date:20100107

There is an alternative through strsplit() when the desired output format is 
numeric (fractional hours on 0-24 scale).

 aa - c(3:00,11:42)
 bb - strsplit(aa,:)
 bb
[[1]]
[1] 3  00

[[2]]
[1] 11 42

 cc - sapply(bb,function(x){as.numeric(x[1])+as.numeric(x[2])/60})
 cc
[1]  3.0 11.7

AM/PM can be dealt with similarly.

 aa - c(3:00pm,11:42am)
 pm - grepl(pm,aa)
 pm
[1]  TRUE FALSE
 bb - strsplit(sub([ap]m$,,aa),:)
 bb
[[1]]
[1] 3  00

[[2]]
[1] 11 42

 cc - sapply(bb,function(x){as.numeric(x[1])+as.numeric(x[2])/60})+12*pm
 cc
[1] 15.0 11.7

Cheers,

M. Kulich



On 7.1.2010 8:26, Dennis Murphy wrote:
 Hi:
 
 Let
 x - '3:00'
 
 The R package for data that are only dates or only times is chron. For
 times,
 it appears that the strings need to be in the form hh:mm:ss on a 24-hour
 clock, so for
 example, 1:30 PM should be expressed as 13:30:00. [I didn't see any option
 for a
 12-hour clock with an optional argument to designate AM or PM...if wrong,
 I'm
 sure I'll be corrected...]
 
 
 Using the x value above, we have
 
 library(chron)
 times(x)
 x - '3:00'
 times(x)
 Error in convert.times(times., fmt) : format h:m:s may be incorrect
 In addition: Warning messages:
 1: In unpaste(times, sep = fmt$sep, fnames = fmt$periods, nfields = 3) :
   wrong number of fields in entry(ies) 1
 2: In convert.times(times., fmt) : NAs introduced by coercion
 3: In convert.times(times., fmt) : NAs introduced by coercion
 4: In convert.times(times., fmt) : NAs introduced by coercion
 
 So '3:00' isn't enough; we need to add on some seconds...
 
 x - paste(x, ':00', sep = '')
 x
 [1] 3:00:00
 times(x) # Now it works.
 [1] 03:00:00
 
 To show you that this works equally well with vectors, suppose the
 input times were a vector
 z - c('3:00', '4:15', '12:25', '16:41')
 
 # Use the same trick as above (paste() is also vectorized)..
 z - paste(z, ':00', sep = '')
 times(z)
 # [1] 03:00:00 04:15:00 12:25:00 16:41:00
 
 
 Consult ?chron and the examples contained within. You can run the
 examples on the help page with example(chron).
 
 HTH,
 Dennis
 
 
 On Wed, Jan 6, 2010 at 9:32 PM, chrisli1223 
 chri...@austwaterenv.com.auwrote:
 

 Hi all,

 I have imported a value 3:00 from Excel into R using read.csv. I want R to
 recognise it as 3:00am (time data). How do I do it?

 Thanks in advance,
 Chris
 --
 View this message in context:
 http://n4.nabble.com/R-treating-time-tp1008608p1008608.html
 Sent from the R help mailing list archive at Nabble.com.

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-- 

Michal Kulich, PhD
Dept. of Probability and Statistics
Charles University
Sokolovska 83
186 75 Praha 8
Czech Republic

Phone  +420-221-913-229
Fax:   +420-283-073-341, +420-222-323-316
Email: kul...@karlin.mff.cuni.cz

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Re: [R] Finally, the first R spam!

2010-01-07 Thread Liviu Andronic

On 1/7/10, David Croll david.cr...@gmx.ch wrote:
  Just for fun (or concern): I received a R spam mail. Perhaps the first in
 history...

No, not quite first. There was one before on Inference with R, at least.
Liviu

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[R] generate XML

2010-01-07 Thread Robert

Finally, I managed to automatically generate rather simple XML code. In R this 
is a matrix. The problem concerns how to write that matrix to file. I use 
write.table and the extension of file .xml Everything works perfect beside 
coding some language letters (Polish). But the problem disappears when I change 
the extension to .txt Therefore I write a file with .txt extension and after 
that I manually change the extension to .xml  - it does not solve the problem. 
Is it possible to write my matrix or txt file to valid xml file? I need to do 
it automatically.

Best,
Robert  

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Re: [R] Building static HTML help pages in R 2.10.x on Windows

On 7.1.2010 9:49, Dieter Menne wrote:
 
 Thanks for that code. I fully agree that the current help system is a step
 back. For stable bookmarking, my workaround is to put
 
 options(help.ports=6800)
 
 into the profile,  so I can created links like
 
 http://127.0.0.1:6800/library/gmodels/html/estimable.html
 
 but this still required that I start RGui and the help system once. 
 
 Dieter

Thanks for this, too. Btw, is there a way to start the dynamic Rhelp server in 
the background without manually launching RGui? That, combined with Dieter's 
suggestion, would bring the help system sort of back to its original state. 

I am sorry to say that the new dynamic help is a HUGE nuisance to me. Had to 
revert back to R 2.9 because of that :-(.

Michal

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Re: [R] Increment in loop - OK

2010-01-07 Thread Muhammad Rahiz


This works.

m - matrix(1:3,3,3)
x1 - list(m, m+1, m+2, m+3, m+4) 


out - list()
for (i in 1:4){
t[[i]] - Reduce(+, x1[c(i:i+1)])
}


Muhammad

--
Muhammad Rahiz  |  Doctoral Student in Regional Climate Modeling

Climate Research Laboratory, School of Geography  the Environment  
Oxford University Centre for the Environment
South Parks Road, Oxford, OX1 3QY, United Kingdom 
Tel: +44 (0)1865-285194	 Mobile: +44 (0)7854-625974

Email: muhammad.ra...@ouce.ox.ac.uk






Muhammad Rahiz wrote:

useRs,

I'm getting limited success in trying to apply increment in a loop.

The following defined function creates a +1 increment

incr - function(x){
eval.parent(substitute(x - x + 1))
print(x) }

How do I apply it in a loop on my test dataset, x1, so that the procedure 
becomes

x1[c(1:2)]
x1[c(2:3)]
x1[c(3:4)]

where x1 = 

  

m - matrix(1:3,3,3)
x1 - list(m, m+1, m+2, m+3, m+4) 





Thanks.


Muhammad




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Re: [R] generate XML

2010-01-07 Thread S Devriese

On 01/07/2010 10:13 AM, Robert wrote:
 Finally, I managed to automatically generate rather simple XML code. In R 
 this is a matrix. The problem concerns how to write that matrix to file. I 
 use write.table and the extension of file .xml Everything works perfect 
 beside coding some language letters (Polish). But the problem disappears when 
 I change the extension to .txt Therefore I write a file with .txt extension 
 and after that I manually change the extension to .xml  - it does not solve 
 the problem. Is it possible to write my matrix or txt file to valid xml file? 
 I need to do it automatically.
 
 Best,
 Robert  
 
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Have you checked the XML package?

If you print the matrix within R, this it look like you want (including
correct langauge encoding? Because in that case, you probably could use
sink (see ?sink).

Stephan

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[R] setting different environments

2010-01-07 Thread Assa Yeroslaviz

Hallo,

I have a set of S4 and S3 classes together in one script.
While running this script I create a lot of new functions and objects
An example for S3 and S4 classes:
## S3 classes
pt - list(x=1,y=2)
class(pt) - xypoint
xpos - function(x, ...) UseMethod(xpos)
xpos.xypoint - function(x) x$x
ypos - function(x, ...) UseMethod(ypos)
ypos.xypoint - function(x) x$y

print.xypoint - function(x) {
  cat(xypoint\n)
  cat(x: , xpos(x),  y: , ypos(x), \n)
}
#
## S4 classes
setClass(point, representation(x=numeric, y=numeric))

## Objekt
new(point, x=3, y=4)
# new(point, x=17, y=5)

## Generics
setGeneric(xcoord, function(object) standardGeneric(xcoord))
setGeneric(ycoord, function(object) standardGeneric(ycoord))
setGeneric(showpoint, function(object) standardGeneric(showpoint))

setMethod(xcoord, point, function(object) obj...@x)
setMethod(ycoord, point, function(object) obj...@y)

setMethod(showpoint, point, function(object) {
  cat(x=, xcoord(object), , y=, ycoord(object), \n)
})
setMethod(show, point, function(object) {
  showpoint(object)
})

setMethod(+, c(point,point), function(e1,e2) {
  newx - xcoord(e1) + xcoord(e2)
  newy - ycoord(e1) + ycoord(e2)
  return(new(point, x=newx, y=newy))
})

setMethod(-, c(point, point), function(e1, e2) {
  newx - xcoord(e1) - xcoord(e2)
  newy - ycoord(e1) - ycoord(e2)
  return(new(point, x=newx, y=newy))
})

setGeneric(point, function(p) standardGeneric(point))
setMethod(f=point, signature=point, definition=function(p) {
points(xcoord(p), ycoord(p))})

This two classes creates various functions and objects. This are being saved
under .GlobalEnv.

My Problem is, that I have a lot of this kind of classes.

I would like to know whether or not there is a possibility to put these
functions and objects in a different environemnt, so that they won'e be
saved under my working directory.

Can I save each class in a different environment?

How, if possible can I than access this functions?

Thanks in advance

Assa

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Re: [R] generate XML

2010-01-07 Thread robert-mcfadden

Dnia 7 stycznia 2010 10:41 S Devriese sdmaill...@gmail.com napisał(a):
 Have you checked the XML package?
 
 If you print the matrix within R, this it look like you want (including
 correct langauge encoding? Because in that case, you probably could use
 sink (see ?sink).
 
 Stephan

Yes. In R I get correct view. How to use sink? I have the object: my.matrix
and I want to create a file item1.xml How to do it?
 

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[R] penalization regression

2010-01-07 Thread Alex Roy

Dear all,
   I am using penalization regression method for my data. I am
wandering the following names are synonymous or not?

Complexity parameter
Penalty parameter
Shrinkage factor
Shrinkage parameter
hyper parameter


Thanks

Alex

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Re: [R] generate XML

2010-01-07 Thread S Devriese

On 01/07/2010 10:57 AM, robert-mcfad...@o2.pl wrote:
 Dnia 7 stycznia 2010 10:41 S Devriese sdmaill...@gmail.com napisał(a):
 Have you checked the XML package?

 If you print the matrix within R, this it look like you want (including
 correct langauge encoding? Because in that case, you probably could use
 sink (see ?sink).

 Stephan
 
 Yes. In R I get correct view. How to use sink? I have the object: my.matrix
 and I want to create a file item1.xml How to do it?
  
 
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you might try

# open file connection
sink(item1.xml)
# print object
my.matrix
# close file connection
sink()

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Re: [R] generate XML

2010-01-07 Thread robert-mcfadden




Dnia 7 stycznia 2010 11:30 S Devriese sdmaill...@gmail.com napisał(a):
 you might try
 
 # open file connection
 sink(item1.xml)
 # print object
 my.matrix
 # close file connection
 sink()

Unfortunately, It does not code letter appropriate. To #print object it's 
better to use write.table. But thank you for help.  

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Re: [R] adding 3D arrows to 3D plots


Eben J. Gering wrote:

Greetings,

I would like to add 3D arrows (i.e. arrow-headed vectors linking X1Y1Z1 to X2,Y2,Z2) to a 3D plot; ideally the sort of plot that can be rotated interactively.  Is this possible using plot3d, or another 3d plotter in R?  
While it is easy to draw segments in plot3d (e.g. below), I haven't figured out how to add arrow heads, or to create 3d arrows from scratch.  


##two headless segments:
library(rgl)
matrix(1:2,2,3)-segment1
matrix(1:3,2,3)-segment2
plot3d(segment2,type=l,col=red,xlim=c(0,3),ylim=c(0,3),zlim=c(0,3))
plot3d(segment1,type=l,add=TRUE,col=blue)

  


There isn't any current code to do that in rgl, but if you have a 
particular shape of arrow in mind, you could probably draw it with some 
combination of functions.  The main problem is that I've never seen any 
very appealing rotatable 3d arrows.  There's a Matlab function to draw 
some here:  
http://www.mathworks.com/matlabcentral/fileexchange/8396-draw-3d-arrows; 
it could probably be translated into rgl if you wanted that.


Duncan Murdoch

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Re: [R] Building static HTML help pages in R 2.10.x on Windows

Michal Kulich wrote:

On 7.1.2010 9:49, Dieter Menne wrote:

Thanks for that code. I fully agree that the current help system is a step
back. For stable bookmarking, my workaround is to put

options(help.ports=6800)

into the profile, so I can created links like

http://127.0.0.1:6800/library/gmodels/html/estimable.html

but this still required that I start RGui and the help system once.

Dieter

Thanks for this, too. Btw, is there a way to start the dynamic Rhelp server in the background without manually launching RGui? That, combined with Dieter's suggestion, would bring the help system sort of back to its original state.

You don't need Rgui, you could run Rterm, which would have a smaller
footprint. It's not very hard to start it and minimize it, but if you
want it running invisibly, you'll need to figure out how to hide the icon.

A disadvantage of doing this is that you won't see help relevant to your
current session, you'll see help relevant to the background task. In
2.10.x there aren't many differences, but you'll find it more limiting
in 2.11.x and later.

Duncan Murdoch

I am sorry to say that the new dynamic help is a HUGE nuisance to me. Had to
revert back to R 2.9 because of that :-(.

Michal

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Re: [R] Calling FING.EXE under RGui.EXE for windows.

I get a problem with shell too:

Under Rgui:

 R.version.string
[1] R version 2.10.1 Patched (2010-01-01 r50884)

 system(C:\\windows\\system32\\find /?, intern = TRUE)
character(0)

 system(cmd /c C:\\windows\\system32\\find /?, intern = TRUE)
character(0)

 shell(C:\\windows\\system32\\find /?)
Warning message:
In shell(C:\\windows\\system32\\find /?) :
 'C:\windows\system32\find /?' execution failed with error code 1

They all work, i.e. they give the required help message, under Rterm
and when I issue this from the Windows console it works:
C:\windows\system32\find /?


2010/1/7 Uwe Ligges lig...@statistik.tu-dortmund.de:


 On 07.01.2010 02:04, Gabor Grothendieck wrote:

 If you have C:\Rtools\bin on your PATH note that it contains a
 UNIX-like find utility that conflicts with the find utility in
 Windows.  If that is the problem then remove that from your PATH and
 then run the batch file.

 The batchfiles distribution at http://batchfiles.googlecode.com  has
 utilities (Rgui.bat, R.bat, Rtools.bat, etc.) that will automatically
 add C:\Rtools\bin to your path temporarily or only while R is running
 so that you can leave it off your PATH.


 I guess it's the use of system() rather than shell() that causes the
 problem. Under Windows, you have to use shell in order to start a command
 interpreter.

 Uwe Ligges


 On Wed, Jan 6, 2010 at 6:51 PM, John Schexnayderjsc...@us.ibm.com
  wrote:

 This is sort of a strange bug.  Not show stopping, but annoying.  I was
 wondering if anyone else has noticed this and reported it before I submit
 a bug report.

 I noticed while running the RGui and attempting to debug one of my
 scripts
 that I encountered a Windows error informing me that Find String [grep]
 Utility has encountered a problem and needs to close.  It is being
 generated by a call to a DOS batch file which contains a call to
 Find.exe.
  It can be reproduced by simply typing  System(find) in RGui.  What I
 found strange is that I have been running this script daily without this
 problem for months.  I now realize I never ran that portion of the script
 while in RGui.exe.  It has always run in batch mode which is done by
 Rterm.exe.

 I have tried this on three separate machines now all running Windows XP
 SP3, with versions of R 2.8.1 and R 2.10.1  If executing System(find)
 under RGui, an error window for the Find String Utility is generated and
 the command is not exectuted.  If the same command is issued in Rterm the
 expected FIND: Parameter format not correct message is properly
 returned.

 It doesn't seem an important bug, but it could be the canary in the mine
 for a larger problem somewhere down the road.

 Re,
 John Schexnayder

 IBM Tape Manufacturing - Information Technology
 San Jose, CA  95138
 jsc...@us.ibm.com

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Re: [R] R treating time

2010-01-07 Thread Meyners, Michael, LAUSANNE, AppliedMathematics

You might check one of the other methods of reading Excel
spreadsheets.  If you google for R Wiki Excel and then click on Cached
(since the R Wiki seems to be down at the moment) various alternatives
are listed.

On Thu, Jan 7, 2010 at 12:32 AM, chrisli1223
chri...@austwaterenv.com.au wrote:

 Hi all,

 I have imported a value 3:00 from Excel into R using read.csv. I want R to
 recognise it as 3:00am (time data). How do I do it?

 Thanks in advance,
 Chris
 --
 View this message in context: 
 http://n4.nabble.com/R-treating-time-tp1008608p1008608.html
 Sent from the R help mailing list archive at Nabble.com.

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[R] table() and setting useNA to be there by default?

2010-01-07 Thread Sean O'Riordain

Good morning,

Is there a way to get table() to default to including NAs  - as in...
table(..., useNA='ifany') or  table(..., useNA='always') or table(...,
exclude=NULL)  ?

I can't see a way under table() or options() or searching the archives
(probably using the wrong keyword?).

 t1 - c(1,2,3,3,3,2,NA,NA,NA,NA)
 table(t1)
t1
1 2 3
1 2 3

I keep forgetting to allow for NAs and I was bitten *again* this
morning... ideally I'd like to be able to set a default in my profile
so that table(t1) will actually do table(t1, exclude=NULL) or
table(t1, useNA='ifany')

I could say something like..

 tab1 - function(t, ...) { table(t, ..., useNA='ifany') }
 tab1(t1)

t
   123 NA
   1234

but this names it as 't' instead of 't1' which is ugly?

Any other suggestions please?

Thanks in advance,
Sean O'Riordain
Dublin
Ireland

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[R] Strange behaviour of as.integer()

2010-01-07 Thread Ulrich Keller

I have encountered a strange behaviour of as.integer() which does not
seem correct to me. Sorry if this is just an indication of me not
understanding floating point arithmetic.

 .57 * 100
[1] 57
 .29 * 100
[1] 29

So far, so good. But:

 as.integer(.57 * 100)
[1] 56
 as.integer(.29 * 100)
[1] 28

Then again:

 all.equal(.57 * 100, as.integer(57))
[1] TRUE
 all.equal(.29 * 100, as.integer(29))
[1] TRUE

This behaviour is the same in R 2.10.1 (Ubuntu and Windows) and 2.9.2
(Windows),
all 32 bit versions. Is this really intended?

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[R] Quantreg - 'could not find functionrq'

2010-01-07 Thread Gough Lauren

Hi all,

 

I'm having some troubles with the Quantreg package.  I am using R
version 2.10.0, and have downloaded the most recent version of Quantreg
(4.44) and SparseM (0.83 - required package).  However, when I try to
run an analysis (e.g. fit1-rq(y~x, tau=0.5)) I get an error message
saying that the function rq could not be found.  I get the same
message when I try to search for any of the other functions that should
be in the package (e.g. help(anova.rq)).

 

I used this package last year and still have the old versions of both
quantreg and SparseM saved on my machine.  When I load these older
packages and attempt an analysis (which, incidentally, worked fine last
February) I get the same error messages as I do with the new versions.  

 

The only think I have changed since last February is the version of R I
am using - is there any reason why quantreg wouldn't work in version
2.10.0?  I'm not very experienced with R so I'm struggling to work out
what may be going wrong - does anyone have any suggestions!?

 

Many thanks

 

Lauren

 

--___

 

Lauren Gough - Postgraduate Research Student  
University of Nottingham, School of Geography,  Nottingham,  NG7 2RD  

Tel: +44 (0)115 8467052
Email: lgx...@nottingham.ac.uk mailto:lgx...@nottingham.ac.uk 

P Consider the environment. Please don't print this e-mail unless you
really need to. 

 

This message has been checked for viruses but the contents of an attachment
may still contain software viruses which could damage your computer system:
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Re: [R] xyplot: adjusting the scale (min, max tick)

2010-01-07 Thread Peter Ehlers



Jay wrote:

Perfect, that piece of code did exactly what I wanted. However, I stumpled
upon a new problem, now my data is plotted on a totally wrong scale. The
y-values are all between 160k and 500k, BUT now with that option I find that
the plots are between 0 and 50 (?!?). What did I do wrong?

This plots the data OK, even thoug it should be between  160k and 500k on
the y-scale:

xyplot(data1[,2]+data1[,3]~data1[,1], data = data1,
type = l,
xlab = x,
ylab = y,
auto.key = list(space=top, lines = T, points = F, text=c(text1,
text2)),
par.settings = simpleTheme(lty = c(1,2)),
scales=list(
  x=list(alternating=FALSE,tick.number = 11),
  y=list(limits=c(0,50))
) 
)   


If I remove the  y=list(limits=c(0,50)) the dat is plotted as it should.


You probably want something like

  y = list(at = seq(100, 200, 25), limits = c(100, 200))

Try this:
x - 1:20
y1 - rnorm(20)*1e3
y2 - rnorm(20)*1e3
xyplot(y1 + y2 ~ x, type='l',
  scales = list(y = list(
 at = seq(-300,400,100),
 limits = c(-500,500)))
)

# or, you could use the ylim argument instead of 'limits=':
xyplot(y1 + y2 ~ x, type='l', ylim = c(-500, 500),
  scales = list(y = list(
 at = seq(-300,400,100)))
)

 -Peter Ehlers




Peter Ehlers wrote:

Have a look at the 'scales' argument. For example:

# default plot
xyplot(Sepal.Length ~ Petal.Length | Species, data = iris)

# modified plot
xyplot(Sepal.Length ~ Petal.Length | Species, data = iris,
 scales=list(y=list(at=c(-5,0,5,10), limits=c(-5,10

  -Peter Ehlers

Jay wrote:

Hi,

I'm terribly sorry but it seems it cannot figure this one out by
myself so, please, if somebody could help I would be very grateful.
So, when I plot with xyplot() I get an y-axis that is very ugly...
starting from a random number and having so many ticks that it becomes
unreadable.

How do I tell xyplot how to draw the axis? E.g., start from 100, end
at 200 with 25 units between ticks/labels?
Can somebody give me an example?

Thanks!

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--
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University of Calgary
403.202.3921

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--
Peter Ehlers
University of Calgary
403.202.3921

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[R] Problems with library(gWidgetsRGtk2) and R2.10.1

2010-01-07 Thread Edouard Chatignoux

 
Hi all,

I've been trying to load the gWidgetsRGtk2 package whith R version 2.10.1 
running under Windows XP, but I get the following error message (in french):

 library(gWidgetsRGtk2)
Error in .Call(name, ..., PACKAGE = PACKAGE) : 
  le nom C de symbole S_gtk_icon_factory_new est introuvable dans la DLL pour 
le package RGtk2
Error : .onAttach a échoué dans 'attachNamespace'
Erreur : le chargement du package / espace de noms a échoué pour 'gWidgetsRGtk2'

which didn't appeared with previous R versions (I tried it ok with R version 
8.1).
Any idea?

Thanks in advance,

Regards


Edouard Chatignoux
Observatoire Régional de Santé d'Ile-de-France
21-23 Rue Miollis - 75732 PARIS CEDEX 15 
Tél. : 01 44 42 64 81 Fax. : 01 44 42 64 71

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Re: [R] Quantreg - 'could not find functionrq'

Are you sure you called 
library(Quantreg) 
before calling any function?
M.

 -Original Message-
 From: r-help-boun...@r-project.org 
 [mailto:r-help-boun...@r-project.org] On Behalf Of Gough Lauren
 Sent: Donnerstag, 7. Januar 2010 13:44
 To: r-help@r-project.org
 Subject: [R] Quantreg - 'could not find functionrq'

 Hi all,

 I'm having some troubles with the Quantreg package.  I am 
 using R version 2.10.0, and have downloaded the most recent 
 version of Quantreg
 (4.44) and SparseM (0.83 - required package).  However, when 
 I try to run an analysis (e.g. fit1-rq(y~x, tau=0.5)) I get 
 an error message saying that the function rq could not be 
 found.  I get the same message when I try to search for any 
 of the other functions that should be in the package (e.g. 
 help(anova.rq)).

 I used this package last year and still have the old versions 
 of both quantreg and SparseM saved on my machine.  When I 
 load these older packages and attempt an analysis (which, 
 incidentally, worked fine last
 February) I get the same error messages as I do with the new 
 versions.  

 The only think I have changed since last February is the 
 version of R I am using - is there any reason why quantreg 
 wouldn't work in version 2.10.0?  I'm not very experienced 
 with R so I'm struggling to work out what may be going wrong 
 - does anyone have any suggestions!?

 Many thanks

 Lauren

 --___

 Lauren Gough - Postgraduate Research Student University of 
 Nottingham, School of Geography,  Nottingham,  NG7 2RD  

 Tel: +44 (0)115 8467052
 Email: lgx...@nottingham.ac.uk mailto:lgx...@nottingham.ac.uk 

 P Consider the environment. Please don't print this e-mail 
 unless you really need to. 

 This message has been checked for viruses but the contents of 
 an attachment may still contain software viruses which could 
 damage your computer system:
 you are advised to perform your own checks. Email 
 communications with the University of Nottingham may be 
 monitored as permitted by UK legislation.
   [[alternative HTML version deleted]]

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

Re: [R] Strange behaviour of as.integer()


On 07/01/2010 7:31 AM, Ulrich Keller wrote:

I have encountered a strange behaviour of as.integer() which does not
seem correct to me. Sorry if this is just an indication of me not
understanding floating point arithmetic.


.57 * 100

[1] 57

.29 * 100

[1] 29

So far, so good. But:


as.integer(.57 * 100)

[1] 56

as.integer(.29 * 100)

[1] 28

Then again:


all.equal(.57 * 100, as.integer(57))

[1] TRUE

all.equal(.29 * 100, as.integer(29))

[1] TRUE

This behaviour is the same in R 2.10.1 (Ubuntu and Windows) and 2.9.2
(Windows),
all 32 bit versions. Is this really intended?


Yes, as the man page states, non-integer values are truncated towards 
zero.  Normal printing rounds them.  So .57*100, which is slightly less 
than 57, is rounded to 57 for printing, but is truncated to 56 by 
as.integer.


 .57*100  57
[1] TRUE

Duncan Murdoch

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Re: [R] Strange behaviour of as.integer()



On Jan 7, 2010, at 7:31 AM, Ulrich Keller wrote:


I have encountered a strange behaviour of as.integer() which does not
seem correct to me. Sorry if this is just an indication of me not
understanding floating point arithmetic.


.57 * 100

[1] 57

.29 * 100

[1] 29

So far, so good. But:


as.integer(.57 * 100)

[1] 56

as.integer(.29 * 100)

[1] 28



From help page for as.integer:
Non-integral numeric values are truncated towards zero (i.e.,  
as.integer(x) equals trunc(x) there), 



Then again:


all.equal(.57 * 100, as.integer(57))

[1] TRUE

all.equal(.29 * 100, as.integer(29))

[1] TRUE

This behaviour is the same in R 2.10.1 (Ubuntu and Windows) and 2.9.2
(Windows),
all 32 bit versions. Is this really intended?



Yes, it works as documented.

--

David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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[R] Odp: Strange behaviour of as.integer()

2010-01-07 Thread Petr PIKAL

Hi

Maybe FAQ 7.31 strikes again.

 .57 * 100==as.integer(57)
[1] FALSE


Regards
Petr


r-help-boun...@r-project.org napsal dne 07.01.2010 13:31:42:

 I have encountered a strange behaviour of as.integer() which does not
 seem correct to me. Sorry if this is just an indication of me not
 understanding floating point arithmetic.
 
  .57 * 100
 [1] 57
  .29 * 100
 [1] 29
 
 So far, so good. But:
 
  as.integer(.57 * 100)
 [1] 56
  as.integer(.29 * 100)
 [1] 28
 
 Then again:
 
  all.equal(.57 * 100, as.integer(57))
 [1] TRUE
  all.equal(.29 * 100, as.integer(29))
 [1] TRUE
 
 This behaviour is the same in R 2.10.1 (Ubuntu and Windows) and 2.9.2
 (Windows),
 all 32 bit versions. Is this really intended?
 
 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide 
http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.

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Re: [R] Quantreg - 'could not find functionrq'

2010-01-07 Thread Meyners, Michael, LAUSANNE, AppliedMathematics



On Jan 7, 2010, at 8:07 AM, Meyners, Michael, LAUSANNE,  
AppliedMathematics wrote:



Are you sure you called
library(Quantreg)
before calling any function?
M.


Are you both using a package with the exact spelling Quantreg? I  
would have expected it to be :


library(quantreg)

--
David.



-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Gough Lauren
Sent: Donnerstag, 7. Januar 2010 13:44
To: r-help@r-project.org
Subject: [R] Quantreg - 'could not find functionrq'

Hi all,



I'm having some troubles with the Quantreg package.  I am
using R version 2.10.0, and have downloaded the most recent
version of Quantreg
(4.44) and SparseM (0.83 - required package).  However, when
I try to run an analysis (e.g. fit1-rq(y~x, tau=0.5)) I get
an error message saying that the function rq could not be
found.  I get the same message when I try to search for any
of the other functions that should be in the package (e.g.
help(anova.rq)).



I used this package last year and still have the old versions
of both quantreg and SparseM saved on my machine.  When I
load these older packages and attempt an analysis (which,
incidentally, worked fine last
February) I get the same error messages as I do with the new
versions.



The only think I have changed since last February is the
version of R I am using - is there any reason why quantreg
wouldn't work in version 2.10.0?  I'm not very experienced
with R so I'm struggling to work out what may be going wrong
- does anyone have any suggestions!?



Many thanks



Lauren



--___



Lauren Gough - Postgraduate Research Student University of
Nottingham, School of Geography,  Nottingham,  NG7 2RD

Tel: +44 (0)115 8467052
Email: lgx...@nottingham.ac.uk mailto:lgx...@nottingham.ac.uk

P Consider the environment. Please don't print this e-mail
unless you really need to.



This message has been checked for viruses but the contents of
an attachment may still contain software viruses which could
damage your computer system:
you are advised to perform your own checks. Email
communications with the University of Nottingham may be
monitored as permitted by UK legislation.
[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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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.


David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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Re: [R] Quantreg - 'could not find functionrq'

Frankly, I have never even heard about this package before and have no
clue what it does, but the error messages nevertheless suggested a
missing call of library. And I didn't bother to check the spelling, my
fault. So I guess you are right... I still didn't check :-) So to the
OP: try 
library(asdf)
with asdf replaced by the correct package name, and mind the spelling!

Michael

 -Original Message-
 From: David Winsemius [mailto:dwinsem...@comcast.net] 
 Sent: Donnerstag, 7. Januar 2010 14:22
 To: Meyners,Michael,LAUSANNE,AppliedMathematics
 Cc: Gough Lauren; r-help@r-project.org
 Subject: Re: [R] Quantreg - 'could not find functionrq'
 
 
 On Jan 7, 2010, at 8:07 AM, Meyners, Michael, LAUSANNE, 
 AppliedMathematics wrote:
 
  Are you sure you called
  library(Quantreg)
  before calling any function?
  M.
 
 Are you both using a package with the exact spelling 
 Quantreg? I would have expected it to be :
 
 library(quantreg)
 
 --
 David.
 
  -Original Message-
  From: r-help-boun...@r-project.org
  [mailto:r-help-boun...@r-project.org] On Behalf Of Gough Lauren
  Sent: Donnerstag, 7. Januar 2010 13:44
  To: r-help@r-project.org
  Subject: [R] Quantreg - 'could not find functionrq'
 
  Hi all,
 
 
 
  I'm having some troubles with the Quantreg package.  I am using R 
  version 2.10.0, and have downloaded the most recent version of 
  Quantreg
  (4.44) and SparseM (0.83 - required package).  However, 
 when I try to 
  run an analysis (e.g. fit1-rq(y~x, tau=0.5)) I get an 
 error message 
  saying that the function rq could not be found.  I get the same 
  message when I try to search for any of the other functions that 
  should be in the package (e.g.
  help(anova.rq)).
 
 
 
  I used this package last year and still have the old 
 versions of both 
  quantreg and SparseM saved on my machine.  When I load these older 
  packages and attempt an analysis (which, incidentally, worked fine 
  last
  February) I get the same error messages as I do with the new 
  versions.
 
 
 
  The only think I have changed since last February is the 
 version of R 
  I am using - is there any reason why quantreg wouldn't work in 
  version 2.10.0?  I'm not very experienced with R so I'm 
 struggling to 
  work out what may be going wrong
  - does anyone have any suggestions!?
 
 
 
  Many thanks
 
 
 
  Lauren
 
 
 
  --___
 
 
 
  Lauren Gough - Postgraduate Research Student University of 
  Nottingham, School of Geography,  Nottingham,  NG7 2RD
 
  Tel: +44 (0)115 8467052
  Email: lgx...@nottingham.ac.uk mailto:lgx...@nottingham.ac.uk
 
  P Consider the environment. Please don't print this e-mail 
 unless you 
  really need to.
 
 
 
  This message has been checked for viruses but the contents of an 
  attachment may still contain software viruses which could 
 damage your 
  computer system:
  you are advised to perform your own checks. Email 
 communications with 
  the University of Nottingham may be monitored as permitted by UK 
  legislation.
 [[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.
 
 
  __
  R-help@r-project.org mailing list
  https://stat.ethz.ch/mailman/listinfo/r-help
  PLEASE do read the posting guide 
  http://www.R-project.org/posting-guide.html
  and provide commented, minimal, self-contained, reproducible code.
 
 David Winsemius, MD
 Heritage Laboratories
 West Hartford, CT
 
 

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[R] vectors into a matrix

2010-01-07 Thread varenda44

Hello all,


Firstly, thanks a lot for all your efforts,
the cbind function was very useful.

I tried all you told me, but I couldn't make it work in the way I wanted.
I mixed two problems I had, a common mistake.
Sorry if I didn't explain myself good enough.

Here, I post a solution for my problem. 
I wanted to avoid the while loop but I've finally used it.
Hopefully it is helpfull for someone else.


CODE:
---


# This could be my data:

VD1 - c(12, 34, 45, 7, 67, 45)
VD2 - c(23, 12, 45, 67, 89, 90)
VD3 - c(14, 11, 10, 19, 20, 27)
VD4 - c(16, 22, 23, 29, 27, 28)


# and this is my objective:
# (in this case it is just for 4 vectors)

AIM - matrix(c(VD1, VD2, VD3, VD4), nrow=4, byrow=TRUE)
print(AIM)

# but I want to use any number of vectors
# VDx when x goes from 1 to n

n - 4  # for this case.

# A solution:
# build an empty matrix with the desired number of rows (vectors)
# then with a while loop fill each row with each vector.

Final.matrix - matrix(, nrow=n, ncol=6, byrow=TRUE)
print(Final.matrix)

y - 1
while (y = n)
{
  c - eval(parse(text=(paste(VD, sep=, y
  Final.matrix[y,] - c
  y - y + 1
}

print(Final.matrix)

# If I set n as 12 I will get the example I explained at first 
# then, by using cbind() and 1:n I add the values of the first column
# as many of you suggested to me

---

If someone comes up with a way to do this avoiding the loop, I'd be very 
interested to get to know the solution.


Kind regards,

Vilen

Forestry Engineer

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[R] How to report or correct translations typos?

2010-01-07 Thread Kenneth Roy Cabrera Torres

Hi R users and developers:

Thanks to Mr Pablo Emilio Verde for his constribution
to the spanish translation for R messages he makes a very
good job.

I find a tiny typo on the translation,
in particular on the es.po file line 7312 it says:
pueto
it should be:
puerto

How can anybody might correct a typo or which is the
best way to correct it on a future patch?

Thank you for your help.

Kenneth

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Re: [R] table() and setting useNA to be there by default?

2010-01-07 Thread Peter Ehlers



Sean O'Riordain wrote:

Good morning,

Is there a way to get table() to default to including NAs  - as in...
table(..., useNA='ifany') or  table(..., useNA='always') or table(...,
exclude=NULL)  ?

I can't see a way under table() or options() or searching the archives
(probably using the wrong keyword?).


t1 - c(1,2,3,3,3,2,NA,NA,NA,NA)
table(t1)

t1
1 2 3
1 2 3

I keep forgetting to allow for NAs and I was bitten *again* this
morning... ideally I'd like to be able to set a default in my profile
so that table(t1) will actually do table(t1, exclude=NULL) or
table(t1, useNA='ifany')

I could say something like..


tab1 - function(t, ...) { table(t, ..., useNA='ifany') }
tab1(t1)


t
   123 NA
   1234

but this names it as 't' instead of 't1' which is ugly?


How about

tab1 - function(...) table(..., useNA='ifany')

 -Peter Ehlers



Any other suggestions please?

Thanks in advance,
Sean O'Riordain
Dublin
Ireland

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--
Peter Ehlers
University of Calgary
403.202.3921

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Re: [R] Building static HTML help pages in R 2.10.x on Windows

2010-01-07 Thread Michael Friendly


Michal Kulich wrote:

On 7.1.2010 9:49, Dieter Menne wrote:

I am sorry to say that the new dynamic help is a HUGE nuisance to me. Had to 
revert back to R 2.9 because of that :-(.

Michal


I too have reverted to 2.9.2 on Win XP because I find html help to be 
far less convenient than the compiled CHM help I had before. CHM help is
so much easier because the Contents, Index and Search panels make it 
easy to *see* all the items defined for a package, and I get a separate 
help window for each package.

I very much appreciate the efforts of the R-core team to move R forward,
but I think the change in help is a step back.


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

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Re: [R] vectors into a matrix

2010-01-07 Thread Dimitris Rizopoulos


you could try something like this:

VD1 - c(12, 34, 45, 7, 67, 45)
VD2 - c(23, 12, 45, 67, 89, 90)
VD3 - c(14, 11, 10, 19, 20, 27)
VD4 - c(16, 22, 23, 29, 27, 28)

n - 4
do.call(rbind, lapply(paste(VD, 1:n, sep = ), get))


I hope it helps.

Best,
Dimitris


varend...@gmail.com wrote:

Hello all,


Firstly, thanks a lot for all your efforts,
the cbind function was very useful.

I tried all you told me, but I couldn't make it work in the way I wanted.
I mixed two problems I had, a common mistake.
Sorry if I didn't explain myself good enough.

Here, I post a solution for my problem. 
I wanted to avoid the while loop but I've finally used it.

Hopefully it is helpfull for someone else.


CODE:
---


# This could be my data:

VD1 - c(12, 34, 45, 7, 67, 45)
VD2 - c(23, 12, 45, 67, 89, 90)
VD3 - c(14, 11, 10, 19, 20, 27)
VD4 - c(16, 22, 23, 29, 27, 28)


# and this is my objective:
# (in this case it is just for 4 vectors)

AIM - matrix(c(VD1, VD2, VD3, VD4), nrow=4, byrow=TRUE)
print(AIM)

# but I want to use any number of vectors
# VDx when x goes from 1 to n

n - 4  # for this case.

# A solution:
# build an empty matrix with the desired number of rows (vectors)
# then with a while loop fill each row with each vector.

Final.matrix - matrix(, nrow=n, ncol=6, byrow=TRUE)
print(Final.matrix)

y - 1
while (y = n)
{
  c - eval(parse(text=(paste(VD, sep=, y
  Final.matrix[y,] - c
  y - y + 1
}

print(Final.matrix)

# If I set n as 12 I will get the example I explained at first 
# then, by using cbind() and 1:n I add the values of the first column

# as many of you suggested to me

---

If someone comes up with a way to do this avoiding the loop, I'd be very 
interested to get to know the solution.



Kind regards,

Vilen

Forestry Engineer

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Re: [R] Naming functions for the purpose of profiling

2010-01-07 Thread Magnus Torfason

I wanted to send an update on my exploits in trying to get rid of 
Anonymous entries in my Rprof.out file (see my prior mail below). 
Basically, I have now found a way to dynamically name a function, and 
even if it is not the cleanest way, I think it will help me in some of 
my profiling needs, and may help others as well. I'm including some 
demonstration code that addresses the issues I wanted to solve:


##
# Demonstration of function names in profiling output
a.func - function()  for (i in 1:100) b = 100^100

# Here, the function name ends up in Rprof.out
# (This is the straight-forward example)
Rprof(Rprof-simple-a.out)
a.func()
Rprof(NULL)

# This doesn't work
# (Function shows up as 'Anonymous' in Rprof.out)
b = list()
b$func = a.func
Rprof(Rprof-simple-b.out)
b$func()
Rprof(NULL)

# By assigning to a variable, the anonymous function gets an
# explicit name (Function shows up as 'c.func' in Rprof.out)
c.func = b$func
Rprof(Rprof-simple-c.out)
c.func()
Rprof(NULL)

# This example is a bit contrived, but works nevertheless
# The anonymous function is assigned to an explicit variable,
# but the variable name can by generated dynamically
# (Function shows up as 'd.func' in Rprof.out, and the stack
# also includes calls to 'eval' as expected)
d = list()
d$func = b$func
Rprof(Rprof-simple-d.out)
desired.func.name = d.func
eval(parse(text=paste(
desired.func.name, = d$func; ,desired.func.name,(),
sep=)))
Rprof(NULL)
##

And thanks to Jim Holtman who contacted me off-line and gave me some 
helpful advice on profiling in general.


Best,
Magnus


On 1/5/2010 2:58 PM, Magnus Torfason wrote:

Hi all,

I have some long-running code that I'm trying to profile. I am seeing a
lot of time spent inside the Anonymous function. Of course, this can
in fact be any of several functions, but I am unable to see how I could
use the information from Rprof.out to discern which function is taking
the most time. An example line from my Rprof.out is:

rbernoulli Anonymous runOneRound FUN lapply sfLapply doTryCatch
tryCatchOne tryCatchList tryCatch try eval.with.vis eval.with.vis source

In my case, the Anonymous functions seem to be any of several
work-horse functions, that are part of a list, and different cases are
dispatched to different functions. I could of course get them all out of
the list and rewrite the dispatch code, but that does not seem like a
neat way do address this. So I am wondering if there is any way to
explicitly set the name of a function in a way that leads to it being
picked up by the profiler?

The same problem seems to apply to Anonymous functions that are
generated on the fly in an apply call or elsewhere.

Of course, having source files and line numbers included in the
profiling output would solve this issue, but it seems to me that R
probably does not have any awareness of where a function was written
down (and of course, even the text of a function can be constructed
dynamically within a program). So I guess that is not a viable approach.

Thanks in advance for any help on this, and any pointers on the best
references for advanced profiling issues would be appreciated as well (I
know of summaryRprof of course, but it can be difficult to get the full
picture from the summaryRprof output if the calling structure is
complicated).

Best,
Magnus


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Re: [R] How to report or correct translations typos?


On 07/01/2010 9:04 AM, Kenneth Roy Cabrera Torres wrote:

Hi R users and developers:

Thanks to Mr Pablo Emilio Verde for his constribution
to the spanish translation for R messages he makes a very
good job.

I find a tiny typo on the translation,
in particular on the es.po file line 7312 it says:
pueto
it should be:
puerto

How can anybody might correct a typo or which is the
best way to correct it on a future patch?
  


You can see the translation teams listed on 
http://developer.r-project.org/TranslationTeams.html.  You send your 
corrections to them (as you have already done; this message is just to 
confirm you've done what you should do).


Duncan Murdoch

Thank you for your help.

Kenneth

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[R] Extract p-value from linear model

2010-01-07 Thread Trafim Vanishek

Dear all,

I have the following question.
Is it possible in R to call for the p-value directly in a model like this

a - c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
b - c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)

summary(lm(a~(b+0)))

or even in this
a - c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
b - c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)

summary(lm(a~b))

to call the p-values directly for every estimated parameter.
Thanks a lot for the help!

[[alternative HTML version deleted]]

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Re: [R] How to report or correct translations typos? [SOLVED]

2010-01-07 Thread Kenneth Roy Cabrera Torres

Thank you Dr. Murdoch.

El jue, 07-01-2010 a las 09:12 -0500, Duncan Murdoch escribió:
 On 07/01/2010 9:04 AM, Kenneth Roy Cabrera Torres wrote:
  Hi R users and developers:
 
  Thanks to Mr Pablo Emilio Verde for his constribution
  to the spanish translation for R messages he makes a very
  good job.
 
  I find a tiny typo on the translation,
  in particular on the es.po file line 7312 it says:
  pueto
  it should be:
  puerto
 
  How can anybody might correct a typo or which is the
  best way to correct it on a future patch?

 
 You can see the translation teams listed on 
 http://developer.r-project.org/TranslationTeams.html.  You send your 
 corrections to them (as you have already done; this message is just to 
 confirm you've done what you should do).
 
 Duncan Murdoch
  Thank you for your help.
 
  Kenneth
 
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Re: [R] vectors into a matrix

2010-01-07 Thread Marc Schwartz


On Jan 7, 2010, at 8:03 AM, varend...@gmail.com wrote:


Hello all,


Firstly, thanks a lot for all your efforts,
the cbind function was very useful.

I tried all you told me, but I couldn't make it work in the way I  
wanted.

I mixed two problems I had, a common mistake.
Sorry if I didn't explain myself good enough.

Here, I post a solution for my problem.
I wanted to avoid the while loop but I've finally used it.
Hopefully it is helpfull for someone else.


CODE:
---


# This could be my data:

VD1 - c(12, 34, 45, 7, 67, 45)
VD2 - c(23, 12, 45, 67, 89, 90)
VD3 - c(14, 11, 10, 19, 20, 27)
VD4 - c(16, 22, 23, 29, 27, 28)


# and this is my objective:
# (in this case it is just for 4 vectors)

AIM - matrix(c(VD1, VD2, VD3, VD4), nrow=4, byrow=TRUE)
print(AIM)

# but I want to use any number of vectors
# VDx when x goes from 1 to n

n - 4  # for this case.

# A solution:
# build an empty matrix with the desired number of rows (vectors)
# then with a while loop fill each row with each vector.

Final.matrix - matrix(, nrow=n, ncol=6, byrow=TRUE)
print(Final.matrix)

y - 1
while (y = n)
{
 c - eval(parse(text=(paste(VD, sep=, y
 Final.matrix[y,] - c
 y - y + 1
}

print(Final.matrix)

# If I set n as 12 I will get the example I explained at first
# then, by using cbind() and 1:n I add the values of the first  
column

# as many of you suggested to me

---

If someone comes up with a way to do this avoiding the loop, I'd be  
very

interested to get to know the solution.


Kind regards,

Vilen

Forestry Engineer



library(fortunes)

 fortune(parse)

If the answer is parse() you should usually rethink the question.
   -- Thomas Lumley
  R-help (February 2005)



An easier way is to use get() along with ls(), using a regex pattern  
in the latter. That will get you the objects which you can then  
manipulate as desired.



# see ?regex
 ls(pattern = ^VD[0-9]+$)
[1] VD1 VD2 VD3 VD4


# This presumes that each vector is the same length, such that using  
sapply() will return a matrix rather than a list.

 t(sapply(ls(pattern = ^VD[0-9]+$), get))
[,1] [,2] [,3] [,4] [,5] [,6]
VD1   12   34   457   67   45
VD2   23   12   45   67   89   90
VD3   14   11   10   19   20   27
VD4   16   22   23   29   27   28

HTH,

Marc Schwartz

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Re: [R] Building static HTML help pages in R 2.10.x on Windows


On 07/01/2010 9:05 AM, Michael Friendly wrote:

Michal Kulich wrote:
 On 7.1.2010 9:49, Dieter Menne wrote:
 
 I am sorry to say that the new dynamic help is a HUGE nuisance to me. Had to revert back to R 2.9 because of that :-(.
 
 Michal


I too have reverted to 2.9.2 on Win XP because I find html help to be 
far less convenient than the compiled CHM help I had before. CHM help is
so much easier because the Contents, Index and Search panels make it 
easy to *see* all the items defined for a package, and I get a separate 
help window for each package.

I very much appreciate the efforts of the R-core team to move R forward,
but I think the change in help is a step back.
  


You can see the items for the package on the index page for the package, 
which is linked from every page.


You can put together a package that displays the help in your favourite 
format, if you don't like the default format.  There's nothing that we 
used in CHM help that couldn't be duplicated in Javascript, without the 
security holes.


I see it as more important that R core enables others to do what they 
want, rather than to maintain ancient designs.


Duncan Murdoch

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[R] diag, diag- and [ , [-

2010-01-07 Thread bergarog

Dear all
I have the following problem.

M - matrix(0,3,3) # dimension of M is dinamic and this can lead to the  
next subscript

diag(M[1,1]) - rep(100,1)
#Error in `diag-`(`*tmp*`, value = 100) :
# only matrix diagonals can be replaced

diag(M[1,1,drop=F]) - rep(100,1)
#Error in diag(M[1, 1, drop = F]) - rep(100, 1) :
# incorrect number of subscripts

diag(M[2:3,1:2]) - rep(100,2)
# works fine

Is there a way to usw diag as replacement function when the input matrix is  
subscript to a one by one matrix. I don't want extra if(dim==1)... etc.

Thanks a lot in advance.
Best regards,
Roger

[[alternative HTML version deleted]]

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Re: [R] Extract p-value from linear model

2010-01-07 Thread Peter Ehlers



 coef(summary(lm(..stuff..)))[,4]
or
 coef(summary(lm(..stuff..)))[,4,drop=FALSE]

 -Peter Ehlers

Trafim Vanishek wrote:

Dear all,

I have the following question.
Is it possible in R to call for the p-value directly in a model like this

a - c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
b - c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)

summary(lm(a~(b+0)))

or even in this
a - c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
b - c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)

summary(lm(a~b))

to call the p-values directly for every estimated parameter.
Thanks a lot for the help!

[[alternative HTML version deleted]]

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--
Peter Ehlers
University of Calgary
403.202.3921

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Re: [R] Extract p-value from linear model

2010-01-07 Thread Ted Harding

On 07-Jan-10 14:15:07, Trafim Vanishek wrote:
 Dear all,
 
 I have the following question.
 Is it possible in R to call for the p-value directly in a model like
 this
 
 a - c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
 b - c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)
 
 summary(lm(a~(b+0)))

  summary(lm(a~(b+0)))
  # [...]
  # Coefficients:
  #   Estimate Std. Error t value Pr(|t|)
  # b  0.907770.07134   12.72 4.67e-07 ***
  # ---

  summary(lm(a~(b+0)))$coef[,4]
  # [1] 4.665795e-07

 or even in this
 a - c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
 b - c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)
 
 summary(lm(a~b))
 
 to call the p-values directly for every estimated parameter.
 Thanks a lot for the help!

  summary(lm(a~b))
  # [...]
  # Coefficients:
  # Estimate Std. Error t value Pr(|t|)   
  # (Intercept)   7.7957 2.1661   3.599  0.00699 **
  # b-0.6230 0.4279  -1.456  0.18351   
  # ---

  summary(lm(a~b))$coef[,4]
  # (Intercept)   b 
  # 0.006992306 0.183511560 

Ted.


E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk
Fax-to-email: +44 (0)870 094 0861
Date: 07-Jan-10   Time: 14:39:46
-- XFMail --

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Re: [R] Building static HTML help pages in R 2.10.x on Windows

On 7.1.2010 12:18, Duncan Murdoch wrote:
 You don't need Rgui, you could run Rterm, which would have a smaller
 footprint. It's not very hard to start it and minimize it, but if you
 want it running invisibly, you'll need to figure out how to hide the icon.

This works. Not entirely invisible but not a big deal about that.
The R code run within Rterm is

options(help_type=html,help.ports=6800)
help.start()
library(audio)
wait(-1)

[couldn't find another way to hang R indefinitely in batch mode]

 
 A disadvantage of doing this is that you won't see help relevant to your
 current session, you'll see help relevant to the background task.  In
 2.10.x there aren't many differences, but you'll find it more limiting
 in 2.11.x and later.

Not a problem if one is not switching between different versions of R. The 
current version is on the path and the path will get updated (manually) after a 
new version is installed. Thus, the relevant help will be always displayed.

Thanks, this is a kind of solution. Now I can use bookmarks to HTML help for 
the favorite libraries when working in ESS - the impossibility to set those and 
the need to start Rgui was the big nuisance. 

I am sure the new help system will get gradually improved in the future.

Best,

Michal

-- 

Michal Kulich, PhD
Dept. of Probability and Statistics
Charles University
Sokolovska 83
186 75 Praha 8
Czech Republic
Email: kul...@karlin.mff.cuni.cz

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Re: [R] Building static HTML help pages in R 2.10.x on Windows

On Thu, Jan 7, 2010 at 9:20 AM, Duncan Murdoch murd...@stats.uwo.ca wrote:
 On 07/01/2010 9:05 AM, Michael Friendly wrote:

 Michal Kulich wrote:
  On 7.1.2010 9:49, Dieter Menne wrote:
   I am sorry to say that the new dynamic help is a HUGE nuisance to me.
   Had to revert back to R 2.9 because of that :-(.
   Michal

 I too have reverted to 2.9.2 on Win XP because I find html help to be far
 less convenient than the compiled CHM help I had before. CHM help is
 so much easier because the Contents, Index and Search panels make it easy
 to *see* all the items defined for a package, and I get a separate help
 window for each package.
 I very much appreciate the efforts of the R-core team to move R forward,
 but I think the change in help is a step back.


 You can see the items for the package on the index page for the package,
 which is linked from every page.

 You can put together a package that displays the help in your favourite
 format, if you don't like the default format.  There's nothing that we used
 in CHM help that couldn't be duplicated in Javascript, without the security
 holes.

 I see it as more important that R core enables others to do what they want,
 rather than to maintain ancient designs.

Perhaps the link to the Index could be placed at both the top and
bottom rather than just at the bottom since its a nuisance to have to
scroll down and its less noticeable at the bottom as its typically off
the screen.

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Re: [R] diag, diag- and [ , [-


On 07/01/2010 9:31 AM, berga...@gmail.com wrote:

Dear all
I have the following problem.

M - matrix(0,3,3) # dimension of M is dinamic and this can lead to the  
next subscript


diag(M[1,1]) - rep(100,1)
#Error in `diag-`(`*tmp*`, value = 100) :
# only matrix diagonals can be replaced

diag(M[1,1,drop=F]) - rep(100,1)
#Error in diag(M[1, 1, drop = F]) - rep(100, 1) :
# incorrect number of subscripts

diag(M[2:3,1:2]) - rep(100,2)
# works fine

Is there a way to usw diag as replacement function when the input matrix is  
subscript to a one by one matrix. I don't want extra if(dim==1)... etc.
  


The problem isn't with diag, it's with [-.  When you include drop=F, 
it doesn't appear to handle properly the matrix indexing that diag() uses.


So a simpler example is just

M[1,1, drop=FALSE] - 1

which generates the same error you saw.  I'd call this a bug; I'll look 
into it.  ([- is done internally in some fairly ugly code, so this 
might take a while.)


As a workaround, I think this does what you want:

n - 1
submatrix - M[1:n,1:n,drop=FALSE]
diag(submatrix) - rep(100, n)
M[1:n,1:n] - submatrix

Duncan Murdoch


Thanks a lot in advance.
Best regards,
Roger

[[alternative HTML version deleted]]

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Re: [R] Building static HTML help pages in R 2.10.x on Windows

On 7.1.2010 15:52, Duncan Murdoch wrote:
 Not necessarily.  The current help system can display information about
 the current session, e.g. the result of ls(), as a simple example.  But
 if you use a single background session you won't get relevant information.
 
 Duncan Murdoch

Sorry, I must admit I don't get it.

-- 

Michal Kulich, PhD
Dept. of Probability and Statistics
Charles University
Sokolovska 83
186 75 Praha 8
Czech Republic
Email: kul...@karlin.mff.cuni.cz

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Re: [R] Building static HTML help pages in R 2.10.x on Windows

On 07/01/2010 9:47 AM, Michal Kulich wrote:

On 7.1.2010 12:18, Duncan Murdoch wrote:
You don't need Rgui, you could run Rterm, which would have a smaller
footprint. It's not very hard to start it and minimize it, but if you
want it running invisibly, you'll need to figure out how to hide the icon.

This works. Not entirely invisible but not a big deal about that.
The R code run within Rterm is

options(help_type=html,help.ports=6800)
help.start()
library(audio)
wait(-1)

[couldn't find another way to hang R indefinitely in batch mode]

A disadvantage of doing this is that you won't see help relevant to your

current session, you'll see help relevant to the background task. In
2.10.x there aren't many differences, but you'll find it more limiting
in 2.11.x and later.

Not a problem if one is not switching between different versions of R. The
current version is on the path and the path will get updated (manually) after a
new version is installed. Thus, the relevant help will be always displayed.

Not necessarily. The current help system can display information about
the current session, e.g. the result of ls(), as a simple example. But
if you use a single background session you won't get relevant information.

Duncan Murdoch
Thanks, this is a kind of solution. Now I can use bookmarks to HTML help for the favorite libraries when working in ESS - the impossibility to set those and the need to start Rgui was the big nuisance.

I am sure the new help system will get gradually improved in the future.

Best,

Michal

[R] kriging with geoR package

2010-01-07 Thread patrocle


Hi all,
I have to draw a map of microorganisms repartition in a sample. I use the
image function of geoR package to build the map but there are three
problems:

1) the legend is Horizontal (with or without vert.leg=TRUE)
2) I want to plot the position of organisms and level curves of density on
the map but I don't find the script to insert these data on the map.
3)the grey range are not really represented on the map: I don't have gradual
evolution but only patches

This is the script I use, can you help me on these three points???

image(KC,col=gray[0:5],xlim=c(-1,53),ylim=c(0,53),x.leg=c(51,53),y.leg=c(10,40),vert.leg=T,pch=Â°)

If necessary I can give further informations about my script.

I thank you all for your answers.

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Re: [R] Building static HTML help pages in R 2.10.x on Windows


On 07/01/2010 9:51 AM, Gabor Grothendieck wrote:

On Thu, Jan 7, 2010 at 9:20 AM, Duncan Murdoch murd...@stats.uwo.ca wrote:
 On 07/01/2010 9:05 AM, Michael Friendly wrote:

 Michal Kulich wrote:
  On 7.1.2010 9:49, Dieter Menne wrote:
   I am sorry to say that the new dynamic help is a HUGE nuisance to me.
   Had to revert back to R 2.9 because of that :-(.
   Michal

 I too have reverted to 2.9.2 on Win XP because I find html help to be far
 less convenient than the compiled CHM help I had before. CHM help is
 so much easier because the Contents, Index and Search panels make it easy
 to *see* all the items defined for a package, and I get a separate help
 window for each package.
 I very much appreciate the efforts of the R-core team to move R forward,
 but I think the change in help is a step back.


 You can see the items for the package on the index page for the package,
 which is linked from every page.

 You can put together a package that displays the help in your favourite
 format, if you don't like the default format.  There's nothing that we used
 in CHM help that couldn't be duplicated in Javascript, without the security
 holes.

 I see it as more important that R core enables others to do what they want,
 rather than to maintain ancient designs.

Perhaps the link to the Index could be placed at both the top and
bottom rather than just at the bottom since its a nuisance to have to
scroll down and its less noticeable at the bottom as its typically off
the screen.
Yes, I may do that at some point, to make the layout of the help pages 
more consistent.  Most higher level pages have a consistent header 
(more so in R-devel), but the individual topic pages don't.


What I'd really like is for someone who has good taste to redesign the 
look of the whole system.  I think one or two people are working on 
packages to do this, and I'd much rather spend time providing whatever 
low level support they need, rather than doing it myself.


Duncan Murdoch

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Re: [R] Strange behaviour of as.integer()

2010-01-07 Thread Magnus Torfason

There have been some really great responses to this question. I would 
like to make a minor contribution by throwing the 'gmp' package into the 
mix.


On 1/7/2010 8:12 AM, Duncan Murdoch wrote:

On 07/01/2010 7:31 AM, Ulrich Keller wrote:

as.integer(.57 * 100)

[1] 56


Yes, as the man page states, non-integer values are truncated towards
zero.

  .57*100  57
[1] TRUE


gmp provides the bigz and bigq classes which provide arbitrary precision 
integers and rationals, and would solve Ulrich's original

problem quite effectively:

 library(gmp)

 # bigq will not parse 0.57 but writing such a parser
 # would be a trivial extension.
 x = as.bigq(57)/100
 x
[1] 57/100

 # as.integer(x*100) does not seem to be overloaded correctly, so
 # we need to use as.numeric first, but the end result is 57
 as.integer(as.numeric(x*100))
[1] 57

 # And we conclude by making some comparisons, and finding the that
 # the results are what a fifth-grader would expect, rather than
 # what a CS grad would expect :-)
 x*10057
[1] FALSE
 x*100==57
[1] TRUE

Of course there is still the problem that:
 1+1 == sqrt(2)*sqrt(2)
[1] FALSE
and gmp will not solve this . I don't know if there is an R-package for 
arbitrary-precision reals floating around, but probably not.

However, Wolfram Alpha will return the correct answer:
http://tr.im/1plus1equals2


Best,
Magnus

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[R] building a neural network on a unbalanced data set on R

2010-01-07 Thread Enrico Giorgi


Hello everybody,

 

I work in a production plant as an operations analyst. I have been using R for 
two years, starting with my final dissertation project at college.

 

We have the following problem in our plant. At the end of the production 
process, each joint (that is what we produce) must pass a final electrical 
test. The result can be 0 or 1. We think that this may depend on some raw 
materials parameters, so at first we have built a logistic regression model in 
order to make some forecasts.

 

Now I would like to try with a neural network as well. Of course I would like 
to set the output response as logistic.

But the values fitted on the training set turn out to be all 1s. I think that 
this depends on the following matter. The training data set is made up of 14 0s 
and 54 1s: so it is quite unbalanced. The net by default classifies as 1 all 
observations whose probability of success is greater than 0.5. I think that it 
would be enough to raise the cut-off probability to 0.79, as it is the fraction 
of 1s over the entire data set (54/68). So, a joint should be classified as 1 
only if its probability is larger than 0.79.

 

The problem is that I cannot find out how to set this threshold using the R 
command nnet.

 

Do you have any ideas?

 

Thank you very much.

 

Kind regards.

 


Enrico Giorgi


  
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Re: [R] mean for subset

2010-01-07 Thread Jerry Floren


As a novice R user, I face a similar challenge. I am almost afraid to share
with this group how I solved it. About 65 labs in our proficiency program
submit data on individual Excel spreadsheets with triple replicates. There
always are a few labs that do not complete the full set of three replicates,
and I do not want their data included in my analysis.

First, I combine all the individual spreadsheets into one large Excel
spreadsheet. The replicates are in three columns: rep1, rep2, and rep3. I
sort on each individual rep column in Excel. Then I go to both the top and
the bottom of the list. 

For example, I sort on rep1 and go to the top of the list to delete any rows
where a value for rep1 was not recorded. Then I go to the bottom of the list
and delete any rows where rep1 is text instead of a number, for example,
0.001. I should say that the labs are instructed that they must complete
all three replicates, and they must not enter results as text. Next I repeat
the process for rep2 and rep3. 

I'll do a little more work in Excel on the large, combined table with all
the lab data. I calculate in Excel the mean, standard deviation, and
coefficient of variation for each of the three reps. Finally, I filter all
the data and delete duplicate rows. This is necessary as I sometimes
accidentally copy the same spreadsheet two times from a lab into my large
table. Finally, I save the cleaned up table in *.csv format that is easily
read into R. 

I know that R can do all of these things, but if you are just learning how
to use R it might be easier to do some initial work in Excel, or a similar
spreadsheet, before running your data through R.

I also use MS-Word's mail merge feature to generate my code. I'll get three
or four pages of code doing what I want for a single analytical test, for
example, calcium. Then I'll use the mail merge feature to generate hundreds
of pages of code with the other analytical tests (nitrogen, phosphorus,
potassium, etc.). I just copy and paste the large, merged Word document into
R. R cranks away for 30 minutes and I end up with several large tables (and
these get additional editing in Ecel) and hundreds of beautiful graphs that
would take weeks to create in Excel.

I was amazed that Word would work. I expected all of Word's special print
control codes would mess things up. I just recently received a new laptop
computer, and now I have an occassional problem with Word's pretty print
quotes, but if you know about that problem, it is easy to fix.

Jerry Floren
Minnesota Department of Agriculture 





Matthew Dowle-3 wrote:
 
 
 As can data.table (i.e. do 'having' in one statement) :
 
 DT = data.table(DF)
 DT[,list(n=length(NAME),mean(SCORE)),by=NAME][n==3]
   NAME n   V2
 [1,] James 3 64.0
 [2,]   Tom 3 78.7

 
 but data.table isn't restricted to SQL functions (such as avg),  any R 
 functions can be used, sometimes for their side effects (such as plotting) 
 rather than just returning data.
 
 Further data.table has a thing called 'join inherited scoping'.   Say we 
 knew the specific groups,  we can go directly to them (without even
 looking 
 at the rest of the data in the table) in very short and convenient syntax, 
 which also happens to run quickly on large data sets (but can be useful
 just 
 for the syntax alone) :
 
 setkey(DT,NAME)
 DT[c(James,Tom),mean(SCORE),mult=all]
   NAME   V1
 [1,] James 64.0
 [2,]   Tom 78.7

 
 Notice there is no group by or even a by in the above.  It inherits
 the 
 scope from the join because mult=all means that James matches to 
 multiple rows, as does Tom, creating two groups.  It does it by binary 
 search to the beginning of each group,  binary search to the end of the 
 group,  and runs the R expression inside the scope of that group.
 
 An example of join inherited scoping for the side effects only :
 
 pdf(out.pdf)
 DT[c(James,Tom),plot(SCORE),mult=all]
 NULL data table
 dev.off()
 # out.pdf now contains 2 plots
 
 which you couldn't do in SQL because SQL has no plotting (or any of R's 
 other packages).
 
 It aims to do this quickly.  Where 'quickly' means 1) shorter code is 
 quicker to write, read, debug and maintain  and also  2) quicker to
 compute, 
 and its 1 that often dominates 2.
 
 Finally, consider the following two statements which are both equivalent :
 
 sqldf(select NAME, avg(SCORE) from DF group by NAME having count(*) =
 3)
NAME avg(SCORE)
 1 James   64.0
 2   Tom   78.7
 DT[ J(DT[,length(NAME),by=NAME][V1==3,NAME]), mean(SCORE), mult=all]
NAME avg(SCORE)
 1 James   64.0
 2   Tom   78.7
 
 Now ok I hear you groaning (!) that the 2nd looks (on first glance) ugly, 
 but bear with me ... in the SQL solution do you know for sure that 
 avg(SCORE) isn't computed wastefully for the all the groups that don't
 have 
 count(*)=3 ?  It might well do the 'group by' first for all the groups,
 then 
 do the 'having' afterwards as a 'where' on the result.  It might depend on

Re: [R] Building static HTML help pages in R 2.10.x on Windows


On 07/01/2010 10:00 AM, Michal Kulich wrote:

On 7.1.2010 15:52, Duncan Murdoch wrote:
 Not necessarily.  The current help system can display information about
 the current session, e.g. the result of ls(), as a simple example.  But
 if you use a single background session you won't get relevant information.
 
 Duncan Murdoch


Sorry, I must admit I don't get it.

  
A more useful example than ls() would be methods().   I think it would 
be nice to have a list of methods included in the man page for a generic 
function, and links to their pages if they have their own man pages.  
You might want to list all installed methods, with some sort of 
highlighting to indicate which ones are already attached, or perhaps be 
able to toggle between installed and attached, or whatever.  None of 
that is possible with static help, not even a list of installed methods, 
because someone might install a new package that offers some others 
after the static help has already been built.


You just need to use some imagination.

Duncan Murdoch

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Re: [R] Identifying outliers in non-normally distributed data

2010-01-07 Thread Jerry Floren


Thank you Bert and Steve for your insights and suggestions. Bert, your
suggestion to meet with a professional statician is right on. We have
collected some great data since 2003, but I need professional help. I am
sure some recommendations could be made to improve the laboratory methods
based on the data collected.

Thanks Steve for the link to, The International Harmonized Protocol for the
Proficiency Testing of Analytical Chemistry Laboratories. I have found some
great ideas in that publication.

Thank you both,

Jerry Floren
Minnesota Department of Agriculture



S Ellison wrote:
 
 If you're interested in handling outliers in analytical proficiency
 testing read current and past IUPAC guidance on PT (see
 http://www.iupac.org/objID/Article/pac7801x0145) and particularly
 references 1, 4, 5, and 11 therein, for starters. 
 
 Although one might reasonably ask whether outliers are real or not,
 bitter experience says that the vast majority of them in PT are
 mistakes, so it is very widely accepted in teh PT community that if
 you;re going to use consensus values, you should use some form of robust
 estimate. In that context, outlier rejection is a crude robustification
 - but better methods exist and are recommended.
 
 If you're looking at data which have asymmetry for good reason, do
 something ordinary (like taking logs) to get the underlying distribution
 near-normal before using robust stats. If the asymmetry is just because
 of the outliers, maybe you have a more awkward problem. But even then,
 something like an MM-estimate or (since this is univariate) pretty much
 any robust estimate using a redescending influence function will help.
 
 Steve E
 
 Bert Gunter gunter.ber...@gene.com 12/30/09 7:09 PM 
 Gents:
 
 Whole books could be -- and have been -- written on this matter.
 Personally,
 when scientists start asking me about criteria for outlier removal, it
 sends shivers up my spine and I break into a cold, clammy sweat. What is
 an
 outlier anyway?
 
 Statisticians (of which I'm one) have promulgated the deception that
 outliers can be defined by purely statistical criteria, and that they
 can
 then be removed from the analysis. That is a lie. The only acceptable
 scientific definition of an outlier that can be legitimately removed is
 of
 data that can be confirmed to have been corrupted in some way, for
 example,
 as Jerry describes below. All purely statistical criteria are arbitrary
 in
 some way and therefore potentially dangerous.
 
 The real question is: what is the scientific purpose of the analysis? --
 how
 are the results to be used? There are a variety of effective so-called
 robust/resistant statistical procedures (e.g. see the R packages robust,
 robustbase, and rrcov, among many others) that might then be useful to
 accomplish the purpose even in the presence of unusual values
 (outliers
 is a term I now avoid due to its 'political' implications). This is
 almost
 always a wiser course of action (there are even theoretical
 justifications
 for this) than using statistical criteria to identify and remove the
 unusual values.
 
 However, use of such tools involves subtle issues that probably cannot
 be
 properly aired in a forum such as this. I therefore think you would do
 well
 to get a competent local statistician to consult with on these matters.
 Yes,
 I do believe that scientists often require advanced statistical tools
 that
 go beyond their usual training to properly analyze even what appear to
 be
 straightforward scientific data. It is a conundrum I cannot resolve,
 but
 that does not mean I can deny it. 
 
 Finally, a word of wisdom from a long-ago engineering colleague:
 Whenever I
 see an outlier, I'm never sure whether to throw it away or patent it. 
 
  
 Cheers,
 
 Bert Gunter
 Genentech Nonclinical Statistics
 
 
 
 
 
 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
 On
 Behalf Of Jerry Floren
 Sent: Wednesday, December 30, 2009 9:47 AM
 To: r-help@r-project.org
 Subject: Re: [R] Identifying outliers in non-normally distributed data
 
 
 Greetings:
 
 I could also use guidance on this topic. I provide manure sample
 proficiency
 sets to agricultural labs in the United States and Canada. There are
 about
 65 labs in the program.
 
 My data sets are much smaller and typically non-symmetrical with obvious
 outliers. Usually, there are 30 to 60 sets of data, each with triple
 replicates (90 to 180 observations).
 
 There are definitely outliers caused by the following: reporting in the
 wrong units, sending in the wrong spreadsheet, entering data in the
 wrong
 row, misplacing decimal points, calculation errors, etc. For each
 analysis,
 it is common that two to three labs make these types of errors. 
 
 Since there are replicates, errors like misplaced decimal points are
 more
 obvious. However, most of the outlier errors are repeated for all three
 replicates. 
 
 I use the median and Median Absolute Deviation

[R] Patterns in histogram

2010-01-07 Thread dbeest


I’ve been busy making some histograms and I would like to distinguish
different groups. I’ve been doing it like this: 

a - c(1,1,1,1,2,2,2)
hist(a,breaks=c(0,1,2))
hist(a[3:5],breaks=c(0,1,2),col=red,add=TRUE)

Basically plotting them over each other, I assume there is a better
way…Anyway what I want to do is make them in grayscale which essentially
means giving different groups patterns. I’ve been playing around with
“density” and “angle”

a - c(1,1,1,1,2,2,2)
hist(a,breaks=c(0,1,2))
hist(a[3:5],breaks=c(0,1,2),add=TRUE,,density=3,angle=9)

Although you can make many different combinations with these I wondered if
there are “patterns” (dots for example) available in the similar fashion as
the colors (col=red or pattern=dots)

cheers,

Dennis
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[R] Graph titles from massive

2010-01-07 Thread Trafim Vanishek

Dear all,

I would like to ask you if there is a possibility in R to give the names to
graphs which are not const.
For example,

How to name each plot, or to add notes like a=x[i], b=y[i] in this cycle

x-c(1,2,3,4,5,6)
y-c(7,8,9,10,11,12)

par(mfrow=c(2,3))

for (i in 1:6){
plot(x,y)
}


Thank you for your time and help!

[[alternative HTML version deleted]]

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Re: [R] Building static HTML help pages in R 2.10.x on Windows

2010-01-07 Thread Jonathan Baron

For what it is worth, I would gladly sacrifice this capability in
order to be able to consult all my R help pages through a Firefox
bookmark to the packages listing (which is what I used to do, and will
do again, when I get time to either rebuild from source or get the
forthcoming Fedora RPM, which will have static pages as the default),
without starting an R session.

Jon

On 01/07/10 10:32, Duncan Murdoch wrote:
 A more useful example than ls() would be methods().   I think it would 
 be nice to have a list of methods included in the man page for a generic 
 function, and links to their pages if they have their own man pages.  
 You might want to list all installed methods, with some sort of 
 highlighting to indicate which ones are already attached, or perhaps be 
 able to toggle between installed and attached, or whatever.  None of 
 that is possible with static help, not even a list of installed methods, 
 because someone might install a new package that offers some others 
 after the static help has already been built.
 
 You just need to use some imagination.
 
 Duncan Murdoch

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Re: [R] Graph titles from massive

2010-01-07 Thread jim holtman

use the 'main' parameter:

for (i in 1:6){
plot(x,y,main=paste(Plot:, i))
}

On Thu, Jan 7, 2010 at 11:24 AM, Trafim Vanishek rdapam...@gmail.comwrote:

 Dear all,

 I would like to ask you if there is a possibility in R to give the names to
 graphs which are not const.
 For example,

 How to name each plot, or to add notes like a=x[i], b=y[i] in this cycle

 x-c(1,2,3,4,5,6)
 y-c(7,8,9,10,11,12)

 par(mfrow=c(2,3))

 for (i in 1:6){
 plot(x,y)
 }


 Thank you for your time and help!

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

What is the problem that you are trying to solve?

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Re: [R] Patterns in histogram



On Jan 7, 2010, at 10:42 AM, dbeest wrote:



I’ve been busy making some histograms and I would like to distinguish
different groups. I’ve been doing it like this:

a - c(1,1,1,1,2,2,2)
hist(a,breaks=c(0,1,2))
hist(a[3:5],breaks=c(0,1,2),col=red,add=TRUE)

Basically plotting them over each other, I assume there is a better
way…Anyway what I want to do is make them in grayscale which  
essentially

means giving different groups patterns. I’ve been playing around with
“density” and “angle”

a - c(1,1,1,1,2,2,2)
hist(a,breaks=c(0,1,2))
hist(a[3:5],breaks=c(0,1,2),add=TRUE,,density=3,angle=9)

Although you can make many different combinations with these I  
wondered if
there are “patterns” (dots for example) available in the similar  
fashion as

the colors (col=red or pattern=dots)


I have not been able t find such. But you can also get the shading  
lines to respond to lty and to a very limited extent to lwd, ...  at  
least I was not able to get arbitrarily thick lines on my screen  
graphics device (Quartz). The help pages I looked at suggested that  
different graphics devices might have varying parameters that could be  
fiddled with.


--

David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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Re: [R] Graph titles from massive



On Jan 7, 2010, at 11:24 AM, Trafim Vanishek wrote:


Dear all,

I would like to ask you if there is a possibility in R to give the  
names to

graphs which are not const.
For example,

How to name each plot, or to add notes like a=x[i], b=y[i] in this  
cycle


x-c(1,2,3,4,5,6)
y-c(7,8,9,10,11,12)

par(mfrow=c(2,3))

for (i in 1:6){
plot(x,y)
}


This might be what you want:

 x-c(1,2,3,4,5,6)
 y-c(7,8,9,10,11,12)

 par(mfrow=c(2,3))

 for (i in 1:6){
+ plot(x,y, main=paste(this is plot # , i, sep=))
+ }


I initially thought you wanted the object names to be different for  
which this answer would not be responsive and no answer could be  
provided since that is not how base graphics work. For that you would  
need grid, lattice, or ggplot methods.



David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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[R] logistic regression based on principle component analysis

2010-01-07 Thread 江文恺


Dear all:

I try to analyse a dataset which contain one binary response variable and 
serveral predict variables, but multiple colinear problem exists in my dataset, 
some paper suggest that logistic regression for principle components is suit 
for these noise data,
but i only find R can done principle component regression using pls package, 
is there any package that can do the task i need - logistic regression based on 
principle components,
if not, can anyone give some suggestion about how to use R to do my work.
Thanks very much!
best regards!

wenkai
  
_
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Re: [R] logistic regression based on principle component analysis

2010-01-07 Thread Steve Lianoglou

Hi,

On Thu, Jan 7, 2010 at 11:57 AM, 江文恺 biology0...@hotmail.com wrote:

 Dear all:

 I try to analyse a dataset which contain one binary response variable and 
 serveral predict variables, but multiple colinear problem exists in my 
 dataset, some paper suggest that logistic regression for principle components 
 is suit for these noise data,
 but i only find R can done principle component regression using pls package,
 is there any package that can do the task i need - logistic regression based 
 on principle components,
 if not, can anyone give some suggestion about how to use R to do my work.

Is this any different than first doing PCA to do the dimensionality
reduction (which presumably will take care of your colinearity), then
doing the logistic regression on your reduced input space?

If so: no package is really necessary, right? It's just a two-step
solution you need to write up.

-steve
-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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[R] Is nested namespace supported?

2010-01-07 Thread Peng Yu

I don't find where in the R document the discussion of nested
namespace is. If there is nested namespace supported in R, could
somebody let me know whether the document is?

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[R] faster GLS code

2010-01-07 Thread Carlo Fezzi

Dear helpers,

I wrote a code which estimates a multi-equation model with generalized
least squares (GLS). I can use GLS because I know the covariance matrix of
the residuals a priori. However, it is a bit slow and I wonder if anybody
would be able to point out a way to make it faster (it is part of a bigger
code and needs to run several times).

Any suggestion would be greatly appreciated.

Carlo


***
Carlo Fezzi
Senior Research Associate

Centre for Social and Economic Research
on the Global Environment (CSERGE),
School of Environmental Sciences,
University of East Anglia,
Norwich, NR4 7TJ
United Kingdom.
email: c.fe...@uea.ac.uk
***

Here is an example with 3 equations and 2 exogenous variables:

- start code --


N - 1000   # number of observations
library(MASS)

## parameters ##

# eq. 1
b10 - 7; b11 - 2; b12 - -1

# eq. 2
b20 - 5; b21 - -2; b22 - 1

# eq.3
b30 - 1; b31 - 5; b32 - 2

# exogenous variables

x1 - runif(min=-10,max=10,N)
x2 - runif(min=-5,max=5,N)

# residual covariance matrix
sigma - matrix(c(2,1,0.7,1,1.5,0.5,0.7,0.5,2),3,3)

# residuals
r - mvrnorm(N,mu=rep(0,3), Sigma=sigma)

# endogenous variables

y1 - b10 + b11 * x1 + b12*x2 + r[,1]
y2 - b20 + b21 * x1 + b22*x2 + r[,2]
y3 - b30 + b31 * x1 + b32*x2 + r[,3]

y - cbind(y1,y2,y3)# matrix of endogenous
x - cbind(1,x1, x2)# matrix of exogenous


 MODEL ESTIMATION ###

# build the big X matrix needed for GLS estimation:

X - kronecker(diag(1,3),x)
Y - c(y) # stack the y in a vector

# residual covariance matrix for each observation
covar - kronecker(sigma,diag(1,N))

# GLS betas covariance matrix
inv.sigma - solve(covar)
betav - solve(t(X)%*%inv.sigma%*%X)

# GLS mean parameter estimates
betam - betav%*%t(X)%*%inv.sigma%*%Y

- end of code 

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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] Strange behaviour of as.integer()

2010-01-07 Thread William Dunlap

Use round(), floor(), or ceiling() to convert
numbers with possible fractional parts to numbers
without fraction parts.

as.integer()'s main use is to convert from one
internal representation (i.e., bit pattern)
of a number to another so you can interface to
C or Fortran code.

Note that as.integer(x) also doesn't work when
abs(x)2^31, while round(), floor(), and ceiling()
do work up to c. 2^52.

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 Ulrich Keller
 Sent: Thursday, January 07, 2010 4:32 AM
 To: r-help@r-project.org
 Subject: [R] Strange behaviour of as.integer()
 
 I have encountered a strange behaviour of as.integer() which does not
 seem correct to me. Sorry if this is just an indication of me not
 understanding floating point arithmetic.
 
  .57 * 100
 [1] 57
  .29 * 100
 [1] 29
 
 So far, so good. But:
 
  as.integer(.57 * 100)
 [1] 56
  as.integer(.29 * 100)
 [1] 28
 
 Then again:
 
  all.equal(.57 * 100, as.integer(57))
 [1] TRUE
  all.equal(.29 * 100, as.integer(29))
 [1] TRUE
 
 This behaviour is the same in R 2.10.1 (Ubuntu and Windows) and 2.9.2
 (Windows),
 all 32 bit versions. Is this really intended?
 
 __
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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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and provide commented, minimal, self-contained, reproducible code.

[R] factor graphics with pca in R?

2010-01-07 Thread Martin Ivanov

 Dear R users, 
I need to know whether the factor graphics with principal component analysis 
are implemented in R. I mean the graphs where the variables are represented in 
a correlation circle, as described in more detail in this document: 
http://www.unesco.org/webworld/idams/advguide/Chapt6_4_3.htm

It is not a pain to program it myself, nevertheless it would be a waste of time
 if it is already implemented in R. 

Regards, 
Martin

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Re: [R] logistic regression based on principle component analysis

2010-01-07 Thread Kjetil Halvorsen

for an alternative (lasso) approach, look at the packages (CRAN)
grpreg, grplasso,  glmnet, penalized and certainly some others.

Kjetil B H

On Thu, Jan 7, 2010 at 2:06 PM, Steve Lianoglou
mailinglist.honey...@gmail.com wrote:
 Hi,

 On Thu, Jan 7, 2010 at 11:57 AM, 江文恺 biology0...@hotmail.com wrote:

 Dear all:

 I try to analyse a dataset which contain one binary response variable and 
 serveral predict variables, but multiple colinear problem exists in my 
 dataset, some paper suggest that logistic regression for principle 
 components is suit for these noise data,
 but i only find R can done principle component regression using pls 
 package,
 is there any package that can do the task i need - logistic regression based 
 on principle components,
 if not, can anyone give some suggestion about how to use R to do my work.

 Is this any different than first doing PCA to do the dimensionality
 reduction (which presumably will take care of your colinearity), then
 doing the logistic regression on your reduced input space?

 If so: no package is really necessary, right? It's just a two-step
 solution you need to write up.

 -steve
 --
 Steve Lianoglou
 Graduate Student: Computational Systems Biology
  | Memorial Sloan-Kettering Cancer Center
  | Weill Medical College of Cornell University
 Contact Info: http://cbio.mskcc.org/~lianos/contact

 __
 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] Question on Reduce + rollmean

2010-01-07 Thread Muhammad Rahiz


Dear Gabor  Henrique,

Thanks for your suggestions on the above problem. The following is more 
traditional and unfanciful but it works. Suitable for a prodige like myself...

m - matrix(1:3,3,3)
x1 - list(m, m+1, m+2, m+3, m+4) 


out - list()
for (i in 1:4){
t[[i]] - Reduce(+, x1[c(i:i+1)])
}

Muhammad

Muhammad Rahiz  |  Doctoral Student in Regional Climate Modeling

Climate Research Laboratory, School of Geography  the Environment  
Oxford University Centre for the Environment
South Parks Road, Oxford, OX1 3QY, United Kingdom 
Tel: +44 (0)1865-285194	 Mobile: +44 (0)7854-625974

Email: muhammad.ra...@ouce.ox.ac.uk






Gabor Grothendieck wrote:

Here is a variation which also uses head and tail:

mapply(function(x, y) (x + y)/2, tail(x, -1), head(x, -1), SIMPLIFY = FALSE)


On Mon, Jan 4, 2010 at 12:37 PM, Henrique Dallazuanna www...@gmail.com wrote:
  

For this example try this:

lapply(lapply(list('head', 'tail'), do.call, list(x, n = -1)),
function(x)Reduce('+', x)/2)


On Mon, Jan 4, 2010 at 1:54 PM, Muhammad Rahiz
muhammad.ra...@ouce.ox.ac.uk wrote:


Thanks Gabor,

It works alright. But is there alternative ways to perform rollmean apart
from permutating the data?
Possibly combining the Reduce and rollmean functions?

The easiest but traditional way is

  

(x[[1]]+x[[2]]) / 2
(x[[2]]+x[[3]]) / 2


Muhammad Rahiz  |  Doctoral Student in Regional Climate Modeling

Climate Research Laboratory, School of Geography  the Environment
Oxford University Centre for the Environment
South Parks Road, Oxford, OX1 3QY, United Kingdom Tel: +44 (0)1865-285194
 Mobile: +44 (0)7854-625974
Email: muhammad.ra...@ouce.ox.ac.uk






Gabor Grothendieck wrote:
  

Try apply:

library(zoo) # rollmean

# test data
m - matrix(1:3, 3, 3)
x - list(m, m+3, m+6)

# convert to array
a - array(unlist(x), c(3, 3, 3)); a

# apply rollmean and permute to desired form
aa - apply(a, 1:2, rollmean, k = 2)
aperm(aa, c(2, 3, 1))

The last line outputs:




aperm(aa, c(2, 3, 1))

  

, , 1

[,1] [,2] [,3]
[1,]  2.5  2.5  2.5
[2,]  3.5  3.5  3.5
[3,]  4.5  4.5  4.5

, , 2

[,1] [,2] [,3]
[1,]  5.5  5.5  5.5
[2,]  6.5  6.5  6.5
[3,]  7.5  7.5  7.5


On Sat, Jan 2, 2010 at 10:00 AM, Muhammad Rahiz
muhammad.ra...@ouce.ox.ac.uk wrote:



Let me rephrase;

Given x as


  

x



[[1]]
 V1 V2 V3
[1,]  1  1  1
[2,]  2  2  2
[3,]  3  3  3

[[2]]
 V1 V2 V3
[1,]  4  4  4
[2,]  5  5  5
[3,]  6  6  6

[[3]]
 V1 V2 V3
[1,]  7  7  7
[2,]  8  8  8
[3,]  9  9  9

I'd like to calculate the moving average (interval = 2) i.e.

( x[[1]] + x[[2]] ) / 2
( x[[2]] + x[[3]] ) / 2
... and so on.

The desired output will return

2.5 2.5 2.5
3.5 3.5 3.5
4.5 4.5 4.5

5.5 5.5 5.5
6.5 6.5 6.5
7.5 7.5 7.5




Muhammad Rahiz  |  Doctoral Student in Regional Climate Modeling
Climate Research Laboratory, School of Geography  the Environment
Oxford University Centre for the Environment, University of Oxford
South Parks Road, Oxford, OX1 3QY, United Kingdom
Tel: +44 (0)1865-285194  Mobile: +44 (0)7854-625974
Email: muhammad.ra...@ouce.ox.ac.uk



milton ruser wrote:

  

Dear M.Rahiz,

Unfortunatelly I can't reproduce your example.
PLEASE do read the posting guide

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

bests

milton
On Sat, Jan 2, 2010 at 9:26 AM, Muhammad Rahiz
muhammad.ra...@ouce.ox.ac.ukmailto:muhammad.ra...@ouce.ox.ac.uk
wrote:
Hello useRs,

I'd like to perform a moving average on the dataset, xx. I've tried
combining the functions Reduce and rollmean but it didn't work.





r - function(n) rollmean(n, 2) # where 2 = averaging interval
output  - Reduce(r, x)


  

Error in f(init, x[[i]]) : unused argument(s) (x[[i]])

Is there anything wrong with the code in the first place?

where




x


  

[[1]]
 V1 V2 V3
[1,]  1  1  1
[2,]  2  2  2
[3,]  3  3  3

[[2]]
 V1 V2 V3
[1,]  4  4  4
[2,]  5  5  5
[3,]  6  6  6

[[3]]
 V1 V2 V3
[1,]  7  7  7
[2,]  8  8  8
[3,]  9  9  9

The moving average is to be performed on

1,4,7 = (1+4)/2 , (4+7)/2
2,5,8 = ..
3,6,9 = ..

Thanks

Muhammad

--
Muhammad Rahiz  |  Doctoral Student in Regional Climate Modeling
Climate Research Laboratory, School of Geography  the Environment
Oxford University Centre for the Environment, University of Oxford
South Parks Road, Oxford, OX1 3QY, United Kingdom
Tel: +44 (0)1865-285194  Mobile: +44 (0)7854-625974
Email: muhammad.ra...@ouce.ox.ac.ukmailto:muhammad.ra...@ouce.ox.ac.uk

__
R-help@r-project.orgmailto:R-help@r-project.org mailing list
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PLEASE do read the posting guide

http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.






__

Re: [R] logistic regression based on principle component analysis

2010-01-07 Thread SR Millis

Frank Harrell, Jr shows you how to implement this in R, in his book, Regression 
Modeling Strategies.


~~~
Scott R Millis, PhD, ABPP (CN,CL,RP), CStat, CSci
Professor  Director of Research
Dept of Physical Medicine  Rehabilitation
Dept of Emergency Medicine
Wayne State University School of Medicine
261 Mack Blvd
Detroit, MI 48201
Email:  aa3...@wayne.edu
Email:  srmil...@yahoo.com
Tel: 313-993-8085
Fax: 313-966-7682


--- On Thu, 1/7/10, Kjetil Halvorsen kjetilbrinchmannhalvor...@gmail.com 
wrote:

 From: Kjetil Halvorsen kjetilbrinchmannhalvor...@gmail.com
 Subject: Re: [R] logistic regression based on principle component analysis
 To: Steve Lianoglou mailinglist.honey...@gmail.com
 Cc: r-help@r-project.org, 江文恺 biology0...@hotmail.com
 Date: Thursday, January 7, 2010, 12:27 PM
 for an alternative (lasso) approach,
 look at the packages (CRAN)
 grpreg, grplasso,  glmnet, penalized and certainly
 some others.
 
 Kjetil B H
 
 On Thu, Jan 7, 2010 at 2:06 PM, Steve Lianoglou
 mailinglist.honey...@gmail.com
 wrote:
  Hi,
 
  On Thu, Jan 7, 2010 at 11:57 AM, 江文恺 biology0...@hotmail.com
 wrote:
 
  Dear all:
 
  I try to analyse a dataset which contain one
 binary response variable and serveral predict variables, but
 multiple colinear problem exists in my dataset, some paper
 suggest that logistic regression for principle components is
 suit for these noise data,
  but i only find R can done principle component
 regression using pls package,
  is there any package that can do the task i need -
 logistic regression based on principle components,
  if not, can anyone give some suggestion about how
 to use R to do my work.
 
  Is this any different than first doing PCA to do the
 dimensionality
  reduction (which presumably will take care of your
 colinearity), then
  doing the logistic regression on your reduced input
 space?
 
  If so: no package is really necessary, right? It's
 just a two-step
  solution you need to write up.
 
  -steve
  --
  Steve Lianoglou
  Graduate Student: Computational Systems Biology
   | Memorial Sloan-Kettering Cancer Center
   | Weill Medical College of Cornell University
  Contact Info: http://cbio.mskcc.org/~lianos/contact
 
  __
  R-help@r-project.org
 mailing list
  https://stat.ethz.ch/mailman/listinfo/r-help
  PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
  and provide commented, minimal, self-contained,
 reproducible code.
 
 
 __
 R-help@r-project.org
 mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained,
 reproducible code.


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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] [R-pkgs] fortunes: 250th fortune

2010-01-07 Thread baptiste auguie

Hi,

Thank you for this fun package.
I recently posted a related question on R-help that seemed to pass
unnoticed. Basically, I suggested that the functionality of fortunes
could be extended to R FAQ entries, also allowing contributed packages
to provide their own (fortune or) faq data file. My initial suggestion
is here: http://markmail.org/message/oisbnuugifx5e36k

I played with the fortune() source code and it doesn't take much
effort to amend it for FAQ-like entries (I did not go as far as
converting all the official FAQ entries, that's another problem).
However such an approach is suboptimal in that most of the code would
be duplicated. Would it make sense to write a slightly more general
code working for a wider range of database entries?

Best regards,

baptiste










2010/1/6 Achim Zeileis achim.zeil...@wu-wien.ac.at:
 Dear useRs,

 it's a new year and time for a new CRAN-version of the fortunes package.
 Version 1.3-7 is now online at

  http://CRAN.R-project.org/package=fortunes

 which contains the 250th fortune:

 R fortune(250)

 As Obi-Wan Kenobi may have said in Star Wars: Use the source, Luke!
   -- Barry Rowlingson (answering a question on the documentation of some
      implementation details)
      R-devel (January 2010)

 Actually there is also the 251st...

 Thanks to all that have contributed to the fortunes package in the form of
 creating these nice quote or submitting them to the package.

 Best wishes,
 Z

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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.


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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] Building static HTML help pages in R 2.10.x on Windows


On 07/01/2010 11:36 AM, Jonathan Baron wrote:

For what it is worth, I would gladly sacrifice this capability in
order to be able to consult all my R help pages through a Firefox
bookmark to the packages listing (which is what I used to do, and will
do again, when I get time to either rebuild from source or get the
forthcoming Fedora RPM, which will have static pages as the default),
without starting an R session.
  


What's so hard about leaving an R session running, and using bookmarks 
as Dieter described?


Duncan Murdoch

Jon

On 01/07/10 10:32, Duncan Murdoch wrote:
 A more useful example than ls() would be methods().   I think it would 
 be nice to have a list of methods included in the man page for a generic 
 function, and links to their pages if they have their own man pages.  
 You might want to list all installed methods, with some sort of 
 highlighting to indicate which ones are already attached, or perhaps be 
 able to toggle between installed and attached, or whatever.  None of 
 that is possible with static help, not even a list of installed methods, 
 because someone might install a new package that offers some others 
 after the static help has already been built.
 
 You just need to use some imagination.
 
 Duncan Murdoch




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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] Drop a part of an array\list\vector?

2010-01-07 Thread Idgarad

I did have a verbose description of why but rather then make everyone's eyes
bleed with useless details I ask the following :)
 To make a long story short: How can I make newmcReg[[i]][PreIO308] go
away in the following list... er vector... no wait array dataframe
awww crap...


 summary(newmcReg[[i]])
 UNITBUILD UNITDB ITBUILD   ITDB
 Mode :logical   Mode :logical   Mode :logical   Mode :logical
 FALSE:249   FALSE:249   FALSE:249   FALSE:249
 TRUE :21TRUE :21TRUE :21TRUE :21



  UATBUILD UATDB HOGANCODE  ACF
 Mode :logical   Mode :logical   Mode :logical   Mode :logical
 FALSE:250   FALSE:250   FALSE:208   FALSE:225
 TRUE :20TRUE :20TRUE :62TRUE :45



RCF  ReleaseST1  ReleaseST2  ReleaseBLA
 Mode :logical   Mode :logical   Mode :logical   Mode :logical
 FALSE:186   FALSE:167   FALSE:157   FALSE:228
 TRUE :84TRUE :103   TRUE :113   TRUE :42



 MonthlyST1  MonthlyST2  MonthlyBLA  Small.Bank.Acquisitions
 Mode :logical   Mode :logical   Mode :logical   Min.   :0.
 FALSE:107   FALSE:105   FALSE:147   1st Qu.:0.
 TRUE :163   TRUE :165   TRUE :123   Median :0.
 Mean   :0.1556
 3rd Qu.:0.
 Max.   :1.
  Conversions  Build.New.Environment HLY.NewYear  HLY.MLK
 Min.   :0.0   Mode :logical Mode :logical   Mode :logical
 1st Qu.:0.0   FALSE:262 FALSE:266   FALSE:264
 Median :0.0   TRUE :8   TRUE :4 TRUE :6
 Mean   :0.08889
 3rd Qu.:0.0
 Max.   :1.0
  HLY.PRES   HLY.MEMORIAL  HLY.J4HLY.LABOR
 Mode :logical   Mode :logical   Mode :logical   Mode :logical
 FALSE:264   FALSE:265   FALSE:265   FALSE:265
 TRUE :6 TRUE :5 TRUE :5 TRUE :5



 HLY.COLUMBUS HLY.VETS   HLY.THANKS   HLY.XMAS
 Mode :logical   Mode :logical   Mode :logical   Mode :logical
 FALSE:265   FALSE:265   FALSE:265   FALSE:265
 TRUE :5 TRUE :5 TRUE :5 TRUE :5



 HLY.ELECT   HLY.PATRIOTEOMNEWMF
 Mode :logical   Mode :logical   Mode :logical   Mode :logical
 FALSE:265   FALSE:265   FALSE:210   FALSE:263
 TRUE :5 TRUE :5 TRUE :60TRUE :7



  PreIO47 PreIO151PreIO164PreIO169
 Mode :logical   Mode :logical   Mode :logical   Mode :logical
 FALSE:269   FALSE:269   FALSE:269   FALSE:269
 TRUE :1 TRUE :1 TRUE :1 TRUE :1



  PreIO197PreIO203PreIO209PreIO241
 Mode :logical   Mode :logical   Mode :logical   Mode :logical
 FALSE:269   FALSE:269   FALSE:269   FALSE:269
 TRUE :1 TRUE :1 TRUE :1 TRUE :1



  PreIO261PreIO308
 Mode :logical   Mode :logical
 FALSE:269   FALSE:270
 TRUE :1


(the PreIO are outliers identified from the output of stl() e.g. outliers in
the source data)

[[alternative HTML version deleted]]

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

Re: [R] Question on Reduce + rollmean

That gives an error when I run it.  I think you want this:

m - matrix(1:3,3,3)
x1 - list(m, m+1, m+2, m+3, m+4)

out - list()
for(i in 1:4) out[[i]] - (x1[[i]] + x1[[i+1]]) / 2


On Thu, Jan 7, 2010 at 12:28 PM, Muhammad Rahiz
muhammad.ra...@ouce.ox.ac.uk wrote:
 Dear Gabor  Henrique,

 Thanks for your suggestions on the above problem. The following is more
 traditional and unfanciful but it works. Suitable for a prodige like
 myself...

 m - matrix(1:3,3,3)
 x1 - list(m, m+1, m+2, m+3, m+4)
 out - list()
 for (i in 1:4){
 t[[i]] - Reduce(+, x1[c(i:i+1)])
 }

 Muhammad

 Muhammad Rahiz  |  Doctoral Student in Regional Climate Modeling

 Climate Research Laboratory, School of Geography  the Environment
 Oxford University Centre for the Environment
 South Parks Road, Oxford, OX1 3QY, United Kingdom Tel: +44 (0)1865-285194
  Mobile: +44 (0)7854-625974
 Email: muhammad.ra...@ouce.ox.ac.uk






 Gabor Grothendieck wrote:

 Here is a variation which also uses head and tail:

 mapply(function(x, y) (x + y)/2, tail(x, -1), head(x, -1), SIMPLIFY =
 FALSE)


 On Mon, Jan 4, 2010 at 12:37 PM, Henrique Dallazuanna www...@gmail.com
 wrote:


 For this example try this:

 lapply(lapply(list('head', 'tail'), do.call, list(x, n = -1)),
 function(x)Reduce('+', x)/2)


 On Mon, Jan 4, 2010 at 1:54 PM, Muhammad Rahiz
 muhammad.ra...@ouce.ox.ac.uk wrote:


 Thanks Gabor,

 It works alright. But is there alternative ways to perform rollmean
 apart
 from permutating the data?
 Possibly combining the Reduce and rollmean functions?

 The easiest but traditional way is



 (x[[1]]+x[[2]]) / 2
 (x[[2]]+x[[3]]) / 2


 Muhammad Rahiz  |  Doctoral Student in Regional Climate Modeling

 Climate Research Laboratory, School of Geography  the Environment
 Oxford University Centre for the Environment
 South Parks Road, Oxford, OX1 3QY, United Kingdom Tel: +44
 (0)1865-285194
  Mobile: +44 (0)7854-625974
 Email: muhammad.ra...@ouce.ox.ac.uk






 Gabor Grothendieck wrote:


 Try apply:

 library(zoo) # rollmean

 # test data
 m - matrix(1:3, 3, 3)
 x - list(m, m+3, m+6)

 # convert to array
 a - array(unlist(x), c(3, 3, 3)); a

 # apply rollmean and permute to desired form
 aa - apply(a, 1:2, rollmean, k = 2)
 aperm(aa, c(2, 3, 1))

 The last line outputs:




 aperm(aa, c(2, 3, 1))



 , , 1

    [,1] [,2] [,3]
 [1,]  2.5  2.5  2.5
 [2,]  3.5  3.5  3.5
 [3,]  4.5  4.5  4.5

 , , 2

    [,1] [,2] [,3]
 [1,]  5.5  5.5  5.5
 [2,]  6.5  6.5  6.5
 [3,]  7.5  7.5  7.5


 On Sat, Jan 2, 2010 at 10:00 AM, Muhammad Rahiz
 muhammad.ra...@ouce.ox.ac.uk wrote:



 Let me rephrase;

 Given x as




 x



 [[1]]
  V1 V2 V3
 [1,]  1  1  1
 [2,]  2  2  2
 [3,]  3  3  3

 [[2]]
  V1 V2 V3
 [1,]  4  4  4
 [2,]  5  5  5
 [3,]  6  6  6

 [[3]]
  V1 V2 V3
 [1,]  7  7  7
 [2,]  8  8  8
 [3,]  9  9  9

 I'd like to calculate the moving average (interval = 2) i.e.

 ( x[[1]] + x[[2]] ) / 2
 ( x[[2]] + x[[3]] ) / 2
 ... and so on.

 The desired output will return

 2.5 2.5 2.5
 3.5 3.5 3.5
 4.5 4.5 4.5

 5.5 5.5 5.5
 6.5 6.5 6.5
 7.5 7.5 7.5




 Muhammad Rahiz  |  Doctoral Student in Regional Climate Modeling
 Climate Research Laboratory, School of Geography  the Environment
 Oxford University Centre for the Environment, University of Oxford
 South Parks Road, Oxford, OX1 3QY, United Kingdom
 Tel: +44 (0)1865-285194  Mobile: +44 (0)7854-625974
 Email: muhammad.ra...@ouce.ox.ac.uk



 milton ruser wrote:



 Dear M.Rahiz,

 Unfortunatelly I can't reproduce your example.
 PLEASE do read the posting guide


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

 bests

 milton
 On Sat, Jan 2, 2010 at 9:26 AM, Muhammad Rahiz
 muhammad.ra...@ouce.ox.ac.ukmailto:muhammad.ra...@ouce.ox.ac.uk
 wrote:
 Hello useRs,

 I'd like to perform a moving average on the dataset, xx. I've tried
 combining the functions Reduce and rollmean but it didn't work.





 r - function(n) rollmean(n, 2) # where 2 = averaging interval
 output  - Reduce(r, x)




 Error in f(init, x[[i]]) : unused argument(s) (x[[i]])

 Is there anything wrong with the code in the first place?

 where




 x




 [[1]]
  V1 V2 V3
 [1,]  1  1  1
 [2,]  2  2  2
 [3,]  3  3  3

 [[2]]
  V1 V2 V3
 [1,]  4  4  4
 [2,]  5  5  5
 [3,]  6  6  6

 [[3]]
  V1 V2 V3
 [1,]  7  7  7
 [2,]  8  8  8
 [3,]  9  9  9

 The moving average is to be performed on

 1,4,7 = (1+4)/2 , (4+7)/2
 2,5,8 = ..
 3,6,9 = ..

 Thanks

 Muhammad

 --
 Muhammad Rahiz  |  Doctoral Student in Regional Climate Modeling
 Climate Research Laboratory, School of Geography  the Environment
 Oxford University Centre for the Environment, University of Oxford
 South Parks Road, Oxford, OX1 3QY, United Kingdom
 Tel: +44 (0)1865-285194  Mobile: +44 (0)7854-625974
 Email:
 muhammad.ra...@ouce.ox.ac.ukmailto:muhammad.ra...@ouce.ox.ac.uk

 __
 R-help@r-project.orgmailto:R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting

[R] Return values in fExtremes package

2010-01-07 Thread Tim Smith

Hi,

I was usuing the fExtemes package, and wanted to obtain some of the values 
returned from the function gumbelFit(). For example, in the following code, I 
would like to access 'mu' and 'beta' from the object 'para'. How should I go 
about doing this? Is there any generic method to access the object?
---
 library(fExtremes) 
 ss - gumbelSim(model = list(mu = 0, beta = 1), n = 1000, seed = NULL)
 para - gumbelFit(ss)
 print(para)

Title:
 Gumbel Parameter Estimation 

Call:
 gumbelFit(x = ss)

Estimation Type:
  gum mle 

Estimated Parameters:
 mubeta 
0.005449572 1.010874131 

Description
  Thu Jan 07 13:14:28 2010 

 class(para)
[1] fGEVFIT
attr(,package)
[1] fExtremes

---
thanks!


  
[[alternative HTML version deleted]]

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Re: [R] Question on Reduce + rollmean

2010-01-07 Thread Muhammad Rahiz


Yes, should be
1. out[[i]], instead of t[[i]].
2. x1[c(i:(i+1))]  # For this case, I was trying out the rolling sum.

Muhammad Rahiz  |  Doctoral Student in Regional Climate Modeling

Climate Research Laboratory, School of Geography  the Environment  
Oxford University Centre for the Environment
South Parks Road, Oxford, OX1 3QY, United Kingdom 
Tel: +44 (0)1865-285194	 Mobile: +44 (0)7854-625974

Email: muhammad.ra...@ouce.ox.ac.uk






Gabor Grothendieck wrote:

That gives an error when I run it.  I think you want this:

m - matrix(1:3,3,3)
x1 - list(m, m+1, m+2, m+3, m+4)

out - list()
for(i in 1:4) out[[i]] - (x1[[i]] + x1[[i+1]]) / 2


On Thu, Jan 7, 2010 at 12:28 PM, Muhammad Rahiz
muhammad.ra...@ouce.ox.ac.uk wrote:
  

Dear Gabor  Henrique,

Thanks for your suggestions on the above problem. The following is more
traditional and unfanciful but it works. Suitable for a prodige like
myself...

m - matrix(1:3,3,3)
x1 - list(m, m+1, m+2, m+3, m+4)
out - list()
for (i in 1:4){
t[[i]] - Reduce(+, x1[c(i:i+1)])
}

Muhammad

Muhammad Rahiz  |  Doctoral Student in Regional Climate Modeling

Climate Research Laboratory, School of Geography  the Environment
Oxford University Centre for the Environment
South Parks Road, Oxford, OX1 3QY, United Kingdom Tel: +44 (0)1865-285194
 Mobile: +44 (0)7854-625974
Email: muhammad.ra...@ouce.ox.ac.uk






Gabor Grothendieck wrote:


Here is a variation which also uses head and tail:

mapply(function(x, y) (x + y)/2, tail(x, -1), head(x, -1), SIMPLIFY =
FALSE)


On Mon, Jan 4, 2010 at 12:37 PM, Henrique Dallazuanna www...@gmail.com
wrote:

  

For this example try this:

lapply(lapply(list('head', 'tail'), do.call, list(x, n = -1)),
function(x)Reduce('+', x)/2)


On Mon, Jan 4, 2010 at 1:54 PM, Muhammad Rahiz
muhammad.ra...@ouce.ox.ac.uk wrote:



Thanks Gabor,

It works alright. But is there alternative ways to perform rollmean
apart
from permutating the data?
Possibly combining the Reduce and rollmean functions?

The easiest but traditional way is


  

(x[[1]]+x[[2]]) / 2
(x[[2]]+x[[3]]) / 2



Muhammad Rahiz  |  Doctoral Student in Regional Climate Modeling

Climate Research Laboratory, School of Geography  the Environment
Oxford University Centre for the Environment
South Parks Road, Oxford, OX1 3QY, United Kingdom Tel: +44
(0)1865-285194
 Mobile: +44 (0)7854-625974
Email: muhammad.ra...@ouce.ox.ac.uk






Gabor Grothendieck wrote:

  

Try apply:

library(zoo) # rollmean

# test data
m - matrix(1:3, 3, 3)
x - list(m, m+3, m+6)

# convert to array
a - array(unlist(x), c(3, 3, 3)); a

# apply rollmean and permute to desired form
aa - apply(a, 1:2, rollmean, k = 2)
aperm(aa, c(2, 3, 1))

The last line outputs:





aperm(aa, c(2, 3, 1))


  

, , 1

   [,1] [,2] [,3]
[1,]  2.5  2.5  2.5
[2,]  3.5  3.5  3.5
[3,]  4.5  4.5  4.5

, , 2

   [,1] [,2] [,3]
[1,]  5.5  5.5  5.5
[2,]  6.5  6.5  6.5
[3,]  7.5  7.5  7.5


On Sat, Jan 2, 2010 at 10:00 AM, Muhammad Rahiz
muhammad.ra...@ouce.ox.ac.uk wrote:




Let me rephrase;

Given x as



  

x




[[1]]
 V1 V2 V3
[1,]  1  1  1
[2,]  2  2  2
[3,]  3  3  3

[[2]]
 V1 V2 V3
[1,]  4  4  4
[2,]  5  5  5
[3,]  6  6  6

[[3]]
 V1 V2 V3
[1,]  7  7  7
[2,]  8  8  8
[3,]  9  9  9

I'd like to calculate the moving average (interval = 2) i.e.

( x[[1]] + x[[2]] ) / 2
( x[[2]] + x[[3]] ) / 2
... and so on.

The desired output will return

2.5 2.5 2.5
3.5 3.5 3.5
4.5 4.5 4.5

5.5 5.5 5.5
6.5 6.5 6.5
7.5 7.5 7.5




Muhammad Rahiz  |  Doctoral Student in Regional Climate Modeling
Climate Research Laboratory, School of Geography  the Environment
Oxford University Centre for the Environment, University of Oxford
South Parks Road, Oxford, OX1 3QY, United Kingdom
Tel: +44 (0)1865-285194  Mobile: +44 (0)7854-625974
Email: muhammad.ra...@ouce.ox.ac.uk



milton ruser wrote:


  

Dear M.Rahiz,

Unfortunatelly I can't reproduce your example.
PLEASE do read the posting guide


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

bests

milton
On Sat, Jan 2, 2010 at 9:26 AM, Muhammad Rahiz
muhammad.ra...@ouce.ox.ac.ukmailto:muhammad.ra...@ouce.ox.ac.uk
wrote:
Hello useRs,

I'd like to perform a moving average on the dataset, xx. I've tried
combining the functions Reduce and rollmean but it didn't work.






r - function(n) rollmean(n, 2) # where 2 = averaging interval
output  - Reduce(r, x)



  

Error in f(init, x[[i]]) : unused argument(s) (x[[i]])

Is there anything wrong with the code in the first place?

where





x



  

[[1]]
 V1 V2 V3
[1,]  1  1  1
[2,]  2  2  2
[3,]  3  3  3

[[2]]
 V1 V2 V3
[1,]  4  4  4
[2,]  5  5  5
[3,]  6  6  6

[[3]]
 V1 V2 V3
[1,]  7  7  7
[2,]  8  8  8
[3,]  9  9  9

The moving average is to be performed on

1,4,7 = (1+4)/2 , (4+7)/2
2,5,8 = ..
3,6,9 = ..

Re: [R] Calling FING.EXE under RGui.EXE for windows.

2010-01-07 Thread Uwe Ligges


Argh. I see it as well. Will dig a lit tomorrow.

Uwe





On 07.01.2010 12:25, Gabor Grothendieck wrote:

I get a problem with shell too:

Under Rgui:


R.version.string

[1] R version 2.10.1 Patched (2010-01-01 r50884)


system(C:\\windows\\system32\\find /?, intern = TRUE)

character(0)


system(cmd /c C:\\windows\\system32\\find /?, intern = TRUE)

character(0)


shell(C:\\windows\\system32\\find /?)

Warning message:
In shell(C:\\windows\\system32\\find /?) :
  'C:\windows\system32\find /?' execution failed with error code 1

They all work, i.e. they give the required help message, under Rterm
and when I issue this from the Windows console it works:
C:\windows\system32\find /?


2010/1/7 Uwe Liggeslig...@statistik.tu-dortmund.de:



On 07.01.2010 02:04, Gabor Grothendieck wrote:


If you have C:\Rtools\bin on your PATH note that it contains a
UNIX-like find utility that conflicts with the find utility in
Windows.  If that is the problem then remove that from your PATH and
then run the batch file.

The batchfiles distribution at http://batchfiles.googlecode.com  has
utilities (Rgui.bat, R.bat, Rtools.bat, etc.) that will automatically
add C:\Rtools\bin to your path temporarily or only while R is running
so that you can leave it off your PATH.



I guess it's the use of system() rather than shell() that causes the
problem. Under Windows, you have to use shell in order to start a command
interpreter.

Uwe Ligges



On Wed, Jan 6, 2010 at 6:51 PM, John Schexnayderjsc...@us.ibm.com
  wrote:


This is sort of a strange bug.  Not show stopping, but annoying.  I was
wondering if anyone else has noticed this and reported it before I submit
a bug report.

I noticed while running the RGui and attempting to debug one of my
scripts
that I encountered a Windows error informing me that Find String [grep]
Utility has encountered a problem and needs to close.  It is being
generated by a call to a DOS batch file which contains a call to
Find.exe.
  It can be reproduced by simply typing  System(find) in RGui.  What I
found strange is that I have been running this script daily without this
problem for months.  I now realize I never ran that portion of the script
while in RGui.exe.  It has always run in batch mode which is done by
Rterm.exe.

I have tried this on three separate machines now all running Windows XP
SP3, with versions of R 2.8.1 and R 2.10.1  If executing System(find)
under RGui, an error window for the Find String Utility is generated and
the command is not exectuted.  If the same command is issued in Rterm the
expected FIND: Parameter format not correct message is properly
returned.

It doesn't seem an important bug, but it could be the canary in the mine
for a larger problem somewhere down the road.

Re,
John Schexnayder

IBM Tape Manufacturing - Information Technology
San Jose, CA  95138
jsc...@us.ibm.com

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Re: [R] factor graphics with pca in R?

2010-01-07 Thread Greg Hirson

Take a look at the FactoMineR and vegan packages. They may contain what 
you are looking for.


Greg

On 1/7/10 9:26 AM, Martin Ivanov wrote:

  Dear R users,
I need to know whether the factor graphics with principal component analysis 
are implemented in R. I mean the graphs where the variables are represented in 
a correlation circle, as described in more detail in this document:
http://www.unesco.org/webworld/idams/advguide/Chapt6_4_3.htm

It is not a pain to program it myself, nevertheless it would be a waste of time
  if it is already implemented in R.

Regards,
Martin

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--
Greg Hirson
ghir...@ucdavis.edu

Graduate Student
Agricultural and Environmental Chemistry

1106 Robert Mondavi Institute North
One Shields Avenue
Davis, CA 95616

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Re: [R] How to report or correct translations typos?

2010-01-07 Thread Pablo Emilio Verde

Dear Duncan,

Thank you  for clarifying this issue.

Cheers,

Pablo

- Original Message -
From: Duncan Murdoch murd...@stats.uwo.ca
To: Kenneth Roy Cabrera Torres krcab...@une.net.co
Cc: r-help@r-project.org; pabloemilio.ve...@uni-duesseldorf.de
Sent: Thursday, January 07, 2010 3:12 PM
Subject: Re: [R] How to report or correct translations typos?


 On 07/01/2010 9:04 AM, Kenneth Roy Cabrera Torres wrote:
  Hi R users and developers:
 
  Thanks to Mr Pablo Emilio Verde for his constribution
  to the spanish translation for R messages he makes a very
  good job.
 
  I find a tiny typo on the translation,
  in particular on the es.po file line 7312 it says:
  pueto
  it should be:
  puerto
 
  How can anybody might correct a typo or which is the
  best way to correct it on a future patch?
 

 You can see the translation teams listed on
 http://developer.r-project.org/TranslationTeams.html.  You send your
 corrections to them (as you have already done; this message is just to
 confirm you've done what you should do).

 Duncan Murdoch
  Thank you for your help.
 
  Kenneth
 
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[R] how to read script name in littler

2010-01-07 Thread Fabrizio Pollastri


Hello,

I am using littler to run my R code and I was looking for a way to read 
the running script name, but neither argv nor commandArgs() give me 
this information. Any suggestion? Thanks in advance.


F. Pollastri

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[R] Simple averaging question

2010-01-07 Thread lse1986


I have the following data:

http://i.imagehost.org/0650/Untitled2.jpg

How would i average, say the 5th and the 8th entries?
Thanks in advance
-- 
View this message in context: 
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Sent from the R help mailing list archive at Nabble.com.

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Re: [R] mean for subset

2010-01-07 Thread Matthew Dowle


Did you really say you're using Word's mail merge to construct hundreds of 
pages of R code which you then paste in to R ? It sounds like you just 
missed somehow how to create a function in R.  Did you fully read the book 
Introduction to R ?  Did you know R can read xls directly, and connect to 
spreadsheets as if they were databases, see ?odbcConnectExcel.

Your graphs may exist and be beautiful but are they correct ?   This link 
contains a formal discussion of the topic :
http://www.burns-stat.com/pages/Tutor/spreadsheet_addiction.html


Jerry Floren jerry.flo...@state.mn.us wrote in message 
news:1262877373634-1008892.p...@n4.nabble.com...

 As a novice R user, I face a similar challenge. I am almost afraid to 
 share
 with this group how I solved it. About 65 labs in our proficiency program
 submit data on individual Excel spreadsheets with triple replicates. There
 always are a few labs that do not complete the full set of three 
 replicates,
 and I do not want their data included in my analysis.

 First, I combine all the individual spreadsheets into one large Excel
 spreadsheet. The replicates are in three columns: rep1, rep2, and rep3. I
 sort on each individual rep column in Excel. Then I go to both the top and
 the bottom of the list.

 For example, I sort on rep1 and go to the top of the list to delete any 
 rows
 where a value for rep1 was not recorded. Then I go to the bottom of the 
 list
 and delete any rows where rep1 is text instead of a number, for example,
 0.001. I should say that the labs are instructed that they must complete
 all three replicates, and they must not enter results as text. Next I 
 repeat
 the process for rep2 and rep3.

 I'll do a little more work in Excel on the large, combined table with all
 the lab data. I calculate in Excel the mean, standard deviation, and
 coefficient of variation for each of the three reps. Finally, I filter all
 the data and delete duplicate rows. This is necessary as I sometimes
 accidentally copy the same spreadsheet two times from a lab into my large
 table. Finally, I save the cleaned up table in *.csv format that is easily
 read into R.

 I know that R can do all of these things, but if you are just learning how
 to use R it might be easier to do some initial work in Excel, or a similar
 spreadsheet, before running your data through R.

 I also use MS-Word's mail merge feature to generate my code. I'll get 
 three
 or four pages of code doing what I want for a single analytical test, for
 example, calcium. Then I'll use the mail merge feature to generate 
 hundreds
 of pages of code with the other analytical tests (nitrogen, phosphorus,
 potassium, etc.). I just copy and paste the large, merged Word document 
 into
 R. R cranks away for 30 minutes and I end up with several large tables 
 (and
 these get additional editing in Ecel) and hundreds of beautiful graphs 
 that
 would take weeks to create in Excel.

 I was amazed that Word would work. I expected all of Word's special print
 control codes would mess things up. I just recently received a new laptop
 computer, and now I have an occassional problem with Word's pretty print
 quotes, but if you know about that problem, it is easy to fix.

 Jerry Floren
 Minnesota Department of Agriculture





 Matthew Dowle-3 wrote:


 As can data.table (i.e. do 'having' in one statement) :

 DT = data.table(DF)
 DT[,list(n=length(NAME),mean(SCORE)),by=NAME][n==3]
   NAME n   V2
 [1,] James 3 64.0
 [2,]   Tom 3 78.7


 but data.table isn't restricted to SQL functions (such as avg),  any R
 functions can be used, sometimes for their side effects (such as 
 plotting)
 rather than just returning data.

 Further data.table has a thing called 'join inherited scoping'.   Say we
 knew the specific groups,  we can go directly to them (without even
 looking
 at the rest of the data in the table) in very short and convenient 
 syntax,
 which also happens to run quickly on large data sets (but can be useful
 just
 for the syntax alone) :

 setkey(DT,NAME)
 DT[c(James,Tom),mean(SCORE),mult=all]
   NAME   V1
 [1,] James 64.0
 [2,]   Tom 78.7


 Notice there is no group by or even a by in the above.  It inherits
 the
 scope from the join because mult=all means that James matches to
 multiple rows, as does Tom, creating two groups.  It does it by binary
 search to the beginning of each group,  binary search to the end of the
 group,  and runs the R expression inside the scope of that group.

 An example of join inherited scoping for the side effects only :

 pdf(out.pdf)
 DT[c(James,Tom),plot(SCORE),mult=all]
 NULL data table
 dev.off()
 # out.pdf now contains 2 plots

 which you couldn't do in SQL because SQL has no plotting (or any of R's
 other packages).

 It aims to do this quickly.  Where 'quickly' means 1) shorter code is
 quicker to write, read, debug and maintain  and also  2) quicker to
 compute,
 and its 1 that often dominates 2.

 Finally, consider the following two

Re: [R] Simple averaging question

2010-01-07 Thread Ista Zahn

Assuming the data frame is named X:

mean(X[c(5,8), Time])

See ?'[' for details.

-Ista

On Thu, Jan 7, 2010 at 1:20 PM, lse1986 sam_eden1...@yahoo.co.uk wrote:

 I have the following data:

 http://i.imagehost.org/0650/Untitled2.jpg

 How would i average, say the 5th and the 8th entries?
 Thanks in advance
 --
 View this message in context: 
 http://n4.nabble.com/Simple-averaging-question-tp1009086p1009086.html
 Sent from the R help mailing list archive at Nabble.com.

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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.




-- 
Ista Zahn
Graduate student
University of Rochester
Department of Clinical and Social Psychology
http://yourpsyche.org

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[R] Problem with writeBin and importing into gfortran compiled programs

2010-01-07 Thread jgarcia

Hi all,
I'm having problems trying to export binary arrays from R and importing
them into fortran (linux openSUSE 10.3 (x86_64), gfortran compiler,
fortran 90/95 program).

Let's say the problem can be expressed as:

R part

whini - runif(1000)
writeBin(whini,fwhini.dat)

f90 part

PROGRAM foo
INTEGER, PARAMETER :: DP = KIND(1.0D0)
INTEGER :: status
REAL(DP), DIMENSION(10,100) :: whini
OPEN(UNIT=5, FILE='fwhini.dat', STATUS='OLD', ACTION='READ', 
 FORM='UNFORMATTED', IOSTAT=status)
READ(5) whini
CLOSE(5)
WRITE(*,*) whini
END PROGRAM

Now, if within the R session I check

typeof(whini)
[1] double

and try

whini.copy - readBin(fwhini.dat,what=double(),n=1000)

the copy of whini is right. However, execution of the fortran program
gives the message:

Fortran runtime error: Unformatted file structure has been corrupted.

I've tried also to declare whini in the fortran part as SINGLE precision,
and to force writeBin using the size argument.
size=4 and size=8 give the same error (whini as double in the fortran
part), while size=16 gives the alternative error
Fortran runtime error: I/O past end of record on unformatted file

Please, could you help me with this problem?

Thanks,
Javier
---

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Re: [R] Generating data from Null Distribution

2010-01-07 Thread Greg Snow

Just randomly permute one of your columns (see ?sample) of the raw data (before 
using the table function to get the table).


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

 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
 project.org] On Behalf Of Jim Silverton
 Sent: Wednesday, January 06, 2010 1:17 AM
 To: r-help@r-project.org
 Subject: Re: [R] Generating data from Null Distribution
 
 Hello everyone,
 
 Can someone tell me exactly how to generate data from a null
 distribution
 for the fisher exact test? I know I have to use the hypergrometric but
 exactly what commands do I use?
 
 Jim
 
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 guide.html
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Re: [R] faster GLS code

2010-01-07 Thread Ravi Varadhan

Try this:


X - kronecker(diag(1,3),x)
Y - c(y) # stack the y in a vector

# residual covariance matrix for each observation
covar - kronecker(sigma,diag(1,N))

csig - chol2inv(covar)
betam2 - ginv(csig %*% X) %*% csig %*% Y

This is more than 2 times faster than your code (however, it doesn't compute 
`betav') . 

Here is a timing comparison:

# Your method
# GLS betas covariance matrix
system.time({
inv.sigma - solve(covar)
betav - solve(t(X)%*%inv.sigma%*%X)

# GLS mean parameter estimates
betam - betav%*%t(X)%*%inv.sigma%*%Y
})

# New method
system.time({
csig - chol2inv(covar)
betam2 - ginv(csig %*% X) %*% csig %*% Y
})

all.equal(betam, betam2)

 # GLS betas covariance matrix
 system.time({
+ inv.sigma - solve(covar)
+ betav - solve(t(X)%*%inv.sigma%*%X)
+ 
+ # GLS mean parameter estimates
+ betam - betav%*%t(X)%*%inv.sigma%*%Y
+ })
   user  system elapsed 
   1.140.511.76 
 
 system.time({
+ csig - chol2inv(covar)
+ betam2 - ginv(csig %*% X) %*% csig %*% Y
+ })
   user  system elapsed 
   0.470.080.61 
 
 all.equal(betam, betam2)
[1] TRUE



Hope this helps,
Ravi.


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

Ph. (410) 502-2619
email: rvarad...@jhmi.edu


- Original Message -
From: Carlo Fezzi c.fe...@uea.ac.uk
Date: Thursday, January 7, 2010 12:13 pm
Subject: [R] faster GLS code
To: r-help@r-project.org


 Dear helpers,
  
  I wrote a code which estimates a multi-equation model with generalized
  least squares (GLS). I can use GLS because I know the covariance 
 matrix of
  the residuals a priori. However, it is a bit slow and I wonder if anybody
  would be able to point out a way to make it faster (it is part of a bigger
  code and needs to run several times).
  
  Any suggestion would be greatly appreciated.
  
  Carlo
  
  
  ***
  Carlo Fezzi
  Senior Research Associate
  
  Centre for Social and Economic Research
  on the Global Environment (CSERGE),
  School of Environmental Sciences,
  University of East Anglia,
  Norwich, NR4 7TJ
  United Kingdom.
  email: c.fe...@uea.ac.uk
  ***
  
  Here is an example with 3 equations and 2 exogenous variables:
  
  - start code --
  
  
  N - 1000# number of observations
  library(MASS)
  
  ## parameters ##
  
  # eq. 1
  b10 - 7; b11 - 2; b12 - -1
  
  # eq. 2
  b20 - 5; b21 - -2; b22 - 1
  
  # eq.3
  b30 - 1; b31 - 5; b32 - 2
  
  # exogenous variables
  
  x1 - runif(min=-10,max=10,N)
  x2 - runif(min=-5,max=5,N)
  
  # residual covariance matrix
  sigma - matrix(c(2,1,0.7,1,1.5,0.5,0.7,0.5,2),3,3)
  
  # residuals
  r - mvrnorm(N,mu=rep(0,3), Sigma=sigma)
  
  # endogenous variables
  
  y1 - b10 + b11 * x1 + b12*x2 + r[,1]
  y2 - b20 + b21 * x1 + b22*x2 + r[,2]
  y3 - b30 + b31 * x1 + b32*x2 + r[,3]
  
  y - cbind(y1,y2,y3) # matrix of endogenous
  x - cbind(1,x1, x2) # matrix of exogenous
  
  
   MODEL ESTIMATION ###
  
  # build the big X matrix needed for GLS estimation:
  
  X - kronecker(diag(1,3),x)
  Y - c(y)  # stack the y in a vector
  
  # residual covariance matrix for each observation
  covar - kronecker(sigma,diag(1,N))
  
  # GLS betas covariance matrix
  inv.sigma - solve(covar)
  betav - solve(t(X)%*%inv.sigma%*%X)
  
  # GLS mean parameter estimates
  betam - betav%*%t(X)%*%inv.sigma%*%Y
  
  - end of code 
  
  __
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  PLEASE do read the posting guide 
  and provide commented, minimal, self-contained, reproducible code.

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Re: [R] Building static HTML help pages in R 2.10.x on Windows

2010-01-07 Thread Kevin Wright

Well, among other things, if my global environment becomes
cluttered/corrupt/etc and I quit R, then restart R, the links in my browser
are now dead.  I have to close all the tabs and call help to open them
again.  Also, the R-supplied java tool for searching help is ancient and
underwhelming.  A desktop search tool (X1/Copernic/GoogleDesktop/etc) can be
very handy, but only if it has pre-built help files to index.  Imperfect,
stale, non-dynamic help is better than no help at all!

As others have done, I have switched back to 2.9.2 until I can build all
help files (on Windows).  Thanks to those people who are figuring out how to
do this.

Kevin

On Thu, Jan 7, 2010 at 11:50 AM, Duncan Murdoch murd...@stats.uwo.cawrote:

 On 07/01/2010 11:36 AM, Jonathan Baron wrote:

 For what it is worth, I would gladly sacrifice this capability in
 order to be able to consult all my R help pages through a Firefox
 bookmark to the packages listing (which is what I used to do, and will
 do again, when I get time to either rebuild from source or get the
 forthcoming Fedora RPM, which will have static pages as the default),
 without starting an R session.



 What's so hard about leaving an R session running, and using bookmarks as
 Dieter described?

 Duncan Murdoch

  Jon

 On 01/07/10 10:32, Duncan Murdoch wrote:
  A more useful example than ls() would be methods().   I think it would 
 be nice to have a list of methods included in the man page for a generic 
 function, and links to their pages if they have their own man pages.   You
 might want to list all installed methods, with some sort of  highlighting
 to indicate which ones are already attached, or perhaps be  able to toggle
 between installed and attached, or whatever.  None of  that is possible
 with static help, not even a list of installed methods,  because someone
 might install a new package that offers some others  after the static help
 has already been built.
   You just need to use some imagination.
   Duncan Murdoch


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-- 
Kevin Wright

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[R] Help formating data to display commas

2010-01-07 Thread Anderson, Chris

I'm using the following code to create quartile intervals of my dataset and it 
is working like it is suppose too. In my final output of the data I would like 
currency amounts to be displayed with commas. I have not found an option either 
through FormatC or sprintf that will display the data with commas, they only 
seem to add decimals. Is there a format that will display commas without me 
reverting to the labels statement.  This is an ongoing process where the values 
are updated, so using the labels statement would be too much to manage.


Benchparaq-levels(quantcut(benchmarkPara$Benchmark_Total, q=seq(0,1,by=0.25), 
na.rm=TRUE))

 #,labels=c($267,000-$436,000,$436,000-$559,000,$559,000-$836,000,$836,000-$1,590,000))
 lower -as.numeric(sub(\\((.+),.*, \\1, Benchparaq))
Warning: NAs introduced by coercion
 upper - as.numeric(sub([^,]*,([^]]*)\\], \\1, Benchparaq))
 lower-ifelse(is.na(lower),0,as.numeric(lower))
 upper-ifelse(is.na(upper),0,as.numeric(upper))
 lower
[1]  0 436000 559000 836000
 upper
[1]  436000  559000  836000 159
 Benchparaq-paste($,lower,-,$,upper,sep=)
   lower-NULL
   upper-NULL
 Benchparaq
[1] $0-$436000   $436000-$559000  $559000-$836000  
$836000-$159


Chris Anderson
Data Analyst
Medical Affairs
wk: 925-677-4870
cell: 707-315-8486
Fax:925-677-4670





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[R] %d/%m/%Y can not be displayed in a .rd file

2010-01-07 Thread rusers.sh

Hi all,
  I found the date format (e.g.%d/%m/%Y) in the .rd file cannot be
displayed after building the package. See below,
###.rd file
\examples{
a-10/20/1999
DateConversion(a,DateIn=%m/%d/%Y,DateOut=%d/%m/%Y)
}
The result is 
Examples:
 a-10-20-1999
 DateConversion(a,DateIn=

  ??%m/%d/%Y seems cannot be recognized.
Is there some method to solve this and make it visible?
  Thanks a lot.
-- 
-
Jane Chang
Queen's

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Re: [R] Drop a part of an array\list\vector?



On Jan 7, 2010, at 1:15 PM, Idgarad wrote:

I did have a verbose description of why but rather then make  
everyone's eyes

bleed with useless details I ask the following :)
To make a long story short: How can I make newmcReg[[i]][PreIO308]  
go
away in the following list... er vector... no wait array  
dataframe

awww crap...



The data type returned by summary appears to be    a table, ...   
which means it can be indexed as would be a matrix:



 summary(data.frame( a= c(TRUE, FALSE, TRUE), b= c(TRUE,TRUE,TRUE),  
cc =c(a, b , c) ))

 a  b   cc
 Mode :logical   Mode:logical   a:1
 FALSE:1 TRUE:3 b:1
 TRUE :2 NA's:0 c:1
 NA's :0

 str(summary(data.frame( a= c(TRUE, FALSE, TRUE), b=  
c(TRUE,TRUE,TRUE), cc =c(a, b , c) )))
 'table' chr [1:4, 1:3] Mode :logical   FALSE:1 TRUE : 
2 NA's :0 ...

 - attr(*, dimnames)=List of 2
  ..$ : chr [1:4]
  ..$ : chr [1:3] ab cc

 summary(data.frame( a= c(TRUE, FALSE, TRUE), b= c(TRUE,TRUE,TRUE),  
cc =c(a, b , c) ))[, 1:2]

 ab
 Mode :logical   Mode:logical  
 FALSE:1 TRUE:3
 TRUE :2 NA's:0
 NA's :0 NA

Although there appear to be some underlying print-issues.

--
David




summary(newmcReg[[i]])
UNITBUILD UNITDB ITBUILD   ITDB
Mode :logical   Mode :logical   Mode :logical   Mode :logical
FALSE:249   FALSE:249   FALSE:249   FALSE:249
TRUE :21TRUE :21TRUE :21TRUE :21



 UATBUILD UATDB HOGANCODE  ACF
Mode :logical   Mode :logical   Mode :logical   Mode :logical
FALSE:250   FALSE:250   FALSE:208   FALSE:225
TRUE :20TRUE :20TRUE :62TRUE :45



   RCF  ReleaseST1  ReleaseST2  ReleaseBLA
Mode :logical   Mode :logical   Mode :logical   Mode :logical
FALSE:186   FALSE:167   FALSE:157   FALSE:228
TRUE :84TRUE :103   TRUE :113   TRUE :42



MonthlyST1  MonthlyST2  MonthlyBLA   
Small.Bank.Acquisitions

Mode :logical   Mode :logical   Mode :logical   Min.   :0.
FALSE:107   FALSE:105   FALSE:147   1st Qu.:0.
TRUE :163   TRUE :165   TRUE :123   Median :0.
Mean   :0.1556
3rd Qu.:0.
Max.   :1.
 Conversions  Build.New.Environment HLY.NewYear  HLY.MLK
Min.   :0.0   Mode :logical Mode :logical   Mode :logical
1st Qu.:0.0   FALSE:262 FALSE:266   FALSE:264
Median :0.0   TRUE :8   TRUE :4 TRUE :6
Mean   :0.08889
3rd Qu.:0.0
Max.   :1.0
 HLY.PRES   HLY.MEMORIAL  HLY.J4HLY.LABOR
Mode :logical   Mode :logical   Mode :logical   Mode :logical
FALSE:264   FALSE:265   FALSE:265   FALSE:265
TRUE :6 TRUE :5 TRUE :5 TRUE :5



HLY.COLUMBUS HLY.VETS   HLY.THANKS   HLY.XMAS
Mode :logical   Mode :logical   Mode :logical   Mode :logical
FALSE:265   FALSE:265   FALSE:265   FALSE:265
TRUE :5 TRUE :5 TRUE :5 TRUE :5



HLY.ELECT   HLY.PATRIOTEOMNEWMF
Mode :logical   Mode :logical   Mode :logical   Mode :logical
FALSE:265   FALSE:265   FALSE:210   FALSE:263
TRUE :5 TRUE :5 TRUE :60TRUE :7



 PreIO47 PreIO151PreIO164PreIO169
Mode :logical   Mode :logical   Mode :logical   Mode :logical
FALSE:269   FALSE:269   FALSE:269   FALSE:269
TRUE :1 TRUE :1 TRUE :1 TRUE :1



 PreIO197PreIO203PreIO209PreIO241
Mode :logical   Mode :logical   Mode :logical   Mode :logical
FALSE:269   FALSE:269   FALSE:269   FALSE:269
TRUE :1 TRUE :1 TRUE :1 TRUE :1



 PreIO261PreIO308
Mode :logical   Mode :logical
FALSE:269   FALSE:270
TRUE :1


(the PreIO are outliers identified from the output of stl() e.g.  
outliers in

the source data)

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David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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Re: [R] faster GLS code

2010-01-07 Thread Charles C. Berry


On Thu, 7 Jan 2010, Ravi Varadhan wrote:


Try this:


X - kronecker(diag(1,3),x)
Y - c(y) # stack the y in a vector

# residual covariance matrix for each observation
covar - kronecker(sigma,diag(1,N))

csig - chol2inv(covar)
betam2 - ginv(csig %*% X) %*% csig %*% Y

This is more than 2 times faster than your code (however, it doesn't compute 
`betav') .



Faster still (by a wide margin) if X will truly be of that form:


B - coef(lm(y~0+.,as.data.frame(x)))
all.equal( as.vector((B)), as.vector(betam))

[1] TRUE

When X is of that form, the covariance matrix drops out of the 
computation.


:)

Chuck



Here is a timing comparison:

# Your method
# GLS betas covariance matrix
system.time({
inv.sigma - solve(covar)
betav - solve(t(X)%*%inv.sigma%*%X)

# GLS mean parameter estimates
betam - betav%*%t(X)%*%inv.sigma%*%Y
})

# New method
system.time({
csig - chol2inv(covar)
betam2 - ginv(csig %*% X) %*% csig %*% Y
})

all.equal(betam, betam2)


# GLS betas covariance matrix
system.time({

+ inv.sigma - solve(covar)
+ betav - solve(t(X)%*%inv.sigma%*%X)
+
+ # GLS mean parameter estimates
+ betam - betav%*%t(X)%*%inv.sigma%*%Y
+ })
  user  system elapsed
  1.140.511.76


system.time({

+ csig - chol2inv(covar)
+ betam2 - ginv(csig %*% X) %*% csig %*% Y
+ })
  user  system elapsed
  0.470.080.61


all.equal(betam, betam2)

[1] TRUE





Hope this helps,
Ravi.


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

Ph. (410) 502-2619
email: rvarad...@jhmi.edu


- Original Message -
From: Carlo Fezzi c.fe...@uea.ac.uk
Date: Thursday, January 7, 2010 12:13 pm
Subject: [R] faster GLS code
To: r-help@r-project.org



Dear helpers,

 I wrote a code which estimates a multi-equation model with generalized
 least squares (GLS). I can use GLS because I know the covariance
matrix of
 the residuals a priori. However, it is a bit slow and I wonder if anybody
 would be able to point out a way to make it faster (it is part of a bigger
 code and needs to run several times).

 Any suggestion would be greatly appreciated.

 Carlo


 ***
 Carlo Fezzi
 Senior Research Associate

 Centre for Social and Economic Research
 on the Global Environment (CSERGE),
 School of Environmental Sciences,
 University of East Anglia,
 Norwich, NR4 7TJ
 United Kingdom.
 email: c.fe...@uea.ac.uk
 ***

 Here is an example with 3 equations and 2 exogenous variables:

 - start code --


 N - 1000   # number of observations
 library(MASS)

 ## parameters ##

 # eq. 1
 b10 - 7; b11 - 2; b12 - -1

 # eq. 2
 b20 - 5; b21 - -2; b22 - 1

 # eq.3
 b30 - 1; b31 - 5; b32 - 2

 # exogenous variables

 x1 - runif(min=-10,max=10,N)
 x2 - runif(min=-5,max=5,N)

 # residual covariance matrix
 sigma - matrix(c(2,1,0.7,1,1.5,0.5,0.7,0.5,2),3,3)

 # residuals
 r - mvrnorm(N,mu=rep(0,3), Sigma=sigma)

 # endogenous variables

 y1 - b10 + b11 * x1 + b12*x2 + r[,1]
 y2 - b20 + b21 * x1 + b22*x2 + r[,2]
 y3 - b30 + b31 * x1 + b32*x2 + r[,3]

 y - cbind(y1,y2,y3)# matrix of endogenous
 x - cbind(1,x1, x2)# matrix of exogenous


  MODEL ESTIMATION ###

 # build the big X matrix needed for GLS estimation:

 X - kronecker(diag(1,3),x)
 Y - c(y)  # stack the y in a vector

 # residual covariance matrix for each observation
 covar - kronecker(sigma,diag(1,N))

 # GLS betas covariance matrix
 inv.sigma - solve(covar)
 betav - solve(t(X)%*%inv.sigma%*%X)

 # GLS mean parameter estimates
 betam - betav%*%t(X)%*%inv.sigma%*%Y

 - end of code 

 __
 R-help@r-project.org mailing list

 PLEASE do read the posting guide
 and provide commented, minimal, self-contained, reproducible code.


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



Charles C. Berry(858) 534-2098
Dept of Family/Preventive Medicine
E mailto:cbe...@tajo.ucsd.edu   UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901

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Re: [R] Problem with writeBin and importing into gfortran compiled programs


On 07/01/2010 2:05 PM, jgar...@ija.csic.es wrote:

Hi all,
I'm having problems trying to export binary arrays from R and importing
them into fortran (linux openSUSE 10.3 (x86_64), gfortran compiler,
fortran 90/95 program).

Let's say the problem can be expressed as:

R part

whini - runif(1000)
writeBin(whini,fwhini.dat)

f90 part

PROGRAM foo
INTEGER, PARAMETER :: DP = KIND(1.0D0)
INTEGER :: status
REAL(DP), DIMENSION(10,100) :: whini
OPEN(UNIT=5, FILE='fwhini.dat', STATUS='OLD', ACTION='READ', 
 FORM='UNFORMATTED', IOSTAT=status)
READ(5) whini
CLOSE(5)
WRITE(*,*) whini
END PROGRAM

Now, if within the R session I check

typeof(whini)
[1] double

and try

whini.copy - readBin(fwhini.dat,what=double(),n=1000)

the copy of whini is right. However, execution of the fortran program
gives the message:

Fortran runtime error: Unformatted file structure has been corrupted.

I've tried also to declare whini in the fortran part as SINGLE precision,
and to force writeBin using the size argument.
size=4 and size=8 give the same error (whini as double in the fortran
part), while size=16 gives the alternative error
Fortran runtime error: I/O past end of record on unformatted file

Please, could you help me with this problem?
I've never used Fortran 90, so I can't tell if your type declaration is 
really declaring double precision values.
So what I'd do is to create an array (say the values 1 to 1000) within 
your Fortran program, and write it out.
Then do the same in R, and do a binary compare of the files to see what 
the differences are.  The things to look for are:


Size of values (4 or 8 bytes or something else).

Byte order within values (big or little endian).

R is very flexible in what it writes, and probably Fortran is flexible 
in what it can read, but you need to figure out what the differences are 
before you can match them up.


The viewRaw() function in the hexView package is a simple way to look at 
the bytes in the files.


Duncan Murdoch

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Re: [R] Building static HTML help pages in R 2.10.x on Windows


On 07/01/2010 2:16 PM, Kevin Wright wrote:

Well, among other things, if my global environment becomes
cluttered/corrupt/etc and I quit R, then restart R, the links in my browser
are now dead.

You weren't following Dieter's instructions, then.


  I have to close all the tabs and call help to open them
again.  Also, the R-supplied java tool for searching help is ancient and
underwhelming.


Then contribute a new one.

  A desktop search tool (X1/Copernic/GoogleDesktop/etc) can be
very handy, but only if it has pre-built help files to index.  Imperfect,
stale, non-dynamic help is better than no help at all!
  


Then fix the search tool so it can search dynamic web pages.  They can 
be spidered too, just like static ones.


Duncan Murdoch

As others have done, I have switched back to 2.9.2 until I can build all
help files (on Windows).  Thanks to those people who are figuring out how to
do this.
  
Kevin


On Thu, Jan 7, 2010 at 11:50 AM, Duncan Murdoch murd...@stats.uwo.cawrote:

 On 07/01/2010 11:36 AM, Jonathan Baron wrote:

 For what it is worth, I would gladly sacrifice this capability in
 order to be able to consult all my R help pages through a Firefox
 bookmark to the packages listing (which is what I used to do, and will
 do again, when I get time to either rebuild from source or get the
 forthcoming Fedora RPM, which will have static pages as the default),
 without starting an R session.



 What's so hard about leaving an R session running, and using bookmarks as
 Dieter described?

 Duncan Murdoch

  Jon

 On 01/07/10 10:32, Duncan Murdoch wrote:
  A more useful example than ls() would be methods().   I think it would 
 be nice to have a list of methods included in the man page for a generic 
 function, and links to their pages if they have their own man pages.   You
 might want to list all installed methods, with some sort of  highlighting
 to indicate which ones are already attached, or perhaps be  able to toggle
 between installed and attached, or whatever.  None of  that is possible
 with static help, not even a list of installed methods,  because someone
 might install a new package that offers some others  after the static help
 has already been built.
   You just need to use some imagination.
   Duncan Murdoch


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[R] Debugging issues encountered during the R CMD check process

2010-01-07 Thread Jason Rupert

I read through the Writing R Extensions and the Debugging in R website 
(http://www.stats.uwo.ca/faculty/murdoch/software/debuggingR/), looking for 
some hints about how to solve the issue of debugging problems encountered 
during the R CMD check process, but nothing seems to be mentioned about 
addressing issues encountered. 

Specifically, I am working with the R signal package which is hosted at the 
following location:
http://code.google.com/p/r-signal/

I would like to debug the problem that is shown below, and is encountered when 
I run R CMD check signal. 

Thank you for any insights that are provided as the R signal package is nice 
and it would be good to have it working again with R 2.9.x and beyond. 

Thank you again for the help. 

From the 00check.log

* using log directory 
'/Users/jasonkrupert/Documents/RStuff/Rsignal/r-signal/signal.Rcheck'
* using R version 2.9.2 (2009-08-24)
* using session charset: UTF-8
* checking for file 'signal/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'signal' version '0.6'
* checking package dependencies ... OK
* checking if this is a source package ... WARNING



 
 ### Name: interp
 ### Title: Interpolate / Increase the sample rate
 ### Aliases: interp
 ### Keywords: math
 
 ### ** Examples
 
 
 # The graph shows interpolated signal following through the
 # sample points of the original signal.
 t = seq(0, 2, by = 0.01)
 x = chirp(t,2,.5,10,'quadratic') + sin(2*pi*t*0.4)
 y = interp(x[seq(1, length(x), by = 4)],4,4,1)   # interpolate a sub-sample
Warning in rbind(x, array(val, dim = c(n - nx, NCOL(x :
  number of columns of result is not a multiple of vector length (arg 1)
Warning in Fft(postpad(x, N)) * B :
  longer object length is not a multiple of shorter object length
Error in ifft(Fft(postpad(x, N)) * B) : 
  dims [product 36] do not match the length of object [256]
Calls: interp - fftfilt - fftfiltx - ifft
Execution halted

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[R] weight by obs # in spatial 'nest' in NLME?

2010-01-07 Thread Seth


Hi,

I am constructing a series of nonlinear mixed regression models at multiple
spatial scales on the same data.  The data is a regular grid of cells.  A
coarser scale is achieved, for example, by aggregating cells in blocks that
are 2x2 cells in dimension and averaging dependent and independent data over
this block.  Some 2x2 blocks will be missing data for several expected
reasons and these blocks are of interest and so cannot be easily discarded
(they are also likely not at random).  I would like to take this into
account when fitting the model.  A simple weighting of each block by number
of complete component observations (e.g. no missing data would have a weight
of 2x2=4) seems intuitive.  I've reviewed the NLME documentation and
weighting schemes seem to be the usual variety of accounting for unequal
variance.  Is there a work around to specify the integer weights I described
above?  I've toyed with a work around where I duplicate each block
observation by the number of observations summarized within it.  Of course,
this is difficult to do correctly as the sample size will be inflated and
most statistics not easily interpretable.  Any advice on how to proceed is
welcome.  Thanks. -seth
-- 
View this message in context: 
http://n4.nabble.com/weight-by-obs-in-spatial-nest-in-NLME-tp1009168p1009168.html
Sent from the R help mailing list archive at Nabble.com.

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R-help@r-project.org mailing list
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Re: [R] Debugging issues encountered during the R CMD check process


On 07/01/2010 2:48 PM, Jason Rupert wrote:
I read through the Writing R Extensions and the Debugging in R website (http://www.stats.uwo.ca/faculty/murdoch/software/debuggingR/), looking for some hints about how to solve the issue of debugging problems encountered during the R CMD check process, but nothing seems to be mentioned about addressing issues encountered. 


Specifically, I am working with the R signal package which is hosted at the 
following location:
http://code.google.com/p/r-signal/

I would like to debug the problem that is shown below, and is encountered when I run R CMD check signal. 

Thank you for any insights that are provided as the R signal package is nice and it would be good to have it working again with R 2.9.x and beyond. 

Thank you again for the help. 


From the 00check.log

* using log directory 
'/Users/jasonkrupert/Documents/RStuff/Rsignal/r-signal/signal.Rcheck'
* using R version 2.9.2 (2009-08-24)
* using session charset: UTF-8
* checking for file 'signal/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'signal' version '0.6'
* checking package dependencies ... OK
* checking if this is a source package ... WARNING



 
 ### Name: interp

 ### Title: Interpolate / Increase the sample rate
 ### Aliases: interp
 ### Keywords: math
 
 ### ** Examples
 
 
 # The graph shows interpolated signal following through the

 # sample points of the original signal.
 t = seq(0, 2, by = 0.01)
 x = chirp(t,2,.5,10,'quadratic') + sin(2*pi*t*0.4)
 y = interp(x[seq(1, length(x), by = 4)],4,4,1)   # interpolate a sub-sample
Warning in rbind(x, array(val, dim = c(n - nx, NCOL(x :
  number of columns of result is not a multiple of vector length (arg 1)
Warning in Fft(postpad(x, N)) * B :
  longer object length is not a multiple of shorter object length
Error in ifft(Fft(postpad(x, N)) * B) : 
  dims [product 36] do not match the length of object [256]

Calls: interp - fftfilt - fftfiltx - ifft
Execution halted

  


You'll often get more informative error messages in recent R releases if 
you set the environment variable


R_KEEP_PKG_SOURCE=yes

I don't know if it will help in this case.

Duncan Murdoch

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Re: [R] regex question on escaping . (and a couple other regex questions as well)