[R] installing package from source

[Long Vo]

Hi R users,
Currently I want to fit a FIGARCH model to a dataset. The only package that
allow for it that I could find is fGarch. However it seems that the FIGARCH
model class fitting of this package has been moved to Oxmetrics. I tried to
install the old versions of it using 'tar.gz' files from CRAN archive 
http://cran.r-project.org/src/contrib/Archive/fGarch/
http://cran.r-project.org/src/contrib/Archive/fGarch/   but not sure how
it works. I tried

install.packages(myfilepath\fGarch_260.71.tar.gz, repos = NULL,
type=source)

And received this error:

Warning: invalid package './I:
_R filesGarch_260.71.tar.gz'
Error: ERROR: no packages specified
Warning messages:
1: running command 'I:/01_RFI~1/INSTAL~1/R-30~1.1/bin/i386/R CMD INSTALL
-l I:\01_R files\installment\R-3.0.1\library ./I:
_R files
Garch_260.71.tar.gz' had status 1 
2: In install.packages(I:\001_R files\fGarch_260.71.tar.gz, repos = NULL, 
:
  installation of package ‘./I:
_R filesGarch_260.71.tar.gz’ had non-zero
exit status

Any helps on this?

Regards,
Long



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[R] How can I use a script l (LaTeX \ell) in mathematical annotation of plots?

[Byron Dom]

Original post: On 13/10/2013 18:53, Byron Dom wrote:

 Due to convention a script l - $$\ell$$ (LaTeX \ell) is used to 
 represent a certain quantity in something I'm working on. I'm 
 unable to figure out how to use it in R. It's not included in the 
 list on ?plotmath.

 Can anyone tell me how to use it?  Its unicode is U+2113. This 
 page has a list of various encodings of it: 

 http://www.fileformat.info/info/unicode/char/2113/encoding.htm.  
 Is there a way to include it by using one of these encodings somehow?

-

On 13/10/2013 22:06 Prof Brian Ripley responded:

 What do you want to do with it?  plotmath is about plotting, but you
 have not otherwise mentioned that, let alone the device on which you 
 want to plot.

 Read the help for plotmath: on some plot devices, just use \u2113.  It 
 is not AFAICS in the Adobe symbol encoding.

 -- 
 Brian D. Ripley,                  ripley at stats.ox.ac.uk
 Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
 University of Oxford,             Tel: 
 +44 1865 272861 (self)
 1 South Parks Road,                     +44 1865 272866 
 (PA)
 Oxford OX1 3TG, UK                Fax:  +44 1865 272595

-

My response:

Thanks I worked out how to do it based on your mention of u2113.
See below.

I'm sorry if my information wasn't complete enough. I assumed that 
what I said, combined with the subject (How can I use a script l 
(LaTeX \ell) in
 mathematical annotation of plots?) would have been 
enough.

I just wanted to be able to do this on the default device, which 
displays plots within the R session window. I have a simple path 
to go from there to .png form, which I include in LaTeX documents
and for other purposes. I am using R version 3.0.1 in Windows 7, 
for which I believe the default plot device is windows.

An example of the kind of thing I wanted to do is to include 
ylab = expression(hat(gamma)) (which is equivalent to the LaTex 
\hat{\gamma}}) among the base-graphics plot() arguments. That 
works. In LaTeX a script l is produced with \ell, but 
something like ylab = expression(ell) doesn't work in R. 
I wanted to be able to do the equivalent of that, but to obtain ℓ.

Here are a couple of examples using it that worked:
   plot(1:10,xlab=\u2113)
  
 plot(1:10,xlab=\u2113(\u2113 + 1))
The only (slight) problem with this is the minor aesthetic issue 

that the ℓ one gets this way is in an obviously different font 

from what one gets using the LaTeX \lambda command/symbol.

Strangely, earlier, when I tried 
   plot(1:10,xlab=expression(symbol(\u2113)))
it did the same thing as 
   plot(1:10,xlab=expression(lambda))
So I got a lower-case greek lambda - λ, rather than ℓ
(script l).

When I used the unicode representation for lowercase 
lambda - λ - as follows
  
 plot(1:10,xlab=expression(symbol(\u03bb)))
I got this for an x-axis label: Y+03BB. On the other hand,
the following did work
   plot(1:10,xlab=\u03bb), 
giving me an x-axis label of lambda - λ.
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Re: [R] Function not working as I'd like

[smugg55]

Could you please show me what the code should be then? 



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Re: [R] Scripting call to R-Studio compile PDF

[Adam Hughes]

Thanks for the help guys.  Sorry, I will not post further RStudio questions
here.  Yihui, thanks for the tip.  Looks like these commands would do:

grDevices::pdf.options(useDingbats = FALSE); require(knitr);
opts_knit$set(concordance = TRUE); knit('filename.rnw',
encoding='UTF-8')


pdflatex filename.tex


evince filename.pdf




On Wed, Oct 23, 2013 at 2:20 PM, David Winsemius dwinsem...@comcast.netwrote:


 On Oct 23, 2013, at 10:48 AM, Adam Hughes wrote:

  Sorry, just to clarify:
 
  When I ask how to do this, I mean what does the RStudio compiler
 actually
  do?  Are there a series of commands that are sent to the shell, similar
 to
  how compiling a .tex file is a call to the command line using pdflatex
  foofile.tex.  I'm hoping to just copy these shell commands using a
 python
  script, which is easy.
 

 There is an RStudio mailing list or forum for support of that product.

 
  On Wed, Oct 23, 2013 at 1:39 PM, Adam Hughes hughesada...@gmail.com
 wrote:
 
  Hey everyone,
 
  I have several RStudio (.rnw) files that I am using a script to assemble
  into a composite document.  For this purpose, it would be helpful if the
  script could automatcially make a call to whatever is called when a user
  opens up one of these files and manually clicks Compile PDF.
  Basically,
  this would allow me to refresh all of the reports before assimilating
 their
  pdf's into a composite document.
 
  Does anyone know offhand how to do this, or if I'm offbase in even
 trying?
 
  Thanks
 
 --

 David Winsemius
 Alameda, CA, USA



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[R] Variable operations

[Syamsul Rizal]

Dear All:

I have

v = c(xy, xy^2, z)

dotv = sum(v*v)

I hope, I have the following result:

dotv = x^2*y^2 + x^2*y^4 + z^2  (still in variable x, y and z, not
numeric result)

How to make simple script, so that I have: dotv = x^2*y^2 + x^2*y^4 + z^2

Thanks a lot for your help.

Best regards, Rizal

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Re: [R] Scripting call to R-Studio compile PDF

[Yihui Xie]

Yes, that is pretty much it. Setting the options useDingbats or
concordance is optional. You may or may not really need them. What is
essential is the knit() function.

Regards,
Yihui
--
Yihui Xie xieyi...@gmail.com
Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA


On Wed, Oct 23, 2013 at 6:02 PM, Adam Hughes hughesada...@gmail.com wrote:
 Thanks for the help guys.  Sorry, I will not post further RStudio questions
 here.  Yihui, thanks for the tip.  Looks like these commands would do:

 grDevices::pdf.options(useDingbats = FALSE); require(knitr);
 opts_knit$set(concordance = TRUE); knit('filename.rnw',
 encoding='UTF-8')


 pdflatex filename.tex


 evince filename.pdf


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Re: [R] raster package: merge/mosaic

[halim10-fes]

Hi,

With the 'merge' function using different tolerance level, I've come up with a 
solution.

For e.g. consider r1 and r2 as two raster layers, attributes are as follows:

r1 - raster(xmx=-150, ymn=60, ncols=30, nrows=20)
r1[]-1:ncell(r1)
r1

class   : RasterLayer 
dimensions  : 20, 30, 600  (nrow, ncol, ncell)
resolution  : 1, 1.5  (x, y)
extent  : -180, -150, 60, 90  (xmin, xmax, ymin, ymax)
coord. ref. : +proj=longlat +datum=WGS84 
data source : in memory
names   : layer 
values  : 1, 600  (min, max)


origin(r1)
[1] 0 0
 
r2 - raster(xmn=-100, xmx=-50, ymx=50, ymn=30,ncols=25,nrows=30)
res(r2)-c(xres(r1),yres(r1))
r2[]-1:ncell(r2)
 r2

class   : RasterLayer 
dimensions  : 13, 50, 650  (nrow, ncol, ncell)
resolution  : 1, 1.5  (x, y)
extent  : -100, -50, 30.5, 50  (xmin, xmax, ymin, ymax)
coord. ref. : +proj=longlat +datum=WGS84 
data source : in memory
names   : layer 
values  : 1, 650  (min, max)

origin(r2)
[1] 0.0 0.5

If we try to merge r1 and r2,

merge(r1,r2)
Error in compareRaster(x, extent = FALSE, rowcol = FALSE, orig = TRUE,  : 
  different origin

So, they have different origins. Here the default tolerance value was = 0.05, 
I've changed it to 0.5 after a few trial and error.

So, finally,

merge(r1,r2,tolerance=0.5)

class   : RasterLayer 
dimensions  : 40, 130, 5200  (nrow, ncol, ncell)
resolution  : 1, 1.5  (x, y)
extent  : -180, -50, 30.5, 90.5  (xmin, xmax, ymin, ymax)
coord. ref. : +proj=longlat +datum=WGS84 
data source : in memory
names   : layer 
values  : 1, 650  (min, max)

Worked! 

Hope this might help you to solve your problem. And also see what others 
say...

Regards,

Halim

---
Md. Abdul Halim
Assistant Professor
Department of Forestry and Environmental Science
Shahjalal University of Science and Technology,Sylhet-3114,
Bangladesh.


On Wed, 23 Oct 2013 12:18:40 -0700 (PDT), Carl Witthoft wrote
 According to ?merge,  you could try adjusting the default value of 
 the tolerance argument.
 
 Nora Ernst wrote
  I'm working with raster data (satellite imagery) and the raster package.
  The
 idea is to merge two raster files that are partially overlaping, do
  have the
 same coordinate system and resolution but not the same origin. As
  expected,
 the functions mosaic(r1,r2) as well as merge(r1,r2)) give the error
  message:
  
  Error in compareRaster(x, extent = FALSE, rowcol = FALSE, orig = TRUE,  : 
different origin
  
  
  origin(r1)
  [1] 5.582522e-05 1.124150e-03
  origin(r2)
  [1]  0.001054868 -0.001124150
  
  
 Can  anyone tell me how it is possible to merge rasters with different
 origin?
 
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 package-merge-mosaic-tp4678890p4678899.html Sent from the R help 
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[R] problem with ecdf : missing C_R_approxfun message

[Olivier Eterradossi]

Hi list,

In June 2013, using R.2.15.1 (i386) on Windows 7, I calculated a set of ecdf 
which I stored in lists of records having a size.ecdf field, with following 
structure :

[skip previous structure...]
$ size.ecdf   :function (v)
  ..- attr(*, class)= chr [1:3] ecdf stepfun function
  ..- attr(*, call)=length 2 ecdf(test.moms[, m.pxs])
  .. ..- attr(*, srcref)=Class 'srcref'  atomic [1:8] 12 1 12 36 1 36 12 12
  .. .. .. ..- attr(*, srcfile)=Classes 'srcfilecopy', 'srcfile' 
environment: 0x07d7b3b0
[skip following structure...]

In September I upgraded to R.3.0.1 under the same OS

I need to use my previously recorded ecdfs again, and try to plot one  as in :

 plot(first.list[[1]]$size.ecdf,col=couleurs[1],main=first ecdf)
Which returns :
Erreur dans x(0.5 * (ti.l + ti.r)) : objet 'C_R_approxfun' introuvable
Sorry it's in French  ;-)  , it translates to error in x(0.5 * (ti.l + ti.r)) 
: missing object 'C_R_approxfun' 

The same message prints when trying to use other ecdf methods, or other records 
in my lists.

I first searched the help and archives without success, here are four questions 
I cannot answer :

What is this C_R_approxfun object and what is it intended to do ?
What may have caused it is missing now (and was not in June) ?
Does this mean that I should have recorded other useful parameters in June 
(such as environment parameters) ?
Or anything else I cannot guess ?

Thanks for helping, I'm stuck and I would prefer not to calculate all my old 
ecdfs again !

Regards, Olivier

--
Olivier ETERRADOSSI
Maître-Assistant, HDR
Ecole des Mines d'Alès (C2MA, site de Pau)
Ingénierie de l'aspect visuel et tactile des matériaux
Pôle « Recherche sur les Interactions des Matériaux avec leur Environnement » 
(RIME)
Hélioparc, 2 av. P. Angot, F-64053 PAU CEDEX 9
Tel : 05 59 30 90 35 (direct) - 05 59 30  54 25 (std)
Fax : 05 59 30 63 68
http://www.mines-ales.frhttp://www.mines-ales.fr/
http://www.mines-telecom.frhttp://www.mines-telecom.fr/










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[R] TR: problem with ecdf : missing C_R_approxfun message

[Olivier Eterradossi]

Hi again, this is a follow-up of my previous post :

I've noticed that
 attr(first.list[[1]]$size.ecdf,call)  gives ecdf(test.moms[, m.pxs]) and 
 that there is no test.moms field in my records (a local variable named 
 test.moms was used inside a function, but it was stored under another name in 
 the list, outside the function)

May this be the answer (and I've been stupid not to see this before !) ?

Anyway, trying to change test.moms to the real name of the corresponding 
record field, i.e. :
 attr(first.list[[1]]$size.ecdf,call)-ecdf(first.list[[1]]$true.varname[,m.pxs])

Does not fix the problem.

Is changing the call attribute the thing to do, but done in a wrong way ?
If yes, what is the good way ?
If not, what can be done ?

Thanks again, Olivier


De : Olivier Eterradossi
Envoyé : jeudi 24 octobre 2013 08:54
À : 'r-help@r-project.org'
Objet : problem with ecdf : missing C_R_approxfun message

Hi list,

In June 2013, using R.2.15.1 (i386) on Windows 7, I calculated a set of ecdf 
which I stored in lists of records having a size.ecdf field, with following 
structure :

[skip previous structure...]
$ size.ecdf   :function (v)
  ..- attr(*, class)= chr [1:3] ecdf stepfun function
  ..- attr(*, call)=length 2 ecdf(test.moms[, m.pxs])
  .. ..- attr(*, srcref)=Class 'srcref'  atomic [1:8] 12 1 12 36 1 36 12 12
  .. .. .. ..- attr(*, srcfile)=Classes 'srcfilecopy', 'srcfile' 
environment: 0x07d7b3b0
[skip following structure...]

In September I upgraded to R.3.0.1 under the same OS

I need to use my previously recorded ecdfs again, and try to plot one  as in :

 plot(first.list[[1]]$size.ecdf,col=couleurs[1],main=first ecdf)
Which returns :
Erreur dans x(0.5 * (ti.l + ti.r)) : objet 'C_R_approxfun' introuvable
Sorry it's in French  ;-)  , it translates to error in x(0.5 * (ti.l + ti.r)) 
: missing object 'C_R_approxfun' 

The same message prints when trying to use other ecdf methods, or other records 
in my lists.

I first searched the help and archives without success, here are four questions 
I cannot answer :

What is this C_R_approxfun object and what is it intended to do ?
What may have caused it is missing now (and was not in June) ?
Does this mean that I should have recorded other useful parameters in June 
(such as environment parameters) ?
Or anything else I cannot guess ?

Thanks for helping, I'm stuck and I would prefer not to calculate all my old 
ecdfs again !

Regards, Olivier

--
Olivier ETERRADOSSI
Maître-Assistant, HDR
Ecole des Mines d'Alès (C2MA, site de Pau)
Ingénierie de l'aspect visuel et tactile des matériaux
Pôle « Recherche sur les Interactions des Matériaux avec leur Environnement » 
(RIME)
Hélioparc, 2 av. P. Angot, F-64053 PAU CEDEX 9
Tel : 05 59 30 90 35 (direct) - 05 59 30  54 25 (std)
Fax : 05 59 30 63 68
http://www.mines-ales.frhttp://www.mines-ales.fr/
http://www.mines-telecom.frhttp://www.mines-telecom.fr/










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Re: [R] problem with ecdf : missing C_R_approxfun message

[Prof Brian Ripley]

On 24/10/2013 07:54, Olivier Eterradossi wrote:

Hi list,

In June 2013, using R.2.15.1 (i386) on Windows 7, I calculated a set of ecdf which I 
stored in lists of records having a size.ecdf field, with following structure 
:


Note that R 2.15.1 was not current even then.


[skip previous structure...]
$ size.ecdf   :function (v)
   ..- attr(*, class)= chr [1:3] ecdf stepfun function
   ..- attr(*, call)=length 2 ecdf(test.moms[, m.pxs])
   .. ..- attr(*, srcref)=Class 'srcref'  atomic [1:8] 12 1 12 36 1 36 12 12
   .. .. .. ..- attr(*, srcfile)=Classes 'srcfilecopy', 'srcfile' environment: 
0x07d7b3b0
[skip following structure...]

In September I upgraded to R.3.0.1 under the same OS


And R 3.0.2 has been out for nearly a month now: see the posting guide.


I need to use my previously recorded ecdfs again, and try to plot one  as in :


plot(first.list[[1]]$size.ecdf,col=couleurs[1],main=first ecdf)

Which returns :
Erreur dans x(0.5 * (ti.l + ti.r)) : objet 'C_R_approxfun' introuvable
Sorry it's in French  ;-)  , it translates to error in x(0.5 * (ti.l + ti.r)) : 
missing object 'C_R_approxfun' 

The same message prints when trying to use other ecdf methods, or other records 
in my lists.

I first searched the help and archives without success, here are four questions 
I cannot answer :

What is this C_R_approxfun object and what is it intended to do ?
What may have caused it is missing now (and was not in June) ?
Does this mean that I should have recorded other useful parameters in June 
(such as environment parameters) ?
Or anything else I cannot guess ?

Thanks for helping, I'm stuck and I would prefer not to calculate all my old 
ecdfs again !


You have to.  The ones you have contain references to internal code 
found only in R  3.0.0.


Note that storing objects in .RData is never intended to be a permanent 
form of storage, and you have done a *major* version update.  You should 
expect to have to re-create objects from your scripts.


It is actually rather easy to update the objects.  Consider Fn12 from 
example(ecdf) (which is random, so your mileage will vary).  The data 
are in the environment of Fn12, so


Fn12 - eval(attr(Fn12, call), environment(Fn12))

recreates it.




Regards, Olivier

--
Olivier ETERRADOSSI
Maître-Assistant, HDR
Ecole des Mines d'Alès (C2MA, site de Pau)
Ingénierie de l'aspect visuel et tactile des matériaux
Pôle « Recherche sur les Interactions des Matériaux avec leur Environnement » 
(RIME)
Hélioparc, 2 av. P. Angot, F-64053 PAU CEDEX 9
Tel : 05 59 30 90 35 (direct) - 05 59 30  54 25 (std)
Fax : 05 59 30 63 68
http://www.mines-ales.frhttp://www.mines-ales.fr/
http://www.mines-telecom.frhttp://www.mines-telecom.fr/



--
Brian D. Ripley,  rip...@stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel:  +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax:  +44 1865 272595

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[R] Course: Mixed modelling (with intro MCMC)

[Highland Statistics Ltd]

We would like to announce the following stats course;

Course: Introduction to MCMC, Linear mixed effects models and GLMM with R
When: 20-24 January, 2014
Where: Bangor University, UK
Info: http://www.highstat.com/statscourse.htm
Flyer: http://www.highstat.com/Courses/Flyer2014_02Bangor.pdf

Kind regards,

Alain

--
Dr. Alain F. Zuur
First author of:

1. Analysing Ecological Data (2007)
2. Mixed effects models and extensions in ecology with R (2009)
3. A Beginner's Guide to R (2009)
4. Zero Inflated Models and GLMM with R (2012)
5. A Beginner's Guide to GAM (2012)
6. A Beginner's Guide to GLM and GLMM (2013)

Highland Statistics Ltd.
6 Laverock road
UK - AB41 6FN Newburgh
Tel: 0044 1358 788177
Email: highs...@highstat.com
URL: www.highstat.com
URL: www.brodgar.com

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Re: [R] How can I use a script l (LaTeX \ell) in mathematical annotation of plots?

[Eik Vettorazzi]

this works for me:

plot(1,main=\u2113)

cheers

Am 24.10.2013 01:39, schrieb Byron Dom:
 
 
 Original post: On 13/10/2013 18:53, Byron Dom wrote:
 
 Due to convention a script l - $$\ell$$ (LaTeX \ell) is used to 
 represent a certain quantity in something I'm working on. I'm 
 unable to figure out how to use it in R. It's not included in the 
 list on ?plotmath.

 Can anyone tell me how to use it?  Its unicode is U+2113. This 
 page has a list of various encodings of it: 

  http://www.fileformat.info/info/unicode/char/2113/encoding.htm.  
 Is there a way to include it by using one of these encodings somehow?
 
 -
 
 On 13/10/2013 22:06 Prof Brian Ripley responded:
 
 What do you want to do with it?  plotmath is about plotting, but you
 have not otherwise mentioned that, let alone the device on which you 
 want to plot.

 Read the help for plotmath: on some plot devices, just use \u2113.  It 
 is not AFAICS in the Adobe symbol encoding.

 -- 
 Brian D. Ripley,  ripley at stats.ox.ac.uk
 Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
 University of Oxford, Tel: 
  +44 1865 272861 (self)
 1 South Parks Road, +44 1865 272866 (PA)
 Oxford OX1 3TG, UKFax:  +44 1865 272595
 
 -
 
 My response:
 
 Thanks I worked out how to do it based on your mention of u2113.
 See below.
 
 I'm sorry if my information wasn't complete enough. I assumed that 
 what I said, combined with the subject (How can I use a script l 
 (LaTeX \ell) in
  mathematical annotation of plots?) would have been 
 enough.
 
 I just wanted to be able to do this on the default device, which 
 displays plots within the R session window. I have a simple path 
 to go from there to .png form, which I include in LaTeX documents
 and for other purposes. I am using R version 3.0.1 in Windows 7, 
 for which I believe the default plot device is windows.
 
 An example of the kind of thing I wanted to do is to include 
 ylab = expression(hat(gamma)) (which is equivalent to the LaTex 
 \hat{\gamma}}) among the base-graphics plot() arguments. That 
 works. In LaTeX a script l is produced with \ell, but 
 something like ylab = expression(ell) doesn't work in R. 
 I wanted to be able to do the equivalent of that, but to obtain ℓ.
 
 Here are a couple of examples using it that worked:
plot(1:10,xlab=\u2113)
   
  plot(1:10,xlab=\u2113(\u2113 + 1))
 The only (slight) problem with this is the minor aesthetic issue 
 
 that the ℓ one gets this way is in an obviously different font 
 
 from what one gets using the LaTeX \lambda command/symbol.
 
 Strangely, earlier, when I tried 
plot(1:10,xlab=expression(symbol(\u2113)))
 it did the same thing as 
plot(1:10,xlab=expression(lambda))
 So I got a lower-case greek lambda - λ, rather than ℓ
 (script l).
 
 When I used the unicode representation for lowercase 
 lambda - λ - as follows
   
  plot(1:10,xlab=expression(symbol(\u03bb)))
 I got this for an x-axis label: Y+03BB. On the other hand,
 the following did work
plot(1:10,xlab=\u03bb), 
 giving me an x-axis label of lambda - λ.
   [[alternative HTML version deleted]]
 
 
 
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 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.
 

-- 
Eik Vettorazzi

Department of Medical Biometry and Epidemiology
University Medical Center Hamburg-Eppendorf

Martinistr. 52
20246 Hamburg

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

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Re: [R] labeling abscissa using a function of the plotted scale

[Hurr]

Thanks Jim, maybe now I can start learning.
Next I want to use my choice of n digits or width instead of round.




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Re: [R] RWeka and multicore package

[Luís Paulo F . Garcia]

Dear, Patrick.

I'm using a workaround to work with RWeka and multicore package. The most
important point is not loading the RWeka package and use the namespace in a
encapsulated function. Take a look on this code:


# C4.5 classifier. Return the prediction for a test dataset.
cl.c45 = function(tran, test) {

model = RWeka::J48(Species ~ ., tran);
pred = predict(model, test[,-ncol(test)], type=class);
names(pred) = row.names(test);
return(pred);
}


library(multicore)
aux = mclapply(1:1000, function(i) {
cl.c45(iris, iris)
})

Regards,
Luis








On Tue, Oct 22, 2013 at 7:11 AM, Patrick Connolly 
p_conno...@slingshot.co.nz wrote:

 On Thu, 17-Oct-2013 at 02:21PM -0300, Luís Paulo F. Garcia wrote:

 | I work very mutch with the packages RWeka and multicore. If you try to
 run
 | J48 or any tree of RWeka with multicore we hava some errors.
 |
 | Example I:
 |
 | library(RWeka);
 | library(multicore);
 |
 | mclapply(1:100, function(i) {
 | J48(Species ~., iris);
 | });
 |
 |
 | Output:  Error in .jcall(o, \Ljava/lang/Class;\, \getClass\) : \n
 | java.lang.ClassFormatError: Incompatible magic value 1347093252 in class
 | file java/lang/ProcessEnvironment$StringEnvironment\n
 |
 |
 | Example II:
 |
 | library(multicore);
 |
 | mclapply(1:100, function(i) {
 | RWeka::J48(Species ~., iris);
 | });
 |
 | Output: Erro em .jcall(x$classifier, S, toString) :
 |   RcallMethod: attempt to call a method of a NULL object.
 |
 |
 | Do you know some way to work with parallel processing and RWeka? I tried
 | MPI and SNOW without success.

 Not much help, but I too have not been able to get parallelling RWeka
 to work.  OTOH, what RWeka can do is very fast compared with, say, gbm
 (which does work well with mclapply).

 I suspect that it has something to do with how Java is set up, but I
 know nothing about setting up Java.




 |
 | R version 3.0.2 (2013-09-25) -- Frisbee Sailing
 | Ubuntu 12.04 x64
 |
 |
 | --
 | Lu?s Paulo Faina Garcia
 | Engenheiro de Computa??o - Universidade de S?o Paulo
 | S?o Carlos - SP - Brasil
 |
 |  [[alternative HTML version deleted]]
 |

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


 --
 ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
___Patrick Connolly
  {~._.~}   Great minds discuss ideas
  _( Y )_ Average minds discuss events
 (:_~*~_:)  Small minds discuss people
  (_)-(_)  . Eleanor Roosevelt

 ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.




-- 
Luís Paulo Faina Garcia
Engenheiro de Computação - Universidade de São Paulo
São Carlos - SP - Brasil

[[alternative HTML version deleted]]

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Re: [R] nls model definition help

[S Ellison]

 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
 project.org] On Behalf Of wayne.w.jo...@shell.com
 Sent: 22 October 2013 18:52
 To: R-help@r-project.org
 Subject: [R] nls model definition help
 
 Hi fellow R users,
 
 I'm trying to fit a model using nls with the following model
 definition:
 
 y(t+1)=(th1*x1 + R1*x2) * exp(a1*x3) + (1-th1*x1 + R1*x2)*y(t)
 
 ...

 Any ideas if this is achievable and if not any ideas on how to fit this
 model?
I'm thinking not, as you have that (t+1) back-reference in there which makes 
the calculated y(t) part of the expression. Pretty sure nlm won't handle that 
in the formula interface. 

However, you could use nlm or optim if you write a function to predict y and 
then wrap that in a function to calculate the residual sum of squares (taking 
the parameter vector and y[obs] as parameters), then minimise the residual SS. 
The hessian from either can then be used to estimate standard errors using the 
usual least-squares formulae.

S Ellison


***
This email and any attachments are confidential. Any use...{{dropped:8}}

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Re: [R] data frame pointers?

[Jon BR]

Hi Arun,
That seemed to do the trick - thanks!!

Jonathan


On Wed, Oct 23, 2013 at 11:12 PM, arun smartpink...@yahoo.com wrote:

 HI,

 Better would be:
 res1 - dcast(df,gene~case,value.var=issue,paste,collapse=,,fill=0)

 str(res1)
 #'data.frame':2 obs. of  4 variables:
 # $ gene  : chr  gene1 gene2
 # $ case_1: chr  nsyn,amp 0
 # $ case_2: chr  del 0
 # $ case_3: chr  0 UTR

  write.table(res1,test.txt,sep=\t,quote=FALSE,row.names=FALSE)


 A.K.


 On , arun smartpink...@yahoo.com wrote:
 Hi Jonathan,If you look at the str()
  str(res)
 'data.frame':2 obs. of  4 variables:
  $ gene  : chr  gene1 gene2
  $ case_1:List of 2
   ..$ : chr  nsyn amp
   ..$ : chr
  $ case_2:List of 2
   ..$ : chr del
   ..$ : chr
  $ case_3:List of 2
   ..$ : chr
   ..$ : chr UTR

 In this case,

 capture.output(res,file=test.txt) #should work

 But, if you wanted to use ?write.table() and also to substitute zeros,
 perhaps:


 res[,2:4] - lapply(res[,2:4],function(x) {x1
 -unlist(lapply(x,paste,collapse=,));x1[x1==] - 0; x1})


  str(res)
 #'data.frame':2 obs. of  4 variables:
 # $ gene  : chr  gene1 gene2
 # $ case_1: chr  nsyn,amp 0
 # $ case_2: chr  del 0
 # $ case_3: chr  0 UTR

  write.table(res,test.txt,sep=\t,quote=FALSE,row.names=FALSE)


 A.K.





 On Wednesday, October 23, 2013 10:44 PM, Jon BR jonsle...@gmail.com
 wrote:

 Hi Arun,
Your suggestion using dcast is simple and worked splendidly!
  Unfortunately, the resulting data frame does not play nicely with
 write.table.

 Any idea how to could print this out to a tab-delimited text file, perhaps
 substituting zeros in for the empty cells?

 See the error below:
  write.table(res,test.txt)
 Error in .External2(C_writetable, x, file, nrow(x), p, rnames, sep, eol,
  :
   unimplemented type 'list' in 'EncodeElement'


 Best,
 Jonathan






 On Wed, Oct 23, 2013 at 9:50 PM, arun smartpink...@yahoo.com wrote:

 HI,
 
 You may try:
 library(reshape2)
 df -
 data.frame(case=c(case_1,case_1,case_2,case_3),
 gene=c(gene1,gene1,gene1,gene2), issue=c(nsyn,amp,del,UTR),
 stringsAsFactors=FALSE)
 res - dcast(df,gene~case,value.var=issue,list)
  res
 #   genecase_1 case_2 case_3
 #1 gene1 nsyn, ampdel
 #2 gene2 UTR
 
 
 A.K.
 
 
 
 On Wednesday, October 23, 2013 7:38 PM, Jon BR jonsle...@gmail.com
 wrote:
 Hello,
 I've been running several programs in the unix shell, and it's time to
 combine results from several different pipelines.  I've been writing shell
 scripts with heavy use of awk and grep to make big text files, but I'm
 thinking it would be better to have all my data in one big structure in R
 so that I can query whatever attributes I like, and print several
 corresponding tables to separate files.
 
 I haven't used R in years, so I was hoping somebody might be able to
 suggest a solution or combinatin of functions that could help me get
 oriented..
 
 Right now, I can import my data into a data frame that looks like this:
 
 df -

 data.frame(case=c(case_1,case_1,case_2,case_3),gene=c(gene1,gene1,gene1,gene2),issue=c(nsyn,amp,del,UTR))
  df
 case  gene issue
 1 case_1 gene1  nsyn
 2 case_1 gene1   amp
 3 case_2 gene1   del
 4 case_3 gene2   UTR
 
 
 I'd like to cook up some combination of functions/scripting that can
 convert a table like df to produce a list or a data frame/ matrix that
 looks like df2:
 
  df2
 case_1 case_2 case_3
 gene1 nsyn,ampdel  0
 gene20  0UTR
 
 I can build df2 manually, like this:
 df2

 -data.frame(case_1=c(nsyn,amp,0),case_2=c(del,0),case_3=c(0,UTR))
 rownames(df2)-c(gene1,gene2)
 
 but obviously do not want to do this by hand; I want R to generate df2
 from
 df.
 
 Any pointers/ideas would be most welcome!
 
 Thanks,
 Jonathan
 
 [[alternative HTML version deleted]]
 
 
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[R] Use R to plot a directory tree

[Thaler,Thorn,LAUSANNE,Applied Mathematics]

Dear all,

I was wondering whether (or better: how) I can use R to read recursively a 
directory to get all the sub-folders and files located in the root folder and 
put it into a tree like structure where the leaves are files and intermediate 
nodes are the directories? The idea is that I'd like to plot the structure of a 
certain root folder to be able to restructure the file system.

Any ideas on that? I was googling a lot but apparently I did not use the right 
terms (R tree folder or R tree directory takes me mainly to pages about the 
R-tree a structure for spatial access methods [at least I learnt something 
new ;)])

Any pointer to the right function is highly appreciated.

Cheers,

Thorn Thaler 
NRC Lausanne
Applied Mathematics

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[R] Plot.raster hides the axis layer

[Alaios]

Hi all,
I am trying to plot a raster object (I can explain why but the point is that it 
would be a raster objeçt)..

I have selected a small code to show you exactly the problem


require(raster)
test-matrix(data=runif(1),nrow=100)
m-raster(test)
plot(m,axes=FALSE)
axis(1,at=c(0,1),labels=c(a,b)) # THIS DOES NOT CHANGE THE INVISIBLE AXIS 
WHILE




plot(test,axes=FALSE)
axis(1,at=c(0,1),labels=c(a,b)) # WHEN I AM PLOTTING A NON RASTER OBJECT 
THE AXIS APPEARS.

Can someone explain me what I can do so a raster layer to show correctly the 
axis? Please remember that I have to do that on a raster object so coercing it 
will not help ..

I would like to thank you in advance for your help

Regards
Alex

[[alternative HTML version deleted]]

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Re: [R] Use R to plot a directory tree

[Bert Gunter]

A wild guess -- take a look at the CRAN phylohenetics task view, as
that sounds like the sort of thing that might have tree generation and
manipulation functions.

... but you may do better with some non-R tool out there.

(Hopefully, you'll get a better response, though).

Cheers,
Bert

On Thu, Oct 24, 2013 at 6:13 AM, Thaler,Thorn,LAUSANNE,Applied
Mathematics thorn.tha...@rdls.nestle.com wrote:
 Dear all,

 I was wondering whether (or better: how) I can use R to read recursively a 
 directory to get all the sub-folders and files located in the root folder and 
 put it into a tree like structure where the leaves are files and intermediate 
 nodes are the directories? The idea is that I'd like to plot the structure of 
 a certain root folder to be able to restructure the file system.

 Any ideas on that? I was googling a lot but apparently I did not use the 
 right terms (R tree folder or R tree directory takes me mainly to pages 
 about the R-tree a structure for spatial access methods [at least I learnt 
 something new ;)])

 Any pointer to the right function is highly appreciated.

 Cheers,

 Thorn Thaler
 NRC Lausanne
 Applied Mathematics

 __
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-- 

Bert Gunter
Genentech Nonclinical Biostatistics

(650) 467-7374

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Re: [R] labeling abscissa using a function of the plotted scale

[Hurr]

Thanks Jim, maybe now I can start learning.
Here is a run of my trying to learn:
 xvalue-c(5.2,1.3,9.7,2.8,8.1,4.7,6.6,7.4)
 yvalue-c(9,3,4,7,2,5,3,6)
 plot(xvalue,yvalue)
 axis(1,at=NULL,labels=1/xvalue,digits=5)
Error in axis(1, at = NULL, labels = 1/xvalue, digits = 5) :
  'labels' is supplied and not 'at'
In addition: Warning message:
In axis(1, at = NULL, labels = 1/xvalue, digits = 5) :
  digits is not a graphical parameter

Why can't R automatically compute the spacing when I use the formula?
How can I specify n-digits or width instead of round or nothing? 




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Re: [R] Use R to plot a directory tree

[Marc Schwartz]

One R package that might be of interest would be 'diagram':

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

I would also agree with Bert here and would point you in the direction of 
PSTricks, which can handle these sorts of complex figures. It would of course 
require learning LaTeX, but that is a good thing. :-)

More info here:

  http://tug.org/PSTricks/main.cgi/

and lots of examples with code here:

 http://tug.org/PSTricks/main.cgi?file=examples


I use PSTricks for creating things like subject disposition flow charts for 
clinical study reports.

Regards,

Marc Schwartz

  
On Oct 24, 2013, at 8:47 AM, Bert Gunter gunter.ber...@gene.com wrote:

 A wild guess -- take a look at the CRAN phylohenetics task view, as
 that sounds like the sort of thing that might have tree generation and
 manipulation functions.
 
 ... but you may do better with some non-R tool out there.
 
 (Hopefully, you'll get a better response, though).
 
 Cheers,
 Bert
 
 On Thu, Oct 24, 2013 at 6:13 AM, Thaler,Thorn,LAUSANNE,Applied
 Mathematics thorn.tha...@rdls.nestle.com wrote:
 Dear all,
 
 I was wondering whether (or better: how) I can use R to read recursively a 
 directory to get all the sub-folders and files located in the root folder 
 and put it into a tree like structure where the leaves are files and 
 intermediate nodes are the directories? The idea is that I'd like to plot 
 the structure of a certain root folder to be able to restructure the file 
 system.
 
 Any ideas on that? I was googling a lot but apparently I did not use the 
 right terms (R tree folder or R tree directory takes me mainly to pages 
 about the R-tree a structure for spatial access methods [at least I learnt 
 something new ;)])
 
 Any pointer to the right function is highly appreciated.
 
 Cheers,
 
 Thorn Thaler
 NRC Lausanne
 Applied Mathematics
 
 __
 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.
 
 
 
 -- 
 
 Bert Gunter
 Genentech Nonclinical Biostatistics
 
 (650) 467-7374
 
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Re: [R] Use R to plot a directory tree

[Jan Kim]

perhaps as a somewhat tamer guess than Bert's, it's probably not
very hard to write a function that pieces together a dendrogram
(S3 class provided by the stats package), using the list.dirs and
list.files functions.

This could then be plotted via the plot function, and you could
even designate attributes such as colours, line thicknesses etc.
to highlight e.g. the largest files.

I'm not too sure, though, how useful this would be for plotting
directory trees for restructuring them; any tree that's complex
enough to require the use of such auxiliary tools will very likely
have at least a few hundred files, and thus labels will end up
either overlapping everywhere or illegibly small.

Best regards, Jan

On Thu, Oct 24, 2013 at 09:20:30AM -0500, Marc Schwartz wrote:
 One R package that might be of interest would be 'diagram':
 
   http://cran.r-project.org/web/packages/diagram/
 
 I would also agree with Bert here and would point you in the direction of 
 PSTricks, which can handle these sorts of complex figures. It would of course 
 require learning LaTeX, but that is a good thing. :-)
 
 More info here:
 
   http://tug.org/PSTricks/main.cgi/
 
 and lots of examples with code here:
 
  http://tug.org/PSTricks/main.cgi?file=examples
 
 
 I use PSTricks for creating things like subject disposition flow charts for 
 clinical study reports.
 
 Regards,
 
 Marc Schwartz
 
   
 On Oct 24, 2013, at 8:47 AM, Bert Gunter gunter.ber...@gene.com wrote:
 
  A wild guess -- take a look at the CRAN phylohenetics task view, as
  that sounds like the sort of thing that might have tree generation and
  manipulation functions.
  
  ... but you may do better with some non-R tool out there.
  
  (Hopefully, you'll get a better response, though).
  
  Cheers,
  Bert
  
  On Thu, Oct 24, 2013 at 6:13 AM, Thaler,Thorn,LAUSANNE,Applied
  Mathematics thorn.tha...@rdls.nestle.com wrote:
  Dear all,
  
  I was wondering whether (or better: how) I can use R to read recursively a 
  directory to get all the sub-folders and files located in the root folder 
  and put it into a tree like structure where the leaves are files and 
  intermediate nodes are the directories? The idea is that I'd like to plot 
  the structure of a certain root folder to be able to restructure the file 
  system.
  
  Any ideas on that? I was googling a lot but apparently I did not use the 
  right terms (R tree folder or R tree directory takes me mainly to 
  pages about the R-tree a structure for spatial access methods [at least 
  I learnt something new ;)])
  
  Any pointer to the right function is highly appreciated.
  
  Cheers,
  
  Thorn Thaler
  NRC Lausanne
  Applied Mathematics
  
  __
  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.
  
  
  
  -- 
  
  Bert Gunter
  Genentech Nonclinical Biostatistics
  
  (650) 467-7374
  
  __
  R-help@r-project.org mailing list
  https://stat.ethz.ch/mailman/listinfo/r-help
  PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
  and provide commented, minimal, self-contained, reproducible code.
 
 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.

-- 
 +- Jan T. Kim ---+
 | email: jtt...@gmail.com|
 | WWW:   http://www.jtkim.dreamhosters.com/  |
 *-=  hierarchical systems are for files, not for humans  =-*

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Re: [R] Plot.raster hides the axis layer

[MacQueen, Don]

This is by no means an explanation, but as a possible approach to consider:

 plot(0:1, 0:1, xaxt='n', asp=1)
 axis(1,at=c(0,1),labels=c(a,b))
 plot(m,add=TRUE)


-Don

-- 
Don MacQueen

Lawrence Livermore National Laboratory
7000 East Ave., L-627
Livermore, CA 94550
925-423-1062





On 10/24/13 6:28 AM, Alaios ala...@yahoo.com wrote:

Hi all,
I am trying to plot a raster object (I can explain why but the point is
that it would be a raster objeçt)..

I have selected a small code to show you exactly the problem


require(raster)
test-matrix(data=runif(1),nrow=100)
m-raster(test)
plot(m,axes=FALSE)
axis(1,at=c(0,1),labels=c(a,b)) # THIS DOES NOT CHANGE THE INVISIBLE
AXIS WHILE




plot(test,axes=FALSE)
axis(1,at=c(0,1),labels=c(a,b)) # WHEN I AM PLOTTING A NON RASTER
OBJECT THE AXIS APPEARS.

Can someone explain me what I can do so a raster layer to show correctly
the axis? Please remember that I have to do that on a raster object so
coercing it will not help ..

I would like to thank you in advance for your help

Regards
Alex

   [[alternative HTML version deleted]]


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

[R] R: Optional argument to be used in a subset function

[David Mora]

I'm writing a function that needs an optional variable. If the variable is
given, then a subset must be made using that variable, but if the variable
is not given the subset must be done using all the values for that variable
(ignoring that variable).

Something like this:

*band - function(file, fruit = apple, optional=TRUE) {*

*data - read.csv(file)*

*a - nrow(subset(data, 'Column 1' == fruit  'Column 2'==hot  'Column 3'==
optional))*

*b - nrow(subset(data,'Column 1' == fruit  'Column 2'==cold  'Column 3'==
optional)) *

*z - a+b*

* print(z)*

* }*

What I need is that the function *band(file,orange)*,  subset the data
frame using all possible values for Column 3 but is not doing it.

All ideas are welcome.

Thanks.


David Mora

[[alternative HTML version deleted]]

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

[R] bug in dummy.coef?

[Alexandra Kuznetsova]

Dear all,

Running the following code produces an error in dummy.coef. I guess it might be 
a bug..

 ctl - c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)
 trt - c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
 group - gl(2, 10, 20, labels = c(Ctl,Trt))
 weight - c(ctl, trt)
 x - rnorm(length(weight))
 lm.D9 - lm(weight ~ group + x + I(x^2))
 dummy.coef(lm.D9)
Error in rep.int(xl[[i]][1L], nl) : invalid 'times' value



 sessionInfo()

R version 3.0.1 (2013-05-16)

Platform: x86_64-w64-mingw32/x64 (64-bit)



locale:

[1] LC_COLLATE=Danish_Denmark.1252  LC_CTYPE=Danish_Denmark.1252
LC_MONETARY=Danish_Denmark.1252

[4] LC_NUMERIC=CLC_TIME=Danish_Denmark.1252



attached base packages:

[1] parallel  splines   stats graphics  grDevices utils datasets  
methods   base



other attached packages:

 [1] pbkrtest_0.3-5MASS_7.3-26   Hmisc_3.12-2  Formula_1.1-1 
survival_2.37-4   numDeriv_2012.9-1

 [7] lmerTest_2.0-1lme4_1.1-1Matrix_1.0-12 lattice_0.20-15



loaded via a namespace (and not attached):

[1] cluster_1.14.4 gdata_2.13.2   gplots_2.11.3  grid_3.0.1 gtools_3.0.0   
minqa_1.2.1nlme_3.1-109

[8] rpart_4.1-1tools_3.0.1




With best wishes,
Alexandra

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

[R] ordinal data with binary response

[Kishor Tappita]

Dear R-users,

I am trying to analyze data with ordinal independent variables and
binary response . Could some one suggest me an appropriate statistic
for this kind of analysis.

Thanks,
Regards,
Kishir

__
R-help@r-project.org mailing list
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and provide commented, minimal, self-contained, reproducible code.

[R] track on boats

[Marta Tobeña]

Hi professors
I'm finding the best package in R for manage a big database about vessels. I 
need to divided the travel of each boat into tracks. I have GPS points.

I would join these points in a line on the map. I make that with the function 
lines, but I can't divided by vessel or by track,

I saw several packages, for tracking animals but they had specifically 
variables. And I don't add others like  type,destination or status.

Can you give me a suggestion, please
  
[[alternative HTML version deleted]]

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

Re: [R] XML package not working

[Steven Dwayne Randolph]

Berend Thanks.  I am aware of the missing kb's in the download.  However, 
my problem is that it only happens with this package.  I download other 
packages manually and via command-line install.packages() and 
Do not have any problems with completing full downloads of the entire file.   

Perhaps, if someone has the complete download for the XML package, both in 
*.zip and  *tar formats that they can either email to me or allow me to ftp 
from it would help me to move forward with this resolve.   

 

Thanks... 
 

 Steven

-Original Message-
From: Berend Hasselman [mailto:b...@xs4all.nl] 
Sent: Tuesday, October 22, 2013 12:39 PM
To: Steven Dwayne Randolph
Cc: Ista Zahn; r-help@r-project.org; stevendrando...@aol.com; Piyush Singh - 
Network
Subject: Re: [R] XML package not working


On 22-10-2013, at 15:19, Steven Dwayne Randolph randolph_steve...@lilly.com 
wrote:

 Ista,... Thank you for your response.   Here is what is occurring when I 
 attempt to command-line install.
 --
 
 install.packages('XML')
 Installing package into 'C:/Users/xxx/Documents/R/win-library/3.0'
 (as 'lib' is unspecified)
 trying URL 'http://cran.rstudio.com/bin/windows/contrib/3.0/XML_3.98-1.1.zip'
 Content type 'application/zip' length 4287270 bytes (4.1 Mb) opened 
 URL downloaded 4.1 Mb
 
 Warning in install.packages :
  downloaded length 4276224 != reported length 4287270


Look at what is reported here. The downloaded length is not equal to the 
reported (i.e. actual) length of  the zip.
What is the length if you download the .zip file manually?
So something has gone wrong with the download.
Can you open a .zip file in another program? If so see what happens if you open 
it in that program.
You have to do detective work.

Berend


 Warning in install.packages :
  error 1 in extracting from zip file
 Warning in install.packages :
  cannot open compressed file 'XML/DESCRIPTION', probable reason 'No such file 
 or directory'
 Error in install.packages : cannot open the connection
 
 --
 
 
 STeven
 -Original Message-
 From: Ista Zahn [mailto:istaz...@gmail.com]
 Sent: Tuesday, October 22, 2013 8:09 AM
 To: Steven Dwayne Randolph
 Cc: Duncan Murdoch; r-help@r-project.org; stevendrando...@aol.com; 
 Piyush Singh - Network
 Subject: Re: [R] XML package not working
 
 Hi Steven,
 
 I still don't understand why you are downloading it manually. What 
 happens when you
 
 install.packages(XML)
 
 ?
 
 Best,
 Ista
 
 On Tue, Oct 22, 2013 at 8:03 AM, Steven Dwayne Randolph 
 randolph_steve...@lilly.com wrote:
 Duncan... Thank you.
 
1.   I am able to download the XML file via my corporate network, 
 other packages without this same issue, even rcurl and bitops which are 
 pre-requisites on the same page as XML.
2.   I  have attempted to download this from my own wifi at home 
 using xfinity/Comcast to my personal pc and still get the same error on this 
 package alone.
3.   I am genuinely baffled by this package download and 
 install experience.
 4.  I would gladly build this from source, If indeed I could 
 find the source and then use RTools to compile it.  That has been 
 unsuccessful as well.   Nightmare? Slightly.
 
 Thanks for your response.
 Steven
 
 -Original Message-
 From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
 Sent: Sunday, October 20, 2013 12:13 PM
 To: Steven Dwayne Randolph; r-help@r-project.org; Ista Zahn
 Cc: stevendrando...@aol.com
 Subject: Re: [R] XML package not working
 
 On 13-10-20 9:23 AM, Steven Dwayne Randolph wrote:
 My apologies for not conforming to the posting guideline.
 
 
 Sys.info()
  sysname  release   
version
Windows  7 x64 build 7601, 
 Service Pack 1
 nodename  machine   
  login
xxNU247BZ1S x86-64   
  XX
 user   effective_user
xxxxxx
 
 When I attempt to install a local copy of the xml.zip file:
 
 in read.dcf(file.path(pkgname, DESCRIPTION), c(Package, Type)) :
   cannot open the connection
 In addition: Warning messages:
 1: In unzip(zipname, exdir = dest) : error 1 in extracting from zip 
 file
 2: In read.dcf(file.path(pkgname, DESCRIPTION), c(Package, Type)) :
   cannot open compressed file 'XML/DESCRIPTION', probable reason 'No such 
 file or directory'
 
 I think it is pretty clear that the problem is at your end:  you aren't 
 downloading the file properly, even though everyone else is.  Perhaps you 
 are behind a firewall, or something 

[R] Making a function and applying it over a list(?)

[Lasse Thorst]

Hi All

I've gotten some awesome help getting a formular that finds the intersection of 
two vectors. This works brilliantly, but I can't figure out how to make it run 
over another factor. A simple example looks likes this:

  df - data.frame(
  id   = factor(rep(c(supply, demand), each = 10)),
  price= c(5,7,9,11,13,15,17,19,21,23,20,18,16,14,12,10,8,6,4,2 ),
  quantity = c(3,5,7,13,19,31,37,53,61,67,6,18,20,24,40,46,66,70,76,78)
)

quantity_points - with(
  df,
  seq(min(quantity), max(quantity), length.out = 500)
)

by_id - split(df[, c(price, quantity)], df$id)

interpolated_price - lapply(
  by_id,
  function(x)
  {
with(
  x,
  approx(
quantity,
price,
xout = quantity_points
  )
)$y
  }
)

index_of_equality - with(interpolated_price, which.min(abs(supply - demand)))
quantity_points[index_of_equality]

Question: I need to run this over a larger data frame, where I have the same 
data, but also a new factor variable (called hour). So if you have the original 
data frame and add:

  df - data.frame(
hour = factor(seq(1:20)),
  id   = factor(rep(c(supply, demand), each = 10)),
  price= c(5,7,9,11,13,15,17,19,21,23,20,18,16,14,12,10,8,6,4,2 ),
  quantity = c(3,5,7,13,19,31,37,53,61,67,6,18,20,24,40,46,66,70,76,78)
)

How can I run it for each hour? I tried using:
by_hour - split(df[, c(price, quantity)], df$hour)
mapply(fx, by_hour)

And gathering the above into a fx - function(){the neat code}, but I can't 
get it to work.

Kind Regards,
Lasse

[[alternative HTML version deleted]]

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

Re: [R] R: Optional argument to be used in a subset function

[Berend Hasselman]

On 24-10-2013, at 16:15, David Mora dmv...@gmail.com wrote:

 I'm writing a function that needs an optional variable. If the variable is
 given, then a subset must be made using that variable, but if the variable
 is not given the subset must be done using all the values for that variable
 (ignoring that variable).
 
 Something like this:
 
 *band - function(file, fruit = apple, optional=TRUE) {*
 
 *data - read.csv(file)*
 
 *a - nrow(subset(data, 'Column 1' == fruit  'Column 2'==hot  'Column 3'==
 optional))*
 
 *b - nrow(subset(data,'Column 1' == fruit  'Column 2'==cold  'Column 3'==
 optional)) *
 
 *z - a+b*
 
 * print(z)*
 
 * }*
 
 What I need is that the function *band(file,orange)*,  subset the data
 frame using all possible values for Column 3 but is not doing it.
 
 All ideas are welcome.
 
 Thanks.
 
 
 David Mora
 
   [[alternative HTML version deleted]]
 

Please do not post in HTML.
And make stuff bold: in plain text it is converted to things like this:

* }*

which nonsense for R.

Berend

 __
 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] ordinal data with binary response

[John Sorkin]

Kishor,
It sounds like you will need to use logistic regression. Although the following 
URL might help you better understand logistic regression, 
http://ww2.coastal.edu/kingw/statistics/R-tutorials/logistic.html  it would 
probably be most helpful if you would see help from a local statistician.
John

 
John David Sorkin M.D., Ph.D.
Professor of Medicine
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology and Geriatric 
Medicine
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing) 
 Kishor Tappita kishor.tapp...@gmail.com 10/24/2013 5:15 AM 
Dear R-users,

I am trying to analyze data with ordinal independent variables and
binary response . Could some one suggest me an appropriate statistic
for this kind of analysis.

Thanks,
Regards,
Kishir

__
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Confidentiality Statement:
This email message, including any attachments, is for the sole use of the 
intended recipient(s) and may contain confidential and privileged information.  
Any unauthorized use, disclosure or distribution is prohibited.  If you are not 
the intended recipient, please contact the sender by reply email and destroy 
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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] track on boats

[Adams, Jean]

It is difficult to advise you when you don't provide reproducible data.
 For example, you could include the first 6 lines of your data using
 dput(head(mydata))

If you have GPS points stored as easting, northing, and if you have a
variable that identifies the vessel, and if your data are sorted by date
and time, then you might be able to get the plot you want using something
like this:

plot(easting[vessel=This One], northing[vessel=This One], type=l)

Jean


On Thu, Oct 24, 2013 at 4:40 AM, Marta Tobeña marta_...@hotmail.com wrote:

 Hi professors
 I'm finding the best package in R for manage a big database about vessels.
 I need to divided the travel of each boat into tracks. I have GPS points.

 I would join these points in a line on the map. I make that with the
 function lines, but I can't divided by vessel or by track,

 I saw several packages, for tracking animals but they had specifically
 variables. And I don't add others like  type,destination or status.

 Can you give me a suggestion, please

 [[alternative HTML version deleted]]

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


[[alternative HTML version deleted]]

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

Re: [R] installing package from source

[David Winsemius]

On Oct 23, 2013, at 7:53 PM, Long Vo wrote:

 Hi R users,
 Currently I want to fit a FIGARCH model to a dataset. The only package that
 allow for it that I could find is fGarch. However it seems that the FIGARCH
 model class fitting of this package has been moved to Oxmetrics. I tried to
 install the old versions of it using 'tar.gz' files from CRAN archive 
 http://cran.r-project.org/src/contrib/Archive/fGarch/
 http://cran.r-project.org/src/contrib/Archive/fGarch/   but not sure how
 it works. I tried
 
 install.packages(myfilepath\fGarch_260.71.tar.gz, repos = NULL,
 type=source)
 
 And received this error:
 
 Warning: invalid package './I:
_R filesGarch_260.71.tar.gz'
 Error: ERROR: no packages specified
 Warning messages:
 1: running command 'I:/01_RFI~1/INSTAL~1/R-30~1.1/bin/i386/R CMD INSTALL
 -l I:\01_R files\installment\R-3.0.1\library ./I:
_R files
 Garch_260.71.tar.gz' had status 1 
 2: In install.packages(I:\001_R files\fGarch_260.71.tar.gz, repos = NULL, 
 :
  installation of package ‘./I:
_R filesGarch_260.71.tar.gz’ had non-zero
 exit status
 
 Any helps on this?
 

I've aways specified the package names and their locations separately in my 
call to install.packages, but I don't know if that is always needed. It also 
appears that you have no / separator between your path and the file name.

 Regards,
 Long
 
 
 
 --
 View this message in context: 
 http://r.789695.n4.nabble.com/installing-package-from-source-tp4678928.html
 Sent from the R help mailing list archive at Nabble.com.
 
 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.

David Winsemius
Alameda, CA, USA

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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] ordinal data with binary response

[Kishor Tappita]

Dear John,

Thanks for the information. It is quite helpful.

Regards,
Kishor

On Thu, Oct 24, 2013 at 9:24 PM, John Sorkin
jsor...@grecc.umaryland.edu wrote:
 Kishor,
 It sounds like you will need to use logistic regression. Although the
 following URL might help you better understand logistic regression,
 http://ww2.coastal.edu/kingw/statistics/R-tutorials/logistic.html  it would
 probably be most helpful if you would see help from a local statistician.
 John


 John David Sorkin M.D., Ph.D.
 Professor of Medicine
 Chief, Biostatistics and Informatics
 University of Maryland School of Medicine Division of Gerontology and
 Geriatric Medicine
 Baltimore VA Medical Center
 10 North Greene Street
 GRECC (BT/18/GR)
 Baltimore, MD 21201-1524
 (Phone) 410-605-7119
 (Fax) 410-605-7913 (Please call phone number above prior to faxing)
 Kishor Tappita kishor.tapp...@gmail.com 10/24/2013 5:15 AM 

 Dear R-users,

 I am trying to analyze data with ordinal independent variables and
 binary response . Could some one suggest me an appropriate statistic
 for this kind of analysis.

 Thanks,
 Regards,
 Kishir

 __
 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.


 Confidentiality Statement:

 This email message, including any attachments, is for ...{{dropped:6}}

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

Re: [R] Error in heatmap

[Adams, Jean]

Using your csv file, I get no error running the following code.
 SPIV2 - read.csv(C:/Temp/SPI V2.csv)
 heatmap(as.matrix(SPIV2), na.rm=TRUE)
Perhaps you modified SPIV2 in some way prior to running heatmap()?

Jean




On Tue, Oct 22, 2013 at 10:29 AM, David Romero drom...@mda.cinvestav.mxwrote:

 Hi Jean

 ** **

 Thank you for helping.

 No, there is no empty column or row. I join the data base.

 ** **

 Regards

 ** **

 David

 ** **

 ** **

 ** **

 *De:* Adams, Jean [mailto:jvad...@usgs.gov]
 *Enviado el:* 22 de octubre de 2013 07:03
 *Para:* David Romero
 *CC:* r-h...@stat.math.ethz.ch
 *Asunto:* Re: [R] Error in heatmap

 ** **

 Do you have a row or column that is all missing?

  sum(apply(is.na(as.matrix(SPIV2)), 1, all))  0

  sum(apply(is.na(as.matrix(SPIV2)), 2, all))  0

 ** **

 For example, this code

  m - as.matrix(mtcars)

  m[8, ] - NA

  heatmap(m, na.rm=TRUE)

 throws this error

  Error in hclustfun(distfun(x)) : 

NA/NaN/Inf in foreign function call (arg 11)

 ** **

 Jean

 ** **

 ** **

 On Mon, Oct 21, 2013 at 1:04 PM, David Romero drom...@mda.cinvestav.mx
 wrote:

 Hi,



 Could you please help?



 Heatmap  doesn't work with:



  heatmap(as.matrix(SPIV2),na.rm = T)

 Error in hclustfun(distfun(x)) :

   NA/NaN/Inf in foreign function call (arg 11)



 There are no 0 data rows or column



 Thanks a lot



 Regards

 ---

 David




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 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
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 ** **


[[alternative HTML version deleted]]

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R-help@r-project.org mailing list
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and provide commented, minimal, self-contained, reproducible code.

[R] Nonparametric k-way ANOVA

[Vicent Giner-Bosch]

Sorry if this subject has been already dealt here.

Which are some common tests for nonparametric k-way ANOVA?

I have read about Kruskal-Wallis test as a kind of nonparametric one-way
ANOVA, but I have not found anything about a general-setting (I mean k-way)
nonparametric ANOVA.

Can you recommend me a good R package (or other reliable software) for that?

Looking forward to your answers,


--
vicent
@vginer_upv
about.me/vginer_upv

[[alternative HTML version deleted]]

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

Re: [R] XML package not working

[Henrik Bengtsson]

Have you tried to download from another CRAN mirror, e.g.

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

More mirrors at http://cran.r-project.org/mirrors.html

As already others said, it's very unlikely that this is not an issue
on your end.

/Henrik


On Thu, Oct 24, 2013 at 4:54 AM, Steven Dwayne Randolph
randolph_steve...@lilly.com wrote:
 Berend Thanks.  I am aware of the missing kb's in the download.  However, 
 my problem is that it only happens with this package.  I download other 
 packages manually and via command-line install.packages() and
 Do not have any problems with completing full downloads of the entire file.

 Perhaps, if someone has the complete download for the XML package, both in 
 *.zip and  *tar formats that they can either email to me or allow me to ftp 
 from it would help me to move forward with this resolve.



 Thanks...


  Steven

 -Original Message-
 From: Berend Hasselman [mailto:b...@xs4all.nl]
 Sent: Tuesday, October 22, 2013 12:39 PM
 To: Steven Dwayne Randolph
 Cc: Ista Zahn; r-help@r-project.org; stevendrando...@aol.com; Piyush Singh - 
 Network
 Subject: Re: [R] XML package not working


 On 22-10-2013, at 15:19, Steven Dwayne Randolph randolph_steve...@lilly.com 
 wrote:

 Ista,... Thank you for your response.   Here is what is occurring when I 
 attempt to command-line install.
 --
 
 install.packages('XML')
 Installing package into 'C:/Users/xxx/Documents/R/win-library/3.0'
 (as 'lib' is unspecified)
 trying URL 'http://cran.rstudio.com/bin/windows/contrib/3.0/XML_3.98-1.1.zip'
 Content type 'application/zip' length 4287270 bytes (4.1 Mb) opened
 URL downloaded 4.1 Mb

 Warning in install.packages :
  downloaded length 4276224 != reported length 4287270


 Look at what is reported here. The downloaded length is not equal to the 
 reported (i.e. actual) length of  the zip.
 What is the length if you download the .zip file manually?
 So something has gone wrong with the download.
 Can you open a .zip file in another program? If so see what happens if you 
 open it in that program.
 You have to do detective work.

 Berend


 Warning in install.packages :
  error 1 in extracting from zip file
 Warning in install.packages :
  cannot open compressed file 'XML/DESCRIPTION', probable reason 'No such 
 file or directory'
 Error in install.packages : cannot open the connection

 --
 

 STeven
 -Original Message-
 From: Ista Zahn [mailto:istaz...@gmail.com]
 Sent: Tuesday, October 22, 2013 8:09 AM
 To: Steven Dwayne Randolph
 Cc: Duncan Murdoch; r-help@r-project.org; stevendrando...@aol.com;
 Piyush Singh - Network
 Subject: Re: [R] XML package not working

 Hi Steven,

 I still don't understand why you are downloading it manually. What
 happens when you

 install.packages(XML)

 ?

 Best,
 Ista

 On Tue, Oct 22, 2013 at 8:03 AM, Steven Dwayne Randolph 
 randolph_steve...@lilly.com wrote:
 Duncan... Thank you.

1.   I am able to download the XML file via my corporate network, 
 other packages without this same issue, even rcurl and bitops which are 
 pre-requisites on the same page as XML.
2.   I  have attempted to download this from my own wifi at home 
 using xfinity/Comcast to my personal pc and still get the same error on 
 this package alone.
3.   I am genuinely baffled by this package download and 
 install experience.
 4.  I would gladly build this from source, If indeed I 
 could find the source and then use RTools to compile it.  That has been 
 unsuccessful as well.   Nightmare? Slightly.

 Thanks for your response.
 Steven

 -Original Message-
 From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
 Sent: Sunday, October 20, 2013 12:13 PM
 To: Steven Dwayne Randolph; r-help@r-project.org; Ista Zahn
 Cc: stevendrando...@aol.com
 Subject: Re: [R] XML package not working

 On 13-10-20 9:23 AM, Steven Dwayne Randolph wrote:
 My apologies for not conforming to the posting guideline.


 Sys.info()
  sysname  release  
 version
Windows  7 x64 build 7601, 
 Service Pack 1
 nodename  machine  
   login
xxNU247BZ1S x86-64  
   XX
 user   effective_user
xxxxxx

 When I attempt to install a local copy of the xml.zip file:

 in read.dcf(file.path(pkgname, DESCRIPTION), c(Package, Type)) :
   cannot open the connection
 In addition: Warning messages:
 1: In unzip(zipname, exdir = dest) : error 1 in extracting from zip
 file
 2: In 

Re: [R] installing package from source

[Marc Schwartz]

On Oct 24, 2013, at 11:38 AM, David Winsemius dwinsem...@comcast.net wrote:

 
 On Oct 23, 2013, at 7:53 PM, Long Vo wrote:
 
 Hi R users,
 Currently I want to fit a FIGARCH model to a dataset. The only package that
 allow for it that I could find is fGarch. However it seems that the FIGARCH
 model class fitting of this package has been moved to Oxmetrics. I tried to
 install the old versions of it using 'tar.gz' files from CRAN archive 
 http://cran.r-project.org/src/contrib/Archive/fGarch/
 http://cran.r-project.org/src/contrib/Archive/fGarch/   but not sure how
 it works. I tried
 
 install.packages(myfilepath\fGarch_260.71.tar.gz, repos = NULL,
 type=source)
 
 And received this error:
 
 Warning: invalid package './I:
_R filesGarch_260.71.tar.gz'
 Error: ERROR: no packages specified
 Warning messages:
 1: running command 'I:/01_RFI~1/INSTAL~1/R-30~1.1/bin/i386/R CMD INSTALL
 -l I:\01_R files\installment\R-3.0.1\library ./I:
_R files
 Garch_260.71.tar.gz' had status 1 
 2: In install.packages(I:\001_R files\fGarch_260.71.tar.gz, repos = NULL, 
 :
 installation of package ‘./I:
_R filesGarch_260.71.tar.gz’ had non-zero
 exit status
 
 Any helps on this?
 
 
 I've aways specified the package names and their locations separately in my 
 call to install.packages, but I don't know if that is always needed. It also 
 appears that you have no / separator between your path and the file name.


Long is trying to install a rather old version of the source R package that 
contains FORTRAN code on Windows.

Besides the immediate error in the way the path was constructed in the 
install.packages() call, using a single backslash, which needs to be escaped:

  
http://cran.r-project.org/bin/windows/base/rw-FAQ.html#R-can_0027t-find-my-file

there are likely to be issues from trying to install an old version of the 
package on a newer version of R, perhaps the lack of the requisite development 
tools for compiling FORTRAN:

  
http://cran.r-project.org/bin/windows/base/rw-FAQ.html#Can-I-install-packages-into-libraries-in-this-version_003f

and other issues as well.

Depending upon how far back you need to go in package versions, there may be 
pre-compiled Windows binaries (.zip files) available in directories here:

  http://cran.r-project.org/bin/windows/contrib/



Regards,

Marc Schwartz


 
 Regards,
 Long

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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Problem with coordinates when trying to draw lines into a raster (image) file

[Adams, Jean]

Rick,

This uses a different approach than what you propose, but it gets the job
done and perhaps you will find it helpful.

Jean

library(jpeg)
# download image from internet for use in example
# http://www.tootsie.com/wallpaper/wp_concord2_1344x1008.jpg
img - readJPEG(c:/temp/wp_concord2_1344x1008.jpg)
# define location of two yellow gumballs, could use locator() to get these
coordinates
px.x - c(172, 576)
px.y - c(433, 657)
# set up plot
par(xaxs=i, yaxs=i)
eqscplot(x, y, type=n, xlim=c(0, 1334), ylim=c(0, 1008))
# add image
rasterImage(img, 0, 0, 1334, 1008)
# add line connecting two yellow gumballs
lines(px.x, px.y, lwd=5, col=yellow)



On Mon, Oct 21, 2013 at 8:57 AM, Rick Turner ricktur...@btconnect.comwrote:


Hi All,

I am struggling with something, and could use some help

I have a scenario where I need to draw lines onto a base image using R
 –
briefly, the image has what amounts to an outline ‘map’ of
 locations, and
the lines will correspond to ‘routes’ between two locations.

The locations are known in terms of image pixel coordinates – let’s
 call
them (px1, py1) and (px2, py2), but when I try and plot a line into the
image using these coordinates, the visual positions are incorrect –
 the
start and end points of the line are offset from the desired position,
 and
the amount of offset changes as I resize the window. I've tried such
 things
as normalising them into the [0,1] range used by the viewport but this
 does
not correct the problem.

So,  I  figured  that I must have made some mistake with my scaling of
coordinates from image to viewport, but I cannot find where or what.
 I’ve
fiddled around a bit (well, a lot!) but cannot get the desired result.
 So,
it is time to ask for help, hence this message….

Any  suggestions  gratefully  received…   I’ve done a fair amount
 of R
programming, but have not used these extended graphics capabilities
 much at
all, so I really am getting frustrated

Regards and thanks in advance,
Rick


  
--

The code segment in question is:

# load packages

library(jpeg)

library(grid)


# read the image file

baseimg - readJPEG(loc_map.jpg, native=FALSE)

xsize - ncol(baseimg)   # Get image size – this one
 is 1344
px wide

ysize - nrow(baseimg) # and 1008 px high


# create a viewport

xrange - c(0, xsize)# set up the viewport
 range to
match the image size

yrange - c(0, ysize)

vp  -  viewport(x=0.5,  y=0.5,  width=0.9, height=0.9, xscale=xrange,
yscale=yrange)

pushViewport(vp)

grid.rect(gp=gpar(lty=dashed))# draw a dashed line around it.


# display the base image

grid.raster(baseimg)


# First location – image pixel coordinates (748, 177). Normalise
 these to
[0,1] to

# match the viewpoint coordinate scheme. Note that we need to invert the

# y coordinate as R coords run from bottom up, but image ones are top
 down

px1 - (748/xsize)#
 748/1344 ~=
0.556, so in range [0,1]

py1 - (1.0 - (177/ysize))   # 1-(177/1008)
 ~=
0.824, so also in range [0,1]


# position of the St Johns Hill enterance (image coords

# [769, 892]) normalised to the viewport

  x2 - (769/xsize)

  y2 - (1.0 - (892/ysize))


  # draw a line from pixel (px1,py1) to pixel (px2,py2) in blue

  xx - c(px1, px2)

  yy - c(py1, py2)

  grid.lines(xx, yy, gp=gpar(col=blue))
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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.


[[alternative HTML version deleted]]

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

Re: [R] Nonparametric k-way ANOVA

[peter dalgaard]

On Oct 24, 2013, at 18:59 , Vicent Giner-Bosch wrote:

 Sorry if this subject has been already dealt here.
 
 Which are some common tests for nonparametric k-way ANOVA?
 
 I have read about Kruskal-Wallis test as a kind of nonparametric one-way
 ANOVA, but I have not found anything about a general-setting (I mean k-way)
 nonparametric ANOVA.
 
 Can you recommend me a good R package (or other reliable software) for that?

Can you provide reliable _theory_ for it? 

Some people have tried just to do ANOVA decompositions after replacing 
observations by their ranks, and referring sums of squares to chi-squared 
distributions. However, that derivation only holds under the global null 
hypothesis. In general, it is problematic to define additivity and interaction 
in a nonparametric setting since there are no parameters that effects can be 
additive in!

Stratified tests do exist and make OK sense. In those, you split data into 
groups and do the rank sums within groups, then look at a weighted sum of the  
group rank sums, work out the mean and variance assuming no effect in any 
group, etc. For a two-way layout without replications, this is friedman.test(). 
I believe the coin package implements some more general cases.

-pd


 
 Looking forward to your answers,
 
 
 --
 vicent
 @vginer_upv
 about.me/vginer_upv
 
   [[alternative HTML version deleted]]
 
 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd@cbs.dk  Priv: pda...@gmail.com

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

Re: [R] installing package from source

[Prof Brian Ripley]

On 24/10/2013 18:25, Marc Schwartz wrote:


On Oct 24, 2013, at 11:38 AM, David Winsemius dwinsem...@comcast.net wrote:



On Oct 23, 2013, at 7:53 PM, Long Vo wrote:


Hi R users,
Currently I want to fit a FIGARCH model to a dataset. The only package that
allow for it that I could find is fGarch. However it seems that the FIGARCH
model class fitting of this package has been moved to Oxmetrics. I tried to
install the old versions of it using 'tar.gz' files from CRAN archive
http://cran.r-project.org/src/contrib/Archive/fGarch/
http://cran.r-project.org/src/contrib/Archive/fGarch/   but not sure how
it works. I tried

install.packages(myfilepath\fGarch_260.71.tar.gz, repos = NULL,
type=source)

And received this error:

Warning: invalid package './I:
_R filesGarch_260.71.tar.gz'
Error: ERROR: no packages specified
Warning messages:
1: running command 'I:/01_RFI~1/INSTAL~1/R-30~1.1/bin/i386/R CMD INSTALL
-l I:\01_R files\installment\R-3.0.1\library ./I:
_R files
Garch_260.71.tar.gz' had status 1
2: In install.packages(I:\001_R files\fGarch_260.71.tar.gz, repos = NULL,
:
installation of package ‘./I:
_R filesGarch_260.71.tar.gz’ had non-zero
exit status

Any helps on this?



I've aways specified the package names and their locations separately in my call to 
install.packages, but I don't know if that is always needed. It also appears that you 
have no / separator between your path and the file name.



Long is trying to install a rather old version of the source R package that 
contains FORTRAN code on Windows.

Besides the immediate error in the way the path was constructed in the 
install.packages() call, using a single backslash, which needs to be escaped:

   
http://cran.r-project.org/bin/windows/base/rw-FAQ.html#R-can_0027t-find-my-file

there are likely to be issues from trying to install an old version of the 
package on a newer version of R, perhaps the lack of the requisite development 
tools for compiling FORTRAN:

   
http://cran.r-project.org/bin/windows/base/rw-FAQ.html#Can-I-install-packages-into-libraries-in-this-version_003f

and other issues as well.

Depending upon how far back you need to go in package versions, there may be 
pre-compiled Windows binaries (.zip files) available in directories here:

   http://cran.r-project.org/bin/windows/contrib/


I don't think so: see NEWS

CHANGES IN R 3.0.0:

  SIGNIFICANT USER-VISIBLE CHANGES:

• Packages need to be (re-)installed under this version (3.0.0) of
  R.

so only those under bin/windows/contrib/3.0 will work, and there is only 
one for each package.



--
Brian D. Ripley,  rip...@stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel:  +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax:  +44 1865 272595

__
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] How can I use a script l (LaTeX \ell) in mathematical annotation of plots?

[Byron Dom]

Thanks. That works for me too.

I had worked that out based on Brian's response to my original post.

If you read thru my response to him in detail, you'll see:

 Here are a couple of examples using it that worked:
    plot(1:10,xlab=\u2113)
   
  plot(1:10,xlab=\u2113(\u2113 + 1))





From: Eik Vettorazzi e.vettora...@uke.de
To: Byron Dom byron_...@yahoo.com; r help r-help@r-project.org 
Cc: rip...@stats.ox.ac.uk rip...@stats.ox.ac.uk 
Sent: Thursday, October 24, 2013 2:50 AM
Subject: Re: [R] How can I use a script l (LaTeX \ell) in mathematical 
annotation of plots?


this works for me:

plot(1,main=\u2113)

cheers


Am 24.10.2013 01:39, schrieb Byron Dom:
 
 
 Original post: On 13/10/2013 18:53, Byron Dom wrote:
 
 Due to convention a script l - $$\ell$$ (LaTeX \ell) is used to 
 represent a certain quantity in something I'm working on. I'm 
 unable to figure out how to use it in R. It's not included in the 
 list on ?plotmath.

 Can anyone tell me how to use it?  Its unicode is U+2113. This 
 page has a list of various encodings of it: 

  http://www.fileformat.info/info/unicode/char/2113/encoding.htm.  
 Is there a way to include it by using one of these encodings somehow?
 
 -
 
 On 13/10/2013 22:06 Prof Brian Ripley responded:
 
 What do you want to do with it?  plotmath is about plotting, but you
 have not otherwise mentioned that, let alone the device on which you 
 want to plot.

 Read the help for plotmath: on some plot devices, just use \u2113.  It 
 is not AFAICS in the Adobe symbol encoding.

 -- 
 Brian D. Ripley,                  ripley at stats.ox.ac.uk
 Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
 University of Oxford,             Tel: 
  +44 1865 272861 (self)
 1 South Parks Road,                     +44 1865 272866 (PA)
 Oxford OX1 3TG, UK                Fax:  +44 1865 272595
 
 -
 
 My response:
 
 Thanks I worked out how to do it based on your mention of u2113.
 See below.
 
 I'm sorry if my information wasn't complete enough. I assumed that 
 what I said, combined with the subject (How can I use a script l 
 (LaTeX \ell) in
  mathematical annotation of plots?) would have been 
 enough.
 
 I just wanted to be able to do this on the default device, which 
 displays plots within the R session window. I have a simple path 
 to go from there to .png form, which I include in LaTeX documents
 and for other purposes. I am using R version 3.0.1 in Windows 7, 
 for which I believe the default plot device is windows.
 
 An example of the kind of thing I wanted to do is to include 
 ylab = expression(hat(gamma)) (which is equivalent to the LaTex 
 \hat{\gamma}}) among the base-graphics plot() arguments. That 
 works. In LaTeX a script l is produced with \ell, but 
 something like ylab = expression(ell) doesn't work in R. 
 I wanted to be able to do the equivalent of that, but to obtain ℓ.
 
 Here are a couple of examples using it that worked:
    plot(1:10,xlab=\u2113)
   
  plot(1:10,xlab=\u2113(\u2113 + 1))
 The only (slight) problem with this is the minor aesthetic issue 
 
 that the ℓ one gets this way is in an obviously different font 
 
 from what one gets using the LaTeX \lambda command/symbol.
 
 Strangely, earlier, when I tried 
    plot(1:10,xlab=expression(symbol(\u2113)))
 it did the same thing as 
    plot(1:10,xlab=expression(lambda))
 So I got a lower-case greek lambda - λ, rather than ℓ
 (script l).
 
 When I used the unicode representation for lowercase 
 lambda - λ - as follows
   
  plot(1:10,xlab=expression(symbol(\u03bb)))
 I got this for an x-axis label: Y+03BB. On the other hand,
 the following did work
    plot(1:10,xlab=\u03bb), 
 giving me an x-axis label of lambda - λ.
     [[alternative HTML version deleted]]
 
 
 
 __
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 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.
 

-- 
Eik Vettorazzi

Department of Medical Biometry and Epidemiology
University Medical Center Hamburg-Eppendorf

Martinistr. 52
20246 Hamburg

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

Besuchen Sie uns auf: www.uke.de
_

Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; 
Gerichtsstand: Hamburg
Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Prof. Dr. Dr. Uwe 
Koch-Gromus, Joachim Prölß, Rainer Schoppik
_

SAVE PAPER - THINK BEFORE PRINTING

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Re: [R] installing package from source

[Marc Schwartz]

On Oct 24, 2013, at 1:11 PM, Prof Brian Ripley rip...@stats.ox.ac.uk wrote:

 On 24/10/2013 18:25, Marc Schwartz wrote:
 
 On Oct 24, 2013, at 11:38 AM, David Winsemius dwinsem...@comcast.net wrote:
 
 
 On Oct 23, 2013, at 7:53 PM, Long Vo wrote:
 
 Hi R users,
 Currently I want to fit a FIGARCH model to a dataset. The only package that
 allow for it that I could find is fGarch. However it seems that the FIGARCH
 model class fitting of this package has been moved to Oxmetrics. I tried to
 install the old versions of it using 'tar.gz' files from CRAN archive
 http://cran.r-project.org/src/contrib/Archive/fGarch/
 http://cran.r-project.org/src/contrib/Archive/fGarch/   but not sure how
 it works. I tried
 
 install.packages(myfilepath\fGarch_260.71.tar.gz, repos = NULL,
 type=source)
 
 And received this error:
 
 Warning: invalid package './I:
_R filesGarch_260.71.tar.gz'
 Error: ERROR: no packages specified
 Warning messages:
 1: running command 'I:/01_RFI~1/INSTAL~1/R-30~1.1/bin/i386/R CMD INSTALL
 -l I:\01_R files\installment\R-3.0.1\library ./I:
_R files
 Garch_260.71.tar.gz' had status 1
 2: In install.packages(I:\001_R files\fGarch_260.71.tar.gz, repos = NULL,
 :
 installation of package ‘./I:
_R filesGarch_260.71.tar.gz’ had non-zero
 exit status
 
 Any helps on this?
 
 
 I've aways specified the package names and their locations separately in my 
 call to install.packages, but I don't know if that is always needed. It 
 also appears that you have no / separator between your path and the file 
 name.
 
 
 Long is trying to install a rather old version of the source R package that 
 contains FORTRAN code on Windows.
 
 Besides the immediate error in the way the path was constructed in the 
 install.packages() call, using a single backslash, which needs to be escaped:
 
   
 http://cran.r-project.org/bin/windows/base/rw-FAQ.html#R-can_0027t-find-my-file
 
 there are likely to be issues from trying to install an old version of the 
 package on a newer version of R, perhaps the lack of the requisite 
 development tools for compiling FORTRAN:
 
   
 http://cran.r-project.org/bin/windows/base/rw-FAQ.html#Can-I-install-packages-into-libraries-in-this-version_003f
 
 and other issues as well.
 
 Depending upon how far back you need to go in package versions, there may be 
 pre-compiled Windows binaries (.zip files) available in directories here:
 
   http://cran.r-project.org/bin/windows/contrib/
 
 I don't think so: see NEWS
 
 CHANGES IN R 3.0.0:
 
  SIGNIFICANT USER-VISIBLE CHANGES:
 
• Packages need to be (re-)installed under this version (3.0.0) of
  R.
 
 so only those under bin/windows/contrib/3.0 will work, and there is only one 
 for each package.
 


Ah, OK. Thanks for noting that Prof. Ripley.

So, Long will need to make some decisions here and it may be worth contacting 
the fGARCH package maintainer to get any relevant insights into potential 
gotchas installing an older version of the package on a recent version of R, 
even from source after installing the needed tools, or having to revert to an 
older version of R to support the installation of the older package.

Older Windows binaries of R releases are available from:

  http://cran.r-project.org/bin/windows/base/old/

and R 2.6.1 would be about the release that corresponds to the particular 
version of fGARCH being used above, which is late 2007.

Regards,

Marc

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Re: [R] Error in scan?

[Carl Witthoft]

Obviously row 11 is incomplete.
It may contain nothing more than a space or an EOL.

Using the fill=TRUE argument to 'scan' or 'read.table'  is your friend
here.



--
View this message in context: 
http://r.789695.n4.nabble.com/Error-in-scan-tp4678976p4678982.html
Sent from the R help mailing list archive at Nabble.com.

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[R] Text in a plot without x axis

[Ahmed Attia]

Dear R users,

Can I add a text to a plot without x axis?

I saw a function that enables placing the text with mouse

text(location, text to place, pos, ...)

locator(1)

but it did not work out.

-- 
Ahmed M. Attia


Research Assistant
Dept. Of SoilCrop Sciences
Texas AM University
ahmed.at...@ag.tamu.edu
Cell phone: 001-979-248-5215

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Re: [R] test wilcoxon sur R help!

[arun]

Hi,
Try:
fun1 - function(dat){
mat1 - combn(colnames(dat1),2)
 res - sapply(seq_len(ncol(mat1)),function(i) {x1- dat[,mat1[,i]]; 
wilcox.test(x1[,1],x1[,2])$p.value})
names(res) - apply(mat1,2,paste,collapse=_)
res
}

set.seed(432)
dat1 - as.data.frame(matrix(sample(18*10,18*10,replace=FALSE),ncol=18))

  fun1(dat1) #gives the p-value for each pair of columns




Hi, 

I want to make a wilcoxon test, i have 18 columns each column 
corresponds to a different sample and i want to compare one to each 
other with a wilcoxon test in one step this is possible ? or do i 
compare two by tow? 

Does it exist a code for automation this test? like this i dont have to type 
the code for each couple. 

thanks! 
denisse

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Re: [R] Error in heatmap

[Adams, Jean]

David,

You should cc r-help on all correspondence so others can follow the thread.

The error appears to be a result of the missing values yielded by the
dist() function on your matrix.
See https://stat.ethz.ch/pipermail/r-help/2009-July/204443.html.

Jean


On Thu, Oct 24, 2013 at 1:25 PM, David Romero drom...@mda.cinvestav.mxwrote:

 Hi,

 ** **

 The difference is:

 row.names=1

 for csv reading. 

 The first column is a numeric row name, it mustn't take part of the
 heatmap. 

 ** **

 I change it to text and try with and without  row.names=1

 Both give me error.

 ** **

 Regards

 ** **

 David

 ** **

 *De:* Adams, Jean [mailto:jvad...@usgs.gov]
 *Enviado el:* 24 de octubre de 2013 11:52
 *Para:* David Romero
 *CC:* R help

 *Asunto:* Re: [R] Error in heatmap

 ** **

 Using your csv file, I get no error running the following code.

  SPIV2 - read.csv(C:/Temp/SPI V2.csv)

  heatmap(as.matrix(SPIV2), na.rm=TRUE)

 Perhaps you modified SPIV2 in some way prior to running heatmap()?

 ** **

 Jean

 ** **

 ** **

 ** **

 On Tue, Oct 22, 2013 at 10:29 AM, David Romero drom...@mda.cinvestav.mx
 wrote:

 Hi Jean

  

 Thank you for helping.

 No, there is no empty column or row. I join the data base.

  

 Regards

  

 David

  

  

  

 *De:* Adams, Jean [mailto:jvad...@usgs.gov]
 *Enviado el:* 22 de octubre de 2013 07:03
 *Para:* David Romero
 *CC:* r-h...@stat.math.ethz.ch
 *Asunto:* Re: [R] Error in heatmap

  

 Do you have a row or column that is all missing?

  sum(apply(is.na(as.matrix(SPIV2)), 1, all))  0

  sum(apply(is.na(as.matrix(SPIV2)), 2, all))  0

  

 For example, this code

  m - as.matrix(mtcars)

  m[8, ] - NA

  heatmap(m, na.rm=TRUE)

 throws this error

  Error in hclustfun(distfun(x)) : 

NA/NaN/Inf in foreign function call (arg 11)

  

 Jean

  

  

 On Mon, Oct 21, 2013 at 1:04 PM, David Romero drom...@mda.cinvestav.mx
 wrote:

 Hi,



 Could you please help?



 Heatmap  doesn't work with:



  heatmap(as.matrix(SPIV2),na.rm = T)

 Error in hclustfun(distfun(x)) :

   NA/NaN/Inf in foreign function call (arg 11)



 There are no 0 data rows or column



 Thanks a lot



 Regards

 ---

 David




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 ** **


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[R] Custom x axis in a boxplot

[Ahmed Attia]

Dear R users,

How can I customize x axis in a boxplot?

xaxt=n to suppress x axis, but I would like to customize x axis for
different groups.

Thanks

-- 
Ahmed M. Attia


Research Assistant
Dept. Of SoilCrop Sciences
Texas AM University
ahmed.at...@ag.tamu.edu
Cell phone: 001-979-248-5215
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Re: [R] Nonparametric k-way ANOVA

[Cade, Brian]

Depends on what the original poster really wants with a nonparametric
k-way ANOVA.  If what they are really looking for is an approach that has
fewer distributional assumptions, then it is possible to perform
permutation tests for linear models parameterized for k-way anova that
would eliminated the normal distribution assumption for the error term but
would certainly involve estimating parameters (including possible
interactions.)   Marti Anderson and Pierre Legendre have implemented these
sorts of permutation tests for models involving means and I've implemented
them for models of quantiles.

Brian

Brian S. Cade, PhD

U. S. Geological Survey
Fort Collins Science Center
2150 Centre Ave., Bldg. C
Fort Collins, CO  80526-8818

email:  ca...@usgs.gov brian_c...@usgs.gov
tel:  970 226-9326



On Thu, Oct 24, 2013 at 12:00 PM, peter dalgaard pda...@gmail.com wrote:


 On Oct 24, 2013, at 18:59 , Vicent Giner-Bosch wrote:

  Sorry if this subject has been already dealt here.
 
  Which are some common tests for nonparametric k-way ANOVA?
 
  I have read about Kruskal-Wallis test as a kind of nonparametric one-way
  ANOVA, but I have not found anything about a general-setting (I mean
 k-way)
  nonparametric ANOVA.
 
  Can you recommend me a good R package (or other reliable software) for
 that?

 Can you provide reliable _theory_ for it?

 Some people have tried just to do ANOVA decompositions after replacing
 observations by their ranks, and referring sums of squares to chi-squared
 distributions. However, that derivation only holds under the global null
 hypothesis. In general, it is problematic to define additivity and
 interaction in a nonparametric setting since there are no parameters that
 effects can be additive in!

 Stratified tests do exist and make OK sense. In those, you split data into
 groups and do the rank sums within groups, then look at a weighted sum of
 the  group rank sums, work out the mean and variance assuming no effect in
 any group, etc. For a two-way layout without replications, this is
 friedman.test(). I believe the coin package implements some more general
 cases.

 -pd


 
  Looking forward to your answers,
 
 
  --
  vicent
  @vginer_upv
  about.me/vginer_upv
 
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  and provide commented, minimal, self-contained, reproducible code.

 --
 Peter Dalgaard, Professor,
 Center for Statistics, Copenhagen Business School
 Solbjerg Plads 3, 2000 Frederiksberg, Denmark
 Phone: (+45)38153501
 Email: pd@cbs.dk  Priv: pda...@gmail.com

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Re: [R] Text in a plot without x axis

[David Carlson]

You should provide an example of what you are trying to do. Try
this

 plot(0, 1, xlab=, xaxt=n)
 text(locator(1), This is my text, xpd=TRUE)

The xpd= parameter controls the clipping region. The default
xpd=FALSE clips text to the plot region. You were not clear, but
if you were trying to plot outside the axes, you need xpd=TRUE
to clip to the figure region or xpd=NA to clip to the device
region.

-
David L Carlson
Associate Professor of Anthropology
Texas AM University
College Station, TX 77840-4352

-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Ahmed Attia
Sent: Thursday, October 24, 2013 2:10 PM
To: r-help@r-project.org
Subject: [R] Text in a plot without x axis

Dear R users,

Can I add a text to a plot without x axis?

I saw a function that enables placing the text with mouse

text(location, text to place, pos, ...)

locator(1)

but it did not work out.

-- 
Ahmed M. Attia


Research Assistant
Dept. Of SoilCrop Sciences
Texas AM University
ahmed.at...@ag.tamu.edu
Cell phone: 001-979-248-5215

__
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code.

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Re: [R] labeling abscissa using a function of the plotted scale

[David Winsemius]

On Oct 24, 2013, at 7:00 AM, Hurr wrote:

 Thanks Jim, maybe now I can start learning.
 Here is a run of my trying to learn:
 xvalue-c(5.2,1.3,9.7,2.8,8.1,4.7,6.6,7.4)
 yvalue-c(9,3,4,7,2,5,3,6)
 plot(xvalue,yvalue)
 axis(1,at=NULL,labels=1/xvalue,digits=5)
 Error in axis(1, at = NULL, labels = 1/xvalue, digits = 5) :
  'labels' is supplied and not 'at'
 In addition: Warning message:
 In axis(1, at = NULL, labels = 1/xvalue, digits = 5) :
  digits is not a graphical parameter
 
 Why can't R automatically compute the spacing when I use the formula?

I don't see any formula. If you are talking about the expression `1/xvalue`, it 
is going to be a decimal fraction and it will be coerced to a character value 
before being assigned to 'labels'. As explained in the help page for `axis`, 
when at is left as NULL, the positions will be computed from par(xaxt). But 
you gave only a numeric argument to labels and did not tell axis where you 
wanted these values were to be placed. If those values were interpreted as 
being positions they would have been off the left side of the paper.

 If you don't like the way 'axis' works, you are welcome to write a new axis 
function that processes numeric arguments to labels differently. But in this 
case you appear to think that R kept a record someplace of the argument to x in 
the preceding plot. _That_ is wishful thinking on your part. If you want a 
plotting paradigm that may record x and y values, then look at lattice or 
ggplot2. Base graphics is mostly ( memoryless ) ink-on-paper, although there 
may be some information accessible via `par`.

 How can I specify n-digits or width instead of round or nothing? 

?sprintf
?formatC
 
-- 

David Winsemius
Alameda, CA, USA

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Re: [R] Custom x axis in a boxplot

[David Carlson]

?axis

-
David L Carlson
Associate Professor of Anthropology
Texas AM University
College Station, TX 77840-4352

-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Ahmed Attia
Sent: Thursday, October 24, 2013 2:24 PM
To: r-help@r-project.org
Subject: [R] Custom x axis in a boxplot

Dear R users,

How can I customize x axis in a boxplot?

xaxt=n to suppress x axis, but I would like to customize x
axis for
different groups.

Thanks

-- 
Ahmed M. Attia


Research Assistant
Dept. Of SoilCrop Sciences
Texas AM University
ahmed.at...@ag.tamu.edu
Cell phone: 001-979-248-5215

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Re: [R] test wilcoxon sur R help!

[Rui Barradas]

Hello,

There's a bug in your function, it should be 'dat', not 'dat1'. In the 
line marked, below.


fun1 - function(dat){
mat1 - combn(colnames(dat),2)  # Here, 'dat' not 'dat1'
	res - sapply(seq_len(ncol(mat1)),function(i) {x1- dat[,mat1[,i]]; 
wilcox.test(x1[,1],x1[,2])$p.value})

names(res) - apply(mat1,2,paste,collapse=_)
res
}


Hope this helps,

Rui Barradas

Em 24-10-2013 20:16, arun escreveu:

Hi,
Try:
fun1 - function(dat){
mat1 - combn(colnames(dat1),2)
  res - sapply(seq_len(ncol(mat1)),function(i) {x1- dat[,mat1[,i]]; 
wilcox.test(x1[,1],x1[,2])$p.value})
names(res) - apply(mat1,2,paste,collapse=_)
res
}

set.seed(432)
dat1 - as.data.frame(matrix(sample(18*10,18*10,replace=FALSE),ncol=18))

   fun1(dat1) #gives the p-value for each pair of columns




Hi,

I want to make a wilcoxon test, i have 18 columns each column
corresponds to a different sample and i want to compare one to each
other with a wilcoxon test in one step this is possible ? or do i
compare two by tow?

Does it exist a code for automation this test? like this i dont have to type 
the code for each couple.

thanks!
denisse

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Re: [R] Help parsing from .txt

[arun]

Hi,
You may try:
?list.files()
nm1 - list.files(pattern=.txt)

res - lapply(nm1,function(x) {
                                ln1 - readLines(x)
 indx1 - grep(DATE PROCESSED,ln1)
 indx2 - grep([A-Z],ln1)
 ln2 - if(max(indx2)==indx1) 
ln1[1:length(ln1)] else ln1[1:(indx2[match(indx1,indx2)+1]-1)]
 ln2 - ln2[ln2!=]
 indx3 - grepl([A-Z],ln2)
 indx4 - cumsum(c(TRUE,diff(which(!indx3))1))
                                mat1 - do.call(cbind, split(ln2[!indx3],indx4))
 colnames(mat1) -  ln2[indx3][-1]
 
write.table(mat1,paste0(ln2[indx3][1],.txt),row.names=FALSE,quote=FALSE,sep=\t)})



A.K.


I have a number of .txt files (1,200) from which I need to parse a 
number of pieces of information.  The files are read into R as such: 

TITLE 
EXAMPLE 
example 1 
example 2 
RELATED TITLE 
related title 1 
DATE PROCESSED 
06/12/2011 

Some of the files have examples 1-4, others 1-12 and beyond.   

How can I create a script that will grab the information from 
the different .txt files, put it in a matrix, and spit it out in a .csv 
file with appropriately named columns (the column titles are in CAPS 
above, where the information that will in the column is lower case). 

Thanks in advance.

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Re: [R] track on boats

[Michael Sumner]

There are several packages for track data on CRAN and they don't all
force the data to have specific variables beyond position,
date-time, track ID. With trip you can do this easily enough, but
depending on your needs adehabitatLT or move might be better.  I wrote
trip so I know that you can do this (pseudo code that assumes columns
X, Y, date, ID for the obvious components), you get plot
control of separate lines and basic data QC for free (welcome or not):

library(trip)
d - read.csv(myfile.csv)
## sort out date-times
d$datetime - as.POSIXct(d$date, [format etc])

## specify the X/Y coordinates (use your relevant column names)
coordinates(d) - c(X, Y)

## create trip object
tr - trip(d, c(datetime, ID))

(If your data are out of order by ID,time or if there are duplicates
or missing values or other problems that will complain and not make
assumptions, but these are things that should be dealt with explicitly
IMO.)

## then you can plot the separate tracks in a minimal way
plot(tr)
lines(tr)

There is general support for reading and manipulating spatial data
with packages sp, raster, maptools and friends. See the Spatial and
SpatioTemporal Task Views, and consider R-Sig-Geo rather than R-help
for questions like this.  I agree that Animal Tracking is too
specific for your needs, but there's certainly room for generalizing
this to other domains easily enough. The trip package is too simple
and awkward for many things, but for basic use there's no built-in
assumptions that track data are from animals (though the label on the
lid does specify that).

HTH




On Fri, Oct 25, 2013 at 3:08 AM, Adams, Jean jvad...@usgs.gov wrote:
 It is difficult to advise you when you don't provide reproducible data.
  For example, you could include the first 6 lines of your data using
  dput(head(mydata))

 If you have GPS points stored as easting, northing, and if you have a
 variable that identifies the vessel, and if your data are sorted by date
 and time, then you might be able to get the plot you want using something
 like this:

 plot(easting[vessel=This One], northing[vessel=This One], type=l)

 Jean


 On Thu, Oct 24, 2013 at 4:40 AM, Marta Tobeña marta_...@hotmail.com wrote:

 Hi professors
 I'm finding the best package in R for manage a big database about vessels.
 I need to divided the travel of each boat into tracks. I have GPS points.

 I would join these points in a line on the map. I make that with the
 function lines, but I can't divided by vessel or by track,

 I saw several packages, for tracking animals but they had specifically
 variables. And I don't add others like  type,destination or status.

 Can you give me a suggestion, please

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




-- 
Michael Sumner
Hobart, Australia
e-mail: mdsum...@gmail.com

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Re: [R] track on boats

[MacQueen, Don]

A good choice might be to store your data in objects of class
   SpatialLinesDataFrame

Then you can assign any attributes you want to each line, such as your
vessel, type, destination, or status.

This will make it relatively easy to, for example, plot subsets of tracks
specified by different attributes.

SpatialLinesDataFrame objects are defined in the sp package.

For further help, I would suggest the r-sig-geo mailing list. Also look at
the CRAN Task View Spatial.

-Don

-- 
Don MacQueen

Lawrence Livermore National Laboratory
7000 East Ave., L-627
Livermore, CA 94550
925-423-1062





On 10/24/13 2:40 AM, Marta Tobeña marta_...@hotmail.com wrote:

Hi professors
I'm finding the best package in R for manage a big database about
vessels. I need to divided the travel of each boat into tracks. I have
GPS points.

I would join these points in a line on the map. I make that with the
function lines, but I can't divided by vessel or by track,

I saw several packages, for tracking animals but they had specifically
variables. And I don't add others like  type,destination or status.

Can you give me a suggestion, please
 
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Re: [R] How to calculate running 8-hour averages of temperature

[arun]

Hi,
You may try
?rollmean from library(zoo)
?SMA from library(TTR)
dat1 - structure(...
library(zoo)

res1 - rollmean(dat1[-c(1:5),2],8)
library(TTR)
res2 - SMA(dat1[-c(1:5),2],8)
 all.equal(res1,res2[!is.na(res2)])
#[1] TRUE



A.K.

Hi, 

How can I calculate running 8-hour averages of temperature 
values that start at specific date and time? In the example data set 
shown below I want to start the calculation on May 31, at 5pm (row 6). 
Reproducible data is provided. 

Thanks 
structure(list(date = structure(c(644148000, 644151600, 644155200, 
644158800, 644162400, 644166000, 644169600, 644173200, 644176800, 
644180400, 644184000, 644187600, 644191200, 644194800, 644198400, 
644202000, 644205600, 644209200, 644212800, 644216400, 64422, 
644223600, 644227200, 644230800, 644234400, 644238000, 644241600, 
644245200, 644248800, 644252400, 644256000), class = c(POSIXct, 
POSIXt), tzone = ), temp = c(17.7, 18.3, 18.9, 19.7, 19.5, 
19, 18.8, 18, 16.3, 15.1, 13.9, 12.7, 11.9, 10.6, 10, 8.7, 7.8, 
8.0, 9.2, 12.4, 14.5, 15.9, 17.4, 18.6, 18.3, 18.4, 18.5, 
20.4, 19.7, 18.9, 18.1)), .Names = c(date, temp), row.names = 3613:3643, 
class = data.frame)

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Re: [R] bug in dummy.coef?

[Rolf Turner]

I agree that this seems to be a bug, but OTOH the help for dummy.coef() 
*does* say:

 The method used has some limitations, and will give incomplete results 
 for terms such as |poly(x, 2)|.

(Note that it says it will give incomplete results not throw an error!)

Looking into the code of dummy.coef.lm() I find that the problem seems 
to reside in all.vars().
When all.vars(Terms) is applied inside dummy.coef.lm() it returns

 [1] group x

rather than
 [1] group  x  I(x^2)

which is what I think it should return.  The workings of all.vars() are 
buried in
the bowels of the internal structure, so I can take it no farther.  
Whether there
is a practical way to make all.vars() do the right thing in this 
setting I know
not.  Perhaps one of the Big Guns can provide some insight.

As a workaround, you can do:

 x2 - x^2
 lm.D9 - lm(weight ~ group + x + x2)
 dummy.coef(lm.D9)

This worked for me, at least.

 cheers,

 Rolf Turner


On 10/24/13 21:51, Alexandra Kuznetsova wrote:
 Dear all,

 Running the following code produces an error in dummy.coef. I guess it might 
 be a bug..

 ctl - c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)
 trt - c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
 group - gl(2, 10, 20, labels = c(Ctl,Trt))
 weight - c(ctl, trt)
 x - rnorm(length(weight))
 lm.D9 - lm(weight ~ group + x + I(x^2))
 dummy.coef(lm.D9)
 Error in rep.int(xl[[i]][1L], nl) : invalid 'times' value



 sessionInfo()
 R version 3.0.1 (2013-05-16)

 Platform: x86_64-w64-mingw32/x64 (64-bit)



 locale:

 [1] LC_COLLATE=Danish_Denmark.1252  LC_CTYPE=Danish_Denmark.1252
 LC_MONETARY=Danish_Denmark.1252

 [4] LC_NUMERIC=CLC_TIME=Danish_Denmark.1252



 attached base packages:

 [1] parallel  splines   stats graphics  grDevices utils datasets  
 methods   base



 other attached packages:

   [1] pbkrtest_0.3-5MASS_7.3-26   Hmisc_3.12-2  Formula_1.1-1 
 survival_2.37-4   numDeriv_2012.9-1

   [7] lmerTest_2.0-1lme4_1.1-1Matrix_1.0-12 lattice_0.20-15



 loaded via a namespace (and not attached):

 [1] cluster_1.14.4 gdata_2.13.2   gplots_2.11.3  grid_3.0.1 gtools_3.0.0  
  minqa_1.2.1nlme_3.1-109

 [8] rpart_4.1-1tools_3.0.1

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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] labeling abscissa using a function of the plotted scale

[Jim Lemon]

On 10/25/2013 01:00 AM, Hurr wrote:

Thanks Jim, maybe now I can start learning.
Here is a run of my trying to learn:

xvalue-c(5.2,1.3,9.7,2.8,8.1,4.7,6.6,7.4)
yvalue-c(9,3,4,7,2,5,3,6)
plot(xvalue,yvalue)
axis(1,at=NULL,labels=1/xvalue,digits=5)

Error in axis(1, at = NULL, labels = 1/xvalue, digits = 5) :
   'labels' is supplied and not 'at'
In addition: Warning message:
In axis(1, at = NULL, labels = 1/xvalue, digits = 5) :
   digits is not a graphical parameter



Why can't R automatically compute the spacing when I use the formula?
How can I specify n-digits or width instead of round or nothing?


Hi Hurr,
Let's see, suppose I answered your message like this:

answer1-NULL

You would be in the same position as the axis function. You have to tell 
the axis function where the labels are to be placed, or it can't place 
them there. Now for your second question. Suppose my answer was 
something like this:


answer2-wpsovmeksjhfhtieur # language = Magungian

You might well respond that you don't understand Magungian. The argument 
digits doesn't tell the axis function anything useful. If you want 
labels with a certain number of digits, create them before you call the 
axis function:


mylabels-round(1/xvalue,digits=5)

The round function understands Magungian.

Jim

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Re: [R] labeling abscissa using a function of the plotted scale

[Hurr]

Thanks David, did I use incorrect english to call labels = 1/xvalue a
formula or function?
Seems to me an obvious first try would be to place the labels where 
they would have been placed without the formula.
I haven't yet, but I will study from your suggestions.




--
View this message in context: 
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Sent from the R help mailing list archive at Nabble.com.

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Re: [R] bug in dummy.coef?

[David Winsemius]

On Oct 24, 2013, at 1:51 AM, Alexandra Kuznetsova wrote:

 Dear all,
 
 Running the following code produces an error in dummy.coef. I guess it might 
 be a bug..
 
 ctl - c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)
 trt - c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
 group - gl(2, 10, 20, labels = c(Ctl,Trt))
 weight - c(ctl, trt)
 x - rnorm(length(weight))
 lm.D9 - lm(weight ~ group + x + I(x^2))
 dummy.coef(lm.D9)
 Error in rep.int(xl[[i]][1L], nl) : invalid 'times' value

As Rolf Turner pointed out the help page says there are limitations to that 
function and its only desiged for specific purposes. What are you trying to 
accomplish?

-- 

David Winsemius
Alameda, CA, USA

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Re: [R] labeling abscissa using a function of the plotted scale

[David Winsemius]

On Oct 24, 2013, at 3:56 PM, Hurr wrote:

 Thanks David, did I use incorrect english to call e a
 formula or function?

Incorrect R terminology. A function in R is a specific sort of object and a 
formula is a different sort of object.  R terminology for the use of labels = 
1/xvalue inside the arguments to a function may be something along the lines 
of assignment in a pairlist. I was rather loosely calling it an expression.

 Seems to me an obvious first try would be to place the labels where 
 they would have been placed without the formula.

And as I said in the context you have failed to include was that R does not 
rememeber or store the locations where where they would have been placed 
without the formula. It doesn't have access to the arguments used in the prior 
plot call.

 I haven't yet, but I will study from your suggestions.

 
 --
 View this message in context: 
 http://r.789695.n4.nabble.com/labeling-abscissa-using-a-function-of-the-plotted-scale-tp4678075p4679004.html
 Sent from the R help mailing list archive at Nabble.com.

Nabble is not R-help. Please read the Posting Guide that Nabble suppresses in 
its effort to masquerade as Rhelp.

This should have appeared at the bottom of every posting were it not for Nabble 
suppressing it:

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

-- 
David Winsemius
Alameda, CA, USA

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

Re: [R] Making a function and applying it over a list(?)

[Christoph Häni]

You could store your first approach in a function and lapply it to
your by_hour variable:

  df - data.frame(
hour = factor(rep(1:5,4)),
  id   = factor(rep(c(supply, demand), each = 10)),
  price= c(5,7,9,11,13,15,17,19,21,23,
20,18,16,14,12,10,8,6,4,2 ),
  quantity = c(3,5,7,13,19,31,37,53,61,67,6,18,20,24,40,46,66,70,76,78)
)

myfu - function(x){

df - x # for simplicity

quantity_points - with(
  df,
  seq(min(quantity), max(quantity), length.out = 500)
)

by_id - split(df[, c(price, quantity)], df$id)

interpolated_price - lapply(
  by_id,
  function(x)
  {
with(
  x,
  approx(
quantity,
price,
xout = quantity_points
  )
)$y
  }
)

index_of_equality - with(interpolated_price, which.min(abs(supply - demand)))
quantity_points[index_of_equality]

}

by_hour - split(df,df$hour)

lapply(by_hour,myfu)


Was that what you were looking for?

Cheers,
Christoph


2013/10/24 Lasse Thorst l...@energidanmark.dk:
 Hi All

 I've gotten some awesome help getting a formular that finds the intersection 
 of two vectors. This works brilliantly, but I can't figure out how to make it 
 run over another factor. A simple example looks likes this:

   df - data.frame(
   id   = factor(rep(c(supply, demand), each = 10)),
   price= c(5,7,9,11,13,15,17,19,21,23,20,18,16,14,12,10,8,6,4,2 ),
   quantity = c(3,5,7,13,19,31,37,53,61,67,6,18,20,24,40,46,66,70,76,78)
 )

 quantity_points - with(
   df,
   seq(min(quantity), max(quantity), length.out = 500)
 )

 by_id - split(df[, c(price, quantity)], df$id)

 interpolated_price - lapply(
   by_id,
   function(x)
   {
 with(
   x,
   approx(
 quantity,
 price,
 xout = quantity_points
   )
 )$y
   }
 )

 index_of_equality - with(interpolated_price, which.min(abs(supply - demand)))
 quantity_points[index_of_equality]

 Question: I need to run this over a larger data frame, where I have the same 
 data, but also a new factor variable (called hour). So if you have the 
 original data frame and add:

   df - data.frame(
 hour = factor(seq(1:20)),
   id   = factor(rep(c(supply, demand), each = 10)),
   price= c(5,7,9,11,13,15,17,19,21,23,20,18,16,14,12,10,8,6,4,2 ),
   quantity = c(3,5,7,13,19,31,37,53,61,67,6,18,20,24,40,46,66,70,76,78)
 )

 How can I run it for each hour? I tried using:
 by_hour - split(df[, c(price, quantity)], df$hour)
 mapply(fx, by_hour)

 And gathering the above into a fx - function(){the neat code}, but I can't 
 get it to work.

 Kind Regards,
 Lasse

 [[alternative HTML version deleted]]

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Re: [R] bug in dummy.coef?

[Alexandra Kuznetsova]

Dear all,

Running the following code produces an error in dummy.coef. I guess it might be 
a bug..
 ctl - c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)
 trt - c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
 group - gl(2, 10, 20, labels = c(Ctl,Trt))
 weight - c(ctl, trt)
 x - rnorm(length(weight))
 lm.D9 - lm(weight ~ group + x + I(x^2))
 dummy.coef(lm.D9)
Error in rep.int(xl[[i]][1L], nl) : invalid 'times' value

 sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=Danish_Denmark.1252  LC_CTYPE=Danish_Denmark.1252
LC_MONETARY=Danish_Denmark.1252
[4] LC_NUMERIC=CLC_TIME=Danish_Denmark.1252

attached base packages:
[1] parallel  splines   stats graphics  grDevices utils datasets  
methods   base

other attached packages:
 [1] pbkrtest_0.3-5MASS_7.3-26   Hmisc_3.12-2  Formula_1.1-1 
survival_2.37-4   numDeriv_2012.9-1
 [7] lmerTest_2.0-1lme4_1.1-1Matrix_1.0-12 lattice_0.20-15

loaded via a namespace (and not attached):
[1] cluster_1.14.4 gdata_2.13.2   gplots_2.11.3  grid_3.0.1 gtools_3.0.0   
minqa_1.2.1nlme_3.1-109
[8] rpart_4.1-1tools_3.0.1


With best wishes,
Alexandra



From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] on behalf of 
Alexandra Kuznetsova [a...@dtu.dk]
Sent: Thursday, October 24, 2013 10:51 AM
To: r-help@r-project.org
Subject: [R] bug in dummy.coef?

Dear all,

Running the following code produces an error in dummy.coef. I guess it might be 
a bug..

 ctl - c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)
 trt - c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
 group - gl(2, 10, 20, labels = c(Ctl,Trt))
 weight - c(ctl, trt)
 x - rnorm(length(weight))
 lm.D9 - lm(weight ~ group + x + I(x^2))
 dummy.coef(lm.D9)
Error in rep.int(xl[[i]][1L], nl) : invalid 'times' value



 sessionInfo()

R version 3.0.1 (2013-05-16)

Platform: x86_64-w64-mingw32/x64 (64-bit)



locale:

[1] LC_COLLATE=Danish_Denmark.1252  LC_CTYPE=Danish_Denmark.1252
LC_MONETARY=Danish_Denmark.1252

[4] LC_NUMERIC=CLC_TIME=Danish_Denmark.1252



attached base packages:

[1] parallel  splines   stats graphics  grDevices utils datasets  
methods   base



other attached packages:

 [1] pbkrtest_0.3-5MASS_7.3-26   Hmisc_3.12-2  Formula_1.1-1 
survival_2.37-4   numDeriv_2012.9-1

 [7] lmerTest_2.0-1lme4_1.1-1Matrix_1.0-12 lattice_0.20-15



loaded via a namespace (and not attached):

[1] cluster_1.14.4 gdata_2.13.2   gplots_2.11.3  grid_3.0.1 gtools_3.0.0   
minqa_1.2.1nlme_3.1-109

[8] rpart_4.1-1tools_3.0.1




With best wishes,
Alexandra

[[alternative HTML version deleted]]

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

Re: [R] Error in heatmap

[David Romero]

Hi Jean,

 

Problem result: the 1st column value must be complete for heatmap to run
correctly.

This solved the same problem I had with vegdist.

 

Thank you for your help.

 

Regards

 

David

 

De: Adams, Jean [mailto:jvad...@usgs.gov] 
Enviado el: 24 de octubre de 2013 14:12
Para: David Romero
CC: R help
Asunto: Re: [R] Error in heatmap

 

David,

 

You should cc r-help on all correspondence so others can follow the thread.

 

The error appears to be a result of the missing values yielded by the dist()
function on your matrix.

See https://stat.ethz.ch/pipermail/r-help/2009-July/204443.html.

 

Jean

 

On Thu, Oct 24, 2013 at 1:25 PM, David Romero drom...@mda.cinvestav.mx
wrote:

Hi,

 

The difference is:

row.names=1

for csv reading. 

The first column is a numeric row name, it mustn't take part of the heatmap.


 

I change it to text and try with and without  row.names=1

Both give me error.

 

Regards

 

David

 

De: Adams, Jean [mailto:jvad...@usgs.gov] 
Enviado el: 24 de octubre de 2013 11:52
Para: David Romero
CC: R help


Asunto: Re: [R] Error in heatmap

 

Using your csv file, I get no error running the following code.

 SPIV2 - read.csv(C:/Temp/SPI V2.csv)

 heatmap(as.matrix(SPIV2), na.rm=TRUE)

Perhaps you modified SPIV2 in some way prior to running heatmap()?

 

Jean

 

 

 

On Tue, Oct 22, 2013 at 10:29 AM, David Romero drom...@mda.cinvestav.mx
wrote:

Hi Jean

 

Thank you for helping.

No, there is no empty column or row. I join the data base.

 

Regards

 

David

 

 

 

De: Adams, Jean [mailto:jvad...@usgs.gov] 
Enviado el: 22 de octubre de 2013 07:03
Para: David Romero
CC: r-h...@stat.math.ethz.ch
Asunto: Re: [R] Error in heatmap

 

Do you have a row or column that is all missing?

 sum(apply(is.na(as.matrix(SPIV2)), 1, all))  0

 sum(apply(is.na(as.matrix(SPIV2)), 2, all))  0

 

For example, this code

 m - as.matrix(mtcars)

 m[8, ] - NA

 heatmap(m, na.rm=TRUE)

throws this error

 Error in hclustfun(distfun(x)) : 

   NA/NaN/Inf in foreign function call (arg 11)

 

Jean

 

 

On Mon, Oct 21, 2013 at 1:04 PM, David Romero drom...@mda.cinvestav.mx
wrote:

Hi,



Could you please help?



Heatmap  doesn't work with:



 heatmap(as.matrix(SPIV2),na.rm = T)

Error in hclustfun(distfun(x)) :

  NA/NaN/Inf in foreign function call (arg 11)



There are no 0 data rows or column



Thanks a lot



Regards

---

David




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

Re: [R] Optional argument to be used in a subset function

[David Mora]

Sorry for the html code:

I'm writing a function that needs an optional variable. If the variable is
given, then a subset must be made using that variable, but if the variable
is not given the subset must be done using all the values for that variable
(ignoring that variable).

Something like this:

band - function(file, fruit = apple, optional=TRUE) {

data - read.csv(file)

a - nrow(subset(data, 'Column 1' == fruit  'Column 2'==hot  'Column
3'== optional))

b - nrow(subset(data,'Column 1' == fruit  'Column 2'==cold  'Column
3'== optional))

z - a+b

 print(z)

 }
*
*
What I need is that the function band(file,orange),  subset the data
frame using all possible values for Column 3 but is not doing it.

All ideas are welcome.

Thanks.

David Mora


On Thu, Oct 24, 2013 at 8:15 AM, David Mora dmv...@gmail.com wrote:

 I'm writing a function that needs an optional variable. If the variable is
 given, then a subset must be made using that variable, but if the variable
 is not given the subset must be done using all the values for that variable
 (ignoring that variable).

 Something like this:

 *band - function(file, fruit = apple, optional=TRUE) {*

 *data - read.csv(file)*

 *a - nrow(subset(data, 'Column 1' == fruit  'Column 2'==hot  'Column
 3'== optional))*

 *b - nrow(subset(data,'Column 1' == fruit  'Column 2'==cold  'Column
 3'== optional)) *

 *z - a+b*

 * print(z)*

 * }*

 What I need is that the function *band(file,orange)*,  subset the
 data frame using all possible values for Column 3 but is not doing it.

 All ideas are welcome.

 Thanks.


 David Mora


[[alternative HTML version deleted]]

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

[R] 'yum install R' failing with tcl/tk issue

[Michael Stauffer]

Hi,

I'm trying to install R on CentOS 6.4.

Following some instructions online, I've done this:

rpm -Uvh
http://download.fedoraproject.org/pub/epel/6/i386/epel-release-6-8.noarch.rpm

yum install R

But yum fails, with this (full output below):

Error: Package: R-core-2.10.0-2.el5.x86_64 (Rocks-6.1)
   Requires: libtcl8.4.so()(64bit)
Error: Package: R-core-2.10.0-2.el5.x86_64 (Rocks-6.1)
   Requires: libtk8.4.so()(64bit)

I have tcl/tk 8.5 already installed. Does anyone have any suggestion?
Thanks!

Full output:

[root@picsl-cluster ~]# yum install R
Repository base is listed more than once in the configuration
Rocks-6.1
  | 1.9 kB 00:00
base
   | 3.7 kB 00:00
Setting up Install Process
Resolving Dependencies
-- Running transaction check
--- Package R.x86_64 0:2.10.0-2.el5 will be installed
-- Processing Dependency: libRmath-devel = 2.10.0-2.el5 for package:
R-2.10.0-2.el5.x86_64
-- Processing Dependency: R-devel = 2.10.0-2.el5 for package:
R-2.10.0-2.el5.x86_64
-- Running transaction check
--- Package R-devel.x86_64 0:2.10.0-2.el5 will be installed
-- Processing Dependency: R-core = 2.10.0-2.el5 for package:
R-devel-2.10.0-2.el5.x86_64
--- Package libRmath-devel.x86_64 0:2.10.0-2.el5 will be installed
-- Processing Dependency: libRmath = 2.10.0-2.el5 for package:
libRmath-devel-2.10.0-2.el5.x86_64
-- Running transaction check
--- Package R-core.x86_64 0:2.10.0-2.el5 will be installed
-- Processing Dependency: libtk8.4.so()(64bit) for package:
R-core-2.10.0-2.el5.x86_64
-- Processing Dependency: libtcl8.4.so()(64bit) for package:
R-core-2.10.0-2.el5.x86_64
-- Processing Dependency: libgfortran.so.1()(64bit) for package:
R-core-2.10.0-2.el5.x86_64
--- Package libRmath.x86_64 0:2.10.0-2.el5 will be installed
-- Running transaction check
--- Package R-core.x86_64 0:2.10.0-2.el5 will be installed
-- Processing Dependency: libtk8.4.so()(64bit) for package:
R-core-2.10.0-2.el5.x86_64
-- Processing Dependency: libtcl8.4.so()(64bit) for package:
R-core-2.10.0-2.el5.x86_64
--- Package compat-libgfortran-41.x86_64 0:4.1.2-39.el6 will be installed
-- Finished Dependency Resolution
Error: Package: R-core-2.10.0-2.el5.x86_64 (Rocks-6.1)
   Requires: libtcl8.4.so()(64bit)
Error: Package: R-core-2.10.0-2.el5.x86_64 (Rocks-6.1)
   Requires: libtk8.4.so()(64bit)
 You could try using --skip-broken to work around the problem
** Found 57 pre-existing rpmdb problem(s), 'yum check' output follows:
foundation-git-1.7.11.4-0.x86_64 has missing requires of perl(SVN::Client)
foundation-git-1.7.11.4-0.x86_64 has missing requires of perl(SVN::Core)
foundation-git-1.7.11.4-0.x86_64 has missing requires of perl(SVN::Delta)
foundation-git-1.7.11.4-0.x86_64 has missing requires of perl(SVN::Ra)
1:guestfish-1.7.17-26.el6.x86_64 has missing requires of libguestfs = ('1',
'1.7.17', '26.el6')
opt-perl-AcePerl-1.92-0.el6.x86_64 has missing requires of
perl(Ace::Browser::LocalSiteDefs)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
perl(Apache::DBI)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
perl(Bio::ASN1::EntrezGene)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
perl(Bio::Expression::Contact)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
perl(Bio::Expression::DataSet)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
perl(Bio::Expression::Platform)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
perl(Bio::Expression::Sample)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
perl(Bio::Phylo::Factory)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
perl(Bio::Phylo::Forest::Tree)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
perl(Bio::Phylo::IO)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
perl(Bio::Phylo::Matrices)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
perl(Bio::Phylo::Matrices::Datum)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
perl(Bio::Phylo::Matrices::Matrix)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
perl(Convert::Binary::C)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of perl(DBD::Pg)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
perl(PostScript::TextBlock)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
perl(Test::Exception)
opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
perl(Test::Warn)
opt-perl-BioPerl-DB-1.006900-0.el6.noarch has missing requires of
perl(DBD::Oracle)
opt-perl-BioPerl-Run-1.006900-0.el6.noarch has missing requires of
perl(Bio::Tools::Run::StandAloneBlastPlus::BlastMethods)
opt-perl-BioPerl-Run-1.006900-0.el6.noarch has missing requires of
perl(Bio::Tools::Run::WrapperBase::CommandExts)
opt-perl-Cache-Cache-1.06-0.el6.noarch has missing requires of
perl(IPC::ShareLite)
opt-perl-DBI-1.622-0.el6.x86_64 has missing requires of perl(Coro)

[R] moving points labels in ordinations

[Peter Nelson]

I'm trying to place labels so as to avoid covering points (and other labels) in 
an ordination plot. I've been trying to use orditkplot() for this  purpose, but 
get an error message, even when I try to replicate the example: 

require(vegan)
data(varespec)
 ord - cca(varespec)
 orditkplot(ord, mar = c(4,4,1,1)+.1, font=3)
Error in structure(.External(.C_dotTclObjv, objv), class = tclObj) : 
  [tcl] invalid command name tk.
In addition: Warning message:
In fun(libname, pkgname) : couldn't connect to display :0
 

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

Re: [R] test wilcoxon sur R help!

[vikram ranga]

Hi,
Check out this function:-
pairwise.wilcox.test {package=stats}.

example(pairwise.wilcox.test)


On Fri, Oct 25, 2013 at 2:15 AM, Rui Barradas ruipbarra...@sapo.pt wrote:
 Hello,

 There's a bug in your function, it should be 'dat', not 'dat1'. In the line
 marked, below.

 fun1 - function(dat){
 mat1 - combn(colnames(dat),2)  # Here, 'dat' not 'dat1'

 res - sapply(seq_len(ncol(mat1)),function(i) {x1- dat[,mat1[,i]];
 wilcox.test(x1[,1],x1[,2])$p.value})
 names(res) - apply(mat1,2,paste,collapse=_)
 res
 }


 Hope this helps,

 Rui Barradas

 Em 24-10-2013 20:16, arun escreveu:

 Hi,
 Try:
 fun1 - function(dat){
 mat1 - combn(colnames(dat1),2)
   res - sapply(seq_len(ncol(mat1)),function(i) {x1- dat[,mat1[,i]];
 wilcox.test(x1[,1],x1[,2])$p.value})
 names(res) - apply(mat1,2,paste,collapse=_)
 res
 }

 set.seed(432)
 dat1 - as.data.frame(matrix(sample(18*10,18*10,replace=FALSE),ncol=18))

fun1(dat1) #gives the p-value for each pair of columns




 Hi,

 I want to make a wilcoxon test, i have 18 columns each column
 corresponds to a different sample and i want to compare one to each
 other with a wilcoxon test in one step this is possible ? or do i
 compare two by tow?

 Does it exist a code for automation this test? like this i dont have to
 type the code for each couple.

 thanks!
 denisse

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


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

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

Re: [R] test wilcoxon sur R help!

[arun]

It looks much better than mine.


with p value adjustment:
p.adjust(fun1(dat1), method = holm, n = 153)
#

dat1$id - 1:10
library(reshape2)
dat2 - melt(dat1,id.var=id)
with(dat2,pairwise.wilcox.test(value,variable))
 with(dat2,pairwise.wilcox.test(value,variable,p.adj=none)) 


A.K.




On Friday, October 25, 2013 12:05 AM, vikram ranga babuaw...@gmail.com wrote:
Hi,
Check out this function:-
pairwise.wilcox.test {package=stats}.

example(pairwise.wilcox.test)


On Fri, Oct 25, 2013 at 2:15 AM, Rui Barradas ruipbarra...@sapo.pt wrote:
 Hello,

 There's a bug in your function, it should be 'dat', not 'dat1'. In the line
 marked, below.

 fun1 - function(dat){
         mat1 - combn(colnames(dat),2)  # Here, 'dat' not 'dat1'

         res - sapply(seq_len(ncol(mat1)),function(i) {x1- dat[,mat1[,i]];
 wilcox.test(x1[,1],x1[,2])$p.value})
         names(res) - apply(mat1,2,paste,collapse=_)
         res
 }


 Hope this helps,

 Rui Barradas

 Em 24-10-2013 20:16, arun escreveu:

 Hi,
 Try:
 fun1 - function(dat){
 mat1 - combn(colnames(dat1),2)
   res - sapply(seq_len(ncol(mat1)),function(i) {x1- dat[,mat1[,i]];
 wilcox.test(x1[,1],x1[,2])$p.value})
 names(res) - apply(mat1,2,paste,collapse=_)
 res
 }

 set.seed(432)
 dat1 - as.data.frame(matrix(sample(18*10,18*10,replace=FALSE),ncol=18))

    fun1(dat1) #gives the p-value for each pair of columns




 Hi,

 I want to make a wilcoxon test, i have 18 columns each column
 corresponds to a different sample and i want to compare one to each
 other with a wilcoxon test in one step this is possible ? or do i
 compare two by tow?

 Does it exist a code for automation this test? like this i dont have to
 type the code for each couple.

 thanks!
 denisse

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



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


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

Re: [R] 'yum install R' failing with tcl/tk issue

[Pascal Oettli]

Hello,

Do you have headers installed (generally tcl-devel and tk-devel)?

Regards,
Pascal


On 25 October 2013 10:33, Michael Stauffer mgsta...@gmail.com wrote:
 Hi,

 I'm trying to install R on CentOS 6.4.

 Following some instructions online, I've done this:

 rpm -Uvh
 http://download.fedoraproject.org/pub/epel/6/i386/epel-release-6-8.noarch.rpm

 yum install R

 But yum fails, with this (full output below):

 Error: Package: R-core-2.10.0-2.el5.x86_64 (Rocks-6.1)
Requires: libtcl8.4.so()(64bit)
 Error: Package: R-core-2.10.0-2.el5.x86_64 (Rocks-6.1)
Requires: libtk8.4.so()(64bit)

 I have tcl/tk 8.5 already installed. Does anyone have any suggestion?
 Thanks!

 Full output:

 [root@picsl-cluster ~]# yum install R
 Repository base is listed more than once in the configuration
 Rocks-6.1
   | 1.9 kB 00:00
 base
| 3.7 kB 00:00
 Setting up Install Process
 Resolving Dependencies
 -- Running transaction check
 --- Package R.x86_64 0:2.10.0-2.el5 will be installed
 -- Processing Dependency: libRmath-devel = 2.10.0-2.el5 for package:
 R-2.10.0-2.el5.x86_64
 -- Processing Dependency: R-devel = 2.10.0-2.el5 for package:
 R-2.10.0-2.el5.x86_64
 -- Running transaction check
 --- Package R-devel.x86_64 0:2.10.0-2.el5 will be installed
 -- Processing Dependency: R-core = 2.10.0-2.el5 for package:
 R-devel-2.10.0-2.el5.x86_64
 --- Package libRmath-devel.x86_64 0:2.10.0-2.el5 will be installed
 -- Processing Dependency: libRmath = 2.10.0-2.el5 for package:
 libRmath-devel-2.10.0-2.el5.x86_64
 -- Running transaction check
 --- Package R-core.x86_64 0:2.10.0-2.el5 will be installed
 -- Processing Dependency: libtk8.4.so()(64bit) for package:
 R-core-2.10.0-2.el5.x86_64
 -- Processing Dependency: libtcl8.4.so()(64bit) for package:
 R-core-2.10.0-2.el5.x86_64
 -- Processing Dependency: libgfortran.so.1()(64bit) for package:
 R-core-2.10.0-2.el5.x86_64
 --- Package libRmath.x86_64 0:2.10.0-2.el5 will be installed
 -- Running transaction check
 --- Package R-core.x86_64 0:2.10.0-2.el5 will be installed
 -- Processing Dependency: libtk8.4.so()(64bit) for package:
 R-core-2.10.0-2.el5.x86_64
 -- Processing Dependency: libtcl8.4.so()(64bit) for package:
 R-core-2.10.0-2.el5.x86_64
 --- Package compat-libgfortran-41.x86_64 0:4.1.2-39.el6 will be installed
 -- Finished Dependency Resolution
 Error: Package: R-core-2.10.0-2.el5.x86_64 (Rocks-6.1)
Requires: libtcl8.4.so()(64bit)
 Error: Package: R-core-2.10.0-2.el5.x86_64 (Rocks-6.1)
Requires: libtk8.4.so()(64bit)
  You could try using --skip-broken to work around the problem
 ** Found 57 pre-existing rpmdb problem(s), 'yum check' output follows:
 foundation-git-1.7.11.4-0.x86_64 has missing requires of perl(SVN::Client)
 foundation-git-1.7.11.4-0.x86_64 has missing requires of perl(SVN::Core)
 foundation-git-1.7.11.4-0.x86_64 has missing requires of perl(SVN::Delta)
 foundation-git-1.7.11.4-0.x86_64 has missing requires of perl(SVN::Ra)
 1:guestfish-1.7.17-26.el6.x86_64 has missing requires of libguestfs = ('1',
 '1.7.17', '26.el6')
 opt-perl-AcePerl-1.92-0.el6.x86_64 has missing requires of
 perl(Ace::Browser::LocalSiteDefs)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Apache::DBI)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::ASN1::EntrezGene)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::Expression::Contact)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::Expression::DataSet)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::Expression::Platform)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::Expression::Sample)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::Phylo::Factory)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::Phylo::Forest::Tree)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::Phylo::IO)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::Phylo::Matrices)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::Phylo::Matrices::Datum)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Bio::Phylo::Matrices::Matrix)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Convert::Binary::C)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of perl(DBD::Pg)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(PostScript::TextBlock)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Test::Exception)
 opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
 perl(Test::Warn)
 opt-perl-BioPerl-DB-1.006900-0.el6.noarch has missing requires of
 perl(DBD::Oracle)
 opt-perl-BioPerl-Run-1.006900-0.el6.noarch has missing requires of
 perl(Bio::Tools::Run::StandAloneBlastPlus::BlastMethods)