[R] How to get a running mean result by R?

[Jie Tang]

Hi R users:
  I have a big data and want to calculate the running mean of this data .
How can I get this kind of result ? I have check the command mean
it seems mean could not get the running mean?

-- 
TANG Jie

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[R] change factor to mtrix

[Gallon Li]

i wish to change a column of factor variable to multiple columns of
zero-ones

for example, my factor could be

ff=c('a','a','b','b','c','c')

then I want to have two columns (for three levels) that are

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

how can i do this fast?

[[alternative HTML version deleted]]

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[R] Instant search for R documentation

[jonathan cornelissen]

Hi, 

I just wanted to share with you that we made a website over the weekend that 
allows instant search of the R documentation on CRAN, see: 
www.Rdocumentation.org. It's a first version, so any 
feedback/comments/criticism most welcome.

Best regards, 

Jonathan  
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Re: [R] Question on Simple Repeated Loops

[Berend Hasselman]

On 12-06-2013, at 04:53, Abdul Rahman bin Kassim (Dr.) rahm...@frim.gov.my 
wrote:

 
 Dear R-User,
 
 Appreciate any helps. It looks simple, but I don't have a clue.
 
 Given that I have a dataframe of tree population with three variables:
 
 sp=species ,
 d0=initial_size
 grow=growth increment from initial size per year
 
 How can I calculate the future growth increment of each tree  for the next 3 
 years.
 
 The following Rscript was written,
 
 #--
 a0 - data.frame(d0=seq(5,50,5) , sp=gl(2,5,10),
   grow=rep(0.5,10))
 a2- list()
 for( i in 1:3){
  a1 - a0$d0+a0$grow
  a2[[i]] - cbind(sp=a0$sp,d0=a1+i,yr=i)
   }
 as.data.frame(do.call(cbind,a2))
 
 as.data.frame(do.call(cbind,a2))
   sp   d0 yr sp   d0 yr sp   d0 yr
 1   1  6.5  1  1  7.5  2  1  8.5  3
 2   1 11.5  1  1 12.5  2  1 13.5  3
 3   1 16.5  1  1 17.5  2  1 18.5  3
 4   1 21.5  1  1 22.5  2  1 23.5  3
 5   1 26.5  1  1 27.5  2  1 28.5  3
 6   2 31.5  1  2 32.5  2  2 33.5  3
 7   2 36.5  1  2 37.5  2  2 38.5  3
 8   2 41.5  1  2 42.5  2  2 43.5  3
 9   2 46.5  1  2 47.5  2  2 48.5  3
 10  2 51.5  1  2 52.5  2  2 53.5  3
 
 #-
 
 but the results did not produce the expected future d0. I think its my R 
 script  d0=a1+i  in the   a2[[i]] - cbind(sp=a0$sp,d0=a1+i,yr=i). 
 Interested to know the correct way of writing the repeated loops in R.
 
 The expected results is:
 
   sp   d0 yr sp   d0 yr sp   d0 yr
 1   1  6.5  1  1  7.0  2  1  7.5  3
 2   1 11.5  1  1 12.0  2  1 12.5  3
 3   1 16.5  1  1 17.0  2  1 17.5  3
 4   1 21.5  1  1 22.0  2  1 22.5  3
 5   1 26.5  1  1 27.0  2  1 27.5  3
 6   2 31.5  1  2 32.0  2  2 32.5  3
 7   2 36.5  1  2 37.0  2  2 37.5  3
 8   2 41.5  1  2 42.0  2  2 42.5  3
 9   2 46.5  1  2 47.0  2  2 47.5  3
 10  2 51.5  1  2 52.0  2  2 52.5  3
 

Why is the expression  a1 - a0$d0+a0$grow inside the for loop?
It doesn't depend on i.

I don't understand your expected result.
Fpr species 1 the initial value in column d0 is 5. I assume that this is in 
year 0.
So with a growth increment of .5 in year 1 I would expect d0 to be 5.5, in year 
2it is  6 and in year 3 it would be 6.5.

So see if this does what you seem to want (and remove the redundant expression 
for a1)

a3- list()
for( i in 1:3){
 a3[[i]] - cbind(sp=a0$sp,d0=a0$d0+i*a0$grow,yr=i)
}
as.data.frame(do.call(cbind,a3))
#sp   d0 yr sp d0 yr sp   d0 yr
# 1   1  5.5  1  1  6  2  1  6.5  3
# 2   1 10.5  1  1 11  2  1 11.5  3
# 3   1 15.5  1  1 16  2  1 16.5  3
# 4   1 20.5  1  1 21  2  1 21.5  3
# 5   1 25.5  1  1 26  2  1 26.5  3
# 6   2 30.5  1  2 31  2  2 31.5  3
# 7   2 35.5  1  2 36  2  2 36.5  3
# 8   2 40.5  1  2 41  2  2 41.5  3
# 9   2 45.5  1  2 46  2  2 46.5  3
# 10  2 50.5  1  2 51  2  2 51.5  3


Berend

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Re: [R] help using code

[Rui Barradas]

Hello,

Simply assign the output of a function to a variable:

xyzuvw - importdata(...)

and then use that output. In this case, a data.frame with, among others, 
vectors 'x' and 'y'.
You need to read an R introductory text. I recommend An Introduction to 
R, file R-intro.pdf in your doc directory.


Rui Barradas


Em 12-06-2013 00:59, John McDermott escreveu:

Hello,

Thanks for the help!

Your answer resolved my problem with the function I listed, but brought up
a larger question. How is the output of the importdata function stored for
use with other functions (as in, how do I call on that data for use with
other functions)? As a simple example I have another function:

meanXY = function(xyzuvw) {
xy = c(mean(xyzuvw$x), mean(xyzuvw$y))
return(xy)
}

I know that the xyzuvw portion is referring to the output of the
importdata function, but I don't know how to call up the necessary data
(hope this makes sense).

Thanks again for the help!

John




On 6/11/13 3:05 PM, Rui Barradas ruipbarra...@sapo.pt wrote:


Hello,

I believe you are making a confusion on how to call a function in R. You
don't replace the argument in the function declaration. what you do is
to call the function like this:

importdata(~/path to/filename.xyzuvwrgb)

leaving the function definition alone.

Hope this helps,

Rui Barradas

Em 11-06-2013 19:52, John McDermott escreveu:

Hi R-helpers,

I inherited some code that I'm trying to use. As a very new R user I'm
having some confusion.

I have some input files in the form: filename.xyzuvwrgb which I'm
trying to
import using:

importdata = function(filename) {

  p = scan(filename,what=list(x = double(), y = double(), z =
double(), u
= double(),v=double(),w=double()),skip=1,flush=TRUE,sep= )

  return(data.frame(x=p$x, y=p$y, z=p$z, u=p$u, v=p$v, w=p$w))

}



For the filename I replaced both with ~/path to/filename.xyzuvwrgb
and I
get the following errors:



Error: unexpected string constant in importdata =
function(~/Desktop/thrustScarp1.xyzuvw



Error: no function to return from, jumping to top level



Error: unexpected '}' in }



I'm assuming it has to do with how I am using/formatted the
function(filename) portion. How can I get this to work?



Thanks for the help!







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Re: [R] change factor to mtrix

[Jim Lemon]

On 06/12/2013 05:47 PM, Gallon Li wrote:

i wish to change a column of factor variable to multiple columns of
zero-ones

for example, my factor could be

ff=c('a','a','b','b','c','c')

then I want to have two columns (for three levels) that are

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

how can i do this fast?


Hi Gallon,
If you want exactly the output shown above, it is not trivial. You could 
convert ff to a factor, then use as.numeric to get:


a = 1
b = 2
c = 3

If you subtract one and display the numbers in two digits of binary:

a = 00
b = 01
c = 10

Then if you apply as.character and strsplit, you can get:

a = 0 0
b = 0 1
c = 1 0

Finally, as.numeric will give you numbers. This does not produce the 
numbers above, but it might give you an idea of what to do.


Jim

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[R] loops for matrices

[maggy yan]

I have to use a loop (while or for) to return the result of hadamard
product. now it returns a matrix, but when I use is.matrix() to check, it
returns FALSE, whats wrong?

Matrix.mul - function(A, B)
{
while(is.matrix(A) == FALSE | is.matrix(B) == FALSE )
 {print(error)
  break}
while(is.matrix(A) == T  is.matrix(B) == T)
 {
  n - dim(A)[1]; m - dim(A)[2];
  p - dim(B)[1]; q - dim(B)[2];
  while(m == p)
   {
C - matrix(0, nrow = n , ncol = q)
for(s in 1:n)
   {
for(t in 1:q)
   {
c - array(0, dim = m )
for(k in 1:m)
   {
c[k] - A[s,k] * B[k, t]

}
C[s, t] - sum(c)
   }
   }
print(C)
break
}
  while(m != p)
   {
print(error)
break
}
  break
  }
}

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[R] Version 1.3.2 of apcluster package (+ last announcement of Webinar)

[Ulrich Bodenhofer]

Dear colleagues,

This is to inform you that Version 1.3.2 of the R package *apcluster* 
has been released on CRAN yesterday (note that it may still take a few 
more hours until the Windows binary will be available). We added a 
plotting function that also allows for plotting clustering results along 
with multi-dimensional data (by superimposing clusters in a scatterplot 
matrix). Moreover, we improved the handling of missing values. For more 
details, see the following URLs:


http://www.bioinf.jku.at/software/apcluster/
http://cran.r-project.org/web/packages/apcluster/index.html

Furthermore, I want to remind you that I will be giving a webinar on the 
apcluster package on Thursday, June 13, 2013, 7:00pm CEST (10:00am PDT). 
The outline of the one-hour webinar is as follows:


- Introduction to affinity propagation (AP) clustering
- The apcluster package, its algorithms, and visualization tools
- Live apcluster demonstration
- Question and Answer period

To register for the webinar, please visit the following URL:
https://www3.gotomeeting.com/register/503109182

The webinar is kindly brought to you by the Orange County R User Group 
and will be moderated by its president, Ray DiGiacomo, Jr.



Best regards,
Ulrich



*Dr. Ulrich Bodenhofer*
Associate Professor
Institute of Bioinformatics

*Johannes Kepler University*
Altenberger Str. 69
4040 Linz, Austria

Tel. +43 732 2468 4526
Fax +43 732 2468 4539
bodenho...@bioinf.jku.at mailto:bodenho...@bioinf.jku.at
http://www.bioinf.jku.at/ http://www.bioinf.jku.at

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Re: [R] loops for matrices

[Rainer Schuermann]

The comments on StackOverflow are fair, I believe...
Please dput() your matrices, so that your code becomes reproducible!


On Wednesday 12 June 2013 11:14:35 maggy yan wrote:
 I have to use a loop (while or for) to return the result of hadamard
 product. now it returns a matrix, but when I use is.matrix() to check, it
 returns FALSE, whats wrong?
 
 Matrix.mul - function(A, B)
 {
 while(is.matrix(A) == FALSE | is.matrix(B) == FALSE )
  {print(error)
   break}
 while(is.matrix(A) == T  is.matrix(B) == T)
  {
   n - dim(A)[1]; m - dim(A)[2];
   p - dim(B)[1]; q - dim(B)[2];
   while(m == p)
{
 C - matrix(0, nrow = n , ncol = q)
 for(s in 1:n)
{
 for(t in 1:q)
{
 c - array(0, dim = m )
 for(k in 1:m)
{
 c[k] - A[s,k] * B[k, t]
 
 }
 C[s, t] - sum(c)
}
}
 print(C)
 break
 }
   while(m != p)
{
 print(error)
 break
 }
   break
   }
 }
 
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Re: [R] Caret train with glmnet give me Error arguments imply differing number of rows

[Ferran Casarramona]

Hi Max,

I think I get the cause of this error. I left unintentionally some NA's in
the y parameter of train().

Here is the example to reproduce it:
X - matrix(seq(1:100, 10, 10)
Y - seq(1:10)
Y[1] - NA
fit - train(X, Y, method=glmnet, preProcess=c(center,scale))

Regards,
  Ferran


2013/6/11 Mxkuhn mxk...@gmail.com

 The data size isn't an issue. Can you send a reproducible example?

 Max


 On Jun 11, 2013, at 10:31 AM, Ferran Casarramona 
 ferran.casarram...@gmail.com wrote:

  Hello,
 
  I'm training a set of data with Caret package using an elastic net
 (glmnet).
  Most of the time train works ok, but when the data set grows in size I
 get
  the following error:
  Error en { :
   task 1 failed - arguments imply differing number of rows: 9, 10
 
  and several warnings like this one:
  1: In eval(expr, envir, enclos) :
   model fit failed for Resample01
 
  My call to train function is like this:
  fit - train(TrainingPreCols, TrainingFrame[,PCol], method=glmnet,
  preProcess = c(center,scale))
 
  When TrainingPreCols is 17420 obs. of 27 variables, the function works
 ok.
  But with a size of 47000 obs of 27 variables I get the former error.
 
  ¿Could be the amount of data the cause of this error?
 
  Any help is appreciated,
   Ferran
 
  P.D.:
  This is my sessionInfo()
  R version 2.15.0 (2012-03-30)
  Platform: x86_64-pc-mingw32/x64 (64-bit)
 
  locale:
  [1] LC_COLLATE=Spanish_Spain.1252  LC_CTYPE=Spanish_Spain.1252
  LC_MONETARY=Spanish_Spain.1252
  [4] LC_NUMERIC=C   LC_TIME=Spanish_Spain.1252
 
  attached base packages:
  [1] stats graphics  grDevices utils datasets  methods   base
 
  other attached packages:
  [1] glmnet_1.9-3Matrix_1.0-12   doSNOW_1.0.7iterators_1.0.6
  snowfall_1.84-4
  [6] snow_0.3-12 caret_5.16-04   reshape2_1.2.2  plyr_1.8
  lattice_0.20-6
  [11] cluster_1.14.4  foreach_1.4.1
 
  loaded via a namespace (and not attached):
  [1] codetools_0.2-8 grid_2.15.0 stringr_0.6.2   tools_2.15.0
 
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Re: [R] How to get a running mean result by R?

[Rui Barradas]

Hello,

You can use, for instance, function ma() in package forecast.

# if not yet installed
#install.packages('forecast', dependencies = TRUE)
library(forecast)

?ma


Hope this helps,

Rui Barradas


Em 12-06-2013 08:21, Jie Tang escreveu:

Hi R users:
   I have a big data and want to calculate the running mean of this data .
How can I get this kind of result ? I have check the command mean
it seems mean could not get the running mean?



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

Re: [R] Bytes to Numeric/Float conversion

[Bikash Agrawal]

Actually I am using rJava, running some map-reduce using R.
The data send is in bytes, but actually it is floating-point number.

On R side, I need to convert this byte into Float. But I couldn't find any
function.
I am try using rawToChar() which convert into character. And later on
as.double to convert it.

But it is not giving the exact value.
Could any one help me out.


On Tue, Jun 11, 2013 at 6:01 PM, Bikash Agrawal er.bikas...@gmail.comwrote:

 Is there any packages available in R, that can convert Bytes array to
 Float.
 Using rJava we can do it. But it is kind of slow. Is there any R
 specific packages.
 I am having problem converting my bytes array to floating point.
 Could any one help me with this problem.

 Thanks
 Bikash

 --
 With Best Regards
 Bikash Agrawal
 Web/Software Developer
 Mobile: +47 92502701
 www.bikashagrawal.com.np




-- 
With Best Regards
Bikash Agrawal
Web/Software Developer
Mobile: +47 92502701
www.bikashagrawal.com.np

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Re: [R] Instant search for R documentation

[Spencer Graves]

On 6/12/2013 1:03 AM, jonathan cornelissen wrote:

Hi,

I just wanted to share with you that we made a website over the weekend that allows 
instant search of the R documentation on CRAN, see: www.Rdocumentation.org. 
It's a first version, so any feedback/comments/criticism most welcome.



  Interesting.  Are you aware of the following:


* help.start()


* The R Wiki (the fourth item under Documentation on the 
left at r-project.org).  Might you want to consider merging your 
rdocumentation.org with this?



  - NOTE:  The R Wiki unfortunately has not gotten the 
attention and development I believe it deserves.  I'm not sure why this 
is.  The standard Wikipedia gets many contributors.  One difference I 
noticed is that to edit this, one needs to login. That's not true for 
Wikimedia projects.  Beyond that, with stardard Mediawiki markup 
language can intimidate some people.  Fortunately, difficulties in using 
the Mediawiki softaware will soon be reduced. One of the primary 
priorities of the software development team at the Wikimedia Foundation 
is modifying the Mediawiki software to include a beta version of a 
visual (WYSIWYG) editor.  I saw a demo of a beta version of this a month 
ago.  It's already available for limited use, but I don't think it's 
quite ready yet.  I think it might be wise to check for it later this year.



* The sos package with its vignette for searching CRAN 
packages and getting the result sorted to place first the package with 
the most matches.



  Hope this helps.
  Spencer


Best regards,

Jonathan
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Re: [R] Add a column to a dataframe based on multiple other column values

[Keith S Weintraub]

Tom,

Here is my solution. Note that I assume the columns are interleaved as you 
describe below. I'm sure others will have better replies.

Note that using dput helps the helpers.

# From dput(mdat)
mdat-structure(list(x1 = c(2L, 2L, 2L, 3L, 3L, 30L, 32L, 33L, 33L), 
y1 = c(100L, 100L, 100L, 0L, 0L, 0L, 100L, 82L, 0L), x2 = c(190L, 
192L, 192L, 195L, 198L, 198L, 868L, 870L, 871L), y2 = c(99L, 
63L, 63L, 99L, 98L, 100L, 100L, 100L, 82L), x3 = c(1430L, 
1431L, 1444L, 1499L, 1500L, 1451L, 1451L, 1490L, 1494L), 
y3 = c(79L, 75L, 51L, 50L, 80L, 97L, 97L, 97L, 85L), output = c(89, 
69, 57, 74.5, 89, 65.6667, 99, 93, 55.6667)), .Names = c(x1, 
y1, x2, y2, x3, y3, output), class = data.frame, row.names = 
c(NA, 
-9L))

mdat.pure-mdat[,-ncol(mdat)]

# Function to apply to rows
theFunk-function(x) {
  nxy-length(x)/2
  idx-seq_len(nxy)
  xvec-x[idx*2 - 1]
  yvec-x[idx*2]
  mean(yvec[xvec10])
}

# Apply the function to rows
output-apply(mdat.pure, 1, theFunk)

Or 

mdat.pure$output-apply(mdat.pure, 1, theFunk)

will put the calculated column at the end of mdat.pure.

Note that I haven't taken account of missing values.

Hope this helps,
KW

--

On Jun 12, 2013, at 6:00 AM, r-help-requ...@r-project.org wrote:

 Message: 35
 Date: Tue, 11 Jun 2013 17:07:12 +0100
 From: Tom Oates toate...@gmail.com
 To: r-help@r-project.org
 Subject: [R] Add a column to a dataframe based on multiple other
   column  values
 Message-ID:
   cagudn1cxlfxxnzdwquo515h_h5qekfmuyg5msdb1qn6gbq7...@mail.gmail.com
 Content-Type: text/plain
 
 Hi
 I have a dataframe as below:
 
 x1y1x2y2x3y3output
 21001909914307989
 21001926314317569
 21001926314445157
 301959914995074.5
 301989815008089
 30019810014519765.6667
 3210086810014519799
 338287010014909793
 3308718214948555.6667
 
 
 In reality the dataframe has pairs of columns x  y up to a large number.
 As you can see from the column labelled output in the dataframe; I want to
 calculate the mean of each row of the yn columns, but only to include each
 yn value in the calculation of the mean if the corresponding xn column
 value is greater than 10.
 So for row 1; you will see that only y2  y3 are included in calculating
 the output column, but for row 6 y1-y3 are all included.
 Because the number of paired x  y columns is large I am not sure the best
 way to achieve this.
 Thanks in advance
 Tom

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

Re: [R] Bytes to Numeric/Float conversion

[Duncan Murdoch]

On 13-06-12 6:54 AM, Bikash Agrawal wrote:

Actually I am using rJava, running some map-reduce using R.
The data send is in bytes, but actually it is floating-point number.

On R side, I need to convert this byte into Float. But I couldn't find any
function.
I am try using rawToChar() which convert into character. And later on
as.double to convert it.

But it is not giving the exact value.
Could any one help me out.



If you want exact transfer from bytes, use raw connections.  For example:

 con - rawConnection(raw(0), r+)
 writeBin(pi, con)
 rawConnectionValue(con)
[1] 18 2d 44 54 fb 21 09 40
 seek(con,0)
[1] 8
 readBin(con, numeric)
[1] 3.141593

Depending on how you created the bytes, you may need to do some fiddling 
with the optional parameters size and endian of readBin to read them 
properly.


Duncan Murdoch

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Re: [R] QR factorization for aov

[peter dalgaard]

On Jun 11, 2013, at 20:26 , Mimi Celis wrote:

 I am looking at the aov function in R. I see that it uses a modified QR 
 factorization routine dqrdc2 based on the Linpack routine dqrdc. Pivoting is 
 done different than the original Linpack function.
 
 My questions:
 
  *   Why is it necessary to modify the pivoting strategy? Something necessary 
 for aov?
  *   Will the LAPACK function dgeqp3 work well or would the pivoting have o 
 be modified?
 


As far as I have understood it, the issue is that to generate the sequential 
ANOVA table based on a single QR factorization, you can't have it swapping 
terms around, because there are cases where the order of terms matters. 

So LAPACK won't do. Or rather, to use it, you'd need to rethink the algoritm; 
you may need refactorizing for each line the ANOVA table. It's not necessarily 
impossible or seriously inefficient, just one of the things that nobody seems 
to have an aching desire to tackle.

-pd

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

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

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

Re: [R] change factor to mtrix

[peter dalgaard]

On Jun 12, 2013, at 09:47 , Gallon Li wrote:

 i wish to change a column of factor variable to multiple columns of
 zero-ones
 
 for example, my factor could be
 
 ff=c('a','a','b','b','c','c')
 
 then I want to have two columns (for three levels) that are
 
 0 0
 0 0
 1 0
 1 0
 0 1
 0 1
 
 how can i do this fast?

Maybe not fast, but quick:

 fff - factor(ff)
 model.matrix(~fff)[,-1]
  fffb fffc
100
200
310
410
501
601

Possibly faster, skipping some red tape:

 CC - contrasts(fff)
 CC
  b c
a 0 0
b 1 0
c 0 1
 CC[fff,]
  b c
a 0 0
a 0 0
b 1 0
b 1 0
c 0 1
c 0 1



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

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

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

Re: [R] Big, complex, well-structured .R file for demonstration?

[Jeff Newmiller]

Just because you have an editor that can let you see the organization within 
the file does not mean the code itself is well-structured. If you do put a lot 
of code in one file, you will be more likely in your next project that builds 
on this one to load code you do not need (bloat), and that is a very practical 
defect in the structure of the current project. Regardless of any arguments you 
can think of to the contrary, that is why single large files with otherwise 
well-structured code are uncommon.
---
Jeff NewmillerThe .   .  Go Live...
DCN:jdnew...@dcn.davis.ca.usBasics: ##.#.   ##.#.  Live Go...
  Live:   OO#.. Dead: OO#..  Playing
Research Engineer (Solar/BatteriesO.O#.   #.O#.  with
/Software/Embedded Controllers)   .OO#.   .OO#.  rocks...1k
--- 
Sent from my phone. Please excuse my brevity.

Thorsten Jolitz tjol...@gmail.com wrote:

Greg Snow 538...@gmail.com writes:

 Some would argue that big and well structured are not compatible.
 Part
 of structuring a project well is knowing when and how to break it
into
 smaller pieces, so those authors who are best at creating well
structured R
 code will often split it between several small files rather than one
big
 file.

As Emacs Org-mode has proven for text files, this structuring into
smaller pieces can be done in one single file too (that is structured
as
a hierarchical outline tree) an this can be even more convenient than
to
deal with many small files. But otherwise I agree with you, its much
better to split a file up before it becomes a growing mess.

 On Tue, Jun 11, 2013 at 9:06 AM, Thorsten Jolitz tjol...@gmail.com
wrote:


 Hi List,

 I'm looking for a rather big, but well structured R file that
contains
 as much of R language features as possible (i.e. that uses a lot of
the
 functionality described in the 'R Reference Card' and, if possible,
S4
 classes too).

 I want to check some code I wrote against such a file and use it for
 demonstration purposes. However, most .R files I find out there are
 rather short without much structure.

 Any links to candidate (open source) files would be appreciated.

 --
 cheers,
 Thorsten

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 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide
 http://www.R-project.org/posting-guide.html
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Re: [R] Combining CSV data

[Shreya Rawal]

Great, thanks Arun, but I seem to be running into this error. Not sure what
did I miss.


result-data.frame(final_ouput[,-5],read.table(text=as.character(final_output$comment),sep=|,fill=TRUE,na.strings=),stringsAsFactors=FALSE)colnames(result)[5:7]-paste0(DataComment,1:3)
Error: unexpected symbol in
result-data.frame(final_ouput[,-5],read.table(text=as.character(final_output$comment),sep=|,fill=TRUE,na.strings=),stringsAsFactors=FALSE)colnames


On Tue, Jun 11, 2013 at 5:09 PM, arun smartpink...@yahoo.com wrote:




 HI,
 You could use:
 result3-
 data.frame(result2[,-5],read.table(text=as.character(result2$comment),sep=|,fill=TRUE,na.strings=),stringsAsFactors=FALSE)
 colnames(result3)[5:7]- paste0(DataComment,1:3)
 A.K.
 
 From: Shreya Rawal rawal.shr...@gmail.com
 To: arun smartpink...@yahoo.com
 Sent: Tuesday, June 11, 2013 4:22 PM
 Subject: Re: [R] Combining CSV data



 Hey Arun,

 I guess you could guide me with this a little bit. I have been working on
 the solution Jim suggested (and also because that I could understand it
 with my little knowledge of R :))

 So with these commands I am able to get the data in this format:

  fileA - read.csv(text = Row_ID_CR,   Data1,Data2,Data3
 + 1,   aa,  bb,  cc
 + 2,   dd,  ee,  ff, as.is = TRUE)
 
  fileB - read.csv(text = Row_ID_N,   Src_Row_ID,   DataN1
 + 1a,   1,   This is comment 1
 + 2a,   1,   This is comment 2
 + 3a,   2,   This is comment 1
 + 4a,   1,   This is comment 3, as.is = TRUE)
 
  # get rid of leading/trailing blanks on comments
  fileB$DataN1 - gsub(^ *| *$, , fileB$DataN1)
 
  # merge together
  result - merge(fileA, fileB, by.x = 'Row_ID_CR', by.y = Src_Row_ID)
 
  # now partition by Row_ID_CR and aggregate the comments
  result2 - do.call(rbind,
 + lapply(split(result, result$Row_ID_CR), function(.grp){
 + cbind(.grp[1L, -c(5,6)], comment = paste(.grp$DataN1, collapse =
 '|'))
 + })
 + )

 Row_ID_CR Data1Data2Data3
 comment
 1 1aa   bb   cc
This is comment 1| This is comment 2| This
 is comment 3
 2 2dd   ee   ff
  This is comment 1| This is Comment 2

 I can even split the last column by
 this: strsplit(as.character(result2$comment), split='\\|')

 [[1]]
 [1] This is comment 1 This is comment 2  This is comment 3

 [[2]]
 [1] This is comment 1 This is comment 2


 but now I am not sure how to combine everything together. I guess by now
 you must have realized how new I am to R :)

 Thanks!!
 Shreya






 On Tue, Jun 11, 2013 at 1:02 PM, arun smartpink...@yahoo.com wrote:

 Hi,
 If the dataset is like this with the comments in the order:
 
 dat2-read.table(text=
 Row_ID_N,  Src_Row_ID,  DataN1
 1a,  1,  This is comment 1
 2a,  1,  This is comment 2
 3a,  2,  This is comment 1
 4a,  1,  This is comment 3
 ,sep=,,header=TRUE,stringsAsFactors=FALSE)
 
 dat3-read.table(text=
 Row_ID_N,  Src_Row_ID,  DataN1
 1a,  1,  This is comment 1
 2a,  1,  This is comment 2
 3a,  2,  This is comment 1   #
 
 4a,  1,  This is comment 3
 5a, 2,  This is comment 2  #
 
 ,sep=,,header=TRUE,stringsAsFactors=FALSE)
 
 
 library(stringr)
 library(plyr)
 fun1- function(data1,data2){
 data2$DataN1- str_trim(data2$DataN1)
 res- merge(data1,data2,by.x=1,by.y=2)
 res1- res[,-5]
 res2-
 ddply(res1,.(Row_ID_CR,Data1,Data2,Data3),summarize,DataN1=list(DataN1))
 Mx1- max(sapply(res2[,5],length))
 res3- data.frame(res2[,-5],do.call(rbind,lapply(res2[,5],function(x){
   c(x,rep(NA,Mx1-length(x)))
 
   })),stringsAsFactors=FALSE)
 colnames(res3)[grep(X,colnames(res3))]-
 paste0(DataComment,gsub([[:alpha:]],,colnames(res3)[grep(X,colnames(res3))]))
 res3
 }
 
 
 fun1(dat1,dat2)
 #  Row_ID_CRData1Data2Data3
 DataComment1
 #1 1   aa   bb   cc This is
 comment 1
 
 #2 2   dd   ee   ff This is
 comment 1
 #   DataComment2  DataComment3
 #1 This is comment 2 This is comment 3
 #2  NA  NA
 
  fun1(dat1,dat3)
 #  Row_ID_CRData1Data2Data3
 DataComment1
 #1 1   aa   bb   cc This is
 comment 1
 
 #2 2   dd   ee   ff This is
 comment 1
  # 

Re: [R] agnes() in package cluster on R 2.14.1 and R 3.0.1

[Martin Maechler]

 Hugo Varet vareth...@gmail.com
 on Tue, 11 Jun 2013 15:15:36 +0200 writes:

 Dear Martin,
 Thank you for your answer. Here is the exact call to agnes():
 setwd(E:/Hugo)
 library(cluster)
 load(mydata.rda)
 tableauTani-dist.binary(mydata, method = 4, diag = FALSE, upper = FALSE)
 resAgnes.Tani-agnes(tableauTani, diss = inherits(tableauTani,
 dist),method = ward)
 classe.agnTani.3 - cutree(resAgnes.Tani, 3)

 I'm going to send you the data in a separated e-mail.

Thank you, Hugo, and I got that alright.

I can see that many of the distances are *identical*, because
your data is completely binary.
From experience, I know that this can lead (for some algorithms)
to arbitrary decisions in clustering, namely when two
*pairs* of observations / clusters have exactly the same
distance, it is somewhat random which of the pair is merged /
fused first, in a bottom up hierarchical algorithm such as agnes().

To reproduce your example (above) I need however to know 
*where* you got the the  dist.binary()  function from.
It is not part of standard R nor of the cluster package.

Regards,
Martin


 Regards,

 Hugo


 Le lundi 10 juin 2013, Martin Maechler maech...@stat.math.ethz.ch a
 écrit :
 Hugo Varet vareth...@gmail.com
 on Sun, 9 Jun 2013 11:43:32 +0200 writes:
 
  Dear R users,
  I discovered something strange using the function agnes() of the
 cluster
  package on R 3.0.1 and on R 2.14.1. Indeed, the clusterings
 obtained are
  different whereas I ran exactly the same code.
 
 hard to believe... but ..
 
  I quickly looked at the source code of the function and I
 discovered that
  there was an important change: agnes() in R 2.14.1 used a FORTRAN
 code
  whereas agnes() in R 3.0.1 uses a C code.
 
 well, it does so quite a bit longer, e.g., also in R 2.15.0
 
  Here is one of the contingency table between R 2.14.1 and R 3.0.1:
  classe.agnTani.2.14.1
  classe.agnTani.3.0.1  12   3
  174   0229
  2 02350
  3  120   0  15
 
  So, I was wondering if it was normal that the C and FORTRAN codes
 give
  different results?
 
 It's not normal, and I'm pretty sure I have had many many
 examples which gave identical results.
 
 Can you provide a reproducible example, please?
 If the example is too large [for dput() ], please send me the *.rda
 file produced from
 save(your data, file=the file I neeed)
 *and* a the exact call to agnes() for your data.
 
 Thank you in advance!
 
 Martin Maechler,
 the one you could have e-mailed directly
 to using   maintainer(cluster) ...
 
 
  Best regards,
  Hugo Varet
 
  [[alternative HTML version deleted]]
 ^ try to avoid, please ^
 
  __
  R-help@r-project.org mailing list
  https://stat.ethz.ch/mailman/listinfo/r-help
  PLEASE do read the posting guide
 http://www.R-project.org/posting-guide.html
  and provide commented, minimal, self-contained, reproducible code.
 
 yes indeed, please.


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

[R] GGally installation problems

[Tim Smith]

Hi,

I was trying to install the GGally package, but was getting errors. Here is 
what I get:

 install.packages(GGally)
Installing package(s) into ‘/Users/ts2w/Library/R/2.15/library’
(as ‘lib’ is unspecified)
Warning in install.packages :
  package ‘GGally’ is not available (for R version 2.15.2)

 install.packages(GGally,repos=http://cran-r.project.org;)
Installing package(s) into ‘/Users/ts2w/Library/R/2.15/library’
(as ‘lib’ is unspecified)
Warning in install.packages :
  cannot open: HTTP status was '404 Not Found'
Warning in install.packages :
  cannot open: HTTP status was '404 Not Found'
Warning in install.packages :
  unable to access index for repository http://cran-r.project.org/src/contrib
Warning in install.packages :
  package ‘GGally’ is not available (for R version 2.15.2)
Warning in install.packages :
  cannot open: HTTP status was '404 Not Found'
Warning in install.packages :
  cannot open: HTTP status was '404 Not Found'
Warning in install.packages :
  unable to access index for repository 
http://cran-r.project.org/bin/macosx/leopard/contrib/2.15

thanks.

[[alternative HTML version deleted]]

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

Re: [R] Combining CSV data

[arun]

HI Shreya,
#Looks like you run the two line code as a single line.

result3- 
data.frame(result2[,-5],read.table(text=as.character(result2$comment),sep=|,fill=TRUE,na.strings=),stringsAsFactors=FALSE)


colnames(result3)[5:7]- paste0(DataComment,1:3)

 result3
#  Row_ID_CR Data1    Data2    Data3  DataComment1
#1 1    aa   bb   cc This is comment 1
#2 2    dd   ee   ff This is comment 1
#   DataComment2  DataComment3
#1 This is comment 2 This is comment 3
#2  NA  NA



A.K.



From: Shreya Rawal rawal.shr...@gmail.com
To: arun smartpink...@yahoo.com 
Cc: R help r-help@r-project.org; jim holtman jholt...@gmail.com 
Sent: Wednesday, June 12, 2013 8:58 AM
Subject: Re: [R] Combining CSV data



Great, thanks Arun, but I seem to be running into this error. Not sure what did 
I miss.

 result-data.frame(final_ouput[,-5],read.table(text=as.character(final_output$comment),sep=|,fill=TRUE,na.strings=),stringsAsFactors=FALSE)colnames(result)[5:7]-paste0(DataComment,1:3)
Error: unexpected symbol in 
result-data.frame(final_ouput[,-5],read.table(text=as.character(final_output$comment),sep=|,fill=TRUE,na.strings=),stringsAsFactors=FALSE)colnames



On Tue, Jun 11, 2013 at 5:09 PM, arun smartpink...@yahoo.com wrote:




HI,
You could use:
result3- 
data.frame(result2[,-5],read.table(text=as.character(result2$comment),sep=|,fill=TRUE,na.strings=),stringsAsFactors=FALSE)
colnames(result3)[5:7]- paste0(DataComment,1:3)

A.K.

From: Shreya Rawal rawal.shr...@gmail.com
To: arun smartpink...@yahoo.com
Sent: Tuesday, June 11, 2013 4:22 PM

Subject: Re: [R] Combining CSV data



Hey Arun,

I guess you could guide me with this a little bit. I have been working on the 
solution Jim suggested (and also because that I could understand it with my 
little knowledge of R :))

So with these commands I am able to get the data in this format:

 fileA - read.csv(text = Row_ID_CR,   Data1,    Data2,    Data3
+ 1,                   aa,          bb,          cc
+ 2,                   dd,          ee,          ff, as.is = TRUE)
 
 fileB - read.csv(text = Row_ID_N,   Src_Row_ID,   DataN1
+ 1a,               1,                   This is comment 1
+ 2a,               1,                   This is comment 2
+ 3a,               2,                   This is comment 1
+ 4a,               1,                   This is comment 3, as.is = TRUE)
 
 # get rid of leading/trailing blanks on comments
 fileB$DataN1 - gsub(^ *| *$, , fileB$DataN1)
 
 # merge together
 result - merge(fileA, fileB, by.x = 'Row_ID_CR', by.y = Src_Row_ID)
 
 # now partition by Row_ID_CR and aggregate the comments
 result2 - do.call(rbind, 
+     lapply(split(result, result$Row_ID_CR), function(.grp){
+         cbind(.grp[1L, -c(5,6)], comment = paste(.grp$DataN1, collapse = 
'|'))
+     })
+ )

Row_ID_CR                 Data1        Data2        Data3                      
                           comment
1         1                    aa           bb           cc                    
                          This is comment 1| This is comment 2| This is 
comment 3
2         2                    dd           ee           ff                    
                            This is comment 1| This is Comment 2

I can even split the last column by this: 
strsplit(as.character(result2$comment), split='\\|')

[[1]]
[1] This is comment 1 This is comment 2  This is comment 3

[[2]]
[1] This is comment 1 This is comment 2


but now I am not sure how to combine everything together. I guess by now you 
must have realized how new I am to R :)

Thanks!!
Shreya






On Tue, Jun 11, 2013 at 1:02 PM, arun smartpink...@yahoo.com wrote:

Hi,
If the dataset is like this with the comments in the order:

dat2-read.table(text=
Row_ID_N,  Src_Row_ID,  DataN1
1a,  1,  This is comment 1
2a,  1,  This is comment 2
3a,  2,  This is comment 1
4a,  1,  This is comment 3
,sep=,,header=TRUE,stringsAsFactors=FALSE)

dat3-read.table(text=
Row_ID_N,  Src_Row_ID,  DataN1
1a,  1,  This is comment 1
2a,  1,  This is comment 2
3a,  2,  This is comment 1   #

4a,  1,  This is comment 3
5a, 2,  This is comment 2  #

,sep=,,header=TRUE,stringsAsFactors=FALSE)


library(stringr)
library(plyr)
fun1- function(data1,data2){
    data2$DataN1- str_trim(data2$DataN1)  
    res- merge(data1,data2,by.x=1,by.y=2)
    res1- res[,-5]
    res2- 
ddply(res1,.(Row_ID_CR,Data1,Data2,Data3),summarize,DataN1=list(DataN1))
    Mx1- max(sapply(res2[,5],length))
    res3- data.frame(res2[,-5],do.call(rbind,lapply(res2[,5],function(x){
  

Re: [R] Combining CSV data

[Shreya Rawal]

Ah that makes sense. This looks perfect now. Thanks for your help on this!



On Wed, Jun 12, 2013 at 9:10 AM, arun smartpink...@yahoo.com wrote:

 HI Shreya,
 #Looks like you run the two line code as a single line.

 result3-

 data.frame(result2[,-5],read.table(text=as.character(result2$comment),sep=|,fill=TRUE,na.strings=),stringsAsFactors=FALSE)


 colnames(result3)[5:7]- paste0(DataComment,1:3)

  result3
 #  Row_ID_CR Data1Data2Data3
 DataComment1
 #1 1aa   bb   cc This is
 comment 1
 #2 2dd   ee   ff This is
 comment 1
 #   DataComment2  DataComment3
 #1 This is comment 2 This is comment 3
 #2  NA  NA



 A.K.


 
 From: Shreya Rawal rawal.shr...@gmail.com
 To: arun smartpink...@yahoo.com
 Cc: R help r-help@r-project.org; jim holtman jholt...@gmail.com
 Sent: Wednesday, June 12, 2013 8:58 AM
 Subject: Re: [R] Combining CSV data



 Great, thanks Arun, but I seem to be running into this error. Not sure
 what did I miss.

 
 result-data.frame(final_ouput[,-5],read.table(text=as.character(final_output$comment),sep=|,fill=TRUE,na.strings=),stringsAsFactors=FALSE)colnames(result)[5:7]-paste0(DataComment,1:3)
 Error: unexpected symbol in
 result-data.frame(final_ouput[,-5],read.table(text=as.character(final_output$comment),sep=|,fill=TRUE,na.strings=),stringsAsFactors=FALSE)colnames



 On Tue, Jun 11, 2013 at 5:09 PM, arun smartpink...@yahoo.com wrote:


 
 
 HI,
 You could use:
 result3-
 data.frame(result2[,-5],read.table(text=as.character(result2$comment),sep=|,fill=TRUE,na.strings=),stringsAsFactors=FALSE)
 colnames(result3)[5:7]- paste0(DataComment,1:3)
 
 A.K.
 
 From: Shreya Rawal rawal.shr...@gmail.com
 To: arun smartpink...@yahoo.com
 Sent: Tuesday, June 11, 2013 4:22 PM
 
 Subject: Re: [R] Combining CSV data
 
 
 
 Hey Arun,
 
 I guess you could guide me with this a little bit. I have been working on
 the solution Jim suggested (and also because that I could understand it
 with my little knowledge of R :))
 
 So with these commands I am able to get the data in this format:
 
  fileA - read.csv(text = Row_ID_CR,   Data1,Data2,Data3
 + 1,   aa,  bb,  cc
 + 2,   dd,  ee,  ff, as.is = TRUE)
 
  fileB - read.csv(text = Row_ID_N,   Src_Row_ID,   DataN1
 + 1a,   1,   This is comment 1
 + 2a,   1,   This is comment 2
 + 3a,   2,   This is comment 1
 + 4a,   1,   This is comment 3, as.is =
 TRUE)
 
  # get rid of leading/trailing blanks on comments
  fileB$DataN1 - gsub(^ *| *$, , fileB$DataN1)
 
  # merge together
  result - merge(fileA, fileB, by.x = 'Row_ID_CR', by.y = Src_Row_ID)
 
  # now partition by Row_ID_CR and aggregate the comments
  result2 - do.call(rbind,
 + lapply(split(result, result$Row_ID_CR), function(.grp){
 + cbind(.grp[1L, -c(5,6)], comment = paste(.grp$DataN1, collapse
 = '|'))
 + })
 + )
 
 Row_ID_CR Data1Data2Data3
 comment
 1 1aa   bb   cc
This is comment 1| This is comment 2| This
 is comment 3
 2 2dd   ee   ff
  This is comment 1| This is Comment 2
 
 I can even split the last column by
 this: strsplit(as.character(result2$comment), split='\\|')
 
 [[1]]
 [1] This is comment 1 This is comment 2  This is comment 3
 
 [[2]]
 [1] This is comment 1 This is comment 2
 
 
 but now I am not sure how to combine everything together. I guess by now
 you must have realized how new I am to R :)
 
 Thanks!!
 Shreya
 
 
 
 
 
 
 On Tue, Jun 11, 2013 at 1:02 PM, arun smartpink...@yahoo.com wrote:
 
 Hi,
 If the dataset is like this with the comments in the order:
 
 dat2-read.table(text=
 Row_ID_N,  Src_Row_ID,  DataN1
 1a,  1,  This is comment 1
 2a,  1,  This is comment 2
 3a,  2,  This is comment 1
 4a,  1,  This is comment 3
 ,sep=,,header=TRUE,stringsAsFactors=FALSE)
 
 dat3-read.table(text=
 Row_ID_N,  Src_Row_ID,  DataN1
 1a,  1,  This is comment 1
 2a,  1,  This is comment 2
 3a,  2,  This is comment 1   #
 
 4a,  1,  This is comment 3
 5a, 2,  This is comment 2  #
 
 ,sep=,,header=TRUE,stringsAsFactors=FALSE)
 
 
 library(stringr)
 library(plyr)
 fun1- function(data1,data2){
 data2$DataN1- str_trim(data2$DataN1)
 res- merge(data1,data2,by.x=1,by.y=2)
 res1- res[,-5]
 res2-
 

Re: [R] survreg with measurement uncertainties

[Andrews, Chris]

survreg allows interval censored data, if that is how you want to represent 
measurement uncertainty.  See

?Surv

-Original Message-
From: Kyle Penner [mailto:kpen...@as.arizona.edu] 
Sent: Tuesday, June 11, 2013 8:02 PM
To: r-help@r-project.org
Subject: [R] survreg with measurement uncertainties

Hello,

I have some measurements that I am trying to fit a model to.  I also have 
uncertainties for these measurements.  Some of the measurements are not well 
detected, so I'd like to use a limit instead of the actual measurement.  (I am 
always dealing with upper limits, i.e. left censored data.)

I have successfully run survreg using the combination of well detected 
measurements and limits, but I would like to include the measurement 
uncertainty (for the well detected measurements) in the fitting.  As far as I 
can tell, survreg doesn't support this.  Does anyone have a suggestion for how 
to accomplish this?

Thanks,

Kyle


**
Electronic Mail is not secure, may not be read every day, and should not be 
used for urgent or sensitive issues 
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Re: [R] help using code

[John Kane]

Have a look at http://www.burns-stat.com/documents/tutorials/impatient-r/ . I 
think the section on blank screen syndrome may help.

John Kane
Kingston ON Canada


 -Original Message-
 From: montana3...@gmail.com
 Sent: Tue, 11 Jun 2013 16:59:34 -0700
 To: ruipbarra...@sapo.pt
 Subject: Re: [R] help using code
 
 Hello,
 
 Thanks for the help!
 
 Your answer resolved my problem with the function I listed, but brought
 up
 a larger question. How is the output of the importdata function stored
 for
 use with other functions (as in, how do I call on that data for use with
 other functions)? As a simple example I have another function:
 
 meanXY = function(xyzuvw) {
   xy = c(mean(xyzuvw$x), mean(xyzuvw$y))
   return(xy)
 }
 
 I know that the xyzuvw portion is referring to the output of the
 importdata function, but I don't know how to call up the necessary data
 (hope this makes sense).
 
 Thanks again for the help!
 
 John
 
 
 
 
 On 6/11/13 3:05 PM, Rui Barradas ruipbarra...@sapo.pt wrote:
 
 Hello,
 
 I believe you are making a confusion on how to call a function in R. You
 don't replace the argument in the function declaration. what you do is
 to call the function like this:
 
 importdata(~/path to/filename.xyzuvwrgb)
 
 leaving the function definition alone.
 
 Hope this helps,
 
 Rui Barradas
 
 Em 11-06-2013 19:52, John McDermott escreveu:
 Hi R-helpers,
 
 I inherited some code that I'm trying to use. As a very new R user I'm
 having some confusion.
 
 I have some input files in the form: filename.xyzuvwrgb which I'm
 trying to
 import using:
 
 importdata = function(filename) {
 
  p = scan(filename,what=list(x = double(), y = double(), z =
 double(), u
 = double(),v=double(),w=double()),skip=1,flush=TRUE,sep= )
 
  return(data.frame(x=p$x, y=p$y, z=p$z, u=p$u, v=p$v, w=p$w))
 
 }
 
 
 
 For the filename I replaced both with ~/path to/filename.xyzuvwrgb
 and I
 get the following errors:
 
 
 
 Error: unexpected string constant in importdata =
 function(~/Desktop/thrustScarp1.xyzuvw
 
 
 
 Error: no function to return from, jumping to top level
 
 
 
 Error: unexpected '}' in }
 
 
 
 I'm assuming it has to do with how I am using/formatted the
 function(filename) portion. How can I get this to work?
 
 
 
 Thanks for the help!
 
 
 
 
 
 
 
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Re: [R] survreg with measurement uncertainties

[Terry Therneau]

I will assume that you are talking about uncertainty in the response.  Then one simple way 
to fit the model is to use case weights that are proprional to 1/variance, along with 
+cluster(id) in the model statement to get a correct variance for this case.  In linear 
models this would be called the White or Horvitz-Thompsen or GEE working 
independence variance estimate, depending on which literature you happen to be reading 
(economics, survey sampling, or biostat).


Now if you are talking about errors in the predictor variables, that is a much 
harder problem.

Terry Therneau


On 06/12/2013 05:00 AM, Kyle Penner wrote:

Hello,

I have some measurements that I am trying to fit a model to.  I also
have uncertainties for these measurements.  Some of the measurements
are not well detected, so I'd like to use a limit instead of the
actual measurement.  (I am always dealing with upper limits, i.e. left
censored data.)

I have successfully run survreg using the combination of well detected
measurements and limits, but I would like to include the measurement
uncertainty (for the well detected measurements) in the fitting.  As
far as I can tell, survreg doesn't support this.  Does anyone have a
suggestion for how to accomplish this?

Thanks,

Kyle


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

Re: [R] ggpairs in GGally replaces plotmatrix in ggplot2

[John Kane]

Thanks, I obviously read the help incorrectly. It does give the same results as 
plotmatrix(dat1)

I take back some of the nasty thoughts I was thinking about ggpairs(). 

Any idea of the problem with RSudio? Keith notices the same speed difference 
(but no crash) on a Mac while I'm runnng Ubuntu 12.10.

John Kane
Kingston ON Canada


 -Original Message-
 From: istaz...@gmail.com
 Sent: Tue, 11 Jun 2013 17:54:55 -0400
 To: kw1...@gmail.com
 Subject: Re: [R] ggpairs in GGally replaces plotmatrix in ggplot2
 
 I think the ggpairs equivalent is
 
 ggpairs(dat1, upper=list(continuous=points), axisLabels=show)
 
 oddly enough.
 
 ggpairs(dat1)
 
 should default to the same graph as
 
 plotmatrix(dat1)
 
 but there seems to be a conflict between the default
 axisLabels=internal and density plots. Or something. There is a bug
 report at https://github.com/ggobi/ggally/issues/18 that may be
 related.
 
 Best,
 Ista
 
 On Tue, Jun 11, 2013 at 4:07 PM, Keith S Weintraub kw1...@gmail.com
 wrote:
 Yes. I was able to run it in RStudio but it did seem much slower than in
 R.app (on the Mac).
 
 Note that the it that I ran still didn't give the same results as
 plotmatrix.
 
 Thanks,
 KW
 
 --
 
 On Jun 11, 2013, at 11:16 AM, John Kane jrkrid...@inbox.com wrote:
 
 Note that the code below might not work in RStudio.  I am gettting an
 intermittant crash when I use the ggpairs() command in RStudio and
 sometimes I get a density plot and sometimes not.  Also the command is
 taking 3-5 minutes to execute.
 
 This may just be a peculiarity of my machine but the code works fine
 and fairly fast in a terminal.
 
 John Kane
 Kingston ON Canada
 
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Re: [R] Add a column to a dataframe based on multiple other column values

[arun]

HI,
You could also try:
dat2- dat1[-ncol(dat1)]
fun1- function(dat,value){
    datNew- dat
    n1- ncol(datNew)
    indx1- seq(1,n1,by=2)
    indx2- indx1+1
    datNew[indx2][datNew[indx1] value]-NA
    dat$output-rowMeans(datNew[indx2],na.rm=TRUE)
    dat 
    }
    fun1(dat2,10)
 # x1  y1  x2  y2   x3 y3   output
#1  2 100 190  99 1430 79 89.0
#2  2 100 192  63 1431 75 69.0
#3  2 100 192  63 1444 51 57.0
#4  3   0 195  99 1499 50 74.5
#5  3   0 198  98 1500 80 89.0
#6 30   0 198 100 1451 97 65.7
#7 32 100 868 100 1451 97 99.0
#8 33  82 870 100 1490 97 93.0
#9 33   0 871  82 1494 85 55.7
A.K.




- Original Message -
From: arun smartpink...@yahoo.com
To: Tom Oates toate...@gmail.com
Cc: R help r-help@r-project.org
Sent: Tuesday, June 11, 2013 5:23 PM
Subject: Re: [R] Add a column to a dataframe based on multiple other column 
values

HI,
May be this helps:
dat1- read.table(text=
x1    y1    x2    y2    x3    y3    output
2    100    190    99    1430    79    89
2    100    192    63    1431    75    69
2    100    192    63    1444    51    57
3    0    195    99    1499    50    74.5
3    0    198    98    1500    80    89
30    0    198    100    1451    97    65.6667
32    100    868    100    1451    97    99
33    82    870    100    1490    97    93
33    0    871    82    1494    85    55.6667
,sep=,header=TRUE)

dat1$output2-apply(dat1[,-7],1,function(x) 
{indx-((seq(x)-1)%%2+1);indx1-indx==1; 
indx2-indx==2;mean(x[indx2][x[indx1]10])})
 dat1
#  x1  y1  x2  y2   x3 y3   output  output2
#1  2 100 190  99 1430 79 89.0 89.0
#2  2 100 192  63 1431 75 69.0 69.0
#3  2 100 192  63 1444 51 57.0 57.0
#4  3   0 195  99 1499 50 74.5 74.5
#5  3   0 198  98 1500 80 89.0 89.0
#6 30   0 198 100 1451 97 65.7 65.7
#7 32 100 868 100 1451 97 99.0 99.0
#8 33  82 870 100 1490 97 93.0 93.0
#9 33   0 871  82 1494 85 55.7 55.7
A.K.



- Original Message -
From: Tom Oates toate...@gmail.com
To: r-help@r-project.org
Cc: 
Sent: Tuesday, June 11, 2013 12:07 PM
Subject: [R] Add a column to a dataframe based on multiple other column
    values

Hi
I have a dataframe as below:

x1    y1    x2    y2    x3    y3    output
2    100    190    99    1430    79    89
2    100    192    63    1431    75    69
2    100    192    63    1444    51    57
3    0    195    99    1499    50    74.5
3    0    198    98    1500    80    89
30    0    198    100    1451    97    65.6667
32    100    868    100    1451    97    99
33    82    870    100    1490    97    93
33    0    871    82    1494    85    55.6667


In reality the dataframe has pairs of columns x  y up to a large number.
As you can see from the column labelled output in the dataframe; I want to
calculate the mean of each row of the yn columns, but only to include each
yn value in the calculation of the mean if the corresponding xn column
value is greater than 10.
So for row 1; you will see that only y2  y3 are included in calculating
the output column, but for row 6 y1-y3 are all included.
Because the number of paired x  y columns is large I am not sure the best
way to achieve this.
Thanks in advance
Tom

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[R] Windows R_LIBS_USER confusion under R-3.0.1

[Paul Johnson]

I would appreciate ideas about MS Windows install issues. I'm at our stats
summer camp and have been looking at a lot of Windows R installs and there
are some wrinkles about R_LIBS_USER.

On a clean Win7 or Win8 system, with R-3.0.1, we see the user library for
packages defaulting to  $HOME/R/win-library.

I think that's awesome, the way it should be. Yea! But it does not appear
that way on all systems, and I think it is because of lingering
after-effects of previous R installs.

In previous versions of R, R_LIBS_USER defaulted to
$HOME/AppData/Roaming/... That was not so great because it was (default)
hidden to the students and they were disoriented about how something that
does not exist (or show) could hold packages. Aside from teaching them how
to configure the file manager, we could navigate that.

The problem is that with R-3.0.1, sometimes we are seeing the user package
installs going into $HOME/AppData/Roaming/

In the user account, there is no $HOME/.Rprofile or $HOME/.Renviron.

I hate to tell non-expert users that they ought to go fishing in the
Windows registry, but I'm starting to suspect that is what they ought to
do.  What do you think?

PJ

-- 
Paul E. Johnson
Professor, Political Science  Assoc. Director
1541 Lilac Lane, Room 504  Center for Research Methods
University of Kansas University of Kansas
http://pj.freefaculty.org   http://quant.ku.edu

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Re: [R] assigning global columns selection for all subset functions in script

[bcrombie]

Thanks very much, John.  This is very helpful.

Burnette

From: John Kane [via R] [mailto:ml-node+s789695n4669297...@n4.nabble.com]
Sent: Tuesday, June 11, 2013 5:35 PM
To: Crombie, Burnette N
Subject: Re: assigning global columns selection for all subset functions in 
script

index the columns to select
lets say you want to select a set of colmns 2,4,6,8
Try something like this. (not run)
mycols  -  c(2,4,6,8)
select(mydata[ , mycols] , mdata$x == 3)
John Kane
Kingston ON Canada

 -Original Message-
 From: [hidden email]/user/SendEmail.jtp?type=nodenode=4669297i=0
 Sent: Tue, 11 Jun 2013 09:18:25 -0700 (PDT)
 To: [hidden email]/user/SendEmail.jtp?type=nodenode=4669297i=1
 Subject: [R] assigning global columns selection for all subset functions
 in script

 How do I let R know that I always want to select the same columns in my
 subset functions (below), so that I don't have to keep copy/pasting the
 same
 selection? (thanks)
 devUni2 - subset(devUni1, dind02 != 52,
 select=c(paidhre,earnhre,earnwke,uhourse,hourslw,otc,ind02,dind02,occ00,docc00,lfsr94,class94,relref95,smsastat,state,weight,year))
 devUni3 - subset(devUni2, lfsr94 == 1 | lfsr94 == 2 ,
 select=c(paidhre,earnhre,earnwke,uhourse,hourslw,otc,ind02,dind02,occ00,docc00,lfsr94,class94,relref95,smsastat,state,weight,year))
 devUni4 - subset(devUni3, class94  6 ,
 select=c(paidhre,earnhre,earnwke,uhourse,hourslw,otc,ind02,dind02,occ00,docc00,lfsr94,class94,relref95,smsastat,state,weight,year))
 devUni5 - subset(devUni4, relref95  10 | relref95 ==13 | relref95
 =14,
 select=c(paidhre,earnhre,earnwke,uhourse,hourslw,otc,ind02,dind02,occ00,docc00,lfsr94,class94,relref95,smsastat,state,weight,year))



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Re: [R] [R-SIG-Mac] problem with the installation of r commander on a mac

[Susanne.Ettinger]

Dear all,

I am trying to install R and the Rcmdr package on a MacOSX 10.8.4.

It appears that I keep getting the error message Erreur : le chargement du 
package ou de l'espace de noms a échoué pour 'Rcmdr' no matter what my 
approach is. Even downloading XQuartz-2.7.4 did not help.

I found the same problem outlined on the following website 

https://stat.ethz.ch/pipermail/r-help/2012-October/325305.html

and was wondering whether a solution to the problem has been stated since then 
and if you could help me with instructions how to proceed ?

Thank you very much for your help !

Kind regards,
Susanne

__

Susanne ETTINGER
Postdoctoral researcher
-
Laboratoire Magmas et Volcans
UBP - UMR6524 CNRS - M163 IRD
5, rue Kessler
63038 Clermont-Ferrand
-
Tel : ++33 (0)6.18.27.54.93
Fax : ++33 (0)4.73.34.67.44
-
susanne.ettin...@gmail.com
__

The eye sees only what the mind is prepared to comprehend.
Robertson Davies

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[R] Permutation test for GLM with proportional data

[Kota Hattori]

Dear all,

I am trying to run permutation tests for GLM using the glmperm package. When I 
created my model,
I followed The R book and Mixed effects models and extensions in ecology with 
R. In both books, response
variables were specified by using cbind(). That is, response variable is in a 
matrix. This approach is not
a problem at all to run glm(). However, when I run  glm.perm(), it seems that 
response variable with cbind() is not good.
This is because glm.perm asks a vector of response variable, not a matrix.  
Does glm() generate a vector for 
a response variable using cbind()? If it does, is there any way to extract the 
vector? Alternatively, I would like to know if
there are other options to run permutation tests for GLM with proportion data. 
Thank you for reading this message.

Yours,
Kota

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Re: [R] assigning global columns selection for all subset functions in script

[bcrombie]

Thanks, David.  I appreciate your help.  Your solution is the idea I also had 
but wasn't quite sure if it was allowed in this case.  That's a simple fix.

Burnette

From: David Winsemius [via R] [mailto:ml-node+s789695n4669295...@n4.nabble.com]
Sent: Tuesday, June 11, 2013 5:31 PM
To: Crombie, Burnette N
Subject: Re: assigning global columns selection for all subset functions in 
script


On Jun 11, 2013, at 9:18 AM, bcrombie wrote:

 How do I let R know that I always want to select the same columns in my
 subset functions (below), so that I don't have to keep copy/pasting the same
 selection? (thanks)
 devUni2 - subset(devUni1, dind02 != 52,
 select=c(paidhre,earnhre,earnwke,uhourse,hourslw,otc,ind02,dind02,occ00,docc00,lfsr94,class94,relref95,smsastat,state,weight,year))

Perhaps:

devUni3 - subset(devUni2, lfsr94 == 1 | lfsr94 == 2 ,
select=names(devUni2) )

Or just create a character vector:

desired - names(devUni2)
devUni3 - subset(devUni2, lfsr94 == 1 | lfsr94 == 2 , select=desired )

Because I am lazy I exprimented a bit to avoid adding all those quote marks:

desired - expression(paidhre, earnhre,earnwke,uhourse,hourslw,otc,ind02, 
dind02,occ00,docc00,lfsr94,class94,relref95,smsastat,state,weight,year)

as.character(as.list(desired))
 [1] paidhre  earnhre  earnwke  uhourse  hourslw  otc  ind02
 [8] dind02   occ00docc00   lfsr94   class94  relref95 
smsastat
[15] stateweight   year

 devUni4 - subset(devUni3, class94  6 ,
 select=c(paidhre,earnhre,earnwke,uhourse,hourslw,otc,ind02,dind02,occ00,docc00,lfsr94,class94,relref95,smsastat,state,weight,year))
 devUni5 - subset(devUni4, relref95  10 | relref95 ==13 | relref95 =14,
 select=c(paidhre,earnhre,earnwke,uhourse,hourslw,otc,ind02,dind02,occ00,docc00,lfsr94,class94,relref95,smsastat,state,weight,year))


--

David Winsemius
Alameda, CA, USA

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Re: [R] odds ratio per standard deviation

[Greg Snow]

Without context this is a shot in the dark, but my guess is this is
referring to something like a logistic regression where the odds ratio
(exponential of the coefficient) refers to the change in odds for the
outcome for a 1 unit change in x.  Now often a 1 unit change in x is very
meaningful, but other times it is not that meaningful, e.g. if x is
measuring the size of diamonds in carats and the data does not span an
entire carat, or x is measured in days and our x variable spans years.  In
these cases it can make more sense to talk about the change in the odds
relative to a different step size than just a 1 unit change in x, a
reasonable thing to use is the change in odds for a one standard deviation
change in x (much smaller than 1 for the diamonds, much larger for the
days), this may be the odds ratio per standard deviation that you mention.


On Tue, Jun 11, 2013 at 7:38 PM, vinhnguyen04x imvi...@yahoo.com.vn wrote:

 Hi all

 i have a question:

 why and when do we use odds ratio per standard deviation instead of odds
 ratio?



 --
 View this message in context:
 http://r.789695.n4.nabble.com/odds-ratio-per-standard-deviation-tp4669315.html
 Sent from the R help mailing list archive at Nabble.com.

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-- 
Gregory (Greg) L. Snow Ph.D.
538...@gmail.com

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[R] Fw: Hi, can you supply tablet pc?

[lv]

Hi, Kejora here.

I didn't get your reply.

Tq,
Kejora

---

From: l...@asquote.com
To: r-h...@stat.math.ethz.ch
Date: 2013-06-07
Subject: Hi, can you supply tablet pc?

Hi. Kejora here.

I find you on google. Aere you doing distributing business?
We have a clients who need tablet pc urgently(first order about 500 pcs).
If you can provide, please send you products with price(!!!) to me.
Quadcore with 3G are prefered.

Tell me your phone or skype if you like to. I'll call you if your price is
good.

Thanks,
Kejora

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[R] Proper way to implement package internal functions

[Bryan Hanson]

[previously posted on Stack Overflow: 
http://stackoverflow.com/questions/17034309/hiding-undocumented-functions-in-a-package-use-of-function-name
 ]

I've got some functions I need to make available in a package, and I don't want 
to export them or write much documentation for them. I'd just hide them inside 
another function but they need to be available to several functions so doing it 
that way becomes a scoping and maintenance issue. What is the right way to do 
this?  By that I mean do they need special names, do they go somewhere other 
than the R subdirectory, can I put them in a single file, etc? I've checked out 
the manuals (e.g. Writing R Extensions 1.6.1), and what I'm after is like the 
.internals concept in the core, but I don't see any instructions about how to 
do this generally.

For example, if I have functions foo1 and foo2 in a file foofunc.R, and these 
are intended for internal use only, should they be called foo1 or .foo1?  And 
the file that holds them, should it be .foofunc.R or foofunc-internals?  What 
should the Rd look like, or do I even need one?

I know people do this in packages all the time and I feel like I've seen this 
somewhere, but I can't find any resources just now.  Perhaps a suggestion of a 
package that does things this way which I could study would be sufficient.

Thanks, Bryan
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Re: [R] Proper way to implement package internal functions

[Duncan Murdoch]

On 12/06/2013 10:44 AM, Bryan Hanson wrote:

[previously posted on Stack Overflow: 
http://stackoverflow.com/questions/17034309/hiding-undocumented-functions-in-a-package-use-of-function-name
 ]

I've got some functions I need to make available in a package, and I don't want 
to export them or write much documentation for them. I'd just hide them inside 
another function but they need to be available to several functions so doing it 
that way becomes a scoping and maintenance issue. What is the right way to do 
this?  By that I mean do they need special names, do they go somewhere other 
than the R subdirectory, can I put them in a single file, etc? I've checked out 
the manuals (e.g. Writing R Extensions 1.6.1), and what I'm after is like the 
.internals concept in the core, but I don't see any instructions about how to 
do this generally.

For example, if I have functions foo1 and foo2 in a file foofunc.R, and these 
are intended for internal use only, should they be called foo1 or .foo1?  And 
the file that holds them, should it be .foofunc.R or foofunc-internals?  What 
should the Rd look like, or do I even need one?

I know people do this in packages all the time and I feel like I've seen this 
somewhere, but I can't find any resources just now.  Perhaps a suggestion of a 
package that does things this way which I could study would be sufficient.


The best way to do this is simply not to export those functions in your 
NAMESPACE file.  If you want to use a naming convention
internally to remind yourself that those are private, you can do so, but 
R doesn't force one on you, and there are no really popular conventions 
in use.   R won't complain if you don't document those functions at all.


There may have been other advice in the version 1.6.1 manual, but that 
is seriously out of date, more than 10 years old.  I recommend that you 
update to 3.0.1.


Duncan Murdoch

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Re: [R] [R-SIG-Mac] problem with the installation of r commander on a mac

[John Fox]

Dear Susanne,

Installation instructions for the Rcmdr are at
http://socserv.socsci.mcmaster.ca/jfox/Misc/Rcmdr/installation-notes.html,
but you've apparently done what you normally need to do to get it to work.
Though you don't say so, I assume that you have the latest versions of R
(3.0.1) and the Rcmdr (1.9-6), and that you've not only downloaded XQuartz,
but installed it (a necessary step on Mac OS X 10.8).

Beyond that, you haven't provided much detail about the error, but I suspect
that for some reason XQuartz isn't finding your display. One way to check
whether the error is particular to the Rcmdr is to try to load the tcltk
package in R directly via library(tcltk). You might also try starting the
XQuartz app *before* you start R.

It's a bit disconcerting that others have occasionally reported a similar
problem, solved the problem, but, as far as I know, failed to post the
solution to this list, which seems to me a common courtesy. If I knew the
solution, I could add it to the Rcmdr installation notes.

I'm not a frequent user of Mac OS X, and I've never experienced problems
installing the Rcmdr on it. I imagine that other list members will be able
to offer more concrete help.

Best,
 John

---
John Fox
Senator McMaster Professor of Social Statistics
Department of Sociology
McMaster University
Hamilton, Ontario, Canada



 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
 project.org] On Behalf Of Susanne.Ettinger
 Sent: Wednesday, June 12, 2013 10:06 AM
 To: r-help@r-project.org
 Subject: Re: [R] [R-SIG-Mac] problem with the installation of r
 commander on a mac
 
 Dear all,
 
 I am trying to install R and the Rcmdr package on a MacOSX 10.8.4.
 
 It appears that I keep getting the error message Erreur : le
 chargement du package ou de l'espace de noms a échoué pour 'Rcmdr' no
 matter what my approach is. Even downloading XQuartz-2.7.4 did not
 help.
 
 I found the same problem outlined on the following website
 
 https://stat.ethz.ch/pipermail/r-help/2012-October/325305.html
 
 and was wondering whether a solution to the problem has been stated
 since then and if you could help me with instructions how to proceed ?
 
 Thank you very much for your help !
 
 Kind regards,
 Susanne
 
 __
 
 Susanne ETTINGER
 Postdoctoral researcher
 -
 Laboratoire Magmas et Volcans
 UBP - UMR6524 CNRS - M163 IRD
 5, rue Kessler
 63038 Clermont-Ferrand
 -
 Tel : ++33 (0)6.18.27.54.93
 Fax : ++33 (0)4.73.34.67.44
 -
 susanne.ettin...@gmail.com
 __
 
 The eye sees only what the mind is prepared to comprehend.
 Robertson Davies
 
 __
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 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/posting-
 guide.html
 and provide commented, minimal, self-contained, reproducible code.

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Re: [R] simulation from truncated skew normal

[Mikhail Umorin]

I am not aware of any such command so, I think, you may have to write one 
yourself: 
invert the CDF and use uniform random variable (runif) to sample

Mikhail

On Tuesday, June 11, 2013 16:18:59 cassie jones wrote:
 Hello R-users,
 
 I am trying to simulate from truncated skew normal distribution. I know
 there are ways to simulate from skewed normal distribution such as rsn(sn)
 or rsnorm(VGAM), but I could not find any command to simulate from a
 truncated skew-normal distribution. Does anyone know how to do that? Any
 help is appreciated.
 
 Thanks in advance.
 
 Cassie
 
   [[alternative HTML version deleted]]
 
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Re: [R] Proper way to implement package internal functions

[Bryan Hanson]

Thanks Duncan...

Silly me, it's section 1.6.1 not version 1.6.1!

So this warning from check is not a problem in the long run:

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘ang0to2pi’ ‘dAB’ ‘doBoxesIntersect’ ...
All user-level objects in a package should have documentation entries.

if I understand correctly.  I guess the reason I didn't find any documentation 
is the wide lattitude which is possible.

Thank you.  Bryan

On Jun 12, 2013, at 10:57 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote:

 On 12/06/2013 10:44 AM, Bryan Hanson wrote:
 [previously posted on Stack Overflow: 
 http://stackoverflow.com/questions/17034309/hiding-undocumented-functions-in-a-package-use-of-function-name
  ]
 
 I've got some functions I need to make available in a package, and I don't 
 want to export them or write much documentation for them. I'd just hide them 
 inside another function but they need to be available to several functions 
 so doing it that way becomes a scoping and maintenance issue. What is the 
 right way to do this?  By that I mean do they need special names, do they go 
 somewhere other than the R subdirectory, can I put them in a single file, 
 etc? I've checked out the manuals (e.g. Writing R Extensions 1.6.1), and 
 what I'm after is like the .internals concept in the core, but I don't see 
 any instructions about how to do this generally.
 
 For example, if I have functions foo1 and foo2 in a file foofunc.R, and 
 these are intended for internal use only, should they be called foo1 or 
 .foo1?  And the file that holds them, should it be .foofunc.R or 
 foofunc-internals?  What should the Rd look like, or do I even need one?
 
 I know people do this in packages all the time and I feel like I've seen 
 this somewhere, but I can't find any resources just now.  Perhaps a 
 suggestion of a package that does things this way which I could study would 
 be sufficient.
 
 The best way to do this is simply not to export those functions in your 
 NAMESPACE file.  If you want to use a naming convention
 internally to remind yourself that those are private, you can do so, but R 
 doesn't force one on you, and there are no really popular conventions in use. 
   R won't complain if you don't document those functions at all.
 
 There may have been other advice in the version 1.6.1 manual, but that is 
 seriously out of date, more than 10 years old.  I recommend that you update 
 to 3.0.1.
 
 Duncan Murdoch

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Re: [R] How to get a running mean result by R?

[William Dunlap]

Look at the filter() function.

Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com


 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On 
 Behalf
 Of Jie Tang
 Sent: Wednesday, June 12, 2013 12:21 AM
 To: r-help@r-project.org
 Subject: [R] How to get a running mean result by R?
 
 Hi R users:
   I have a big data and want to calculate the running mean of this data .
 How can I get this kind of result ? I have check the command mean
 it seems mean could not get the running mean?
 
 --
 TANG Jie
 
   [[alternative HTML version deleted]]
 
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Re: [R] odds ratio per standard deviation

[Ted Harding]

[Replies transposed so as to achieve bottom-posting ... ]

On 12-Jun-2013 14:53:02 Greg Snow wrote:
 
 On Tue, Jun 11, 2013 at 7:38 PM, vinhnguyen04x imvi...@yahoo.com.vn wrote:
 
 Hi all
 i have a question:

 why and when do we use odds ratio per standard deviation instead of odds
 ratio?
 --
 View this message in context:
 http://r.789695.n4.nabble.com/odds-ratio-per-standard-deviation-tp4669315.htm
 l
 Sent from the R help mailing list archive at Nabble.com.
 __
 
 Without context this is a shot in the dark, but my guess is this is
 referring to something like a logistic regression where the odds ratio
 (exponential of the coefficient) refers to the change in odds for the
 outcome for a 1 unit change in x.  Now often a 1 unit change in x is very
 meaningful, but other times it is not that meaningful, e.g. if x is
 measuring the size of diamonds in carats and the data does not span an
 entire carat, or x is measured in days and our x variable spans years.  In
 these cases it can make more sense to talk about the change in the odds
 relative to a different step size than just a 1 unit change in x, a
 reasonable thing to use is the change in odds for a one standard deviation
 change in x (much smaller than 1 for the diamonds, much larger for the
 days), this may be the odds ratio per standard deviation that you mention.
 -- 
 Gregory (Greg) L. Snow Ph.D.
 538...@gmail.com

I think there is one comment that needs to be made about this!

The odds ratio per unit change in x means exactly what it says,
and can be converted into the odds ratio per any other amount of
change in x very easily. With x originally in (say) days, and
with estimated logistic regression logodds = a + b*x, if you
change your unit of x to, say weeks, so that x' = x/7, then this
is equivalent to changing b to b' = 7*b. Now just take your sliderule;
no need for R (oops, now off-topic ... ).

Another comment: I do not favour blindly standardising a variable
relative to its standard deviation in the data. The SD may be what
it is for any number of reasons, ranging from x being randomly sampled
fron a population to x being assigned specific values in a designed
experiment.

Since, for exactly the same meanings of the variables in the regression,
the standard deviation may change from one set of data to another of
exactly the same kind, the odds per standard deviation could vary
from dataset to dataset of the same investigation, and even vary
dramatically. That looks like a situation to avoid, unless it is very
carefully discussed!

The one argument that might give some sense to odds ratio per standard
deviation could apply when x has been sampled from a population in
which the variation of x can be approximately described by a Normal
distribution. Then odds ratio per standard deviation refers to
a change from, say, the mean/median of the population to the 84th
percentile, or from the 31st percentile to the 69th percentile,
or from the 69th percentile to the 93rd percentile, etc.
But these steps cover somewhat different proportions of the populatipn:
50th to 85th = 35%; 31st to 69th = 38%; 69th to 93rd = 24%. So you are
still facing issues of what you mean, or what you want to mean.

Simpler to stick to the original odds per unit of x and then apply
it to whatever multiple of the unit you happen to be interested in
as a change (along with the reasons for that interest).

Ted.

-
E-Mail: (Ted Harding) ted.hard...@wlandres.net
Date: 12-Jun-2013  Time: 17:14:00
This message was sent by XFMail

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Re: [R] agnes() in package cluster on R 2.14.1 and R 3.0.1

[Hugo Varet]

Dear Martin,
Thank you for your answer. I got the dist.binary() function in the ade4
package. It gives several distances for binary data. I agree with you, some
individuals probably share the same profile in my data.
Regards,
Hugo

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[R] Default colors for barplot() XXXX

[Dan Abner]

Hi everyone,

I have the following call to the barplot() function which produces the
desired stacked bar chart. HOWEVER, barplot() chooses 4 different shades of
gray for the stacks. If I want to use the legend=NULL argument in
combination with a separate call to legend() to customize the legend, how
do I figure out exactly what shades of gray barplot() has choosen? Can
these color names be extracted from the barplot after saving it as an
object?

barplot(table(credit_rating_num,clu_),
 xlab=Cluster Label,
 ylab=Frequency,
 ylim=c(0,7000),
 legend=c(C2,C3,C4,C5))

Thank you,

Dan

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[R] Functions within functions - environments

[Rik Verdonck]

Dear list,


I have a problem with nested functions and I don't manage to get it
solved. I know I should be looking in environments, and I have tried a
lot, but it keeps on erroring. 
An easy version of the problem is as follows:



innerfunction-function()
{
print(paste(a,  from inner function))
print(paste(b,  from inner function))
setwd(wd)
}


middlefunction-function()
{
b=b
print(paste(b,  from middle function))
innerfunction()
}


outerfunction-function()
{
a=a
print(paste(a, from outer function))
middlefunction()
}

outerfunction()



Here, R will tell me that the inner function has no clue what a or b is.
So what I want, is the inner function to recognize a and b.
Any suggestions?

Many thanks!
Rik




-- 


Rik Verdonck



Research group of Molecular Developmental Physiology and Signal
Transduction
KULeuven, Faculty of Science
Naamsestraat 59,  Bus 02465
B-3000 Leuven,Belgium
Tel. +32 16 32 39 65
Fax +32 16 32 39 02

http://bio.kuleuven.be/df/JV/index2.htm
rik.verdo...@bio.kuleuven.be





  Please consider the environment before printing this e-mail

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[R] How to cast a numeric argument to a two-dimensional array in an inline C function?

[Mikhail Umorin]

Hello --

For convenience, I would like to use a two dimensional array 
inside an inline C function. However, any numeric array in R 
is passed to C code as double *. So, how can I cast a (double 
*) to a double[][]?

thank you for your time, 

Mikhail

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Re: [R] Functions within functions - environments

[Rui Barradas]

Hello,

See the help page for parent.frame, and use its argument to go back to 
the frames of variables 'a' and 'b':



innerfunction-function()
{
env1 - parent.frame(1)  # for 'b'
env2 - parent.frame(2)  # for 'a'
print(paste(env2$a,  from inner function))
print(paste(env1$b,  from inner function))
setwd(wd)
}


Now it complains about 'wd'.
(Are you sure you want to hard code the number of frames to go back to? 
It seems better to write normal functions, i.e., functions with 
arguments. innerfunction would have 2 args and middlefunction just one, 
'a'.)


Hope this helps,

Rui Barradas

Em 12-06-2013 18:42, Rik Verdonck escreveu:

Dear list,


I have a problem with nested functions and I don't manage to get it
solved. I know I should be looking in environments, and I have tried a
lot, but it keeps on erroring.
An easy version of the problem is as follows:



innerfunction-function()
{
 print(paste(a,  from inner function))
 print(paste(b,  from inner function))
 setwd(wd)
}


middlefunction-function()
{
 b=b
 print(paste(b,  from middle function))
 innerfunction()
}


outerfunction-function()
{
 a=a
 print(paste(a, from outer function))
 middlefunction()
}

outerfunction()



Here, R will tell me that the inner function has no clue what a or b is.
So what I want, is the inner function to recognize a and b.
Any suggestions?

Many thanks!
Rik






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

Re: [R] Default colors for barplot() XXXX

[Marc Schwartz]

On Jun 12, 2013, at 12:37 PM, Dan Abner dan.abne...@gmail.com wrote:

 Hi everyone,
 
 I have the following call to the barplot() function which produces the
 desired stacked bar chart. HOWEVER, barplot() chooses 4 different shades of
 gray for the stacks. If I want to use the legend=NULL argument in
 combination with a separate call to legend() to customize the legend, how
 do I figure out exactly what shades of gray barplot() has choosen? Can
 these color names be extracted from the barplot after saving it as an
 object?
 
 barplot(table(credit_rating_num,clu_),
 xlab=Cluster Label,
 ylab=Frequency,
 ylim=c(0,7000),
 legend=c(C2,C3,C4,C5))
 
 Thank you,
 
 Dan



The help file defines the 'col' argument as:


col a vector of colors for the bars or bar components. By default, grey is 
used if height is a vector, and a gamma-corrected grey palette if height is a 
matrix.


However, that is lacking a bit of detail in the latter case, albeit one of the 
examples on the page uses the gray.colors() function. 

The easiest way to get that detail (in this case or for any function more 
generally) is to look at the source code for the function, within which you 
would see:

...
else if (is.matrix(height)) {
if (is.null(col)) 
col - gray.colors(nrow(height))
...


A better approach would be to simply take proactive control of the colors when 
you call barplot() and define the 'col' argument to colors of your choosing, 
which you can then use in the call to legend().

Regards,

Marc Schwartz

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Re: [R] Functions within functions - environments

[William Dunlap]

A function looks up free variables in the environment in which the function
was defined, not in the environment in which the function was called.  The
latter is called something like 'dynamic scoping' and usually leads to trouble,
the former is 'lexical scoping' and leads to predictable results.  You can do
dynamic scoping in R (using get(), assign(), and parent.frame()), but it
leads to code that only works correctly in favorable circumstances.  You should 
pass
data from the caller to the callee via the argument list, not via free 
variables.

To use lexical scoping define your functions as:

outerfunction-function()
{
 middlefunction-function()
 {
  innerfunction-function()
  {
  print(paste(a,  from inner function))
  print(paste(b,  from inner function))
  # setwd(wd) # wd was not defined in your mail
}
b=b
print(paste(b,  from middle function))
innerfunction()
 }
 a=a
 print(paste(a, from outer function))
 middlefunction()
}

 outerfunction()
[1] a  from outer function
[1] b  from middle function
[1] a  from inner function
[1] b  from inner function

(One can change the environment of a function after it is defined, but
there is not often a need to do that.)

Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com


 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On 
 Behalf
 Of Rik Verdonck
 Sent: Wednesday, June 12, 2013 10:42 AM
 To: r-help@r-project.org
 Subject: [R] Functions within functions - environments
 
 Dear list,
 
 
 I have a problem with nested functions and I don't manage to get it
 solved. I know I should be looking in environments, and I have tried a
 lot, but it keeps on erroring.
 An easy version of the problem is as follows:
 
 
 
 innerfunction-function()
 {
 print(paste(a,  from inner function))
 print(paste(b,  from inner function))
 setwd(wd)
 }
 
 
 middlefunction-function()
 {
 b=b
 print(paste(b,  from middle function))
 innerfunction()
 }
 
 
 outerfunction-function()
 {
 a=a
 print(paste(a, from outer function))
 middlefunction()
 }
 
 outerfunction()
 
 
 
 Here, R will tell me that the inner function has no clue what a or b is.
 So what I want, is the inner function to recognize a and b.
 Any suggestions?
 
 Many thanks!
 Rik
 
 
 
 
 --
 
 
 Rik Verdonck
 
 
 
 Research group of Molecular Developmental Physiology and Signal
 Transduction
 KULeuven, Faculty of Science
 Naamsestraat 59,  Bus 02465
 B-3000 Leuven,Belgium
 Tel. +32 16 32 39 65
 Fax +32 16 32 39 02
 
 http://bio.kuleuven.be/df/JV/index2.htm
 rik.verdo...@bio.kuleuven.be
 
 
 
 
 
   Please consider the environment before printing this e-mail
 
   [[alternative HTML version deleted]]
 
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and provide commented, minimal, self-contained, reproducible code.

[R] grDevices::convertColor XYZ space is it really xyY?

[Bryan Hanson]

grDevices::convertColor has arguments 'from' and 'to' which can take on value 
'XYZ'.  Can someone confirm that 'XYZ' is the same as the CIE chromaticity 
coordinates that are also sometimes refered to as 'xyY' in the literature?  Or 
are these the CIE tristimulus values?  It looks to me like the first case is 
true, but I would appreciate hearing from one of the people in the know.  
Thanks, Bryan

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

Re: [R] grDevices::convertColor XYZ space is it really xyY?

[Duncan Murdoch]

On 12/06/2013 2:45 PM, Bryan Hanson wrote:

grDevices::convertColor has arguments 'from' and 'to' which can take on value 
'XYZ'.  Can someone confirm that 'XYZ' is the same as the CIE chromaticity 
coordinates that are also sometimes refered to as 'xyY' in the literature?  Or 
are these the CIE tristimulus values?  It looks to me like the first case is 
true, but I would appreciate hearing from one of the people in the know.  
Thanks, Bryan


According to the referenced web page from ?convertColor (i.e. 
http://www.brucelindbloom.com/), XYZ is not xyY, though the conversion 
looks pretty simple.


Duncan Murdoch

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

Re: [R] grDevices::convertColor XYZ space is it really xyY?

[Ken Knonlauch]

Bryan Hanson hanson at depauw.edu writes:

 
 grDevices::convertColor has arguments 'from' and 'to' which can 
take on value 'XYZ'.  Can 
someone confirm
 that 'XYZ' is the same as the CIE chromaticity coordinates 
 are also sometimes refered to 
as 'xyY' in
 the literature?  Or are these the CIE tristimulus values?  
It looks to me like the first case is 
true, but I
 would appreciate hearing from one of the people in 
 know.  Thanks, Bryan
 
 

I.'d look at the code or put in some known data to test it, 
but XYZ are tristimulus values and xyY are chromaticity
coordinated and the luminance which is the Y tristimulus
value for the CIE 1931 standard observer.

Ken

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

[R] Fetching and Saving warnings from a function

[Christofer Bogaso]

Hello again,

Let say I have following user defined function:

Myfn - function(x) {
if (x  0) {
warning(Negative value)
}
return(x)
}

Now I want to create some function which will save the Warnings from
'Myfn', so that I can use those warnings later for more analysis. Therefore
I was thinking of following type of function:

ProposedWarningStoreFunction - function() {
  ....
}

therefore,if I run 'ProposedWarningStoreFunction', I should get following
kind of results:

Warnings - ProposedWarningStoreFunction({Result - Myfn(-4)})

 Result
 -4

 Warnings
In Myfn(-3) : Negative value

Can somebody here point me how to achieve this? Or is it possible to
achieve at all?

Thank you for your help.

[[alternative HTML version deleted]]

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

[R] How to fit the cumulative probability distributive functiion with the gamma distribution?

[Kaptue Tchuente, Armel]

Hello everyone,



I'm trying to fit the PDF of time series datasets with the gamma distribution.

Nonetheless, this isn't possible for several datasets since the gamma 
distribution can only been used to fit continuous distribution. For instance, 
gam-fitdrib(hist-c(24,7,4,1,2,1,0,0,0,1,0,0),gamma) will yield an error 
message.

To solve this issue, I decided to fit the cumulative distributive function i.e. 
gam-fitdistr(hist_cum-c(24,31,35,36,38,39,39,39,40,40,40)).

Now I don't know how to obtain the corresponding CDF of the gamma distribution 
which will fit the empirical CDF.

I have already tried some instructions like pgamma(seq(4,4*12,4), 
scale=1/gam$estimate[2],shape=gam$estimate[1]) without success as you can see 
on this picture 
https://docs.google.com/file/d/0BwjZP-sfazLMaDM2bHBDYnFOSWs/edit?usp=sharing 
where the curve in blue was supposed to be the fitted gamma CDF.

I said was supposed because I was obliged to use the instruction par(new=T) 
in order to super-impose the fitted gamma CDF



Cheers



Armel


[[alternative HTML version deleted]]

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

Re: [R] Fetching and Saving warnings from a function

[William Dunlap]

?withCallingHandlers

E.g.,
R f - function(expr) {
  warnings - character()
  withCallingHandlers(expr, warning=function(e){
 warnings - c(warnings, conditionMessage(e))
 invokeRestart(muffleWarning)
  })
  warnings
}
R f(1:10)
character(0)
R f(warning(Hmm))
[1] Hmm
R f({warning(Hmm); x - 666 ; warning(Possible problem)})
[1] Hmm  Possible problem
R x
[1] 666

Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com


 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On 
 Behalf
 Of Christofer Bogaso
 Sent: Wednesday, June 12, 2013 12:07 PM
 To: r-help
 Subject: [R] Fetching and Saving warnings from a function
 
 Hello again,
 
 Let say I have following user defined function:
 
 Myfn - function(x) {
 if (x  0) {
 warning(Negative value)
 }
 return(x)
 }
 
 Now I want to create some function which will save the Warnings from
 'Myfn', so that I can use those warnings later for more analysis. Therefore
 I was thinking of following type of function:
 
 ProposedWarningStoreFunction - function() {
   ....
 }
 
 therefore,if I run 'ProposedWarningStoreFunction', I should get following
 kind of results:
 
 Warnings - ProposedWarningStoreFunction({Result - Myfn(-4)})
 
  Result
  -4
 
  Warnings
 In Myfn(-3) : Negative value
 
 Can somebody here point me how to achieve this? Or is it possible to
 achieve at all?
 
 Thank you for your help.
 
   [[alternative HTML version deleted]]
 
 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.

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

Re: [R] survreg with measurement uncertainties

[Kyle Penner]

Hi Terry,

Thanks for your quick reply.  I am talking about uncertainty in the
response.  I have 2 follow up questions:

1) my understanding from the documentation is that 'id' in cluster(id)
should be the same when the predictors are not independent.  Is this
correct?  (To be more concrete: my data are brightnesses at different
wavelengths.  Each brightness is an independent measurement, so the
elements of id should all be different?)

2) I tested survreg with uncertainties on an example where I already
know the answer (and where I am not using limits), and it does not
converge.  Below is the code I used, does anything jump out as
incorrect?

data = c(144.53, 1687.68, 5397.91)
err = c(8.32, 471.22, 796.67)
model = c(71.60, 859.23, 1699.19)
id = c(1, 2, 3)

This works (2.9 is the answer from simple chi_sq fitting):

survreg(Surv(time = data, event = c(1,1,1))~model-1, dist='gaussian',
init=c(2.9))

This does not converge (2.1 is the answer from chi_sq fitting):

survreg(Surv(time = data, event = c(1,1,1))~model-1+cluster(id),
weights=1/(err^2), dist='gaussian', init=c(2.1))

And this does, but the answer it returns is wonky:

data[2] = 3*err[2] # data[2] is very close to 3*err[2] already
survreg(Surv(time = data, event = c(1,2,1))~model-1+cluster(id),
weights=1/(err^2), dist='gaussian', init=c(2.1))

Thanks,

Kyle

On Wed, Jun 12, 2013 at 6:51 AM, Terry Therneau thern...@mayo.edu wrote:
 I will assume that you are talking about uncertainty in the response.  Then
 one simple way to fit the model is to use case weights that are proprional
 to 1/variance, along with +cluster(id) in the model statement to get a
 correct variance for this case.  In linear models this would be called the
 White or Horvitz-Thompsen or GEE working independence variance
 estimate, depending on which literature you happen to be reading (economics,
 survey sampling, or biostat).

 Now if you are talking about errors in the predictor variables, that is a
 much harder problem.

 Terry Therneau



 On 06/12/2013 05:00 AM, Kyle Penner wrote:

 Hello,

 I have some measurements that I am trying to fit a model to.  I also
 have uncertainties for these measurements.  Some of the measurements
 are not well detected, so I'd like to use a limit instead of the
 actual measurement.  (I am always dealing with upper limits, i.e. left
 censored data.)

 I have successfully run survreg using the combination of well detected
 measurements and limits, but I would like to include the measurement
 uncertainty (for the well detected measurements) in the fitting.  As
 far as I can tell, survreg doesn't support this.  Does anyone have a
 suggestion for how to accomplish this?

 Thanks,

 Kyle

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Re: [R] Creating a new var from conditional values in other vars

[arun]

Hi,
Try this:
set.seed(25)
dat1- 
data.frame(A=sample(1:30,100,replace=TRUE),B=sample(1:35,100,replace=TRUE),C=sample(1:25,100,replace=TRUE))


dat1$pattern-with(dat1,ifelse(A20  B=2.5  C=20,Normal,ifelse(A 20  B 
2.5  C 20,Increased,ifelse(A =20  B 2.5  C =20,Low,Other
head(dat1)
#   A  B  C pattern
#1 13 20  5   Other
#2 21 15  4 Low
#3  5 24  1   Other
#4 27 13  6 Low
#5  4  4 10   Other
#6 30 19 22   Other
A.K.




I am newbie to R coming from SAS (basic user). Quite a difficult move 
I have a dataframe named kappa exported from csv file 
kappa-read.csv(kappacsv, header=TRUE, sep=;, dec=.) 
kappa contains 3 numeric vars (A,B and C) 
I want to create a new var called pattern depending on the values of the 
conditions in A, B and C 
I have tried many ways one has been this: 
kappa$pattern1-99 # create a new numeric var in kappa dataframe 

if (A=20  B=2.5  C =20){kappa$pattern-Normal} 
else if (A 20  B 2.5  C 20){kappa$pattern-Increased} 
else if (A =20  B 2.5  C =20){kappa$pattern-Low} 
else {kappa$pattern-“Other”} 
  
The code does not work and I get errors all the time. 
Any help will be greatly appreciated 
Thanks

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Re: [R] grDevices::convertColor XYZ space is it really xyY?

[Bryan Hanson]

Ken, I followed your suggestion and perhaps I don't understand what to expect 
from convertColor or maybe I'm not using it correctly.  Consider the following 
tests:

D65 - c(0.3127, 0.329, 0.3583) # D65 chromaticity coordinates
X - D65[1]*D65[3]/D65[2] # conversion per brucelindbloom.com
Y - D65[3]
Z - D65[3]*D65[3]/D65[2]
XYZ - data.frame(X = X, Y = Y, Z = Z) # D65 in tristimulus values (?)
colnames(XYZ) - c(X, Y, Z)

tst1 - convertColor(XYZ, from = XYZ, to = sRGB)
tst2 - convertColor(D65, from = XYZ, to = sRGB)
# none of these are 1,1,1, namely white (they are ~ 0.6, 0.6, 0.6)

So it looks like D65, a white standard, does not come back to something near 
white in the sRGB space.  What am I doing wrong here, or what do I 
misunderstand?  Please don't say everything!

Thanks, Bryan

On Jun 12, 2013, at 2:57 PM, Ken Knonlauch ken.knobla...@inserm.fr wrote:

 Bryan Hanson hanson at depauw.edu writes:
 
 
 grDevices::convertColor has arguments 'from' and 'to' which can 
 take on value 'XYZ'.  Can 
 someone confirm
 that 'XYZ' is the same as the CIE chromaticity coordinates 
 are also sometimes refered to 
 as 'xyY' in
 the literature?  Or are these the CIE tristimulus values?  
 It looks to me like the first case is 
 true, but I
 would appreciate hearing from one of the people in 
 know.  Thanks, Bryan
 
 
 
 I.'d look at the code or put in some known data to test it, 
 but XYZ are tristimulus values and xyY are chromaticity
 coordinated and the luminance which is the Y tristimulus
 value for the CIE 1931 standard observer.
 
 Ken
 
 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.

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

Re: [R] grDevices::convertColor XYZ space is it really xyY?

[Ken Knoblauch]

You seem to treating the input values as xyY when they should be XYZ
(case matters).
So, I would do something like this

D65 - c(0.3127, 0.329, 0.3583)

X - 100 * D65[1]
Y - 100 * D65[2]
Z - 100 * D65[3]
XYZ - data.frame(X = X, Y = Y, Z = Z)

convertColor(XYZ, from = XYZ, to = sRGB)
 [,1] [,2] [,3]
[1,]111


Quoting Bryan Hanson han...@depauw.edu:

Ken, I followed your suggestion and perhaps I don't understand what   
to expect from convertColor or maybe I'm not using it correctly.
Consider the following tests:


D65 - c(0.3127, 0.329, 0.3583) # D65 chromaticity coordinates
X - D65[1]*D65[3]/D65[2] # conversion per brucelindbloom.com
Y - D65[3]
Z - D65[3]*D65[3]/D65[2]
XYZ - data.frame(X = X, Y = Y, Z = Z) # D65 in tristimulus values (?)
colnames(XYZ) - c(X, Y, Z)

tst1 - convertColor(XYZ, from = XYZ, to = sRGB)
tst2 - convertColor(D65, from = XYZ, to = sRGB)
# none of these are 1,1,1, namely white (they are ~ 0.6, 0.6, 0.6)

So it looks like D65, a white standard, does not come back to   
something near white in the sRGB space.  What am I doing wrong here,  
 or what do I misunderstand?  Please don't say everything!


Thanks, Bryan

On Jun 12, 2013, at 2:57 PM, Ken Knonlauch ken.knobla...@inserm.fr wrote:


Bryan Hanson hanson at depauw.edu writes:



grDevices::convertColor has arguments 'from' and 'to' which can

take on value 'XYZ'.  Can
someone confirm

that 'XYZ' is the same as the CIE chromaticity coordinates

are also sometimes refered to
as 'xyY' in

the literature?  Or are these the CIE tristimulus values?

It looks to me like the first case is
true, but I

would appreciate hearing from one of the people in

know.  Thanks, Bryan





I.'d look at the code or put in some known data to test it,
but XYZ are tristimulus values and xyY are chromaticity
coordinated and the luminance which is the Y tristimulus
value for the CIE 1931 standard observer.

Ken

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







--
Kenneth Knoblauch
Inserm U846
Stem-cell and Brain Research Institute
Department of Integrative Neurosciences
18 avenue du Doyen Lépine
69500 Bron
France
tel: +33 (0)4 72 91 34 77
fax: +33 (0)4 72 91 34 61
portable: +33 (0)6 84 10 64 10
http://www.sbri.fr/members/kenneth-knoblauch.html

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

Re: [R] grDevices::convertColor XYZ space is it really xyY?

[Bryan Hanson]

Thank you Ken.

90% of my problem was missing the factor of 100.  I was just inputing xyY as a 
test, I wasn't sure whether the docs were being clear about nomenclature.  
Speaking thereof, the D65 values used in the example: I thought they were 
chromaticity coordinates, but apparently they are tristimulus values - is that 
correct?

Thanks again.  This solves several problems in a package I am developing.  Bryan

On Jun 12, 2013, at 4:36 PM, Ken Knoblauch ken.knobla...@inserm.fr wrote:

 You seem to treating the input values as xyY when they should be XYZ
 (case matters).
 So, I would do something like this
 
 D65 - c(0.3127, 0.329, 0.3583)
 
 X - 100 * D65[1]
 Y - 100 * D65[2]
 Z - 100 * D65[3]
 XYZ - data.frame(X = X, Y = Y, Z = Z)
 
 convertColor(XYZ, from = XYZ, to = sRGB)
 [,1] [,2] [,3]
 [1,]111
 
 
 Quoting Bryan Hanson han...@depauw.edu:
 
 Ken, I followed your suggestion and perhaps I don't understand what  to 
 expect from convertColor or maybe I'm not using it correctly.   Consider the 
 following tests:
 
 D65 - c(0.3127, 0.329, 0.3583) # D65 chromaticity coordinates
 X - D65[1]*D65[3]/D65[2] # conversion per brucelindbloom.com
 Y - D65[3]
 Z - D65[3]*D65[3]/D65[2]
 XYZ - data.frame(X = X, Y = Y, Z = Z) # D65 in tristimulus values (?)
 colnames(XYZ) - c(X, Y, Z)
 
 tst1 - convertColor(XYZ, from = XYZ, to = sRGB)
 tst2 - convertColor(D65, from = XYZ, to = sRGB)
 # none of these are 1,1,1, namely white (they are ~ 0.6, 0.6, 0.6)
 
 So it looks like D65, a white standard, does not come back to  something 
 near white in the sRGB space.  What am I doing wrong here,  or what do I 
 misunderstand?  Please don't say everything!
 
 Thanks, Bryan
 
 On Jun 12, 2013, at 2:57 PM, Ken Knonlauch ken.knobla...@inserm.fr wrote:
 
 Bryan Hanson hanson at depauw.edu writes:
 
 
 grDevices::convertColor has arguments 'from' and 'to' which can
 take on value 'XYZ'.  Can
 someone confirm
 that 'XYZ' is the same as the CIE chromaticity coordinates
 are also sometimes refered to
 as 'xyY' in
 the literature?  Or are these the CIE tristimulus values?
 It looks to me like the first case is
 true, but I
 would appreciate hearing from one of the people in
 know.  Thanks, Bryan
 
 
 
 I.'d look at the code or put in some known data to test it,
 but XYZ are tristimulus values and xyY are chromaticity
 coordinated and the luminance which is the Y tristimulus
 value for the CIE 1931 standard observer.
 
 Ken
 
 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.
 
 
 
 
 
 -- 
 Kenneth Knoblauch
 Inserm U846
 Stem-cell and Brain Research Institute
 Department of Integrative Neurosciences
 18 avenue du Doyen Lépine
 69500 Bron
 France
 tel: +33 (0)4 72 91 34 77
 fax: +33 (0)4 72 91 34 61
 portable: +33 (0)6 84 10 64 10
 http://www.sbri.fr/members/kenneth-knoblauch.html
 
 
 This message was sent using IMP, the Internet Messaging Program.
 
 

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

Re: [R] grDevices::convertColor XYZ space is it really xyY?

[Ken Knoblauch]

If they sum to 1 then they are one and the same.  Look at how
chromaticity coordinates are defined in terms of the tristimulus
values.

Quoting Bryan Hanson han...@depauw.edu:


Thank you Ken.

90% of my problem was missing the factor of 100.  I was just   
inputing xyY as a test, I wasn't sure whether the docs were being   
clear about nomenclature.  Speaking thereof, the D65 values used in   
the example: I thought they were chromaticity coordinates, but   
apparently they are tristimulus values - is that correct?


Thanks again.  This solves several problems in a package I am   
developing.  Bryan


On Jun 12, 2013, at 4:36 PM, Ken Knoblauch ken.knobla...@inserm.fr wrote:


You seem to treating the input values as xyY when they should be XYZ
(case matters).
So, I would do something like this

D65 - c(0.3127, 0.329, 0.3583)

X - 100 * D65[1]
Y - 100 * D65[2]
Z - 100 * D65[3]
XYZ - data.frame(X = X, Y = Y, Z = Z)

convertColor(XYZ, from = XYZ, to = sRGB)
[,1] [,2] [,3]
[1,]111


Quoting Bryan Hanson han...@depauw.edu:

Ken, I followed your suggestion and perhaps I don't understand   
what  to expect from convertColor or maybe I'm not using it   
correctly.   Consider the following tests:


D65 - c(0.3127, 0.329, 0.3583) # D65 chromaticity coordinates
X - D65[1]*D65[3]/D65[2] # conversion per brucelindbloom.com
Y - D65[3]
Z - D65[3]*D65[3]/D65[2]
XYZ - data.frame(X = X, Y = Y, Z = Z) # D65 in tristimulus values (?)
colnames(XYZ) - c(X, Y, Z)

tst1 - convertColor(XYZ, from = XYZ, to = sRGB)
tst2 - convertColor(D65, from = XYZ, to = sRGB)
# none of these are 1,1,1, namely white (they are ~ 0.6, 0.6, 0.6)

So it looks like D65, a white standard, does not come back to
something near white in the sRGB space.  What am I doing wrong   
here,  or what do I misunderstand?  Please don't say everything!


Thanks, Bryan

On Jun 12, 2013, at 2:57 PM, Ken Knonlauch ken.knobla...@inserm.fr wrote:


Bryan Hanson hanson at depauw.edu writes:



grDevices::convertColor has arguments 'from' and 'to' which can

take on value 'XYZ'.  Can
someone confirm

that 'XYZ' is the same as the CIE chromaticity coordinates

are also sometimes refered to
as 'xyY' in

the literature?  Or are these the CIE tristimulus values?

It looks to me like the first case is
true, but I

would appreciate hearing from one of the people in

know.  Thanks, Bryan





I.'d look at the code or put in some known data to test it,
but XYZ are tristimulus values and xyY are chromaticity
coordinated and the luminance which is the Y tristimulus
value for the CIE 1931 standard observer.

Ken

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PLEASE do read the posting guide   
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--
Kenneth Knoblauch
Inserm U846
Stem-cell and Brain Research Institute
Department of Integrative Neurosciences
18 avenue du Doyen Lépine
69500 Bron
France
tel: +33 (0)4 72 91 34 77
fax: +33 (0)4 72 91 34 61
portable: +33 (0)6 84 10 64 10
http://www.sbri.fr/members/kenneth-knoblauch.html


This message was sent using IMP, the Internet Messaging Program.









--
Kenneth Knoblauch
Inserm U846
Stem-cell and Brain Research Institute
Department of Integrative Neurosciences
18 avenue du Doyen Lépine
69500 Bron
France
tel: +33 (0)4 72 91 34 77
fax: +33 (0)4 72 91 34 61
portable: +33 (0)6 84 10 64 10
http://www.sbri.fr/members/kenneth-knoblauch.html

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

Re: [R] [R-SIG-Mac] problem with the installation of r commander on a mac

[John Fox]

Dear Susanne,

You started this thread on r-help (though R-SIG-Mac would have been more
appropriate), and so I'm copying my response to the r-help list. People will
find it confusing if the messages are simply kept private.

It's not obvious to me exactly what your problem is now. In particular, is
the Rcmdr package working when you start XQuartz before R? 

I see that you've installed and loaded the FactoMineR package. Presumably
the Rcmdr package was already installed. Then you executed an R script
provided by the authors of the FactoMineR package, which reinstalls and then
modifies the Rcmdr package. I think that this is ill-advised (as opposed to
providing an Rcmdr plug-in package for FactoMineR, as used to be the case),
and if you're having problems with their script, you should really contact
the authors. 

If I read the messages correctly, the script produces warnings, not errors,
oddly relating to the language you're using (odd because the authors of the
FactoMineR package are French) and it's possible that everything will work
correctly despite the warnings.

I hope this helps,
 John

 -Original Message-
 From: Susanne.Ettinger [mailto:susanne.ettin...@gmail.com]
 Sent: Wednesday, June 12, 2013 11:44 AM
 To: John Fox
 Subject: Re: [R] [R-SIG-Mac] problem with the installation of r
 commander on a mac
 
 Dear John,
 
 thank you very much for your quick reply - I realize I sent this email
 to the list without being a member, but I am a very beginner and
 started this morning the installation process of R.
 
 I have been printing out any possibly available information on how to
 get started with R and I am following the exercices exposed in the book
 written by Cornillon et al. (2012) to use FactoMineR to do some PCA
 analysis on vulnerability data.
 
 I downloaded the 3.0.1 version of R and have the 1.9-6 package of
 Rcmdr. I also checked into the library(tcltk) but do not get an error
 message, this seems to work fine.
 
 Since I open XQuartz before starting the Rcmdr library, I am getting a
 different error message than the ones of this morning. This is what it
 looks like :
 
 
install.packages()
   --- SVP sélectionner un miroir CRAN pour cette session ---
   essai de l'URL 'http://cran.univ-
 lyon1.fr/bin/macosx/contrib/3.0/FactoMineR_1.25.tgz'
   Content type 'application/x-gzip' length 3397827 bytes (3.2 Mb)
   URL ouverte
   ==
   downloaded 3.2 Mb
 
 
 
 
   Les packages binaires téléchargés sont dans
   /var/folders/06/z7b6z3y102xgxls2xh251p5wgp/T//Rtmp13nIpm/downl
 oaded_packages
library(FactoMineR)
   Le chargement a nécessité le package : car
   Le chargement a nécessité le package : MASS
   Le chargement a nécessité le package : nnet
   Le chargement a nécessité le package : ellipse
 
 
   Attachement du package : ‘ellipse’
 
 
   L'objet suivant est masqué from ‘package:car’:
 
 
   ellipse
 
 
   Le chargement a nécessité le package : lattice
   Le chargement a nécessité le package : cluster
   Le chargement a nécessité le package : scatterplot3d
   Le chargement a nécessité le package : leaps
source(http://factominer.free.fr/install-facto-fr.r;)
   essai de l'URL 'http://cran.univ-
 lyon1.fr/bin/macosx/contrib/3.0/Rcmdr_1.9-6.tgz'
   Content type 'application/x-gzip' length 3759850 bytes (3.6 Mb)
   URL ouverte
   ==
   downloaded 3.6 Mb
 
 
 
 
   The downloaded binary packages are in
   /var/folders/06/z7b6z3y102xgxls2xh251p5wgp/T//Rtmp13nIpm/downl
 oaded_packages
   essai de l'URL 'http://cran.univ-
 lyon1.fr/bin/macosx/contrib/3.0/FactoMineR_1.25.tgz'
   Content type 'application/x-gzip' length 3397827 bytes (3.2 Mb)
   URL ouverte
   ==
   downloaded 3.2 Mb
 
 
 
 
   The downloaded binary packages are in
   /var/folders/06/z7b6z3y102xgxls2xh251p5wgp/T//Rtmp13nIpm/downl
 oaded_packages
   Avis dans grepl(\n, lines, fixed = TRUE) :
 la chaîne de caractères entrée 1 est incorrecte dans cet
 environnement linguistique
   Avis dans grepl(\n, lines, fixed = TRUE) :
 la chaîne de caractères entrée 5 est incorrecte dans cet
 environnement linguistique
   Avis dans grepl(\n, lines, fixed = TRUE) :
 la chaîne de caractères entrée 31 est incorrecte dans cet
 environnement linguistique
   Avis dans grepl(\n, lines, fixed = TRUE) :
 la chaîne de caractères entrée 35 est incorrecte dans cet
 environnement linguistique
   Avis dans grepl(\n, lines, fixed = TRUE) :
 la chaîne de caractères entrée 81 est incorrecte dans cet
 environnement linguistique
   Avis dans grepl(\n, lines, fixed = TRUE) :
 la chaîne de caractères entrée 84 est incorrecte dans cet
 environnement linguistique
   Avis dans 

[R] how to maximize the log-likelihood function with EM algorithm

[Anhai Jin]

Hi R users,

I am trying to fit a Mixed Markov Model and ran into trouble with maximizing 
the log-likelihood function. I attached my R codes and the problem I have right 
now is that the maximization may end in some local maximum by specifying 
different start values. I am thinking if we can improve the maximization with 
EM algorithm. Any help will be greatly appreciated!

purch_1 = c(0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1)
purch_2 = c(0,0,1,1,0,0,1,1,0,0,1,1,0,0,1,1,0,0,1,1,0,0,1,1,0,0,1,1,0,0,1,1)
purch_3 = c(0,0,0,0,1,1,1,1,0,0,0,0,1,1,1,1,0,0,0,0,1,1,1,1,0,0,0,0,1,1,1,1)
purch_4 = c(0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1)
purch_5 = c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1)
freq = 
c(352,44,26,14,20,5,7,12,14,5,5,5,5,3,3,7,21,3,4,3,5,2,3,5,9,2,0,6,5,5,7,24)

switch_1 = c(0,1,1,0,0,1,1,0,0,1,1,0,0,1,1,0,0,1,1,0,0,1,1,0,0,1,1,0,0,1,1,0)
switch_2 = c(0,0,1,1,1,1,0,0,0,0,1,1,1,1,0,0,0,0,1,1,1,1,0,0,0,0,1,1,1,1,0,0)
switch_3 = c(0,0,0,0,1,1,1,1,1,1,1,1,0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,0,0,0,0)
switch_4 = c(0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,0,0,0,0,0,0,0)

full = 
cbind(purch_1,purch_2,purch_3,purch_4,purch_5,freq,switch_1,switch_2,switch_3,switch_4)

markovdata = data.frame(full)

library(maxLik)
set.seed(123)

loglikelihood = function(param) {

pi_1   = 
param[1]
p0_1  = 
param[2]
p00_1   = 
param[3]
p11_1   = 
param[4]
p0_2  = 
param[5]
p00_2 = param[6]
p11_2 = param[7]

y = 
markovdata$freq*

log(

pi_1*

(p0_1^(1-markovdata$purch_1)) 
*((1-p0_1)^markovdata$purch_1)

*


((p00_1^(1-markovdata$switch_1))*((1-p00_1)^markovdata$switch_1))   
 ^ (1-markovdata$purch_1)

*


((p11_1^(1-markovdata$switch_1))*((1-p11_1)^markovdata$switch_1))   
 ^ markovdata$purch_1

*


((p00_1^(1-markovdata$switch_2))*((1-p00_1)^markovdata$switch_2))   
 ^ (1-markovdata$purch_2)

*


((p11_1^(1-markovdata$switch_2))*((1-p11_1)^markovdata$switch_2))   
 ^ markovdata$purch_2

*


((p00_1^(1-markovdata$switch_3))*((1-p00_1)^markovdata$switch_3))   
 ^ (1-markovdata$purch_3)

*


((p11_1^(1-markovdata$switch_3))*((1-p11_1)^markovdata$switch_3))   
 ^ markovdata$purch_3

*


((p00_1^(1-markovdata$switch_4))*((1-p00_1)^markovdata$switch_4))   
 ^ (1-markovdata$purch_4)

*


((p11_1^(1-markovdata$switch_4))*((1-p11_1)^markovdata$switch_4))   
 ^ markovdata$purch_4

+

(1-pi_1)*
 

[R] Cannot install RPostgreSQL

[Drew]

Hello everyone,

I am extremely new to R. I have yet to write any complicated code myself,
however I have been learning largely by reading code that has already been
written. Long story short, I have been running a code that makes use of the
RPostgreSQL package for some time now. For some reason I just recently
started to get an error. Whenever I try to load the RPostgreSQL package I
get:

 library(RPostgreSQL)
Error in library(RPostgreSQL) : there is no package called ‘RPostgreSQL’

I also tried install.packages(RPostgreSQL) and
install.packages(RPostgreSQL). I've attached a text document of the
resulting error here.

Error.txt http://r.789695.n4.nabble.com/file/n4669380/Error.txt  

I'm running R version 2.15.1 on Ubuntu. I can't seem to find a solution to
the problem online. And let me be clear, I was able to load this package
without an issue no longer than a week ago. Any help you can offer would be
much appreciated.

Thanks,

Drew



--
View this message in context: 
http://r.789695.n4.nabble.com/Cannot-install-RPostgreSQL-tp4669380.html
Sent from the R help mailing list archive at Nabble.com.

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

[R] rewrite script to eliminate constant object reference

[bcrombie]

I'm adding a column (region) to a data frame (devUni8), and the (region)
column will be populated by a numeric code that is a function of another
column (state) in that data frame.  See part of the script below. 

How can I rewrite this so that I could apply the conditions to any data
frame without having to keep typing its name (in this case, devUni8$). 
I've heard the attach() function is to be avoided, and I'm not good at with,
while, or if statements right now.  I've tried some other things but keep
getting object not found errors.  Assistance appreciated. Thanks.

#Create Region Variable
#
devUni8$region=0

#Assign Northeast States
#   
devUni8$region[devUni8$state = 11  devUni8$state = 23 | devUni8$state =
51  devUni8$state = 55] = 1   

#Assign Southeast States
#
devUni8$region[devUni8$state = 56  devUni8$state = 64 ] = 2



--
View this message in context: 
http://r.789695.n4.nabble.com/rewrite-script-to-eliminate-constant-object-reference-tp4669393.html
Sent from the R help mailing list archive at Nabble.com.

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

Re: [R] [R-SIG-Mac] problem with the installation of r commander on a mac

[Milan Bouchet-Valat]

Le mercredi 12 juin 2013 à 16:52 -0400, John Fox a écrit :
 Dear Susanne,
 
 You started this thread on r-help (though R-SIG-Mac would have been more
 appropriate), and so I'm copying my response to the r-help list. People will
 find it confusing if the messages are simply kept private.
 
 It's not obvious to me exactly what your problem is now. In particular, is
 the Rcmdr package working when you start XQuartz before R? 
 
 I see that you've installed and loaded the FactoMineR package. Presumably
 the Rcmdr package was already installed. Then you executed an R script
 provided by the authors of the FactoMineR package, which reinstalls and then
 modifies the Rcmdr package. I think that this is ill-advised (as opposed to
 providing an Rcmdr plug-in package for FactoMineR, as used to be the case),
 and if you're having problems with their script, you should really contact
 the authors. 
 
 If I read the messages correctly, the script produces warnings, not errors,
 oddly relating to the language you're using (odd because the authors of the
 FactoMineR package are French) and it's possible that everything will work
 correctly despite the warnings.
It's possible that the file
http://factominer.free.fr/add-menu-facto-fr.txt that the FactoMineR
script downloads is not read using the correct encoding (it is in
CP2152), and thus contains invalid UTF-8 characters.

So indeed I would reinstall Rcmdr using
install.packages(Rcmdr)

and load Rcmdr separately using
library(Rcmdr)

If that works, the bug is in FactoMineR's nonstandard way of installing
a menu. A workaround might be to use their English install script:
source(http://factominer.free.fr/install-facto.r;)


Regards

 I hope this helps,
  John
 
  -Original Message-
  From: Susanne.Ettinger [mailto:susanne.ettin...@gmail.com]
  Sent: Wednesday, June 12, 2013 11:44 AM
  To: John Fox
  Subject: Re: [R] [R-SIG-Mac] problem with the installation of r
  commander on a mac
  
  Dear John,
  
  thank you very much for your quick reply - I realize I sent this email
  to the list without being a member, but I am a very beginner and
  started this morning the installation process of R.
  
  I have been printing out any possibly available information on how to
  get started with R and I am following the exercices exposed in the book
  written by Cornillon et al. (2012) to use FactoMineR to do some PCA
  analysis on vulnerability data.
  
  I downloaded the 3.0.1 version of R and have the 1.9-6 package of
  Rcmdr. I also checked into the library(tcltk) but do not get an error
  message, this seems to work fine.
  
  Since I open XQuartz before starting the Rcmdr library, I am getting a
  different error message than the ones of this morning. This is what it
  looks like :
  
  
   install.packages()
  --- SVP sélectionner un miroir CRAN pour cette session ---
  essai de l'URL 'http://cran.univ-
  lyon1.fr/bin/macosx/contrib/3.0/FactoMineR_1.25.tgz'
  Content type 'application/x-gzip' length 3397827 bytes (3.2 Mb)
  URL ouverte
  ==
  downloaded 3.2 Mb
  
  
  
  
  Les packages binaires téléchargés sont dans
  /var/folders/06/z7b6z3y102xgxls2xh251p5wgp/T//Rtmp13nIpm/downl
  oaded_packages
   library(FactoMineR)
  Le chargement a nécessité le package : car
  Le chargement a nécessité le package : MASS
  Le chargement a nécessité le package : nnet
  Le chargement a nécessité le package : ellipse
  
  
  Attachement du package : ‘ellipse’
  
  
  L'objet suivant est masqué from ‘package:car’:
  
  
  ellipse
  
  
  Le chargement a nécessité le package : lattice
  Le chargement a nécessité le package : cluster
  Le chargement a nécessité le package : scatterplot3d
  Le chargement a nécessité le package : leaps
   source(http://factominer.free.fr/install-facto-fr.r;)
  essai de l'URL 'http://cran.univ-
  lyon1.fr/bin/macosx/contrib/3.0/Rcmdr_1.9-6.tgz'
  Content type 'application/x-gzip' length 3759850 bytes (3.6 Mb)
  URL ouverte
  ==
  downloaded 3.6 Mb
  
  
  
  
  The downloaded binary packages are in
  /var/folders/06/z7b6z3y102xgxls2xh251p5wgp/T//Rtmp13nIpm/downl
  oaded_packages
  essai de l'URL 'http://cran.univ-
  lyon1.fr/bin/macosx/contrib/3.0/FactoMineR_1.25.tgz'
  Content type 'application/x-gzip' length 3397827 bytes (3.2 Mb)
  URL ouverte
  ==
  downloaded 3.2 Mb
  
  
  
  
  The downloaded binary packages are in
  /var/folders/06/z7b6z3y102xgxls2xh251p5wgp/T//Rtmp13nIpm/downl
  oaded_packages
  Avis dans grepl(\n, lines, fixed = TRUE) :
la chaîne de caractères entrée 1 est incorrecte dans cet
  environnement linguistique
  Avis dans grepl(\n, lines, fixed = TRUE) :
la chaîne de caractères entrée 5 est incorrecte dans cet
  

Re: [R] rewrite script to eliminate constant object reference

[Greg Snow]

If you want an easy way to change the name of the data frame for assignment
then you may want a macro.  There is an article in the R journal (
http://cran.r-project.org/doc/Rnews/Rnews_2001-3.pdf) on creating macros
and there are tools that help with creating macros in the gtools package.

Though what you are trying to do may work a little better using
`findInterval` or `merge`.


On Wed, Jun 12, 2013 at 2:36 PM, bcrombie bcrom...@utk.edu wrote:

 I'm adding a column (region) to a data frame (devUni8), and the (region)
 column will be populated by a numeric code that is a function of another
 column (state) in that data frame.  See part of the script below.

 How can I rewrite this so that I could apply the conditions to any data
 frame without having to keep typing its name (in this case, devUni8$).
 I've heard the attach() function is to be avoided, and I'm not good at
 with,
 while, or if statements right now.  I've tried some other things but keep
 getting object not found errors.  Assistance appreciated. Thanks.

 #Create Region Variable
 #
 devUni8$region=0

 #Assign Northeast States
 #
 devUni8$region[devUni8$state = 11  devUni8$state = 23 | devUni8$state =
 51  devUni8$state = 55] = 1

 #Assign Southeast States
 #
 devUni8$region[devUni8$state = 56  devUni8$state = 64 ] = 2



 --
 View this message in context:
 http://r.789695.n4.nabble.com/rewrite-script-to-eliminate-constant-object-reference-tp4669393.html
 Sent from the R help mailing list archive at Nabble.com.

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




-- 
Gregory (Greg) L. Snow Ph.D.
538...@gmail.com

[[alternative HTML version deleted]]

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

Re: [R] rewrite script to eliminate constant object reference

[Jim Holtman]

Check out 'with' and 'within'.


Sent from my Verizon Wireless 4G LTE Smartphone

 Original message 
From: bcrombie bcrom...@utk.edu 
Date: 06/12/2013  16:36  (GMT-05:00) 
To: r-help@r-project.org 
Subject: [R] rewrite script to eliminate constant object reference 
 
I'm adding a column (region) to a data frame (devUni8), and the (region)
column will be populated by a numeric code that is a function of another
column (state) in that data frame.  See part of the script below. 

How can I rewrite this so that I could apply the conditions to any data
frame without having to keep typing its name (in this case, devUni8$). 
I've heard the attach() function is to be avoided, and I'm not good at with,
while, or if statements right now.  I've tried some other things but keep
getting object not found errors.  Assistance appreciated. Thanks.

#Create Region Variable
#
devUni8$region=0

#Assign Northeast States
#   
devUni8$region[devUni8$state = 11  devUni8$state = 23 | devUni8$state =
51  devUni8$state = 55] = 1   

#Assign Southeast States
#
devUni8$region[devUni8$state = 56  devUni8$state = 64 ] = 2



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Re: [R] rewrite script to eliminate constant object reference

[Ista Zahn]

Hi,

Here are some examples using the mtcars dataset that you can modify to work
with your data.

## Here is my first try using within.
## Somehow the elements of region that
## should be zero are converted to NA

mtcars - within(mtcars, {
region - 0
region[gear==4carb==4] - 1
region[gear==3carb==1] - 2
})

## Here is a second try with an ugly
## hack to fix the NA problem

mtcars - within(mtcars, {
region - NA
region[gear==4carb==4] - 1
region[gear==3carb==1] - 2
region[is.na(region)] - 0
})


## Here is an alternative using with
## instead of within
mtcars$region - 0
mtcars$region[with(mtcars, gear==4carb==4)] - 1
mtcars$region[with(mtcars, gear==3carb==1)] - 2


Best,
Ista


On Wed, Jun 12, 2013 at 4:36 PM, bcrombie bcrom...@utk.edu wrote:

 I'm adding a column (region) to a data frame (devUni8), and the (region)
 column will be populated by a numeric code that is a function of another
 column (state) in that data frame.  See part of the script below.

 How can I rewrite this so that I could apply the conditions to any data
 frame without having to keep typing its name (in this case, devUni8$).
 I've heard the attach() function is to be avoided, and I'm not good at
 with,
 while, or if statements right now.  I've tried some other things but keep
 getting object not found errors.  Assistance appreciated. Thanks.

 #Create Region Variable
 #
 devUni8$region=0

 #Assign Northeast States
 #
 devUni8$region[devUni8$state = 11  devUni8$state = 23 | devUni8$state =
 51  devUni8$state = 55] = 1

 #Assign Southeast States
 #
 devUni8$region[devUni8$state = 56  devUni8$state = 64 ] = 2



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Re: [R] new data

[arun]

Hi,
Try this:


final3New-read.table(file=real_data_cecilia.txt,sep=\t)
final3New1-read.csv(real_data_cecilia_new.csv)
fun2-function(dat){
        indx- duplicated(dat)|duplicated(dat,fromLast=TRUE)    
        dat1- subset(dat[indx,],dummy==1)
        dat2- dat1[order(dat1$dimension),]
        indx1- as.numeric(row.names(dat2))
        names(indx1)- (seq_along(indx1)-1)%/%2+1
        dat3- dat[c(indx1,indx1+1),]
        dat3$id- names(c(indx1,indx1+1))
        lst1- lapply(split(dat3,dat3$id),function(x){
                x1- x[-1,]
                x2- x1[which.min(abs(x1$dimension[1]-x1$dimension[-1]))+1,]
                x3- subset(x,dummy==1)
                rowNx2- as.numeric(row.names(x2))
                rowNx3- as.numeric(row.names(x3))
                x4- x3[which.min(abs(rowNx2-rowNx3)),]
                x5- rbind(x4,x2)
                x6- x[is.na(match(row.names(x),row.names(x5))),]
                  })
      dat4- do.call(rbind,lst1)
      row.names(dat4)- gsub(.*\\.,,row.names(dat4))
      indxNew1- sort(as.numeric(unique(row.names(dat4
      dat0- subset(dat[indx,],dummy==0)
     if(nrow(dat0)0){    
      dat20-dat0[order(dat0$dimension),]
      indx0- as.numeric(row.names(dat20))
      names(indx0)- (seq_along(indx0)-1)%/%2+1
      dat30- dat[c(indx0-1,indx0),]
      dat30$id- names(c(indx0-1,indx0))
      lst0- lapply(split(dat30,dat30$id),function(x) {
                    x1- subset(x,dummy==1)
                    x2- subset(x,dummy==0)
                    x3- x1[which.min(abs(x1$dimension- unique(x2$dimension))),]
                    rowNx2- as.numeric(row.names(x2))
                    rowNx3- as.numeric(row.names(x3))
                    x4- x2[which.min(abs(rowNx2-rowNx3)),]
                    x5- rbind(x3,x4)
                    x6- x[is.na(match(row.names(x),row.names(x5))),]
                    })
    dat40- do.call(rbind,lst0)
    row.names(dat40)- gsub(.*\\.,,row.names(dat40))
    indxNew0- sort(as.numeric(unique(row.names(dat40
    res1Del-dat[indxNew1,]
    res0Del-dat[indxNew0,]
    indx10-sort(as.numeric(union(row.names(res0Del),row.names(res1Del
    if(length(indx10)%%2==1){
    res10Del-unique(rbind(res1Del,res0Del))
  indx10New- sort(as.numeric(row.names(res10Del)))
     resF- dat[-indx10New,]
    resF
    }
    else{
    resF- dat[-indx10,]
    resF
    }
    }
    else{
    resF- dat[-indxNew1,]
    }
    }

###Old Function
fun3- function(dat){
  indx- duplicated(dat)
      dat1- subset(dat[indx,],dummy==1)
      dat0- subset(dat[indx,],dummy==0)
      indx1- as.numeric(row.names(dat1))
     indx11- sort(c(indx1,indx1+1))
     indx0- as.numeric(row.names(dat0))
     indx00- sort(c(indx0,indx0-1))
      indx10- sort(c(indx11,indx00))
     res - dat[-indx10,]
    res
    }
##Applying fun1() (from previous post)       
res5Percent- fun1(final3New,0.05,50)
res5Percent1- fun1(final3New1,0.05,50)
res10Percent- fun1(final3New,0.10,200)
res10Percent1- fun1(final3New1,0.10,200)
res20Percent- fun1(final3New,0.20,100)
res20Percent1- fun1(final3New1,0.20,100)

###Applying fun2()
res5F2- fun2(res5Percent)
res5F2_1- fun2(res5Percent1)
res10F2- fun2(res10Percent)
res10F2_1- fun2(res10Percent1)
res20F2- fun2(res20Percent)
res20F2_1- fun2(res20Percent1)
    
#Applying fun3()
res5F3- fun3(res5Percent)
res5F3_1- fun3(res5Percent1)
res10F3- fun3(res10Percent)
res10F3_1- fun3(res10Percent1)
res20F3- fun3(res20Percent)
res20F3_1- fun3(res20Percent1)

vec1- rep(c(res5F2,res10F2,res20F2),2)
vec2- rep(c(res5F3,res10F3,res20F3),2)
vec1[4:6]-paste(vec1[4:6],_1,sep=)
vec2[4:6]-paste(vec2[4:6],_1,sep=)
 resTbl-data.frame( 
Dataset=rep(rep(c(final3New,final3New1),each=3),2),Funct=rep(c(fun2,fun3),each=6),do.call(rbind,lapply(as.list(c(vec1,vec2)),function(x)
 
{x1-get(x);c(N_row=nrow(x1),Sub0_Nrow=nrow(subset(x1,dummy==0)),Sub1_Nrow=nrow(subset(x1,dummy==1)),Uniq_Nrow=nrow(unique(x1)))})),stringsAsFactors=FALSE)
 row.names(resTbl)- c(vec1,vec2)
resTbl
# Dataset Funct N_row Sub0_Nrow Sub1_Nrow Uniq_Nrow
#res5F2 final3New  fun2   276   138   138   276
#res10F2    final3New  fun2   454   227   227   454
#res20F2    final3New  fun2   284   142   142   284
#res5F2_1  final3New1  fun2   288   144   144   288
#res10F2_1 final3New1  fun2   488   244   244   488
#res20F2_1 final3New1  fun2   310   155   155   310
#res5F3 final3New  fun3   276   138   138   276
#res10F3    final3New  fun3   452   226   226   452
#res20F3    final3New  fun3   284   142   142   284
#res5F3_1  final3New1  fun3   288   144   144   288
#res10F3_1 final3New1  fun3   488   244   244   488
#res20F3_1 final3New1  fun3   310   155   155   310
 head(res5F2_1,4)
#  firm year industry dummy dimension
#1 500622043 2004    1 1  1172
#2 501611886 2004    1 0  1183
#3 500778787 2004    1 1  5680
#4 

Re: [R] Proper way to implement package internal functions

[Rolf Turner]

On 13/06/13 03:34, Bryan Hanson wrote:

SNIP

So this warning from check is not a problem in the long run:

* checking for missing documentation entries ... WARNING
Undocumented code objects:
   ‘ang0to2pi’ ‘dAB’ ‘doBoxesIntersect’ ...
All user-level objects in a package should have documentation entries.

if I understand correctly.  I guess the reason I didn't find any documentation 
is the wide lattitude which is possible.

I think you *might* get flak about the warnings if you submit your package
to CRAN.  I find such warnings annoying, anyhow.

To avoid them you can create a *.Rd file listing all the undocumented 
functions

in your package with an alias for the name of each such function and a
usage line for each such function.  Only a mild pain in the pohutukawa,
and it only needs to be done once.  (Possibly with some updating if new
undocumented functions are added to the package.)

The *.Rd file can be called anything you like (as long as it ends in 
.Rd and

doesn't conflict with other *.Rd filled.  However a fairly common convention
is to name the file melvin-internal.Rd where melvin is the name of your
package.

cheers,

Rolf Turner

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Re: [R] Proper way to implement package internal functions

[Michael Weylandt]

On Jun 12, 2013, at 16:34, Bryan Hanson han...@depauw.edu wrote:

 Thanks Duncan...
 
 Silly me, it's section 1.6.1 not version 1.6.1!
 
 So this warning from check is not a problem in the long run:
 
 * checking for missing documentation entries ... WARNING
 Undocumented code objects:
  ‘ang0to2pi’ ‘dAB’ ‘doBoxesIntersect’ ...
 All user-level objects in a package should have documentation entries.

What does your NAMESPACE file say?

MW
 
 if I understand correctly.  I guess the reason I didn't find any 
 documentation is the wide lattitude which is possible.
 
 Thank you.  Bryan
 
 On Jun 12, 2013, at 10:57 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote:
 
 On 12/06/2013 10:44 AM, Bryan Hanson wrote:
 [previously posted on Stack Overflow: 
 http://stackoverflow.com/questions/17034309/hiding-undocumented-functions-in-a-package-use-of-function-name
  ]
 
 I've got some functions I need to make available in a package, and I don't 
 want to export them or write much documentation for them. I'd just hide 
 them inside another function but they need to be available to several 
 functions so doing it that way becomes a scoping and maintenance issue. 
 What is the right way to do this?  By that I mean do they need special 
 names, do they go somewhere other than the R subdirectory, can I put them 
 in a single file, etc? I've checked out the manuals (e.g. Writing R 
 Extensions 1.6.1), and what I'm after is like the .internals concept in the 
 core, but I don't see any instructions about how to do this generally.
 
 For example, if I have functions foo1 and foo2 in a file foofunc.R, and 
 these are intended for internal use only, should they be called foo1 or 
 .foo1?  And the file that holds them, should it be .foofunc.R or 
 foofunc-internals?  What should the Rd look like, or do I even need one?
 
 I know people do this in packages all the time and I feel like I've seen 
 this somewhere, but I can't find any resources just now.  Perhaps a 
 suggestion of a package that does things this way which I could study would 
 be sufficient.
 
 The best way to do this is simply not to export those functions in your 
 NAMESPACE file.  If you want to use a naming convention
 internally to remind yourself that those are private, you can do so, but R 
 doesn't force one on you, and there are no really popular conventions in 
 use.   R won't complain if you don't document those functions at all.
 
 There may have been other advice in the version 1.6.1 manual, but that is 
 seriously out of date, more than 10 years old.  I recommend that you update 
 to 3.0.1.
 
 Duncan Murdoch
 
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Re: [R] Creating a new var from conditional values in other vars

[arun]

Hi `Bangali`,
You can type in the R Console ?with() 
?ifelse()
The details and some examples are there.


In addition to ?with(), you can use: ?within

dat1-within(dat1,pattern-ifelse(A20  B=2.5  C=20,Normal,ifelse(A 20  
B 2.5  C 20,Increased,ifelse(A =20  B 2.5  C =20,Low,Other

library(plyr)
?mutate()
dat1New-mutate(dat1,pattern=ifelse(A20  B=2.5  C=20,Normal,ifelse(A 20 
 B 2.5  C 20,Increased,ifelse(A =20  B 2.5  C =20,Low,Other
identical(dat1,dat1New)
#[1] TRUE
dat2-transform(dat1,pattern=ifelse(A20  B=2.5  C=20,Normal,ifelse(A 20 
 B 2.5  C 20,Increased,ifelse(A =20  B 2.5  C =20,Low,Other 
 identical(dat1,dat2)
#[1] TRUE
A.K.




Arun, 

Many thanks! The code works perfectly well. It seems that ifelse
 + with do the trick much better than if/else statement. Now  I need to 
understand the mechanichs of what you did. Can you provide a link on how
 to use with 
- Original Message -
From: arun smartpink...@yahoo.com
To: R help r-help@r-project.org
Cc: 
Sent: Wednesday, June 12, 2013 4:03 PM
Subject: Re: Creating a new var from conditional values in other vars

Hi,
Try this:
set.seed(25)
dat1- 
data.frame(A=sample(1:30,100,replace=TRUE),B=sample(1:35,100,replace=TRUE),C=sample(1:25,100,replace=TRUE))


dat1$pattern-with(dat1,ifelse(A20  B=2.5  C=20,Normal,ifelse(A 20  B 
2.5  C 20,Increased,ifelse(A =20  B 2.5  C =20,Low,Other
head(dat1)
#   A  B  C pattern
#1 13 20  5   Other
#2 21 15  4 Low
#3  5 24  1   Other
#4 27 13  6 Low
#5  4  4 10   Other
#6 30 19 22   Other
A.K.




I am newbie to R coming from SAS (basic user). Quite a difficult move 
I have a dataframe named kappa exported from csv file 
kappa-read.csv(kappacsv, header=TRUE, sep=;, dec=.) 
kappa contains 3 numeric vars (A,B and C) 
I want to create a new var called pattern depending on the values of the 
conditions in A, B and C 
I have tried many ways one has been this: 
kappa$pattern1-99 # create a new numeric var in kappa dataframe 

if (A=20  B=2.5  C =20){kappa$pattern-Normal} 
else if (A 20  B 2.5  C 20){kappa$pattern-Increased} 
else if (A =20  B 2.5  C =20){kappa$pattern-Low} 
else {kappa$pattern-“Other”} 
  
The code does not work and I get errors all the time. 
Any help will be greatly appreciated 
Thanks

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Re: [R] Proper way to implement package internal functions

[Bryan Hanson]

Hi Rolf...  Thanks.  I discovered the approach you described by looking at the 
source for spatstat, which as it turns out does exactly that.  I also 
discovered by testing that if you don't export a pattern, but rather export the 
specific names, not including the functions one wants to hide, that the warning 
goes away.  Since it is less work to change the export statement compared to 
even a minimal Rd, that's the way I went.  It's interesting that there is not 
more info about these options available.  Thanks, Bryan

On Jun 12, 2013, at 6:46 PM, Rolf Turner rolf.tur...@xtra.co.nz wrote:

 On 13/06/13 03:34, Bryan Hanson wrote:
 
SNIP
 So this warning from check is not a problem in the long run:
 
 * checking for missing documentation entries ... WARNING
 Undocumented code objects:
   ‘ang0to2pi’ ‘dAB’ ‘doBoxesIntersect’ ...
 All user-level objects in a package should have documentation entries.
 
 if I understand correctly.  I guess the reason I didn't find any 
 documentation is the wide lattitude which is possible.
 I think you *might* get flak about the warnings if you submit your package
 to CRAN.  I find such warnings annoying, anyhow.
 
 To avoid them you can create a *.Rd file listing all the undocumented 
 functions
 in your package with an alias for the name of each such function and a
 usage line for each such function.  Only a mild pain in the pohutukawa,
 and it only needs to be done once.  (Possibly with some updating if new
 undocumented functions are added to the package.)
 
 The *.Rd file can be called anything you like (as long as it ends in .Rd and
 doesn't conflict with other *.Rd filled.  However a fairly common convention
 is to name the file melvin-internal.Rd where melvin is the name of your
 package.
 
cheers,
 
Rolf Turner

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[R] identify data points by certain criteria

[Ye Lin]

Hey I want to identify data points by criteria, here is an example of my
1min data

Time Var1  Var2
00:001  0
00:010  0
00:021  0
00:031  0
00:040  0
00:051  0
00:061  0
00:071  0
00:081  0
00:090  0
00:101  0
00:111  0
00:121  0
00:130  0

I want to identify the data points where Var1=0 and Var2=0, ( in this
example shud be the points highlighted above), then calculate the time
duration between these data points, (in this example, shud be 3min, 5 min
and 4min), then identify the starting point of the max time duration ( in
this example shud be the starting point of 5-min-duration, return the data
points at 00:09), finally return the value in Time column ( in this
example shud be 00:09)

Thanks for your help!

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Re: [R] identify data points by certain criteria

[David Winsemius]

On Jun 12, 2013, at 5:55 PM, Ye Lin wrote:

 Hey I want to identify data points by criteria, here is an example of my
 1min data
 
 Time Var1  Var2
 00:001  0
 00:010  0
 00:021  0
 00:031  0
 00:040  0
 00:051  0
 00:061  0
 00:071  0
 00:081  0
 00:090  0
 00:101  0
 00:111  0
 00:121  0
 00:130  0
 
 I want to identify the data points where Var1=0 and Var2=0, ( in this
 example shud be the points highlighted above), then calculate the time
 duration between these data points, (in this example, shud be 3min, 5 min
 and 4min), then identify the starting point of the max time duration ( in
 this example shud be the starting point of 5-min-duration, return the data
 points at 00:09), finally return the value in Time column ( in this
 example shud be 00:09)
 

While you are waiting for an answer you might want to read the Posting Guide:

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

Points to pay special attention to: Plain-text. Posting code. Posting examples 
in form that can be pasted into console session (dump or dput functions). 
Providing context for problem (such as describing the conventions for your 
time-scale)  and your background (since this looks like a homework exercise.)



 Thanks for your help!
 
   [[alternative HTML version deleted]]
 
 __


David Winsemius
Alameda, CA, USA

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Re: [R] Cannot install RPostgreSQL

[Pascal Oettli]

Hello,

If you carefully check the error message, it is clearly written:

RS-PostgreSQL.h:23:26: fatal error: libpq-fe.h: No such file or directory

Some header files are missing.
Here is the result of a quick search on the web: libpq-dev for Ubuntu.

If I may suggest, you should upgrade the version of R.

Regards,
Pascal


On 13/06/13 03:13, Drew wrote:

Hello everyone,

I am extremely new to R. I have yet to write any complicated code myself,
however I have been learning largely by reading code that has already been
written. Long story short, I have been running a code that makes use of the
RPostgreSQL package for some time now. For some reason I just recently
started to get an error. Whenever I try to load the RPostgreSQL package I
get:


library(RPostgreSQL)

Error in library(RPostgreSQL) : there is no package called ‘RPostgreSQL’

I also tried install.packages(RPostgreSQL) and
install.packages(RPostgreSQL). I've attached a text document of the
resulting error here.

Error.txt http://r.789695.n4.nabble.com/file/n4669380/Error.txt

I'm running R version 2.15.1 on Ubuntu. I can't seem to find a solution to
the problem online. And let me be clear, I was able to load this package
without an issue no longer than a week ago. Any help you can offer would be
much appreciated.

Thanks,

Drew



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Re: [R] odds ratio per standard deviation

[vinhnguyen04x]

L. Snow,
Ted,

Many thanks, I am sorry to made a question without context. I use three
parameters of facial temperature, heart rate, and respiratory rate to
distinguish infectious patients from healthy subjects. So I use logistic
regression to generate a classification model and calculate the odds ratio
for these three parameters. In my case, I would like to know what kinds of
odds ratio can be used, odds ratio per standard deviation or odds ratio. 

Thanks you in advance for your help




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Re: [R] identify data points by certain criteria

[arun]

Hi,
Not clear about the 'Time' column.
dat1- read.table(text=
Time    Var1  Var2
00:00    1  0
00:01    0  0
00:02    1  0
00:03    1  0
00:04    0  0
00:05    1  0
00:06    1  0
00:07    1  0
00:08    1  0
00:09    0  0
00:10    1  0
00:11    1  0
00:12    1  0
00:13    0  0
,sep=,header=TRUE,stringsAsFactors=FALSE)


indx-which(rowSums(dat1[,-1])==0)
dat1[indx[which.max(c(1,diff(as.numeric(gsub(.*:,,dat1[,1][indx])],]
#    Time Var1 Var2
#10 00:09    0    0
dat1[indx[which.max(c(1,diff(as.numeric(gsub(.*:,,dat1[,1][indx])],Time]
#[1] 00:09


A.K.



- Original Message -
From: Ye Lin ye...@lbl.gov
To: R help r-help@r-project.org
Cc: 
Sent: Wednesday, June 12, 2013 8:55 PM
Subject: [R] identify data points by certain criteria

Hey I want to identify data points by criteria, here is an example of my
1min data

Time     Var1      Var2
00:00    1              0
00:01    0              0
00:02    1              0
00:03    1              0
00:04    0              0
00:05    1              0
00:06    1              0
00:07    1              0
00:08    1              0
00:09    0              0
00:10    1              0
00:11    1              0
00:12    1              0
00:13    0              0

I want to identify the data points where Var1=0 and Var2=0, ( in this
example shud be the points highlighted above), then calculate the time
duration between these data points, (in this example, shud be 3min, 5 min
and 4min), then identify the starting point of the max time duration ( in
this example shud be the starting point of 5-min-duration, return the data
points at 00:09), finally return the value in Time column ( in this
example shud be 00:09)

Thanks for your help!

    [[alternative HTML version deleted]]

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