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t.test in a loop

1 message · Pushpike J Thilakarathne

Original
Pushpike J Thilakarathne
# 
Hi, can u send a sample data set then I can setup it out.

Pushpike.

________________________________________________________________

O. Pushpike J. Thilakarathne, 
L-BioStat, Catholic University of Leuven.
U.Z. Sint-Rafa?l (2nd Floor)
Kapucijnenvoer 35,   
B-3000 Leuven,            
BELGIUM.
Tel : + 32 (0) 16 33 68 87  
Fax: + 32 (0) 16 33 70 15  
URL [L-BioStat] : http://med.kuleuven.be/biostat/


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Today's Topics:

   1. t.test in a loop (Michael Pearmain)
   2. Re: evaluation revisited (Wacek Kusnierczyk)
   3. Re: evaluation revisited (Wacek Kusnierczyk)
   4. Re: t.test in a loop (Thomas Lumley)
   5. Re: for/if loop (Zhou Fang)
   6. putting match.call to good use (Harald Eikrem)
   7. Re: for/if loop (jim holtman)
   8. Re: evaluation revisited (Gabor Grothendieck)
   9. Re: evaluation revisited (Wacek Kusnierczyk)
  10. Character SNP data to binary MAF data (Hadassa Brunschwig)
  11. initial value in 'vmmin' is not finite (June Wong)
  12. putting match.call to good use (Harald Eikrem)
  13. Re: Mystery Error in midnightStandard (Ted Byers)
  14. Re: initial value in 'vmmin' is not finite (Prof Brian Ripley)
  15. plot slideshow (diego Diego)
  16. Re: Re : Need help on running Heckman Correction Estimation
      using R (Arne Henningsen)
  17. StepAIC with coxph (Michele Santacatterina)
  18. Merge two vectors into one. (patricia garc?a gonz?lez)
  19. Re: putting match.call to good use (Prof Brian Ripley)
  20. Re: Merge two vectors into one. (G?bor Cs?rdi)
  21. Re: Merge two vectors into one. (Dimitris Rizopoulos)
  22. Re: Merge two vectors into one. (patricia garc?a gonz?lez)
  23. Re: plot slideshow (stephen sefick)
  24. Re: Mystery Error in midnightStandard (Yohan Chalabi)
  25. Re: putting match.call to good use (Peter Dalgaard)
  26. Re: plot slideshow (David Winsemius)
  27. Re: putting match.call to good use (Dieter Menne)
  28. Re: OT: Adding verbatim R code text into LaTeX documents:
      texttt; verb or url? (JLucke at ria.buffalo.edu)
  29. Re: putting match.call to good use (Prof Brian Ripley)
  30. Grouping problem (venkata kirankumar)
  31. help with plot layout (mauede at alice.it)
  32. Newbie question about "grouping" (Rixon, John C.)
  33. Logical subset of the columns in a dataframe (Mark Na)
  34. Re: Grouping problem (David Winsemius)
  35. Re: Grouping problem (hadley wickham)
  36. Re: Newbie question about "grouping" (David Winsemius)
  37. Re: Newbie question about "grouping" (Thomas Lumley)
  38. Re: Newbie question about "grouping" (hadley wickham)
  39. Re: Logical subset of the columns in a dataframe
      (Prof Brian Ripley)
  40. Re: Mystery Error in midnightStandard (Ted Byers)
  41. Re: Logical subset of the columns in a dataframe (David Winsemius)
  42. Re: Mystery Error in midnightStandard (Yohan Chalabi)
  43. constrainOptim (June Wong)
  44. Re: constrainOptim (Ravi Varadhan)
  45. repeated measures design for GAM? (Strubbe Diederik)
  46. Repeated measures design for GAM? - corrected question...
      (Strubbe Diederik)
  47. Sweave problem with greek text (constantine)
  48. Re: StepAIC with coxph (Ravi Varadhan)
  49. Re: Repeated measures design for GAM? - corrected question...
      (Simon Wood)
  50. gls prediction using the correlation structure in nlme (Dr Carbon)
  51. [R-pkgs] AdMit version 1-01.01 (ARDIA David)
  52. Re: help with plot layout (Greg Snow)
  53. stack data sets (Nidhi Kohli)
  54. stack data sets (Nidhi Kohli)
  55. Re: constrainOptim (Ben Bolker)
  56. Saving plot into file without showing it (julien cuisinier)
  57. Get median of each column (Frank Zhang)
  58. R compilation (Attiglah, Mama)
  59. Re: Get median of each column (jim holtman)
  60. Re: Saving plot into file without showing it (jim holtman)
  61. Re: Get median of each column (Stephan Kolassa)
  62. Re: Saving plot into file without showing it (Stephan Kolassa)
  63. Re: Repeated measures design for GAM? - corrected question...
      (Strubbe Diederik)
  64. Re: Get median of each column (Rolf Turner)
  65. Re: Power analysis for MANOVA? (Stephan Kolassa)
  66. Re: Get median of each column (Stephan Kolassa)
  67. Neighborhood distance calculator (Kumudan)
  68. Cor(df,method = "kendall") (glenn)
  69. Re: R compilation (stephen sefick)
  70. Re: Neighborhood distance calculator (roger koenker)
  71.  Newbie Question About Histograms (pfc_ivan)
  72.  Help with normal distribution in random samples...
      (Sea Captain 1779)
  73.  Text data (Alice Lin)
  74. Re: Newbie Question About Histograms (Peter Alspach)
  75. Changing histogram stack in qplot (Jason Rupert)
  76. Re: Neighborhood distance calculator (Antonio, Fabio Di Narzo)
  77. Re: Text data (jim holtman)
  78. Re: Help with normal distribution in random samples...
      (Mike Lawrence)
  79. Re: Text data (Nutter, Benjamin)
  80. Re: Help with normal distribution in random samples...
      (Nordlund, Dan (DSHS/RDA))
  81. Re: Changing histogram stack in qplot (hadley wickham)
  82. Re: Memory issue? (Ubuntu Diego)
  83. Re: Newbie Question About Histograms (pfc_ivan)
  84. Re: rproxy.dll (Cl?ment D)
  85. Re: for/if loop (SnowManPaddington)
  86. Re: Newbie Question About Histograms (Eik Vettorazzi)
  87. Re: Using R in a web application (Gad Abraham)
  88. Re: Changing histogram stack in qplot (Jason Rupert)
  89.  Dynamic random effects model (Joseph Magagnoli)
  90. Re: [SPAM] - Re:  for/if loop - Bayesian Filter detected spam
      (davidr at rhotrading.com)
  91. questions about histogram (Wenxia Li)
  92. Re: [SPAM] - Re: for/if loop - Bayesian Filter detected spam
      (Henrik Bengtsson)
  93. Re: questions about histogram (jim holtman)
  94. Re: questions about histogram (Wenxia Li)
  95. Re: questions about histogram (Jorge Ivan Velez)
  96. Re: glm binomial loglog (NOT cloglog) link (Jorge Ivan Velez)
  97. Re: Faced Problems with RODBC package 1.2-5 and 1.2-4 for
      windows (Mark Wardle)
  98. Re: using Sweave with a master file that has several iputted
      .tex files (cameron.bracken)
  99.  standard error of logit parameters (Bomee Park)
  100.  Ignore text when reading data (beyar)
  101. Re: Ignore text when reading data (Remko Duursma)
  102. Re: Ignore text when reading data (Remko Duursma)
  103. Re: Ignore text when reading data (jim holtman)
  104. Re: Ignore text when reading data (beyar)
  105. Question about collapse/aggregate and avoidance of loops
      (Weiss, Bernd )
  106. Re :   standard error of logit parameters (justin bem)
  107. Re: t.test in a loop (Petr PIKAL)
  108. Re: Re :   standard error of logit parameters
      (markleeds at verizon.net)
  109. Odp: Question about collapse/aggregate and avoidance of
      loops (Petr PIKAL)
  110. Odp:  stack data sets (Petr PIKAL)
  111. Re: Character SNP data to binary MAF data (Hadassa Brunschwig)
  112. Re: Odp: Question about collapse/aggregate and avoidance of
      loops (Bernd Weiss)
  113. Re: Character SNP data to binary MAF data (Barry Rowlingson)
  114. Re: Character SNP data to binary MAF data (Thomas Lumley)
  115. Re: Character SNP data to binary MAF data (Patrick Aboyoun)
  116. Re: Question about collapse/aggregate and avoidance of loops
      (Patrick Burns)
  117. Re: Character SNP data to binary MAF data (Barry Rowlingson)
  118. Multiple tables (Gerit Offermann)
  119.  Text in a character vector to indicate "ifelse" argument
      (joe1985)
  120. Re: help with plot layout (Jim Lemon)
  121. Re: convergence problem gamm / lme (geert aarts)
  122. Odp: Text in a character vector to indicate "ifelse"
      argument (Petr PIKAL)
  123. Graphic device & graphics primitives (Sigbert Klinke)


----------------------------------------------------------------------

Message: 1
Date: Wed, 28 Jan 2009 11:25:22 +0000
From: Michael Pearmain <mpearmain at google.com>
Subject: [R] t.test in a loop
To: r-help at r-project.org
Message-ID:
	<2763e000901280325y4c8801dctc02a0aa48a9d45b6 at mail.gmail.com>
Content-Type: text/plain

Hi All,
I've been having a little trouble with creating a loop that will run a a
series of t.tests for inspection,
Below is the code i've tried, and some checks i've looked at.

I've used the get(paste()) idea as i was told previously that the use of the
eval should try and be avoided.


I've run a single syntax to check that my systax is correct and works
without any problems
Can anyone offer any advice?

Many thanks

Mike
num [1:9913] 0 0 0 0 0 0 0 0 0 0 ...
Min. 1st Qu.  Median    Mean 3rd Qu.    Max.
 0.0000  0.0000  0.0000  0.2368  0.0000  1.0000
[1] "News"              "Entertainment"     "Communicate"
 [4] "Lifestyle"         "Games"             "Music"
 [7] "Money"             "Celebrity"         "Shopping"
[10] "Sport"             "Film"              "Travel"
[13] "Cars"              "Property"          "Chat"
[16] "Bet.Play.Win"      "config"            "exposed"
[19] "site"              "referrer"          "started"
[22] "last_viewed"       "num_views"         "secs_since_viewed"
[25] "register"          "secs.na"           "power"
[28] "tt"
+
t.test(get(paste("channel.data.train$",i,"~channel.data.train$power",sep="")))
+ }
Error in get(paste("channel.data.train$", i, "~channel.data.train$power",
 :
  variable "channel.data.train$News~channel.data.train$power" was not found



-- 
Michael Pearmain
Senior Analytics Research Specialist


Google UK Ltd
Belgrave House
76 Buckingham Palace Road
London SW1W 9TQ
United Kingdom
t +44 (0) 2032191684
mpearmain at google.com

If you received this communication by mistake, please don't forward it to
anyone else (it may contain confidential or privileged information), please
erase all copies of it, including all attachments, and please let the sender
know it went to the wrong person. Thanks.




------------------------------

Message: 2
Date: Wed, 28 Jan 2009 12:26:53 +0100
From: Wacek Kusnierczyk <Waclaw.Marcin.Kusnierczyk at idi.ntnu.no>
Subject: Re: [R] evaluation revisited
To: Gabor Grothendieck <ggrothendieck at gmail.com>
Cc: r-help at r-project.org
Message-ID: <498040FD.1010506 at idi.ntnu.no>
Content-Type: text/plain; charset=ISO-8859-1
Gabor Grothendieck wrote:
really?  eval.parent is just a regular r function, a wrapper for eval
with envir=parent.frame().  the arguments to eval.parent are passed to
eval *unevaluated* (as promises), and are only evaluated when eval needs
them.  here's a modified eval.parent:

my.eval.parent = function(expr, n=1) {
    print('foo')
    p = parent.frame(n+1)
    eval(expr, p) }

my.eval.parent({print(1); 2})
# prints 'foo' before printing 1 and returning 2
well, when you are in the debugger and look at the value of the
arguments you actually force the promises, so no wonder you see them
evaluated.  if you don't look at them, they're not evaluated:

trace(eval)
trace(parent.frame)
eval.parent({print(1);2})
# calling parent.frame
# calling eval
# printing 1 (after parent.frame and eval have been called)
# returning 2

vQ



------------------------------

Message: 3
Date: Wed, 28 Jan 2009 12:35:03 +0100
From: Wacek Kusnierczyk <Waclaw.Marcin.Kusnierczyk at idi.ntnu.no>
Subject: Re: [R] evaluation revisited
To: Gabor Grothendieck <ggrothendieck at gmail.com>
Cc: R help <R-help at stat.math.ethz.ch>
Message-ID: <498042E7.9050600 at idi.ntnu.no>
Content-Type: text/plain; charset=ISO-8859-1
Wacek Kusnierczyk wrote:
to be strict, the argument n to eval.parent is not further passed to
eval, and is evaluated before eval is called.  the above referred to the
'expr' argument to eval.parent.  one more example:

my.eval.parent = function(expr, n=1) {
    print('foo')
    p = parent.frame(n+1)
    eval(expr, p) }
trace(eval)
my.eval.parent({print('expr'); 1}, {print('n'); 1})
# "foo"
# "n"
# trace eval(expr, p)
# "expr"
# 1


vQ



------------------------------

Message: 4
Date: Wed, 28 Jan 2009 03:57:55 -0800 (PST)
From: Thomas Lumley <tlumley at u.washington.edu>
Subject: Re: [R] t.test in a loop
To: Michael Pearmain <mpearmain at google.com>
Cc: r-help at r-project.org
Message-ID:
	<Pine.LNX.4.43.0901280357550.12037 at hymn14.u.washington.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
On Wed, 28 Jan 2009, Michael Pearmain wrote:

            

      
      
      
    

        
There's the additional problem that if your code worked it would do 16 t-tests but only report the last one.

Assuming you want them printed

for(v in names(channel.data.train)[1:16]) {
   print(v)
   print(t.test(channel.data.train[[v]]~channel.data.train$power)
}

or
for(v in names(channel.data.train)[1:16]){
   test <- eval(bquote(.(v)~power, data=channel.data.train)
   print(eval(test))
}

This sort of use of eval is fairly harmless.

        -thomas

            

      
      
      
    

        

      
      
    

        
Thomas Lumley			Assoc. Professor, Biostatistics
tlumley at u.washington.edu	University of Washington, Seattle



------------------------------

Message: 5
Date: Wed, 28 Jan 2009 12:07:40 +0000
From: Zhou Fang <zhou.zfang at gmail.com>
Subject: Re: [R] for/if loop
To: r-help at r-project.org
Message-ID: <49804A8C.1030807 at gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

What are you trying to do with
 > for (pp in 1:pp+1){
?

Also, note that 1:rr+1 and 1:(rr+1) mean different things.

Zhou



------------------------------

Message: 6
Date: Wed, 28 Jan 2009 13:34:55 +0100
From: "Harald Eikrem" <heikrem at c2i.net>
Subject: [R] putting match.call to good use
To: r-help at r-project.org
Message-ID: <web-124267531 at mailbe01.swip.net>
Content-Type: text/plain; charset="iso-8859-15"



------------------------------

Message: 7
Date: Wed, 28 Jan 2009 07:36:52 -0500
From: jim holtman <jholtman at gmail.com>
Subject: Re: [R] for/if loop
To: SnowManPaddington <wiwiana at gmail.com>
Cc: r-help at r-project.org
Message-ID:
	<644e1f320901280436w24c9f77chc9aeae47aeff5f4a at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Within the loops you are changing the loop variables (pp & rr).  Why
are you doing this?  THis might be causing your problem of what sounds
like an infinite loop.  You probably want to rethink what you are
trying to do in the loop.

        
On Wed, Jan 28, 2009 at 3:21 AM, SnowManPaddington <wiwiana at gmail.com> wrote:

            

      
      
      
    

        

      
      
    

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

What is the problem that you are trying to solve?



------------------------------

Message: 8
Date: Wed, 28 Jan 2009 08:04:03 -0500
From: Gabor Grothendieck <ggrothendieck at gmail.com>
Subject: Re: [R] evaluation revisited
To: Wacek Kusnierczyk <Waclaw.Marcin.Kusnierczyk at idi.ntnu.no>
Cc: r-help at r-project.org
Message-ID:
	<971536df0901280504pf93398fjbbc2153eed8f3264 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

On Wed, Jan 28, 2009 at 6:26 AM, Wacek Kusnierczyk

        
<Waclaw.Marcin.Kusnierczyk at idi.ntnu.no> wrote:

            

      
      
      
    

        
Yes, you're right about the mechanism although quoting the
help page its nevertheless true that it:
"evaluates its first argument in the current scope before
passing it to the evaluator"



------------------------------

Message: 9
Date: Wed, 28 Jan 2009 14:29:02 +0100
From: Wacek Kusnierczyk <Waclaw.Marcin.Kusnierczyk at idi.ntnu.no>
Subject: Re: [R] evaluation revisited
To: Gabor Grothendieck <ggrothendieck at gmail.com>
Cc: r-help at r-project.org
Message-ID: <49805D9E.9000901 at idi.ntnu.no>
Content-Type: text/plain; charset=ISO-8859-1

        
Gabor Grothendieck wrote:

            

      
      
      
    

        
... where 'current scope' is as clear as the sky over trondheim right
now [1], the issue being:

- is 'current scope' the scope in which eval (the above quote refers to
eval) is called (as it seems to be meant), or
- the scope *within* the call to eval (which would be intuitively
obvious, since when eval 'evaluates' it must have already been entered
and not yet left, so we're inside the eval-call scope).

another example of how quoting an r help page helps provided you already
know the answer. 
must admit that 'eval evaluates its argument before passing it to the
evaluator' is quite funny a quote;  so eval is able to evaluate without
an evaluator?  magic!

*what* is it that is true, quoting the help page?

vQ






[1]
http://www.yr.no/place/Norway/S%C3%B8r-Tr%C3%B8ndelag/Trondheim/Trondheim/



------------------------------

Message: 10
Date: Wed, 28 Jan 2009 15:36:03 +0200
From: Hadassa Brunschwig <hadassa.brunschwig at mail.huji.ac.il>
Subject: [R] Character SNP data to binary MAF data
To: r-help at r-project.org
Message-ID:
	<db80b30d0901280536v610e265w105cd60a133b03ef at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi

I am sure there is a function out there already but I couldn't find it.
I have SNP data, that is, a matrix which contains in each row two
characters (they are different in each row) and I would like to
convert this matrix to a binary one according to the minor allele
frequency. For non-geneticists: I want to have a binary matrix
for which in each row the 0 stands for the less frequent character
and 1 for the more frequent character.

Thanks for any suggestions.
Hadassa

-- 
Hadassa Brunschwig
PhD Student
Department of Statistics
The Hebrew University of Jerusalem
http://www.stat.huji.ac.il



------------------------------

Message: 11
Date: Wed, 28 Jan 2009 14:15:20 +0000
From: June Wong <neptune545 at hotmail.com>
Subject: [R] initial value in 'vmmin' is not finite
To: <r-help at r-project.org>
Message-ID: <BAY136-W36F4FAD45683269D9C3DBC8AC80 at phx.gbl>
Content-Type: text/plain


Dear r helpers

I run the following code for nested logit and got a message that 

Error in optim(c(0, 0, 0, 0, 0.1, -2, -0.2), fr, hessian = TRUE, method = "BFGS") :   initial value in 'vmmin' is not finite
What does this mean? and how can I correct it?

Thank you
June

            

      
      
      
    

        
4])+(pr4*yogurt[,4])+ lsum = log(likelihood)+ return(-colSums(lsum))+ }> p = optim(c(0,0,0,0,0.1,-2,-0.2),fr, hessian = TRUE, method = "BFGS")Error in optim(c(0, 0, 0, 0, 0.1, -2, -0.2), fr, hessian = TRUE, method = "BFGS") :   initial value in 'vmmin' is not finite

_________________________________________________________________






------------------------------

Message: 12
Date: Wed, 28 Jan 2009 15:29:44 +0100
From: Harald Eikrem <heikrem at c2i.net>
Subject: [R] putting match.call to good use
To: r-help at r-project.org
Message-ID: <49806BD8.1090804 at c2i.net>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

( I just became aware the mailer enforces html bodies, as such removed 
by the list handler.  Sorry about that.  My message was )

I have this function

slm <- function(fun=lm, ...) {
   #ilm <- eval(match.call()[-1]);  # no way
   ilm <- eval(parse(text=sub("^list", deparse(substitute(fun)), 
deparse(substitute(...())))));
   ...

The latter actually does the trick, but recognising how some gurus hate 
parse, I would like to know if this can anyhow be done with match.call, 
or any other reasonable solution.

The issue here is that lm (and likewise glm, bayesglm, etc.) returns the 
function call, which needs to show up as the original args to slm of course.

   ~~harald e



------------------------------

Message: 13
Date: Wed, 28 Jan 2009 09:30:58 -0500
From: Ted Byers <r.ted.byers at gmail.com>
Subject: Re: [R] Mystery Error in midnightStandard
To: Yohan Chalabi <chalabi at phys.ethz.ch>
Cc: R-help Forum <r-help at r-project.org>
Message-ID:
	<4f1819890901280630l24b48a9ah66273c6425620fad at mail.gmail.com>
Content-Type: text/plain

Hi Yohan,  Thanks.

        
On Wed, Jan 28, 2009 at 4:57 AM, Yohan Chalabi <chalabi at phys.ethz.ch> wrote:

        

            

      
      
      
    

        
It is certain that all entries have the same format, but I'm starting to
think that the error message is something of a red herring.  Consider this:

            

      
      
      
    

        
[1] "2009-0-3"

            

      
      
      
    

        
GMT
[1] [NA]

            

      
      
      
    

        
[1] "2009-0-4"

            

      
      
      
    

        
GMT
[1] [2009-01-01]

            

      
      
      
    

        
[1] "2009-0-3"

            

      
      
      
    

        
GMT
[1] [NA]

            

      
      
      
    

        
Error in midnightStandard(charvec, format) :
  'charvec' has non-NA entries of different number of characters
In addition: Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf



The first values for year, week and day are the values on which my loop
dies.  It returns 'NA' here.  It seems clear that it is returning NA because
the date that data corresponds to is 2008-12-31.

The error is being produced by difftimeDate rather than timeDate (as shown
by the above session).  But that represents a flaw in the function design.
It should fail when taking the elapsed time between a null and the present,
but if I wrote such a function, I'd have it return null (perhaps with a
warning) rather than just die.

A bigger issue is that timeDate ought never give null here (which is what I
assume 'NA' means), since all the data comes from transaction data with real
dates, so the elapsed time, measured in weeks, ought to always be a valid
real number that is positive semidefinite.  I have not yet come to any
conclusions as to how it ought to behave (whether to return new years day,
along with a warning, or to return the date requested by reinvoking itself
with the year and week adjusted so a valid date is returned).

On a practical side, how would I test date2 to see if it is null, so I can
give it a sensible default value?

A more troubling thought is that with this handling of dates in this
combination of SQL (my group by clause uses
YEAR(transaction_date),WEEK(transaction_date)) to get the data and R to
process it, the week containing new years day will ALWAYS be split in two at
the first second of the new year. I'm going to have to either figure out a
way to correct this, or ignore it (as it doesn't actually make things wrong,
but rather it splits a sample into two unequal parts).

Thoughts?

Thanks

Ted




------------------------------

Message: 14
Date: Wed, 28 Jan 2009 14:35:11 +0000 (GMT)
From: Prof Brian Ripley <ripley at stats.ox.ac.uk>
Subject: Re: [R] initial value in 'vmmin' is not finite
To: June Wong <neptune545 at hotmail.com>
Cc: r-help at r-project.org
Message-ID: <alpine.OSX.1.00.0901281432210.97827 at tystie.local>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed

        
On Wed, 28 Jan 2009, June Wong wrote:

        

            

      
      
      
    

        
It means that your function at your starting values is evaluating to a 
non-finite value (+/-Inf, NA, NaN).

Your example is unreadable, and we don't have the file so cannot help 
you debug this.

            

      
      
      
    

        
,!

            

      
      
      
    

        

      
      
    

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



------------------------------

Message: 15
Date: Wed, 28 Jan 2009 11:44:31 -0300
From: diego Diego <dhabbyc at gmail.com>
Subject: [R] plot slideshow
To: r-help at r-project.org
Message-ID:
	<e76ec2580901280644q24a8fe9cm2fdd3b919996f413 at mail.gmail.com>
Content-Type: text/plain

Dear R experts:
 I've seen that it's possible to make a sort of "slideshow" with several
R-plots (each slide is activated by a click on the mouse). How can I put
this on a R-script???


Regards.

D.




------------------------------

Message: 16
Date: Wed, 28 Jan 2009 09:48:06 -0500
From: Arne Henningsen <arne.henningsen at googlemail.com>
Subject: Re: [R] Re : Need help on running Heckman Correction
	Estimation	using R
To: r-help at r-project.org, justin bem <justin_bem at yahoo.fr>,	Kishore
	<gladikishore at gmail.com>
Cc: Ott Toomet <ott.toomet at ut.ee>
Message-ID: <200901280948.06591.arne.henningsen at googlemail.com>
Content-Type: text/plain;  charset="iso-8859-15"

Hi Kishore and Justin,

The sample selection stuff has been separated from the micEcon package about 
one year ago. It is available in the sampleSelection package [1,2,3] now. The 
sample selection package is thoroughly described in a (freely available) paper 
published in the Journal of Statistical Software [4]. We recommend using the 
"selection" command rather than the "heckit" command, because the former can 
be used to estimate the model not only by the two-step method but also by ML.

[1] http://www.sampleselection.org/
[2] http://r-forge.r-project.org/projects/sampleselection/
[3] http://cran.r-project.org/web/packages/sampleSelection/index.html
[4] http://www.jstatsoft.org/v27/i07

Best wishes,
Arne

        
On Tuesday 27 January 2009 06:02:46, justin bem wrote:

            

      
      
      
    

        

      
      
    

        
-- 
Arne Henningsen
http://www.arne-henningsen.name/



------------------------------

Message: 17
Date: Wed, 28 Jan 2009 15:50:11 +0100
From: Michele Santacatterina <miksanta at gmail.com>
Subject: [R] StepAIC with coxph
To: R-help at r-project.org
Message-ID:
	<1f0555cf0901280650q4dae0443mca01c02e6d4c0582 at mail.gmail.com>
Content-Type: text/plain

Hi,

i'm trying to apply StepAIC with coxph...but i have the same error:

stepAIC(fitBMT)
Start:  AIC=327.77
Surv(TEMPO,morto==1) ? VOD + SESSO + ETA + ........

Error in dropterm.default(fit,scope$drop, scale=scale,trace=max(0,  :
number of rows in use has changed: remove missing values?

anybody know this error??

Thanks.

Michele




------------------------------

Message: 18
Date: Wed, 28 Jan 2009 14:54:19 +0000
From: patricia garc?a gonz?lez <kurtney_84 at hotmail.com>
Subject: [R] Merge two vectors into one.
To: <r-help at r-project.org>
Message-ID: <BAY106-W17030B9E71F42E0796554CF6C80 at phx.gbl>
Content-Type: text/plain


Hi all, 

I have two vectors like this:


      x <- c( "Y", "H", NA,  NA )

    y <- c( NA,  "H", NA,  "B" )

And would like to make one vector with the common elements, and the element available only in one of the vectors.


      res <- c( "Y",  "H", NA,  "B" )


Thanks, 

Patricia

            

      
      
      
    

        
[,!

            

      
      
      
    

        

      
      
    

        
_________________________________________________________________





------------------------------

Message: 19
Date: Wed, 28 Jan 2009 15:00:42 +0000 (GMT)
From: Prof Brian Ripley <ripley at stats.ox.ac.uk>
Subject: Re: [R] putting match.call to good use
To: Harald Eikrem <heikrem at c2i.net>
Cc: r-help at r-project.org
Message-ID: <alpine.OSX.1.00.0901281452150.97868 at tystie.local>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed

        
On Wed, 28 Jan 2009, Harald Eikrem wrote:

        

            

      
      
      
    

        
The way to do this is eval(substitute()).  E.g. from the new Rd2HTML

         Rd <- eval(substitute(parse_Rd(f, encoding = enc),
                              list(f = Rd,enc = 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



------------------------------

Message: 20
Date: Wed, 28 Jan 2009 16:01:11 +0100
From: G?bor Cs?rdi <csardi at rmki.kfki.hu>
Subject: Re: [R] Merge two vectors into one.
To: patricia garc?a gonz?lez <kurtney_84 at hotmail.com>
Cc: r-help at r-project.org
Message-ID:
	<d70c15d40901280701t7ab41b20rf14de15ef41105e8 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Is position important? The vectors always have the same length? They
always have the same entry if both are not NA?

If yes, yes and yes, then

res <- ifelse( is.na(x), y, x)

does what you want. Otherwise please explain better what you want.

Gabor

On Wed, Jan 28, 2009 at 3:54 PM, patricia garc?a gonz?lez

        
<kurtney_84 at hotmail.com> wrote:

            

      
      
      
    

        
-- 
Gabor Csardi <Gabor.Csardi at unil.ch>     UNIL DGM



------------------------------

Message: 21
Date: Wed, 28 Jan 2009 16:01:08 +0100
From: Dimitris Rizopoulos <d.rizopoulos at erasmusmc.nl>
Subject: Re: [R] Merge two vectors into one.
To: patricia garc?a gonz?lez  <kurtney_84 at hotmail.com>
Cc: r-help at r-project.org
Message-ID: <49807334.2070501 at erasmusmc.nl>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

you could start by something like the following:

x <- c("Y", "H", NA, NA)
y <- c(NA, "H", NA, "B")

ifelse(is.na(x), y, x)


I hope it helps.

Best,
Dimitris

        
patricia garc?a gonz?lez wrote:

            

      
      
      
    

        
!

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        
-- 
Dimitris Rizopoulos
Assistant Professor
Department of Biostatistics
Erasmus Medical Center

Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands
Tel: +31/(0)10/7043478
Fax: +31/(0)10/7043014



------------------------------

Message: 22
Date: Wed, 28 Jan 2009 15:04:14 +0000
From: patricia garc?a gonz?lez <kurtney_84 at hotmail.com>
Subject: Re: [R] Merge two vectors into one.
To: <csardi at rmki.kfki.hu>
Cc: r-help at r-project.org
Message-ID: <BAY106-W11D32EFEDD34EB887498B4F6C80 at phx.gbl>
Content-Type: text/plain


Hi, 



Sorry, the answers are yes yes yes. And thank you for your idea it works perfectly.


Regards



Patricia

            

      
      
      
    

        
_________________________________________________________________





------------------------------

Message: 23
Date: Wed, 28 Jan 2009 10:10:40 -0500
From: stephen sefick <ssefick at gmail.com>
Subject: Re: [R] plot slideshow
To: diego Diego <dhabbyc at gmail.com>
Cc: r-help at r-project.org
Message-ID:
	<c502a9e10901280710t40ddac82n137de355fe620613 at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

I know you probably want to do this in R, but you could do this in
power point or the openoffice variant rather easily.

Stephen

        
On Wed, Jan 28, 2009 at 9:44 AM, diego Diego <dhabbyc at gmail.com> wrote:

            

      
      
      
    

        

      
      
    

        
-- 
Stephen Sefick

Let's not spend our time and resources thinking about things that are
so little or so large that all they really do for us is puff us up and
make us feel like gods.  We are mammals, and have not exhausted the
annoying little problems of being mammals.

								-K. Mullis



------------------------------

Message: 24
Date: Wed, 28 Jan 2009 16:28:28 +0100
From: Yohan Chalabi <chalabi at phys.ethz.ch>
Subject: Re: [R] Mystery Error in midnightStandard
To: Ted Byers <r.ted.byers at gmail.com>
Cc: R-help Forum <r-help at r-project.org>
Message-ID: <20090128162828.36d5648f at mimi>
Content-Type: text/plain; charset=US-ASCII

            

      
      
      
    

        
TB> It is certain that all entries have the same format, but I'm
   TB> starting to
   TB> think that the error message is something of a red herring.
   TB> Consider this:
   TB>
   TB> > year = 2009
   TB> > week = 0
   TB> > day = 3
   TB> > datestr = sprintf(%i-%i-%i,year,week,day);datestr
   TB> [1] 2009-0-3
   TB> > date1 = timeDate(datestr, format = %Y-%U-%w);
   TB> > date1
   TB> GMT
   TB> [1] [NA]
   TB> > day = 4
   TB> > datestr = sprintf(%i-%i-%i,year,week,day);datestr
   TB> [1] 2009-0-4
   TB> > date1 = timeDate(datestr, format = %Y-%U-%w);
   TB> > date1
   TB> GMT
   TB> [1] [2009-01-01]
   TB> >
   TB> > datestr = sprintf(%i-%i-%i,year,week,3);datestr
   TB> [1] 2009-0-3
   TB> > date2 = timeDate(datestr, format = %Y-%U-%w);date2
   TB> GMT
   TB> [1] [NA]
   TB> > difftimeDate(date2,date1, units = weeks)
   TB> Error in midnightStandard(charvec, format) :
   TB> 'charvec' has non-NA entries of different number of characters
   TB> In addition: Warning messages:
   TB> 1: In min(x) : no non-missing arguments to min; returning Inf
   TB> 2: In max(x) : no non-missing arguments to max; returning -Inf
   TB>
   TB>
   TB>
   TB> The first values for year, week and day are the values on
   TB> which my loop
   TB> dies.  It returns 'NA' here.  It seems clear that it is
   TB> returning NA because
   TB> the date that data corresponds to is 2008-12-31.
   TB>
   TB> The error is being produced by difftimeDate rather than timeDate
   TB> (as shown
   TB> by the above session).  But that represents a flaw in the
   TB> function design.

This is not a flaw in timeDate. it behaves the same way as
'as.POSIXct' 

strptime(datestr, format = "%Y-%U-%w")

Instead of claiming that there is a flaw in the function you could have
suggested an 'is.na' method for 'timeDate'.

I will add an 'is.na' method in the dev version of 'timeDate'.

regards,
Yohan 

   TB> It should fail when taking the elapsed time between a null
   TB> and the present,
   TB> but if I wrote such a function, I'd have it return null
   TB> (perhaps with a
   TB> warning) rather than just die.
   TB>
   TB> A bigger issue is that timeDate ought never give null here
   TB> (which is what I
   TB> assume 'NA' means), since all the data comes from transaction
   TB> data with real
   TB> dates, so the elapsed time, measured in weeks, ought to always
   TB> be a valid
   TB> real number that is positive semidefinite.  I have not yet
   TB> come to any
   TB> conclusions as to how it ought to behave (whether to return
   TB> new years day,
   TB> along with a warning, or to return the date requested by
   TB> reinvoking itself
   TB> with the year and week adjusted so a valid date is returned).
   TB>
   TB> On a practical side, how would I test date2 to see if it is
   TB> null, so I can
   TB> give it a sensible default value?
   TB>
   TB> A more troubling thought is that with this handling of dates
   TB> in this
   TB> combination of SQL (my group by clause uses
   TB> YEAR(transaction_date),WEEK(transaction_date)) to get the data
   TB> and R to
   TB> process it, the week containing new years day will ALWAYS be
   TB> split in two at
   TB> the first second of the new year. I'm going to have to either
   TB> figure out a
   TB> way to correct this, or ignore it (as it doesn't actually make
   TB> things wrong,
   TB> but rather it splits a sample into two unequal parts).




-- 
PhD student
Swiss Federal Institute of Technology
Zurich

www.ethz.ch



------------------------------

Message: 25
Date: Wed, 28 Jan 2009 16:29:37 +0100
From: Peter Dalgaard <P.Dalgaard at biostat.ku.dk>
Subject: Re: [R] putting match.call to good use
To: Prof Brian Ripley <ripley at stats.ox.ac.uk>
Cc: r-help at r-project.org, Harald Eikrem <heikrem at c2i.net>
Message-ID: <498079E1.4020109 at biostat.ku.dk>
Content-Type: text/plain; charset=UTF-8

        
Prof Brian Ripley wrote:

            

      
      
      
    

        
I don't understand the

   substitute(...())

bit (looks like an unexpected feature), but I suspect that it might also
be a good idea to read and understand the first dozen lines or so of the
lm function itself.

-- 
   O__  ---- Peter Dalgaard             ?ster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark      Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)              FAX: (+45) 35327907



------------------------------

Message: 26
Date: Wed, 28 Jan 2009 10:30:59 -0500
From: David Winsemius <dwinsemius at comcast.net>
Subject: Re: [R] plot slideshow
To: diego Diego <dhabbyc at gmail.com>
Cc: r-help at r-project.org
Message-ID: <68773229-5537-40A1-AFB9-2F956556487B at comcast.net>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes

If you investigate how the call:

demo(graphics)

... works, you find that the first interactive event is handled by the  
code at the end of the demo function, Just type:

demo

The rest of the interactive events are handled by this single line at  
the beginning of the graphics.R code that creates an implicit loop:

oask <- devAskNewPage(dev.interactive(orNone = TRUE))

You could have found this by looking at the Writing R Extensions  
documentation and then noting that demos are placed in demo  
subdirectories of the packages. Going to a package that you knew  
contained a working demo, in this cases the graphics package, you  
would find a graphics.R demo script.

-- 
David Winsemius

        
On Jan 28, 2009, at 9:44 AM, diego Diego wrote:

        

            

      
      
      
    

        

      
      
    

        
------------------------------

Message: 27
Date: Wed, 28 Jan 2009 15:34:47 +0000 (UTC)
From: Dieter Menne <dieter.menne at menne-biomed.de>
Subject: Re: [R] putting match.call to good use
To: r-help at stat.math.ethz.ch
Message-ID: <loom.20090128T153337-162 at post.gmane.org>
Content-Type: text/plain; charset=us-ascii

Prof Brian Ripley <ripley <at> stats.ox.ac.uk> writes:

            

      
      
      
    

        
What is Rd2HTML? 

Dieter



------------------------------

Message: 28
Date: Wed, 28 Jan 2009 10:43:16 -0500
From: JLucke at ria.buffalo.edu
Subject: Re: [R] OT: Adding verbatim R code text into LaTeX documents:
	texttt; verb or url?
To: "Peter Dunn" <PDunn2 at usc.edu.au>
Cc: R Help <r-help at r-project.org>, r-help-bounces at r-project.org
Message-ID:
	<OFDE86EA96.6227F93B-ON8525754C.0055A1EF-8525754C.005676E8 at ria.buffalo.edu>
	
Content-Type: text/plain

LaTeX offers a verbatim environment. 

\begin{verbatim} 
This is maintained verbatim, Latex commands and environments are typeset 
as written without any processing. 
\end{verbatim}

Be sure to use the package verbatim.
---Joe



"Peter Dunn" <PDunn2 at usc.edu.au> 
Sent by: r-help-bounces at r-project.org
01/28/2009 01:41 AM

To
"R Help" <r-help at r-project.org>
cc

Subject
[R] OT: Adding verbatim R code text into LaTeX documents: texttt; verb or 
url?






Hi all

I use Sweave extensively to mix R and LaTeX, and often have R code 
appearing in my LaTeX document.

Just a quick question then: What is the best way to add example of R 
commands into LaTeX in-line?  (That is, not using Sweave.)  For example, 
suppose I wish to place in my document this instruction:



...is done in R using the command  \verb|lm( y ~ var.one + var.two )| as 
follows:



I used  \verb  above, but I see three options:  \verb, \url (package url), 
or \texttt; there are probably others.

Here are my comments on these three:

- Using \texttt is OK, but it disappears my tildes and can hyphenate

- Using \verb is good, but it can hyphenate.

- Using \url is very good, but it:
* disappears my spaces; so for the above example, the spaces added for 
clarity are gone.
* Minor:  I like my verbatim text a little smaller (\small size), and 
change the font size for verbatim using 
\def\verbatim at font{\small\ttfamily} but \url seems to ignore this and 
appears larger than if I used \text or \verb.

Also, using \url often adds line-breaks mid-variable at the dots (for 
example, splitting  var.one  to have "var." on one line, and "one" on the 
next). I'm not sure this is a problem or not; here it is just an 
observation.

Ideally, one would want a LaTeX function, say \rcode{}, that displayed 
in-text using non-proportional font, kept tildes, kept spacing, uses my 
verb-font changes, and broke at sensible places for R.  (I don't want 
much, do I?)

So two questions:

* What do other people do?  Maybe there is a solution I have over-looked.

* Is there an easy solution?  I suppose writing such a command in LaTeX is 
possible, but there is strong evidence to reject the hypothesis that I 
would be able to write one.  Maybe one of the above choices are easily 
adopted.

If no easy solutions exist or emerge, I'm happy to run with \url.

Thanks again.

P.

Peter Dunn
Biostatistician
School of Health and Sport Science
Faculty of Science, Health and Education
University of the Sunshine Coast

Tel: +61 7 5456 5085
Fax: +61 7 5430 2896
Email: pdunn2 at usc.edu.au
www.usc.edu.au


CRICOS Provider Number: 01595D

This communication is intended for the recipient only and should not be 
forwarded, distributed or otherwise read by others without express 
permission. The views expressed in this email are not necessarily those of 
the University of the Sunshine Coast.

-- 




------------------------------

Message: 29
Date: Wed, 28 Jan 2009 15:44:10 +0000 (GMT)
From: Prof Brian Ripley <ripley at stats.ox.ac.uk>
Subject: Re: [R] putting match.call to good use
To: Dieter Menne <dieter.menne at menne-biomed.de>
Cc: r-help at stat.math.ethz.ch
Message-ID: <alpine.OSX.1.00.0901281540450.97868 at tystie.local>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed

        
On Wed, 28 Jan 2009, Dieter Menne wrote:

        

            

      
      
      
    

        
A function in the R-devel version of R (is 'new' not rather a hint?).

            

      
      
      
    

        
o	parse_Rd(), an experimental parser for Rd files, and Rd2txt(),
 	Rd2HTML(), Rd2latex() and Rd2ex(), even more experimental
 	converters, have been added to package 'tools'.

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



------------------------------

Message: 30
Date: Wed, 28 Jan 2009 21:17:35 +0530
From: venkata kirankumar <kiran4u2all at gmail.com>
Subject: [R] Grouping problem
To: r-help at r-project.org
Message-ID:
	<27f678620901280747x1374203di84e0710fb5b7b9a3 at mail.gmail.com>
Content-Type: text/plain

Hi all,
I have a problem with grouping like I have to give count of employes in each
department like

if in one company there is departments like
Mechanical, Computer, Fitting, electronics and Chemical

hear I have to retreave the number of employes in each department and as
well as
I have to retreave number of John's in each department

is there any function is there which can solve my problem
i tried with    subset();
but it is retreaving one department's data only
can anyone suggest what I have to do for this


thanks in advance




------------------------------

Message: 31
Date: Wed, 28 Jan 2009 16:51:35 +0100
From: <mauede at alice.it>
Subject: [R] help with plot layout
To: <r-help at stat.math.ethz.ch>
Cc: gunter.berton at gene.com
Message-ID:
	<6B32C438581E5D4C8A34C377C3B334A401752993 at FBCMST11V04.fbc.local>
Content-Type: text/plain; charset="iso-8859-1"

It takes a lot of sweat to generate a composite plot with R ...  sigh.
I though I was almost done when I met the umpteenth hurdle. I cannot place a nice title on the 2nd plot (raw signal)
on the layout. I do not have control on where either the "main" option of "plot" function, or "title", place the text
string which keeps dysplaying chopped from above. I also tried "text", changing many times the string coordinates, but could not see any text anywhere on the canvas . 
By the way, since the layout breaks the canvas into 4 parts, are the text coordinates absolute (referred to the canvas) or 
relative (referred to the part) ?
Please, find attached the generated drawing. The generating script is i the following.
Thank you so much,
Maura

##################################################################
 WavMaxNumCoef <- 30
 setwd("C:/Documents and Settings/Monville/SpAn-Tests/16440-Raw-Dir")

 xx <- read.table("Interp-Amp-PhasePlus16440.txt",header=TRUE, sep=" ")
 NumCycles <- max(xx[,"cycle"])
 TickPos <- vector(length=NumCycles)
 TickCoord <- vector(length=NumCycles)
 for(i in 1:NumCycles) {
    TickPos[i] <- xx[min(which(xx[,"cycle"] == i)),1]
 }

 aa <- read.table( "16440-Alpha.txt" )
 xaa <- seq(1:length(t(aa)))

 vv <- read.table("16440-Vanishing-Moments")
 vvLab <- seq(1,WavMaxNumCoef/2,1)
 vvCounts <- vector(length=WavMaxNumCoef/2)
 for(k in 1:(WavMaxNumCoef/2)) {
    vvCounts[k] <- length(which(vv[] == k))
 }
 yyLab <- seq(1,length(t(vv)),2)

 bb <- read.table("16440-Length")
 bbLab <- seq(min(bb),max(bb),1)
 bb <- sort(t(bb))
 bbCounts <- as.numeric(vector(length=(max(bb)-min(bb)+1)))
 for(k in 1:length(bbCounts)) {
    bbCounts[k] <- length(which(bb[] == (k +min(bb) -1)))
 }
 zzLab <- seq(1,max(bbCounts),1)

# DEFINE LAYOUT
 x11(width=22,height=14)
 nf <- layout(matrix(c(1,3,2,4),2,2,byrow=TRUE), c(3,1), c(2,2),FALSE)
 layout.show(nf)

# PLOT DONOHO ALPHA
 par(mar=c(10,4,2,5),xaxt="n",cex.axis=1,pty="m")
 plot(xaa,t(aa),type="h")
 par (xaxt="s",xaxp=c(0,95.964,24),xaxs="i")
 axis(1,at=TickPos,labels=as.character(TickPos),col="red",col.axis="red",font.axis=1)

# PLOT RAW SIGNAL
 par(mar=c(3,4,0,5),xaxt="n",cex.axis=1,pty="m")
 plot(xx[,1],xx[,2],pch=3,type="l",frame.plot=FALSE,xpd=TRUE)
 title("Raw Signal 16440",cex.main=1.0,font=2)
 par (xaxt="s",xaxp=c(0,95.964,24),xaxs="i")
 axis(1,at=TickPos,labels=as.character(TickPos),col="red",col.axis="red", font.axis=1)

# PLOT VANISHING MOMENT DISTRIBUTION
 par(mar=c(1,0,2,3),xaxt="n",yaxt="n",cex.axis=0.7,pty="m")
 barplot(vvCounts,width=1,space=0,horiz=TRUE,axes=FALSE)
 par(xaxt="s",yaxt="s",crt=180,srt=270,adj=1,las=3,xpd=TRUE)
 text(x=25.5,y=15.3,pos=4,"Wavelet Vanishing Moments Distribution",cex=1.0,font=2)
 axis(2,at=vvLab-1,labels=as.character(vvLab),col="red",col.axis="red",font.axis=1,xpd=TRUE,
      cex.lab=1)
 axis(3,at=yyLab-1,labels=as.character(yyLab),col="red",col.axis="red",font.axis=1,xpd=TRUE,
      cex.lab=0.8,cex.axis=0.8)

# PLOT CYCLES LENGTH
 par(mar=c(0,0,1,3),xaxt="n",yaxt="n",cex.axis=1)
 barplot(bbCounts,width=1,axes=FALSE,space=0,horiz=TRUE)
 par(xaxt="s",yaxt="s",crt=180,srt=270,adj=1,las=3,cex.lab=0.1,xpd=TRUE)
 text(x=15.5,y=65.3,pos=4,"Cycles Length Distribution",cex=1.0,font=2)
 axis(2,at=as.numeric(bbLab)-41,labels=bbLab,col="red",col.axis="red",font.axis=1,
      lab=c(10,10,15),cex.lab=0.7,cex.axis=0.6)
 axis(3,at=zzLab,labels=as.character(zzLab),col="red",col.axis="red",font.axis=1,xpd=TRUE,
      cex.lab=1,cex.axis=0.8)


# cords <-locator(n=3)






e tutti i telefonini TIM!
Vai su 

------------------------------

Message: 32
Date: Wed, 28 Jan 2009 09:13:51 -0500
From: "Rixon, John C." <JCRixon at wellington.com>
Subject: [R] Newbie question about "grouping"
To: <r-help at r-project.org>
Message-ID:
	<761B467185125146B58FC9540C493F6A07B46196 at PROD-MSG-CLU-03.messaging.wellmanage.com>
	
Content-Type: text/plain

Hi folks:

I am a SQL guy who just downloaded and installed R yesterday.  I am
trying to evaluate some "complex" aggregations we are currently
performing with Syncsort (and have tried in Oracle) with R.  I have
loaded data in a dataframe and have performed some of the simple
aggregations on a subset of data.  What I do not see how to do though,
is to "group" the aggregations on a particular key value (e.g., sum
market_value over account_id).

If you can point me in the right direction I'd very much appreciate it.

Thanks!

John




------------------------------

Message: 33
Date: Wed, 28 Jan 2009 17:11:04 +0100
From: Mark Na <mtb954 at gmail.com>
Subject: [R] Logical subset of the columns in a dataframe
To: r-help at r-project.org
Message-ID:
	<e40d78ce0901280811l5edc87f4lc42485ed6cbe3e33 at mail.gmail.com>
Content-Type: text/plain

Hi R-helpers,

I've been struggling with a problem for most of the day (!) so am finally
resorting to R-help.

I would like to subset the columns of my dataframe based on the frequency
with which the columns contain non-zero values. For example, let's say that
I want to retain only those columns which contain non-zero values in at
least 1% of their rows.

In Excel I would calculate a row at the bottom of my data sheet and use the
following function

=countif(range,">0")

to identify the number of non-zero cells in each column. Then, I would
divide that by the number of rows to obtain the frequency of non-zero values
in each column. Then, I would delete those columns with frequencies < 0.01.

But, I'd like to do this in R. I think the missing link is an analog to
Excel's countif function. Any ideas?

Thanks! Mark




------------------------------

Message: 34
Date: Wed, 28 Jan 2009 11:11:59 -0500
From: David Winsemius <dwinsemius at comcast.net>
Subject: Re: [R] Grouping problem
To: venkata kirankumar <kiran4u2all at gmail.com>
Cc: r-help at r-project.org
Message-ID: <B0F494E3-C48F-4B55-B222-E1705451D746 at comcast.net>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes

A vague answer is the best you should hope for with such a vague  
question with no sample data:

?table
?xtabs
?"=="

A search on "Frequency tables from factors" should get you to the  
intro to R section with that name.

-- 
David Winsemius

        
On Jan 28, 2009, at 10:47 AM, venkata kirankumar wrote:

        

            

      
      
      
    

        
If you had offered the code that was doing this, there may have been a  
person who could explain how it could be modified to return a more  
desirable value.

            

      
      
      
    

        

      
      
    

        
------------------------------

Message: 35
Date: Wed, 28 Jan 2009 10:12:59 -0600
From: hadley wickham <h.wickham at gmail.com>
Subject: Re: [R] Grouping problem
To: venkata kirankumar <kiran4u2all at gmail.com>
Cc: r-help at r-project.org
Message-ID:
	<f8e6ff050901280812p596c0fecr5627386123116a64 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

You might want to have a look at the plyr package,
http://had.co.nz/plyr, which includes tools for performing this sort
of grouping.

Hadley

On Wed, Jan 28, 2009 at 9:47 AM, venkata kirankumar

        
<kiran4u2all at gmail.com> wrote:

            

      
      
      
    

        

      
      
    

        
-- 
http://had.co.nz/



------------------------------

Message: 36
Date: Wed, 28 Jan 2009 11:16:30 -0500
From: David Winsemius <dwinsemius at comcast.net>
Subject: Re: [R] Newbie question about "grouping"
To: "Rixon, John C." <JCRixon at wellington.com>
Cc: r-help at r-project.org
Message-ID: <78B3843E-0007-495B-A052-8C9E3AC82788 at comcast.net>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes


?by
?aggregate
?ave

Further specifics might be forthcoming if self-contained example data  
and desired output were offered. The help pages will have worked  
examples, of course.

-- 
David Winsemius

        
On Jan 28, 2009, at 9:13 AM, Rixon, John C. wrote:

        

            

      
      
      
    

        

      
      
    

        
------------------------------

Message: 37
Date: Wed, 28 Jan 2009 08:18:15 -0800 (PST)
From: Thomas Lumley <tlumley at u.washington.edu>
Subject: Re: [R] Newbie question about "grouping"
To: "Rixon, John C." <JCRixon at wellington.com>
Cc: r-help at r-project.org
Message-ID: <Pine.LNX.4.43.0901280818150.7342 at hymn14.u.washington.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed

Some useful commands are:

by(), aggregate(), ave(), split().

eg
   by(market_value, account_id, sum)

         -thomas

        
On Wed, 28 Jan 2009, Rixon, John C. wrote:

        

            

      
      
      
    

        

      
      
    

        
Thomas Lumley			Assoc. Professor, Biostatistics
tlumley at u.washington.edu	University of Washington, Seattle



------------------------------

Message: 38
Date: Wed, 28 Jan 2009 10:20:15 -0600
From: hadley wickham <h.wickham at gmail.com>
Subject: Re: [R] Newbie question about "grouping"
To: "Rixon, John C." <JCRixon at wellington.com>
Cc: r-help at r-project.org
Message-ID:
	<f8e6ff050901280820r3098ae20raf6b2e770a1c2d64 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

        
On Wed, Jan 28, 2009 at 8:13 AM, Rixon, John C. <JCRixon at wellington.com> wrote:

            

      
      
      
    

        
Have a look at the plyr package, http://had.co.nz/plyr, and associated
documentation. If you're doing pivot table type aggregations, you
might also want to have a look at the reshape package,
http://had.co.nz/reshape.


Hadley

-- 
http://had.co.nz/



------------------------------

Message: 39
Date: Wed, 28 Jan 2009 16:24:11 +0000 (GMT)
From: Prof Brian Ripley <ripley at stats.ox.ac.uk>
Subject: Re: [R] Logical subset of the columns in a dataframe
To: Mark Na <mtb954 at gmail.com>
Cc: r-help at r-project.org
Message-ID:
	<alpine.LFD.2.00.0901281621030.31070 at gannet.stats.ox.ac.uk>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed

        
On Wed, 28 Jan 2009, Mark Na wrote:

        

            

      
      
      
    

        
Use something like

     DF[sapply(DF, function(x) mean(x) >= 0.01)]

Since logical values are converted to 0/1, mean() gives the frequency 
(and sum() the count).

            

      
      
      
    

        

      
      
    

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



------------------------------

Message: 40
Date: Wed, 28 Jan 2009 11:25:55 -0500
From: Ted Byers <r.ted.byers at gmail.com>
Subject: Re: [R] Mystery Error in midnightStandard
To: Yohan Chalabi <chalabi at phys.ethz.ch>
Cc: R-help Forum <r-help at r-project.org>
Message-ID:
	<4f1819890901280825w3cfa983bi8c68f1b85c22d378 at mail.gmail.com>
Content-Type: text/plain

Hi Yohan,

        
On Wed, Jan 28, 2009 at 10:28 AM, Yohan Chalabi <chalabi at phys.ethz.ch>wrote:

        

            

      
      
      
    

        
That the two behave the same doesn't change the assessment that the design
is flawed.  That doesn't mean that the function is wrong.  It means only
that the behaviour can be made more useful.  For example, in SQL, if a given
calculation returns NULL, and the result is subsequently used in another
calculation, the result that returns is also NULL.  That is quite useful,
and admits algorithms that can react appropriately to NULLs when necessary.
That is arguably better than forcing the code to fail the moment a NULL is
used in a secondary calculation.  In C++, OTOH, one can catch the problem
earlier using, e.g., exceptions, again allowing the program to complete even
when problems arise for certain values or combinations thereof.

As a software engineer, I understand the issues involved in creating
libraries.  If I want to incorporate the functionality of a given standard
suite of functions (e.g. ANSI C standard library functions, or posix
functions), my first step would be to ensure I can duplicate how they
behave.  But I would not stop there.  There are, for example, serious design
flaws in many ANSI C functions that, ignored, introduce serious security
defects in applications that use them.  I would therefore refactor them to
eliminate the security defects.  If they can not be eliminated, I would
replace the function in question by a similar function that does not have
that security defect.

Posix is a useful, but old, standard, and I am merely suggesting that once
you have duplicated it, look beyond it to ways it can be improved upon.
There is more to the design of a function than whether or not it gives the
right result with good input.  There is how it behaves when there is a
problem with the inputs and whether or not you force the calling code to die
when a problem arises or you give the calling code a way to react to such
problems.  When I add functions to my own C++ or Java libraries, I normally
include more bad input data in the unit tests than good data (though the
latter is sufficient to ensure correct results are invariably obtained),
precisely so I can document how it behaves when there is a problem and give
coders who use it a variety of options to use to deal with them.

            

      
      
      
    

        
At the time, I did not know about is.na.  I have spent the past hour trying
is.na, but to no avail.  I guess that is no surprise to you, but that it
would fail is not reflected in the R documentation of is.na.  That mentions
S3, but not S4.  As I just recently started using R, I have not yet looked
at what S3 and S4 are, so that is a few more hours of study before I get
this problem solved.

            

      
      
      
    

        
Thanks.  I'll benefit from that once it makes it into the production
release.  In the mean time, I need to find a way to make something similar
now, in my script.

Thanks

Ted




------------------------------

Message: 41
Date: Wed, 28 Jan 2009 11:35:19 -0500
From: David Winsemius <dwinsemius at comcast.net>
Subject: Re: [R] Logical subset of the columns in a dataframe
To: Mark Na <mtb954 at gmail.com>
Cc: r-help at r-project.org
Message-ID: <AA1C6FDC-927E-468F-B31A-0A8EA38FC2E3 at comcast.net>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes

One approach to such a problem would be to use a logical vector inside  
the function colSums.

?colSums

 > DF <- data.frame(XX= runif(20), YY=runif(20))

 > colSums(DF > 0.5)
XX YY
11  9

 > colSums(DF > -Inf)
XX YY
20 20
 >
 > colSums(DF> 0.5)/colSums(DF > -Inf) #could have used DF >= min(DF)  
in the denominator
   XX   YY
0.55 0.45



-- 
David Winsemius

        
On Jan 28, 2009, at 11:11 AM, Mark Na wrote:

        

            

      
      
      
    

        
I don't think that would do what you describe unless you were only  
working with single column ranges. Functions on ranges in Excel are  
not calculated by column.

            

      
      
      
    

        

      
      
    

        
------------------------------

Message: 42
Date: Wed, 28 Jan 2009 17:48:24 +0100
From: Yohan Chalabi <chalabi at phys.ethz.ch>
Subject: Re: [R] Mystery Error in midnightStandard
To: Ted Byers <r.ted.byers at gmail.com>
Cc: R-help Forum <r-help at r-project.org>
Message-ID: <20090128174824.561e94cb at mimi>
Content-Type: text/plain; charset=US-ASCII

            

      
      
      
    

        
TB> That the two behave the same doesn't change the assessment
   TB> that the design
   TB> is flawed.  That doesn't mean that the function is wrong.
   TB> It means only
   TB> that the behaviour can be made more useful.  For example,
   TB> in SQL, if a given
   TB> calculation returns NULL, and the result is subsequently used
   TB> in another
   TB> calculation, the result that returns is also NULL.  That is
   TB> quite useful,
   TB> and admits algorithms that can react appropriately to NULLs
   TB> when necessary.
   TB> That is arguably better than forcing the code to fail the
   TB> moment a NULL is
   TB> used in a secondary calculation.  In C++, OTOH, one can catch
   TB> the problem
   TB> earlier using, e.g., exceptions, again allowing the program
   TB> to complete even
   TB> when problems arise for certain values or combinations thereof.
   TB>
   TB> As a software engineer, I understand the issues involved
   TB> in creating
   TB> libraries.  If I want to incorporate the functionality of a
   TB> given standard
   TB> suite of functions (e.g. ANSI C standard library functions,
   TB> or posix
   TB> functions), my first step would be to ensure I can duplicate
   TB> how they
   TB> behave.  But I would not stop there.  There are, for example,
   TB> serious design
   TB> flaws in many ANSI C functions that, ignored, introduce
   TB> serious security
   TB> defects in applications that use them.  I would therefore
   TB> refactor them to
   TB> eliminate the security defects.  If they can not be eliminated,
   TB> I would
   TB> replace the function in question by a similar function that
   TB> does not have
   TB> that security defect.
   TB>
   TB> Posix is a useful, but old, standard, and I am merely suggesting
   TB> that once
   TB> you have duplicated it, look beyond it to ways it can be
   TB> improved upon.
   TB> There is more to the design of a function than whether or not
   TB> it gives the
   TB> right result with good input.  There is how it behaves when
   TB> there is a
   TB> problem with the inputs and whether or not you force the
   TB> calling code to die
   TB> when a problem arises or you give the calling code a way to
   TB> react to such
   TB> problems.  When I add functions to my own C++ or Java libraries,
   TB> I normally
   TB> include more bad input data in the unit tests than good data
   TB> (though the
   TB> latter is sufficient to ensure correct results are invariably
   TB> obtained),
   TB> precisely so I can document how it behaves when there is a
   TB> problem and give
   TB> coders who use it a variety of options to use to deal with them.
   TB>
   TB>
   TB> >
   TB> > strptime(datestr, format = %Y-%U-%w)
   TB> >
   TB> > Instead of claiming that there is a flaw in the function
   TB> you could have
   TB> > suggested an 'is.na' method for 'timeDate'.
   TB> >
   TB>
   TB> At the time, I did not know about is.na.  I have spent the
   TB> past hour trying
   TB> is.na, but to no avail.  I guess that is no surprise to you,
   TB> but that it
   TB> would fail is not reflected in the R documentation of is.na.
   TB> That mentions
   TB> S3, but not S4.  As I just recently started using R, I have
   TB> not yet looked
   TB> at what S3 and S4 are, so that is a few more hours of study
   TB> before I get
   TB> this problem solved.
   TB>
   TB>
   TB> >
   TB> > I will add an 'is.na' method in the dev version of 'timeDate'.
   TB> >
   TB> >
   TB> Thanks.  I'll benefit from that once it makes it into the
   TB> production
   TB> release.  In the mean time, I need to find a way to make
   TB> something similar
   TB> now, in my script.

setMethod("is.na", "timeDate", function(x) is.na(as.POSIXct(x)))

   TB>
   TB> Thanks




-- 
PhD student
Swiss Federal Institute of Technology
Zurich

www.ethz.ch



------------------------------

Message: 43
Date: Wed, 28 Jan 2009 16:55:40 +0000
From: June Wong <neptune545 at hotmail.com>
Subject: [R] constrainOptim
To: <r-help at r-project.org>
Message-ID: <BAY136-W82AA69673D0B171ED34178AC80 at phx.gbl>
Content-Type: text/plain


Dear R helpers

I have a question regarding the constrainOptim. 
I'm coding the nested logit and would like to set a bound of rho to (0,1] as an extreme value distribution where rho = exp(lambda)/1+exp(lambda)
I wonder if I can do that directly in optim (say rho > 0 & <= 1) or need to use constrainOptim
I read the help but still don't know how to set ui and ci

Thanks,
June

_________________________________________________________________





------------------------------

Message: 44
Date: Wed, 28 Jan 2009 12:07:14 -0500
From: Ravi Varadhan <rvaradhan at jhmi.edu>
Subject: Re: [R] constrainOptim
To: June Wong <neptune545 at hotmail.com>
Cc: r-help at r-project.org
Message-ID: <f6d1b5dede2.49804a72 at johnshopkins.edu>
Content-Type: text/plain; charset=us-ascii

For simple box constraints, i.e. lower and upper limits directly on the parameters themselves, you don't need ConstrOptim.  You can get the job done with the "L-BFGS-B" algorithm in optim() or using nlminb() or using the spg() function in the BB package.  In this case the feasible region is a hyper-rectangle (could be infinite in some dimensions).

ConstrOptim() is useful when you have more general linear inequality constraints, i.e. constraints on linear combinations of parameters. In this case the feasible region is a convex polytope.  

Best,
Ravi.

____________________________________________________________________

Ravi Varadhan, Ph.D.
Assistant Professor,
Division of Geriatric Medicine and Gerontology
School of Medicine
Johns Hopkins University

Ph. (410) 502-2619
email: rvaradhan at jhmi.edu


----- Original Message -----
From: June Wong <neptune545 at hotmail.com>
Date: Wednesday, January 28, 2009 11:57 am
Subject: [R] constrainOptim
To: r-help at r-project.org

            

      
      
      
    

        

      
      
    

        
------------------------------

Message: 45
Date: Wed, 28 Jan 2009 18:07:28 +0100
From: "Strubbe Diederik" <diederik.strubbe at ua.ac.be>
Subject: [R] repeated measures design for GAM?
To: <r-help at R-project.org>
Message-ID:
	<C9854550FEF14846A136100B3EC52F73B6B5AC at xmail05.ad.ua.ac.be>
Content-Type: text/plain

Dear all,

I have a question on the use of GAM with repeated measures. My dataset is as follows:
- a number of study areas where bird abundance has been determined. Counts have been performed in 3 consecutive years and there were 2 counts per year (i.e. in total 6 counts).
- a number of environmental predictors that do not change over year Xi).
When using a GLM, a repeated measures design would like: (for example)

lme(Bird_abundance = study_area + count + X1 + X2 + X3,random = ~time|cow).

However, I have found no analogue design for a GAM. For now, I have averaged my bird abundances but I wondered whether a more subtle and elegant strategy exists...?

Many thanks,


Diederik 



Diederik Strubbe
Evolutionary Ecology Group
Department of Biology, University of Antwerp
Universiteitsplein 1
B-2610 Antwerp, Belgium
http://webhost.ua.ac.be/deco
tel : 32 3 820 23 85





------------------------------

Message: 46
Date: Wed, 28 Jan 2009 18:09:38 +0100
From: "Strubbe Diederik" <diederik.strubbe at ua.ac.be>
Subject: [R] Repeated measures design for GAM? - corrected question...
To: <r-help at R-project.org>
Message-ID:
	<C9854550FEF14846A136100B3EC52F73B6B5AD at xmail05.ad.ua.ac.be>
Content-Type: text/plain

Dear all,

I have a question on the use of GAM with repeated measures. My dataset is as follows:
- a number of study areas where bird abundance has been determined. Counts have been performed in 3 consecutive years and there were 2 counts per year (i.e. in total 6 counts).
- a number of environmental predictors that do not change over year Xi).
When using a GLM, a repeated measures design would like: (for example)

lme(Bird_abundance = study_area + count +year+ X1 + X2 + X3,random = ~count|study_area).

However, I have found no analogue design for a GAM. For now, I have averaged my bird abundances but I wondered whether a more subtle and elegant strategy exists...?

Many thanks,


Diederik

Diederik Strubbe
Evolutionary Ecology Group
Department of Biology, University of Antwerp
Universiteitsplein 1
B-2610 Antwerp, Belgium
http://webhost.ua.ac.be/deco
tel : 32 3 820 23 85





------------------------------

Message: 47
Date: Wed, 28 Jan 2009 19:16:30 +0200
From: constantine <costas.magnuse at gmail.com>
Subject: [R] Sweave problem with greek text
To: r-help at r-project.org
Message-ID:
	<30ddfdae0901280916i1e92e040s336ec0227305723 at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

Dear Sweave and R aficionados,


I am using R and Latex for many years, writing texts in greek. I tried
to combine them with Sweave, but without any success.

Could you provide me with any help?

Usually my LaTeX files are like this iso-8859-7 encoded .tex file:
http://costis.name/0various/lists/R/sweave/successful.greek.tex ,
which happily produces
http://costis.name/0various/lists/R/sweave/successful.greek.pdf .

I tried using Sweave on the iso-8859-7 encoded .Rnw file:
http://costis.name/0various/lists/R/sweave/unsuccessful.sweave.Rnw ,
but I am getting misencoded greek text and also misencoded R code as
it appears in  http://costis.name/0various/lists/R/sweave/unsuccessful.sweave.pdf
.

The .tex file that Sweave produces is located at
http://costis.name/0various/lists/R/sweave/unsuccessful.sweave.tex
I am also the latex R error code
http://costis.name/0various/lists/R/sweave/unsuccessful.sweave.log
In the above example I am not using the kerkis font-package. When I
am,  I am getting no output at all, and a latex error of "Corrupted
NFSS tables".

I can understand that the whole problem is an encoding issue, but what
should I do in order to use Sweave with greek text flawlessly?
One solution is to edit the .tex file produced by Sweave, but this
solution is by far counter-productive.



Thank you very much in advance,



Constantine Tsardounis
http://www.costis.name



PS.: I am having no problem to run Sweave in 100% English texts.
I postscript the following files:
* unsuccessful.sweave.Rnw
* unsuccessful.sweave.tex
* successful.greek.tex


########################
unsuccessful.sweave.Rnw
########################
\documentclass[a4paper,12pt]{book}
\usepackage[greek]{babel}
\usepackage[iso-8859-7]{inputenc}
% \usepackage{kerkis}
\begin{document}
\section{\textlatin{Sweave}}
\subsection{\textlatin{in Greek}}
???? ???, ???? ????? ????????.

<<>>=
data(airquality)
library(ctest)
kruskal.test(Ozone ~ Month, data = airquality)
@

\subsection{\textlatin{in English}}
\textlatin{Hello to all, now I am writing in English.}
\end{document}


########################
unsuccessful.sweave.tex
########################
\documentclass[a4paper,12pt]{book}
\usepackage[greek]{babel}
\usepackage[iso-8859-7]{inputenc}
% \usepackage{kerkis}
\usepackage{/usr/share/R/share/texmf/Sweave}
\begin{document}
\section{\textlatin{Sweave}}
\subsection{\textlatin{in Greek}}
?????(c)?' ???'??, ???????' ?????????? ???????????(c)????.

\begin{Schunk}
\begin{Sinput}

            

      
      
      
    

        
\end{Sinput}
\begin{Soutput}
	Kruskal-Wallis rank sum test

data:  Ozone by Month
Kruskal-Wallis chi-squared = 29.2666, df = 4, p-value = 6.901e-06
\end{Soutput}
\end{Schunk}

\subsection{\textlatin{in English}}
\textlatin{Hello to all, now I am writing in English.}
\end{document}


########################
successful.greek.tex
########################
\documentclass[a4paper,12pt]{book}
\usepackage[greek]{babel}
\usepackage[iso-8859-7]{inputenc}
\usepackage{kerkis}
\begin{document}
\section{\textlatin{Sweave}}
\subsection{\textlatin{in Greek}}
???? ???, ???? ????? ????????.

\subsection{\textlatin{in English}}
\textlatin{Hello to all, now I am writing in English.}
\end{document}



------------------------------

Message: 48
Date: Wed, 28 Jan 2009 12:17:05 -0500
From: Ravi Varadhan <rvaradhan at jhmi.edu>
Subject: Re: [R] StepAIC with coxph
To: Michele Santacatterina <miksanta at gmail.com>
Cc: R-help at r-project.org
Message-ID: <f6b1f699771b.49804cc1 at johnshopkins.edu>
Content-Type: text/plain; charset=iso-8859-1

Michele,

This error means that some of the variables in your formula have missing values, and hence when these terms or added/dropped you have a different sample size.  Hence, the AIC cannot be compared between different models.  The solution is to create a compelete-data dataframe for the largest model, i.e none of the variables in the largest model should have any missing values.  Then run stepAIC on this dataframe. 

Best,
Ravi.

____________________________________________________________________

Ravi Varadhan, Ph.D.
Assistant Professor,
Division of Geriatric Medicine and Gerontology
School of Medicine
Johns Hopkins University

Ph. (410) 502-2619
email: rvaradhan at jhmi.edu


----- Original Message -----
From: Michele Santacatterina <miksanta at gmail.com>
Date: Wednesday, January 28, 2009 9:51 am
Subject: [R] StepAIC with coxph
To: R-help at r-project.org

            

      
      
      
    

        

      
      
    

        
------------------------------

Message: 49
Date: Wed, 28 Jan 2009 17:30:02 +0000
From: Simon Wood <s.wood at bath.ac.uk>
Subject: Re: [R] Repeated measures design for GAM? - corrected
	question...
To: r-help at r-project.org
Message-ID: <200901281730.02975.s.wood at bath.ac.uk>
Content-Type: text/plain;  charset="iso-8859-1"

`gamm' in package `mgcv' will let you specify random effects as part of a 
generalized additive mixed model, but I must admit that I'm a bit confused 
about what `Bird_abundance' is here, and how it differs from `Count'.

best,
Simon

        
On Wednesday 28 January 2009 17:09, Strubbe Diederik wrote:

            

      
      
      
    

        

      
      
    

        
--

            

      
      
      
    

        
------------------------------

Message: 50
Date: Wed, 28 Jan 2009 09:51:29 -0800
From: Dr Carbon <drcarbon at gmail.com>
Subject: [R] gls prediction using the correlation structure in nlme
To: r-help at r-project.org, jcp at research.bell-labs.com,
	bates at stat.wisc.edu
Message-ID:
	<e89bb7ac0901280951j725ef225r87965bfd08595b71 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

How does one coerce predict.gls to incorporate the fitted correlation
structure from the gls object into predictions? In the example below
the AR(1) process with phi=0.545 is not used with predict.gls. Is
there another function that does this? I'm going to want to fit a few
dozen models varying in order from AR(1) to AR(3) and would like to
look at the fits with the correlation structure included.

Thanks in advance.

-JC

PS I am including the package maintainers on this post - does this
constitute a maintainer-specific question in r-help etiquette?

# example
set.seed(123)
x <- arima.sim(list(order = c(1,0,0), ar = 0.7), n = 100)
y <-x + arima.sim(list(order = c(1,0,0), ar = 0.7), n = 100)
x <- c(x)
y <- c(y)
lm1 <- lm(y~x)
ar(residuals(lm1)) # indicates an ar1 model
cs1 <- corARMA(p=1)
fm1 <- gls(y~x,corr=cs1)
summary(fm1)
# get fits
fits <- predict(fm1)
# use coef to get fits
fits2 <- coef(fm1)[1] + (coef(fm1)[2] * x)
plot(fits,fits2)



------------------------------

Message: 51
Date: Mon, 26 Jan 2009 14:55:21 +0100
From: "ARDIA David" <david.ardia at unifr.ch>
Subject: [R] [R-pkgs] AdMit version 1-01.01
To: <r-packages at r-project.org>
Message-ID:
	<2AA9A291D7760C40B00A75A149DB5D37062033 at EXCHANGE4.unifr.ch>
Content-Type: text/plain; charset="us-ascii"

Dear all,

The new version of AdMit (version 1.01-01) is now available from CRAN.

SUMMARY
The package provides functions to perform the fitting of an adaptive
mixture of Student-t distributions to a target density through its 
kernel function. The mixture approximation can then be used as the importance
density in importance sampling or as the candidate density in the
Metropolis-Hastings algorithm to obtain quantities of interest for 
the target density itself. We believe that this approach may be applicable in
many fields of research and hope that the R package AdMit will be
fruitful for many researchers like econometricians or applied statisticians.


MODIFICATIONS
o change in AdMit.R to deal with convergence problems for simple cases.

o the documentation file has been improved (thanks to Achim Zeilis for
comments).

o a package vignette has been added.

o a paper describing the package in detail has been published in  the
Journal of Statistical Software: http://www.jstatsoft.org/v29/i03.

Abstract:
This paper presents the R package AdMit which provides functions to
approximate and sample from a certain target distribution given only a
kernel of the target density function. The core algorithm consists in
the function AdMit which fits an adaptive mixture of Student-t
distributions to the density of interest via its kernel function. Then,
importance sampling or the independence chain Metropolis-Hastings
algorithm are used to obtain quantities of interest for the target
density, using the fitted mixture as the importance or candidate
density. The estimation procedure is fully automatic and thus avoids the
time-consuming and difficult task of tuning a sampling algorithm. The
relevance of the package is shown in two examples. The first aims at
illustrating in detail the use of the functions provided by the
package in a bivariate bimodal distribution. The second shows the
relevance of the adaptive mixture procedure through the Bayesian
estimation of a mixture of ARCH model fitted to foreign exchange
log-returns data. The methodology is compared to standard cases of
importance sampling and the Metropolis-Hastings algorithm using a naive
candidate and with the Griddy-Gibbs approach.

o creation of /doc folder with AdMitJSS.txt and AdMitRnews.txt files
(the R codes used for JSS and Rnews papers).

o CITATION file simplified.

o 'coda' package is now Suggests


REFERENCES
Ardia D, Hoogerheide LF, van Dijk HK (2008). AdMit: Adaptive Mixture of
Student-t Distributions in R. R package version 1.01-01.
URL http://CRAN.R-project.org/package=AdMit.

Ardia D, Hoogerheide LF, van Dijk HK (2009). Adaptive Mixture of
Student-t Distributions as a Flexible Candidate Distribution for
Efficient Simulation: The R Package AdMit. Journal of Statistical
Software, 29(3), 1-32.
URL http://www.jstatsoft.org/v29/i03/.

Hoogerheide LF (2006). Essays on Neural Network Sampling Methods and
Instrumental Variables. Ph.D. thesis, Tinbergen Institute, Erasmus
University Rotterdam. Book nr. 379 of the Tinbergen Institute Research
Series.

Hoogerheide LF, Kaashoek JF, van Dijk HK (2007). On the Shape of
Posterior Densities and Credible Sets in Instrumental Variable
Regression Models with Reduced Rank: An Application of Flexible Sampling
Methods using Neural Networks.
Journal of Econometrics, 139(1), 154-180. doi:10.1016/j.jeconom.2006.06.009.

Hoogerheide LF, van Dijk HK (2008a). Bayesian Forecasting of Value at
Risk and Expected Shorfall Using Adaptive Importance Sampling. Technical
Report 2008-092/4, Tinbergen Institute, Erasmus University Rotterdam.
URL http://www.tinbergen.nl/ discussionpapers/08092.pdf.

Hoogerheide LF, van Dijk HK (2008b). Possibly Ill-Behaved Posteriors in
Econometric Models: On the Connection Between Model Structures,
Non-Elliptical Credible Sets and Neural Network Simulation Techniques."
Technical Report 2008-036/4, Tinbergen Institute, Erasmus University
Rotterdam.
URL http://www.tinbergen.nl/discussionpapers/08036.pdf.

Best regards,

David Ardia (package's maintainer)
Lennart F. Hoogerheide
Herman K. van Dijk


_______________________________________________
R-packages mailing list
R-packages at r-project.org
https://stat.ethz.ch/mailman/listinfo/r-packages



------------------------------

Message: 52
Date: Wed, 28 Jan 2009 11:20:08 -0700
From: Greg Snow <Greg.Snow at imail.org>
Subject: Re: [R] help with plot layout
To: "mauede at alice.it" <mauede at alice.it>, "r-help at stat.math.ethz.ch"
	<r-help at stat.math.ethz.ch>
Cc: "gunter.berton at gene.com" <gunter.berton at gene.com>
Message-ID:
	<B37C0A15B8FB3C468B5BC7EBC7DA14CC61C939DBFA at LP-EXMBVS10.CO.IHC.COM>
Content-Type: text/plain; charset="us-ascii"

We don't have your data, so we cannot reproduce what you are doing and the plot was stripped off before we saw it (only certain types of attachments are allowed, and some e-mail programs don't give the correct information about attachments so even those types can be stripped if it is not clear what they are).

Here are some possible hints that may help (if I have guessed correctly about what you are trying to do).

Read the help page for par, looking at the information on margins and outer margins, this can be used to give you more room for your titles (also the xpd argument if you are placing things outside the plot area).  Also look at the various cex arguments for controlling sizes.

Try using mtext instead of text to manually add titles or other text in the margins.

Sometimes using the outer margins works better than using the regular margins (sometimes not).

The text function uses the user coordinates of the current plot, the functions grconvertX and grconvertY can be used to convert between the different coordinate systems.

Hope this helps,

-- 
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.snow at imail.org
801.408.8111

            

      
      
      
    

        
------------------------------

Message: 53
Date: Wed, 28 Jan 2009 13:25:32 -0500 (EST)
From: Nidhi Kohli <nidhik at umd.edu>
Subject: [R] stack data sets
To: r-help at stat.math.ethz.ch, r-help at r-project.org
Message-ID: <20090128132532.BIX30409 at po3.mail.umd.edu>
Content-Type: text/plain; charset=us-ascii

Hi All,

I'm generating 10 different data sets with 1 and 0 in a matrix form and writing the output in separate files. Now I need to stack all these data sets in one vector and I know that stack only operates on list or data frame however I got these data sets by converting list to a matrix so can't go backwards now. Is there a way i can still use Stack?

Please see the program:

#Importing psych & ltm library for all the simulation related functions
library(ltm)
library(psych)
# Settting the working directory path to C:/NCME
path="C:/NCME"
setwd(path)
#IRT Data Simulation Routine#
n.exams = 500   #Sets number of examinees to be generated#
n.items = 20     #Sets number of items to be generated#
#The following intialize empty (NA) vectors or matrices#
beta.values = rep(NA,n.items)
resp.prob=matrix(rep(NA, n.exams*n.items), nrow=n.exams, ncol=n.items)
Observed_Scores=matrix(rep(NA, n.exams*n.items), nrow=n.exams, ncol=n.items)
str(Observed_Scores)
for (k in 1:10)
{
#Setting the starting point for seed
set.seed(k)
#filling item parameters into beta.values
beta.values = runif(n.items,-2,2)
#Calculating Threshold
thresh.values = .5 * beta.values

#Using the function to generate the Parallel Model CTT data
GenData <- congeneric.sim(N=500, loads = rep(.5,20), err=NULL, short = FALSE)

#Storing Observed Score in a variable
Observed_Scores = GenData[[3]]
#Exporting Observed scores to output file
ObservedScores_Data <- paste("Observed_Scores_",k,".dat")
write.table(Observed_Scores,ObservedScores_Data,row.name=FALSE,col.name=FALSE)
Zero = 0
One = 1
for (t in 1:20)
{
for (s in 1:500)
{
if (Observed_Scores[s,t]<= thresh.values[t])
resp.prob[s,t] = Zero
else
resp.prob[s,t] = One

}
}
ResponseData <- paste("ResponseMatrix_",k,".dat")
ThreshData <- paste("Threshold_",k,".dat")
write.table(resp.prob,ResponseData,row.name=FALSE,col.name=FALSE)
write.table(thresh.values,ThreshData,row.name=FALSE,col.name=FALSE)

#####STACKING ALL THE OUTPUTS#########
CommonFile <- stack(resp.prob)
######################################

#Rounding upto 2 decimal places while showing the correlation matrix
round(cor(GenData$observed),2)
#Factor Score
FactorScore=factor.pa(GenData$observed,1,scores = "TRUE")
round(cor(FactorScore$scores,GenData$latent),2)
filename_fs <- paste("FactorScore_",k,".dat")
#Exporting Factor Scores to Output file
write.table(FactorScore$scores,filename_fs,col.name=FALSE, row.name=FALSE)
}


Thank you
Nidhi



------------------------------

Message: 54
Date: Wed, 28 Jan 2009 13:25:32 -0500 (EST)
From: Nidhi Kohli <nidhik at umd.edu>
Subject: [R] stack data sets
To: r-help at stat.math.ethz.ch, r-help at r-project.org
Message-ID: <20090128132532.BIX30409 at po3.mail.umd.edu>
Content-Type: text/plain; charset=us-ascii

Hi All,

I'm generating 10 different data sets with 1 and 0 in a matrix form and writing the output in separate files. Now I need to stack all these data sets in one vector and I know that stack only operates on list or data frame however I got these data sets by converting list to a matrix so can't go backwards now. Is there a way i can still use Stack?

Please see the program:

#Importing psych & ltm library for all the simulation related functions
library(ltm)
library(psych)
# Settting the working directory path to C:/NCME
path="C:/NCME"
setwd(path)
#IRT Data Simulation Routine#
n.exams = 500   #Sets number of examinees to be generated#
n.items = 20     #Sets number of items to be generated#
#The following intialize empty (NA) vectors or matrices#
beta.values = rep(NA,n.items)
resp.prob=matrix(rep(NA, n.exams*n.items), nrow=n.exams, ncol=n.items)
Observed_Scores=matrix(rep(NA, n.exams*n.items), nrow=n.exams, ncol=n.items)
str(Observed_Scores)
for (k in 1:10)
{
#Setting the starting point for seed
set.seed(k)
#filling item parameters into beta.values
beta.values = runif(n.items,-2,2)
#Calculating Threshold
thresh.values = .5 * beta.values

#Using the function to generate the Parallel Model CTT data
GenData <- congeneric.sim(N=500, loads = rep(.5,20), err=NULL, short = FALSE)

#Storing Observed Score in a variable
Observed_Scores = GenData[[3]]
#Exporting Observed scores to output file
ObservedScores_Data <- paste("Observed_Scores_",k,".dat")
write.table(Observed_Scores,ObservedScores_Data,row.name=FALSE,col.name=FALSE)
Zero = 0
One = 1
for (t in 1:20)
{
for (s in 1:500)
{
if (Observed_Scores[s,t]<= thresh.values[t])
resp.prob[s,t] = Zero
else
resp.prob[s,t] = One

}
}
ResponseData <- paste("ResponseMatrix_",k,".dat")
ThreshData <- paste("Threshold_",k,".dat")
write.table(resp.prob,ResponseData,row.name=FALSE,col.name=FALSE)
write.table(thresh.values,ThreshData,row.name=FALSE,col.name=FALSE)

#####STACKING ALL THE OUTPUTS#########
CommonFile <- stack(resp.prob)
######################################

#Rounding upto 2 decimal places while showing the correlation matrix
round(cor(GenData$observed),2)
#Factor Score
FactorScore=factor.pa(GenData$observed,1,scores = "TRUE")
round(cor(FactorScore$scores,GenData$latent),2)
filename_fs <- paste("FactorScore_",k,".dat")
#Exporting Factor Scores to Output file
write.table(FactorScore$scores,filename_fs,col.name=FALSE, row.name=FALSE)
}


Thank you
Nidhi



------------------------------

Message: 55
Date: Wed, 28 Jan 2009 18:54:27 +0000 (UTC)
From: Ben Bolker <bolker at ufl.edu>
Subject: Re: [R] constrainOptim
To: r-help at stat.math.ethz.ch
Message-ID: <loom.20090128T184853-604 at post.gmane.org>
Content-Type: text/plain; charset=us-ascii

June Wong <neptune545 <at> hotmail.com> writes:

            

      
      
      
    

        
an extreme value distribution

            

      
      
      
    

        
use constrainOptim

            

      
      
      
    

        
optim() can do box constraints (i.e., independent inequality
constraints on parameters): use method="L-BFGS-B" and
the lower and upper arguments to set the bounds for
each parameter (to -Inf and Inf if there are no bounds).
If you want to set bounds on rho you have to use rho as
the parameter in your model -- this is tricky if you
can't solve for rho, but in your case lambda=log(rho/(1-rho))

  Ben Bolker



------------------------------

Message: 56
Date: Wed, 28 Jan 2009 18:26:57 +0100
From: julien cuisinier <j_cuisinier at hotmail.com>
Subject: [R] Saving plot into file without showing it
To: <r-help at r-project.org>
Message-ID: <COL102-W425B97D7E5E340366CB9128FC80 at phx.gbl>
Content-Type: text/plain


Hi List,


My apologies in advance if question is simplistic, I am quite new to R graphics capabilities and I could not find anything in past threads...

I use R 2.8.1 under Mac OS X, but I would preferrably have a cross platform answer as I use also R under Windows

I produce plots using R & save them in a file

e.g. below:

y <- rnorm(1000)
x <- rnorm(1000)
plot(x,y)
dev.copy2pdf()

Until there fine, it create a pdf file that is composed of my plot...My "issues" are the following:
1. If I want to produce the plot & save it directly in a pdf file without viewing it, how do I do that? 
2. Can I create several plots in a row (without showing them in Quartz or whatever other graphic device) and save them all in separate files after creation? for example a function that would save me in separate files all what is visible through dev.list()


Let's keep the example of saving in pdf format here...I do not have target file type for saving the graphics. The point is that I would have another piece of code (HTML I guess, not developed yet) fetching all the charts and presenting it nicely.


Any feedback is appreciated

Many thanks
Julien

_________________________________________________________________

 charlas.




------------------------------

Message: 57
Date: Wed, 28 Jan 2009 08:48:16 -0800 (PST)
From: Frank Zhang <frankyuzhang at yahoo.com>
Subject: [R] Get median of each column
To: r-help at r-project.org
Message-ID: <724831.30195.qm at web33007.mail.mud.yahoo.com>
Content-Type: text/plain

I am new to R. How can I get column median? Thanks.Frank


      



------------------------------

Message: 58
Date: Wed, 28 Jan 2009 18:37:58 -0000
From: "Attiglah, Mama" <Mama_Attiglah at ssga.com>
Subject: [R] R compilation
To: <r-sig-finance at stat.math.ethz.ch>
Cc: r-help at r-project.org, r-sig-hpc at r-project.org,
	r-sig-db at stat.math.ethz.ch
Message-ID:
	<AD34C27D4F3A0649ACE5DB999EC62E50E050BA at LCPPW1089.corp.statestr.com>
Content-Type: text/plain;	charset="iso-8859-1"


Hi Mates, 
I have a very long R code that needs to go to production but my portfolio managers do not use R language and the software is not supported by my bank. 
Is there any way I can compile the code to an executable file and make it usable to my portfolio managers who have no knowledge at all of R? 

Thanks 

Mama 
 ----- 
Mama Attiglah, PhD
Quantitative Strategist
Liability Driven Investment 
State Street Global Advisors 
25 Bank Street, London E14 5NU 
+44(0)20 7698 6290 (Direct Line)
+44 (0)207 004 2968 (Direct Fax) 
Authorised and regulated by the Financial Services Authority.
State Street Global Advisors Limited, a company registered in England with company number 2509928
and VAT number 5576591 81 and whose registered office is...{{dropped:12}}



------------------------------

Message: 59
Date: Wed, 28 Jan 2009 14:38:15 -0500
From: jim holtman <jholtman at gmail.com>
Subject: Re: [R] Get median of each column

Cc: r-help at r-project.org
Message-ID:
	<644e1f320901281138m7935f39cr77e92d9ccb67b35b at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

?apply

            

      
      
      
    

        
[,1] [,2] [,3] [,4] [,5]
[1,]    1    6   11   16   21
[2,]    2    7   12   17   22
[3,]    3    8   13   18   23
[4,]    4    9   14   19   24
[5,]    5   10   15   20   25

            

      
      
      
    

        
[1]  3  8 13 18 23

            

      
      
      
    

        
wrote:

            

      
      
      
    

        

      
      
    

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

What is the problem that you are trying to solve?



------------------------------

Message: 60
Date: Wed, 28 Jan 2009 14:39:40 -0500
From: jim holtman <jholtman at gmail.com>
Subject: Re: [R] Saving plot into file without showing it
To: julien cuisinier <j_cuisinier at hotmail.com>
Cc: r-help at r-project.org
Message-ID:
	<644e1f320901281139h134ba472nb3673fddbfc79e05 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

pdf("yourFile.pdf")
plot(1)
plot(2)
plot(3)
.....
dev.off()

On Wed, Jan 28, 2009 at 12:26 PM, julien cuisinier

        
<j_cuisinier at hotmail.com> wrote:

            

      
      
      
    

        

      
      
    

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

What is the problem that you are trying to solve?



------------------------------

Message: 61
Date: Wed, 28 Jan 2009 20:39:09 +0100
From: Stephan Kolassa <Stephan.Kolassa at gmx.de>
Subject: Re: [R] Get median of each column

Cc: "r-help at r-project.org" <r-help at r-project.org>
Message-ID: <4980B45D.4000204 at gmx.de>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Assuming your data are in a data.frame called dataset,

apply(dataset,2,median)

should work. Look at

?apply

HTH,
Stephan


Frank Zhang schrieb:

            

      
      
      
    

        

      
      
    

        
------------------------------

Message: 62
Date: Wed, 28 Jan 2009 20:40:33 +0100
From: Stephan Kolassa <Stephan.Kolassa at gmx.de>
Subject: Re: [R] Saving plot into file without showing it
To: julien cuisinier <j_cuisinier at hotmail.com>
Cc: r-help at r-project.org
Message-ID: <4980B4B1.9090504 at gmx.de>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Try

pdf("foo.pdf")
   plot(x)
dev.off()

Other possibilities are jpeg(), tiff(), postscript() etc.

HTH,
Stephan

julien cuisinier schrieb:

            

      
      
      
    

        

      
      
    

        
------------------------------

Message: 63
Date: Wed, 28 Jan 2009 20:44:53 +0100
From: "Strubbe Diederik" <diederik.strubbe at ua.ac.be>
Subject: Re: [R] Repeated measures design for GAM? - corrected
	question...
To: <r-help at R-project.org>
Message-ID:
	<C9854550FEF14846A136100B3EC52F73B6B5AF at xmail05.ad.ua.ac.be>
Content-Type: text/plain

Dear Simon,
Many thanks for pointing me to the GAMM! For clarification, Bird_abundance are breeding densities ( e.g. 1.25 BP/ha, 2.20 BP/ha,...) and count is just the actual survey(e.g. first_survey,...). The dataset looks like
Bird_abundance	Study_area	YEAR	COUNT	X1	X2	X3	X4 
0.15	area_1	2004	first_survey	?	?	?	?
1.26	area_1	2004	second_survey	?	?	?	?
2.47	area_1	2005	third_survey	?	?	?	?
0.00	area_1	2005	fourth_survey	?	?	?	?
0.23	area_1	2006	fifht_survey	?	?	?	?
2.64	area_1	2006	sixth_survey	?	?	?	?
4.14	area_2	2004	first_survey	?	?	?	?
5.00	area_2	2004	second_survey	?	?	?	?
6.80	area_2	2005	third_survey	?	?	?	?
0.15	area_2	2005	fourth_survey	?	?	?	?
0.25	area_2	2006	fifht_survey	?	?	?	?
2.36	area_2	2006	sixth_survey	?	?	?	?
2.59	area_3	2004	first_survey	?	?	?	?
6.31	area_3	2004	second_survey	?	?	?	?
0.15	area_3	2005	third_survey	?	?	?	?
2.85	area_3	2005	fourth_survey	?	?	?	?
2.48	area_3	2006	fifht_survey	?	?	?	?
1.23	area_3	2006	sixth_survey	?	?	?	?
?	?	?	?	?	?	?	?

Am I correct in assuming the following is a valid syntax for this repeated measures design?:

model <-gamm(Bird_abundance ~ YEAR + s(X1)+ s(X2)+ s(X3)+ s(X4),random=list(count=~1,park=~1))

best wishes and thanks again,

Diederik





Diederik Strubbe
Evolutionary Ecology Group
Department of Biology, University of Antwerp
Universiteitsplein 1
B-2610 Antwerp, Belgium
http://webhost.ua.ac.be/deco
tel : 32 3 820 23 85



-----Original Message-----
From: Strubbe Diederik
Sent: Wed 28-1-2009 18:09
To: r-help at R-project.org
Subject: Repeated measures design for GAM? - corrected question...

Dear all,

I have a question on the use of GAM with repeated measures. My dataset is as follows:
- a number of study areas where bird abundance has been determined. Counts have been performed in 3 consecutive years and there were 2 counts per year (i.e. in total 6 counts).
- a number of environmental predictors that do not change over year Xi).
When using a GLM, a repeated measures design would like: (for example)

lme(Bird_abundance = study_area + count +year+ X1 + X2 + X3,random = ~count|study_area).

However, I have found no analogue design for a GAM. For now, I have averaged my bird abundances but I wondered whether a more subtle and elegant strategy exists...?

Many thanks,


Diederik

Diederik Strubbe
Evolutionary Ecology Group
Department of Biology, University of Antwerp
Universiteitsplein 1
B-2610 Antwerp, Belgium
http://webhost.ua.ac.be/deco
tel : 32 3 820 23 85







------------------------------

Message: 64
Date: Thu, 29 Jan 2009 08:53:44 +1300
From: Rolf Turner <r.turner at auckland.ac.nz>
Subject: Re: [R] Get median of each column
To: Stephan Kolassa <Stephan.Kolassa at gmx.de>
Cc: "r-help at r-project.org" <r-help at r-project.org>
Message-ID: <81B1D521-D4BE-451D-BC74-38B17F9D2EBE at auckland.ac.nz>
Content-Type: text/plain; charset="US-ASCII"; format=flowed

        
On 29/01/2009, at 8:39 AM, Stephan Kolassa wrote:

        

            

      
      
      
    

        
Note that apply() works with ***matrices***.  The foregoing code will
work, given that all columns of ``dataset'' are numeric, due to the
fact that apply will *coerce* a data frame to a matrix.

However it should always be remembered that

[[elided Yahoo spam]]

cheers,

	Rolf Turner

######################################################################
Attention:\ This e-mail message is privileged and confid...{{dropped:9}}



------------------------------

Message: 65
Date: Wed, 28 Jan 2009 21:21:07 +0100
From: Stephan Kolassa <Stephan.Kolassa at gmx.de>
Subject: Re: [R] Power analysis for MANOVA?
To: adik at ilovebacon.org
Cc: r-help at r-project.org
Message-ID: <4980BE33.3020008 at gmx.de>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi Adam,

first: I really don't know much about MANOVA, so I sadly can't help you 
without learning about it an Pillai's V... which I would be glad to do, 
[[elided Yahoo spam]]

Second: you seem to be doing a kind of "post-hoc power analysis", "my 
result isn't significant, perhaps that's due to low power? Let's look at 
the power of my experiment!" My impression is that "post-hoc power 
analysis" and its interpretation is, shall we say, not entirely accepted 
within the statistical community, see:

Hoenig, J. M., & Heisey, D. M. (2001, February). The abuse of power: The 
pervasive fallacy of power calculations for data analysis. The American 
Statistician, 55 (1), 1-6

And this:
http://staff.pubhealth.ku.dk/~bxc/SDC-courses/power.pdf

However, I am sure that lots of people can discuss this more competently 
than me...

Best wishes
Stephan


Adam D. I. Kramer schrieb:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        
------------------------------

Message: 66
Date: Wed, 28 Jan 2009 21:28:00 +0100
From: Stephan Kolassa <Stephan.Kolassa at gmx.de>
Subject: Re: [R] Get median of each column
To: Rolf Turner <r.turner at auckland.ac.nz>
Cc: "r-help at r-project.org" <r-help at r-project.org>
Message-ID: <4980BFD0.5070301 at gmx.de>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Thank you, Rolf, for this well-deserved spanking :-)

I promise to amend my ways and think before I send in the future.

Best,
Stephan

Rolf Turner schrieb:

            

      
      
      
    

        
[[elided Yahoo spam]]

            

      
      
      
    

        
------------------------------

Message: 67
Date: Wed, 28 Jan 2009 14:33:47 -0600
From: Kumudan <cybermails at gmail.com>
Subject: [R] Neighborhood distance calculator
To: r-help at r-project.org
Message-ID:
	<d5081b140901281233v44dca65es7ced065502379055 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi all,

I am new to R, hence this question. I have a set of points with X and
Y coordinates. I would like to build an R code to calculate the
distances of points within a specified neighborhood (circular range)
for each point. I would like the code to be a function, so that I can
call the function, specifying parameters (data file, distance), from
another piece of code. Also, I would like the output to be as:

output = list(array)
.........code...........
........new code.....
return(output)

Something like this--
[[1496]]
[1] 1490 1491 1492 1493 1494 1495

The most important thing, however, is that I want to run the code for
100,000+ points. The current code I have calculates the neighborhood
distances for all the points with ever point, and then selects only
those points within the specified distance parameter. This code
crashes when I have over 40,000 points. Therefore, I need to figure
out a way to preclude the step where it calculates all of the paired
distances, and rather only those points within the specified distance
parameter. Please, see below for the existing code, and a sample data.
Thanks a lot for your time and effort.

Best,
Kumudan

Kumudan Grubh
EEB Graduate student
Iowa State University

-------------------------------------------------------------------------------------------------------------------------------------------------------
#--Code--
#transform coordinates in kilometers, and redefine origin
newx=(XCOORD-min(XCOORD))/1000
newy=(YCOORD-min(YCOORD))/1000
plot(newx,newy,pch=20,xlab="X coordinate (km)",ylab="Y coordinate (km)")

#set of new locations to be used from here on
tr.locs=cbind(newx,newy)

#the functions necessary for estimation are written in an external
program. All you need to do is to run this program one. To do this,
you could "source" this code
source("D:/...../Functions_distance.R")

#define distance-based neighborhood
nb.tr=dist.neighbors(tr.locs,2)
----------------------------------------------------------------------------------------------------------------------------------------------------------
#---Function_distance.R   <- Function to calculate distance of pairs
of neighbors
#start by defining neighbors
library(spatstat)#need this to compute distances between all points in a data

dist.neighbors=function(data,distance)
#distance is set by user
{
#data has the x and y on the first two columns. Could have more than
two columns, or exactly two columns, it doesn't matter.
#produces a "list" object with a vector of the neighbors for each location
#distance defines the range within which we define neighbors
nd=length(data[,1])
nbmat=list(array)
dist=pairdist(data[,1:2])
  for(i in 1:nd){
  nbmat[[i]]=0
 	for(j in 1:nd) if((dist[i,j]<distance)&(i!=j)) nbmat[[i]]=c(nbmat[[i]],j)
 	nbmat[[i]]=nbmat[[i]][nbmat[[i]]!=0]}
return(nbmat)		
}
------------------------------------------------------------------------------------------------------------------------------------

Data
-----------------------------------------------------------------------------------
XCOORD	YCOORD
544312.87500000000	4851169.00000000000
542705.87500000000	4851165.00000000000
541068.87500000000	4851155.00000000000
537861.81250000000	4851123.00000000000
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571901.87500000000	4827229.50000000000
570293.87500000000	4827212.50000000000
568683.87500000000	4827208.50000000000
567078.87500000000	4827184.50000000000
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563834.87500000000	4827155.50000000000
562230.87500000000	4827134.50000000000
560626.87500000000	4827118.50000000000
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557407.87500000000	4827100.50000000000
555792.87500000000	4827098.50000000000
554127.87500000000	4827090.50000000000
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546074.81250000000	4827034.50000000000
581561.93750000000	4826547.50000000000
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559031.81250000000	4820684.50000000000
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578390.81250000000	4820097.50000000000
577590.81250000000	4820082.50000000000
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575188.81250000000	4820052.50000000000
574385.81250000000	4820040.50000000000
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570360.81250000000	4819985.50000000000
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567142.81250000000	4819976.50000000000
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563887.81250000000	4819912.50000000000
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562270.81250000000	4819901.50000000000
561466.81250000000	4819893.50000000000
560662.81250000000	4819885.50000000000
559848.81250000000	4819882.50000000000
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560678.75000000000	4817479.50000000000
559056.75000000000	4817467.50000000000
557445.75000000000	4817453.50000000000
555831.75000000000	4817436.50000000000
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577645.75000000000	4816860.50000000000
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575228.75000000000	4816846.50000000000
570389.75000000000	4816784.50000000000
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562297.75000000000	4816695.50000000000
560687.75000000000	4816678.50000000000
559875.75000000000	4816670.50000000000
559063.75000000000	4816662.50000000000
557453.75000000000	4816645.50000000000
556645.75000000000	4816637.50000000000
555838.75000000000	4816629.50000000000



------------------------------

Message: 68
Date: Wed, 28 Jan 2009 20:41:08 +0000
From: glenn <g1enn.roberts at btinternet.com>
Subject: [R] Cor(df,method = "kendall")
To: "r-help at r-project.org" <r-help at r-project.org>
Message-ID: <C5A67364.1140%g1enn.roberts at btinternet.com>
Content-Type: text/plain

Hi All,

Does anyone know of any issues at all with using;

Cor(df,method = ?kendall?)

On a dataframe (df) 13 columns wide say?

Seems to hang my system for a while in calculating the correlation matrix ?
appreciate it is doing some ranking calculations so I am expecting too much
that it should return immediately ? In particular trying to use function in
Excel (reval) and I am getting OLE error boxes as RGUI hangs.

Many Thanks.

Glenn




------------------------------

Message: 69
Date: Wed, 28 Jan 2009 15:46:43 -0500
From: stephen sefick <ssefick at gmail.com>
Subject: Re: [R] R compilation
To: "Attiglah, Mama" <Mama_Attiglah at ssga.com>
Cc: r-sig-finance at stat.math.ethz.ch, r-help at r-project.org,
	r-sig-hpc at r-project.org, r-sig-db at stat.math.ethz.ch
Message-ID:
	<c502a9e10901281246u2d14b1d7od4161f733f9bfc0f at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

yes, first don't crosspost.  It all depends on what OS .. blah, blah,
blah.  You must read the posting guide because it will up your chances
of a reply.

        
On Wed, Jan 28, 2009 at 1:37 PM, Attiglah, Mama <Mama_Attiglah at ssga.com> wrote:

            

      
      
      
    

        
------------------------------

Message: 70
Date: Wed, 28 Jan 2009 14:51:25 -0600
From: roger koenker <rkoenker at uiuc.edu>
Subject: Re: [R] Neighborhood distance calculator
To: Kumudan <cybermails at gmail.com>
Cc: r-help <r-help at r-project.org>
Message-ID: <FEEDB763-0E6E-4E7F-8A6D-C10B94884FC3 at uiuc.edu>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes

If you are willing to dig into the adjacency information returned from
tri.mesh in the tripack package, this could be done quite efficiently.

url:    www.econ.uiuc.edu/~roger            Roger Koenker
email    rkoenker at uiuc.edu            Department of Economics
vox:     217-333-4558                University of Illinois
fax:       217-244-6678                Champaign, IL 61820

        
On Jan 28, 2009, at 2:33 PM, Kumudan wrote:

        

            

      
      
      
    

        

      
      
    

        
------------------------------

Message: 71
Date: Wed, 28 Jan 2009 12:03:50 -0800 (PST)
From: pfc_ivan <pfc_ivan at hotmail.com>
Subject: [R]  Newbie Question About Histograms
To: r-help at r-project.org
Message-ID: <21713626.post at talk.nabble.com>
Content-Type: text/plain; charset=us-ascii


Hello everyone. Just have a question , cant figure out how to make this
histogram. 

I have this table, that i stored in a variable name new.data2. Table looks
like this

Year GeoArea SmpNo Month Gear Maturity Length Age YearC
1989       1   362    10   22        1    225   1  1988
1991       1   267    10   10        1    191   1  1990
1991       1   267    10   10        1    202   1  1990
1992       1   305    10    8        1    162   1  1991
1992       1   305    10    8        1    165   1  1991
1992       1   305    10    8        1    166   1  1991
1992       1   305    10    8        1    167   1  1991
1992       1   305    10    8        1    167   1  1991
1992       1   305    10    8        1    169   1  1991
1992       1   305    10    8        1    170   1  1991

Now I need to make a histogram of Length vs YearC. I would guess that Length
would be on the Y-axis and YearC variable would be on X-axis. I have tried
many different combinations with command 'hist' but im always getting error
" 'x' must be numeric " ... I think im getting that error because of the
header which is not numeric. Any help would be appreciated. Thanks guys. 

Ivan.
-- 
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------------------------------

Message: 72
Date: Wed, 28 Jan 2009 12:04:18 -0800 (PST)
From: Sea Captain 1779 <dbowen at measinc.com>
Subject: [R]  Help with normal distribution in random samples...
To: r-help at r-project.org
Message-ID: <21713636.post at talk.nabble.com>
Content-Type: text/plain; charset=us-ascii


Hi!!!

First time 'R' user looking for a little assistance.  Here is what I have so
far:

practice1 = matrix ((runif(5000, min =0, max = 12)), 100)

which is creating 50 samples, for 100 cases, distributed between 0-12.  What
I would like is to be able to set the mean and SD so that the data is
normally distributed around lets say 7.  Any help I can get with achieving
[[elided Yahoo spam]]

-Dan
-- 
View this message in context: http://www.nabble.com/Help-with-normal-distribution-in-random-samples...-tp21713636p21713636.html
Sent from the R help mailing list archive at Nabble.com.



------------------------------

Message: 73
Date: Wed, 28 Jan 2009 12:37:57 -0800 (PST)
From: Alice Lin <alice.ly at gmail.com>
Subject: [R]  Text data
To: r-help at r-project.org
Message-ID: <21714334.post at talk.nabble.com>
Content-Type: text/plain; charset=us-ascii


i have a data column of text entries:
26M_AN_C.bmp
22M_AN_C.bmp
20M_HA_O.bmp
20M_AN_C.bmp
26M_HA_O.bmp
22M_HA_O.bmp
31M_AN_C.bmp
38M_HA_O.bmp
.
.
.
.


And I would like to sort by the middle tag: AN, HA, etc.
Is there a way to parse text data in R? 

In excel, I would have used the "left" and "right" function to cut out just
the middle two letters out and put into another column to sort by. 

Thanks!

-- 
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Sent from the R help mailing list archive at Nabble.com.



------------------------------

Message: 74
Date: Thu, 29 Jan 2009 10:10:38 +1300
From: "Peter Alspach" <PAlspach at hortresearch.co.nz>
Subject: Re: [R] Newbie Question About Histograms
To: "pfc_ivan" <pfc_ivan at hotmail.com>, <r-help at r-project.org>
Message-ID:
	<EC0F8FF776F3F74E9C63CE16641C9628037A486D at AKLEXB02.hort.net.nz>
Content-Type: text/plain;	charset="us-ascii"

Kia ora Ivan

I think you might want a barplot.

?hist

under 'See Also:' states:

     Typical plots with vertical bars are _not_ histograms.  Consider
     'barplot' or 'plot(*, type = "h")' for such bar plots.

[The online help in R is good.]

HTH ....

Peter Alspach

            

      
      
      
    

        

      
      
    

        
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------------------------------

Message: 75
Date: Wed, 28 Jan 2009 13:11:57 -0800 (PST)

Subject: [R] Changing histogram stack in qplot
To: R-help at r-project.org
Message-ID: <186567.94177.qm at web56006.mail.re3.yahoo.com>
Content-Type: text/plain

I've been using qplot pretty successfully to generate stacked histograms.  However, it appears that I need to tweak the colors a little.  

I've got three temperature variables (characters not numeric) and I need to change from the default qplot colors to the following:
Low = Blue
Middle = black
High = Red

Here is pseudo code of what I have currently:qplot(Run, data = TestData, breaks = hist_breaks, ,  
          fill = TestData$Temperature, 
          main = short_title) +
          scale_x_continuous("Run, Radians") + scale_y_continuous("Frequency") + 
          scale_fill_discrete("Temperature")

Thanks for any advice and insights.




      



------------------------------

Message: 76
Date: Wed, 28 Jan 2009 16:14:48 -0500
From: "Antonio, Fabio Di Narzo" <antonio.fabio at gmail.com>
Subject: Re: [R] Neighborhood distance calculator
To: roger koenker <rkoenker at uiuc.edu>
Cc: r-help <r-help at r-project.org>, Kumudan <cybermails at gmail.com>
Message-ID:
	<b0808fdc0901281314j20f9f995hd3b68d345a961cc at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

The tseriesChaos package has an internal function "find_knearests"
which deals with a similar problem using a box-assisted search
strategy to alleviate time complexity explosion.
However, you will have to dig into the C sources, as these have no man pages.

HTH,
f.

2009/1/28 roger koenker <rkoenker at uiuc.edu>:

            

      
      
      
    

        
-- 
Antonio, Fabio Di Narzo
Ph.D. student at
Department of Statistical Sciences
University of Bologna, Italy



------------------------------

Message: 77
Date: Wed, 28 Jan 2009 16:18:41 -0500
From: jim holtman <jholtman at gmail.com>
Subject: Re: [R] Text data
To: Alice Lin <alice.ly at gmail.com>
Cc: r-help at r-project.org
Message-ID:
	<644e1f320901281318m7550429y763caa0c96824316 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

This will sort on those characters:

            

      
      
      
    

        
+ 22M_AN_C.bmp
+ 20M_HA_O.bmp
+ 20M_AN_C.bmp
+ 26M_HA_O.bmp
+ 22M_HA_O.bmp
+ 31M_AN_C.bmp
+ 38M_HA_O.bmp"))

            

      
      
      
    

        
[1] "AN" "AN" "HA" "AN" "HA" "HA" "AN" "HA"

            

      
      
      
    

        
[1] "26M_AN_C.bmp" "22M_AN_C.bmp" "20M_AN_C.bmp" "31M_AN_C.bmp"
"20M_HA_O.bmp" "26M_HA_O.bmp" "22M_HA_O.bmp" "38M_HA_O.bmp"

            

      
      
      
    

        

        
On Wed, Jan 28, 2009 at 3:37 PM, Alice Lin <alice.ly at gmail.com> wrote:

            

      
      
      
    

        

      
      
    

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

What is the problem that you are trying to solve?



------------------------------

Message: 78
Date: Wed, 28 Jan 2009 17:23:35 -0400
From: Mike Lawrence <mike at thatmike.com>
Subject: Re: [R] Help with normal distribution in random samples...
To: Sea Captain 1779 <dbowen at measinc.com>
Cc: r-help at r-project.org
Message-ID:
	<8ae7763a0901281323u3e87e032gc8ceff5673246c8a at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

?rnorm

        
On Wed, Jan 28, 2009 at 4:04 PM, Sea Captain 1779 <dbowen at measinc.com> wrote:

            

      
      
      
    

        
[[elided Yahoo spam]]

            

      
      
      
    

        

      
      
    

        
-- 
Mike Lawrence
Graduate Student
Department of Psychology
Dalhousie University
www.thatmike.com

Looking to arrange a meeting? Check my public calendar:
http://www.thatmike.com/mikes-public-calendar

~ Certainty is folly... I think. ~



------------------------------

Message: 79
Date: Wed, 28 Jan 2009 16:26:58 -0500
From: "Nutter, Benjamin" <NutterB at ccf.org>
Subject: Re: [R] Text data
To: "Alice Lin" <alice.ly at gmail.com>, r-help at r-project.org
Message-ID:
	<07773E68C32A644CA47651463E79E5C202476EDF at CCHSCLEXMB68.cc.ad.cchs.net>
Content-Type: text/plain; charset=us-ascii

Jim's solution is more elegant than the following (and probably more
efficient) but you could also try the following (This let's you sort by
AN/HN, and then by the number at the start of the filename):

            

      
      
      
    

        
"20M_AN_C.bmp", "26M_HA_O.bmp", "22M_HA_O.bmp",
             "31M_AN_C.bmp", "38M_HA_O.bmp")

            

      
      
      
    

        
[1] 20M_AN_C.bmp" "22M_AN_C.bmp" "26M_AN_C.bmp" "31M_AN_C.bmp"
"20M_HA_O.bmp"
[6] "22M_HA_O.bmp" "26M_HA_O.bmp" "38M_HA_O.bmp"

-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
On Behalf Of Alice Lin
Sent: Wednesday, January 28, 2009 3:38 PM
To: r-help at r-project.org
Subject: [R] Text data


i have a data column of text entries:
26M_AN_C.bmp
22M_AN_C.bmp
20M_HA_O.bmp
20M_AN_C.bmp
26M_HA_O.bmp
22M_HA_O.bmp
31M_AN_C.bmp
38M_HA_O.bmp
.
.
.
.


And I would like to sort by the middle tag: AN, HA, etc.
Is there a way to parse text data in R? 

In excel, I would have used the "left" and "right" function to cut out
just
the middle two letters out and put into another column to sort by. 

Thanks!

-- 
View this message in context:
http://www.nabble.com/Text-data-tp21714334p21714334.html
Sent from the R help mailing list archive at Nabble.com.

______________________________________________
R-help at 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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------------------------------

Message: 80
Date: Wed, 28 Jan 2009 13:26:55 -0800
From: "Nordlund, Dan (DSHS/RDA)" <NordlDJ at dshs.wa.gov>
Subject: Re: [R] Help with normal distribution in random samples...
To: "Sea Captain 1779" <dbowen at measinc.com>, r-help at r-project.org
Message-ID:
	<941871A13165C2418EC144ACB212BDB0BEB2A5 at dshsmxoly1504g.dshs.wa.lcl>
Content-Type: text/plain; charset=iso-8859-1

            

      
      
      
    

        
[[elided Yahoo spam]]

            

      
      
      
    

        
Use rnorm() instead of runif().

Hope this is helpful,

A different Dan

Daniel J. Nordlund
Washington State Department of Social and Health Services
Planning, Performance, and Accountability
Research and Data Analysis Division
Olympia, WA  98504-5204





------------------------------

Message: 81
Date: Wed, 28 Jan 2009 15:32:13 -0600
From: hadley wickham <h.wickham at gmail.com>
Subject: Re: [R] Changing histogram stack in qplot

Cc: R-help at r-project.org
Message-ID:
	<f8e6ff050901281332r4aeee3b7jc7b8398791f3c57b at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi Jason,

You'll need scale_fill_manual(values = c(low = "blue", middle =
"black", high = "red"))

See http://had.co.nz/ggplot2/scale_manual.html for more examples/details.

Regards,

Hadley


wrote:

            

      
      
      
    

        

      
      
    

        
-- 
http://had.co.nz/



------------------------------

Message: 82
Date: Wed, 28 Jan 2009 16:33:48 -0500
From: Ubuntu Diego <ubuntu.diego at gmail.com>
Subject: Re: [R] Memory issue?
To: "r-help at r-project.org" <r-help at r-project.org>
Message-ID: <1233178428.12820.38.camel at Halley>
Content-Type: text/plain

I had similar issues with memory occupancy. You should explicitly call
gc() to call the garbage collector (free memory routine) after you do
rm() of the big objects. 

D.



------------------------------

Message: 83
Date: Wed, 28 Jan 2009 13:08:33 -0800 (PST)
From: pfc_ivan <pfc_ivan at hotmail.com>
Subject: Re: [R] Newbie Question About Histograms
To: r-help at r-project.org
Message-ID: <21714995.post at talk.nabble.com>
Content-Type: text/plain; charset=us-ascii



Also I forgot to say that The Y-axis values for each YearC would be the mean
value of all the Lenghts that happen in that YearC. Basically I cant figure
out how to put the mean values of Lengths for each YearC on Y axis. 

Thanks in advance!
-- 
View this message in context: http://www.nabble.com/Newbie-Question-About-Histograms-tp21713626p21714995.html
Sent from the R help mailing list archive at Nabble.com.



------------------------------

Message: 84
Date: Wed, 28 Jan 2009 13:14:48 -0800 (PST)
From: Cl?ment D <dudouet at gmail.com>
Subject: Re: [R] rproxy.dll
To: r-help at r-project.org
Message-ID: <21715182.post at talk.nabble.com>
Content-Type: text/plain; charset=UTF-8

        
Duncan Murdoch-2 wrote:

            

      
      
      
    

        

      
      
    

        
Hi!

Since rproxy.dll has been replaced by rscproxy, how can I use the (R)-D COM
dll?

Cheers!

Cl?ment D
-- 
View this message in context: http://www.nabble.com/rproxy.dll-tp20165941p21715182.html
Sent from the R help mailing list archive at Nabble.com.



------------------------------

Message: 85
Date: Wed, 28 Jan 2009 13:59:03 -0800 (PST)
From: SnowManPaddington <wiwiana at gmail.com>
Subject: Re: [R] for/if loop
To: r-help at r-project.org
Message-ID: <21715928.post at talk.nabble.com>
Content-Type: text/plain; charset=us-ascii


Hi ya, I've revised the code (and finally know what I m doing.. :-D)

The good news is.. I dont get any error message, but the bad news is the
following optim generate no results. I still think there is something to do
[[elided Yahoo spam]]



pp=1
rr=1

for (ii in 1:n){
	if (!(panel[ii] == pp)){
		hll[pp,1] == sum(lselb1[rr:ii-1])
		hll[pp,2] == sum(lselb2[rr:ii-1])
		rr==ii
		pp==pp+1
		}
	
	if (ii==n){
		hll[pp,1] == sum(lselb1[rr:ii])
		hll[pp,2] == sum(lselb2[rr:ii])
		rr==ii
		pp==pp+1
		}
	ii=ii+1
}





pp=1
rr=1

for (ii in 1:n){
	if (!(panel[ii] == pp)){
		hll[pp,1] == sum(lselb1[rr:ii-1])
		hll[pp,2] == sum(lselb2[rr:ii-1])
		rr==ii
		pp==pp+1
		}
	
	if (ii==n){
		hll[pp,1] == sum(lselb1[rr:ii])
		hll[pp,2] == sum(lselb2[rr:ii])
		rr==ii
		pp==pp+1
		}
	ii=ii+1
}

        
SnowManPaddington wrote:

            

      
      
      
    

        
[[elided Yahoo spam]]

            

      
      
      
    

        
-- 
View this message in context: http://www.nabble.com/for-if-loop-tp21701496p21715928.html
Sent from the R help mailing list archive at Nabble.com.



------------------------------

Message: 86
Date: Wed, 28 Jan 2009 23:24:12 +0100
From: Eik Vettorazzi <E.Vettorazzi at uke.uni-hamburg.de>
Subject: Re: [R] Newbie Question About Histograms
To: pfc_ivan <pfc_ivan at hotmail.com>
Cc: r-help at r-project.org
Message-ID: <4980DB0C.10307 at uke.uni-hamburg.de>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

How about

 > dta<-read.table("clipboard",header=T)
 > means<-aggregate(dta$Length,by=list(YearC=dta$YearC),FUN=mean)
 > barplot(means[,2],names.arg=means[,1])

you may have a look at ?barplot to see (lots of) options for fine tuning 
the plot.

hth.

pfc_ivan schrieb:

            

      
      
      
    

        
------------------------------

Message: 87
Date: Thu, 29 Jan 2009 09:28:42 +1100
From: Gad Abraham <gabraham at csse.unimelb.edu.au>
Subject: Re: [R] Using R in a web application
To: Will Glass-Husain <wglasshusain at gmail.com>
Cc: r-help at stat.math.ethz.ch
Message-ID: <4980DC1A.8000006 at csse.unimelb.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

        
Will Glass-Husain wrote:

            

      
      
      
    

        
Have a look at Rserve (http://www.rforge.net/Rserve), I've never used it 
but it might be useful to you.


-- 
Gad Abraham
Dept. CSSE and NICTA
The University of Melbourne
Parkville 3010, Victoria, Australia
email: gabraham at csse.unimelb.edu.au
web: http://www.csse.unimelb.edu.au/~gabraham



------------------------------

Message: 88
Date: Wed, 28 Jan 2009 14:37:15 -0800 (PST)

Subject: Re: [R] Changing histogram stack in qplot
To: R-help at r-project.org
Message-ID: <370998.28760.qm at web56006.mail.re3.yahoo.com>
Content-Type: text/plain

Worked beautifully!  Thank you again for providing such a flexible package.

        
--- On Wed, 1/28/09, hadley wickham <h.wickham at gmail.com> wrote:

        
From: hadley wickham <h.wickham at gmail.com>
Subject: Re: [R] Changing histogram stack in qplot

Cc: R-help at r-project.org
Date: Wednesday, January 28, 2009, 3:32 PM

Hi Jason,

You'll need scale_fill_manual(values = c(low = "blue", middle =
"black", high = "red"))

See http://had.co.nz/ggplot2/scale_manual.html for more examples/details.

Regards,

Hadley


wrote:

            

      
      
      
    

        
histograms.  However, it appears that I need to tweak the colors a little.

            

      
      
      
    

        
need to change from the default qplot colors to the following:

            

      
      
      
    

        
breaks = hist_breaks, ,

            

      
      
      
    

        
scale_y_continuous("Frequency") +

            

      
      
      
    

        

      
      
    

        
http://www.R-project.org/posting-guide.html

        

      
      
    

        
-- 
http://had.co.nz/



      



------------------------------

Message: 89
Date: Wed, 28 Jan 2009 16:39:06 -0600
From: Joseph Magagnoli <jcm331 at gmail.com>
Subject: [R]  Dynamic random effects model
To: r-help at r-project.org
Message-ID:
	<9729f0ae0901281439h784649d2o3d6d29ec9f0c7794 at mail.gmail.com>
Content-Type: text/plain

All R experts,
How do I fit a dynamic Random effects model with a binary dependent variable
in R
Thanks
JCM




------------------------------

Message: 90
Date: Wed, 28 Jan 2009 16:41:40 -0600
From: <davidr at rhotrading.com>
Subject: Re: [R] [SPAM] - Re:  for/if loop - Bayesian Filter detected
	spam
To: "SnowManPaddington" <wiwiana at gmail.com>, <r-help at r-project.org>
Message-ID:
	<F9F2A641C593D7408925574C05A7BE77022A612A at rhopost.rhotrading.com>
Content-Type: text/plain;	charset="us-ascii"

Well, maybe you are just bad at typing then ;-)

The lines rr==ii, pp==pp+1, etc. are not setting rr and pp but comparing
them.
Probably you want rr <- ii and pp <- pp+1, etc.
And the last line of your loop 'ii=ii+1' means that,
since the for statement is already incrementing ii,
you are incrementing it twice and skipping the even indices. Omit this
line probably.
You are also forgetting(?) the operator precedence in
sum(lselb1[rr:ii-1]) and similar lines.
Note that this is equivalent to sum(lselb1[(rr-1):(ii-1)]); is that what
you meant?
Or did you want sum(lselb1[rr:(ii-1)])?
You are changing some variables but not asking R to print anything as
far as I can see.
To see the results, ask R to print hll.

HTH,
-- David

-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
On Behalf Of SnowManPaddington
Sent: Wednesday, January 28, 2009 3:59 PM
To: r-help at r-project.org
Subject: [SPAM] - Re: [R] for/if loop - Bayesian Filter detected spam


Hi ya, I've revised the code (and finally know what I m doing.. :-D)

The good news is.. I dont get any error message, but the bad news is the
following optim generate no results. I still think there is something to
do
[[elided Yahoo spam]]



pp=1
rr=1

for (ii in 1:n){
	if (!(panel[ii] == pp)){
		hll[pp,1] == sum(lselb1[rr:ii-1])
		hll[pp,2] == sum(lselb2[rr:ii-1])
		rr==ii
		pp==pp+1
		}
	
	if (ii==n){
		hll[pp,1] == sum(lselb1[rr:ii])
		hll[pp,2] == sum(lselb2[rr:ii])
		rr==ii
		pp==pp+1
		}
	ii=ii+1
}





pp=1
rr=1

for (ii in 1:n){
	if (!(panel[ii] == pp)){
		hll[pp,1] == sum(lselb1[rr:ii-1])
		hll[pp,2] == sum(lselb2[rr:ii-1])
		rr==ii
		pp==pp+1
		}
	
	if (ii==n){
		hll[pp,1] == sum(lselb1[rr:ii])
		hll[pp,2] == sum(lselb2[rr:ii])
		rr==ii
		pp==pp+1
		}
	ii=ii+1
}

        
SnowManPaddington wrote:

            

      
      
      
    

        
loop

            

      
      
      
    

        
panel

            

      
      
      
    

        
I

            

      
      
      
    

        
language
[[elided Yahoo spam]]

            

      
      
      
    

        
know

            

      
      
      
    

        
-- 
View this message in context:
http://www.nabble.com/for-if-loop-tp21701496p21715928.html
Sent from the R help mailing list archive at Nabble.com.

______________________________________________
R-help at 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.



------------------------------

Message: 91
Date: Wed, 28 Jan 2009 17:50:03 +0800
From: Wenxia Li <ringingfeeling at gmail.com>
Subject: [R] questions about histogram
To: r-help at r-project.org
Message-ID: <D05E2017-A927-4F62-A5A2-11C4CE9281F9 at gmail.com>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes

Hi all,

I'm a new R user. I have the following information about a data set  
and how to make a histogram?
data             number of observations
0-2                     25
2-10                  10
10-100             10
100-1000          5

I tried barplot(height=...,width=...,...), the output looks right but  
the x-axis is missing. How to fix it?
Also can I use<hist> to draw it?

Thanks!

WX



------------------------------

Message: 92
Date: Wed, 28 Jan 2009 15:08:14 -0800
From: Henrik Bengtsson <hb at stat.berkeley.edu>
Subject: Re: [R] [SPAM] - Re: for/if loop - Bayesian Filter detected
	spam
To: davidr at rhotrading.com
Cc: r-help at r-project.org, SnowManPaddington <wiwiana at gmail.com>
Message-ID:
	<59d7961d0901281508w1f304b74r3c30c6b91ec03e93 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

        
On Wed, Jan 28, 2009 at 2:41 PM,  <davidr at rhotrading.com> wrote:

            

      
      
      
    

        
That is actually not the case (because of the scoping rules for for(),
I think).  Example:

            

      
      
      
    

        
[1] 1
[1] 2
[1] 3
[1] 4
[1] 5

Another "counter intuitive" (though it isn't) example:

for (ii in 1:3) {
  cat("Outer ii:",ii,"\n");
  for (ii in ii:3) {
    cat("  Inner ii:",ii,"\n");
  }
}

Outer ii: 1
  Inner ii: 1
  Inner ii: 2
  Inner ii: 3
Outer ii: 2
  Inner ii: 2
  Inner ii: 3
Outer ii: 3
  Inner ii: 3

My $.02

/Henrik

            

      
      
      
    

        
[[elided Yahoo spam]]

            

      
      
      
    

        
[[elided Yahoo spam]]

            

      
      
      
    

        

      
      
    

        
------------------------------

Message: 93
Date: Wed, 28 Jan 2009 18:08:53 -0500
From: jim holtman <jholtman at gmail.com>
Subject: Re: [R] questions about histogram
To: Wenxia Li <ringingfeeling at gmail.com>
Cc: r-help at r-project.org
Message-ID:
	<644e1f320901281508t7bc7d8b2i7314b11d1da76e17 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Try this:

            

      
      
      
    

        
+ 2-10                  10
+ 10-100             10
+ 100-1000          5"))

            

      
      
      
    

        
V1 V2
1      0-2 25
2     2-10 10
3   10-100 10
4 100-1000  5

            

      
      
      
    

        
+ 2-10                  10
+ 10-100             10
+ 100-1000          5"))

            

      
      
      
    

        

        
On Wed, Jan 28, 2009 at 4:50 AM, Wenxia Li <ringingfeeling at gmail.com> wrote:

            

      
      
      
    

        

      
      
    

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

What is the problem that you are trying to solve?



------------------------------

Message: 94
Date: Wed, 28 Jan 2009 18:24:43 +0800
From: Wenxia Li <ringingfeeling at gmail.com>
Subject: Re: [R] questions about histogram
To: r-help at r-project.org
Message-ID: <9AA09DFB-A859-4ECA-B13D-BB329DF696FB at gmail.com>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes

it's a frequency histogram. The total area of the bars is 1, and the  
area of each bar represents its frequency, i.e.  
25/50,10/50,10/50,5/50, respectively. And the width of the bars are  
different.

        
On Jan 28, 2009, at 5:50 PM, Wenxia Li wrote:

        

            

      
      
      
    

        
------------------------------

Message: 95
Date: Wed, 28 Jan 2009 18:31:12 -0500
From: Jorge Ivan Velez <jorgeivanvelez at gmail.com>
Subject: Re: [R] questions about histogram
To: Wenxia Li <ringingfeeling at gmail.com>
Cc: r-help at r-project.org
Message-ID:
	<317737de0901281531n606d2484we61f1ff628c8747 at mail.gmail.com>
Content-Type: text/plain

Dear Wenxia,
Take a look at this post:

http://www.nabble.com/Histogram-for-grouped-data-in-R-to21624806.html#a21624806


HTH,

Jorge

        
On Wed, Jan 28, 2009 at 4:50 AM, Wenxia Li <ringingfeeling at gmail.com> wrote:

        

            

      
      
      
    

        

      
      
    

        
------------------------------

Message: 96
Date: Wed, 28 Jan 2009 21:30:04 -0500
From: Jorge Ivan Velez <jorgeivanvelez at gmail.com>
Subject: Re: [R] glm binomial loglog (NOT cloglog) link
To: William Simpson <william.a.simpson at gmail.com>
Cc: r-help at r-project.org
Message-ID:
	<317737de0901281830o468390b9occ3745a48c8cd268 at mail.gmail.com>
Content-Type: text/plain

Dear Bill,
Perhaps the "cloglog" function in the "VGAM" package might be useful for
you.

HTH,

Jorge


On Fri, Jan 23, 2009 at 11:32 AM, William Simpson <

        
william.a.simpson at gmail.com> wrote:

        

            

      
      
      
    

        

      
      
    

        
------------------------------

Message: 97
Date: Thu, 29 Jan 2009 02:31:18 +0000
From: Mark Wardle <mark at wardle.org>
Subject: Re: [R] Faced Problems with RODBC package 1.2-5 and 1.2-4 for
	windows
To: Nikhil Bhide <nikhil.bhide at tcs.com>
Cc: r-help at r-project.org
Message-ID:
	<b59a37130901281831m7fe573eby34b789e4f877168b at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

You need to include much more information.

Try creating a reproducible example - you may find the answer in the
process of doing this.

You may find the posting guide for the mailing list to be helpful -
you've had no replies because you haven't explained your problem well
enough.

Mark

2009/1/28 Nikhil Bhide <nikhil.bhide at tcs.com>:

            

      
      
      
    

        

      
      
    

        
-- 
Dr. Mark Wardle
Specialist registrar, Neurology
Cardiff, UK



------------------------------

Message: 98
Date: Wed, 28 Jan 2009 18:56:09 -0800 (PST)
From: "cameron.bracken" <cameron.bracken at gmail.com>
Subject: Re: [R] using Sweave with a master file that has several
	iputted .tex files
To: r-help at r-project.org
Message-ID: <21719963.post at talk.nabble.com>
Content-Type: text/plain; charset=us-ascii

        
Mark Wardle wrote:

            

      
      
      
    

        
The pgfSweave package is specifically designed for speeding up the
compilation time in large documents.  It is still in development (not on
CRAN) but might be worth checking out:

https://www.rforge.net/pgfSweave/

-Cameron Bracken
-- 
View this message in context: http://www.nabble.com/using-Sweave-with-a-master-file-that-has-several-iputted-.tex-files-tp21690580p21719963.html
Sent from the R help mailing list archive at Nabble.com.



------------------------------

Message: 99
Date: Wed, 28 Jan 2009 21:01:56 -0600
From: Bomee Park <bombom at stanford.edu>
Subject: [R]  standard error of logit parameters
To: r-help at R-project.org
Message-ID: <FD57ADE8-5658-4C1F-BD41-93454A60C0DF at stanford.edu>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes

Hi everyone.

I am now estimating the parameters for a logit model, and trying to  
get the estimates by laximizing the log_likelihood.
The nlm function works nicely for maximizing the -(log_likelihood) and  
returns the parameter estimates that minimize the static, and the  
gradients also, but don't have any clue how I can get the standard  
error for the parameters.

Any help will be greatly appreciated.
Thanks.



------------------------------

Message: 100
Date: Wed, 28 Jan 2009 16:45:41 -0800 (PST)
From: beyar <bxx at mailinator.com>
Subject: [R]  Ignore text when reading data
To: r-help at r-project.org
Message-ID: <21718709.post at talk.nabble.com>
Content-Type: text/plain; charset=us-ascii


Hi,
I have tab delimited text files containing numerical data,
like below, but many more columns.

As you can see, the first few lines are heading and file data.  I need to
skip these lines.  2 lines above where the numbers start is what I want to
use as my header rows.  I then want to ignore the next line (containing
units) and start importing data.  

The header row repeats.  i want to ignore the blank rows and text in the
data and then continue reading.  Is there an easy way to do this?  

thanks
Beyar


-------------------------
main data file - file 1
by mr x
etc


Time	out1	
Sec	mm
0.82495117	-0.020977303
1.3554688	-0.059330709
1.826416	-0.021419302
2.3295898	-0.051521059
2.8347168	-0.020661414


Time	out1	
Sec	mm
3.8679199	-0.000439643
4.3322754	-0.063477799
4.8015137	-0.024581354
5.3286133	-0.067487299
5.8212891	-0.011978489

-----------------------------------------------

-- 
View this message in context: http://www.nabble.com/Ignore-text-when-reading-data-tp21718709p21718709.html
Sent from the R help mailing list archive at Nabble.com.



------------------------------

Message: 101
Date: Thu, 29 Jan 2009 14:28:05 +1100
From: Remko Duursma <remkoduursma at gmail.com>
Subject: Re: [R] Ignore text when reading data
To: beyar <bxx at mailinator.com>
Cc: r-help at r-project.org
Message-ID:
	<80b45a8c0901281928x3143dbf9x3d9848011d3dce1f at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

# replace this bit, replace it with your file name
myfile <- textConnection(
"Time    out1
Sec     mm
0.82495117      -0.020977303
1.3554688       -0.059330709
1.826416        -0.021419302
2.3295898       -0.051521059
2.8347168       -0.020661414


Time    out1
Sec     mm
3.8679199       -0.000439643
4.3322754       -0.063477799
4.8015137       -0.024581354
5.3286133       -0.067487299
5.8212891       -0.011978489")

# which lines not to read
notread <- c(which(r==""),grep("Time ",r),grep("Sec ",r))

# read the data as text
mydata <- r[setdiff(1:length(r),notread)]

# make it into a dataframe (I think this can be done prettier, but whatever)
z <- paste(mydata, collapse="\n")
read.table(textConnection(z))


greetings
Remko

-------------------------------------------------
Remko Duursma
Post-Doctoral Fellow

Centre for Plant and Food Science
University of Western Sydney
Hawkesbury Campus
Richmond NSW 2753

Dept of Biological Science
Macquarie University
North Ryde NSW 2109
Australia

Mobile: +61 (0)422 096908

        
On Thu, Jan 29, 2009 at 11:45 AM, beyar <bxx at mailinator.com> wrote:

            

      
      
      
    

        

      
      
    

        
------------------------------

Message: 102
Date: Thu, 29 Jan 2009 14:29:01 +1100
From: Remko Duursma <remkoduursma at gmail.com>
Subject: Re: [R] Ignore text when reading data
To: beyar <bxx at mailinator.com>
Cc: r-help at r-project.org
Message-ID:
	<80b45a8c0901281929x4f536cccw3cd028b8286852e4 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Sorry, forgot this line after the textConnection bit:

r <- readLines(myfile)


-------------------------------------------------
Remko Duursma
Post-Doctoral Fellow

Centre for Plant and Food Science
University of Western Sydney
Hawkesbury Campus
Richmond NSW 2753

Dept of Biological Science
Macquarie University
North Ryde NSW 2109
Australia

Mobile: +61 (0)422 096908

        
On Thu, Jan 29, 2009 at 2:28 PM, Remko Duursma <remkoduursma at gmail.com> wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        
------------------------------

Message: 103
Date: Wed, 28 Jan 2009 22:37:44 -0500
From: jim holtman <jholtman at gmail.com>
Subject: Re: [R] Ignore text when reading data
To: beyar <bxx at mailinator.com>
Cc: r-help at r-project.org
Message-ID:
	<644e1f320901281937n750e9133geb9984b87ed3f59b at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Try this:

            

      
      
      
    

        
+ by mr x
+ etc
+
+
+ Time    out1
+ Sec     mm
+ 0.82495117      -0.020977303
+ 1.3554688       -0.059330709
+ 1.826416        -0.021419302
+ 2.3295898       -0.051521059
+ 2.8347168       -0.020661414
+
+
+ Time    out1
+ Sec     mm
+ 3.8679199       -0.000439643
+ 4.3322754       -0.063477799
+ 4.8015137       -0.024581354
+ 5.3286133       -0.067487299
+ 5.8212891       -0.011978489"))

            

      
      
      
    

        
Time         out1
1  0.8249512 -0.020977303
2  1.3554688 -0.059330709
3  1.8264160 -0.021419302
4  2.3295898 -0.051521059
5  2.8347168 -0.020661414
6  3.8679199 -0.000439643
7  4.3322754 -0.063477799
8  4.8015137 -0.024581354
9  5.3286133 -0.067487299
10 5.8212891 -0.011978489

            

      
      
      
    

        

        
On Wed, Jan 28, 2009 at 7:45 PM, beyar <bxx at mailinator.com> wrote:

            

      
      
      
    

        

      
      
    

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

What is the problem that you are trying to solve?



------------------------------

Message: 104
Date: Wed, 28 Jan 2009 20:09:59 -0800 (PST)
From: beyar <bxx at mailinator.com>
Subject: Re: [R] Ignore text when reading data
To: r-help at r-project.org
Message-ID: <21720588.post at talk.nabble.com>
Content-Type: text/plain; charset=us-ascii


thanks to all for the solutions.  Especially to Jim H for this one which
worked perfectly...
(i only had to change the seperater on the header to /t as there are spaces
in header names)




----------------
Try this:

            

      
      
      
    

        
+ by mr x
+ etc
+
+
+ Time    out1
+ Sec     mm
+ 0.82495117      -0.020977303
+ 1.3554688       -0.059330709
+ 1.826416        -0.021419302
+ 2.3295898       -0.051521059
+ 2.8347168       -0.020661414
+
+
+ Time    out1
+ Sec     mm
+ 3.8679199       -0.000439643
+ 4.3322754       -0.063477799
+ 4.8015137       -0.024581354
+ 5.3286133       -0.067487299
+ 5.8212891       -0.011978489"))

            

      
      
      
    

        

        
beyar wrote:

            

      
      
      
    

        
-- 
View this message in context: http://www.nabble.com/Ignore-text-when-reading-data-tp21718709p21720588.html
Sent from the R help mailing list archive at Nabble.com.



------------------------------

Message: 105
Date: Thu, 29 Jan 2009 07:52:37 +0100
From: "Weiss, Bernd " <bernd.weiss at uni-koeln.de>
Subject: [R] Question about collapse/aggregate and avoidance of loops
To: r-help at r-project.org
Message-ID: <49815235.2000303 at uni-koeln.de>
Content-Type: text/plain; charset=ISO-8859-15; format=flowed

Dear all,

given the following data

## original data
id <- c(1,1,1,2,2,3)
author <- c("A","B","C","D","E","F")
tmp <- data.frame(id,author)
tmp


 > tmp
   id author
1  1      A
2  1      B
3  1      C
4  2      D
5  2      E
6  3      F

What is the best (most efficient/vectorized/avoiding loops) approach to 
obtain the following data frame?

id 	author
1	"A, B, C"
2 	"D, E"
3	"F"


Thanks for your help,

Bernd





 > version
                _
platform       i386-pc-mingw32
arch           i386
os             mingw32
system         i386, mingw32
status         Patched
major          2
minor          8.1
year           2008
month          12
day            22
svn rev        47296
language       R
version.string R version 2.8.1 Patched (2008-12-22 r47296)



------------------------------

Message: 106
Date: Thu, 29 Jan 2009 06:54:49 +0000 (GMT)
From: justin bem <justin_bem at yahoo.fr>
Subject: [R] Re :   standard error of logit parameters
To: R Maillist <r-help at stat.math.ethz.ch>
Message-ID: <609242.98892.qm at web23208.mail.ird.yahoo.com>
Content-Type: text/plain

Run 


outfit<-nlm(..., hessian=T) and then standards error are
se<-diag(solve(outfit$hessian))


? 
Justin BEM
BP 1917 Yaound??
T??l (237) 76043774

? 



________________________________
De : Bomee Park <bombom at stanford.edu>
?? : r-help at r-project.org
Envoy?? le : Jeudi, 29 Janvier 2009, 4h01mn 56s
Objet? : [R] standard error of logit parameters

Hi everyone.

I am now estimating the parameters for a logit model, and trying to get the estimates by laximizing the log_likelihood.
The nlm function works nicely for maximizing the -(log_likelihood) and returns the parameter estimates that minimize the static, and the gradients also, but don't have any clue how I can get the standard error for the parameters.

Any help will be greatly appreciated.
Thanks.

______________________________________________
R-help at 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.


      



------------------------------

Message: 107
Date: Thu, 29 Jan 2009 08:17:48 +0100
From: Petr PIKAL <petr.pikal at precheza.cz>
Subject: Re: [R] t.test in a loop
To: Michael Pearmain <mpearmain at google.com>
Cc: r-help at r-project.org
Message-ID:
	<OF1FE4CBEF.AEE8B85E-ONC125754D.0027723A-C125754D.0028054F at precheza.cz>
	
Content-Type: text/plain; charset="US-ASCII"

Hi 

r-help-bounces at r-project.org napsal dne 28.01.2009 12:57:55:

            

      
      
      
    

        
a

            

      
      
      
    

        
of the

            

      
      
      
    

        
t-tests

            

      
      
      
    

        
Another option is to use lapply

lapply(channel.data.train[, 1:16], function(x) 
t.test((x)~channel.data.train$power)

Regards
Petr

            

      
      
      
    

        
t.test(get(paste("channel.data.train$",i,"~channel.data.train$power",sep="")))

            

      
      
      
    

        
"~channel.data.train$power",

            

      
      
      
    

        
found

            

      
      
      
    

        
to

            

      
      
      
    

        
please

            

      
      
      
    

        
sender

            

      
      
      
    

        

      
      
    

        
http://www.R-project.org/posting-guide.html

        

      
      
    

            

      
      
      
    

        

      
      
    

        
http://www.R-project.org/posting-guide.html

        

      
      
    

        
------------------------------

Message: 108
Date: Thu, 29 Jan 2009 01:29:48 -0600 (CST)
From: markleeds at verizon.net
Subject: Re: [R] Re :   standard error of logit parameters
To: justin bem <justin_bem at yahoo.fr>
Cc: R Maillist <r-help at stat.math.ethz.ch>
Message-ID:
	<1961203354.65345681233214188971.JavaMail.javamailuser at localhost>
Content-Type: text/plain; charset=UTF-8; format=flowed; delsp=no

I'm sure below is fine but  john fox's CAR book has some nice examples 
of how to compute the logit parameters and variances from scratch using 
iteratively weighted least squares.

        
On Thu, Jan 29, 2009 at  1:54 AM, justin bem wrote:

        

            

      
      
      
    

        

      
      
    

        
------------------------------

Message: 109
Date: Thu, 29 Jan 2009 08:38:57 +0100
From: Petr PIKAL <petr.pikal at precheza.cz>
Subject: [R] Odp: Question about collapse/aggregate and avoidance of
	loops
To: "Weiss, Bernd " <bernd.weiss at uni-koeln.de>
Cc: r-help at r-project.org
Message-ID:
	<OFCB718E52.0A552D54-ONC125754D.0029CE12-C125754D.0029F514 at precheza.cz>
	
Content-Type: text/plain; charset="US-ASCII"

Hi

r-help-bounces at r-project.org napsal dne 29.01.2009 07:52:37:

            

      
      
      
    

        
Not sure if it is most efficient but

 aggregate(tmp$author, list(tmp$id), function(x) paste(x, collapse=","))

can do the trick

Regards
Petr

            

      
      
      
    

        

      
      
    

        
http://www.R-project.org/posting-guide.html

        

      
      
    

        
------------------------------

Message: 110
Date: Thu, 29 Jan 2009 08:50:03 +0100
From: Petr PIKAL <petr.pikal at precheza.cz>
Subject: [R] Odp:  stack data sets
To: Nidhi Kohli <nidhik at umd.edu>, r-help at stat.math.ethz.ch
Message-ID:
	<OF8ECC66A1.290C3232-ONC125754D.002A39DA-C125754D.002AF935 at precheza.cz>
	
Content-Type: text/plain; charset="US-ASCII"

Hi

r-help-bounces at r-project.org napsal dne 28.01.2009 19:25:32:

            

      
      
      
    

        
sets

            

      
      
      
    

        
It is rather difficult to understand what you want to do. The code you 
provide do not work as I presume only you have C:/NCME path and your data.

Stack works with data frames as you point out. However if your matrix has 
appropriate form and names you can easily transform it to data frame and 
use stack.


pg <- unstack(PlantGrowth)
pg<-as.matrix(pg)
pg
      ctrl trt1 trt2
 [1,] 4.17 4.81 6.31
 [2,] 5.58 4.17 5.12
...
 [9,] 5.33 4.32 5.80
[10,] 5.14 4.69 5.26

            

      
      
      
    

        
Error in rep.int(names(x), lapply(x, length)) : invalid 'times' value

            

      
      
      
    

        
ctrl trt1 trt2
1  4.17 4.81 6.31
2  5.58 4.17 5.12
...
9  5.33 4.32 5.80
10 5.14 4.69 5.26

            

      
      
      
    

        
values  ind
1    4.17 ctrl
2    5.58 ctrl
3    5.18 ctrl
4    6.11 ctrl
5    4.50 ctrl
6    4.61 ctrl
....

Regards
Petr

            

      
      
      
    

        
ncol=n.items)

            

      
      
      
    

        
FALSE)

            

      
      
      
    

        
write.table(Observed_Scores,ObservedScores_Data,row.name=FALSE,col.name=FALSE)

            

      
      
      
    

        
row.name=FALSE)

            

      
      
      
    

        

      
      
    

        
http://www.R-project.org/posting-guide.html

        

      
      
    

        
------------------------------

Message: 111
Date: Thu, 29 Jan 2009 10:08:47 +0200
From: Hadassa Brunschwig <hadassa.brunschwig at mail.huji.ac.il>
Subject: Re: [R] Character SNP data to binary MAF data
To: Jorge Ivan Velez <jorgeivanvelez at gmail.com>
Cc: r-help at r-project.org
Message-ID:
	<db80b30d0901290008j2f25ab58mcbe87677c55c1c52 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi

An example is as follows. Consider the character 3x6 matrix:

a A a T A t
G g t T T t
A a C C c c

For each row I would like to identify the most frequent letter and
assign a 1 to it and 0
to the less frequent character. That is, in row 1 the most frequent
letter is A (I do not differentiate between capital and non-capital
letters), in row 2 T and in row 3 C. After the binary conversion
the resulting matrix would look like that:

1 1 1 0 1 0
0 0 1 1 1 1
0 0 1 1 1 1

Any suggestions on how to do that (and I am sure I am not the first
one to try this).

Thanks
Hadassa


On Thu, Jan 29, 2009 at 1:50 AM, Jorge Ivan Velez

        
<jorgeivanvelez at gmail.com> wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        
-- 
Hadassa Brunschwig
PhD Student
Department of Statistics
The Hebrew University of Jerusalem
http://www.stat.huji.ac.il



------------------------------

Message: 112
Date: Thu, 29 Jan 2009 09:14:49 +0100
From: Bernd Weiss <bernd.weiss at uni-koeln.de>
Subject: Re: [R] Odp: Question about collapse/aggregate and avoidance
	of	loops
To: r-help at r-project.org, petr.pikal at precheza.cz,
	markleeds at verizon.net
Message-ID: <49816579.2000102 at uni-koeln.de>
Content-Type: text/plain; charset=UTF-8; format=flowed

markleeds at verizon.net schrieb:

            

      
      
      
    

        
Dear Mark & Petr,

Thank your very much! I like both solutions. Petr's is the more obvious 
one but Mark's solution is good for rethinking my understanding of 
lapply :-)

Again, thank you very much.

Bernd



------------------------------

Message: 113
Date: Thu, 29 Jan 2009 08:28:44 +0000
From: Barry Rowlingson <b.rowlingson at lancaster.ac.uk>
Subject: Re: [R] Character SNP data to binary MAF data
To: Hadassa Brunschwig <hadassa.brunschwig at mail.huji.ac.il>
Cc: r-help at r-project.org
Message-ID:
	<d8ad40b50901290028j3b97129bo34100a6606467217 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

2009/1/29 Hadassa Brunschwig <hadassa.brunschwig at mail.huji.ac.il>:

            

      
      
      
    

        
What if there's a tie for most frequent? Do you want 1s for all the
most frequent characters? Or choose one randomly? Or zeroes?

 Examples: what do the following become:

 A A C C T G
 A A C C T T
 A A A A A A

Or are such cases not possible?

 Some hints for you to work on this yourself:

   help('table') - the table function works out counts of elements of vectors
   help('tolower') - for changing upper to lower case
   help('apply') - for working on rows of data frames

 then check out any basic R tutorial on subscripting and replacement,
and you may need to work out how to loop over things with 'for'. You
should be able to make a working solution in a dozen or so lines of R.
Don't be surprised if some R guru on here does it in 2 or 3 lines of
[[elided Yahoo spam]]

Barry



------------------------------

Message: 114
Date: Thu, 29 Jan 2009 00:33:31 -0800 (PST)
From: Thomas Lumley <tlumley at u.washington.edu>
Subject: Re: [R] Character SNP data to binary MAF data
To: Hadassa Brunschwig <hadassa.brunschwig at mail.huji.ac.il>
Cc: r-help at r-project.org
Message-ID:
	<Pine.LNX.4.43.0901290033310.11961 at hymn32.u.washington.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed


The first step is to convert your data to all uppercase with toupper().

Then it depends on how tidy the data are: are there missing data, are some SNPs monomorphic in your sample, etc.

If there are no missing data you can use

N<-ncol(the_data)
halfN <- N/2

maf_one_row <-function(arow) {
    rval<-numeric(N)
    if (sum(i<-arow=="A")>halfN) {
         rval[]<-1
    } else if (sum(i<-arow=="C")>halfN){
         rval[i]<-1
    } else if (sum(i<-arow=="T"))>halfN){
         rval[i]<-1
    } else if (sum(i<-arow=="G")>halfN){
         rval[i]<-1
    }
    rval
}

apply(the_data, 1, maf_one_row)

YOu could also use table() to find the two alleles, but you have to make sure that the code still works when there is only one allele.

      -thomas

        
On Thu, 29 Jan 2009, Hadassa Brunschwig wrote:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        
Thomas Lumley			Assoc. Professor, Biostatistics
tlumley at u.washington.edu	University of Washington, Seattle



------------------------------

Message: 115
Date: Thu, 29 Jan 2009 00:41:09 -0800
From: Patrick Aboyoun <paboyoun at fhcrc.org>
Subject: Re: [R] Character SNP data to binary MAF data
To: r-help at r-project.org
Cc: Thomas Lumley <tlumley at u.washington.edu>,	Hadassa Brunschwig
	<hadassa.brunschwig at mail.huji.ac.il>
Message-ID: <20090129004109.s7162gkn2uc4gsko at webmail.fhcrc.org>
Content-Type: text/plain;	charset=ISO-8859-1;	DelSp="Yes";
	format="flowed"

Hadassa,
You may want to check out the snpMatrix package in Bioconductor

http://bioconductor.org/packages/2.3/bioc/html/snpMatrix.html
http://bioconductor.org/packages/2.4/bioc/html/snpMatrix.html

It contains classes that manage this type of information and should  
minimize your coding effort.


Patrick


Quoting Thomas Lumley <tlumley at u.washington.edu>:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        
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Message: 116
Date: Thu, 29 Jan 2009 08:46:01 +0000
From: Patrick Burns <pburns at pburns.seanet.com>
Subject: Re: [R] Question about collapse/aggregate and avoidance of
	loops
To: "Weiss, Bernd " <bernd.weiss at uni-koeln.de>
Cc: r-help at r-project.org
Message-ID: <49816CC9.9060905 at pburns.seanet.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

I think you are looking for

split(author, id)


Patrick Burns
patrick at burns-stat.com
+44 (0)20 8525 0696
http://www.burns-stat.com
(home of "The R Inferno" and "A Guide for the Unwilling S User")

        
Weiss, Bernd wrote:

            

      
      
      
    

        

      
      
    

        
------------------------------

Message: 117
Date: Thu, 29 Jan 2009 08:53:05 +0000
From: Barry Rowlingson <b.rowlingson at lancaster.ac.uk>
Subject: Re: [R] Character SNP data to binary MAF data
To: Patrick Aboyoun <paboyoun at fhcrc.org>
Cc: r-help at r-project.org, Thomas Lumley <tlumley at u.washington.edu>,
	Hadassa Brunschwig <hadassa.brunschwig at mail.huji.ac.il>
Message-ID:
	<d8ad40b50901290053m2f937ddft8923db40c1a1b7c3 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

2009/1/29 Patrick Aboyoun <paboyoun at fhcrc.org>:

            

      
      
      
    

        
It's not that much effort - this code turns all ties into 1s:

snp2maf=function(m){
m=toupper(m)
return(t(apply(m,1,makeBin)))
}

makeBin = function(chars){
tc = table(chars)
maxV = names(tc[tc==max(tc)])
matches = match(chars,maxV)
r=as.integer(!is.na(matches))
return(r)
}

 then:

            

      
      
      
    

        
[,1] [,2] [,3] [,4] [,5]
 [1,] "t"  "g"  "g"  "g"  "t"
 [2,] "a"  "G"  "a"  "C"  "c"
 [3,] "A"  "T"  "c"  "c"  "C"
 [4,] "g"  "T"  "c"  "A"  "C"
 [5,] "G"  "C"  "G"  "g"  "G"
 [6,] "G"  "t"  "T"  "a"  "C"
 [7,] "A"  "G"  "T"  "g"  "T"
 [8,] "T"  "a"  "C"  "a"  "T"
 [9,] "t"  "g"  "g"  "c"  "T"
[10,] "A"  "t"  "t"  "c"  "A"

            

      
      
      
    

        
[,1] [,2] [,3] [,4] [,5]
 [1,]    0    1    1    1    0
 [2,]    1    0    1    1    1
 [3,]    0    0    1    1    1
 [4,]    0    0    1    0    1
 [5,]    1    0    1    1    1
 [6,]    0    1    1    0    0
 [7,]    0    1    1    1    1
 [8,]    1    1    0    1    1
 [9,]    1    1    1    0    1
[10,]    1    1    1    0    1

            

      
      
      
    

        
Barry



------------------------------

Message: 118
Date: Thu, 29 Jan 2009 10:19:37 +0100
From: "Gerit Offermann" <gerit.offermann at gmx.de>
Subject: [R] Multiple tables
To: R-help at r-project.org
Message-ID: <20090129091937.122580 at gmx.net>
Content-Type: text/plain; charset="iso-8859-1"

Dear list,

I have a set of 100+ variables. I would like to have one by one crosstables for each variable. I started with
table(variable1, variable2)
table(variable1, variable3)
table(variable1, variable4)
...
table(variable2, variable3)
table(variable2, variable4)
...

It seems rather tedious.

Any better ideas around?

Thanks for any help!
Gerit
-- 
NUR NOCH BIS 31.01.! GMX FreeDSL - Telefonanschluss + DSL 
f?r nur 16,37 EURO/mtl.!* http://dsl.gmx.de/?ac=OM.AD.PD003K11308T4569a



------------------------------

Message: 119
Date: Thu, 29 Jan 2009 01:25:13 -0800 (PST)
From: joe1985 <johannes at dsr.life.ku.dk>
Subject: [R]  Text in a character vector to indicate "ifelse" argument
To: r-help at r-project.org
Message-ID: <21722983.post at talk.nabble.com>
Content-Type: text/plain; charset=UTF-8


Hello

I have a data set that looks like this;

            

      
      
      
    

        
dato         chr                      status           PRRSvac
PRRSsanVac PRRSsanDk PRRSdk
33  2007-12-03 090432                    R?d SPF        
34  2007-02-09 090432              R?d SPF+sanDK        
35  2002-12-17 090432                 R?d SPF+DK        
36  2002-11-27 090432              R?d SPF+sanDK        
37  2002-07-23 090432                 R?d SPF+DK        
38  2001-08-23 090432                    R?d SPF        
39  2000-01-01 090432          SPF-X,  PRRS-neg.        
40  1999-05-01 090432           MS-X,  PRRS-neg.        
81  2001-08-23 022458                    R?d SPF        
82  1999-01-22 022458          SPF-X,  PRRS-neg.       
130 2008-10-16 080385 R?d SPF+Myc+Ap2+Nys+DK+Vac       
131 2003-03-18 080385     R?d SPF+Myc+Ap2+DK+Vac        
132 2002-11-01 080385         R?d SPF+Myc+DK+Vac        
133 2002-02-07 080385            R?d SPF+Myc+Vac        
134 2000-09-19 080385         MS-X,  PRRS-pos VAC       
135 1999-01-22 080385            MS-X,  PRRS-neg        
176 2008-10-28 013168 R?d SPF+Myc+Ap2+Nys+DK+Vac        
177 2003-05-23 013168     R?d SPF+Myc+Ap2+DK+Vac        
178 2002-11-01 013168         R?d SPF+Myc+DK+Vac        
179 2001-07-03 013168            R?d SPF+Myc+Vac        
180 2000-09-01 013168         MS-X,  PRRS-pos VAC      
181 2000-06-02 013168            MS-X,  PRRS-neg        
182 2000-04-03 013168     SKM-X,  +Ap2,  PRRS-neg       
183 1999-01-22 013168            MS-X,  PRRS-neg        

Where I have used;

b2$PRRSvac <- ifelse(b2$status=='PRRS-pos VAC' | b2$status=='Vac',1,0)
b2$PRRSdk <- ifelse(b2$status=='PRRS-pos DK' | b2$status=='DK',1,0)
b2$PRRSsanVac <- ifelse(b2$status=='sanVac',1,0)
b2$PRRSsanDk <- ifelse(b2$status=='sanDK',1,0)

to creat the last four variables, but it wont work!!! The variable status
has class "character". 

Can anyone help me?