object.

How can I distinguish these two cases?


Look at typeof(substitute(object)).  For example,

 f - function(object) typeof(substitute(object))
 f(aname)
[1] symbol
 f(aname+1)
[1] language

That will tell you if an object was passed by name, or if you got an 
expression to produce the object.


One problem with this approach is that it only looks at the direct 
call to f, for example


 g - function(x) f(x)
 g(aname + 1)
[1] symbol

because substitute looks at the f(x) call, not the g(aname + 1) call.

Duncan Murdoch




For example, I can use the following to get the name of the argument:

foo.glm - function(object) {
oname - as.character(sys.call())[2]
oname
}

  indep - glm(Freq ~ mental + ses, family = poisson, data = Mental)
  foo.glm(indep)
[1] indep

But in foo.glm() I want to avoid using this as oname:
  foo.glm(glm(formula = Freq ~ mental + ses, family = poisson, data 
= Mental))
[1] glm(formula = Freq ~ mental + ses, family = poisson, data = 
Mental)


Here is Mental, if it matters.

 dput(Mental)
structure(list(ses = structure(c(1L, 1L, 1L, 1L, 2L, 2L, 2L,
2L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 6L, 6L, 6L,
6L), .Label = c(1, 2, 3, 4, 5, 6), class = c(ordered,
factor)), mental = structure(c(1L, 2L, 3L, 4L, 1L, 2L, 3L,
4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L,
4L), .Label = c(Well, Mild, Moderate, Impaired), class = 
c(ordered,

factor)), Freq = c(64L, 94L, 58L, 46L, 57L, 94L, 54L, 40L,
57L, 105L, 65L, 60L, 72L, 141L, 77L, 94L, 36L, 97L, 54L, 78L,
21L, 71L, 54L, 71L)), .Names = c(ses, mental, Freq), row.names 
= c(NA,

-24L), class = data.frame)






--
Michael Friendly Email: friendly AT yorku DOT ca 
Professor, Psychology Dept.

York University  Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Streethttp://www.math.yorku.ca/SCS/friendly.html
Toronto, ONT  M3J 1P3 CANADA

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Re: [R] function arguments: name of an object vs. call producing theobject?

2010-03-16 Thread Bert Gunter

Michael:

Well, several possibilities come to mind, but their appropriateness depends
on what your argument could be.

1) The deparse(substitute(...)) construction will get you the character
string that was used as the argument and you can grep for ~ in it.

2) Or maybe check the class of the argument (e.g. if it's a formula it will
inherit from formula).

3) Or create separate (S3) methods foo.glm, foo.formula, etc. for the
different classes that you wish to consider. This might be the cleanest
approach, but it requires more planning.

HTH

Bert Gunter
Genentech Nonclinical Biostatistics
 
 
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Michael Friendly
Sent: Tuesday, March 16, 2010 5:27 AM
To: R-Help
Subject: [R] function arguments: name of an object vs. call producing
theobject?

In a function, say foo.glm for glm objects I want to use the name of the 
object as a label for some output,
but *only* if a glm object was passed as an argument, not a call to 
glm() producing that object.
How can I distinguish these two cases?

For example, I can use the following to get the name of the argument:

foo.glm - function(object) {
oname - as.character(sys.call())[2]
oname
}

  indep - glm(Freq ~ mental + ses, family = poisson, data = Mental)
  foo.glm(indep)
[1] indep

But in foo.glm() I want to avoid using this as oname:
  foo.glm(glm(formula = Freq ~ mental + ses, family = poisson, data = 
Mental))
[1] glm(formula = Freq ~ mental + ses, family = poisson, data = Mental)

Here is Mental, if it matters.

 dput(Mental)
structure(list(ses = structure(c(1L, 1L, 1L, 1L, 2L, 2L, 2L,
2L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 6L, 6L, 6L,
6L), .Label = c(1, 2, 3, 4, 5, 6), class = c(ordered,
factor)), mental = structure(c(1L, 2L, 3L, 4L, 1L, 2L, 3L,
4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L,
4L), .Label = c(Well, Mild, Moderate, Impaired), class = 
c(ordered,
factor)), Freq = c(64L, 94L, 58L, 46L, 57L, 94L, 54L, 40L,
57L, 105L, 65L, 60L, 72L, 141L, 77L, 94L, 36L, 97L, 54L, 78L,
21L, 71L, 54L, 71L)), .Names = c(ses, mental, Freq), row.names = 
c(NA,
-24L), class = data.frame)

-- 
Michael Friendly Email: friendly AT yorku DOT ca 
Professor, Psychology Dept.
York University  Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Streethttp://www.math.yorku.ca/SCS/friendly.html
Toronto, ONT  M3J 1P3 CANADA

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Re: [R] Help with calculating entropy of data

2010-03-16 Thread Marsh



mnstn wrote:
 
 Hello All,
 My question is not directly related to R but rather on which statistical
 method I should look in to for capturing the entropy of a data-set as a
 number. In this figure http://www.twitpic.com/18sob5 are two data sets
 blue and green (x-axis is time) that fluctuate between (-1,+1). Clearly,
 green has 4 jumps while blue has 1 (and a some?). Intuitively, green has
 more entropy than blue. Is there a robust statistical quantity that can
 capture their relative flexibilities? Additionally I am hoping this method
 will differentiate between two cases where both spend 50% of time in each
 of the states -1 and +1 but one has more jumps than the other. I am
 guessing the limits of that quantity are 0 (no change) and N-1 (for N time
 steps). 
 Sigma( mod(value(t)-value(t-1))/2 )? I am just thinking out loud here.
 
 I have about 200 such plots and I would like to arrange them in order of
 their entropy. 
 
 Thanks and I sincerely apologize if you feel this is not the right place
 to ask this question.
 MoonStone
 

Google information theory and entropy, and you'll find lots of stuff. If
memory serves me, Henri Theil's book, Economics and Information Theory,
has a good discussion of this kind of stuff.

Marsh Feldman
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[R] nested looping functions and dataframes

2010-03-16 Thread Lanna Jin


Hey All,

So, I am confused how exactly to use nesting loop functions in R to spit out
data frames.  I've managed to create a working function for my data set that
generates a data frame for a given set of Year i and Location j; but how
would I do it for all Years and Locations?

Here is my working function:

test-function(i,j){
a-x[which(x$Year==i  x$Location==j),]
b-as.data.frame(as.matrix(table(a$Species,a$Species)))
c-b[-which(b$Var1==b$Var2),-3]
c$Year-i; c$Location-j
return(c)
}

Where, x is a dataframe that looks like the following:

 head(x,n=20)
   Year LocationSpecies
66 1998   PIPE_7  ACMI2
67 1998   PIPE_7  AMAR2
68 1998   PIPE_7  AMCA6
69 1998   PIPE_7   ANCY
70 1998   PIPE_7   ASVE
71 1998   PIPE_7   BOCU
72 1998   PIPE_7   CIFL
73 1998   PIPE_7  DAPU5
74 1998   PIPE_7 DICHANTHEL
75 1998   PIPE_7  GABO2
76 1998   PIPE_7  HEHE5
77 1998   PIPE_7   LIAS
78 1998   PIPE_7   LIPY
79 1998   PIPE_7  PAVI2
80 1998   PIPE_7   PHPI
81 1998   PIPE_7  PHVI5
82 1998   PIPE_7   RAPI
83 1998   PIPE_7  SOCA6
84 1998   PIPE_7  VIPE2
85 1998   PIPE_7   ZIAU

and when feeding x into my function test with the parameters i = 1998 and
j = PIPE_7, I get the following dataframe, c:

 head(test(1998,PIPE_7),n=20)
 Var1  Var2 Year Location
2   AMAR2 ACMI2 1998   PIPE_7
3   AMCA6 ACMI2 1998   PIPE_7
4ANCY ACMI2 1998   PIPE_7
5ASVE ACMI2 1998   PIPE_7
6BOCU ACMI2 1998   PIPE_7
7CIFL ACMI2 1998   PIPE_7
8   DAPU5 ACMI2 1998   PIPE_7
9  DICHANTHEL ACMI2 1998   PIPE_7
10  GABO2 ACMI2 1998   PIPE_7
11  HEHE5 ACMI2 1998   PIPE_7
12   LIAS ACMI2 1998   PIPE_7
13   LIPY ACMI2 1998   PIPE_7
14  PAVI2 ACMI2 1998   PIPE_7
15   PHPI ACMI2 1998   PIPE_7
16  PHVI5 ACMI2 1998   PIPE_7
17   RAPI ACMI2 1998   PIPE_7
18  SOCA6 ACMI2 1998   PIPE_7
19  VIPE2 ACMI2 1998   PIPE_7
20   ZIAU ACMI2 1998   PIPE_7
21  ACMI2 AMAR2 1998   PIPE_7


I have searched through the R-help archives for hints, which have not been
successful in answering my question.  As a new user to R and programming
languages, I truly appreciate your help and thank you for your patience. 

Thanks in advance for your response,
Lanna Jin

-
Lanna Jin

lanna...@gmail.com
510-898-8525
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Re: [R] Error in library(eda) : there is no package called 'eda'




On 15.03.2010 21:44, Phil Spector wrote:

Peter -
While the message hasn't been shown in more recent versions
of R, older ( 2.9) versions of R used to print the following:


library(eda)

Warning message:
package 'eda' has been merged into 'stats'


... which happened for R-1.9.0 roughly 6 years ago.

Uwe Ligges





So I would guess the functions you're looking for are now automatically
loaded when you start R.
- Phil Spector
Statistical Computing Facility
Department of Statistics
UC Berkeley
spec...@stat.berkeley.edu


On Mon, 15 Mar 2010, Peter Lauren wrote:


I am using RGui version 2.10.1 (2009-12-14) for Windows.? When I enter
the call
?
library(eda)
?
the following message ensues.
?
Error in library(eda) : there is no package called 'eda'
?
I thought that eda was a standard library for exploratory data
analysis.? However I could not find it in the list of packages in the
pull-down menu either.
?
Any assistance with finding this package would be greatly appreciated.
?
Many thanks in advance,
Peter Lauren.
?
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Re: [R] nested looping functions and dataframes

2010-03-16 Thread Phil Spector


Lanna -
   Here's one way:

makeframe = function(x){
   b = as.data.frame(as.matrix(table(x$Species,x$Species)))
   b = b[!(b$Var1 == b$Var2),-3]
   data.frame(Year=x$Year[1],Location=x$Location[1],b)
}

result = lapply(split(x,list(x$Year,x$Location)),makeframe)

result will be a list of data frames, one for each 
Year/Location combination.You can find the data frame

for a particular Year/Location combination as

Year = 1998
Location = 'PIPE_7'
result[[paste(Year,Location,sep='.')]]

Hope this helps.

- Phil Spector
 Statistical Computing Facility
 Department of Statistics
 UC Berkeley
 spec...@stat.berkeley.edu


On Tue, 16 Mar 2010, Lanna Jin wrote:



Hey All,

So, I am confused how exactly to use nesting loop functions in R to spit out
data frames.  I've managed to create a working function for my data set that
generates a data frame for a given set of Year i and Location j; but how
would I do it for all Years and Locations?

Here is my working function:

test-function(i,j){
a-x[which(x$Year==i  x$Location==j),]
b-as.data.frame(as.matrix(table(a$Species,a$Species)))
c-b[-which(b$Var1==b$Var2),-3]
c$Year-i; c$Location-j
return(c)
}

Where, x is a dataframe that looks like the following:


head(x,n=20)

  Year LocationSpecies
66 1998   PIPE_7  ACMI2
67 1998   PIPE_7  AMAR2
68 1998   PIPE_7  AMCA6
69 1998   PIPE_7   ANCY
70 1998   PIPE_7   ASVE
71 1998   PIPE_7   BOCU
72 1998   PIPE_7   CIFL
73 1998   PIPE_7  DAPU5
74 1998   PIPE_7 DICHANTHEL
75 1998   PIPE_7  GABO2
76 1998   PIPE_7  HEHE5
77 1998   PIPE_7   LIAS
78 1998   PIPE_7   LIPY
79 1998   PIPE_7  PAVI2
80 1998   PIPE_7   PHPI
81 1998   PIPE_7  PHVI5
82 1998   PIPE_7   RAPI
83 1998   PIPE_7  SOCA6
84 1998   PIPE_7  VIPE2
85 1998   PIPE_7   ZIAU

and when feeding x into my function test with the parameters i = 1998 and
j = PIPE_7, I get the following dataframe, c:


head(test(1998,PIPE_7),n=20)

Var1  Var2 Year Location
2   AMAR2 ACMI2 1998   PIPE_7
3   AMCA6 ACMI2 1998   PIPE_7
4ANCY ACMI2 1998   PIPE_7
5ASVE ACMI2 1998   PIPE_7
6BOCU ACMI2 1998   PIPE_7
7CIFL ACMI2 1998   PIPE_7
8   DAPU5 ACMI2 1998   PIPE_7
9  DICHANTHEL ACMI2 1998   PIPE_7
10  GABO2 ACMI2 1998   PIPE_7
11  HEHE5 ACMI2 1998   PIPE_7
12   LIAS ACMI2 1998   PIPE_7
13   LIPY ACMI2 1998   PIPE_7
14  PAVI2 ACMI2 1998   PIPE_7
15   PHPI ACMI2 1998   PIPE_7
16  PHVI5 ACMI2 1998   PIPE_7
17   RAPI ACMI2 1998   PIPE_7
18  SOCA6 ACMI2 1998   PIPE_7
19  VIPE2 ACMI2 1998   PIPE_7
20   ZIAU ACMI2 1998   PIPE_7
21  ACMI2 AMAR2 1998   PIPE_7


I have searched through the R-help archives for hints, which have not been
successful in answering my question.  As a new user to R and programming
languages, I truly appreciate your help and thank you for your patience.

Thanks in advance for your response,
Lanna Jin

-
Lanna Jin

lanna...@gmail.com
510-898-8525
--
View this message in context: 
http://n4.nabble.com/nested-looping-functions-and-dataframes-tp1595166p1595166.html
Sent from the R help mailing list archive at Nabble.com.

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[R] bottlenecks in R script

2010-03-16 Thread Joe Calderon

hello *, im running into two major bottlenecks an R script.

1. going through a 40mb file and reading in via readLines() 1 line at
a time is almost an order of magnitude slow than the equivalent in
python, im wondering if there are alternatives to readLines(), doing
more lines at a time helps a bit

2. generating date sequences takes a long time, im basically doing
something like seq.Date(Sys.Date(), length.out = 300, by ='day') a lot
while digging into it, i strace'd the running process and it seems the
bulk of the time is spent checking for /etc/localtime

stat(/etc/localtime, {st_mode=S_IFREG|0644, st_size=2819, ...}) = 0


strace -cp 2964
Process 2964 attached - interrupt to quit
^CProcess 2964 detached
% time seconds  usecs/call callserrors syscall
-- --- --- - - 
 94.610.006387   0 55872   stat
  2.580.000174   0   568   read
  1.420.96   0   285   write
  1.390.94   1   137   brk
-- --- --- - - 
100.000.006751 56862   total



has anybody ran into similar problems?

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Re: [R] aggregate without removing empty subset

2010-03-16 Thread Henrique Dallazuanna

If the factor have only level:

apply(m1, 2, tapply, addNA(part2), mean)[-2,,drop = FALSE]


On Tue, Mar 16, 2010 at 12:43 PM, Christophe Genolini
cgeno...@u-paris10.fr wrote:
 As I told you in private, thanks, it works perfectly.

 More precisely, I am working with 3D array. Your code works well (both on
 matrix or on array).
 But when part is a factor with only one value, the result has not a correct
 dimension (vector if m is a matrix, a matrix if m is an array).
 Any way to fix that ?

 m1 - matrix(1:12,4)
 m2 - array(1:24,dim=c(4,3,2))
 part1 - factor(c(A,B,A,B),levels=c(A,B,C))
 part2 - factor(c(A,A,A,A),levels=c(A))

 apply(m1, 2, tapply, part1, mean) ##Perfect (dim=c(3,3))
 apply(m1, 2, tapply, part2, mean) ## dim=NULL...

 apply(m2, c(2,3), tapply, part1, mean) ## Perfect (dim=c(3,3,2))
 apply(m2, c(2,3), tapply, part2, mean) ## dim=c(3,2)


 Christophe

 Try this:

 apply(m, 2, tapply, part, mean)

 On Mon, Mar 15, 2010 at 2:10 PM, Christophe Genolini
 cgeno...@u-paris10.fr wrote:


 Hi the list,

 As it is say in its doc, the aggregate function remove empty subsets. Is it
 possible to NOT remove empty subset ?
 --- 8 ---
 m - matrix(1:12,4)
 part - factor(c(A,B,A,B),levels=c(A,B,C))
 aggregate(m,list(part),mean)

 ### I get:
 #   Group.1 V1 V2 V3
 # 1       A  2  6 10
 # 2       B  3  7 11
 #
 ### I would like:
 #   Group.1 V1 V2 V3
 # 1       A  2  6 10
 # 2       B  3  7 11
 # 3       C NA NA NA
 --- 8 --


 Thanks
 Christophe

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-- 
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O

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Re: [R] unknown compression




On 16.03.2010 14:35, R Heberto Ghezzo, Dr wrote:

Thanks to Uwe Ligges, simply putting
library(xxx)
dump(ls(pos=2)),file=xxx.r)
gives a file with all the 'pure R' function in a package
This just solved my problem, as an added curiosity or just for completion sake, 
if the package 'xxx'
has some C/Fortran code , ie an /lib/xxx.dll in Windows, will Rcmd INSTALL xxx 
work when xxx has
a R; man and lib subfolders? not a src subfolder since I have the dll not the 
original C/for


No, it won't work that way.
But you could use some trick in order to inject the library. Since 
that one was compiled and linked against an ancient version of R, there 
is always the risk that your library won't work at all or causes 
crashes, of course.


As an example see package rcom that does such nasty things by delivering 
the files somewhere in ./inst and ciopies on installation to ./libs 
using its configure.win file.


Best,
Uwe Ligges








Thanks
Heberto Ghezzo



From: Uwe Ligges [lig...@statistik.tu-dortmund.de]
Sent: Sunday, March 14, 2010 2:04 PM
To: R Heberto Ghezzo, Dr
Subject: Re: [R] unknown compression

On 13.03.2010 22:33, R Heberto Ghezzo, Dr wrote:

Hello Uwe / Rohlf
Yes I know that, the problem here is that I have a package, old, it says Built: 
R 2.0.0; ; 2004-11-15 14:58:41; windows
   it is not in CRAN the author and manteiner can not be reached, so I have no 
way of obtaining the source tarball. The only solution is to decompress the 
pair .rdb .rdx if it is possible?


In that case you can load the package and save all functions from that
environment into a new package.

The tool to load the serialized databases is lazyLoad() - or more low
level lazyLoadDBfetch(), both not intended to be called by a user.

Best wishes,
Uwe




Thanks for any help
Heberto Ghezzo


From: Uwe Ligges [lig...@statistik.tu-dortmund.de]
Sent: Saturday, March 13, 2010 3:37 PM
To: R Heberto Ghezzo, Dr
Cc: r-help@r-project.org
Subject: Re: [R] unknown compression

On 12.03.2010 21:34, R Heberto Ghezzo, Dr wrote:

Hello, I am trying to modify some functions in an existing package. I can get a 
function by just typing the name in the console, but how can I get all the 
functions in a package? the ./R/ subdirectory has files xx.rdb and xx.rdx which 
I can not decompress with 7-zip or with unzip, unrar etc. The help files are 
compressed with gzip in the ./man/ folder and can be unzipped easily.


You are looking in a binary package.

Instead of that, just download a source package (i.e. a not yet compiled
one) from CRAN where you find the sources in plain text.

Uwe Ligges


Thanks for your help
heberto.ghe...@mcgill.ca
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Re: [R] Error in pruning hclust object using maptree package




On 15.03.2010 16:37, Keith wrote:

Dear R users,

Due to too many children in my clustering result, I would like to prune
the tree-like hclust object into a certain groups. However, an error:

  clip.clust: no data provided for hclust object

always shows up.

Firstly, I tried the example in the maptree package, and it worked well.
Then, I tried to used the example in stats package to generate a hclust
object and tried the clip.clust method again, and the error still
occurred. Here is the example:

  hc - hclust(dist(USArrests), ave)
  pr - clip.clust(hc, k=4)
Error in clip.clust(hc, k = 4) :
clip.clust: no data provided for hclust object


Have you read ?clip.clust ??
It says for argument data:
 data   clustered dataset for hclust application.

whic means you need to provide data as the error message suggests as well.

 pr - clip.clust(hc, k=4, data=USArrests)
 pr$membership

works for me.

Uwe Ligges








Does anyone have the idea? My environment is
R version 2.10.1 (2009-12-14)
x86_64-pc-linux-gnu
[1] maptree_1.4-6

Best regards,
Keith

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Re: [R] Package documentation in dissertation

2010-03-16 Thread statmobile

Thanks Gabor, that looks to be exactly what I was seeking.  I'll play
around with that.

Thanks,
Brian

On Tue, Mar 16, 2010 at 05:19:23AM -0400, Gabor Grothendieck wrote:
 See:
 https://stat.ethz.ch/pipermail/r-help/2005-April/070581.html
 
 On Mon, Mar 15, 2010 at 11:16 PM, statmobile statmob...@gmail.com wrote:
  Hey Gabor,
 
  Thanks, I tried that, although I can't compile it directly.  Do you know
  where I can get the R LaTeX definitions in order to compile that?
 
  Thanks!
 
  Gabor Grothendieck wrote:
 
  Try:
 
  R CMD Rdconv --type=latex myfile.Rd
 
 
  On Mon, Mar 15, 2010 at 8:46 PM, statmobile statmob...@gmail.com wrote:
 
  Hey Everyone,
 
  I wrote up a library for my dissertation work, and I'd love to include it
  as
  an appendix.  I have found ways to export the Rd files as html, txt and
  pdf/ps, but not a raw tex export.  I've had to resort to dumping it into
  text files, and just using verbatim in my LaTeX code.  Does anybody have
  any
  recommendations or experiences with dealing with this?
 
  Please CC me on any response, as I only get summary emails from the list.
 
  Thanks in advance!
  Brian
 
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  PLEASE do read the posting guide
  http://www.R-project.org/posting-guide.html
  and provide commented, minimal, self-contained, reproducible code.
 
 
 

-- 
Brian J. Lopes
PhD Student
Department of Statistics and Operations Research
University of North Carolina at Chapel Hill

To know that we know what we know, and that we do not know what we do
not know, that is true knowledge --Henry David Thoreau (quoting
Confucius): Walden

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Re: [R] nested looping functions and dataframes

2010-03-16 Thread Lanna Jin

Thanks Phil,

That worked wonders!

Best,
Lanna

2010/3/16 Phil Spector spec...@stat.berkeley.edu

 Lanna -
   Here's one way:

 makeframe = function(x){
   b = as.data.frame(as.matrix(table(x$Species,x$Species)))
   b = b[!(b$Var1 == b$Var2),-3]
   data.frame(Year=x$Year[1],Location=x$Location[1],b)
 }

 result = lapply(split(x,list(x$Year,x$Location)),makeframe)

 result will be a list of data frames, one for each Year/Location
 combination.You can find the data frame
 for a particular Year/Location combination as

Year = 1998
Location = 'PIPE_7'
result[[paste(Year,Location,sep='.')]]

 Hope this helps.

- Phil Spector
 Statistical Computing Facility
 Department of Statistics
 UC Berkeley
 spec...@stat.berkeley.edu


 On Tue, 16 Mar 2010, Lanna Jin wrote:


 Hey All,

 So, I am confused how exactly to use nesting loop functions in R to spit
 out
 data frames.  I've managed to create a working function for my data set
 that
 generates a data frame for a given set of Year i and Location j; but how
 would I do it for all Years and Locations?

 Here is my working function:

 test-function(i,j){
 a-x[which(x$Year==i  x$Location==j),]
 b-as.data.frame(as.matrix(table(a$Species,a$Species)))
 c-b[-which(b$Var1==b$Var2),-3]
 c$Year-i; c$Location-j
 return(c)
 }

 Where, x is a dataframe that looks like the following:

 head(x,n=20)

  Year LocationSpecies
 66 1998   PIPE_7  ACMI2
 67 1998   PIPE_7  AMAR2
 68 1998   PIPE_7  AMCA6
 69 1998   PIPE_7   ANCY
 70 1998   PIPE_7   ASVE
 71 1998   PIPE_7   BOCU
 72 1998   PIPE_7   CIFL
 73 1998   PIPE_7  DAPU5
 74 1998   PIPE_7 DICHANTHEL
 75 1998   PIPE_7  GABO2
 76 1998   PIPE_7  HEHE5
 77 1998   PIPE_7   LIAS
 78 1998   PIPE_7   LIPY
 79 1998   PIPE_7  PAVI2
 80 1998   PIPE_7   PHPI
 81 1998   PIPE_7  PHVI5
 82 1998   PIPE_7   RAPI
 83 1998   PIPE_7  SOCA6
 84 1998   PIPE_7  VIPE2
 85 1998   PIPE_7   ZIAU

 and when feeding x into my function test with the parameters i = 1998
 and
 j = PIPE_7, I get the following dataframe, c:

 head(test(1998,PIPE_7),n=20)

Var1  Var2 Year Location
 2   AMAR2 ACMI2 1998   PIPE_7
 3   AMCA6 ACMI2 1998   PIPE_7
 4ANCY ACMI2 1998   PIPE_7
 5ASVE ACMI2 1998   PIPE_7
 6BOCU ACMI2 1998   PIPE_7
 7CIFL ACMI2 1998   PIPE_7
 8   DAPU5 ACMI2 1998   PIPE_7
 9  DICHANTHEL ACMI2 1998   PIPE_7
 10  GABO2 ACMI2 1998   PIPE_7
 11  HEHE5 ACMI2 1998   PIPE_7
 12   LIAS ACMI2 1998   PIPE_7
 13   LIPY ACMI2 1998   PIPE_7
 14  PAVI2 ACMI2 1998   PIPE_7
 15   PHPI ACMI2 1998   PIPE_7
 16  PHVI5 ACMI2 1998   PIPE_7
 17   RAPI ACMI2 1998   PIPE_7
 18  SOCA6 ACMI2 1998   PIPE_7
 19  VIPE2 ACMI2 1998   PIPE_7
 20   ZIAU ACMI2 1998   PIPE_7
 21  ACMI2 AMAR2 1998   PIPE_7


 I have searched through the R-help archives for hints, which have not been
 successful in answering my question.  As a new user to R and programming
 languages, I truly appreciate your help and thank you for your patience.

 Thanks in advance for your response,
 Lanna Jin

 -
 Lanna Jin

 lanna...@gmail.com
 510-898-8525
 --
 View this message in context:
 http://n4.nabble.com/nested-looping-functions-and-dataframes-tp1595166p1595166.html
 Sent from the R help mailing list archive at Nabble.com.

 __
 R-help@r-project.org mailing list
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 PLEASE do read the posting guide
 http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.




-- 
Lanna Jin

lanna...@gmail.com
510-898-8525

[[alternative HTML version deleted]]

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[R] Changing global variables from functions

2010-03-16 Thread jtouyz


Hey all,
I'm relatively new to the R-environment. I'm having a bit of trouble with
encapsulation.
I have a globally declared variable that doesn't update it when I change it
in a function. For example when I run the following function 

deckn-NULL
deck1-1  #52 card deck
deck-function()
{
#Creating a standard deck
deck1-c(1:52)
deckn-deck1
#Creating n decks
for (i in 2:num_decks)
{
deckn-c(deckn,52*i+deck1-1)
}
}
deckn
NULL

it returns NULL for deckn instead of a vector of values. Is there an easy
fix to update deckn in the function so that it outputs a vector of values (
I don't wish the function to return a value just update the current one)? 

Thanks in advance,
Josh Elliott
-- 
View this message in context: 
http://n4.nabble.com/Changing-global-variables-from-functions-tp1595002p1595002.html
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[R] Writting in the file

2010-03-16 Thread rizesimoes


   Hi user

   I'm learning how to use R and I have a problem with the format file. How do
   I to write in a file? I have some variables which I would like to write in a
   file.

   Â

   Att.

   Marize SimÃµes
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Re: [R] bottlenecks in R script

Check out read.csv.sql in the sqldf package.  It reads a file directly
into sqlite without going through R and then from there into R.  It
sets up the database and file layouts in the database for you and also
destroys the database when finished so reading is just a matter of one
line of R code.  It also has the capability of reading any portion of
the file that can be specified in sql. See examples on home page:
http://sqldf.googlecode.com

On Tue, Mar 16, 2010 at 12:51 PM, Joe Calderon calderon@gmail.com wrote:
 hello *, im running into two major bottlenecks an R script.

 1. going through a 40mb file and reading in via readLines() 1 line at
 a time is almost an order of magnitude slow than the equivalent in
 python, im wondering if there are alternatives to readLines(), doing
 more lines at a time helps a bit

 2. generating date sequences takes a long time, im basically doing
 something like seq.Date(Sys.Date(), length.out = 300, by ='day') a lot
 while digging into it, i strace'd the running process and it seems the
 bulk of the time is spent checking for /etc/localtime

 stat(/etc/localtime, {st_mode=S_IFREG|0644, st_size=2819, ...}) = 0


 strace -cp 2964
 Process 2964 attached - interrupt to quit
 ^CProcess 2964 detached
 % time     seconds  usecs/call     calls    errors syscall
 -- --- --- - - 
  94.61    0.006387           0     55872           stat
  2.58    0.000174           0       568           read
  1.42    0.96           0       285           write
  1.39    0.94           1       137           brk
 -- --- --- - - 
 100.00    0.006751                 56862           total



 has anybody ran into similar problems?

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Re: [R] Regarding variable importance in the randomForest package

2010-03-16 Thread Liaw, Andy

Seems like you're new to R as well?  The first argument should contain
only the predictor variables, but you used the entire data frame that
contains the response.

Andy 

 -Original Message-
 From: r-help-boun...@r-project.org 
 [mailto:r-help-boun...@r-project.org] On Behalf Of Corinne Staley
 Sent: Monday, March 15, 2010 9:52 PM
 To: r-help@r-project.org
 Subject: [R] Regarding variable importance in the randomForest package
 
 For anyone who is knowledgeable about the randomForest 
 package in R, I have
 a question:
 
 When I look at the variable importance for data, I see that 
 my response
 variable is included along with my predictor variables. That is, I am
 getting a MeanDecreaseGini for my response variable, and 
 therefore it seems
 as though it is being treated as a predictor variable.
 
 my code (just in case it helps) :
 comm.RF-randomForest(model.data,y=model.data$Comm_Heir,mtry=8
,importance=T)
 
 Apologies if it's a stupid question, but I'm new to 
 randomForests. Hopefully
 that makes sense and if anyone can let me know how remedy 
 this situation, I
 would be so grateful.
 
 Cheers!
 
   [[alternative HTML version deleted]]
 
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Notice:  This e-mail message, together with any attachme...{{dropped:10}}

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Re: [R] inner join sqldf

Its unlikely that the inner join is what you want. prochi has only 5
levels so the result is going to be enormous.  In the second statement
you are trying to union incompatible tables.  Get an introductory book
on SQL and read up on how it works.

On Mon, Mar 15, 2010 at 10:39 AM, Newbie19_02 nvanzuy...@gmail.com wrote:

 Dear Gabor,

 require(sqldf)

 file(description=http://n4.nabble.com/file/n1593282/test_sql_psd.txt;,
 open=)
 file(description=http://n4.nabble.com/file/n1593282/test_sql_tsf.txt;,
 open=)

 test_sql_psd -
 read.table(file=http://n4.nabble.com/file/n1593282/test_sql_psd.txt;,
 header=TRUE, sep=\t, dec=., na.strings=NA,
 check.names=TRUE, quote= \')


 test_sql_tsf
 -read.table(http://n4.nabble.com/file/n1593282/test_sql_tsf.txt; ,
 header=TRUE, sep=\t, dec=., na.strings=NA, check.names=TRUE, quote=
 \')




 test_sql_innerjoin - sqldf(select * from test_sql_psd inner join
 test_sql_tsf
 on test_sql_psd.prochi=test_sql_tsf.prochi)

 Please note that in my previous email I said that I had used union and it
 had worked.  In fact it did not.

 test_sql_union-sqldf(select * from test_sql_tsf union select * from
 test_sql_psd)
 did not work because of the following error:  Error in
 sqliteExecStatement(con, statement, bind.data) :
  RS-DBI driver: (error in statement: SELECTs to the left and right of UNION
 do not have the same number of result columns)


 Please let me know if this works otherwise I'll amend the code again.

 Thanks,
 natalie
 --
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[R] simple line graphics, labels and legend

2010-03-16 Thread Ivan Calandra

Dear users,

I think my questions are pretty simple, but I got lost in the hundreds 
of par() and plot() arguments and plot functions, so I don't know in 
which direction I should go.

Here is my sample dataset:
test - structure(list(DIET = structure(c(1L, 1L, 1L, 1L, 1L, 3L, 3L, 
3L, 3L, 3L, 2L, 2L, 2L, 2L, 2L, 4L, 4L, 4L, 4L, 4L), .Label = c(G, 
GG, L, LG), class = factor), SILIKATG = c(0.0152, 0.0161, 
0.0141, 0.0131, 0.0108, 0, 0, 0, 0, 1e-04, 0.0056, 0.0078, 0.0072, 
0.0047, 0.0091, 3e-04, 5e-04, 0, 0.0013, 0.0012)), .Names = c(DIET, 
SILIKATG), row.names = c(1L, 2L, 3L, 4L, 5L, 31L, 32L, 33L, 34L, 35L, 
61L, 62L, 63L, 64L, 65L, 101L, 102L, 103L, 104L, 105L), class = 
data.frame)

1. The first plot I want to do is:
plot(test$SILIKATG, ylim=c(0,0.02), type=l)

It looks the way I want to, but my question is:*
How to change the labels on the x-axis? I would like to have the groups 
(G, GG, L, LG) labeled on the x-axis instead of the 5, 10, 
15, 20 of Index. And if possible with ticks to delimit the groups. *

I've tried:plot(test$SILIKATG~test$DIET, ylim=c(0,0.02), 
type=l)But I get boxplots...

2. The second graph is an alternative, and I would like to use both for now:
I first modify the data:
selectG - test[test$DIET==G,]; selectG$DIET - factor(selectG$DIET, 
levels=G)
I do it for each group and:
plot(selectG$SILIKATG, type=p, ylim=c(0,0.02), pch=1, col=black); 
points(selectGG$SILIKATG, type=p, ylim=c(0,0.02), pch=2, col=red)
And so on for each group, and then add the legend with:
legend(x=topright, legend=c(G, GG, L, LG), pch=1:4, 
col=c(black, red, green, blue))

My question here is: *
Isn't there an easier way to do all of it?!
I'm quite sure there's a way where I don't have to select each group and 
plot it separately. And I guess something more automatic also exists 
(e.g. the legend so that I don't have to give the names of the groups 
and the colors and symbols used etc).

*Thank you all in advance for your help.
Regards,
Ivan

-- 
Ivan CALANDRA
PhD Student
University of Hamburg
Biozentrum Grindel und Zoologisches Museum
Abt. Säugetiere
Martin-Luther-King-Platz 3
D-20146 Hamburg, GERMANY
+49(0)40 42838 6231
ivan.calan...@uni-hamburg.de

**
http://www.for771.uni-bonn.de
http://webapp5.rrz.uni-hamburg.de/mammals/eng/mitarbeiter.php


[[alternative HTML version deleted]]

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

Re: [R] Changing global variables from functions



On Mar 16, 2010, at 11:04 AM, jtouyz wrote:



Hey all,
I'm relatively new to the R-environment. I'm having a bit of trouble  
with

encapsulation.
I have a globally declared variable that doesn't update it when I  
change it

in a function.



For example when I run the following function


deckn-NULL
deck1-1  #52 card deck
deck-function()

{
#Creating a standard deck
deck1-c(1:52)
deckn-deck1
   #Creating n decks
   for (i in 2:num_decks)


# could be wrong but it appears that you are expecting the act of  
putting num_ in front of decks to be interpreted by R as returning  
the length of deckn or deck1. That is a higher level of abstraction  
than is yet available in any computer language with which I am  
familiar. Or perhaps you were intending to use Greg Snow's soon to be  
released mind-reading package so that R could know that you wanted it  
to be 6?.


Perhaps instead (depending on what the real problem (unstated as yet)  
might be:


  for (i in 2:length(deck1) )  # or some other object or function  
that returns a numeric value.



   {
   deckn-c(deckn,52*i+deck1-1)



   }
}

deckn


You would have needed to assign a return-ed value to deckn in the  
outer environment. The deckn object would have disappeared at the end  
of the function call, and it would not have needed to be named  
deckn, either.



Try instead:

deckn-NULL
deck-function(num_decks=6)
{
#Creating a standard deck
deck1-c(1:52)
deckn-deck1
   #Creating n decks
   for (i in 2:num_decks)
   {
   deckn-c(deckn,52*i+deck1-1)
   }; return(deckn)
}
deckn - deck()
deckn

Which has a gap between 52 and 104 because of your logic, not mine.



NULL


it returns NULL for deckn instead of a vector of values. Is there an  
easy
fix to update deckn in the function so that it outputs a vector of  
values (
I don't wish the function to return a value just update the current  
one)?


You could, of course, explain what you are trying to do.



Thanks in advance,
Josh Elliott
--


David Winsemius, MD
West Hartford, CT

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

[R] an ordinal regression MCMC run high correlation

2010-03-16 Thread ping chen

I am trying to model  a clusterd ordinal response data (either 1, 2 or 3) 
called , the correponding physician of the patient is also in the data.
 
Since it is ordinal, I used the ordinal logit model
 
topbox[i]~discrete with probability P[j,1],p[j,2], p[j,3], j is the 
corresponding physician of the ith patient
 
C[j] is the physician effect , a1 and a1+theta is the common cutpoints for all 
physicians

I generate 10,000 iteration and there are still high autocorrelation of a1 and 
tau. I thought 10,000 is a pretty big number and the chain converges really 
slow. I am a new MCMC user and don't know other ways to solve this problem.
Will someone please give some suggestions that may apply to this specific 
modeling?

model  {
for ( i in 1:N) {
response[i]~dcat( p[physician[i], ] )
}

for (j in 1:Nt) {
p[j,1]-1-Q[j,1]
p[j,2]-Q[j,1]-Q[j,2]
p[j,3]-Q[j,2]
logit(Q[j,1])--c[j]
logit(Q[j,2])--(c[j]+theta)
score[j]-0.5*p[j,2]+p[j,3]
c[j]~dnorm(a1, tau)
}
a1~dnorm(0, 1.0E-06)
theta~dnorm(0, 1.0E-06)I(0,)
tau~dgamma(0.001,0.001)
}

list(N=667,Nt=50)

 
Thanks, Ping




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Re: [R] Changing global variables from functions

2010-03-16 Thread jtouyz


Hi David,
Thank you for your response. 
Yes, num_decks was previously defined in my program, I apologize for the
confusion as it is an integral value.
This is only one portion of my program that is being used to simulate card
counting in blackjack.

The basic idea was to modify deckn without having to return a value from the
function deck(). That is whenever deck() was run it would write over
whatever was in deckn (instead of having to input deckn-deck().)
It seems from your response that this may not be possible and return is
always required.
If I have erred, please let me know.

Thanks once again,
Josh Elliott


David Winsemius wrote:
 
 
 On Mar 16, 2010, at 11:04 AM, jtouyz wrote:
 

 Hey all,
 I'm relatively new to the R-environment. I'm having a bit of trouble  
 with
 encapsulation.
 I have a globally declared variable that doesn't update it when I  
 change it
 in a function.
 
 For example when I run the following function

 deckn-NULL
 deck1-1  #52 card deck
 deck-function()
 {
 #Creating a standard deck
 deck1-c(1:52)
 deckn-deck1
#Creating n decks
for (i in 2:num_decks)
 
 # could be wrong but it appears that you are expecting the act of  
 putting num_ in front of decks to be interpreted by R as returning  
 the length of deckn or deck1. That is a higher level of abstraction  
 than is yet available in any computer language with which I am  
 familiar. Or perhaps you were intending to use Greg Snow's soon to be  
 released mind-reading package so that R could know that you wanted it  
 to be 6?.
 
 Perhaps instead (depending on what the real problem (unstated as yet)  
 might be:
 
for (i in 2:length(deck1) )  # or some other object or function  
 that returns a numeric value.
 
{
deckn-c(deckn,52*i+deck1-1)
 
}
 }
 deckn
 
 You would have needed to assign a return-ed value to deckn in the  
 outer environment. The deckn object would have disappeared at the end  
 of the function call, and it would not have needed to be named  
 deckn, either.
 
 
 Try instead:
 
 deckn-NULL
 deck-function(num_decks=6)
 {
 #Creating a standard deck
 deck1-c(1:52)
 deckn-deck1
 #Creating n decks
 for (i in 2:num_decks)
 {
 deckn-c(deckn,52*i+deck1-1)
 }; return(deckn)
 }
 deckn - deck()
 deckn
 
 Which has a gap between 52 and 104 because of your logic, not mine.
 
 
 NULL

 it returns NULL for deckn instead of a vector of values. Is there an  
 easy
 fix to update deckn in the function so that it outputs a vector of  
 values (
 I don't wish the function to return a value just update the current  
 one)?
 
 You could, of course, explain what you are trying to do.
 

 Thanks in advance,
 Josh Elliott
 -- 
 
 David Winsemius, MD
 West Hartford, CT
 
 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide
 http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.
 
 

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http://n4.nabble.com/Changing-global-variables-from-functions-tp1595002p1595356.html
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] Constrained non linear regression using ML

2010-03-16 Thread Corrado


Dear R users,

I have to fit the non linear regression:

y~1-exp(-(k0+k1*p1+k2*p2+  +kn*pn))

where ki=0 for each i in [1  n] and pi are on R+.

I am using, at the moment, nls, but I would rather use a Maximum 
Likelhood based algorithm. The error is not necessarily normally 
distributed.


y is approximately beta distributed, and the volume of data is medium to 
large (the y,pi may have ~ 40,000 elements).


I have studied the packages in the task views Optimisation and Robust 
Statistical Methods, but I did look like what I was looking for was 
there. Maybe I am wrong.


The nearest thing was nlrob, but even that does not allow for 
constraints, as far as I can understand.


Any suggestion?

Regards

--
Corrado Topi
PhD Researcher
Global Climate Change and Biodiversity
Area 18,Department of Biology
University of York, York, YO10 5YW, UK
Phone: + 44 (0) 1904 328645, E-mail: ct...@york.ac.uk

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

[R] Problems with loading arm

2010-03-16 Thread Gregory Wawro


Hello,

I recently updated to R 2.10 on my 64 bit Dell Precision T7400 running
Enterprise Linux and now I can't get the arm library to load when I run
R using Wine.  Prior to the update I was able to use arm without any
trouble.  My main goal is to use arm with WinBUGS on this machine,
calling it from R for Windows, which is executed with wine.  After the
update, when I try to load the arm library, I get the following:


library(arm)

Loading required package: MASS
Loading required package: Matrix
Loading required package: lattice
Loading required package: lme4
Loading required package: R2WinBUGS
Loading required package: coda

Attaching package: 'coda'


The following object(s) are masked from package:lme4 :

 HPDinterval

Loading required package: abind
Loading required package: car
Error in packageDescription(arm, lib = mylib)$Version :
  $ operator is invalid for atomic vectors
In addition: Warning message:
In packageDescription(arm, lib = mylib) : no package 'arm' was found
Error : .onAttach failed in 'attachNamespace'
Error: package/namespace load failed for 'arm'

I tried reinstalling arm (and updating all packages), but I still get
the same error.

I've tried loading arm in R running under linux pointing to the library 
location that R for Windows is reading from and it loads fine.  I've tried 
loading arm in R for Windows referencing the library location where I've 
installed arm for R for linux, and get the following:



library(arm)

Loading required package: MASS
Loading required package: Matrix
Loading required package: lattice
Loading required package: lme4
Error in library.dynam(lib, package, package.lib) :
  shared library 'lme4' not found
Error: package 'lme4' could not be loaded

I installed lme4 in the same directory as arm (i.e., myrlibrary/), but R
claims it can't find it, even though it shows up in the window when I
click on Load Packages  I'm assuming this has something to do with
a shared library problem.

I've spent the past two days googling, reading manuals and standard
references, and I'm stumped.  Does anyone have any suggestions about how
I might fix this problem.

Best,
Greg

.

Gregory Wawro   gj...@columbia.edu
Associate Professor phone:  212-854-8540
Dept. of Political Science  fax:212-222-0598
741 International Affairs   http://www.columbia.edu/~gjw10/
Columbia University
New York, NY 10027

.

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

Re: [R] Changing global variables from functions



On Mar 16, 2010, at 2:43 PM, jtouyz wrote:



Hi David,
Thank you for your response.
Yes, num_decks was previously defined in my program, I apologize for  
the

confusion as it is an integral value.
This is only one portion of my program that is being used to  
simulate card

counting in blackjack.

The basic idea was to modify deckn without having to return a value  
from the

function deck(). That is whenever deck() was run it would write over
whatever was in deckn (instead of having to input deckn-deck().)
It seems from your response that this may not be possible and  
return is

always required.
If I have erred, please let me know.


R is supposed to be used as a functional language. The use of the  
- operator is deprecated, so I did not mention that strategy. You  
could also have simply run the loop without the functional wrapper.


--
david.


Thanks once again,
Josh Elliott


David Winsemius wrote:



On Mar 16, 2010, at 11:04 AM, jtouyz wrote:



Hey all,
I'm relatively new to the R-environment. I'm having a bit of trouble
with
encapsulation.
I have a globally declared variable that doesn't update it when I
change it
in a function.



For example when I run the following function


deckn-NULL
deck1-1  #52 card deck
deck-function()

{
#Creating a standard deck
deck1-c(1:52)
deckn-deck1
  #Creating n decks
  for (i in 2:num_decks)


# could be wrong but it appears that you are expecting the act of
putting num_ in front of decks to be interpreted by R as  
returning

the length of deckn or deck1. That is a higher level of abstraction
than is yet available in any computer language with which I am
familiar. Or perhaps you were intending to use Greg Snow's soon to be
released mind-reading package so that R could know that you wanted it
to be 6?.

Perhaps instead (depending on what the real problem (unstated as yet)
might be:

  for (i in 2:length(deck1) )  # or some other object or function
that returns a numeric value.


  {
  deckn-c(deckn,52*i+deck1-1)



  }
}

deckn


You would have needed to assign a return-ed value to deckn in the
outer environment. The deckn object would have disappeared at the end
of the function call, and it would not have needed to be named
deckn, either.


Try instead:

deckn-NULL
deck-function(num_decks=6)
{
#Creating a standard deck
deck1-c(1:52)
deckn-deck1
   #Creating n decks
   for (i in 2:num_decks)
   {
   deckn-c(deckn,52*i+deck1-1)
   }; return(deckn)
}
deckn - deck()
deckn

Which has a gap between 52 and 104 because of your logic, not mine.



NULL


it returns NULL for deckn instead of a vector of values. Is there an
easy
fix to update deckn in the function so that it outputs a vector of
values (
I don't wish the function to return a value just update the current
one)?


You could, of course, explain what you are trying to do.



Thanks in advance,
Josh Elliott
--


David Winsemius, MD
West Hartford, CT

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.




--
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http://n4.nabble.com/Changing-global-variables-from-functions-tp1595002p1595356.html
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and provide commented, minimal, self-contained, reproducible code.


David Winsemius, MD
West Hartford, CT

__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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[R] How can I save the result for goodness of fit test

2010-03-16 Thread pinusan


Dear All,
I run the goodness of fit test using goodfit() in vcd package.
The result is as follow: 

Goodness-of-fit test for poisson distribution

 X^2 df  P( X^2)
Pearson 1.053348  2 0.5905661
Warning message:
In summary.goodfit(gf) : Chi-squared approximation may be incorrect

I want to save the the test statistics(X^2), df, and p-value. How can I save
the result. Actually, I want to make a table.

In addition, there is warning message In summary.goodfit(gf) : Chi-squared
approximation may be incorrect.
How can I interpret this result. 

Have a nice day.

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

Re: [R] OT Really: Odds Are, It's Wrong...

2010-03-16 Thread Johannes Hüsing


Dieter Menne schrieb:

Marc Schwartz-3 wrote:
  

I thought that readers of R-Help might find the following article at
ScienceNews of interest:

  Odds Are, It's Wrong
  Science fails to face the shortcomings of statistics
  By Tom Siegfried
  March 27th, 2010; Vol.177 #7 (p. 26)
 
http://www.sciencenews.org/view/feature/id/57091/title/Odds_are,_its_wrong






Too bad the article is so long that all my p-value-greedy colleagues from
the medical faculty won't read it. 


Journals should apply a post-hoc Bonferroni-correction by the number of
p-values cited in an article.

  


The main problem is the multitude of p-value not cited. I have little 
problems
with scientists publishing all their findings with p-values (or 
confidence intervals)

but big problems with people who use them as a filter.

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

Re: [R] Changing global variables from functions



On Mar 16, 2010, at 3:11 PM, David Winsemius wrote:



On Mar 16, 2010, at 2:43 PM, jtouyz wrote:



Hi David,
Thank you for your response.
Yes, num_decks was previously defined in my program, I apologize  
for the

confusion as it is an integral value.
This is only one portion of my program that is being used to  
simulate card

counting in blackjack.

The basic idea was to modify deckn without having to return a value  
from the

function deck(). That is whenever deck() was run it would write over
whatever was in deckn (instead of having to input deckn-deck().)
It seems from your response that this may not be possible and  
return is

always required.
If I have erred, please let me know.


R is supposed to be used as a functional language. The use of the  
- operator is deprecated, so I did not mention that strategy.  
You could also have simply run the loop without the functional  
wrapper.



I wondered if a sampling without replacement strategy might work to  
provide with indexing:


num_deck # what fills shoes these days.
( table((1:52)[sample(1:(52*num_decks), 52*num_decks) %% 52])

 1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23  
24 25 26 27 28 29 30
 6  6  6  6  6  6  6  6  6  6  6  6  6  6  6  6  6  6  6  6  6  6  6   
6  6  6  6  6  6  6

31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51
 6  6  6  6  6  6  6  6  6  6  6  6  6  6  6  6  6  6  6  6  6
--
David.



--
david.


Thanks once again,
Josh Elliott


David Winsemius wrote:



On Mar 16, 2010, at 11:04 AM, jtouyz wrote:



Hey all,
I'm relatively new to the R-environment. I'm having a bit of  
trouble

with
encapsulation.
I have a globally declared variable that doesn't update it when I
change it
in a function.



For example when I run the following function


deckn-NULL
deck1-1  #52 card deck
deck-function()

{
#Creating a standard deck
deck1-c(1:52)
deckn-deck1
 #Creating n decks
 for (i in 2:num_decks)


# could be wrong but it appears that you are expecting the act of
putting num_ in front of decks to be interpreted by R as  
returning

the length of deckn or deck1. That is a higher level of abstraction
than is yet available in any computer language with which I am
familiar. Or perhaps you were intending to use Greg Snow's soon to  
be
released mind-reading package so that R could know that you wanted  
it

to be 6?.

Perhaps instead (depending on what the real problem (unstated as  
yet)

might be:

 for (i in 2:length(deck1) )  # or some other object or function
that returns a numeric value.


 {
 deckn-c(deckn,52*i+deck1-1)



 }
}

deckn


You would have needed to assign a return-ed value to deckn in the
outer environment. The deckn object would have disappeared at the  
end

of the function call, and it would not have needed to be named
deckn, either.


Try instead:

deckn-NULL
deck-function(num_decks=6)
{
#Creating a standard deck
deck1-c(1:52)
deckn-deck1
  #Creating n decks
  for (i in 2:num_decks)
  {
  deckn-c(deckn,52*i+deck1-1)
  }; return(deckn)
}
deckn - deck()
deckn

Which has a gap between 52 and 104 because of your logic, not mine.



NULL


it returns NULL for deckn instead of a vector of values. Is there  
an

easy
fix to update deckn in the function so that it outputs a vector of
values (
I don't wish the function to return a value just update the current
one)?


You could, of course, explain what you are trying to do.



Thanks in advance,
Josh Elliott
--


David Winsemius, MD
West Hartford, CT

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.




--
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http://n4.nabble.com/Changing-global-variables-from-functions-tp1595002p1595356.html
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


David Winsemius, MD
West Hartford, CT

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David Winsemius, MD
West Hartford, CT

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[R] Retrieving latitude and longitude via Google Maps API

2010-03-16 Thread Nutter, Benjamin

Does anyone have any experience retrieving latitutde and longitude for
an address from the Google Maps API?  

I'd like to have an R script that submits a street address, city, state,
and zip code and returns the coordinates.  So far, I've been submitting
the coordinates from another program, then loading the coordinates in R
and merging them back into the data frame I want to use.  It'd be nice
to be able to do it all in one script, but I'm not comprehending the API
thing very well.

I'm using R 2.9.1 on Windows XP.  Any suggestions or pointers?

Benjamin

 
 
  Benjamin Nutter |  Biostatistician  |  Quantitative Health Sciences
  Cleveland Clinic  |  9500 Euclid Ave.   |  Cleveland, OH 44195  |
(216) 445-1365


===

P Please consider the environment before printing this e-mail

Cleveland Clinic is ranked one of the top hospitals
in America by U.S.News  World Report (2009).  
Visit us online at http://www.clevelandclinic.org for
a complete listing of our services, staff and
locations.


Confidentiality Note:  This message is intended for use\...{{dropped:13}}

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[R] Fw: an ordinal regression MCMC run high correlation

2010-03-16 Thread ping chen

I tried thinning of the mcmc run with 500,000 iteration. It looks like 100 or 
200 is enough to remove the autocorrelation of a1 and tau. 
Is that too much thining? 

--- On Tue, 3/16/10, ping chen chen1984...@yahoo.com.cn wrote:

 From: ping chen chen1984...@yahoo.com.cn
 Subject: an ordinal regression MCMC run high correlation
 To: r-help@r-project.org
 Cc: chen1984...@yahoo.com.cn
 Date: Tuesday, March 16, 2010, 12:19 PM
 I am trying to model  a clusterd
 ordinal response data (either 1, 2 or 3) called , the
 correponding physician of the patient is also in the data.

 Since it is ordinal, I used the ordinal logit model

 topbox[i]~discrete with probability P[j,1],p[j,2], p[j,3],
 j is the corresponding physician of the ith patient

 C[j] is the physician effect , a1 and a1+theta is the
 common cutpoints for all physicians

 I generate 10,000 iteration and there are still high
 autocorrelation of a1 and tau. I thought 10,000 is a pretty
 big number and the chain converges really slow. I am a new
 MCMC user and don't know other ways to solve this problem.
 Will someone please give some suggestions that may apply to
 this specific modeling?

 model  {
 for ( i in 1:N) {
 response[i]~dcat( p[physician[i], ] )
 }

 for (j in 1:Nt) {
 p[j,1]-1-Q[j,1]
 p[j,2]-Q[j,1]-Q[j,2]
 p[j,3]-Q[j,2]
 logit(Q[j,1])--c[j]
 logit(Q[j,2])--(c[j]+theta)
 score[j]-0.5*p[j,2]+p[j,3]
 c[j]~dnorm(a1, tau)
 }
 a1~dnorm(0, 1.0E-06)
 theta~dnorm(0, 1.0E-06)I(0,)
 tau~dgamma(0.001,0.001)
 }

 list(N=667,Nt=50)

 Thanks, Ping

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Re: [R] Error in pruning hclust object using maptree package

2010-03-16 Thread Keith


My bad.

I did read the help. However, I didn't pay enough attention to the data 
argument, and it seems it doesn't need to use data argument in the 
earlier version.


I also noticed this argument afterwards. Now it works for me as well. 
Thanks a lot.


Uwe Ligges wrote:



On 15.03.2010 16:37, Keith wrote:

Dear R users,

Due to too many children in my clustering result, I would like to prune
the tree-like hclust object into a certain groups. However, an error:

  clip.clust: no data provided for hclust object

always shows up.

Firstly, I tried the example in the maptree package, and it worked well.
Then, I tried to used the example in stats package to generate a hclust
object and tried the clip.clust method again, and the error still
occurred. Here is the example:

  hc - hclust(dist(USArrests), ave)
  pr - clip.clust(hc, k=4)
Error in clip.clust(hc, k = 4) :
clip.clust: no data provided for hclust object


Have you read ?clip.clust ??
It says for argument data:
 data clustered dataset for hclust application.

whic means you need to provide data as the error message suggests as 
well.


 pr - clip.clust(hc, k=4, data=USArrests)
 pr$membership

works for me.

Uwe Ligges








Does anyone have the idea? My environment is
R version 2.10.1 (2009-12-14)
x86_64-pc-linux-gnu
[1] maptree_1.4-6

Best regards,
Keith

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Re: [R] Conditional variable assignment



On Mar 16, 2010, at 3:44 PM, Hosack, Michael wrote:


Hi everyone,

Once again I am stuck with a problem I can't seem to figure out. I  
suppose this learning curve levels off eventually, lol. I am  
learning on my own with absolutely no background in programming, so  
if I seem to request help a lot it's not because I am seeking others  
to do the work for me. I need to assign one of two arrival times to  
the 'ARRIVE' variable of my dataframe, and I want a value assigned  
only to the first element of each 'MM' by 'DD' variable grouping.  
The value used (either 0700 or 1430) will be conditional on the  
value in the 'TOD' variable, such that if 'TOD' == 1,  
'ARRIVE'-0700, and if 'TOD'==2, 'ARRIVE'-1430. I want the  
remaining three 'MM' by 'DD' values for each unique grouping to  
remain NA for now, because I intend to calculate them later. I  
have tried ifelse statements with ddply, for loops, etc. to no  
avail. Any help would be greatly appreciated.


Logical indexing;

dfrm[!duplicated(paste(dfrm$MM, dfrm$DD)), ARRIVE] - 0700
dfrm$ARRIVE[dfrm$ARRIVE == 0700  dfrm$TOD==2] - 1430

--

David Winsemius, MD
West Hartford, CT

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Re: [R] Constrained non linear regression using ML

2010-03-16 Thread Ravi Varadhan

I have an algorithm that can perform nonlinear optimization, with
linear/nonlinear, equality and/or inequality constraints.  From your
description, it seems like this algorithm would work for your problem.
Contact me if you are interested and I will send you the code.

Ravi.

-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Corrado
Sent: Tuesday, March 16, 2010 2:59 PM
To: r-help@r-project.org
Subject: [R] Constrained non linear regression using ML

Dear R users,

I have to fit the non linear regression:

y~1-exp(-(k0+k1*p1+k2*p2+  +kn*pn))

where ki=0 for each i in [1  n] and pi are on R+.

I am using, at the moment, nls, but I would rather use a Maximum 
Likelhood based algorithm. The error is not necessarily normally 
distributed.

y is approximately beta distributed, and the volume of data is medium to 
large (the y,pi may have ~ 40,000 elements).

I have studied the packages in the task views Optimisation and Robust 
Statistical Methods, but I did look like what I was looking for was 
there. Maybe I am wrong.

The nearest thing was nlrob, but even that does not allow for 
constraints, as far as I can understand.

Any suggestion?

Regards

-- 
Corrado Topi
PhD Researcher
Global Climate Change and Biodiversity
Area 18,Department of Biology
University of York, York, YO10 5YW, UK
Phone: + 44 (0) 1904 328645, E-mail: ct...@york.ac.uk

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Re: [R] OT Really: Odds Are, It's Wrong...

2010-03-16 Thread Dieter Menne



Johannes Huesing wrote:
 
 I have little  problems with scientists publishing all their findings with
 p-values (or 
 confidence intervals) but big problems with people who use them as a
 filter.
 

While I am aware that CI and p-values have a common root, I do not to throw
both into one pot for the average medical end-user. 

When two treatments for blood pressure show a significant differences, this
only tells you that the sponsor had a lot of money to show his expensive new
product is worth the money.  When you tell the medical doctor that the CI of
the difference has a range 1.1 mmHg , she would say: I don't care, it's not
relevant, both products are good enough for me.

I tend to strongly stress the difference between relevance (medically
weighted CI) and significance (pure numerics) in lectures. After all, it's
difficult enough when doing sample size estimation to get something like a
medically relevant difference.

So I have to pay back by giving them a medically-to-be-weighted difference
after study end.

Dieter
 

-- 
View this message in context: 
http://n4.nabble.com/OT-Sorta-Odds-Are-It-s-Wrong-tp1593626p1595554.html
Sent from the R help mailing list archive at Nabble.com.

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Re: [R] Retrieving latitude and longitude via Google Maps API

2010-03-16 Thread Phil Spector


Benjamin -
   Perhaps this will get you started:


addr = '1600 Pennsylvania Avenue, Washington, DC'
url = paste('http://maps.google.com/maps/api/geocode/xml?address=',

+  addr,'sensor=false',sep='')

library(XML)
doc = xmlTreeParse(url)
root = xmlRoot(doc)
lat = xmlValue(root[['result']][['geometry']][['location']][['lat']])
long = xmlValue(root[['result']][['geometry']][['location']][['lng']])
lat 

[1] 38.8976500

long

[1] -77.0356669

- Phil Spector
 Statistical Computing Facility
 Department of Statistics
 UC Berkeley
 spec...@stat.berkeley.edu



On Tue, 16 Mar 2010, Nutter, Benjamin wrote:


Does anyone have any experience retrieving latitutde and longitude for
an address from the Google Maps API?

I'd like to have an R script that submits a street address, city, state,
and zip code and returns the coordinates.  So far, I've been submitting
the coordinates from another program, then loading the coordinates in R
and merging them back into the data frame I want to use.  It'd be nice
to be able to do it all in one script, but I'm not comprehending the API
thing very well.

I'm using R 2.9.1 on Windows XP.  Any suggestions or pointers?

Benjamin



 Benjamin Nutter |  Biostatistician  |  Quantitative Health Sciences
 Cleveland Clinic  |  9500 Euclid Ave.   |  Cleveland, OH 44195  |
(216) 445-1365


===

P Please consider the environment before printing this e-mail

Cleveland Clinic is ranked one of the top hospitals
in America by U.S.News  World Report (2009).
Visit us online at http://www.clevelandclinic.org for
a complete listing of our services, staff and
locations.


Confidentiality Note:  This message is intended for use\...{{dropped:13}}

__
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__
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Re: [R] Constrained non linear regression using ML

Check out the betareg package.

On Tue, Mar 16, 2010 at 2:58 PM, Corrado ct...@york.ac.uk wrote:
 Dear R users,

 I have to fit the non linear regression:

 y~1-exp(-(k0+k1*p1+k2*p2+  +kn*pn))

 where ki=0 for each i in [1  n] and pi are on R+.

 I am using, at the moment, nls, but I would rather use a Maximum Likelhood
 based algorithm. The error is not necessarily normally distributed.

 y is approximately beta distributed, and the volume of data is medium to
 large (the y,pi may have ~ 40,000 elements).

 I have studied the packages in the task views Optimisation and Robust
 Statistical Methods, but I did look like what I was looking for was there.
 Maybe I am wrong.

 The nearest thing was nlrob, but even that does not allow for constraints,
 as far as I can understand.

 Any suggestion?

 Regards

 --
 Corrado Topi
 PhD Researcher
 Global Climate Change and Biodiversity
 Area 18,Department of Biology
 University of York, York, YO10 5YW, UK
 Phone: + 44 (0) 1904 328645, E-mail: ct...@york.ac.uk

 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.


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Re: [R] Retrieving latitude and longitude via Google Maps API

2010-03-16 Thread Michael Denslow

Hi Benjamin,


 On Tue, 16 Mar 2010, Nutter, Benjamin wrote:

 Does anyone have any experience retrieving latitutde and longitude for
 an address from the Google Maps API?

This thread from r-sig-geo may be of interest:
https://stat.ethz.ch/pipermail/r-sig-geo/2010-March/thread.html#7788

Hope this helps,
Michael

 I'd like to have an R script that submits a street address, city, state,
 and zip code and returns the coordinates.  So far, I've been submitting
 the coordinates from another program, then loading the coordinates in R
 and merging them back into the data frame I want to use.  It'd be nice
 to be able to do it all in one script, but I'm not comprehending the API
 thing very well.

 I'm using R 2.9.1 on Windows XP.  Any suggestions or pointers?

 Benjamin



  Benjamin Nutter |  Biostatistician  |  Quantitative Health Sciences
  Cleveland Clinic  |  9500 Euclid Ave.   |  Cleveland, OH 44195  |
 (216) 445-1365


 ===

 P Please consider the environment before printing this e-mail

 Cleveland Clinic is ranked one of the top hospitals
 in America by U.S.News  World Report (2009).
 Visit us online at http://www.clevelandclinic.org for
 a complete listing of our services, staff and
 locations.


 Confidentiality Note:  This message is intended for use\...{{dropped:13}}

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


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




-- 
Michael Denslow

I.W. Carpenter Jr. Herbarium [BOON]
Department of Biology
Appalachian State University
Boone, North Carolina U.S.A.
-- AND --
Communications Manager
Southeast Regional Network of Expertise and Collections
sernec.org

36.214177, -81.681480 +/- 3103 meters

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[R] Re : Eliminate border in wireframe plot

2010-03-16 Thread Seth W Bigelow

Scott:

This may work for you. Just include the statement
par.settings - par.set1 in your wire graph statement

par.set1 -list(
axis.line=list(col=transparent),  # Get rid 
of box around fig?
clip=list(panel=FALSE), # disarm 
lurking panel settings?
 
)



Dr. Seth  W. Bigelow
Biologist, USDA-FS Pacific Southwest Research Station
1731 Research Park Drive, Davis California
sbige...@fs.fed.us /  ph. 530 759 1718
[[alternative HTML version deleted]]

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[R] Is there a way to edit a specific line in a function (e.g: doing function-text-edit-function) ?

Hello,

Let's say we have the following function:

foo - function(x)

{


line1 - x


line2 - 0


line3 - line1 + line2


return(line3)

}

 And that we want to change the second line to be:

line2 - 2

 How would you do that?

The two ways I know of are either to use

fix(foo)

 And change the function.

Or to just write the function again.

Is there another way?

*What I would like* is for some way to represent the function as a vector of
strings (well, characters), then change one of it's values, and then turn it
into a function again.

The reason I am asking is that I just published a post online where I used a
function to which I did a minor tweak (so to improve it's output for my
particular case).
This tweaking was just adding one line of code, to a function who's length
is 187 lines of code. So instead of repasting all the function on my blog, I
decided to just explain how to edit it.  But I would rather have a simple
code that edited the function for the reader.


Thanks,
Tal

Contact
Details:---
Contact me: tal.gal...@gmail.com |  972-52-7275845
Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
www.r-statistics.com (English)
--

[[alternative HTML version deleted]]

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Re: [R] Is there a way to edit a specific line in a function (e.g: doing function-text-edit-function) ?

2010-03-16 Thread Henrique Dallazuanna

Try this:

body(foo)[[grep('^line2', body(foo))]][[3]] - 2

On Tue, Mar 16, 2010 at 6:31 PM, Tal Galili tal.gal...@gmail.com wrote:
 Hello,

 Let's say we have the following function:

 foo - function(x)

 {


    line1 - x


    line2 - 0


    line3 - line1 + line2


    return(line3)

 }

  And that we want to change the second line to be:

    line2 - 2

  How would you do that?

 The two ways I know of are either to use

 fix(foo)

  And change the function.

 Or to just write the function again.

 Is there another way?

 *What I would like* is for some way to represent the function as a vector of
 strings (well, characters), then change one of it's values, and then turn it
 into a function again.

 The reason I am asking is that I just published a post online where I used a
 function to which I did a minor tweak (so to improve it's output for my
 particular case).
 This tweaking was just adding one line of code, to a function who's length
 is 187 lines of code. So instead of repasting all the function on my blog, I
 decided to just explain how to edit it.  But I would rather have a simple
 code that edited the function for the reader.


 Thanks,
 Tal

 Contact
 Details:---
 Contact me: tal.gal...@gmail.com |  972-52-7275845
 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
 www.r-statistics.com (English)
 --

        [[alternative HTML version deleted]]

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




-- 
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O

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Re: [R] R on Linux - a primer

2010-03-16 Thread Emmanuel Charpentier

Le dimanche 14 mars 2010 à 18:04 -0400, Axel Urbiz a écrit :
 Hi,
 
 I'm looking to move from Windows into a 64-bit Linux environment. Which is
 the best Linux Flavor to use within R? To install R on this environment, do
 I need to do any compiling?

I'd like to add two cents of folly to the (wise) advice you've received
already.

Indeed , Ubuntu is one very good distribution whose management system
has made the care and feeding of a Linux system a *lot* easier for the
not-so-system-oriented people like yours truly. Whereas my first
contacts with a Unix-like system were about 30 years ago (Oh my, how
time flies, and how far away are Xenix and our 68000 systems ...), I'm
*still* not fond of system maintenance for it's own sake. Ubuntu added
an (almost) fool-proof maintenance system to an excellent distribution
called Debian, thus lowering the Linux entry bar to as low as it can be
humanely made. Some pretended that Ubuntu was a code word for I'm too
stupid to configure Debian ; quite untrue ! It only means I'm too
busy|lazy to configure Debian, which is a Good Thing (TM).

But Debian has its strong points,  and one of them is *extremely* strong
for an R user : Dirk Eddelbuettel (whose name I'm almost surely
misspelling (sorry, Dirk !)) has created a marvelous system called
cran2deb which routinely creates binary Debian packages from (almost)
the 2000+ R packages available nowadays.

That might look small change : the basic tools used for
developing/compiling most R packages are small beer (at least by today's
standards).But some of them might depend on fiendishly
difficult-to-maintain foreign libraries. Dirk's cran2deb takes care of
that and creates any information that Debian's dpkg maintenance system
needs to automate *your* R maintenance chores by integrating them in
Debian's maintenance scheme, which is as automatic as you can get
without becoming an incomprehensible beast.

In fact, cran2deb is so good that Im seriously tempted to go back to
Debian (after almost 8 years of Debian use, Ubuntu's ease-of-use, easy
access to no-so-exotic hardware drivers (and the then-incessant
politically correct yack-yacking on some Debian mailing lists...) made
me switch to an early Ubuntu distribution). I did not yet switch back
(mostly for not-so-superficial hardware support reasons), but I
maintain a backup Debian installation for the hell of it and to test
waters. So far, they have been a lot less rough than they used to be,
but there are still occasional rows (e. g. a recent gotcha with
openoffice.org, which would have render myself unable to work with those
d*mn Word files for about a month, or forced me to do a maual repair
(which I hate...)).

So consider Debian as a (desirable) alternative to Ubuntu.

HTH,

Emmanuel Charpentier, DDS, MSc
affiliation withdrawn,
notwithstanding Frank Harrell's
whims...

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[R] using RKWard for a function plot

2010-03-16 Thread KAYVEN RIESE



Is it possible to use the RKWard GUI to just plot a function?  I will have 
some exponential function, I need to plot u as a function of y where



 u=   -2yg  exp(-y^2/beta)
   -
   f

  where everything else other than u and y are various constants.

*--*
  Kayven Riese, BSCS, MS (Physiology and Biophysics)
  (415) 902 5513 cellular
  http://kayve.net
  Webmaster http://ChessYoga.org

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Re: [R] using RKWard for a function plot

2010-03-16 Thread KAYVEN RIESE


On Tue, 16 Mar 2010, KAYVEN  RIESE wrote:



Is it possible to use the RKWard GUI to just plot a function?  I will have 
some exponential function, I need to plot u as a function of y where



u=   -2yg  exp(-y^2/beta)
  -
  f

 where everything else other than u and y are various constants.

*--*
 Kayven Riese, BSCS, MS (Physiology and Biophysics)
 (415) 902 5513 cellular
 http://kayve.net
 Webmaster http://ChessYoga.org
*--*



*--*
  Kayven Riese, BSCS, MS (Physiology and Biophysics)
  (415) 902 5513 cellular
  http://kayve.net
  Webmaster http://ChessYoga.org

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[R] [R-pkgs] New package: ordinal

2010-03-16 Thread Rune Haubo

This is to announce the new R-package ‘ordinal’ that implements
cumulative link (mixed) models for ordinal (ordered categorical) data
(http://www.cran.r-project.org/package=ordinal/).

The main features are:
-   scale (multiplicative) as well as location (additive) effects
-   nominal effects for a subset of the predictors (denoted partial
proportional odds when the link is the logistic)
-   structured thresholds, e.g. assuming symmetry or equidistant thresholds
-   random effects via the Laplace approximation and adaptive
Gauss-Hermite quadrature in the location-part of the model.
-   a range of standard link functions
-   flexible link functions where an extra link function-parameter
bridges the log-log, probit and c-loglog links (log-gamma), and
cloglog and logistic links (Aranda-Ordaz)
-   a suite of optimizers including an efficient Newton scheme.
-   works for binomial observations (a special case of ordinal data).
-   a suite of methods including anova, addterm, dropterm, profile,
confint, plot.profile, predict, in addition to the standard print and
summary methods.
-   an important special case is the proportional odds model (with
random effects).
-   a range of examples illustrates how to use the functions.

Future additions will include:
-   more general random effect structures: multiple (crossed and nested)
and vector-valued random effects.
-   profile methods for variance parameters in mixed effect models.
-   helpful package vignettes.
-   implementation of core functions in C.

Comments, critique, suggestions, wishes and contributions are always
highly appreciated.

Kind regards
Rune

-- 
Rune Haubo Bojesen Christensen

PhD student, M.Sc. Eng.
Phone: (+45) 45 25 33 63
Mail: rhbc at imm.dtu.dk

DTU Informatics, Section for Statistics
Technical University of Denmark, Build. 305, Room 122,
DK-2800 Kgs. Lyngby, Denmark

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Re: [R] Is there a way to edit a specific line in a function (e.g: doing function-text-edit-function) ?

That did it.
Thanks Henrique!

Tal

Contact
Details:---
Contact me: tal.gal...@gmail.com |  972-52-7275845
Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
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--




On Tue, Mar 16, 2010 at 11:34 PM, Henrique Dallazuanna www...@gmail.comwrote:

 Try this:

 body(foo)[[grep('^line2', body(foo))]][[3]] - 2

 On Tue, Mar 16, 2010 at 6:31 PM, Tal Galili tal.gal...@gmail.com wrote:
  Hello,
 
  Let's say we have the following function:
 
  foo - function(x)
 
  {
 
 
 line1 - x
 
 
 line2 - 0
 
 
 line3 - line1 + line2
 
 
 return(line3)
 
  }
 
   And that we want to change the second line to be:
 
 line2 - 2
 
   How would you do that?
 
  The two ways I know of are either to use
 
  fix(foo)
 
   And change the function.
 
  Or to just write the function again.
 
  Is there another way?
 
  *What I would like* is for some way to represent the function as a vector
 of
  strings (well, characters), then change one of it's values, and then turn
 it
  into a function again.
 
  The reason I am asking is that I just published a post online where I
 used a
  function to which I did a minor tweak (so to improve it's output for my
  particular case).
  This tweaking was just adding one line of code, to a function who's
 length
  is 187 lines of code. So instead of repasting all the function on my
 blog, I
  decided to just explain how to edit it.  But I would rather have a simple
  code that edited the function for the reader.
 
 
  Thanks,
  Tal
 
  Contact
  Details:---
  Contact me: tal.gal...@gmail.com |  972-52-7275845
  Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
  www.r-statistics.com (English)
 
 --
 
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 --
 Henrique Dallazuanna
 Curitiba-Paraná-Brasil
 25° 25' 40 S 49° 16' 22 O


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Re: [R] Is there a way to edit a specific line in a function (e.g: doing function-text-edit-function) ?

2010-03-16 Thread Duncan Murdoch


On 16/03/2010 5:31 PM, Tal Galili wrote:

Hello,

Let's say we have the following function:

foo - function(x)

{


line1 - x


line2 - 0


line3 - line1 + line2


return(line3)

}

 And that we want to change the second line to be:

line2 - 2

 How would you do that?

The two ways I know of are either to use

fix(foo)

 And change the function.

Or to just write the function again.


That's the best way.


Is there another way?


You can use findLineNum to find where that line of source appears in 
your workspace.  For example, if I source your input from the above, the 
line that interests you is line 9 of my foo.R input file.  Then


 source(c:/temp/foo.R)
 findLineNum(foo.R#9)
c:\temp\foo.R#9:
 foo step 3 in environment: R_GlobalEnv
 body(foo)[[3]]
line2 - 0

Now I can replace step 3 using

body(foo)[[3]] - quote(line2 - 2)

If the line you want is nested deep within a block structure, you might 
need to use a vector index to get to it, e.g. after wrapping that line 
in an if() { }, I see


 findLineNum(foo.R#10)
c:\temp\foo.R#10:
 foo step 3,3,2 in environment: R_GlobalEnv
 body(foo)[[c(3,3,2)]] - quote(line2 - 2)
 foo
function (x)
{
line1 - x
if (x  0) {
line2 - 2
}
line3 - line1 + line2
return(line3)
}

The findLineNum() function depends on having source references in the 
function, so it won't work on functions in packages unless you build 
them with the option to keep package source refs.  (And then you need 
special contortions to tell it to look in the namespace for the 
function, and to edit a function in the namespace.  Better not to do that.)


Duncan Murdoch






*What I would like* is for some way to represent the function as a vector of
strings (well, characters), then change one of it's values, and then turn it
into a function again.

The reason I am asking is that I just published a post online where I used a
function to which I did a minor tweak (so to improve it's output for my
particular case).
This tweaking was just adding one line of code, to a function who's length
is 187 lines of code. So instead of repasting all the function on my blog, I
decided to just explain how to edit it.  But I would rather have a simple
code that edited the function for the reader.


Thanks,
Tal

Contact
Details:---
Contact me: tal.gal...@gmail.com |  972-52-7275845
Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
www.r-statistics.com (English)
--

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Re: [R] How can I save the result for goodness of fit test