date:20120111




On 10.01.2012 22:40, R. Michael Weylandt michael.weyla...@gmail.com wrote:

What lists are you referring to when you state: there are many packages that do not 
show up in the list of binaries. They do in the list of sources? CRAN? To see all 
packages installed on your machine try

rownames(installed.packages(())

I think available.packages() will give packages available from your local CRAN 
mirror.

Just a hunch, but if you are seeing different behaviors between home and work 
it may well be that a work-firewall is blocking packages which contain 
pre-compiled DLLs/SOs while allowing the source code through.

Also, if you aren't on Windows the vast majority of packages are quite easy to 
learn compile yourself

Michael

On Jan 10, 2012, at 4:01 PM, natalia nordennatnor...@gmail.com  wrote:


Thank you very much for your answers. I could do it by downloading the
package I needed manually and then installing it through the Terminal. Yet
the fundamental problem remains. I downloaded R 2.14.1 several times from
different mirrors



I think you should change the mirror for the installation of packages, 
not for downloading R.


Uwe Ligges




and there are many packages that do not show up in the
list of binaries. They do in the list of sources, but then I have a
problem compiling the package... I did not have this problem from my home
computer when I installed R 2.14.0.

Best,
Natalia


El 10/01/12 14:52, Ken Hutchisonvicvoncas...@gmail.com  escribió:


Maybe check your proxy settings in your browser and make sure you're
connecting to the mirror.
   Ken

Sent from my iPhone

On Jan 10, 2012, at 8:35 AM, natalia nordennatnor...@gmail.com  wrote:


Hello,

I was using version 2.13.2 and I have just downloaded the latest version
2.14.1. However, I'm trying to install the packages I was using and
when I
look for them in the packages list, I can´t find many in the CRAN
binaries
(e.g. vegan). I do find them in the CRAN sources but the installation
fails. I tried downloading the version 2.14.0 and I had the same
problem. I
re-installed the old version, and now it works again. Is this a problem
with
2.14?
Thank you for your help.
Natalia Norden



Natalia Norden
Profesor Asistente
Departamento de Ecología y Territorio
Facultad de Estudios Ambientales y Rurales
Pontificia Universidad Javeriana
Bogotá, Colombia
Tel: 320 83 20  Ext: 2448
www.phylodiversity.net/nnorden/



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Re: [R] Max value of an integer

2012-01-11 Thread Berend Hasselman


rmx wrote
 
 Hi.
 Is there any constant that represents the maximum value of an integer?
 If I need to setup by myself what is the maximum value?
 

?.Machine

i.e.

.Machine$integer.max

Berend


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Re: [R] 2 sample wilcox.test != kruskal.test

2012-01-11 Thread Łukasz Ręcławowicz

2012/1/11 syrvn ment...@gmx.net

 Hi,

 thanks for your answer. Unfortunately I cannot reproduce your results.

 In my example the results still differ when I use your approach:

  x - c(10,11,15,8,16,12,20)
  y - c(10,14,18,25,28,30,35)
  f - as.factor(c(rep(a,7), rep(b,7)))
  d - c(x,y)
  kruskal.test(x,y)


Try to compare  wilcox.test and right formula in kruskal, I got:
 all.equal(wilcox.test(x,y, correct =
F,exact=F)$p.value,kruskal.test(d~f)$p.value)
[1] TRUE

-- 
Mi³ego dnia

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Re: [R] 64bit R under 32bit winxp

2012-01-11 Thread Prof Brian Ripley


On 11/01/2012 08:55, Jeff Newmiller wrote:

You cannot install 64-bit R on 32-bit OS,


Technically, you can (but by default the packaged installers will refuse 
to do so).  What you cannot do is run 64-bit R on a 32-bit version of 
Windows: the OS will refuse to run the executables (and if it is old 
enough, not even recognize them).


The only reason for mentioning this is for the record.  People do drag 
up R-help postings from years past (someone recently sent me a response 
to one from the 1990s).


We do plan to allow both versions of R to be installed on 32-bit Windows 
in the future (with a warning).  You still will not be able to run them, 
but you will be able to make binary packages for both versions: also 
this could be useful for system-wide installations from a 32-bit server OS.


 but you can install a 32-bit R on a 64-bit OS, and you can later 
install 64-bit R as well. That is, installing 32-bit R does not 
interfere with your option to later install a 64-bit R.

---
Jeff NewmillerThe .   .  Go Live...
DCN:jdnew...@dcn.davis.ca.us Basics: ##.#.   ##.#.  Live Go...
   Live:   OO#.. Dead: OO#..  Playing
Research Engineer (Solar/BatteriesO.O#.   #.O#.  with
/Software/Embedded Controllers)   .OO#.   .OO#.  rocks...1k
---
Sent from my phone. Please excuse my brevity.

孟欣lm_meng...@163.com  wrote:


Hi all:


My OS is 32bit winxp,but I wanna install 64bit R2.14.1.


 From the following website,it says You can also go back and add
64-bit components to a 32-bit install, or vice versa
http://cran.r-project.org/bin/windows/rw-FAQ.html#Can-both-32_002d-and-64_002dbit-R-be-installed-on-the-same-machine_003f




Does it mean that I can install and run 64bit R2.14.1 under 32bit
winxp?If so,how can I add 64-bit components to a 32-bit install?




Many thanks for your help.




My best
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Re: [R] 2 sample wilcox.test != kruskal.test

2012-01-11 Thread Meyners, Michael

The devil is in the details (and in the arguments in Lukasz code). The defaults 
for the two functions are different: wilcox.test uses an exact test (which is 
not available in kruskal.test afaik) for your data, and uses the continuity 
correction if the normal approximation is requested (neither available in 
kruskal.test). See the manual (in particular ?wilcox.test) for details, or the 
pertinent literature for the theoretical background.

HTH, Michael


 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
 project.org] On Behalf Of Lukasz Reclawowicz
 Sent: Wednesday, January 11, 2012 12:00
 To: syrvn
 Cc: r-help@r-project.org
 Subject: Re: [R] 2 sample wilcox.test != kruskal.test
 
 2012/1/11 syrvn ment...@gmx.net
 
  Hi,
 
  thanks for your answer. Unfortunately I cannot reproduce your
 results.
 
  In my example the results still differ when I use your approach:
 
   x - c(10,11,15,8,16,12,20)
   y - c(10,14,18,25,28,30,35)
   f - as.factor(c(rep(a,7), rep(b,7))) d - c(x,y)
   kruskal.test(x,y)
 
 
 Try to compare  wilcox.test and right formula in kruskal, I got:
  all.equal(wilcox.test(x,y, correct =
 F,exact=F)$p.value,kruskal.test(d~f)$p.value)
 [1] TRUE
 
 --
 Mi³ego dnia
 
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[R] Constructing a data.frame from csv files

2012-01-11 Thread Vincy Pyne

Dear R helpers,

Following is my R code where I am trying to calculate returns and then trying 
to create a data.frame. Since, I am not aware how many instruments I will be 
dealing so I have constructed a function. My R code is as follows -

library(plyr)

mydata - data.frame(instru_name = 
c(instru_A,instru_A,instru_A,instru_A,instru_A,instru_A,instru_A,instru_A,instru_A,instru_A,instru_A,instru_A,instru_A,instru_A,instru_B,instru_B,instru_B,instru_B,instru_B,instru_B,instru_B,instru_B,instru_B,instru_B,instru_B,instru_B,instru_B,instru_B),
 date = c(10-Jan-12,9-Jan-12,8-Jan-12, 7-Jan-12, 
6-Jan-12,5-Jan-12,4-Jan-12,3-Jan-12,2-Jan-12,1-Jan-12, 31-Dec-11, 
30-Dec-11,29-Dec-11,28-Dec-11,10-Jan-12,9-Jan-12,8-Jan-12, 
7-Jan-12,6-Jan-12,5-Jan-12,4-Jan-12,3-Jan-12,2-Jan-12,1-Jan-12,31-Dec-11,30-Dec-11,29-Dec-11,28-Dec-11),
 price = c(11.9,10.5,13,14.5,14.4,14.8,10.1,12,14.3, 
10.7,11.2,10.2,10.2,10.8,41.9,40.5,43,44.5,44.4,48.8,42.1,44,46.3,48.7,46.2,44.2,42.2,40.8))

attach(mydata)

opt_return_volatilty = function(price, instru_name)

{

price_returns = matrix(data = NA, nrow = (length(price)-1), ncol = 1)
    for (i in(1:(length(price)-1)))
    {
    price_returns[i] = log(price[i]/price[i+1])
    }
volatility = sd(price_returns)
entity_returns = unique(instru_name)
colnames(price_returns) = entity_returns

write.csv(price_returns, file = paste(entity_returns, .csv, sep = ), 
row.names = FALSE)

return(data.frame(list(volatility = volatility)))

}

entity_volatility - ddply(.data=mydata, .variables = instru_name,
    .fun=function(x) opt_return_volatilty(price = x$price, 
instru_name = x$instru_name))


 entity_volatility
  instru_name volatility
1    instru_A 0.17746897
2    instru_B 0.06565341                
                
                
fileNames - list.files(pattern = instru.*.csv)

 fileNames
[1] instru_A.csv instru_B.csv

# 
_

# MY QUERY

# I need to construct the data frame consisting of all the returns. I.e. I need 
to have # a data.frame like 

instru_A instru_B
0.125163143  0.033983853 
-0.2135741  -0.059898142 
-0.109199292    -0.034289073  
0.006920443  0.00224972 
-0.027398974    -0.094490843  

I am using following Code 

input - do.call(rbind, lapply(fileNames, function(.name)
    {
    .data - read.csv(.name, header = TRUE, as.is = TRUE)
    .data$file - .name
    .data
    }))

# I get following error.
    
    Error in match.names(clabs, names(xi)) : 
  names do not match previous names

  
 Kindly guide

Regards

Vincy

 

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Re: [R] Problem with segmented

2012-01-11 Thread Vito Muggeo (UniPa)


dear Phil,
I am not able to read the error message.. did you forget it?

However: does x exist in the workspace?

The following lines work:

myreg2 = lm(y ~ x, data=xy)
mysegmented = segmented(myreg2, seg.Z=~x, psi=c(245000))

myreg2 = lm(xy$y ~ xy$x)
x-xy$x
mysegmented = segmented(myreg2, seg.Z=~x, psi=c(245000))


The following line does *not* work (as specified in ?segmented, argument 
seg.Z)


myreg2 = lm(xy$y ~ xy$x)
mysegmented = segmented(myreg2, seg.Z=~xy$x, psi=c(245000)) #error


Hope to have been clear,
vito



Il 10/01/2012 17.17, Filoche ha scritto:

Hi everyone.

I'm trying to use the segmented function with the following data:


For instance, I use segmented package as follow:

myreg2 = lm(xy$y ~ xy$x)
mysegmented = segmented(myreg2, seg.Z=~x, psi=c(245000), control =
seg.control(display=FALSE))

Which get me to the following error :


As a break point, a starting guess of 245000 seems fair.

Anyone has an idea why I'm getting such error?

Regards,
Phil

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viale delle Scienze, edificio 13
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Re: [R] runif with condition

2012-01-11 Thread Duncan Murdoch


On 12-01-11 5:12 AM, peter dalgaard wrote:


On Jan 10, 2012, at 18:11 , AlanM wrote:


I have to disagree with what's been posted, but I think some very interesting
points have been addressed.  I'd like to add my two cents.

Consider the pair {X, 1-X} where X is sampled from a uniform(0,1)
distribution.  The quantity 1- X also comes from a uniform(0,1) distribution
and therefore is probabilistic and not deterministic.

The sum of independent random variables is itself a random variable.


Also of non-independent ones, provided you allow the possibility of a 
degenerate distribution, as in the case above.


If X1,
X2  X3 are


independent and


uniformly distributed, then the distribution of Y = X1 + X2 + X3
can be determined (i.e. Y is probabilistic and NOT deterministic).  Y is a
random variable, but it is correlated with X1, X2 and X3.  The set {X1, X2,
X3, 100 - (X1 + X2 + X3) } contains 4 random variables, however they are
neither independent or identically distributed.



Yes. You can achieve various properties like X1+X2+X3+X4=100, X1,...,X4 
identically distributed, but not independent and not uniform. (Generate 4 
independent variables from some distribution on the positive axis and rescale 
to the required sum.)

You can't have X1,...,X4 all uniform on (0,100), even if non-independent, with 
a sum of 100, because the mean of the sum would be the sum of the means, i.e., 
200!

Whether you can have X1,...,X4, exchangeable and uniform on (0,50) is, er, an 
interesting question. (I would say probably not, but I can't think of an 
argument.)


I think it probably is possible -- it's basically a 4 dimensional 
copula, and those are pretty flexible.  We have a construction for 2D, 
and I think I have one in 3D.  (In 3D, the intersection of the plane 
X+Y+Z=100 with the cube [0,50]^3 is a regular hexagon; you just need to 
spread the mass over the hexagon in the right way to get uniform marginals.)


I think the shape W+X+Y+Z=100 makes when it intersects with the 4-cube 
is a regular octahedron in some projection, but I don't know how to 
distribute mass over it for uniform marginals.


Duncan Murdoch






If you are curious, check this out.

Deriving the Probability Density for Sums of Uniform Random Variables
Edward J. Lusk and Haviland Wright
The American Statistician
Vol. 36, No. 2 (May, 1982), pp. 128-130

Thanks to the OP.  This has become an interesting thread.

-Alan Mitchell

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Re: [R] 2 sample wilcox.test != kruskal.test

2012-01-11 Thread syrvn

Hi Michael and Mi³ego dnia,

yes right. I get identical results now! thanks a lot!

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[R] spplot : help with legend

2012-01-11 Thread Ana

Hi!

I am looking for some examples on how to plot using spplot the overlay
of :polygon+point+point
both point files are different files with different coordinates.

I am planning on doing something like this:

polygon.file=readShapeSpatial(polygons)
l1 = list(sp.points, points.file1, pch = 19,col = red)
l2 = list(sp.points, points.file2, pch = 19,col = green)

spplot(polygon.file, common,col=black, sp.layout = list(l1,l2))

However I didn't find any help on how to do the legend, except for
these examples:
http://www.nceas.ucsb.edu/scicomp/usecases/CreateMapsWithRGraphics
http://casoilresource.lawr.ucdavis.edu/drupal/node/962

It seems there is a way to do it, but too confusing for me (mapLegendGrob2)

Any help is appreciated!

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[R] get the percentage rank of a value based on an empirical data vector

2012-01-11 Thread Martin Batholdy

Hi,

I have a vector with values:

x - rnorm(1000, 5, 2)


and one single value:
y - 6.2

now I would like to know the percent rank of y based on the 'population'-vector 
x.
Is there a convenient function that calculates the percent rank of a y for the 
given vector x?


thanks!
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Re: [R] Constructing a data.frame from csv files

2012-01-11 Thread jim holtman

The error message says it all:  the dataframes that you are creating,
and then trying to 'rbind', do not have the same columns.  You need to
at least show what the first couple of lines of each of you input
files are, or output the names of the columns as you are reading the
files.  This is some elementary debugging that you will have to learn.

On Wed, Jan 11, 2012 at 7:38 AM, Vincy Pyne vincy_p...@yahoo.ca wrote:
 Dear R helpers,

 Following is my R code where I am trying to calculate returns and then trying 
 to create a data.frame. Since, I am not aware how many instruments I will be 
 dealing so I have constructed a function. My R code is as follows -

 library(plyr)

 mydata - data.frame(instru_name = 
 c(instru_A,instru_A,instru_A,instru_A,instru_A,instru_A,instru_A,instru_A,instru_A,instru_A,instru_A,instru_A,instru_A,instru_A,instru_B,instru_B,instru_B,instru_B,instru_B,instru_B,instru_B,instru_B,instru_B,instru_B,instru_B,instru_B,instru_B,instru_B),
  date = c(10-Jan-12,9-Jan-12,8-Jan-12, 7-Jan-12, 
 6-Jan-12,5-Jan-12,4-Jan-12,3-Jan-12,2-Jan-12,1-Jan-12, 
 31-Dec-11, 
 30-Dec-11,29-Dec-11,28-Dec-11,10-Jan-12,9-Jan-12,8-Jan-12, 
 7-Jan-12,6-Jan-12,5-Jan-12,4-Jan-12,3-Jan-12,2-Jan-12,1-Jan-12,31-Dec-11,30-Dec-11,29-Dec-11,28-Dec-11),
  price = c(11.9,10.5,13,14.5,14.4,14.8,10.1,12,14.3, 
 10.7,11.2,10.2,10.2,10.8,41.9,40.5,43,44.5,44.4,48.8,42.1,44,46.3,48.7,46.2,44.2,42.2,40.8))

 attach(mydata)

 opt_return_volatilty = function(price, instru_name)

 {

 price_returns = matrix(data = NA, nrow = (length(price)-1), ncol = 1)
     for (i in(1:(length(price)-1)))
     {
     price_returns[i] = log(price[i]/price[i+1])
     }
 volatility = sd(price_returns)
 entity_returns = unique(instru_name)
 colnames(price_returns) = entity_returns

 write.csv(price_returns, file = paste(entity_returns, .csv, sep = ), 
 row.names = FALSE)

 return(data.frame(list(volatility = volatility)))

 }

 entity_volatility - ddply(.data=mydata, .variables = instru_name,
     .fun=function(x) opt_return_volatilty(price = x$price, 
 instru_name = x$instru_name))


 entity_volatility
   instru_name volatility
 1    instru_A 0.17746897
 2    instru_B 0.06565341


 fileNames - list.files(pattern = instru.*.csv)

 fileNames
 [1] instru_A.csv instru_B.csv

 # 
 _

 # MY QUERY

 # I need to construct the data frame consisting of all the returns. I.e. I 
 need to have # a data.frame like

 instru_A instru_B
 0.125163143  0.033983853
 -0.2135741  -0.059898142
 -0.109199292    -0.034289073
 0.006920443  0.00224972
 -0.027398974    -0.094490843

 I am using following Code

 input - do.call(rbind, lapply(fileNames, function(.name)
     {
     .data - read.csv(.name, header = TRUE, as.is = TRUE)
     .data$file - .name
     .data
     }))

 # I get following error.

     Error in match.names(clabs, names(xi)) :
   names do not match previous names


  Kindly guide

 Regards

 Vincy



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Data Munger Guru

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

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Re: [R] How to make this for() loop memory efficient?

2012-01-11 Thread Martin Morgan


On 01/11/2012 12:09 AM, iliketurtles wrote:

Ray, your solution works and is indeed faster than mine!

It looks like it's going to take a few days to to 400,000 rows, still, which
is unfortunate.

Steve, thanks for your help, I'll definitely self-teach plyr and data.table.


I added a column with the first two digits of the module

  data$XX - substr(L[,2], 1, 2)

then created a data frame that summarized the first module of each call 
and the length of the phone call


  df - with(data,
 data.frame(FirstModule=tapply(XX, `phone calls`, `[[`, 1),
Length=tapply(XX, `phone calls`, length)))

then summarized the length of the phone calls associated with each module

  with(df, tapply(Length, FirstModule, mean))

resulting in

 with(df, tapply(Length, FirstModule, mean))
  82   84   92   93   94   96   97
1.00 2.00 1.75 1.67 1.00 1.22 1.67

Martin



-


Isaac
Research Assistant
Quantitative Finance Faculty, UTS
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http://r.789695.n4.nabble.com/How-to-make-this-for-loop-memory-efficient-tp4283594p4284716.html
Sent from the R help mailing list archive at Nabble.com.

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--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793

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Re: [R] get the percentage rank of a value based on an empirical data vector

2012-01-11 Thread R. Michael Weylandt michael.weyla...@gmail.com



On Jan 11, 2012, at 8:12 AM, Martin Batholdy wrote:


Hi,

I have a vector with values:

x - rnorm(1000, 5, 2)


and one single value:
y - 6.2

now I would like to know the percent rank of y based on the  
'population'-vector x.
Is there a convenient function that calculates the percent rank of a  
y for the given vector x?


Two options :
1) sort x and use findInterval, divide the index by length(x) and  
multiply by 100

(It can all be done as a one-liner.)

2) I generally reach for the `ecdf` function making machine when I  
see sample quantile problems and see if I can cast the problem in  
terms for which it applies.


For my random draw I get:
 findInterval(6.2, sort(x))
[1] 704
 xecdf - ecdf(x)
 xecdf(6.2)
[1] 0.704

--
David Winsemius, MD
West Hartford, CT

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[R] Help with speed (replacing the loop?)

2012-01-11 Thread Dimitri Liakhovitski

Dear R-ers,

I have a loop below that loops through my numeric variables in data
frame x and through levels of the factor group and multiplies (group
by group) the values of numeric variables in x by the corresponding
group-specific values from data frame y. In reality, my:
dim(x) is 300,000 rows by 100 variables, and
dim(y) is 120 levels of group by 100 variables.
So, my huge data frame x takes up a lot of space in memory. This is
why I am actually replacing values of a and b in x with newly
calculated values, rather than adding them.
The code does what I need, but it takes forever.

Is there maybe a more speedy way to achieve what I need?
Thanks a lot!
Dimitri


# Example data:
x-data.frame(group=c(rep(group1,5),rep(group2,5)),
a=1:10,b=seq(10,100,by=10))
x$group-as.factor(x$group)
y-data.frame(group=c(group1,group2),a=c(10,20),b=c(2,3))
y$group-as.factor(y$group)
(x);(y)

# My code:
myvars-c(a,b)
for(var in myvars){
for(group in levels(y$group)){
  temp-x[x$group %in% group,var]
  temp-temp * y[y$group %in% group,var]
  x[x$group %in% group,var]-temp
}
}
(x)
-- 
Dimitri Liakhovitski

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Re: [R] R problem: unable to read data in the xls-format in the PerformAnalytics package

2012-01-11 Thread Joshua Ulrich

On Wed, Jan 11, 2012 at 2:41 AM, ysei...@bluewin.ch ysei...@bluewin.ch wrote:
 Hallo

 I have the following problem

 1) Problem: I am unable to read data in the xls-format in the PerformAnalytics
 package.
 While it works well for several commands, e.g.
 t(table.Stats(msci_ret))

 it does not work for other
 commands, e.g.
 x
 - msci_ret[, c(CH), drop = FALSE]
 table.Drawdowns(x)

 The error code is:
 Error in checkData(R) :

 The data cannot be
 converted into a time series.  If you are trying to pass in names from a data 
 object with one
 column, you should use the form 'data[rows, columns, drop = FALSE]'.  
 Rownames should have standard date formats, such
 as '1985-03-15'.



 2) I guess it is the German data format after I transform the data from ts 
 -- xls.
 Jan 1970
 -0.025317808
 -0.0488751680 -0.006219300 -0.0737541890 -0.015215166 Feb 1970 -0.016650677 
 -0.0289782710 -0.053743041
 0.0548771330
 0.012912517
 Mrz 1970 -0.000312907  0.0094675260  0.025474411  0.0060957210  0.040465110 
 ...
 Okt 2010
 0.029227924
 0.0572494500  0.024199223  0.0386233850 -0.016248884 Nov 2010 -0.023411677  
 0.0133836160 -0.024089614
 0.0011141310
 0.060007812
 Dez 2010  0.019613741  0.0375536810  0.065130745  0.0647369970  0.041147678

 ... but I am not
 sure, perhaps
 it is something else.

 3) What I did: I save excel-data (6 raw time series with a header line) in 
 the csv-
 format and read it in R, first in ts, and then converting it to csv:
 msci_ret = ts(msci_ret, start=1970, frequency=12)
 msci_ret -
 as.xts(msci_ret)

Please provide a reproducible example (your file was not attached).
Use dput() to include a _small_ sample of your data.  My guess is that
Excel is not saving the dates to the CSV in a standard date format.

 Apparently, I do not understand exactly how to generate a date format for 
 monthly data
 which can be read unter PerformanceAnalytics.
 I attach my csv data.
 Thanks for your help!
 yvonne

Best,
--
Joshua Ulrich  |  FOSS Trading: www.fosstrading.com

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Re: [R] get the percentage rank of a value based on an empirical data vector

If performance is an issue, I think mean(x  y) will be as quick as it can be 
done in R alone (you could do it in C in a single pass if needed which might be 
a good first exercise in using compiled code)

Michael

On Jan 11, 2012, at 8:58 AM, David Winsemius dwinsem...@comcast.net wrote:

 
 On Jan 11, 2012, at 8:12 AM, Martin Batholdy wrote:
 
 Hi,
 
 I have a vector with values:
 
 x - rnorm(1000, 5, 2)
 
 
 and one single value:
 y - 6.2
 
 now I would like to know the percent rank of y based on the 
 'population'-vector x.
 Is there a convenient function that calculates the percent rank of a y for 
 the given vector x?
 
 Two options :
 1) sort x and use findInterval, divide the index by length(x) and multiply by 
 100
 (It can all be done as a one-liner.)
 
 2) I generally reach for the `ecdf` function making machine when I see 
 sample quantile problems and see if I can cast the problem in terms for which 
 it applies.
 
 For my random draw I get:
  findInterval(6.2, sort(x))
 [1] 704
  xecdf - ecdf(x)
  xecdf(6.2)
 [1] 0.704
 
 -- 
 David Winsemius, MD
 West Hartford, CT
 
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[R] general question on Spotfire

2012-01-11 Thread John Smith

Dear R users,

I have been using R for 10 years, and I love it very much. But in my daily
job for drug discovery, some people use Spotfire. I tried Spotfire on
couple of data sets. It sounds I still need do some data manipulation
before plot figures. For example, I can not plot figure with data arranged
in rows (is this true, or I am stupid?).   So far I don't feel any benefit
Spotfire can provide over R. I am just wondering whether it just because I
am new to Spotfire, or it's true that Spotfire is not a good tool for
statistician.

Also could anyone give me any suggestion how to learn Spotfire?

Thanks

John

[[alternative HTML version deleted]]

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Re: [R] Help with speed (replacing the loop?)

2012-01-11 Thread Steve Lianoglou

Hi,

On Wed, Jan 11, 2012 at 9:57 AM, Dimitri Liakhovitski
dimitri.liakhovit...@gmail.com wrote:
 Dear R-ers,

 I have a loop below that loops through my numeric variables in data
 frame x and through levels of the factor group and multiplies (group
 by group) the values of numeric variables in x by the corresponding
 group-specific values from data frame y. In reality, my:
 dim(x) is 300,000 rows by 100 variables, and
 dim(y) is 120 levels of group by 100 variables.
 So, my huge data frame x takes up a lot of space in memory. This is
 why I am actually replacing values of a and b in x with newly
 calculated values, rather than adding them.
 The code does what I need, but it takes forever.

 Is there maybe a more speedy way to achieve what I need?
 Thanks a lot!

Here's an all-middle-steps included way to do so using data.table. If
you use more data.table-centric idioms (using `:=` operator and other
ways to `merge`) you can likely eek out less memory and higher speed,
but I'll leave it like so for pedagogical purposes ;-)


library(data.table)

## your data
xx - data.table(group=c(rep(group1,5),rep(group2,5)),
 a=1:10, b=seq(10,100,by=10), key=group)
yy - data.table(group=c(group1,group2), a=c(10,20), b=c(2,3),
 key=group)

## temp data.table to get your ducks in a row
m - merge(xx, yy, by=group, suffixes=c(.x, .y))

## your answers will be in the aa and bb columns
result - transform(m, aa=a.x * a.y, bb=b.x * b.y)



Truth be told, if you use normal data.frames, the code will look very
similar to above, so you can try that, too.

HTH,
-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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Re: [R] general question on Spotfire

2012-01-11 Thread Duncan Murdoch


On 12-01-11 10:13 AM, John Smith wrote:

Dear R users,

I have been using R for 10 years, and I love it very much. But in my daily
job for drug discovery, some people use Spotfire. I tried Spotfire on
couple of data sets. It sounds I still need do some data manipulation
before plot figures. For example, I can not plot figure with data arranged
in rows (is this true, or I am stupid?).   So far I don't feel any benefit
Spotfire can provide over R. I am just wondering whether it just because I
am new to Spotfire, or it's true that Spotfire is not a good tool for
statistician.

Also could anyone give me any suggestion how to learn Spotfire?


Shouldn't you be asking this question to Spotfire users?

Duncan Murdoch

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Re: [R] plotOHLC(alpha3): Error in plotOHLC(alpha3) : x is not a open/high/low/close time series

2012-01-11 Thread Joshua Ulrich

Hi Ted,

On Tue, Jan 10, 2012 at 1:59 PM, Ted Byers r.ted.by...@gmail.com wrote:
 R version 2.12.0, 64 bit on Windows.

 Here is a short script that illustrates the problem:
 library(tseries)
 library(xts)
 setwd('C:\\cygwin\\home\\Ted\\New.Task\\NKs-01-08-12\\NKs\\tests')
 x = read.table(quotes_h.2.dat, header = FALSE, sep=\t, skip=0)
 str(x)
 y - data.frame(as.POSIXlt(paste(x$V2,substr(x$V4,4,8),sep=
 ),format='%Y-%m-%d %H:%M'),x$V5)
 colnames(y) - c(tickdate,price)
 str(y)
 plot(y)
 z - as.irts(y)
 str(z)
 plot(z)
 str(alpha3)
 List of 2
 $ time : POSIXt[1:98865], format: 2010-06-30 15:47:00 2010-06-30
 15:53:00 2010-06-30 17:36:00 ...
 $ value: num [1:98865, 1:4] 9215 9220 9205 9195 9195 ...
  ..- attr(*, dimnames)=List of 2
  .. ..$ : NULL
  .. ..$ : chr [1:4] z.Open z.High z.Low z.Close
 - attr(*, class)= chr ts
 - attr(*, tsp)= num [1:3] 1 2 1

This is a big clue.  Your alpha3 object is a list with two elements 1)
the datetime, and 2) the OHLC values as a ts object.  There's no
as.xts() method for this type of object.

 alpha3 - as.xts(to.minutes3(z,OHLC = TRUE))

Look at str(z).  Why did you convert z to an irts object instead of
directly to an xts object?  to.minutes() expects an xts object.  Try
something like this instead:
z - xts(y[,2], y[,1])
alpha3 - to.minutes3(z, OHLC=TRUE)

 plotOHLC(alpha3)
 Error in plotOHLC(alpha3) : x is not a open/high/low/close time series

 The file quotes_h.2.dat contains real time tick data for futures contracts,
 so the above manipulation is my attempt to just get a time series with one
 column being a date/time and the other being tick price.  I believe I have
 to use read.table to make a data frame, and then the manipulations to
 combine the date and time fields from that feed, along with the price.

 My first attempt at using to.minutes3 (and I am interested in the other
 'to.period' functions too), is to get a regular time series to which I can
 apply rollapply, along with a function in which I use various autoregression
 methods, along with forecasting for as long as the 95% confidence intervals
 is reasonably close - I want to know how far into the future the forecast
 contains useful information.  And then, I want to create a plot in which I
 do the autoregression, and then plot the actual and forecast prices (along
 with the confidence interval), as a function of time, embed that in a
 function, which rollappply works with, so I can have a plot comprised of all
 those individual plots (plotting only the comparison of actual and forecast
 values).

 It seems everything works adequately until I try the plotOHLC function
 itself, which gives me the error in the subject line.

 I would ask for two things:
 1) what the fix is to get rid of that error plotOHLC gives me
 2) some tips on the 'walk-forward' method I am looking at using.

 Thanks
 Ted


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--
Joshua Ulrich  |  FOSS Trading: www.fosstrading.com

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Re: [R] Help with speed (replacing the loop?)

2012-01-11 Thread Dimitri Liakhovitski

Thanks a lot, Steve. I have one question (below):


 
 library(data.table)

 ## your data
 xx - data.table(group=c(rep(group1,5),rep(group2,5)),
                 a=1:10, b=seq(10,100,by=10), key=group)
 yy - data.table(group=c(group1,group2), a=c(10,20), b=c(2,3),
                 key=group)

 ## temp data.table to get your ducks in a row
 m - merge(xx, yy, by=group, suffixes=c(.x, .y))


Dimitri: The step above (merge) - I was thinking of it but decided
against it because my xx already fills up tons of memory. When I merge
xx and yy that doubles the number of variables - I am afraid my memory
won't hold that much stuff...


 ## your answers will be in the aa and bb columns
 result - transform(m, aa=a.x * a.y, bb=b.x * b.y)

 

 Truth be told, if you use normal data.frames, the code will look very
 similar to above, so you can try that, too.

 HTH,
 -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



-- 
Dimitri Liakhovitski
marketfusionanalytics.com

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Re: [R] get the percentage rank of a value based on an empirical data vector

2012-01-11 Thread Martin Batholdy

  findInterval(6.2, sort(x))
 [1] 704
  xecdf - ecdf(x)
  xecdf(6.2)
 [1] 0.704


thanks, that helped a lot!




On 11.01.2012, at 14:58, David Winsemius wrote:

 
 On Jan 11, 2012, at 8:12 AM, Martin Batholdy wrote:
 
 Hi,
 
 I have a vector with values:
 
 x - rnorm(1000, 5, 2)
 
 
 and one single value:
 y - 6.2
 
 now I would like to know the percent rank of y based on the 
 'population'-vector x.
 Is there a convenient function that calculates the percent rank of a y for 
 the given vector x?
 
 Two options :
 1) sort x and use findInterval, divide the index by length(x) and multiply by 
 100
 (It can all be done as a one-liner.)
 
 2) I generally reach for the `ecdf` function making machine when I see 
 sample quantile problems and see if I can cast the problem in terms for which 
 it applies.
 
 For my random draw I get:
  findInterval(6.2, sort(x))
 [1] 704
  xecdf - ecdf(x)
  xecdf(6.2)
 [1] 0.704
 
 -- 
 David Winsemius, MD
 West Hartford, CT
 

__
R-help@r-project.org mailing list
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Re: [R] CairoPDF and greek letter spacing

2012-01-11 Thread Walker, John Stephen

Thanks for the input, but I can confirm the either form of the paste command 
i.e. expression(paste(Length (, mu*m, ))) or my original which had 
expression(paste(Length (, mu, m))), and the expression command alone have 
the same effect. It may be limited to Linux machines 
(which I did state I used  in my first post) as when I previously used an OS X 
machine I didn't see the bug.   I don't use OS X anymore, I've implemented a 
completely Linux based 
lab and would like to get this sorted out. Any suggestions? Rolf, if you can 
repoduce it then I think we have a bug report but to whom? R or Cairo?

John




From: David Winsemius [dwinsem...@comcast.net]
Sent: Monday, January 09, 2012 10:36 PM
To: Rolf Turner
Cc: Walker, John Stephen; r-help@r-project.org
Subject: Re: [R] CairoPDF and greek letter spacing

On Jan 10, 2012, at 12:22 AM, Rolf Turner wrote:

 On 10/01/12 15:25, David Winsemius wrote:

 On Jan 9, 2012, at 8:19 PM, Rolf Turner wrote:

 On 10/01/12 11:40, John Walker wrote:
 I have a small problem with R graphics output. When I use the
 lattice
 package and CairoPDF to generate publication quality graphs I
 often use
 the expression to create an axis title that has microlitres or
 micrometers as a unit. I use something like the following
 'expression(paste(Length (, mu,m )))' as an argument to the
 xlabel
 function. The command works but the mu and 'm' have a space between
 them. It looks like 'u m' rather than 'um'. It only seems to
 happen with
 the CairoPDF output on my linux machine, it's fine on the X11
 device.
 I've fixed it in the past by importing the pdf into inkscape and
 manually adjusting the spacing (it's more difficult than it sounds
 because I can't actually adjust the spacing but have to delete
 the mu
 and re-enter it).  Is there something I'm doing wrong? Is this a
 known
 bug?  How can I fix it?
 I can't help, but I can confirm the problem, for what *that* is
 worth.

 It seems be an unfortunate interaction between lattice graphics and
 the cairo_pdf() device.

 The space between the mu and the m does not appear with
 ``ordinary'' R graphics, irrespective of device, nor does it appear
 with lattice graphics and, e.g. the pdf() device.  But it does
 appear
 with lattice graphics *and* the cairo_pdf() device.

 That probably means that the problem is subtle and will be difficult
 to impossible to fix. :-(

 Doubtful. Do either of you realize that `paste` is a plotmath
 function that is misused more often than correctly used (at least
 as judged by the number o errors submitted to r-help)? I see no
 workable example, but if I did I would be trying instead :

 expression(Length~mu*m)

 You meant expression(Length==mu*m).

I thought what was wanted:

main=expression(Length~group((,mu*m,))) # Or

main=expression(Length~(*mu*m*))


And on a Mac (Leopard, R 2.14.1 Patched)  I could not get a different
display on the screen device and either pdf or cairo_pdf so your
experience may have something to do with the as yet unstated OSes.


  And yes that helps a bit, but there's
 still a bit more space between the mu and the m than one would like.

 Compare:

require(lattice)
cairo_pdf(file=mung.pdf)

 print
 (xyplot
 (y~x,data=data.frame(x=1:10,y=1:10),main=expression(Length==mu*m)))
dev.off()
 and
pdf(file=gorp.pdf)

 print
 (xyplot
 (y~x,data=data.frame(x=1:10,y=1:10),main=expression(Length==mu*m)))
dev.off()

 There's not much in it, but there's just enough to be annoying.

cheers,

Rolf

 P. S.  And I have never been able to figure out *anything* about how
 paste() and
 expression() interact.  It is a complete mystery, and a matter of
 trying things more
 or less at random until something more or less works.

R. T.

 P^2. S.  I just realised that there's more space between the letters
 of Length in
 the cairo_pdf version, as well.  Which is, I guess, The
 Explanation.  Is it a font thing?

R. T.

David Winsemius, MD
West Hartford, CT

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Re: [R] general question on Spotfire

2012-01-11 Thread John Smith

I am struggling whether I should learn Spotfire or not. I just want some
statisticians inputs.

Thanks



On Wed, Jan 11, 2012 at 10:28 AM, Duncan Murdoch
murdoch.dun...@gmail.comwrote:

 On 12-01-11 10:13 AM, John Smith wrote:

 Dear R users,

 I have been using R for 10 years, and I love it very much. But in my daily
 job for drug discovery, some people use Spotfire. I tried Spotfire on
 couple of data sets. It sounds I still need do some data manipulation
 before plot figures. For example, I can not plot figure with data arranged
 in rows (is this true, or I am stupid?).   So far I don't feel any benefit
 Spotfire can provide over R. I am just wondering whether it just because I
 am new to Spotfire, or it's true that Spotfire is not a good tool for
 statistician.

 Also could anyone give me any suggestion how to learn Spotfire?


 Shouldn't you be asking this question to Spotfire users?

 Duncan Murdoch


[[alternative HTML version deleted]]

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[R] Generating unque patient IDs

2012-01-11 Thread Ayyappa Chaturvedula

Dear group,

I am trying to prepare a NONMEM friendly dataset for population PK
analysis. My patient IDs are 10 digit long and NONMEM is losing precison
and rouding the last couple of digits.  I need to generate unique Patient
IDs fromt he current 10-digit IDs.  Ihave total 250 subjects so I
appreciate if anybody can suggest me a way to code this in R.

Regards,
Ayyappa

[[alternative HTML version deleted]]

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Re: [R] Help with speed (replacing the loop?)

2012-01-11 Thread Steve Lianoglou

Hi,

On Wed, Jan 11, 2012 at 10:50 AM, Dimitri Liakhovitski
dimitri.liakhovit...@gmail.com wrote:
 Thanks a lot, Steve. I have one question (below):


 
 library(data.table)

 ## your data
 xx - data.table(group=c(rep(group1,5),rep(group2,5)),
                 a=1:10, b=seq(10,100,by=10), key=group)
 yy - data.table(group=c(group1,group2), a=c(10,20), b=c(2,3),
                 key=group)

 ## temp data.table to get your ducks in a row
 m - merge(xx, yy, by=group, suffixes=c(.x, .y))


 Dimitri: The step above (merge) - I was thinking of it but decided
 against it because my xx already fills up tons of memory. When I merge
 xx and yy that doubles the number of variables - I am afraid my memory
 won't hold that much stuff...

Fair enough ... how about just using `match`, then, ie:

R aa - x$a * y$a[match(x$group, y$group)]

Should do the trick, no?

-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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Re: [R] general question on Spotfire

2012-01-11 Thread peter dalgaard

On Jan 11, 2012, at 16:28 , Duncan Murdoch wrote:

On 12-01-11 10:13 AM, John Smith wrote:
Dear R users,

I have been using R for 10 years, and I love it very much. But in my daily
job for drug discovery, some people use Spotfire. I tried Spotfire on
couple of data sets. It sounds I still need do some data manipulation
before plot figures. For example, I can not plot figure with data arranged
in rows (is this true, or I am stupid?). So far I don't feel any benefit
Spotfire can provide over R. I am just wondering whether it just because I
am new to Spotfire, or it's true that Spotfire is not a good tool for
statistician.

Also could anyone give me any suggestion how to learn Spotfire?

Shouldn't you be asking this question to Spotfire users?

Just to clue in the casual reader, Spotfire embeds a version of S+, which is,
er, sort of, like, a predecessor to R, so John is not completely off target.

Documents comparing R and S+ should be useful to him. There are books that are
bilingual, such as Venables and Ripley MASS and S Programming, but I also
spotted this on TIBCO's own site:

http://spotfire.tibco.com/community/blogs/stn/archive/2010/11/04/differences-between-r-and-spotfire-s.aspx

Also, there are (claimed to be) facilities to integrate R itself in Spotfire,
which could be a rather expedient solution.

Duncan Murdoch

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

Re: [R] Help with speed (replacing the loop?)

2012-01-11 Thread Jeff Newmiller

It is common that performance problems are addressed by using more memory. If 
your algorithm needs to join those tables and do calculations, then you can 
either pay the piper in memory (usually the most appropriate answer) or you can 
reinvent those optimized algorithms in a compiled language and figure out how 
to thread them together to minimize memory use (a dangerous course of action). 
Try working on chunks of xx? Or getting more memory in your computer?
---
Jeff NewmillerThe .   .  Go Live...
DCN:jdnew...@dcn.davis.ca.usBasics: ##.#.   ##.#.  Live Go...
  Live:   OO#.. Dead: OO#..  Playing
Research Engineer (Solar/BatteriesO.O#.   #.O#.  with
/Software/Embedded Controllers)   .OO#.   .OO#.  rocks...1k
--- 
Sent from my phone. Please excuse my brevity.

Dimitri Liakhovitski dimitri.liakhovit...@gmail.com wrote:

Thanks a lot, Steve. I have one question (below):


 
 library(data.table)

 ## your data
 xx - data.table(group=c(rep(group1,5),rep(group2,5)),
                 a=1:10, b=seq(10,100,by=10), key=group)
 yy - data.table(group=c(group1,group2), a=c(10,20), b=c(2,3),
                 key=group)

 ## temp data.table to get your ducks in a row
 m - merge(xx, yy, by=group, suffixes=c(.x, .y))


Dimitri: The step above (merge) - I was thinking of it but decided
against it because my xx already fills up tons of memory. When I merge
xx and yy that doubles the number of variables - I am afraid my memory
won't hold that much stuff...


 ## your answers will be in the aa and bb columns
 result - transform(m, aa=a.x * a.y, bb=b.x * b.y)

 

 Truth be told, if you use normal data.frames, the code will look very
 similar to above, so you can try that, too.

 HTH,
 -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



-- 
Dimitri Liakhovitski
marketfusionanalytics.com

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[R] Odp: Generating unque patient IDs

2012-01-11 Thread Petr PIKAL

Hi
 
 Dear group,
 
 I am trying to prepare a NONMEM friendly dataset for population PK
 analysis. My patient IDs are 10 digit long and NONMEM is losing precison
 and rouding the last couple of digits.  I need to generate unique 
Patient
 IDs fromt he current 10-digit IDs.  Ihave total 250 subjects so I
 appreciate if anybody can suggest me a way to code this in R.

I would start with

?abbreviate
and check uniqueness with 
?unique or ?duplicated

Regards
Petr


 
 Regards,
 Ayyappa
 
[[alternative HTML version deleted]]
 
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[R] test for condition during whole r session or after each command

2012-01-11 Thread Jannis


Dear List,


is there any way to test for certain conditions during the whole r 
session or after the execution of each command? I am debugging my code 
and sometimes a certain logical error causes a program error much later 
in the script/function so especially with loops etc it is hard to 
backtrace the condition or situation that actually created the error.



Any ideas?
Jannis

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Re: [R] Odp: Generating unque patient IDs

2012-01-11 Thread jim holtman

Does this do it for you:

 sprintf(%010.0f, seq(10.0, length = 250, by = 1.0))
  [1] 10 11 12 13 14
15 16
  [8] 17 18 19 100010 100011
100012 100013
 [15] 100014 100015 100016 100017 100018
100019 100020
 [22] 100021 100022 100023 100024 100025
100026 100027
 [29] 100028 100029 100030 100031 100032
100033 100034
 [36] 100035 100036 100037 100038 100039
100040 100041
 [43] 100042 100043 100044 100045 100046
100047 100048
 [50] 100049 100050 100051 100052 100053
100054 100055
 [57] 100056 100057 100058 100059 100060
100061 100062
 [64] 100063 100064 100065 100066 100067
100068 100069
 [71] 100070 100071 100072 100073 100074
100075 100076
 [78] 100077 100078 100079 100080 100081
100082 100083
 [85] 100084 100085 100086 100087 100088
100089 100090
 [92] 100091 100092 100093 100094 100095
100096 100097

On Wed, Jan 11, 2012 at 11:32 AM, Petr PIKAL petr.pi...@precheza.cz wrote:
 Hi

 Dear group,

 I am trying to prepare a NONMEM friendly dataset for population PK
 analysis. My patient IDs are 10 digit long and NONMEM is losing precison
 and rouding the last couple of digits.  I need to generate unique
 Patient
 IDs fromt he current 10-digit IDs.  Ihave total 250 subjects so I
 appreciate if anybody can suggest me a way to code this in R.

 I would start with

 ?abbreviate
 and check uniqueness with
 ?unique or ?duplicated

 Regards
 Petr



 Regards,
 Ayyappa

    [[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.



-- 
Jim Holtman
Data Munger Guru

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

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Re: [R] Generating unque patient IDs



On Jan 11, 2012, at 11:12 AM, Ayyappa Chaturvedula wrote:


Dear group,

I am trying to prepare a NONMEM friendly dataset for population PK
analysis. My patient IDs are 10 digit long and NONMEM is losing  
precison

and rouding the last couple of digits.


Are you sure?

I need to generate unique Patient
IDs fromt he current 10-digit IDs.  Ihave total 250 subjects so I
appreciate if anybody can suggest me a way to code this in R.


They should not be input or managed as numbers but rather as character  
variables. If you want them output without quotes, then fine, R can do  
that when specified.



--
David Winsemius, MD
West Hartford, CT

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Re: [R] Help with speed (replacing the loop?)

2012-01-11 Thread Dimitri Liakhovitski

Thanks a lot, Steve!
match sounds very promising - that means I only need a loop across predictors.

As far as get more memory advice is concerned: I already have more memory :)

On Wed, Jan 11, 2012 at 11:14 AM, Steve Lianoglou
mailinglist.honey...@gmail.com wrote:
 Hi,

 On Wed, Jan 11, 2012 at 10:50 AM, Dimitri Liakhovitski
 dimitri.liakhovit...@gmail.com wrote:
 Thanks a lot, Steve. I have one question (below):


 
 library(data.table)

 ## your data
 xx - data.table(group=c(rep(group1,5),rep(group2,5)),
                 a=1:10, b=seq(10,100,by=10), key=group)
 yy - data.table(group=c(group1,group2), a=c(10,20), b=c(2,3),
                 key=group)

 ## temp data.table to get your ducks in a row
 m - merge(xx, yy, by=group, suffixes=c(.x, .y))


 Dimitri: The step above (merge) - I was thinking of it but decided
 against it because my xx already fills up tons of memory. When I merge
 xx and yy that doubles the number of variables - I am afraid my memory
 won't hold that much stuff...

 Fair enough ... how about just using `match`, then, ie:

 R aa - x$a * y$a[match(x$group, y$group)]

 Should do the trick, no?

 -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



-- 
Dimitri Liakhovitski
marketfusionanalytics.com

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Re: [R] Odp: Generating unque patient IDs

Unfortunately the rounding effect (which I assumed was related to  
the automatic conversion from integer to numeric) is only going to  
show up above 2147483647L, so I question whether you really  
demonstrated a solution to what I understood was the fundamental  
problem.


--
David.

On Jan 11, 2012, at 11:50 AM, jim holtman wrote:


Does this do it for you:


sprintf(%010.0f, seq(10.0, length = 250, by = 1.0))

 [1] 10 11 12 13 14
15 16
 [8] 17 18 19 100010 100011
100012 100013
[15] 100014 100015 100016 100017 100018
100019 100020
[22] 100021 100022 100023 100024 100025
100026 100027
[29] 100028 100029 100030 100031 100032
100033 100034
[36] 100035 100036 100037 100038 100039
100040 100041
[43] 100042 100043 100044 100045 100046
100047 100048
[50] 100049 100050 100051 100052 100053
100054 100055
[57] 100056 100057 100058 100059 100060
100061 100062
[64] 100063 100064 100065 100066 100067
100068 100069
[71] 100070 100071 100072 100073 100074
100075 100076
[78] 100077 100078 100079 100080 100081
100082 100083
[85] 100084 100085 100086 100087 100088
100089 100090
[92] 100091 100092 100093 100094 100095
100096 100097

On Wed, Jan 11, 2012 at 11:32 AM, Petr PIKAL  
petr.pi...@precheza.cz wrote:

Hi


Dear group,

I am trying to prepare a NONMEM friendly dataset for population PK
analysis. My patient IDs are 10 digit long and NONMEM is losing  
precison

and rouding the last couple of digits.  I need to generate unique

Patient

IDs fromt he current 10-digit IDs.  Ihave total 250 subjects so I
appreciate if anybody can suggest me a way to code this in R.


I would start with

?abbreviate
and check uniqueness with
?unique or ?duplicated

Regards
Petr




Regards,
Ayyappa

   [[alternative HTML version deleted]]

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

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

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


__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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--
Jim Holtman
Data Munger Guru

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

__
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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
West Hartford, CT

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[R] rgl/ x11 problem

2012-01-11 Thread jack hietpas

Hello- I am having problems with plot3d... I keep receiving the follow
messages:

when I attempt to load the package: library(rgl, pos=4), I get this error
message:

[6] WARNING: Warning in rgl.init(initValue) :
Warning in rgl.init(initValue) :
Warning in rgl.init(initValue) :
Warning in rgl.init(initValue) : RGL: no suitable visual available
Warning in fun(...) : error in rgl_init

When I attempt to use the plot3d function, I get this message:
[7] ERROR:  rgl_dev_getcurrent

This is a new problem, I have been using these packages/ functions without
problems for at least a year.  I am using Rcommander on Ubuntu 11.10.

I have read that this may be an X11 problem, if so, I don't know how to fix
this.  Any help would be very much appreciated. Thanks for your time,

-jack

[[alternative HTML version deleted]]

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Re: [R] CairoPDF and greek letter spacing

2012-01-11 Thread Chris Campbell

As a workaround you could use escape characters, then adjust the font style as 
necessary.

cairo_pdf(file = zend.pdf)
print(xyplot(y ~ x, 
  data = data.frame(x = 1:10, y = 1:10),
  main = Length (\u03BCm)))
dev.off()

Regards

Chris Campbell
MANGO SOLUTIONS
Data Analysis that Delivers
+44 1249 767700

-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On 
Behalf Of Walker, John Stephen
Sent: 11 January 2012 16:01
To: David Winsemius; Rolf Turner
Cc: r-help@r-project.org
Subject: Re: [R] CairoPDF and greek letter spacing

Thanks for the input, but I can confirm the either form of the paste command 
i.e. expression(paste(Length (, mu*m, ))) or my original which had 
expression(paste(Length (, mu, m))), and the expression command alone have 
the same effect. It may be limited to Linux machines 
(which I did state I used  in my first post) as when I previously used an OS X 
machine I didn't see the bug.   I don't use OS X anymore, I've implemented a 
completely Linux based 
lab and would like to get this sorted out. Any suggestions? Rolf, if you can 
repoduce it then I think we have a bug report but to whom? R or Cairo?

John




From: David Winsemius [dwinsem...@comcast.net]
Sent: Monday, January 09, 2012 10:36 PM
To: Rolf Turner
Cc: Walker, John Stephen; r-help@r-project.org
Subject: Re: [R] CairoPDF and greek letter spacing

On Jan 10, 2012, at 12:22 AM, Rolf Turner wrote:

 On 10/01/12 15:25, David Winsemius wrote:

 On Jan 9, 2012, at 8:19 PM, Rolf Turner wrote:

 On 10/01/12 11:40, John Walker wrote:
 I have a small problem with R graphics output. When I use the 
 lattice package and CairoPDF to generate publication quality graphs 
 I often use the expression to create an axis title that has 
 microlitres or micrometers as a unit. I use something like the 
 following 'expression(paste(Length (, mu,m )))' as an argument 
 to the xlabel function. The command works but the mu and 'm' have a 
 space between them. It looks like 'u m' rather than 'um'. It only 
 seems to happen with the CairoPDF output on my linux machine, it's 
 fine on the X11 device.
 I've fixed it in the past by importing the pdf into inkscape and 
 manually adjusting the spacing (it's more difficult than it sounds 
 because I can't actually adjust the spacing but have to delete the 
 mu and re-enter it).  Is there something I'm doing wrong? Is this a 
 known bug?  How can I fix it?
 I can't help, but I can confirm the problem, for what *that* is 
 worth.

 It seems be an unfortunate interaction between lattice graphics and 
 the cairo_pdf() device.

 The space between the mu and the m does not appear with 
 ``ordinary'' R graphics, irrespective of device, nor does it appear 
 with lattice graphics and, e.g. the pdf() device.  But it does 
 appear with lattice graphics *and* the cairo_pdf() device.

 That probably means that the problem is subtle and will be difficult 
 to impossible to fix. :-(

 Doubtful. Do either of you realize that `paste` is a plotmath 
 function that is misused more often than correctly used (at least as 
 judged by the number o errors submitted to r-help)? I see no workable 
 example, but if I did I would be trying instead :

 expression(Length~mu*m)

 You meant expression(Length==mu*m).

I thought what was wanted:

main=expression(Length~group((,mu*m,))) # Or

main=expression(Length~(*mu*m*))


And on a Mac (Leopard, R 2.14.1 Patched)  I could not get a different display 
on the screen device and either pdf or cairo_pdf so your experience may have 
something to do with the as yet unstated OSes.


  And yes that helps a bit, but there's still a bit more space between 
 the mu and the m than one would like.

 Compare:

require(lattice)
cairo_pdf(file=mung.pdf)

 print
 (xyplot
 (y~x,data=data.frame(x=1:10,y=1:10),main=expression(Length==mu*m)))
dev.off()
 and
pdf(file=gorp.pdf)

 print
 (xyplot
 (y~x,data=data.frame(x=1:10,y=1:10),main=expression(Length==mu*m)))
dev.off()

 There's not much in it, but there's just enough to be annoying.

cheers,

Rolf

 P. S.  And I have never been able to figure out *anything* about how
 paste() and
 expression() interact.  It is a complete mystery, and a matter of 
 trying things more or less at random until something more or less 
 works.

R. T.

 P^2. S.  I just realised that there's more space between the letters 
 of Length in the cairo_pdf version, as well.  Which is, I guess, The 
 Explanation.  Is it a font thing?

R. T.

David Winsemius, MD
West Hartford, CT

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Re: [R] Odp: Generating unque patient IDs

2012-01-11 Thread jim holtman

One of the reasons that I specified the 'seq' command as it was was to
make sure it used numerics:

 x - seq(123456789012.0, length = 10, by = 1.0)
 x
 [1] 123456789012 123456789013 123456789014 123456789015 123456789016
123456789017 123456789018
 [8] 123456789019 123456789020 123456789021
 str(x)
 num [1:10] 123456789012 123456789013 123456789014 123456789015 123456789016 ...


On Wed, Jan 11, 2012 at 12:14 PM, David Winsemius
dwinsem...@comcast.net wrote:
 Unfortunately the rounding effect (which I assumed was related to the
 automatic conversion from integer to numeric) is only going to show up above
 2147483647L, so I question whether you really demonstrated a solution to
 what I understood was the fundamental problem.

 --
 David.

 On Jan 11, 2012, at 11:50 AM, jim holtman wrote:

 Does this do it for you:

 sprintf(%010.0f, seq(10.0, length = 250, by = 1.0))

  [1] 10 11 12 13 14
 15 16
  [8] 17 18 19 100010 100011
 100012 100013
 [15] 100014 100015 100016 100017 100018
 100019 100020
 [22] 100021 100022 100023 100024 100025
 100026 100027
 [29] 100028 100029 100030 100031 100032
 100033 100034
 [36] 100035 100036 100037 100038 100039
 100040 100041
 [43] 100042 100043 100044 100045 100046
 100047 100048
 [50] 100049 100050 100051 100052 100053
 100054 100055
 [57] 100056 100057 100058 100059 100060
 100061 100062
 [64] 100063 100064 100065 100066 100067
 100068 100069
 [71] 100070 100071 100072 100073 100074
 100075 100076
 [78] 100077 100078 100079 100080 100081
 100082 100083
 [85] 100084 100085 100086 100087 100088
 100089 100090
 [92] 100091 100092 100093 100094 100095
 100096 100097

 On Wed, Jan 11, 2012 at 11:32 AM, Petr PIKAL petr.pi...@precheza.cz
 wrote:

 Hi


 Dear group,

 I am trying to prepare a NONMEM friendly dataset for population PK
 analysis. My patient IDs are 10 digit long and NONMEM is losing precison
 and rouding the last couple of digits.  I need to generate unique

 Patient

 IDs fromt he current 10-digit IDs.  Ihave total 250 subjects so I
 appreciate if anybody can suggest me a way to code this in R.


 I would start with

 ?abbreviate
 and check uniqueness with
 ?unique or ?duplicated

 Regards
 Petr



 Regards,
 Ayyappa

   [[alternative HTML version deleted]]


 __
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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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 --
 Jim Holtman
 Data Munger Guru

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


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 David Winsemius, MD
 West Hartford, CT




-- 
Jim Holtman
Data Munger Guru

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

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Re: [R] Odp: Generating unque patient IDs

2012-01-11 Thread Ayyappa Chaturvedula


Dear all,
I am sorry if I misstated the problem. The roundig issue is with  
NONMEM software not with R. But the suggestions are helpful.


Regards,Ayyappa Chaturvedula

On Jan 11, 2012, at 12:14 PM, David Winsemius dwinsem...@comcast.net  
wrote:


Unfortunately the rounding effect (which I assumed was related to  
the automatic conversion from integer to numeric) is only going to  
show up above 2147483647L, so I question whether you really  
demonstrated a solution to what I understood was the fundamental  
problem.


--
David.

On Jan 11, 2012, at 11:50 AM, jim holtman wrote:


Does this do it for you:


sprintf(%010.0f, seq(10.0, length = 250, by = 1.0))

[1] 10 11 12 13 14
15 16
[8] 17 18 19 100010 100011
100012 100013
[15] 100014 100015 100016 100017 100018
100019 100020
[22] 100021 100022 100023 100024 100025
100026 100027
[29] 100028 100029 100030 100031 100032
100033 100034
[36] 100035 100036 100037 100038 100039
100040 100041
[43] 100042 100043 100044 100045 100046
100047 100048
[50] 100049 100050 100051 100052 100053
100054 100055
[57] 100056 100057 100058 100059 100060
100061 100062
[64] 100063 100064 100065 100066 100067
100068 100069
[71] 100070 100071 100072 100073 100074
100075 100076
[78] 100077 100078 100079 100080 100081
100082 100083
[85] 100084 100085 100086 100087 100088
100089 100090
[92] 100091 100092 100093 100094 100095
100096 100097

On Wed, Jan 11, 2012 at 11:32 AM, Petr PIKAL  
petr.pi...@precheza.cz wrote:

Hi


Dear group,

I am trying to prepare a NONMEM friendly dataset for population PK
analysis. My patient IDs are 10 digit long and NONMEM is losing  
precison

and rouding the last couple of digits.  I need to generate unique

Patient

IDs fromt he current 10-digit IDs.  Ihave total 250 subjects so I
appreciate if anybody can suggest me a way to code this in R.


I would start with

?abbreviate
and check uniqueness with
?unique or ?duplicated

Regards
Petr




Regards,
Ayyappa

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--
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David Winsemius, MD
West Hartford, CT



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Re: [R] Generating unque patient IDs

2012-01-11 Thread Chris Campbell

Dear Ayyappa

Unique identifiers can be created from numbers using factor. These are coded as 
integers in R which you could use to relabel your dataset.

 x - rep(16:18, each = 2)
 x
[1] 16 16 17 17 18 18
 y - factor(x)
 levels(y)
[1] 16 17 18
 z - as.numeric(y)
 z
[1] 1 1 2 2 3 3

Regards, 

Chris Campbell
MANGO SOLUTIONS
Data Analysis that Delivers
+44 1249 767700

-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On 
Behalf Of Ayyappa Chaturvedula
Sent: 11 January 2012 16:12
To: r-help@r-project.org
Subject: [R] Generating unque patient IDs

Dear group,

I am trying to prepare a NONMEM friendly dataset for population PK analysis. My 
patient IDs are 10 digit long and NONMEM is losing precison and rouding the 
last couple of digits.  I need to generate unique Patient IDs fromt he current 
10-digit IDs.  Ihave total 250 subjects so I appreciate if anybody can suggest 
me a way to code this in R.

Regards,
Ayyappa

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This message is intended for the use o...{{dropped:10}}

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Re: [R] 2 sample wilcox.test != kruskal.test

2012-01-11 Thread Nordlund, Dan (DSHS/RDA)

 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
 project.org] On Behalf Of syrvn
 Sent: Tuesday, January 10, 2012 10:28 AM
 To: r-help@r-project.org
 Subject: [R] 2 sample wilcox.test != kruskal.test

 Hello,

 I think I am right in saying that a 2 sample wilcox.test is equal to a
 2
 sample kruskal.test and

 a 2 sample t.test is equal to a 2 sample anova. This is also stated in
 the
 ?kruskal.test man page:

 The Wilcoxon rank sum test (wilcox.test) as the special case for two
 samples; lm together with anova for performing one-way location
 analysis
 under normality assumptions; with Student's t test (t.test) as the
 special
 case for two samples.

 From this example it seems like it doesn't but I cannot figure out
 what I am
 doing wrong.

 x - c(10,11,15,8,16,12,20)
 y - c(10,14,18,25,28,30,35)
 f - c(rep(a,7), rep(b,7))
 d - c(x,y)

 wilcox.test(x,y)
 kruskal.test(x,y)
 kruskal.test(x~y)
 kruskal.test(f~d)

 t.test(x,y)
 anova(lm(x~y))
 summary(aov(lm(x~y)))

 And why does kruskal.test(x~y) differ from kruskal.test(f~d)??

You have received answers about the kruskal.test.  But, to make a final point, 
if your purpose for these statements

 t.test(x,y)
 anova(lm(x~y))
 summary(aov(lm(x~y)))

Was to compare the t.test results with anova, you have misspecified the call to 
lm(). To get comparable results you should look at

t.test(x,y)
summary(lm(d ~ as.factor(f)))

The difference between the two is that t.test() use the Welch adjustment to the 
degrees of freedom.

Hope this is helpful,

Dan

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

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Re: [R] general question on Spotfire

2012-01-11 Thread Bert Gunter

Peter et. al:

1. I agree with Duncan: wrong list.

2. AFAIK, Spotfire **already** can interface with R.

-- Bert

On Wed, Jan 11, 2012 at 8:17 AM, peter dalgaard pda...@gmail.com wrote:

On Jan 11, 2012, at 16:28 , Duncan Murdoch wrote:

On 12-01-11 10:13 AM, John Smith wrote:
Dear R users,

Also could anyone give me any suggestion how to learn Spotfire?

Shouldn't you be asking this question to Spotfire users?

Just to clue in the casual reader, Spotfire embeds a version of S+, which is,
er, sort of, like, a predecessor to R, so John is not completely off target.

Documents comparing R and S+ should be useful to him. There are books that
are bilingual, such as Venables and Ripley MASS and S Programming, but I
also spotted this on TIBCO's own site:

http://spotfire.tibco.com/community/blogs/stn/archive/2010/11/04/differences-between-r-and-spotfire-s.aspx

Also, there are (claimed to be) facilities to integrate R itself in Spotfire,
which could be a rather expedient solution.

Duncan Murdoch

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

Bert Gunter
Genentech Nonclinical Biostatistics

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

Re: [R] stacked barplot colour coding

2012-01-11 Thread Jean V Adams

acacia21 wrote on 01/09/2012 07:01:28 PM:

 Hi all,
 i'm fairly new to R and its graphing, but having unsuccessfully 
'googled'
 and checked this forum to find answer to my problem, i'm posting my 
question
 here.
 
 I'm trying to plot stacked barplot. I have simple data that looks like 
this:
 bgag
 0.41   2.81
 0.37   2.91
 0.31   2.06
 0.32   2.39
 
 every row indicates a factor (1,2,3,4, see below in names.arg). Now when 
i
 plot this using following function for stacked barplots:
 plot-barplot(t(data), main=txt, ylim=c(0,10), col=c(white, grey90),
 ylab=Total biomass (g), space=0.1, names.arg=c(1, 2, 3, 4)) 
 
 i get a lovely stacked graph and it color-codes with white (bg) and 
grey90
 (ag) in each individual stacked bar.  I have a total of 4 stacked bars 
as i
 have 4 factors. Now here is the question: i would like to add density 
lines
 across entire stacked bar or any other graphic feature to distinguish
 between bars 1 and 2 as they indicate same factor and  3 and 4 that 
indicate
 different factor. Is there any way to do that? Surely it's possible, but 
not
 so obvious for the beginner =)
 
 thank you very much


One workaround is to create a second matrix of data, with zeroes for the 
bars where you don't want to add emphasis.  Then, overlay a second bar 
plot with density lines for emphasis.

df - data.frame(bg=c(0.41, 0.37, 0.31, 0.32), ag=c(2.81, 2.91, 2.06, 
2.39))
# matrix for full barplot
m - t(df)
# matrix for subset of barplot to add angled lines to
mlines - m
mlines[, 3:4] - 0

barplot(m, space=0.1, col=c(white, grey90), ylim=c(0, 10), 
ylab=Total biomass (g), names.arg=c(1, 2, 3, 4)) 
barplot(mlines, space=0.1, col=black, density=10, angle=35, add=TRUE)

Jean

P.S.  You should avoid creating objects that have the same names as 
currently existing functions, e.g., data and plot.

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Re: [R] general question on Spotfire

2012-01-11 Thread Louis Bajuk-Yorgan

Hello,

I am a Product Manager at Spotfire, focused on integrating statistical 
capabilities from R  S+ into Spotfire, so I will make a few comments:

1. We have a quite a few customers who use Spotfire and R side-by-side for 
doing ad hoc data analysis. Sometimes by the same user, sometimes by different 
users collaborating in a group. Each fills a different niche (with Spotfire 
focusing on highly interactive visualizations), and often different users are 
more comfortable with one or the other. Sometimes users will do their initial 
data manipulation and analysis in R, and then move the data into Spotfire for 
further interaction, and presentation to other, non-R users. 

2. Our focus at Spotfire has been on integrating R  S+ (as Peter mentions 
below), so that it's easy to create and share interactive Spotfire applications 
that leverage analytics from R  S+. We want to help customers put the power of 
R  S+ into the hands of more users, in applications that are friendly and 
familiar to them. 

If you'd like more info on that, check out the info on the Statistics Services 
product at spotfire.tibco.com, or this recorded webcast: 
http://www.screencast.com/t/So5Kz7gJI4

Regards
Lou
--
Lou Bajuk-Yorgan
Sr. Director, Product Management
Spotfire, TIBCO Software
206-802-2328
lba...@tibco.com
http://spotfire.tibco.com

-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On 
Behalf Of peter dalgaard
Sent: Wednesday, January 11, 2012 8:17 AM
To: Duncan Murdoch
Cc: r-help@r-project.org
Subject: Re: [R] general question on Spotfire


On Jan 11, 2012, at 16:28 , Duncan Murdoch wrote:

 On 12-01-11 10:13 AM, John Smith wrote:
 Dear R users,
 
 I have been using R for 10 years, and I love it very much. But in my 
 daily job for drug discovery, some people use Spotfire. I tried 
 Spotfire on couple of data sets. It sounds I still need do some data 
 manipulation before plot figures. For example, I can not plot figure with 
 data arranged
 in rows (is this true, or I am stupid?).   So far I don't feel any benefit
 Spotfire can provide over R. I am just wondering whether it just 
 because I am new to Spotfire, or it's true that Spotfire is not a 
 good tool for statistician.
 
 Also could anyone give me any suggestion how to learn Spotfire?
 
 Shouldn't you be asking this question to Spotfire users?

Just to clue in the casual reader, Spotfire embeds a version of S+, which is, 
er, sort of, like, a predecessor to R, so John is not completely off target. 

Documents comparing R and S+ should be useful to him. There are books that are 
bilingual, such as Venables and Ripley MASS and S Programming, but I also 
spotted this on TIBCO's own site: 

http://spotfire.tibco.com/community/blogs/stn/archive/2010/11/04/differences-between-r-and-spotfire-s.aspx

Also, there are (claimed to be) facilities to integrate R itself in Spotfire, 
which could be a rather expedient solution.


 Duncan Murdoch
 
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 PLEASE do read the posting guide 
 http://www.R-project.org/posting-guide.html
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--
Peter Dalgaard, Professor
Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 
Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd@cbs.dk  Priv: pda...@gmail.com

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Re: [R] Plot maps with R

2012-01-11 Thread hwright

Dear Alex
Two other packages that create maps are:
 maps
 mapproj


alaios wrote
 
 Dear all I would like to use R and make some maps.
 I want to have strict control, over the details of the produced map, like
 remove borders, city names, add markers, add labels.
 
 Is there any package apart Rgooglemaps that can do something like that?
 
 B.R
 Alex
 
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-
---
Heather A. Wright, PhD candidate
Ecology and Evolution of Plankton
Stazione Zoologica Anton Dohrn
Villa Comunale
80121 - Napoli, Italy
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Re: [R] plotOHLC(alpha3): Error in plotOHLC(alpha3) : x is not a open/high/low/close time series

2012-01-11 Thread Ted Byers

Hi Joshua,

Thanks.

I had used irts because I thought I had to.  The tick data I have has some
minutes in which there is no data, and others when there are hundreds, or
even thousands.  If xts supports irregular data, the that is one less step
for me to worry about.

Alas, your suggestion didn't help:

 z - xts(y[,2], y[,1]) 
 alpha3 - to.minutes3(z, OHLC=TRUE) 
 plotOHLC(alpha3)
Error in plotOHLC(alpha3) : x is not a open/high/low/close time series
 str(alpha3)
An ‘xts’ object from 2010-06-30 15:47:00 to 2011-10-31 15:14:00 containing:
  Data: num [1:98865, 1:4] 9215 9220 9205 9195 9195 ...
 - attr(*, dimnames)=List of 2
  ..$ : NULL
  ..$ : chr [1:4] z.Open z.High z.Low z.Close
  Indexed by objects of class: [POSIXct,POSIXt] TZ: 
  xts Attributes:  
 NULL

Is there anything else I might try?

Thanks again,

Ted

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[R] Assist me on how I can arrange trend data of rainfall and temperature for analysis

2012-01-11 Thread MukhalaC

I am a student doing my MSc Research Methods, i am working on my thesis
research on analysing and modelling of crop failure risks due to drought in
selected districts in Malawi. The analysis and modelling will focus on two
crop stages of development: just after planting and flowering stages. I have
rainfall, temperature, Relative humidity, wind speed, coordinate location
data for the past 30 years for each of the district i have chosen based on
the Malawi National Program action against climate change. I wish to model
using the extreme value statistical theory in R by extRemes package. How do
I arrange this data? How do I produce maps using R?

I am a good user of R however; I have just been exposed to this wonderful
and powerful open statistical software recently. I am good using it in
analysing designed experimental data.

Would anyone good in the area I have indicated help me. My email address is
mukha...@yahoo.co.uk.

I appreciate in advance.

-
Collins Tamonde Mukhala
MSc Research Methods student
Jomo Kenyatta University of Agriculture and Technology
P.O. Box 62000-00200
City Square, Nairobi
Kenya
Main Campus-Juja
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[R] Accomplishing a loop on multiple columns

2012-01-11 Thread Nerak

Hello,
I have a question concerning ‘for loops’ on multiple columns. 
I made 91 columns with results (all made together with a for loop) and I
want to us lm to fit the model.
I want to compare the results of all these calculated columns (91) with one
column with observed values. I use the function lm to fit the model and
calculate r.squared. I manage to do this for each column separately:

For example: my calculated results are in the dataframe ‘results6”, my
observed results in data, (data$observed). 
#To calculate R2 for column 1:
lm.modelobs1 - lm(results6[,c(1)] ~ data$observed)
R2.1 - summary(lm.modelobs1)[r.squared]
#To calculate R2 for column 91:
lm.modelobs91 - lm(results6[,c(91)] ~ data$observed)
R2.91 - summary(lm.modelobs91)[r.squared]

But I think there has to be a method to do this automatically and not 91
times.
I tried to use a for loop:
###(length(C) = 91)
results7-data.frame(lm.modelobs=rep(NA,length(C)))
for (i in (1:91))
{
results7$lm.modelobs[i] - lm(results6[i] ~ data$observed)
R2.[i] - summary(lm.modelobs[i])[r.squared]
}

I also tried just to calculate results7$lm.modelobs[i] without directly
calculating r.squared but I also didn’t manage. It seems like it’s not
possible to use the referral to a column in a for loop or a function. (if I
just ask R the data in column 5 with ‘ results6[5]  ’, that works. ‘
results6[,c(5)]’ gives the same but replacing results6[i] by
results6[,c([i])] in the for loop is apparently also no a solution).  I’m
looking for a manner to repeat a calculation/function on several columns. I
kind of need this as well further in my script, not only in this part…

I would greatly appreciate any suggestions!
Thanks!
Nerak


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Re: [R] 64bit R under 32bit winxp

2012-01-11 Thread 孟欣

Thanks





At 2012-01-11 16:55:32,Jeff Newmiller jdnew...@dcn.davis.ca.us wrote:
You cannot install 64-bit R on 32-bit OS, but you can install a 32-bit R on a 
64-bit OS, and you can later install 64-bit R as well. That is, installing 
32-bit R does not interfere with your option to later install a 64-bit R.
---
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DCN:jdnew...@dcn.davis.ca.usBasics: ##.#.   ##.#.  Live Go...
  Live:   OO#.. Dead: OO#..  Playing
Research Engineer (Solar/BatteriesO.O#.   #.O#.  with
/Software/Embedded Controllers)   .OO#.   .OO#.  rocks...1k
--- 
Sent from my phone. Please excuse my brevity.

ÃÏÐÀ lm_meng...@163.com wrote:

Hi all:


My OS is 32bit winxp,but I wanna install 64bit R2.14.1.


From the following website,it says You can also go back and add
64-bit components to a 32-bit install, or vice versa
http://cran.r-project.org/bin/windows/rw-FAQ.html#Can-both-32_002d-and-64_002dbit-R-be-installed-on-the-same-machine_003f




Does it mean that I can install and run 64bit R2.14.1 under 32bit
winxp?If so,how can I add 64-bit components to a 32-bit install?




Many thanks for your help.




My best
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Re: [R] Max value of an integer

2012-01-11 Thread Mikko Korpela

On 01/11/2012 12:01 PM, Rui Esteves wrote:

 Is there any constant that represents the maximum value of an integer?

Yes, there is (assuming you refer to the 'integer' type). See ?.Machine.

 .Machine$integer.max
[1] 2147483647
 as.integer(2147483647)
[1] 2147483647
 as.integer(2147483648)
[1] NA
Warning message:
NAs introduced by coercion

Double-precision numbers (i.e. the 'numeric' type) are able to represent
a larger range of integer values, from  -(2^.Machine$double.digits) to
+(2^.Machine$double.digits). If you go outside that range, some integers
are not exactly representable.

 options(digits = 22)
 print(max.num - 2 ^ .Machine$double.digits)
[1] 9007199254740992
 (max.num) - (max.num - 1)
[1] 1
 (max.num + 1) - (max.num)
[1] 0
 (max.num + 2) - (max.num + 1)
[1] 2

 If I need to setup by myself what is the maximum value?

I don't understand what you mean.

-- 
Mikko Korpela

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Re: [R] Getting Sphericity Tests for Within Subject Repeated Measure Anova (using car package)

2012-01-11 Thread maximilian.mueller

Dear John,

thanks for your help and sorry for answering this late. My question is a
follow up question of an older thread posted several mongths ago, but your
statement helped a lot.

Thanks,
Max



-
M a x i m i l i a n  M ue l l e r

PhD-Student
Department of Business Studies
Leuphana Universität Lüneburg

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[R] Problem concerning withRestarts and R2WinBUGS

2012-01-11 Thread Jongerling, J. (Joran)

Dear R-users,



I have a question regarding the withRestarts function in R. I´m running a 
simulation code in which I analyse data using both lme and R2WinBUGS. Now, I 
want to run this code for 1000 replications, however the model I´m using is a 
little ´sensitive´, so sometimes the WinBUGS analysis crashes. In that case I 
want the code to ignore the current results, and redo all steps. This means 
drawing new data, analysing the data with lme, and than analysing the data 
using WinBUGS. So basically, I want my code to continue untill I get 1000 
succesful replications, and ignore the replications that failed. I figured I 
might be able to do so by putting the data generation and analysis steps in a 
second function embedded in the overall one, and calling this second function 
using the withRestarts and invokeRestart options, but I can´t get this to work. 
Can somebody help me figure this out by telling me if this is even possible, 
and if so, how withRestarts and invokeRestarts should be called to do this? 
Alternatively, if any of you know an other way to aqcuire the desired effect 
I´m also very interested.



Kind regards,

Joran Jongerling

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Re: [R] RGL- Drawing Circle

2012-01-11 Thread gli

thanks Duncan.  I think want my circle to be in user coordinates.  I tried
the first code u gave me and it gives me a circle. but how can i: 

1) change the radius ?

2) place the circle at a given x,y,z coordinate?

3) turn it 90 degree up like these circle plate bus stop?
http://www.geocities.co.jp/yuganatabi/bus-stop-aba.html

4) and finally, set the orientation angle of the circle plate?

grateful if u give me some directions or at least let me know if it is
possible or not.

graham

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Re: [R] Accomplishing a loop on multiple columns

2012-01-11 Thread iliketurtles

Lists are the answer.


LIST-list()
 for(i in 1:ncol(results6))
 {
  LIST[[i]]-lm(results6[,i]~data$observed)
 }

You'll now have a 91 entry list of lm(). You can then do something like
this:

LIST2-list()
 for(i in 1:length(LIST))
 {
  LIST2[[i]]-LIST[[i]]$r.squared
 }

This should now be a list of 91 R-squared, which you can unlist() and save
in matrix form if you want. 

-


Isaac
Research Assistant
Quantitative Finance Faculty, UTS
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Re: [R] odfWeave UTF-8 error and latin characters

2012-01-11 Thread staffan7s

Hello,

I am using R and Libreoffice on Ubuntu 11.10 (64-bit) and have been
experiencing similar problems with character encoding (Swedish utf8) in
odfWeave. Here is an example of what it looks like:

Should be: Hör Ärland dåligt?
Appears as: HÃ¶r Ãrland dÃ¥ligt?

I found a (pretty clumsy) solution which I post below. Has anyone been able
to solve this in a more elegant way?

Setup:

 sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
 [1] LC_CTYPE=sv_SE.UTF-8   LC_NUMERIC=C  
other attached packages:
[1] odfWeave_0.7.17 XML_3.2-0   lattice_0.19-30

Problem:

I have some R syntax for tables in the file in.odt:

vl5, echo=FALSE, results=xml=
irre - xtabs(~Species, data=iris) 
irre - data.frame(irre) 
colnames(irre) - c(växt, antal) 
row.names(irre) - c(å, ä, ö) 
odfTable(irre)
odfTableCaption(Tabell åäö)
@

Running odfWeave on this with odfWeave(in.odt, out.odt) yields lots of
output, ending with this Warning message: ‘content.Rnw’ has unknown
encoding: assuming Latin-1. 

On opening the output file (odt.out), Swedish characters appear jumbled. I
had a look at the content.Rnw file, which was correctly coded with utf-8.
The same was true for the content.xml file in the odt source (this had to be
unzipped).

I then tried downgrading to XML 3.2, as suggested elsewhere. This didn't
help. I then looked for tools for converting an odt file from one kind of
encoding to another, again to no avail.

Solution:

Save the odt file in flat xml format (Libreoffice  save as  second last
option). Convert the resulting .fodt file FROM utf-8 TO latin 1 (aka
ISO_8859-1) with iconv from a bash terminal:

iconv -t ISO_8859-1 -f UTF-8 -o converted.fodt out.fodt

This produces a correctly encoded file!




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Re: [R] Constructing a data.frame from csv files

2012-01-11 Thread Vincy Pyne

Dear Sir,
Thanks a lot for your guidance. I have understood my mistake. It was naming the 
columns viz.   colnames(price_returns) = entity_returns which was creating the 
problems. Code is running excellently once I got rid of this particular line. I 
will use melt from reshape etc to get the required data.frame.

Thanks again.
With warm regards
Vincy
--- On Wed, 1/11/12, jim holtman jholt...@gmail.com wrote:

From: jim holtman jholt...@gmail.com
Subject: Re: [R] Constructing a data.frame from csv files
To: Vincy Pyne vincy_p...@yahoo.ca
Cc: r-help@r-project.org
Received: Wednesday, January 11, 2012, 1:49 PM

The error message says it all:  the dataframes that you are creating,
and then trying to 'rbind', do not have the same columns.  You need to
at least show what the first couple of lines of each of you input
files are, or output the names of the columns as you are reading the
files.  This is some elementary debugging that you will have to learn.

On Wed, Jan 11, 2012 at 7:38 AM, Vincy Pyne vincy_p...@yahoo.ca wrote:
 Dear R helpers,

 Following is my R code where I am trying to calculate returns and then trying 
 to create a data.frame. Since, I am not aware how many instruments I will be 
 dealing so I have constructed a function. My R code is as follows -

 library(plyr)

 mydata - data.frame(instru_name = 
 c(instru_A,instru_A,instru_A,instru_A,instru_A,instru_A,instru_A,instru_A,instru_A,instru_A,instru_A,instru_A,instru_A,instru_A,instru_B,instru_B,instru_B,instru_B,instru_B,instru_B,instru_B,instru_B,instru_B,instru_B,instru_B,instru_B,instru_B,instru_B),
  date = c(10-Jan-12,9-Jan-12,8-Jan-12, 7-Jan-12, 
 6-Jan-12,5-Jan-12,4-Jan-12,3-Jan-12,2-Jan-12,1-Jan-12, 
 31-Dec-11, 
 30-Dec-11,29-Dec-11,28-Dec-11,10-Jan-12,9-Jan-12,8-Jan-12, 
 7-Jan-12,6-Jan-12,5-Jan-12,4-Jan-12,3-Jan-12,2-Jan-12,1-Jan-12,31-Dec-11,30-Dec-11,29-Dec-11,28-Dec-11),
  price = c(11.9,10.5,13,14.5,14.4,14.8,10.1,12,14.3, 
 10.7,11.2,10.2,10.2,10.8,41.9,40.5,43,44.5,44.4,48.8,42.1,44,46.3,48.7,46.2,44.2,42.2,40.8))

 attach(mydata)

 opt_return_volatilty = function(price, instru_name)

 {

 price_returns = matrix(data = NA, nrow = (length(price)-1), ncol = 1)
     for (i in(1:(length(price)-1)))
     {
     price_returns[i] = log(price[i]/price[i+1])
     }
 volatility = sd(price_returns)
 entity_returns = unique(instru_name)
 colnames(price_returns) = entity_returns

 write.csv(price_returns, file = paste(entity_returns, .csv, sep = ), 
 row.names = FALSE)

 return(data.frame(list(volatility = volatility)))

 }

 entity_volatility - ddply(.data=mydata, .variables = instru_name,
     .fun=function(x) opt_return_volatilty(price = x$price, 
 instru_name = x$instru_name))


 entity_volatility
   instru_name volatility
 1    instru_A 0.17746897
 2    instru_B 0.06565341


 fileNames - list.files(pattern = instru.*.csv)

 fileNames
 [1] instru_A.csv instru_B.csv

 # 
 _

 # MY QUERY

 # I need to construct the data frame consisting of all the returns. I.e. I 
 need to have # a data.frame like

 instru_A instru_B
 0.125163143  0.033983853
 -0.2135741  -0.059898142
 -0.109199292    -0.034289073
 0.006920443  0.00224972
 -0.027398974    -0.094490843

 I am using following Code

 input - do.call(rbind, lapply(fileNames, function(.name)
     {
     .data - read.csv(.name, header = TRUE, as.is = TRUE)
     .data$file - .name
     .data
     }))

 # I get following error.

     Error in match.names(clabs, names(xi)) :
   names do not match previous names


  Kindly guide

 Regards

 Vincy



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What is the problem that you are trying to solve?
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Re: [R] Problem with segmented

2012-01-11 Thread Filoche

Hi there.

Here's the error message.

Error in seg.lm.fit(y, XREG, Z, PSI, weights, offs, opz) : 
  (Some) estimated psi out of its range

I have tried many ways to specify the arguments, but apparently the error
message is related to the estimated break point being invalid. However, my
estimation fall within range of my data.

Thank for your help,
Phil

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[R] New to R, Curious about Project Idea

2012-01-11 Thread arbeaupg

Good morning,

I am a student whom is currently working on a term project for my GIS
Program. I am looking for a software package which can aid me in my project,
and I was curious if R would be able to address my goals.

My project includes  power outage data from a hydro company (point data,
with UTM coordinates attached), which is available in an Access database, or
in a Shapefile. 

I would like to be able to take this poweroutage data, and then perform a
spatial analysis of this data, perhaps as a hot-spot analysis, or in a
points per raster square style analysis. 

With the completed analysis, I would like to be able to use an open source
web mapping platform to display it for the 'company' I am performing this
for as part of my project. 


Any insight you could provide me would be greatly, greatly appreciated.

Thanks,

Phil

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[R] meta-analysis normal quantile plot metafor

2012-01-11 Thread Ricc

Hello,

I once used the metawin software to perform a meta-analysis (see
metawinsoft, Rosenberg et al.) and produced normal qqplot to test for
a potential bias in the dataset.
I now want to re-use the same dataset with the package metafor by W.
Viechtbauer (great package btw).

I run the qqnorm.rma.uni function. I use standardized effect sizes as
in metawin.

QQplot generated with metafor differs from the plot obtained with
metawin: most of the datapoint fall outside the confidence envelope
(using the same confidence level). I don't understand very well how
the pseudo confidence envelope was created in metafor. Is it more
conservative than that from metawin or created using the package
envelope ? Unfortunately I do not have access to metawin's code so
that I cannot compare implementations but the manual let me think that
metawin print classical confidence interval...

Thanks for input !
Ricc

More precisions:
R version 2.13.1 (2011-07-08)
Platform: x86_64-pc-linux-gnu (64-bit)
metafor_1.6-0

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Re: [R] fix and edit don't work: unable to open X Input Method-segfault

2012-01-11 Thread Patrick Connolly

On Sun, 08-Jan-2012 at 03:32PM -0600, Paul Johnson wrote:

| I can't run fix() or edit() anymore. Did I break my system?
| 

| I'm running Debian Linux with R-2.14.1. As far as I can tell, the R
| packages came from Debian's testing wheezy repository.  I would
| like to know if users on other types of systems see the same
| problem. If no, then, obviously, it is a Debian-only issue and I

I compiled R-2.14.1 on CentOS and on Kubuntu (64 bit) without any
problem.  Since Kubuntu is a Debian based distro, I don't think it's a
Debian problem.  However, if R-2.14.0 still works for you but R-2.14.1
does not, that's an indication that it would be the debs you used.

| can approach it from that point of view.  And if no other Debian
| users see same, it means it is a me-only problem, and that's
| discouraging :)

[...]

|  sessionInfo()
| R version 2.14.1 (2011-12-22)
| Platform: x86_64-pc-linux-gnu (64-bit)
| 
| locale:
|  [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
|  [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
|  [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
|  [7] LC_PAPER=C LC_NAME=C
|  [9] LC_ADDRESS=C   LC_TELEPHONE=C
| [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
| 
| attached base packages:
| [1] grid  stats graphics  grDevices utils datasets  methods
| [8] base
| 
| other attached packages:
| [1] ggplot2_0.8.9 proto_0.3-9.2 reshape_0.8.4 plyr_1.6
|  fix(mpg)
| Error in dataentry(datalist, modes) : invalid device
| In addition: Warning message:
| In edit.data.frame(get(subx, envir = parent), title = subx, ...) :
|   unable to open X Input Method

That looks like an OS issue (assuming it's not a problem with the deb).  

| 
| Same happens no matter what packages are loaded, so far as I can tell.
|  Here it is without ggplot2, in case you were suspicious of those
| particular datasets.
| 
| 
|  library(datasets)
|  datasets()
| Error: could not find function datasets

No surprise there.  Everyone will get that message since there is no
datasets function.


|  help(package=datasets)
|  fix(CO2)
| Error in dataentry(datalist, modes) : invalid device
| In addition: Warning message:
| In edit.data.frame(get(subx, envir = parent), title = subx, ...) :
|   unable to open X Input Method

There's that X message again.

[...]


HTH


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

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Re: [R] rjags installation trouble

2012-01-11 Thread Martyn Plummer

It looks like you are cross-linking to an earlier version of the JAGS
library at run time. Check

/sbin/ldconfig -p | grep jags -

When compiling rjags, you can hard-code the location of the jags library
using the [GNU-specific] configure option --enable-rpath.

Martyn

On Tue, 2012-01-10 at 10:40 -0500, Ben Bolker wrote:
 Trying to install latest rjags (3-5) from CRAN with JAGS 3.2.0
 installed on Ubuntu 10.04, with r-devel ... the bottom line is that it
 fails while loading with
 
  /libs/rjags.so: undefined symbol: _ZN7Console15checkAdaptationERb
 
   Has anyone else seen this or is it a glitch somewhere in my system?
 
   thanks
 Ben Bolker
 
 ==
 bolker@ubuntu-10-new:~/R/pkgs/rjags$ jags
 Welcome to JAGS 3.2.0 on Tue Jan 10 10:38:31 2012
 JAGS is free software and comes with ABSOLUTELY NO WARRANTY
 Loading module: basemod: ok
 Loading module: bugs: ok
 .
 
 ===
 
 install.packages(rjags) starts out fine:
 
 Installing package(s) into
 ‘/mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library’
 (as ‘lib’ is unspecified)
 trying URL 'http://probability.ca/cran/src/contrib/rjags_3-5.tar.gz'
 Content type 'application/x-gzip' length 66429 bytes (64 Kb)
 opened URL
 ==
 downloaded 64 Kb
 
 * installing *source* package ‘rjags’ ...
 ** package ‘rjags’ successfully unpacked and MD5 sums checked
 checking for prefix by checking for jags... /usr/bin/jags
 
   [snip snip]
 
 ** libs
 g++ -I/usr/local/lib/R/include -DNDEBUG -I/usr/include/JAGS
 -I/usr/local/include-fpic  -g -O2  -c jags.cc -o jags.o
 g++ -I/usr/local/lib/R/include -DNDEBUG -I/usr/include/JAGS
 -I/usr/local/include-fpic  -g -O2  -c parallel.cc -o parallel.o
 g++ -shared -L/usr/local/lib -o rjags.so jags.o parallel.o -L/usr/lib -ljags
 installing to /mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags/libs
 ** R
 
   [snip snip]
 
   but fails at:
 
 ** building package indices
 Error : .onLoad failed in loadNamespace() for 'rjags', details:
   call: dyn.load(file, DLLpath = DLLpath, ...)
   error: unable to load shared object
 '/mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags/libs/rjags.so':
 
 /mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags/libs/rjags.so:
 undefined symbol: _ZN7Console15checkAdaptationERb
 ERROR: installing package indices failed
 * removing ‘/mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags’
 * restoring previous
 ‘/mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags’
 
 The downloaded source packages are in
   ‘/tmp/RtmpSKHIz5/downloaded_packages’
 Warning message:
 In install.packages(rjags) :
   installation of package ‘rjags’ had non-zero exit status
  sessionInfo()
 R Under development (unstable) (2012-01-01 r58032)
 Platform: i686-pc-linux-gnu (32-bit)
 
 locale:
  [1] LC_CTYPE=en_CA.utf8   LC_NUMERIC=C
  [3] LC_TIME=en_CA.utf8LC_COLLATE=en_CA.utf8
  [5] LC_MONETARY=en_CA.utf8LC_MESSAGES=en_CA.utf8
  [7] LC_PAPER=CLC_NAME=C
  [9] LC_ADDRESS=C  LC_TELEPHONE=C
 [11] LC_MEASUREMENT=en_CA.utf8 LC_IDENTIFICATION=C
 
 attached base packages:
 [1] stats graphics  grDevices utils datasets  methods   base
 
 loaded via a namespace (and not attached):
 [1] tools_2.15.0


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[R] turning a list of vectors into a data.frame (as rows of the DF)?

2012-01-11 Thread Chris Conner

As a newer R practicioner, it seems I stump myself weekly (at least) with 
issues that have spinning my wheels.  Here is yet another... I'm trying to turn 
a list of numeric vectors (of uneual length) inot a dataframe.  Each vector 
held in the list represents a row, and there are some rows of unequal length.  
I would like NAs as placeholders for missing data in the shorter vectors.  I 
think I'm missing something quite basic.
 
v1 - c(1,2,3,4)
v2 - c(1,2)
lst1 - list(v1,v2)
 
Of course there is the intuitive:
 
as.data.frame(lst1)
 
However, the recycling rule (expectedly) reclycles 1,2 versus using NAs as 
placeholders.
 
Then, looking into Teetor's R Cookbook, there is a piece of code that looked 
(from the description) like it might do the trick:
 
do.call(rbind, Map(as.data.frame,lst1)
 
But I get the error:
Error in match.names(clabs, names(xi)) : 
  names do not match previous names
 
Thinking the source of the error had to do with the vectors of unequal lenght, 
I tried Hadley's rbind.fill thusly:
 
library(reshape)
do.call(rbind.fill, Map(as.data.frame,lst1)
 
Which produced a dataset, but gain, not in the desired format.
 
Thanks in advance to anyone that can bring my frustrations to end!
C
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Re: [R] general question on Spotfire

2012-01-11 Thread Spencer Graves

Roughly 5 years ago, a Spotfire rep at the Joint Statistical Meetings
told me they routinely interfaced with both R and S-Plus. I'm not 100%
certain, but I believe they have many customers who use that facility
today. Spencer

On 1/11/2012 10:37 AM, Bert Gunter wrote:

Peter et. al:

1. I agree with Duncan: wrong list.

2. AFAIK, Spotfire **already** can interface with R.

-- Bert

On Wed, Jan 11, 2012 at 8:17 AM, peter dalgaardpda...@gmail.com wrote:

On Jan 11, 2012, at 16:28 , Duncan Murdoch wrote:

On 12-01-11 10:13 AM, John Smith wrote:

Dear R users,

Also could anyone give me any suggestion how to learn Spotfire?

Shouldn't you be asking this question to Spotfire users?

Just to clue in the casual reader, Spotfire embeds a version of S+, which is,
er, sort of, like, a predecessor to R, so John is not completely off target.

Documents comparing R and S+ should be useful to him. There are books that are
bilingual, such as Venables and Ripley MASS and S Programming, but I also
spotted this on TIBCO's own site:

http://spotfire.tibco.com/community/blogs/stn/archive/2010/11/04/differences-between-r-and-spotfire-s.aspx

Also, there are (claimed to be) facilities to integrate R itself in Spotfire,
which could be a rather expedient solution.

Duncan Murdoch

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

--
Spencer Graves, PE, PhD
President and Chief Technology Officer
Structure Inspection and Monitoring, Inc.
751 Emerson Ct.
San José, CA 95126
ph: 408-655-4567
web: www.structuremonitoring.com

[R] Confidence Interval from Moments?

2012-01-11 Thread lambdatau

Hi all,

I'm wondering whether it is possible to construct a confidence interval
using only the mean, variance, skewness and kurtosis, i.e. without any of
the population?

If anyone could help with this it'd be much appreciated (even if just a
confirmation of it being impossible!).

Thanks.

--
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[R] Getting a root edge error when trying to read the phylocom megatree into R

2012-01-11 Thread Megan Bartlett

Hi,

I'm trying to use the picante package in R to build phylogenetic trees,
based on a list of taxa I have data for and the phylocom APG3 megatree
(version R20091110; http://www.phylodiversity.net/phylomatic/). However,
trying to read the tree in R using:

read.tree(R20091110.new.txt)

Gives the error message:

Error in if (sum(obj[[i]]$edge[, 1] == ROOT) == 1  dim(obj[[i]]$edge)[1]
  :
  missing value where TRUE/FALSE needed

This seems like such a basic question, but I don't know what the problem
with the root edge is. Are there any modifications you have to make to the
megatree in order to read it in R? Thanks so much for your help!

Best,

Megan Bartlett

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Re: [R] Restricting R session




On 10.01.2012 20:30, Antonio Rodriges wrote:

Hello,

Is it possible to use R on public server where each user has its own
restricted R session?


This entirely depends on the definition of restricted, otherwise the 
answer is yes.




In particular, how to prohibit some set of functions, for example,
from base package?


You can't: R is free software. Well, of course you could build your own 
version of R that did not ship those functions. Anyway, typical 
restrictions are handled by settig permissions on the file system and/or 
arrange quotas for space / memory / CPU resources.




How to limit session operating memory and CPU time?


Ask he manual of your operating system.

Best,
Uwe Ligges


What additional
security considerations must be taken care of?



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[R] Storing/Restoring R objects

2012-01-11 Thread Rich Shepard


  One of my projects has generated quite a few objects (data frames) related
to one portion of this project. They can be listed with the ls() function. 
What I would like to do is move them to another directory so that data

frames for other portions of the project can be more easily seen and used.

  .RData is a binary file. Are there tools that let me work with this file?
What if I rename it and start a new .RData file when I next invoke R? Could
I then specify which .RData file should be available on demand?

  I have not seen (or remembered if I did) discussions on this topic. Please
advise.

Rich

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Re: [R] plotOHLC(alpha3): Error in plotOHLC(alpha3) : x is not a open/high/low/close time series

2012-01-11 Thread Joshua Ulrich

On Wed, Jan 11, 2012 at 11:10 AM, Ted Byers r.ted.by...@gmail.com wrote:
 Hi Joshua,

 Thanks.

 I had used irts because I thought I had to.  The tick data I have has some
 minutes in which there is no data, and others when there are hundreds, or
 even thousands.  If xts supports irregular data, the that is one less step
 for me to worry about.

 Alas, your suggestion didn't help:

 z - xts(y[,2], y[,1])
 alpha3 - to.minutes3(z, OHLC=TRUE)
 plotOHLC(alpha3)
 Error in plotOHLC(alpha3) : x is not a open/high/low/close time series

plotOHLC requires a 4-column ts object with columns explicitly named
Open, High, Low, Close, in that order.  alpha3, as I've defined above,
will have 4 columns but may not have those explicit column names.  You
would have to set them yourself.

Then you could run:
plotOHLC(as.ts(alpha3))

For example, this works:
library(xts)
data(sample_matrix)
x - as.ts(sample_matrix)
plotOHLC(x)

 str(alpha3)
 An ‘xts’ object from 2010-06-30 15:47:00 to 2011-10-31 15:14:00 containing:
  Data: num [1:98865, 1:4] 9215 9220 9205 9195 9195 ...
  - attr(*, dimnames)=List of 2
  ..$ : NULL
  ..$ : chr [1:4] z.Open z.High z.Low z.Close
  Indexed by objects of class: [POSIXct,POSIXt] TZ:
  xts Attributes:
  NULL

 Is there anything else I might try?

You could try quantmod::chartSeries(to.minutes3(z, OHLC=TRUE)).  I'm
not familiar with the charting capabilities in the tseries package,
but those in quantmod are quite extensive.  See also www.quantmod.com.

 Thanks again,

 Ted


Best,
--
Joshua Ulrich  |  FOSS Trading: www.fosstrading.com

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Re: [R] 2 sample wilcox.test != kruskal.test

2012-01-11 Thread Daniel Nordlund

 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
 On Behalf Of syrvn
 Sent: Wednesday, January 11, 2012 2:36 AM
 To: r-help@r-project.org
 Subject: Re: [R] 2 sample wilcox.test != kruskal.test

 Hi,

 thanks for your answer. Unfortunately I cannot reproduce your results.

 In my example the results still differ when I use your approach:

  x - c(10,11,15,8,16,12,20)
  y - c(10,14,18,25,28,30,35)
  f - as.factor(c(rep(a,7), rep(b,7)))
  d - c(x,y)
  kruskal.test(x,y)

   Kruskal-Wallis rank sum test

 data:  x and y
 Kruskal-Wallis chi-squared = 6, df = 6, p-value = 0.4232

  kruskal.test(x~y)

   Kruskal-Wallis rank sum test

 data:  x by y
 Kruskal-Wallis chi-squared = 6, df = 6, p-value = 0.4232

  kruskal.test(d~f)

   Kruskal-Wallis rank sum test

 data:  d by f
 Kruskal-Wallis chi-squared = 3.6816, df = 1, p-value = 0.05502

  kruskal.test(f~d)

   Kruskal-Wallis rank sum test

 data:  f by d
 Kruskal-Wallis chi-squared = 11.1429, df = 12, p-value = 0.5167

 I know the last kruskal.test(f~d) is not correct as the factor is always
 placed as the second bit but I still tried it that way just to be sure...

 Cheers

You don't provide context, so I don't know what results you can't reproduce.  
But you need to reread the help page for the kruskal.test and look at the 
examples give.  If x and y are the results for two independent groups, then the 
call to the kruskal.test should be either 

kruskal.test(list(x,y)) #or,
kruskal.test(d~f)

Hope this is helpful,

Dan

Daniel Nordlund
Bothell, WA USA

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[R] 2D filter in R?

2012-01-11 Thread Michael

Hi all,

I am looking for a command for doing 2D filtering (rectangular or
Gaussian) in R...

I have looked at ksmooth, filter and convolve but they seem to be 1D...

Any thoughts?

Thanks a lot!

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Re: [R] Problem with segmented

2012-01-11 Thread Sarah Goslee

We really need the small reproducible example requested in the posting
guide, including sample data, the actual R commands you used, the
libraries required, and your OS and version of R.

Sarah

On Wed, Jan 11, 2012 at 9:08 AM, Filoche pmassico...@hotmail.com wrote:
 Hi there.

 Here's the error message.

 Error in seg.lm.fit(y, XREG, Z, PSI, weights, offs, opz) :
  (Some) estimated psi out of its range

 I have tried many ways to specify the arguments, but apparently the error
 message is related to the estimated break point being invalid. However, my
 estimation fall within range of my data.

 Thank for your help,
 Phil


-- 
Sarah Goslee
http://www.functionaldiversity.org

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Re: [R] stacked barplot colour coding

2012-01-11 Thread Richard M. Heiberger

This graph would be easier under lattice graphics.

biomass - data.frame(bg=c(0.41, 0.37, 0.31, 0.32),
  ag=c(2.81, 2.91, 2.06, 2.39))
b2 - stack(biomass)
names(b2) - c(mass, type)
b2$type - factor(b2$type, levels=c(bg,ag))
b2$AB - rep(c(A,A,B,B), 2)
b2$location - rep(1:4, 2)
b2
barchart(mass ~ location | AB, group=type, data=b2,
 horizontal=FALSE, stack=TRUE,
 col=c(white, grey90),
 scales=list(x=list(relation=sliced)),
 ylim=c(0, 10),
 ylab=Total biomass (g))

I did several things above.  First, I gave the data frame a name that has
some semblance
of what the data is (I don't know more about it, but you can do even better
with an appropriate name).

Second, I recognize that there are three factors---using the technical
definition of a factor.  You were using
the term factor very informally and inconsistently.  You said that there
are four factors and also that there are
two factors.  I interpret that as the factor location with 4 levels, and
the factor AB with two levels.
You also have the factor type with two levels, these are the columns of
your original data organization.
I invented the names location, AB, and type.  You can pick more appropriate
names.

Third, since you want to distinguish the AB levels, I did it graphically by
putting them in separate panels.

I suggest you learn lattice graphics.

Rich



On Mon, Jan 9, 2012 at 8:01 PM, acacia21 chriss...@hotmail.com wrote:

 Hi all,
 i'm fairly new to R and its graphing, but having unsuccessfully  'googled'
 and checked this forum to find answer to my problem, i'm posting my
 question
 here.

 I'm trying to plot stacked barplot. I have simple data that looks like
 this:
 bg   ag
 0.412.81
 0.372.91
 0.312.06
 0.322.39

 every row indicates a factor (1,2,3,4, see below in names.arg). Now when i
 plot this using following function for stacked barplots:
 plot-barplot(t(data), main=txt, ylim=c(0,10), col=c(white, grey90),
 ylab=Total biomass (g), space=0.1, names.arg=c(1, 2, 3, 4))

 i get a lovely stacked graph and it color-codes with white (bg) and grey90
 (ag) in each individual stacked bar.  I have a total of 4 stacked bars as i
 have 4 factors. Now here is the question: i would like to add density lines
 across entire stacked bar or any other graphic feature to distinguish
 between bars 1 and 2 as they indicate same factor and  3 and 4 that
 indicate
 different factor. Is there any way to do that? Surely it's possible, but
 not
 so obvious for the beginner =)

 thank you very much


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Re: [R] New to R, Curious about Project Idea

It sounds quite possible but you'll probably get more specialized help
if you ask on the r-sig-geo mailing list.

Michael

On Wed, Jan 11, 2012 at 9:36 AM, arbeaupg parb...@gmail.com wrote:
 Good morning,

 I am a student whom is currently working on a term project for my GIS
 Program. I am looking for a software package which can aid me in my project,
 and I was curious if R would be able to address my goals.

 My project includes  power outage data from a hydro company (point data,
 with UTM coordinates attached), which is available in an Access database, or
 in a Shapefile.

 I would like to be able to take this poweroutage data, and then perform a
 spatial analysis of this data, perhaps as a hot-spot analysis, or in a
 points per raster square style analysis.

 With the completed analysis, I would like to be able to use an open source
 web mapping platform to display it for the 'company' I am performing this
 for as part of my project.


 Any insight you could provide me would be greatly, greatly appreciated.

 Thanks,

 Phil

 --
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Re: [R] Restricting R session

2012-01-11 Thread Antonio Rodriges

Thank you, Uwe,

below are my comments

 In particular, how to prohibit some set of functions, for example,
 from base package?


 You can't: R is free software.

This does not imply it must be inflexible and unsuitable for cloud services

 Well, of course you could build your own
 version of R that did not ship those functions. Anyway, typical restrictions
 are handled by settig permissions on the file system and/or arrange quotas
 for space / memory / CPU resources.

Disk quotas and permissions are helpful in case when R function
depends on disk access. For other functions something more special
must be devised.

 How to limit session operating memory and CPU time?
 Ask he manual of your operating system.

The most straightforward Linux command is ulimit which limits
CPU/memory per shell/user/system wide. However, sessions are child
processes of R and this requires testing whether limits will cover all
sessions or each session separately.

-- 
Kind regards,
Antonio Rodriges

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Re: [R] turning a list of vectors into a data.frame (as rows of the DF)?

Most methods take the rows of data.frame()s to be very significant
(indicating multiple values from a single observation) so what you're
doing seems like it may be against the spirit of R, but if you want
a simple NA padding at the end, this should do it:

listToDF - function(inputList, fill = NA){
# Use fill = NULL for regular recycling behavior
maxLen = max(sapply(inputList, length))
for(i in seq_along(inputList))
inputList[[i]] - c(inputList[[i]], rep(fill, maxLen -
length(inputList[[i]])))
return(as.data.frame(inputList))
}

listToDF(list(x = 1:4, y = 1:2))

Michael

On Wed, Jan 11, 2012 at 2:40 PM, Chris Conner connerpha...@yahoo.com wrote:
 As a newer R practicioner, it seems I stump myself weekly (at least) with 
 issues that have spinning my wheels.  Here is yet another... I'm trying to 
 turn a list of numeric vectors (of uneual length) inot a dataframe.  Each 
 vector held in the list represents a row, and there are some rows of unequal 
 length.  I would like NAs as placeholders for missing data in the shorter 
 vectors.  I think I'm missing something quite basic.

 v1 - c(1,2,3,4)
 v2 - c(1,2)
 lst1 - list(v1,v2)

 Of course there is the intuitive:

 as.data.frame(lst1)

 However, the recycling rule (expectedly) reclycles 1,2 versus using NAs as 
 placeholders.

 Then, looking into Teetor's R Cookbook, there is a piece of code that looked 
 (from the description) like it might do the trick:

 do.call(rbind, Map(as.data.frame,lst1)

 But I get the error:
 Error in match.names(clabs, names(xi)) :
   names do not match previous names

 Thinking the source of the error had to do with the vectors of unequal 
 lenght, I tried Hadley's rbind.fill thusly:

 library(reshape)
 do.call(rbind.fill, Map(as.data.frame,lst1)

 Which produced a dataset, but gain, not in the desired format.

 Thanks in advance to anyone that can bring my frustrations to end!
 C
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Re: [R] Storing/Restoring R objects

R is the natural tool to operate on a .RData file: you can name it
however you wish either with your OS or with the save() command in R.

You can load any .RData files with the load() command but the startup
routine only looks for .RData (to my knowledge) unless you put
specific instructions in your .Rprofile.

What I might suggest is (if there is a natural modularity to your
project) saving the sets of relevant data frames in .RData files
(which can hold multiple objects) and then writing a little prompt to
ask your users which one he would like to load using readline(): e.g.,

cat(Here are available data sets, dir(pattern = .RData), \n)
load(dir()[pmatch(readline(Which data set would you like to load), dir())])

Does this help?

Michael

On Wed, Jan 11, 2012 at 2:56 PM, Rich Shepard rshep...@appl-ecosys.com wrote:
  One of my projects has generated quite a few objects (data frames) related
 to one portion of this project. They can be listed with the ls() function.
 What I would like to do is move them to another directory so that data
 frames for other portions of the project can be more easily seen and used.

  .RData is a binary file. Are there tools that let me work with this file?
 What if I rename it and start a new .RData file when I next invoke R? Could
 I then specify which .RData file should be available on demand?

  I have not seen (or remembered if I did) discussions on this topic. Please
 advise.

 Rich

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Re: [R] Storing/Restoring R objects




On 11.01.2012 20:56, Rich Shepard wrote:

One of my projects has generated quite a few objects (data frames) related
to one portion of this project. They can be listed with the ls()
function. What I would like to do is move them to another directory so
that data
frames for other portions of the project can be more easily seen and used.

.RData is a binary file. Are there tools that let me work with this file?
What if I rename it and start a new .RData file when I next invoke R? Could
I then specify which .RData file should be available on demand?



See ?save and ?load

Uwe Ligges


I have not seen (or remembered if I did) discussions on this topic. Please
advise.

Rich

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Re: [R] RGL- Drawing Circle




On 11.01.2012 15:08, gli wrote:

thanks Duncan.  I think want my circle to be in user coordinates.  I tried
the first code u gave me and it gives me a circle. but how can i:

1) change the radius ?

2) place the circle at a given x,y,z coordinate?

3) turn it 90 degree up like these circle plate bus stop?
http://www.geocities.co.jp/yuganatabi/bus-stop-aba.html

4) and finally, set the orientation angle of the circle plate?



What about readin the help pages for the functions Duncan cited?

Uwe Ligges



grateful if u give me some directions or at least let me know if it is
possible or not.

graham

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Re: [R] New to R, Curious about Project Idea

2012-01-11 Thread Daniel Nordlund

 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
 On Behalf Of arbeaupg
 Sent: Wednesday, January 11, 2012 6:36 AM
 To: r-help@r-project.org
 Subject: [R] New to R, Curious about Project Idea

 Good morning,

 I am a student whom is currently working on a term project for my GIS
 Program. I am looking for a software package which can aid me in my
 project,
 and I was curious if R would be able to address my goals.

 My project includes  power outage data from a hydro company (point data,
 with UTM coordinates attached), which is available in an Access database,
 or
 in a Shapefile.

 I would like to be able to take this poweroutage data, and then perform a
 spatial analysis of this data, perhaps as a hot-spot analysis, or in a
 points per raster square style analysis.

 With the completed analysis, I would like to be able to use an open source
 web mapping platform to display it for the 'company' I am performing this
 for as part of my project.

 Any insight you could provide me would be greatly, greatly appreciated.

 Thanks,

 Phil

Not my area of expertise, but if you go to your favorite CRAN mirror and look 
at the task views, you will find info on spatial analysis.  Also, Googling 'R 
GIS' brings up a ton of hits.

Good luck,

Dan

Daniel Nordlund
Bothell, WA USA

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[R] summarizing a complex dataframe

2012-01-11 Thread Christopher G Oakley

I need some help summarizing complex data frames (small example below):

m1_1 m2_1 m3_1 m1_2 m2_2 m3_2 
i1111222
i1211222   
i2221222


For an arbitrary number of columns (say m1 …. m199) where the column names have 
variable patterns, 

and such that each set of columns is repeated (with potentially unique data) an 
arbitrary number of times (say _1 … _1000),

I would like to summarize by row the mean values of (m1, m2, m3, … m199) over 
all replicates (_1, _2, _3, … _1000). I need to do this with a large number of 
dataframes of variable nrow, ncolumn, and colnames.

I've tried various loops creating new dataframes and reassigning cell values in 
loops or using rbind and bind, but run into trouble in each case.

Any ideas?

Thanks,

Chris 

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Re: [R] Confidence Interval from Moments?

Assuming a distribution defined solely by those moments it is possible
(e.g., z- or t-test confidence intervals) but this isn't really the
place to discuss such things since there's no R content to your
question: try stats.stackexchange.com

Michael

On Wed, Jan 11, 2012 at 4:56 AM, lambdatau lewis@rbs.com wrote:
 Hi all,

 I'm wondering whether it is possible to construct a confidence interval
 using only the mean, variance, skewness and kurtosis, i.e. without any of
 the population?

 If anyone could help with this it'd be much appreciated (even if just a
 confirmation of it being impossible!).

 Thanks.

 --
 View this message in context: 
 http://r.789695.n4.nabble.com/Confidence-Interval-from-Moments-tp4284937p4284937.html
 Sent from the R help mailing list archive at Nabble.com.

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

Re: [R] turning a list of vectors into a data.frame (as rows of the DF)?

2012-01-11 Thread William Dunlap

Perhaps the following does what you want.  It extends
each element of your list to a common length, converts
that to a matrix, then to a data.frame:

  f - function(data) {
nCol - max(vapply(data, length, 0))
data - lapply(data, function(row) c(row, rep(NA, nCol-length(row
data - matrix(unlist(data), nrow=length(data), ncol=nCol, byrow=TRUE)
data.frame(data)
  }
E.g.,
   rawData - list(c(1,2,3), c(11,12), integer(), 31)
   f(rawData)
X1 X2 X3
  1  1  2  3
  2 11 12 NA
  3 NA NA NA
  4 31 NA NA

What sort of data is this?  If it is longitudinal
it might be more straigtforward to store it as a
three-column data.frame (columns subject, time, value).

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 Chris Conner
 Sent: Wednesday, January 11, 2012 11:41 AM
 To: HelpR
 Subject: [R] turning a list of vectors into a data.frame (as rows of the DF)?
 
 As a newer R practicioner, it seems I stump myself weekly (at least) with 
 issues that have spinning my
 wheels.  Here is yet another... I'm trying to turn a list of numeric vectors 
 (of uneual length) inot a
 dataframe.  Each vector held in the list represents a row, and there are some 
 rows of unequal
 length.  I would like NAs as placeholders for missing data in the shorter 
 vectors.  I think I'm
 missing something quite basic.
 
 v1 - c(1,2,3,4)
 v2 - c(1,2)
 lst1 - list(v1,v2)
 
 Of course there is the intuitive:
 
 as.data.frame(lst1)
 
 However, the recycling rule (expectedly) reclycles 1,2 versus using NAs as 
 placeholders.
 
 Then, looking into Teetor's R Cookbook, there is a piece of code that looked 
 (from the description)
 like it might do the trick:
 
 do.call(rbind, Map(as.data.frame,lst1)
 
 But I get the error:
 Error in match.names(clabs, names(xi)) :
   names do not match previous names
 
 Thinking the source of the error had to do with the vectors of unequal 
 lenght, I tried Hadley's
 rbind.fill thusly:
 
 library(reshape)
 do.call(rbind.fill, Map(as.data.frame,lst1)
 
 Which produced a dataset, but gain, not in the desired format.
 
 Thanks in advance to anyone that can bring my frustrations to end!
 C
   [[alternative HTML version deleted]]

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

Re: [R] turning a list of vectors into a data.frame (as rows of the DF)?

2012-01-11 Thread Marc Schwartz

On Jan 11, 2012, at 1:40 PM, Chris Conner wrote:

 As a newer R practicioner, it seems I stump myself weekly (at least) with 
 issues that have spinning my wheels.  Here is yet another... I'm trying to 
 turn a list of numeric vectors (of uneual length) inot a dataframe.  Each 
 vector held in the list represents a row, and there are some rows of unequal 
 length.  I would like NAs as placeholders for missing data in the shorter 
 vectors.  I think I'm missing something quite basic.
  
 v1 - c(1,2,3,4)
 v2 - c(1,2)
 lst1 - list(v1,v2)
  
 Of course there is the intuitive:
  
 as.data.frame(lst1)
  
 However, the recycling rule (expectedly) reclycles 1,2 versus using NAs as 
 placeholders.
  
 Then, looking into Teetor's R Cookbook, there is a piece of code that looked 
 (from the description) like it might do the trick:
  
 do.call(rbind, Map(as.data.frame,lst1)
  
 But I get the error:
 Error in match.names(clabs, names(xi)) : 
   names do not match previous names
  
 Thinking the source of the error had to do with the vectors of unequal 
 lenght, I tried Hadley's rbind.fill thusly:
  
 library(reshape)
 do.call(rbind.fill, Map(as.data.frame,lst1)
  
 Which produced a dataset, but gain, not in the desired format.
  
 Thanks in advance to anyone that can bring my frustrations to end!
 C
   [[alternative HTML version deleted]]


There may be an easier way, but try this:

list2df - function(x)
{
  MAX.LEN - max(sapply(x, length), na.rm = TRUE)
  DF - data.frame(lapply(x, function(x) c(x, rep(NA, MAX.LEN - length(x)
  colnames(DF) - paste(V, seq(ncol(DF)), sep = )  
  DF
}


 list2df(lst1)
  V1 V2
1  1  1
2  2  2
3  3 NA
4  4 NA


HTH,

Marc Schwartz

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Re: [R] rjags installation trouble

2012-01-11 Thread Ben Bolker

On 12-01-11 11:45 AM, Martyn Plummer wrote:
 It looks like you are cross-linking to an earlier version of the JAGS
 library at run time. Check
 
 /sbin/ldconfig -p | grep jags -
 
 When compiling rjags, you can hard-code the location of the jags library
 using the [GNU-specific] configure option --enable-rpath.
 
 Martyn

  Thanks.  I managed to sort it out by assiduously cleaning out all
older versions of JAGS ...

  Ben Bolker

 
 On Tue, 2012-01-10 at 10:40 -0500, Ben Bolker wrote:
 Trying to install latest rjags (3-5) from CRAN with JAGS 3.2.0
 installed on Ubuntu 10.04, with r-devel ... the bottom line is that it
 fails while loading with

  /libs/rjags.so: undefined symbol: _ZN7Console15checkAdaptationERb

   Has anyone else seen this or is it a glitch somewhere in my system?

   thanks
 Ben Bolker

 ==
 bolker@ubuntu-10-new:~/R/pkgs/rjags$ jags
 Welcome to JAGS 3.2.0 on Tue Jan 10 10:38:31 2012
 JAGS is free software and comes with ABSOLUTELY NO WARRANTY
 Loading module: basemod: ok
 Loading module: bugs: ok
 .

 ===

 install.packages(rjags) starts out fine:

 Installing package(s) into
 ‘/mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library’
 (as ‘lib’ is unspecified)
 trying URL 'http://probability.ca/cran/src/contrib/rjags_3-5.tar.gz'
 Content type 'application/x-gzip' length 66429 bytes (64 Kb)
 opened URL
 ==
 downloaded 64 Kb

 * installing *source* package ‘rjags’ ...
 ** package ‘rjags’ successfully unpacked and MD5 sums checked
 checking for prefix by checking for jags... /usr/bin/jags

   [snip snip]

 ** libs
 g++ -I/usr/local/lib/R/include -DNDEBUG -I/usr/include/JAGS
 -I/usr/local/include-fpic  -g -O2  -c jags.cc -o jags.o
 g++ -I/usr/local/lib/R/include -DNDEBUG -I/usr/include/JAGS
 -I/usr/local/include-fpic  -g -O2  -c parallel.cc -o parallel.o
 g++ -shared -L/usr/local/lib -o rjags.so jags.o parallel.o -L/usr/lib -ljags
 installing to /mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags/libs
 ** R

   [snip snip]

   but fails at:

 ** building package indices
 Error : .onLoad failed in loadNamespace() for 'rjags', details:
   call: dyn.load(file, DLLpath = DLLpath, ...)
   error: unable to load shared object
 '/mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags/libs/rjags.so':

 /mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags/libs/rjags.so:
 undefined symbol: _ZN7Console15checkAdaptationERb
 ERROR: installing package indices failed
 * removing ‘/mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags’
 * restoring previous
 ‘/mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags’

 The downloaded source packages are in
  ‘/tmp/RtmpSKHIz5/downloaded_packages’
 Warning message:
 In install.packages(rjags) :
   installation of package ‘rjags’ had non-zero exit status
 sessionInfo()
 R Under development (unstable) (2012-01-01 r58032)
 Platform: i686-pc-linux-gnu (32-bit)

 locale:
  [1] LC_CTYPE=en_CA.utf8   LC_NUMERIC=C
  [3] LC_TIME=en_CA.utf8LC_COLLATE=en_CA.utf8
  [5] LC_MONETARY=en_CA.utf8LC_MESSAGES=en_CA.utf8
  [7] LC_PAPER=CLC_NAME=C
  [9] LC_ADDRESS=C  LC_TELEPHONE=C
 [11] LC_MEASUREMENT=en_CA.utf8 LC_IDENTIFICATION=C

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

 loaded via a namespace (and not attached):
 [1] tools_2.15.0
 
 
 ---
 This message and its attachments are strictly confiden...{{dropped:8}}

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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] Storing/Restoring R objects

2012-01-11 Thread Jeff Newmiller

?save
?load
You may need to create single use environment objects to hold the whole file 
while you separate multiple objects.
---
Jeff NewmillerThe .   .  Go Live...
DCN:jdnew...@dcn.davis.ca.usBasics: ##.#.   ##.#.  Live Go...
  Live:   OO#.. Dead: OO#..  Playing
Research Engineer (Solar/BatteriesO.O#.   #.O#.  with
/Software/Embedded Controllers)   .OO#.   .OO#.  rocks...1k
--- 
Sent from my phone. Please excuse my brevity.

Rich Shepard rshep...@appl-ecosys.com wrote:

One of my projects has generated quite a few objects (data frames)
related
to one portion of this project. They can be listed with the ls()
function. 
What I would like to do is move them to another directory so that data
frames for other portions of the project can be more easily seen and
used.

.RData is a binary file. Are there tools that let me work with this
file?
What if I rename it and start a new .RData file when I next invoke R?
Could
I then specify which .RData file should be available on demand?

I have not seen (or remembered if I did) discussions on this topic.
Please
advise.

Rich

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[R] rjava on FreeBSD

2012-01-11 Thread Hasan Diwan

Trying to install Rjava on FreeBSD 9 and am getting the following error:
 install.packages('rJava')
trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/rJava_0.9-3.tar.gz'
Content type 'application/x-gzip' length 537153 bytes (524 Kb)
opened URL
==
downloaded 524 Kb

* installing *source* package 'rJava' ...
** package 'rJava' successfully unpacked and MD5 sums checked
checking for gcc... gcc46 -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc46 -std=gnu99 accepts -g... yes
checking for gcc46 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc46 -std=gnu99 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking whether time.h and sys/time.h may both be included... yes
configure: checking whether gcc46 -std=gnu99 supports static inline...
yes
checking whether setjmp.h is POSIX.1 compatible... yes
checking whether sigsetjmp is declared... yes
checking whether siglongjmp is declared... yes
checking Java support in R... present:
interpreter : '/usr/local/bin/java'
archiver: '/usr/local/bin/jar'
compiler: '/usr/local/bin/javac'
header prep.: '/usr/local/bin/javah'
cpp flags   : '-I/usr/local/jdk1.6.0/jre/../include
-I/usr/local/jdk1.6.0/jre/../include/freebsd'
java libs   : '-L/usr/local/jdk1.6.0/jre/lib/i386/server
-L/usr/local/jdk1.6.0/jre/lib/i386
-L/usr/local/jdk1.6.0/jre/../lib/i386 -L -L/usr/java/packages/lib/i386
-L/lib -L/usr/lib -L/usr/local/lib -ljvm'
checking whether JNI programs can be compiled... yes
checking JNI data types... configure: error: One or more JNI types
differ from the corresponding native type. You may need to use
non-standard compiler flags or a different compiler in order to fix
this.
ERROR: configuration failed for package 'rJava'
* removing '/usr/local/lib/R/library/rJava'
* removing '/usr/local/lib/R/library/rJava'

The downloaded packages are in
'/tmp/RtmpWtRfKe/downloaded_packages'
Updating HTML index of packages in '.Library'
Warning messages:
1: In install.packages(rJava) :
  installation of package 'rJava' had non-zero exit status
2: In file.create(f.tg) :
  cannot create file '/usr/local/share/doc/R/html/packages.html',
reason 'Permission denied'
3: In make.packages.html(.Library) : cannot update HTML package index


Ok, so I tried doing so as root, because it would solve the
'Permissions denied' issue and was rewarded with:
 install.packages('rJava')
trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/rJava_0.9-3.tar.gz'
Content type 'application/x-gzip' length 537153 bytes (524 Kb)
opened URL
==
downloaded 524 Kb

* installing *source* package 'rJava' ...
** package 'rJava' successfully unpacked and MD5 sums checked
checking for gcc... gcc46 -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc46 -std=gnu99 accepts -g... yes
checking for gcc46 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc46 -std=gnu99 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking whether time.h and sys/time.h may both be included... yes
configure: checking whether gcc46 -std=gnu99

Re: [R] Storing/Restoring R objects