date:20130222


On Feb 21, 2013, at 2:15 PM, William Dunlap wrote:

 Many find the functions in the plyr package more convenient to use than the
 do.call(rbind, lapply(split(...),...) business:
 
 library(plyr)
 ddply(dat1, .(Subject,Block),  summarize, MeanFeature1=mean(Feature1), 
 MeanFeature2=mean(Feature2))
Subject Block MeanFeature1 MeanFeature2
  1   1 1 55.0 29.0
  2   1 2 42.5 38.5
  3   1 3 64.0 14.0
 
 Change the calls to 'mean' to calls to other summary functions like 'sum' or 
 'max' as you wish. 

Apropos something less complex than the do.call( lapply( split...)) business: 
The same sort of operation is provided by `aggregate` when the function to be 
applied on all columns is the same:

 aggregate(dat1[, c('Feature1', 'Feature2')] , dat1[, c(Subject, Block)], 
 FUN=mean)
  Subject Block Feature1 Feature2
1   1 1 55.0 29.0
2   1 2 42.5 38.5
3   1 3 64.0 14.0

-- 
David

 Bill Dunlap
 Spotfire, TIBCO Software
 wdunlap tibco.com
 
 
 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On 
 Behalf
 Of arun
 Sent: Thursday, February 21, 2013 1:45 PM
 To: Johannes Brand
 Cc: R help
 Subject: Re: [R] remove rows in data frame by average
 
 Hi,
 
 May be this helps:
 
 dat1- read.table(text=
 Subject Block Trial Feature1 Feature2
 1  1  1  48  40
 1  1  2   62  18
 1 2  134  43
 1  2  2   51 34
 1  3  1   64  14
 ,sep=,header=TRUE)
 
 
  res1-do.call(rbind,lapply(split(dat1,dat1$Block),function(x)
 data.frame(unique(x[,1:2]),t(colMeans(x[,-c(1:3)])
  res1
 #  Subject Block Feature1 Feature2
 #1   1 1 55.0 29.0
 #2   1 2 42.5 38.5
 #3   1 3 64.0 14.0
 
 
 #With multiple subjects:
 dat2- read.table(text=
 Subject Block Trial Feature1 Feature2
 1  1  1  48  40
 1  1  2   62  18
 1 2  134  43
 1  2  2   51 34
 1  3  1   64  14
 2  1  1   48  35
 2  1  2   54  15
 2  2  1   49  50
 2  2  2   64  40
 2  3  1   38  28
 ,sep=,header=TRUE)
 
  
 res2-do.call(rbind,lapply(split(dat2,list(dat2$Subject,dat2$Block)),function(x)
 data.frame(unique(x[,1:2]),t(colMeans(x[,-c(1:3)])
 res2-do.call(rbind,split(res2,res2$Subject))
 res2
  # Subject Block Feature1 Feature2
 #1   1 1 55.0 29.0
 #2   1 2 42.5 38.5
 #3   1 3 64.0 14.0
 #4   2 1 51.0 25.0
 #5   2 2 56.5 45.0
 #6   2 3 38.0 28.0
 
 
 
 A.K.
 
 
 
 - Original Message -
 From: Johannes Brand brandjohan...@gmx.de
 To: r-help@r-project.org
 Cc:
 Sent: Thursday, February 21, 2013 12:02 PM
 Subject: [R] remove rows in data frame by average
 
 Dear all,
 
 I have a data frame, which looks like this:
 
 Subject | Block | Trial | Feature1 | Feature2 
 1 | 1 | 1 | ... | ...
 1 | 1 | 2 | ... | ...
 1 | 2 | 1 | ... | ...
 1 | 2 | 2 | ... | ...
 1 | 3 | 1 | ... | ...
 ...| ...| ...| ... | ...
 
 Can I remove the Trial column by averaging all the rows and without using
 a for loop?
 
 At the end my data frame should look like this:
 
 Subject | Block | Feature1 | Feature2 
 1 | 1 | ... | ...
 1 | 2 | ... | ...
 1 | 3 | ... | ...
 ...| ...| ... | ...
 
 Thank you a lot for your help.
 
 Best,
 Johannes
 


David Winsemius
Alameda, CA, USA

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[R] Controlling Order of Panels in Lattice Trellis Plots


  With multiple panels in a lattice trellis plot the sequence is, for
example, 1, 10, 11, 12, 2, 3, 4. I want the sequence to be 1, 2, 3, 4, 10,
11, 12.

  Reading ?strip.default and the appropriate section in the Lattice book I'm
not seeing how to specify the 'human' numeric order rather than the computer
numeric order.

  A pointer will be appreciated.

TIA,

Rich

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Re: [R] HELP!!!


On Feb 22, 2013, at 11:02 AM, lara sowale wrote:

 I am sorry to bug you, I am having this error whenever I want to run
 random effects regression in software R: Error in if (sigma2$id  0)
 stop(paste(the estimated variance of the,  :
   missing value where TRUE/FALSE needed.
 
 Please help me look into it.

Please read the Posting Guide and after doing so repost with a question that 
admits of some possiblity of answering.

   [[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.

Yes, and that, too.
-- 
David Winsemius
Alameda, CA, USA

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Re: [R] Controlling Order of Panels in Lattice Trellis Plots


On Feb 22, 2013, at 11:02 AM, Rich Shepard wrote:

  With multiple panels in a lattice trellis plot the sequence is, for
 example, 1, 10, 11, 12, 2, 3, 4. I want the sequence to be 1, 2, 3, 4, 10,
 11, 12.
 

It appears these may be factors. No much in the way of code can be offered 
since you have provided none of hte requested details.


  Reading ?strip.default and the appropriate section in the Lattice book I'm
 not seeing how to specify the 'human' numeric order rather than the computer
 numeric order.
 
  A pointer will be appreciated.
 

 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html

Many pointers have been offered, but you have refused to heed them.

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

-- 

David Winsemius
Alameda, CA, USA

__
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Re: [R] HELP!!!

2013-02-22 Thread jim holtman

Run with:

options(error=utils::recover)

Then at the point of the error you will be able to examine sigma2$id
which is probably not a numeric.  Any time you get an error like this,
if you have been using the above statement in your script (which I
always have turned on), you will be able to discover for yourself most
of your bugs.  Debugging is an important talent to learn if you are
going to be writing programs/scripts.

On Fri, Feb 22, 2013 at 2:02 PM, lara sowale lara.d...@gmail.com wrote:
 I am sorry to bug you, I am having this error whenever I want to run
 random effects regression in software R: Error in if (sigma2$id  0)
 stop(paste(the estimated variance of the,  :
missing value where TRUE/FALSE needed.

 Please help me look into it.

 [[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.



-- 
Jim Holtman
Data Munger Guru

What is the problem that you are trying to solve?
Tell me what you want to do, not how you want to do it.

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Re: [R] Controlling Order of Panels in Lattice Trellis Plots


On Fri, 22 Feb 2013, David Winsemius wrote:


It appears these may be factors. No much in the way of code can be offered
since you have provided none of hte requested details.


  Yes, David, strip labels are factors. What sort of detail would you like
to see to advise me on how to specify the order of these factors?

  Do you want a data set?

  Here is an example command:


xyplot(sb.d$quant ~ sb.d$sampdate | sb.d$site, ylim=range(sb.d$quant), 
xlim=range(sb.d$sampdate), main='Antimony By Time', ylab='Concentraion (mg/L)', 
xlab='Time')


Rich

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Re: [R] HELP!!!

2013-02-22 Thread Nicole Ford

Wow, Jim- fun tid bit!  Unrelated to op, but I will say thank you- as I know it 
will be useful!

~Nicole Ford
Ph.D. Student
Graduate Assistant/ Instructor
Department of Government and International Affairs
University of South Florida
office: SOC 012M
e: nmhi...@mail.usf.edu
http://gia.usf.edu/student/nford/

Sent from my iPhone

On Feb 22, 2013, at 2:23 PM, jim holtman jholt...@gmail.com wrote:

 Run with:
 
 options(error=utils::recover)
 
 Then at the point of the error you will be able to examine sigma2$id
 which is probably not a numeric.  Any time you get an error like this,
 if you have been using the above statement in your script (which I
 always have turned on), you will be able to discover for yourself most
 of your bugs.  Debugging is an important talent to learn if you are
 going to be writing programs/scripts.
 
 On Fri, Feb 22, 2013 at 2:02 PM, lara sowale lara.d...@gmail.com wrote:
 I am sorry to bug you, I am having this error whenever I want to run
 random effects regression in software R: Error in if (sigma2$id  0)
 stop(paste(the estimated variance of the,  :
   missing value where TRUE/FALSE needed.
 
 Please help me look into it.
 
[[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.
 
 
 
 -- 
 Jim Holtman
 Data Munger Guru
 
 What is the problem that you are trying to solve?
 Tell me what you want to do, not how you want to do 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.

[[alternative HTML version deleted]]

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

Re: [R] Controlling Order of Panels in Lattice Trellis Plots

Manually change the ordering of the levels in the factor to that which
you want (see ?factor if necessary) and replot.

-- Bert

On Fri, Feb 22, 2013 at 11:17 AM, David Winsemius
dwinsem...@comcast.net wrote:

On Feb 22, 2013, at 11:02 AM, Rich Shepard wrote:

With multiple panels in a lattice trellis plot the sequence is, for
example, 1, 10, 11, 12, 2, 3, 4. I want the sequence to be 1, 2, 3, 4, 10,
11, 12.

It appears these may be factors. No much in the way of code can be offered
since you have provided none of hte requested details.

Reading ?strip.default and the appropriate section in the Lattice book I'm
not seeing how to specify the 'human' numeric order rather than the computer
numeric order.

A pointer will be appreciated.

PLEASE do read the posting guide http://www.R-project.org/posting-guide.html

Many pointers have been offered, but you have refused to heed them.

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

David Winsemius
Alameda, CA, USA

Bert Gunter
Genentech Nonclinical Biostatistics

Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm

[R] R on mac not installing packages

2013-02-22 Thread londonphd


Hi, I have not been able to use R in my macbook pro. I am getting the
following error message every time i try to install a package

* installing *source* package ‘Hmisc’ ...
** package ‘Hmisc’ successfully unpacked and MD5 sums checked
** libs
*** arch - i386
sh: make: command not found
ERROR: compilation failed for package ‘Hmisc’
* removing ‘/Users/ravshonbek/Library/R/2.15/library/Hmisc’
* installing *source* package ‘quadprog’ ...
** libs
*** arch - i386
sh: make: command not found
ERROR: compilation failed for package ‘quadprog’
* removing ‘/Users/ravshonbek/Library/R/2.15/library/quadprog’
ERROR: dependency ‘Hmisc’ is not available for package ‘its’
* removing ‘/Users/ravshonbek/Library/R/2.15/library/its’
ERROR: dependency ‘quadprog’ is not available for package ‘tseries’
* removing ‘/Users/ravshonbek/Library/R/2.15/library/tseries’

The downloaded source packages are in

‘/private/var/folders/c7/jrjv78_x6f53l3sw_w715gk0gn/T/RtmpS4sYUx/downloaded_packages’


I look forward to your help, plsease




--
View this message in context: 
http://r.789695.n4.nabble.com/R-on-mac-not-installing-packages-tp4659392.html
Sent from the R help mailing list archive at Nabble.com.

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

Re: [R] Getting htmlParse to work with Hebrew? (on windows)

2013-02-22 Thread Lawr Eskin

I thiknk that I have to install Linux on VM... There is a shortest way

by the way, could you please advise how to rebuild 'XML' package for R with
latest libxml sources? Who may do that?
or is it possible to build the new R package based on another non-C sorced
parsers based like on PyPY, erlang and so on?

2013/2/22 Milan Bouchet-Valat nalimi...@club.fr

 Le jeudi 21 fÃ©vrier 2013 Ã  18:53 +0400, Lawr Eskin a Ã©crit :
  iconv trued before in various try, same issue and result with encoding
  = unknown
  now try sub - same issue
 This procedure works on Linux, but not on Windows:

 library(RCurl)
 library(XML)
 u - http://www.cian.ru/cat.php?deal_type=2obl_id=1room1=1;
 a - getURL(u, .encoding=UTF-8)
 a - iconv(a, windows-1251, UTF-8)
 a2 - htmlParse(sub(windows-1251, UTF-8, a))
 a2

 But maybe the problem is more general, and related to conversion between
 encodings on Windows. What looks weird to me is that on Windows, I'm not
 able to save a character string to a file in UTF-8, despite what ?file
 says:
 x - ÐÑÐµ Ð¿ÑÐ°Ð²Ð° Ð·Ð°ÑÐ¸ÑÐµÐ½Ñ
 Encoding(x)
 # UTF-8
 cat(x, con - file(foo, w, encoding=UTF-8)); close(con)
 x2 - readLines(con - file(foo, r, encoding=UTF-8)); close(con)
 Encoding(x2)
 # unknown
 x2
 # [1] U+041AU+0443...

 I know the problem happens on write because the file cannot be read
 correctly on Linux either.

 This Windows machine uses Windows Server 2008 with French_France.1252
 locale.

  2013/2/21 Milan Bouchet-Valat nalimi...@club.fr
  Le jeudi 21 fÃ©vrier 2013 Ã  18:31 +0400, Lawr Eskin a Ã©crit :
   Hi Milan,
  
   a - getURL(con, .encoding = UTF-8)
   Encoding(a)
[1] UTF-8
   a # Here - the UTF-8 codes looks like fine.
   htmlParse(a, encoding = UTF-8) ###again same encoding
  issue
 
  And what if you try this:
  a2 - htmlParse(sub(windows-1251, UTF-8, a))
 
  or this:
  a2 - htmlParse(iconv(a, windows-1251, UTF-8))
 
 
  Cheers
 
 
   why didn't getURL() detect and set a's encoding correctly?
   I think there are page issue because another sites works
  fine
  
   2013/2/21 Milan Bouchet-Valat nalimi...@club.fr
   Le jeudi 21 fÃ©vrier 2013 Ã  16:04 +0400, Lawr Eskin a
  Ã©crit :
Hi Milan!
   
   
 Encoding(a)
[1] unknown
  
   Hm, here I get UTF-8, which is my locale encoding.
  
   I've tried a little more, and I discovered that
  using
   a - getURL(u, .encoding=UTF-8)
   ensures that a is in the correct encoding here. I
  know this is
   not your
   problem, but it might help: check whether
  Encoding(a) is set
   to UTF-8
   or not in that case, and whether this fixes things.
  
   I'm not sure how htmlParse() detects the encoding
  when you
   pass it a
   character vector, but it probably uses Encoding(a),
  since
   that's the
   only reliable information; if it is missing, maybe
  it falls
   back to what
   the contents of the file say (maybe even before what
  the
   encoding
   argument says), which is windows-1251, and may not
  be the
   encoding in
   which getURL() saved the character vector. The
  question would
   then be:
   why didn't getURL() detect and set a's encoding
  correctly?
  
  
   My two cents
  
  
2013/2/21 Milan Bouchet-Valat nalimi...@club.fr
Le jeudi 21 fÃ©vrier 2013 Ã  13:16 +0400,
  Lawr Eskin a
   Ã©crit :
 Hello dear R-help mailing list.


 Looks like the same issue in Russian:



 library(RCurl)

 library(XML)

 u = 
   
  
  http://www.cian.ru/cat.php?deal_type=2obl_id=1room1=1;

 a = getURL(u)

 a # Here - the Russian is fine.

 a2 - htmlParse(a)

 a2 # Here it is a mess...

[R] Fwd: difficulty defining variables as categorical using Gower with DAISY

2013-02-22 Thread Joanna Papakonstantinou


 I am using the iris dataset that contains mixed variables (some columns are 
 numeric and some categorical).
  
 
  iris
 Sepal.Length Sepal.Width Petal.Length Petal.WidthSpecies
 15.1 3.5  1.4 0.2 setosa
 24.9 3.0  1.4 0.2 setosa
 34.7 3.2  1.3 0.2 setosa
 44.6 3.1  1.5 0.2 setosa
 .
 .
 .

 I am trying to use the Gower metric so that I may specify that some columns 
 contain categorical data.
  iris.clust-daisy(iris, metric = gower, stand = FALSE, type = 
  list(factor=Species))
 
But it is saying that the type= I, I, I, I, N
so obviously it is not reading the variable types correctly.

Could someone please tell me how to specify the types correctly?

Thank you.
  
 **
  
 Joanna Papakonstantinou, Ph.D.
 

[[alternative HTML version deleted]]

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Re: [R] Controlling Order of Panels in Lattice Trellis Plots


On Fri, 22 Feb 2013, Bert Gunter wrote:


Manually change the ordering of the levels in the factor to that which you
want (see ?factor if necessary) and replot.


Bert,

  I'll do this.

  I looked at ?factor and will try is.ordered() to see if that makes a
difference.

Many thanks,

Rich

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Re: [R] Controlling Order of Panels in Lattice Trellis Plots


On Feb 22, 2013, at 11:29 AM, Rich Shepard wrote:

 On Fri, 22 Feb 2013, David Winsemius wrote:
 
 It appears these may be factors. No much in the way of code can be offered
 since you have provided none of hte requested details.
 
  Yes, David, strip labels are factors. What sort of detail would you like
 to see to advise me on how to specify the order of these factors?
 
  Do you want a data set?
 
  Here is an example command:
 
 xyplot(sb.d$quant ~ sb.d$sampdate | sb.d$site, ylim=range(sb.d$quant), 
 xlim=range(sb.d$sampdate), main='Antimony By Time', ylab='Concentraion 
 (mg/L)', xlab='Time')

My response can be seen on your cross-posted SO question. 

-- 
David Winsemius
Alameda, CA, USA

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

Re: [R] R on mac not installing packages

The system is reporting that it cannot find `make`. It appears that you have 
not installed XCode on you Mac, or that you did with an earlier version for 
which you have not updated, or something else which has broken your 
installation. Please read the MacOS FAQ. (And post further such question on the 
SIG-Mac mailing list.)

On Feb 22, 2013, at 12:15 PM, londonphd wrote:

 
 Hi, I have not been able to use R in my macbook pro. I am getting the
 following error message every time i try to install a package
 
 * installing *source* package ‘Hmisc’ ...
 ** package ‘Hmisc’ successfully unpacked and MD5 sums checked
 ** libs
 *** arch - i386
 sh: make: command not found
 ERROR: compilation failed for package ‘Hmisc’
 * removing ‘/Users/ravshonbek/Library/R/2.15/library/Hmisc’
 * installing *source* package ‘quadprog’ ...
 ** libs
 *** arch - i386
 sh: make: command not found
 ERROR: compilation failed for package ‘quadprog’
 * removing ‘/Users/ravshonbek/Library/R/2.15/library/quadprog’
 ERROR: dependency ‘Hmisc’ is not available for package ‘its’
 * removing ‘/Users/ravshonbek/Library/R/2.15/library/its’
 ERROR: dependency ‘quadprog’ is not available for package ‘tseries’
 * removing ‘/Users/ravshonbek/Library/R/2.15/library/tseries’
 
 The downloaded source packages are in
 
 ‘/private/var/folders/c7/jrjv78_x6f53l3sw_w715gk0gn/T/RtmpS4sYUx/downloaded_packages’
 
 
 I look forward to your help, plsease
 
 
 
 
 --
 View this message in context: 
 http://r.789695.n4.nabble.com/R-on-mac-not-installing-packages-tp4659392.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

__
R-help@r-project.org mailing list
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Re: [R] Controlling Order of Panels in Lattice Trellis Plots

You do not need to use ordered factors.

newfac - factor(oldfac, lev= ...) ## will do it. e.g.

 x - factor(letters[1:3]) ## default ordering is alphabetic (mod locale)
 x
[1] a b c
Levels: a b c
 y - factor(x,lev=letters[3:1])  ## reorder the levels
 y
[1] a b c
Levels: c b a

-- Bert

On Fri, Feb 22, 2013 at 1:22 PM, Rich Shepard rshep...@appl-ecosys.com wrote:
 On Fri, 22 Feb 2013, Bert Gunter wrote:

 Manually change the ordering of the levels in the factor to that which you
 want (see ?factor if necessary) and replot.


 Bert,

   I'll do this.

   I looked at ?factor and will try is.ordered() to see if that makes a
 difference.

 Many thanks,

 Rich

 __
 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

Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm

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

Re: [R] R on mac not installing packages

2013-02-22 Thread Prof Brian Ripley


On 22/02/2013 21:26, David Winsemius wrote:

The system is reporting that it cannot find `make`. It appears that you have 
not installed XCode on you Mac, or that you did with an earlier version for 
which you have not updated, or something else which has broken your 
installation. Please read the MacOS FAQ. (And post further such question on the 
SIG-Mac mailing list.)


For the record, such information is in the 'R Installation and 
Administration Manual', as from R-patched (and hence R 2.15.3 and R 
3.0.0).  See e.g. 
http://cran.r-project.org/doc/manuals/r-release/R-admin.html#Mac-OS-X .


On recent versions of OS X it is not Xcode you need, but the 'Xcode 
command-line tools'.  These can be installed from inside Xcode 
(Preferences-Downloads-Components) or separately.


For Hmisc you will need a matching Fortran compiler: see that manual.


On Feb 22, 2013, at 12:15 PM, londonphd wrote:



Hi, I have not been able to use R in my macbook pro. I am getting the
following error message every time i try to install a package

* installing *source* package ‘Hmisc’ ...
** package ‘Hmisc’ successfully unpacked and MD5 sums checked
** libs
*** arch - i386
sh: make: command not found
ERROR: compilation failed for package ‘Hmisc’
* removing ‘/Users/ravshonbek/Library/R/2.15/library/Hmisc’
* installing *source* package ‘quadprog’ ...
** libs
*** arch - i386
sh: make: command not found
ERROR: compilation failed for package ‘quadprog’
* removing ‘/Users/ravshonbek/Library/R/2.15/library/quadprog’
ERROR: dependency ‘Hmisc’ is not available for package ‘its’
* removing ‘/Users/ravshonbek/Library/R/2.15/library/its’
ERROR: dependency ‘quadprog’ is not available for package ‘tseries’
* removing ‘/Users/ravshonbek/Library/R/2.15/library/tseries’

The downloaded source packages are in

‘/private/var/folders/c7/jrjv78_x6f53l3sw_w715gk0gn/T/RtmpS4sYUx/downloaded_packages’


I look forward to your help, plsease




--
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David Winsemius
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--
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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Re: [R] Controlling Order of Panels in Lattice Trellis Plots


On Feb 22, 2013, at 1:22 PM, Rich Shepard wrote:

 On Fri, 22 Feb 2013, Bert Gunter wrote:
 
 Manually change the ordering of the levels in the factor to that which you
 want (see ?factor if necessary) and replot.
 
 Bert,
 
  I'll do this.
 
  I looked at ?factor and will try is.ordered() to see if that makes a
 difference.

`is.ordered` will return TRUE if it is an ordered factor. That's not what you 
want to know and using `as.ordered` would also fail to provide the needed 
ordering. You need to provide a proper levels argument to the factor function. 
And you will find that making an ordered factor will probably have undesirable 
side effects.

-- 

David Winsemius
Alameda, CA, USA

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Re: [R] R on mac not installing packages

2013-02-22 Thread Marc Schwartz


On Feb 22, 2013, at 3:46 PM, Prof Brian Ripley rip...@stats.ox.ac.uk wrote:

 On 22/02/2013 21:26, David Winsemius wrote:
 The system is reporting that it cannot find `make`. It appears that you have 
 not installed XCode on you Mac, or that you did with an earlier version for 
 which you have not updated, or something else which has broken your 
 installation. Please read the MacOS FAQ. (And post further such question on 
 the SIG-Mac mailing list.)
 
 For the record, such information is in the 'R Installation and Administration 
 Manual', as from R-patched (and hence R 2.15.3 and R 3.0.0).  See e.g. 
 http://cran.r-project.org/doc/manuals/r-release/R-admin.html#Mac-OS-X .
 
 On recent versions of OS X it is not Xcode you need, but the 'Xcode 
 command-line tools'.  These can be installed from inside Xcode 
 (Preferences-Downloads-Components) or separately.
 
 For Hmisc you will need a matching Fortran compiler: see that manual.


It seems reasonable to ask however, why he is installing source CRAN packages 
on OSX when the default OSX install would be binaries, if he installed R by 
using Simon's OSX binary. 

If he installed R from source, he should have already had the requisite 
compiler related tools installed.

Perhaps I need more coffee late on a Friday, but something seems inconsistent 
here.

Regards,

Marc Schwartz


 
 On Feb 22, 2013, at 12:15 PM, londonphd wrote:
 
 
 Hi, I have not been able to use R in my macbook pro. I am getting the
 following error message every time i try to install a package
 
 * installing *source* package ‘Hmisc’ ...
 ** package ‘Hmisc’ successfully unpacked and MD5 sums checked
 ** libs
 *** arch - i386
 sh: make: command not found
 ERROR: compilation failed for package ‘Hmisc’
 * removing ‘/Users/ravshonbek/Library/R/2.15/library/Hmisc’
 * installing *source* package ‘quadprog’ ...
 ** libs
 *** arch - i386
 sh: make: command not found
 ERROR: compilation failed for package ‘quadprog’
 * removing ‘/Users/ravshonbek/Library/R/2.15/library/quadprog’
 ERROR: dependency ‘Hmisc’ is not available for package ‘its’
 * removing ‘/Users/ravshonbek/Library/R/2.15/library/its’
 ERROR: dependency ‘quadprog’ is not available for package ‘tseries’
 * removing ‘/Users/ravshonbek/Library/R/2.15/library/tseries’
 
 The downloaded source packages are in
 
 ‘/private/var/folders/c7/jrjv78_x6f53l3sw_w715gk0gn/T/RtmpS4sYUx/downloaded_packages’
 
 
 I look forward to your help, plsease

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[R] locating boxplot in bwplot (lattice)

2013-02-22 Thread Elaine Kuo

Hello



I am using lattice bwplot to draw migration distance of three groups of
birds.

The boxplots from the left to right is displayed

in alphabetic order of the boxplot names, as the default setting.



However, I would like the boxplots from the left to right to be displayed
according to the migration distance from the short values to the long ones.

In the data below, from the left to the right should be Gruiformes,
Falconiiformes, and Charadriiformes.



Please kindly advise how to modify the code below.

The data is as below.

Thank you.


Elaine





Code

Library(lattice)

bwplot(migration_distance~bird)





data

migration distance (km)bird group

10987  Charadriiformes

9867Charadriiformes

8702Charadriiformes

9432Charadriiformes

9054Charadriiformes

5087   Falconiiformes

5783   Falconiiformes

5298Falconiiformes

5687   Falconiiformes

3987Gruiformes

3298Gruiformes

3567Gruiformes

3409Gruiformes

3321Gruiformes

3598Gruiformes

[[alternative HTML version deleted]]

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Re: [R] locating boxplot in bwplot (lattice)

2013-02-22 Thread Ben Bolker

Elaine Kuo elaine.kuo.tw at gmail.com writes:

 
 Hello
 
 I am using lattice bwplot to draw migration distance of three groups of
 birds.
 
 The boxplots from the left to right is displayed
 in alphabetic order of the boxplot names, as the default setting.
 
 However, I would like the boxplots from the left to right to be displayed
 according to the migration distance from the short values to the long ones.
 
 In the data below, from the left to the right should be Gruiformes,
 Falconiiformes, and Charadriiformes.
 
 Please kindly advise how to modify the code below.
 

 Define the order of the levels of your factor 
accordingly. Take a look at

http://stackoverflow.com/questions/15033107/
  specifing-order-of-lattice-plot-panels

(broken URL to meet gmane line length limits)

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Re: [R] Controlling Order of Panels in Lattice Trellis Plots


On Fri, 22 Feb 2013, David Winsemius wrote:


`is.ordered` will return TRUE if it is an ordered factor. That's not what
you want to know and using `as.ordered` would also fail to provide the
needed ordering. You need to provide a proper levels argument to the
factor function. And you will find that making an ordered factor will
probably have undesirable side effects.


  Thank you, David. That was the conclusion I was approaching as I tried
is.ordered and as.ordered and saw they did not affec the needed changes.
I'll look at levels or sort the input data file before reading it into R.

Rich

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Re: [R] Controlling Order of Panels in Lattice Trellis Plots


On Fri, 22 Feb 2013, Bert Gunter wrote:


You do not need to use ordered factors.
newfac - factor(oldfac, lev= ...) ## will do it. e.g.


x - factor(letters[1:3]) ## default ordering is alphabetic (mod locale)
x

[1] a b c
Levels: a b c

y - factor(x,lev=letters[3:1])  ## reorder the levels
y

[1] a b c
Levels: c b a


Bert,

  Makes sense. I wonder if this will work when only a portion of the site
IDs need to be explicitly ordered. There are 64 sites in all. Might be
easier to sort the text file.

Thanks again,

Rich

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Re: [R] HELP!!!

2013-02-22 Thread Ben Bolker

David Winsemius dwinsemius at comcast.net writes:

 On Feb 22, 2013, at 11:02 AM, lara sowale wrote:
 
  I am sorry to bug you, I am having this error whenever I want to run
  random effects regression in software R: Error in if (sigma2$id  0)
  stop(paste(the estimated variance of the,  :
missing value where TRUE/FALSE needed.
  
  Please help me look into it.
 
 Please read the Posting Guide and after doing so repost with 
 a question that admits of some possiblity of answering.

  In case you need the URL: http://www.r-project.org/posting-guide.html

  Some google-detection (searching for if sigma2$id error)
suggests that the OP is using the ercomp package, but beyond
that the question is still (as you suggest) unanswerable.

 Ben Bolker

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[R] Issues with installing RBGL package

2013-02-22 Thread jason tyler

Hi all,

I was installing a package *RBGL* of bioconductor. However, I had some
issues while installing it. I asked the devel group of bioconductor and
they told me to consult this group. Here is my conversation with the
bioconductor group related to the problem


*Me-*
I was trying to install the RBGL package using the following command

biocLite(RBGL)

However, I got the following error
*
installing *source* package RBGL ...
untarring boost include tree...
** libs
/usr/bin/clang++ -I/usr/local/Cellar/r/2.15.1/R.framework/Resources/include
-DNDEBUG  -I/usr/local/Cellar/readline/6.2.4/include -isystem
/usr/local/include -I/usr/X11/include   -Irbgl_trimmed_boost_1_49_0 -fPIC
-Os -w -pipe -march=native -Qunused-arguments -mmacosx-version-min=10.7  -c
bbc.cpp -o bbc.o
/usr/bin/clang++ -I/usr/local/Cellar/r/2.15.1/R.framework/Resources/include
-DNDEBUG  -I/usr/local/Cellar/readline/6.2.4/include -isystem
/usr/local/include -I/usr/X11/include   -Irbgl_trimmed_boost_1_49_0 -fPIC
-Os -w -pipe -march=native -Qunused-arguments -mmacosx-version-min=10.7  -c
cliques.cpp -o cliques.o
cliques.cpp:26:31: error: redefinition of 'p' as different kind of symbol
std::pairEdge, bool p;
  ^
rbgl_trimmed_boost_1_49_0/boost/mpl/assert.hpp:149:42: note: previous
definition is here
BOOST_MPL_AUX_ASSERT_CONSTANT( bool, p = !p_type::value );
 ^
rbgl_trimmed_boost_1_49_0/boost/mpl/assert.hpp:56:58: note: expanded from
macro 'BOOST_MPL_AUX_ASSERT_CONSTANT'
#   define BOOST_MPL_AUX_ASSERT_CONSTANT(T, expr) enum { expr }
 ^
cliques.cpp:53:19: error: expression is not assignable
p = edge(*va1, *va2, g);
~ ^
cliques.cpp:54:25: error: member reference base type
'mpl_::assert_arg_pred_notboost::detail::is_iterator_traversalboost::random_access_traversal_tag::anonymous
enum at
  rbgl_trimmed_boost_1_49_0/boost/mpl/assert.hpp:149:5' is not a
structure or union
if ( !p.second ) return FALSE;*


Any suggestions how to overcome this or what is causing this issue?

*Vincent Gray(of bioconductor group) - *
please provide sessionInfo() and result of gcc -v

*Me-*
gcc -v
Using built-in specs.
Target: i686-apple-darwin11
Configured with: /private/var/tmp/llvmgcc42/llvmgcc42-2336.11~28/src/configure
--disable-checking --enable-werror --prefix=/Applications/Xcode.
app/Contents/Developer/usr/llvm-gcc-4.2 --mandir=/share/man
--enable-languages=c,objc,c++,obj-c++ --program-prefix=llvm-
--program-transform-name=/^[cg][^.-]*$/s/$/-4.2/ --with-slibdir=/usr/lib
--build=i686-apple-darwin11 --enable-llvm=/private/var/
tmp/llvmgcc42/llvmgcc42-2336.11~28/dst-llvmCore/Developer/usr/local
--program-prefix=i686-apple-darwin11- --host=x86_64-apple-darwin11
--target=i686-apple-darwin11 --with-gxx-include-dir=/usr/include/c++/4.2.1
Thread model: posix
gcc version 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00)


*sessionInfo() Results*

R version 2.15.1 (2012-06-22)
Platform: x86_64-apple-darwin11.4.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] BiocInstaller_1.8.3

loaded via a namespace (and not attached):
[1] tools_2.15.1

Thanks

Regards,
Jason

*Vincent Gray - *
OK, I didn't read your log too well, so I missed that you are using
clang++.  Theoretically it will work

http://blog.llvm.org/2010/05/clang-builds-boost.html

I am using the gcc supplied in Xcode 4.0.2, with

bash-3.2$ gcc -v
Using built-in specs.
Target: i686-apple-darwin10
Configured with: /var/tmp/gcc/gcc-5666.3~123/src/configure
--disable-checking --enable-werror --prefix=/usr --mandir=/share/man
--enable-languages=c,objc,c++,obj-c++
--program-transform-name=/^[cg][^.-]*$/s/$/-4.2/ --with-slibdir=/usr/lib
--build=i686-apple-darwin10 --program-prefix=i686-apple-darwin10-
--host=x86_64-apple-darwin10 --target=i686-apple-darwin10
--with-gxx-include-dir=/include/c++/4.2.1
Thread model: posix
gcc version 4.2.1 (Apple Inc. build 5666) (dot 3)

this has no problem installing RBGL from source.  your R is a little out of
date but I don't think that's an issue.

I have minimal experience with clang++ and you may have to take this to
R-help or R-devel if you are not going to use Xcode- based compilation, as
that's what we are basing our builds/tests on.  I did try

bash-3.2$ clang++ -v
clang version 3.2 (tags/RELEASE_32/final)
Target: x86_64-apple-darwin10.8.0
Thread model: posix
bash-3.2$ clang++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names
-undefined dynamic_lookup -single_module -multiply_defined suppress
-L/Users/stvjc/ExternalSoft/READLINE-62-DIST/lib -lreadline
-L//Users/stvjc/ExternalSoft/LIBICONV-64/lib -liconv
-L/Users/stvjc/ExternalSoft/jpeg-6b -ljpeg -o cliques.so cliques.o

Re: [R] Help xyplot

2013-02-22 Thread Peter Maclean

Hi Mackay and anybody
(a) Is it possible to select randomly (let say five grids) and plot?
(b) Is it possible to plot five nearest grid in one figure?
The original question and improved codes:


#I am ploting gridded time series data. I would like the actual lat 
#and lon value appear on the graph-if possible inside the graph as 
#numbers. If there is also more elegant ways to plot the graphs I 
#will appreciate more suggestions.
#
library(ggplot2)
library(lattice)
month - c(Jan, Feb, Mar, Apr, May, Jun, Jul,
Aug, Sep, Oct, Nov, Dec)
month - factor(month, levels = month.abb)
data - as.data.frame(expand.grid(lon=seq(4,5, 1), lat=seq(-3,-2,1),
year=seq(2010, 2012,1), month=month))
n=nrow(data)
data$prec - rgamma(n, 2, 0.25)
data$year - factor(data$year)
data$lon  - factor(data$lon)
data$lat  - factor(data$lat)
ndata - data[order(data$lon, data$lat),]
fix(ndata)
max - max(ndata$prec, na.rm=TRUE)
min - min(ndata$prec, na.rm=TRUE)

#Plot the graph and save as pdf by Mackay suggestion
pdf(H:/file.pdf)
library(latticeExtra)
useOuterStrips(
xyplot(prec~month|year*paste(lat,lon), data=ndata,
as.table = T,
type = c(l, l,p), ylim=c(min, max),
layout=c(1,4)) )
dev.off()#The actual data have more than 5 thousand data points, Just want to 
plot a few
#selected randomly. Also, if I can put 5 data points (nearest grids) in one 
graph
#will be more helpful.


Peter Maclean
Department of Economics
UDSM
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[R] Fitting this data with a gaussian would be great

2013-02-22 Thread Samantha Warnes

Hello,I'm still working with this data set, and trying to fit it with a 
nonlinear model. Here is my data
 small - 
 c(507680,507670,508832,510184,511272,513380,515828,519160,525046,534046,547982,567124,590208,614506,637876,656846,669054,672976,668800,656070,637136,614342,590970,570752,554480,542882,535630,531276,528682,527682,527020,526834,526802,526860)


test - glm(dnorm(x), data=small)
Error in formula.default(object, env = baseenv()) : invalid formula


I have tried a variety of options for the formula with the same effect. What I 
want to do with this data is simply fit it with a non linear model, most likely 
a gaussian.


Thanks in advance,
Samantha

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Re: [R] Fitting this data with a gaussian would be great

2013-02-22 Thread Ben Bolker

Samantha Warnes warnes at wisc.edu writes:

 
 Hello,I'm still working with this data set, and 
 trying to fit it with a nonlinear model. Here is my data
  small - c(507680,507670,508832,510184,511272,513380,515828,
  519160,525046,
  534046,547982,567124,590208,614506,637876,656846,669054,672976,668800,
656070,637136,614342,590970,570752,554480,542882,535630,531276,528682,
  527682,527020,526834,526802,526860)
 
 test - glm(dnorm(x), data=small)
 Error in formula.default(object, env = baseenv()) : invalid formula
 

  I'm sorry, but as stated the question doesn't make much sense.
  You haven't stated your nonlinear model at all, and you haven't
said anything about any predictor variables.
  
  If you want fit a *constant* normal model you can

1. Compute the mean and standard deviation of the data (which
are the parameters of the model): mean(small), sd(small)

2. use an intercept-only model with lm(small~1) or glm(small~1)
(although the latter is definitely overkill)

3. You *can* use a nonlinear fitting method to estimate an
intercept-only model

nls(small~a,start=list(a=564000))

but it doesn't really mean much.

  Ben Bolker

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[R] assign index to colnames(matrix)

2013-02-22 Thread Prew, Paul

Hello,  Iâm trying to follow the syntax of a script from a journal website.  
In order to create a regression formula used later in the script, the 
regression matrix must have column names âX1â, âX2â, etc.  I have tried 
to assign these column names to my matrix ScoutRSM.mat using a for loop, but I 
donât know how to interpret the error message.  Suggestions?  Thanks, Paul



== instructions about dimnames(X)[[2]] = X1,X2,...  ===


function(binstr)
{
  # makes formula for regression
  # must make sure dimnames(X)[[2]] = X1,X2,...
  ind-which(binstr==1)
  rht - paste(X, ind, sep=, collapse=+)
  ans-paste(y ~ , rht)
  return(as.formula(ans))
}


###
##  my for loop  ##
###

for (i in 1:dim(ScoutRSM.mat)[2]  {
colnames(ScoutRSM.mat)[i] - paste(X, i, sep = ââ))
}

 for(i in 1:dim(ScoutRSM.mat)[2]) {
+   colnames(ScoutRSM.mat)[i] - paste(X,i, sep = )
+ }
Error in `colnames-`(`*tmp*`, value = X1) :
  length of 'dimnames' [2] not equal to array extent


~~
  ScoutRSM.mat  ~~
~~

 dput(ScoutRSM.mat)
structure(c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, -1, 1, -1, 0, -1, 0, 0, 0, 1, 1, 0, 1, -1, 1, -1, 1, 0, -1,
-0.464, -0.516, -0.48, 1, -0.008, 0.486, 0, 0.524, -0.96, -1,
-0.526, 1, 0.47, 0.49, 0, 0.53, -0.866, -0.6, 0.227, -1, -0.895,
1.289, 0.181, 0.204, -1, 0.199, -0.908, -1, -1, 1.289, 1.289,
0.204, -1, 0.213, -0.922, -1, -0.84, -1, 0.2, -1, -1, 0.05, -1,
1.136, -0.861, -0.861, -1, 1.136, 0.193, 0.047, -1, -1, -0.733,
-1, -0.817, 0.14, -1, 1, 0.127, -0.05, 1, -1, -0.797, -0.797,
0.123, -1, -1, -0.04, 1, 1, -0.75, 0, 0.464, -0.516, 0.48, 0,
0.008, 0, 0, 0, -0.96, -1, 0, 1, -0.47, 0.49, 0, 0.53, 0, 0.6,
-0.227, -1, 0.895, 0, -0.181, 0, 0, 0, -0.908, -1, 0, 1.289,
-1.289, 0.204, 1, 0.213, 0, 1, 0.84, -1, -0.2, 0, 1, 0, 0, 0,
-0.861, -0.861, 0, 1.136, -0.193, 0.047, 1, -1, 0, 1, 0.817,
0.14, 1, 0, -0.127, 0, 0, 0, -0.797, -0.797, 0, -1, 1, -0.04,
-1, 1, 0, 0, -0.105, 0.516, 0.429, 1.289, -0.001, 0.099, 0, 0.104,
0.872, 1, 0.526, 1.289, 0.606, 0.1, 0, 0.113, 0.799, 0.6, 0.39,
0.516, -0.096, -1, 0.008, 0.025, 0, 0.596, 0.827, 0.861, 0.526,
1.136, 0.091, 0.023, 0, -0.53, 0.635, 0.6, 0.379, -0.072, 0.48,
1, -0.001, -0.024, 0, -0.524, 0.765, 0.797, -0.065, -1, -0.47,
-0.02, 0, 0.53, 0.65, 0, -0.19, 1, -0.179, -1.289, -0.181, 0.01,
1, 0.226, 0.782, 0.861, 1, 1.464, 0.249, 0.01, 1, -0.213, 0.676,
1, -0.185, -0.14, 0.895, 1.289, 0.023, -0.01, -1, -0.199, 0.724,
0.797, -0.123, -1.289, -1.289, -0.008, -1, 0.213, 0.692, 0, 0.686,
-0.14, -0.2, -1, -0.127, -0.003, -1, -1.136, 0.686, 0.686, -0.123,
-1.136, -0.193, -0.002, -1, -1, 0.55, 0, 1, 1, 1, 0, 1, 0, 0,
0, 1, 1, 0, 1, 1, 1, 1, 1, 0, 1, 0.215, 0.266, 0.23, 1, 0, 0.236,
0, 0.275, 0.922, 1, 0.277, 1, 0.221, 0.24, 0, 0.281, 0.75, 0.36,
0.051, 1, 0.801, 1.66, 0.033, 0.042, 1, 0.04, 0.825, 1, 1, 1.66,
1.66, 0.042, 1, 0.045, 0.85, 1, 0.705, 1, 0.04, 1, 1, 0.003,
1, 1.292, 0.742, 0.742, 1, 1.292, 0.037, 0.002, 1, 1, 0.537,
1, 0.667, 0.02, 1, 1, 0.016, 0.003, 1, 1, 0.635, 0.635, 0.015,
1, 1, 0.002, 1, 1, 0.563, 0, 0.105, 0.516, -0.429, 0, 0.001,
0, 0, 0, 0.872, 1, 0, 1.289, -0.606, 0.1, 0, 0.113, 0, -0.6,
-0.39, 0.516, 0.096, 0, -0.008, 0, 0, 0, 0.827, 0.861, 0, 1.136,
-0.091, 0.023, 0, -0.53, 0, -0.6, -0.379, -0.072, -0.48, 0, 0.001,
0, 0, 0, 0.765, 0.797, 0, -1, 0.47, -0.02, 0, 0.53, 0, 0, 0.19,
1, 0.179, 0, 0.181, 0, 0, 0, 0.782, 0.861, 0, 1.464, -0.249,
0.01, -1, -0.213, 0, -1, 0.185, -0.14, -0.895, 0, -0.023, 0,
0, 0, 0.724, 0.797, 0, -1.289, 1.289, -0.008, 1, 0.213, 0, 0,
-0.686, -0.14, 0.2, 0, 0.127, 0, 0, 0, 0.686, 0.686, 0, -1.136,
0.193, -0.002, 1, -1, 0, 0, 0.088, -0.516, 0.086, -1.289, 0.001,
0.005, 0, 0.119, -0.751, -0.861, -0.526, 1.464, 0.117, 0.005,
0, -0.113, -0.585, -0.6, 0.086, 0.072, -0.429, 1.289, 0, -0.005,
0, -0.104, -0.695, -0.797, 0.065, -1.289, -0.606, -0.004, 0,
0.113, -0.599, 0, -0.318, 0.072, 0.096, -1, 0.001, -0.001, 0,
-0.596, -0.659, -0.686, 0.065, -1.136, -0.091, -0.001, 0, -0.53,
-0.476, 0, 0.155, 0.14, 0.179, -1.289, -0.023, -0.001, 1, -0.226,
-0.623, -0.686, 0.123, -1.464, -0.249, 0, 1, -0.213, -0.507,
0, -0.464, -0.516, -0.48, 0, -0.008, 0, 0, 0, -0.96, -1, 0, 1,
0.47, 0.49, 0, 0.53, 0, -0.6, 0.227, -1, -0.895, 0, 0.181, 0,
0, 0, -0.908, -1, 0, 1.289, 1.289, 0.204, -1, 0.213, 0, -1, -0.84,
-1, 0.2, 0, -1, 0, 0, 0, -0.861, -0.861, 0, 1.136, 0.193, 0.047,
-1, -1, 0, -1, -0.817, 0.14, -1, 0, 0.127, 0, 0, 0, -0.797, -0.797,
0, -1, -1, -0.04, 1, 1, 0, 0, -0.215, 0.266, -0.23, 0, 0, 0,
0, 0, 0.922, 1, 0, 1, -0.221, 0.24, 0, 0.281, 0, -0.36, -0.051,
1, -0.801, 0, -0.033, 0, 0, 0, 0.825, 1, 0, 1.66, -1.66, 0.042,
-1, 0.045, 0, -1, -0.705, 1, -0.04, 0, -1, 0, 0, 0, 0.742, 0.742,
0, 1.292, -0.037, 0.002, -1, 1, 0, -1, -0.667, 0.02, -1, 0, -0.016,
0,

Re: [R] Controlling Order of Panels in Lattice Trellis Plots

As you appear not to know, or at least have not stated, **what** you
want to do, how can you expect anyone to tell you **how** to do it?

Cheers,
Bert

On Fri, Feb 22, 2013 at 2:33 PM, Rich Shepard rshep...@appl-ecosys.com wrote:
 On Fri, 22 Feb 2013, Bert Gunter wrote:

 You do not need to use ordered factors.
 newfac - factor(oldfac, lev= ...) ## will do it. e.g.

 x - factor(letters[1:3]) ## default ordering is alphabetic (mod locale)
 x

 [1] a b c
 Levels: a b c

 y - factor(x,lev=letters[3:1])  ## reorder the levels
 y

 [1] a b c
 Levels: c b a


 Bert,

   Makes sense. I wonder if this will work when only a portion of the site
 IDs need to be explicitly ordered. There are 64 sites in all. Might be
 easier to sort the text file.

 Thanks again,

 Rich

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-- 

Bert Gunter
Genentech Nonclinical Biostatistics

Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm

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Re: [R] assign index to colnames(matrix)

2013-02-22 Thread Jim Lemon


On 02/23/2013 11:34 AM, Prew, Paul wrote:

Hello,  Iâ€™m trying to follow the syntax of a script from a journal website.  
In order to create a regression formula used later in the script, the 
regression matrix must have column names â€œX1â€�, â€œX2â€�, etc.  I have tried 
to assign these column names to my matrix ScoutRSM.mat using a for loop, but I 
donâ€™t know how to interpret the error message.  Suggestions?  Thanks, Paul



== instructions about dimnames(X)[[2]] = X1,X2,...  ===


function(binstr)
{
   # makes formula for regression
   # must make sure dimnames(X)[[2]] = X1,X2,...
   ind-which(binstr==1)
   rht- paste(X, ind, sep=, collapse=+)
   ans-paste(y ~ , rht)
   return(as.formula(ans))
}


###
##  my for loop  ##
###

for (i in 1:dim(ScoutRSM.mat)[2]  {
colnames(ScoutRSM.mat)[i]- paste(X, i, sep = â€œâ€�))
}


for(i in 1:dim(ScoutRSM.mat)[2]) {

+   colnames(ScoutRSM.mat)[i]- paste(X,i, sep = )
+ }
Error in `colnames-`(`*tmp*`, value = X1) :
   length of 'dimnames' [2] not equal to array extent


Hi Paul,
You don't really need the loop, try:

colnames(ScoutRSM.mat)-paste(X,1:dim(ScoutRSM.mat)[2],sep=)

Jim

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Re: [R] R on mac not installing packages

2013-02-22 Thread londonphd

Many thanks to all who replied to this post. the problem has now been sorted
out. i installed GCC-10.7-v2.pkg, now i can install packages from source 



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[R] help with R CMD check --as-cran

2013-02-22 Thread Tao Wang

Hi Everyone!

This is my first time using R-help. I am trying to do R CMD check before 
uploading my package to CRAN.

R CMD check --as-cran my package folder.

However, it spits out this warning:

pdf is needed for checks on size reduction of PDFs

I searched online but found no clue to solve this problem. Can someone tell me 
what could be wrong with my package?

Thanks a lot!

Tao




UT Southwestern Medical Center
The future of medicine, today.

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[R] Climate Spatial plot

2013-02-22 Thread Bedassa Regassa

Dear Sir,

I am beginner in using R. I am working on climate and like to plot spatial
but I can't able to go ahead. I know it is too simply but not for me. Here
is attached the data and my sample script. I am waiting R-users to solve my
problem.  Your help is valuable for me. Thank you.


-- 
---
*Bedassa Regassa Cheneka*
*Adama Science and Technology Univesity*
*Natural Resource Management*
*P.O.BOX---193*
*Assela *
Ethiopia
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Re: [R] help with R CMD check --as-cran

2013-02-22 Thread Joshua Wiley

Hi Tao,

I wonder if you are on Windows?  If so, make sure you have qpdf
installed, and the location is in your path.

Cheers,

Josh

On Fri, Feb 22, 2013 at 3:32 PM, Tao Wang tao.w...@utsouthwestern.edu wrote:
 Hi Everyone!

 This is my first time using R-help. I am trying to do R CMD check before 
 uploading my package to CRAN.

 R CMD check --as-cran my package folder.

 However, it spits out this warning:

 pdf is needed for checks on size reduction of PDFs

 I searched online but found no clue to solve this problem. Can someone tell 
 me what could be wrong with my package?

 Thanks a lot!

 Tao


 

 UT Southwestern Medical Center
 The future of medicine, today.

 [[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.



--
Joshua Wiley
Ph.D. Student, Health Psychology
Programmer Analyst II, Statistical Consulting Group
University of California, Los Angeles
https://joshuawiley.com/

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Re: [R] help with R CMD check --as-cran


On Feb 22, 2013, at 5:52 PM, Joshua Wiley wrote:

 Hi Tao,
 
 I wonder if you are on Windows?  If so, make sure you have qpdf
 installed, and the location is in your path.
 
 Cheers,
 
 Josh
 
 On Fri, Feb 22, 2013 at 3:32 PM, Tao Wang tao.w...@utsouthwestern.edu wrote:
 Hi Everyone!
 
 This is my first time using R-help. I am trying to do R CMD check before 
 uploading my package to CRAN.
 
 R CMD check --as-cran my package folder.
 
 However, it spits out this warning:
 
 pdf is needed for checks on size reduction of PDFs
 
 I searched online but found no clue to solve this problem. Can someone tell 
 me what could be wrong with my package?


I believe this was crossposted to StackOverflow where the questioner has later 
reported figuring out that warning was inaccurate but harmless.

-- 
David Winsemius
Alameda, CA, USA

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[R] Issue with matrices within nested for-loops

2013-02-22 Thread Jonathan Richar

Greetings!

I am trying to compare simulated environmental conditions from a model
against a recruitment time series for a species of crab by first dropping 5
data points, and then using the remainder to attempt to simulate the
missing data as a measure of best fit and using the following code:


all.mat-as.matrix(comb,ncol=ncol(comb),nrow=nrow(comb))
obs-as.matrix(R2,24,1)
mod-all.mat

results-numeric(ncol(mod))


for(i in mod) {
x-mod[,i]
resid - matrix(NA, 1000, 5)
for(k in 1:1000) {
sub-sample(1:24,19)
fit-lm(obs~x,subset=sub)
cf-coef(fit)
p - cf[1] + cf[2] * x[-sub]
resid[k,] - obs[-sub] - p
}
results[i] - mean(resid^2)
}


where* R2* is a 24x1 matrix with recruitment data, *comb* was a cbind()
object combining two matrices and *all.mat* is the final 565x24 matrix of
modeled environmental scenarios. When the script is run the first 99
scenarios are processed properly and I get readable output. At scenario 100
however, I get this message:

*Error in na.omit.data.frame(list(obs = c(0.414153096303487,
1.39649463342491,  : subscript out of bounds*

Which I understand to mean that the bounds of the indicated vector/matrix
have been violated. I am however at a loss as to how to resolve this. Any
advice would be appreciated

Cheers!

JR

-- 

Jonathan Richar
Doctoral candidate
UAF SFOS Fisheries Division
17101 Pt. Lena Loop Rd.
University of Alaska Fairbanks
Juneau, AK 99801
Phone: (907) 796-5459

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Re: [R] assign index to colnames(matrix)

2013-02-22 Thread Prew, Paul

Jim, thank you, that worked great.

Paul Prew  |  Statistician
651-795-5942   |   fax 651-204-7504 
Ecolab Research Center  | Mail Stop ESC-F4412-A 
655 Lone Oak Drive  |  Eagan, MN 55121-1560 

-Original Message-
From: Jim Lemon [mailto:j...@bitwrit.com.au] 
Sent: Friday, February 22, 2013 7:22 PM
To: Prew, Paul
Cc: r-help@r-project.org
Subject: Re: [R] assign index to colnames(matrix)

On 02/23/2013 11:34 AM, Prew, Paul wrote:
 Hello,  Iâ€™m trying to follow the syntax of a script from a journal 
 website.  In order to create a regression formula used later in the 
 script, the regression matrix must have column names â€œX1â€, 
 â€œX2â€, etc.  I have tried to assign these column names to my matrix 
 ScoutRSM.mat using a for loop, but I donâ€™t know how to interpret the 
 error message.  Suggestions?  Thanks, Paul


 
 == instructions about dimnames(X)[[2]] = X1,X2,...  === 
 

 function(binstr)
 {
# makes formula for regression
# must make sure dimnames(X)[[2]] = X1,X2,...
ind-which(binstr==1)
rht- paste(X, ind, sep=, collapse=+)
ans-paste(y ~ , rht)
return(as.formula(ans))
 }


 ###
 ##  my for loop  ## 
 ###

 for (i in 1:dim(ScoutRSM.mat)[2]  {
 colnames(ScoutRSM.mat)[i]- paste(X, i, sep = â€œâ€)) }

 for(i in 1:dim(ScoutRSM.mat)[2]) {
 +   colnames(ScoutRSM.mat)[i]- paste(X,i, sep = ) }
 Error in `colnames-`(`*tmp*`, value = X1) :
length of 'dimnames' [2] not equal to array extent

Hi Paul,
You don't really need the loop, try:

colnames(ScoutRSM.mat)-paste(X,1:dim(ScoutRSM.mat)[2],sep=)

Jim

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Re: [R] package ReadImages

2013-02-22 Thread John

Petr,

Another program that may be useful is ImageJ which has a great many
useful analytic plugins.  The program is written in Java and it
supports a good many different image file formats.  You should also be
able to use Octave to normalize an image.

JWDougherty

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Re: [R] Issue with matrices within nested for-loops