date:20091118

Hello dear R help group,
I would like to download the tRNA data on:
http://gtrnadb.ucsc.edu/download.html

And then import it into R.

Can anyone direct me as to how to do so?


Thanks,
Tal




--


My contact information:
Tal Galili
E-mail: tal.gal...@gmail.com
Phone number: 972-52-7275845
FaceBook: Tal Galili
My Blogs:
http://www.talgalili.com (Web and general, Hebrew)
http://www.biostatistics.co.il (Statistics, Hebrew)
http://www.r-statistics.com/ (Statistics,R, English)


--


My contact information:
Tal Galili
E-mail: tal.gal...@gmail.com
Phone number: 972-52-7275845
FaceBook: Tal Galili
My Blogs:
http://www.talgalili.com (Web and general, Hebrew)
http://www.biostatistics.co.il (Statistics, Hebrew)
http://www.r-statistics.com/ (Statistics,R, English)

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[R] getting the name of a single object in R for debugging output

2009-11-18 Thread Andrew

I often use a debug flag (set to TRUE) to turn on various debugging print 
statements in my R scripts.  I was thinking I should create a function 
debugPrint(object,debugFlag),
to print out the object name and contents if the debugFlag is set to TRUE.  
Then I wouldn't have to make my script ugly(..er) than it already is by adding 
IF statements all over the place.  I've seen how ls() dumps object names, but 
how do I get access to the character representation of the name of an object.

E.g.

myVar- 10

print(myVar) produces 10

I'd like to print out something like  myVar : 10

I'd appreciate any suggestions.

Regards,

Andrew



  
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[R] Switch Help

2009-11-18 Thread oscar linares

Dear Rexperts,

Given,

aar -function(command) {

switch(command,
  {scrn = cat(scrn  :Screening,\n)}
  {dx   = cat(dx:Diagnosis,\n)}
  {df   = cat(df:Don't Forget,\n)}
)
}

I want to be able to do:

aar(dx) # function does cat(dx:Diagnosis,\n)

aar(c(dx,df))  # function does cat(dx:Diagnosis,\n)
# function does df   = cat(df:Don't
Forget,\n)

BUT IT IS NOT WORKING FOR ME.

Please help:-)

-- 
Oscar
Oscar A. Linares, MD
Translational Medicine Unit
LaPlaisance Bay, Bolles Harbor
Monroe, Michigan

[[alternative HTML version deleted]]

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Re: [R] Lattice plot

Hi,

ggplot2 can also split the graphs in different panels,

d=
read.table(textConnection(
chr start1 end1 meth positive
1   1 10   20  1.5y
2   2 12   18 -0.7n
3   3 22   34  2.0y
4   1 35   70  3.0y
5   1120  140 -1.3n
6   1180  190  0.2y
7   2220  300  0.4y), head=T)

library(ggplot2)
ggplot(data=d) + facet_grid(.~chr) +
 geom_segment(aes(x=start1, xend=end1, y=meth, yend=meth))


HTH,

baptiste


2009/11/17 Tim Smith tim_smith_...@yahoo.com:
 Hi,

 I was trying to get a graph in lattice with the following data frame (7 rows, 
 5 cols):
 chr start1 end1 meth positive
 1   1     10   20  1.5        y
 2   2     12   18 -0.7        n
 3   3     22   34  2.0        y
 4   1     35   70  3.0        y
 5   1    120  140 -1.3        n
 6   1    180  190  0.2        y
 7   2    220  300  0.4        y
 I wanted the panels to be organized by 'chr' - which is ok. Further, I wanted 
 the lines to be discontinuous. For example, in the first row, the x 
 co-ordinate starts with a value of 10 (2nd column) and ends with a value of 
 20 (3rd column). The corresponding y value for this range of x values is 1.5 
 (4th column). Similarly, for the same panel (i.e chr=1), the fourth row would 
 have x co-ordinate range from 35 to 70 with a y co-ordinate of 3.
 If it were only one panel, a similar result could be achieved for the data x2:
 x2
  chr start1 end1 meth positive
 1   1     10   20  1.5        y
 4   1     35   70  3.0        y
 5   1    120  140 -1.3        n
 6   1    180  190  0.2        y


 ## Code courtesy of BAPTISTE AUGUIE
 library(ggplot2)
 ggplot(data=x2) +
  geom_segment(aes(x=start1, xend=end1, y=meth, yend=meth))
 - Can I get lattice to do a similar graph for the panels?
 thanks!



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[R] Odp: recode according to old levels

2009-11-18 Thread Petr PIKAL

Hi


r-help-boun...@r-project.org napsal dne 18.11.2009 09:24:40:

 Dear R-users,
 
 i try to recode a factor according to old levels
 
 F - factor(sample(c(rep(A, 4), rep(B,2), rep(C,5
 
 recode(F, levels(F)[c(1,3)]='X'; else='Y')
 
 i tried to work with eval or expression around levels(F)[c(1,3)], but 
 nothing seems to work.
 

I am not sure if recode does not want as an input a numeric vector. 
However for recoding levels of factor you can add a vector of new levels 
in correct order.

set.seed(111)
F - factor(sample(c(rep(A, 4), rep(B,2), rep(C,5
levels(F)-c(X,X,Y)
F
 [1] Y Y X X X Y X X X Y Y
Levels: X Y

or maybe

levels(F)- ifelse(levels(F) %in% c(A,B), X, Y)

Regards
Petr


 
 Many thanks if anyone could tell me what i've missed and what's the 
 problem here.
 
 best regards
 
 Andreas
 
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Re: [R] recode according to old levels



Andreas Wittmann wrote:

Dear R-users,

i try to recode a factor according to old levels

F - factor(sample(c(rep(A, 4), rep(B,2), rep(C,5

recode(F, levels(F)[c(1,3)]='X'; else='Y')

i tried to work with eval or expression around levels(F)[c(1,3)], but 
nothing seems to work.



I assume that you mean the recode() function in pkg:car?
(You really should say so.)

Here are a couple of ways to recode the factor:

set.seed(6931)
F - factor(sample(rep(c(A,B,C), c(4,2,5
lev - levels(F)

# 1: using car:::recode
F - recode(F, lev[c(1,3)] = 'X'; else = 'Y')

# 2: using base:::levels
levels(F) - list(X = lev[c(1,3)], Y = lev[-c(1,3)])

 -Peter Ehlers



Many thanks if anyone could tell me what i've missed and what's the 
problem here.


best regards

Andreas

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Re: [R] Switch Help

2009-11-18 Thread Colin Millar

I think you just missed some commas out...  

aar -
function(command = c(scrn, dx, df))
{
  command - match.arg(command)
  switch(command,
scrn = cat(scrn  :Screening,\n),
dx   = cat(dx:Diagnosis,\n),
df   = cat(df:Don't Forget,\n)
  )
}

Colin.


Ps you don't need the curly brackets here if theres only one expresion,
and sometimes its good to restrict the inputs to only those you want
So that

aar(something wrong)

# Error in match.arg(command) : 'arg' should be one of scrn, dx,
df


-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf Of oscar linares
Sent: 18 November 2009 10:40
To: r-help@r-project.org
Subject: [R] Switch Help

Dear Rexperts,

Given,

aar -function(command) {

switch(command,
  {scrn = cat(scrn  :Screening,\n)}
  {dx   = cat(dx:Diagnosis,\n)}
  {df   = cat(df:Don't Forget,\n)}
)
}

I want to be able to do:

aar(dx) # function does cat(dx:Diagnosis,\n)

aar(c(dx,df))  # function does cat(dx:Diagnosis,\n)
# function does df   = cat(df:Don't
Forget,\n)

BUT IT IS NOT WORKING FOR ME.

Please help:-)

-- 
Oscar
Oscar A. Linares, MD
Translational Medicine Unit
LaPlaisance Bay, Bolles Harbor
Monroe, Michigan

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Re: [R] Switch Help

If you want type twice commands in function aar, you could try this:

aar -function(command) {
switch(command,
 scrn = cat(scrn  :Screening,\n),
 dx = cat(dx:Diagnosis,\n),
 df = cat(df:Don't Forget,\n))
}

invisible(Vectorize(aar)(c('dx', 'df')))


On Wed, Nov 18, 2009 at 8:39 AM, oscar linares wins...@gmail.com wrote:
 Dear Rexperts,

 Given,

 aar -function(command) {

 switch(command,
  {scrn = cat(scrn  :Screening,\n)}
  {dx   = cat(dx    :Diagnosis,\n)}
  {df   = cat(df    :Don't Forget,\n)}
 )
 }

 I want to be able to do:

 aar(dx) # function does cat(dx    :Diagnosis,\n)

 aar(c(dx,df))  # function does cat(dx    :Diagnosis,\n)
                        # function does df   = cat(df    :Don't
 Forget,\n)

 BUT IT IS NOT WORKING FOR ME.

 Please help:-)

 --
 Oscar
 Oscar A. Linares, MD
 Translational Medicine Unit
 LaPlaisance Bay, Bolles Harbor
 Monroe, Michigan

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-- 
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O

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Re: [R] Switch Help

2009-11-18 Thread Colin Millar

And if you want to do both do

invisible( lapply(c(scrn,dx), aar) )

but I think you will have to use multiple ifs rather than switch if you
intend to add more functionality...


.
.
.

I think you just missed some commas out...  

aar -
function(command = c(scrn, dx, df)) {
  command - match.arg(command)
  switch(command,
scrn = cat(scrn  :Screening,\n),
dx   = cat(dx:Diagnosis,\n),
df   = cat(df:Don't Forget,\n)
  )
}

Colin.


Ps you don't need the curly brackets here if theres only one expresion,
and sometimes its good to restrict the inputs to only those you want So
that

aar(something wrong)

# Error in match.arg(command) : 'arg' should be one of scrn, dx,
df


-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf Of oscar linares
Sent: 18 November 2009 10:40
To: r-help@r-project.org
Subject: [R] Switch Help

Dear Rexperts,

Given,

aar -function(command) {

switch(command,
  {scrn = cat(scrn  :Screening,\n)}
  {dx   = cat(dx:Diagnosis,\n)}
  {df   = cat(df:Don't Forget,\n)}
)
}

I want to be able to do:

aar(dx) # function does cat(dx:Diagnosis,\n)

aar(c(dx,df))  # function does cat(dx:Diagnosis,\n)
# function does df   = cat(df:Don't
Forget,\n)

BUT IT IS NOT WORKING FOR ME.

Please help:-)

-- 
Oscar
Oscar A. Linares, MD
Translational Medicine Unit
LaPlaisance Bay, Bolles Harbor
Monroe, Michigan

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Re: [R] getting the name of a single object in R for debugging output

Try this:

debugPrint - function(x, ...){
print(sprintf(%s: %d, deparse(substitute(x)), x), ...)
}

On Wed, Nov 18, 2009 at 8:35 AM, Andrew nodeco...@yahoo.com wrote:
 I often use a debug flag (set to TRUE) to turn on various debugging print 
 statements in my R scripts.  I was thinking I should create a function 
 debugPrint(object,debugFlag),
 to print out the object name and contents if the debugFlag is set to TRUE.  
 Then I wouldn't have to make my script ugly(..er) than it already is by 
 adding IF statements all over the place.  I've seen how ls() dumps object 
 names, but how do I get access to the character representation of the name of 
 an object.

 E.g.

 myVar- 10

 print(myVar) produces 10

 I'd like to print out something like  myVar : 10

 I'd appreciate any suggestions.

 Regards,

 Andrew




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-- 
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O

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Re: [R] (exact) confidence bounds for lognormal parameters \mu and \sigma

2009-11-18 Thread Krusty the Klown


Thank you,
it is what I was looking for:

library(fitdistrplus)
x-rlnorm(100)
res-mledist(x, distr=lnorm)
res

Anyway, the results do not provide confidence intervals, but mle estimates
and the hessian matrix, whose extradiagonal elements are null... is it
correct?
http://www.weibull.com/LifeDataWeb/confidence_bounds_log.htm
http://www.weibull.com/LifeDataWeb/confidence_bounds_log.htm 

I will investigate...


David Scott-6 wrote:
 
 Krusty the Klown wrote:
 Dear all,
 a statistical question: how can I compute exact confidence intervals for
 the
 lognormal distribution parameters? I found something only on 
 www.weibull.com www.weibull.com . Does exist a package in R which can
 compute them?
 Thanks in advance,
 KTK
 
 I think fitdistrplus can do this
 
 David Scott
 -- 
 _
 David Scott   Department of Statistics
   The University of Auckland, PB 92019
   Auckland 1142,NEW ZEALAND
 Phone: +64 9 923 5055, or +64 9 373 7599 ext 85055
 Email:d.sc...@auckland.ac.nz,  Fax: +64 9 373 7018
 
 Director of Consulting, Department of Statistics
 
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[R] How to install older version of R?

2009-11-18 Thread Pan,

Dear list

This is much like a linux problem, but I can't find any reference for
it. My OS is ubuntu 9.04 and a version of 2.9.2 of R has been already
installed in. Now, I need to install the version of 2.7.1. I google a
lot of websites and it seems like without a painless way provided me to
do it.
If any one offer me some suggestions/reference, I will appreciate.

Jia-Chiun Pan

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Re: [R] (exact) confidence bounds for lognormal parameters \mu and \sigma

2009-11-18 Thread Krusty the Klown


Sorry, probbaly it is...:blush:

Krusty the Klown wrote:
 
 Anyway, the results do not provide confidence intervals, but mle estimates
 and the hessian matrix, whose extradiagonal elements are null... is it
 correct?
  http://www.weibull.com/LifeDataWeb/confidence_bounds_log.htm
 http://www.weibull.com/LifeDataWeb/confidence_bounds_log.htm 
 
 

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http://old.nabble.com/%28exact%29-confidence-bounds-for-lognormal-parameters-%5Cmu-and-%5Csigma-tp26394177p26404958.html
Sent from the R help mailing list archive at Nabble.com.

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Re: [R] Switch Help

2009-11-18 Thread Alain Guillet


I believe that is what you want:

aar -function(command) {
   for(i in command){
   cat(i,:,switch(EXPR=i,
scrn = Screening,
dx = Diagnosis,
df = Don't Forget),
   \n)
   }
}

 aar(c(dx,df))
dx : Diagnosis
df : Don't Forget


Alain

oscar linares wrote:

Dear Rexperts,

Given,

aar -function(command) {

switch(command,
  {scrn = cat(scrn  :Screening,\n)}
  {dx   = cat(dx:Diagnosis,\n)}
  {df   = cat(df:Don't Forget,\n)}
)
}

I want to be able to do:

aar(dx) # function does cat(dx:Diagnosis,\n)

aar(c(dx,df))  # function does cat(dx:Diagnosis,\n)
# function does df   = cat(df:Don't
Forget,\n)

BUT IT IS NOT WORKING FOR ME.

Please help:-)

  


--
Alain Guillet
Statistician and Computer Scientist

SMCS - Institut de statistique - Université catholique de Louvain
Bureau c.316
Voie du Roman Pays, 20
B-1348 Louvain-la-Neuve
Belgium

tel: +32 10 47 30 50

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Re: [R] Lattice plot

2009-11-18 Thread Deepayan Sarkar

On Wed, Nov 18, 2009 at 4:14 AM, Tim Smith tim_smith_...@yahoo.com wrote:
 Hi,

 I was trying to get a graph in lattice with the following data frame (7 rows, 
 5 cols):
 chr start1 end1 meth positive
 1   1     10   20  1.5        y
 2   2     12   18 -0.7        n
 3   3     22   34  2.0        y
 4   1     35   70  3.0        y
 5   1    120  140 -1.3        n
 6   1    180  190  0.2        y
 7   2    220  300  0.4        y
 I wanted the panels to be organized by 'chr' - which is ok. Further, I wanted 
 the lines to be discontinuous. For example, in the first row, the x 
 co-ordinate starts with a value of 10 (2nd column) and ends with a value of 
 20 (3rd column). The corresponding y value for this range of x values is 1.5 
 (4th column). Similarly, for the same panel (i.e chr=1), the fourth row would 
 have x co-ordinate range from 35 to 70 with a y co-ordinate of 3.



You could do it with

library(latticeExtra)
segplot(meth ~ start1 + end1 | factor(chr), bar, type = g)

but as Baptiste said, ggplot2 can do conditioning just as well.

-Deepayan


 If it were only one panel, a similar result could be achieved for the data x2:
 x2
  chr start1 end1 meth positive
 1   1     10   20  1.5        y
 4   1     35   70  3.0        y
 5   1    120  140 -1.3        n
 6   1    180  190  0.2        y


 ## Code courtesy of BAPTISTE AUGUIE
 library(ggplot2)
 ggplot(data=x2) +
  geom_segment(aes(x=start1, xend=end1, y=meth, yend=meth))
 - Can I get lattice to do a similar graph for the panels?
 thanks!



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Re: [R] lattice barchart

2009-11-18 Thread Deepayan Sarkar

On Tue, Nov 17, 2009 at 3:31 PM, Wilberforce
will.pa...@matrixknowledge.com wrote:

 I have a data frame with two factors and want to create panel barcharts with
 one factor defining the panels and the other the vertical categories by
 which I can count the rows of data in each combination of factors. How do I
 do this?

 I have been trying to use barchart(~factor1|factor2) but it does not give
 the panels as I want them.

 The data looks like this:

 Factor1    Factor2
 A             y
 B             y
 A             x
 B             y
 C             x
 etc...

You need to tabulate your data first; barchart() won't do that for you.

Start with

barchart(xtabs(~Factor1 + Factor2, your.data))

and try using

as.data.frame(xtabs(~Factor1 + Factor2, your.data))

as the data= argument for more flexibility.

-Deepayan

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Re: [R] specifying group plots using panel.groups

2009-11-18 Thread Deepayan Sarkar

On Mon, Nov 16, 2009 at 9:47 PM, wintere ericawint...@gmail.com wrote:

 Hi,

 I am trying to plot two types of data on the same graph: points and
 distributions. I am attempting to use the panel.groups function, but cannot
 seem to get it to work. I have a melted data set and put in a FLAG column to
 separate my data into the two groups that I would like to plot, point data
 (FLAG=0) and the distribution(FLAG=1). Here is the code i am using in R:

Reproducible example please.

-Deepayan


 stripplot(
 variable~value,
 conf(RunlogBootCL),
 groups=FLAG,
 panel=panel.superpose,
 panel.groups=function(x,y, group.number, ...){
 if(group.number==1)panel.xyplot(x,y, group.number...)
 else if(group.number==0)panel.covplot(x,y, group.number...)},
 ref=1,
 cex = 0.5,
 col=black,
 main='Covariate Effects on Clearance',
 xlab='relative clearance',
 fill='transparent'
 )

 For some reason I can only get one or the other to plot!! (points or
 distributions). Can you please direct me to my error?! thanks!


 --
 View this message in context: 
 http://old.nabble.com/specifying-group-plots-using-panel.groups-tp26374674p26374674.html
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[R] boxplot

2009-11-18 Thread Sukhbir Rattan

Hi,

I have simple query

In which package drawBoxplot function is available?


Regards,
Sukhbir Singh Rattan

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[R] parsing numeric values

Dear list,

I'm seeking advice to extract some numeric values from a log file
created by an external program. Consider the following example,

input -
readLines(textConnection(
some text
  ax =1.3770E-03 bx =3.4644E-07
  ay =1.9412E-04 by =4.8840E-08

other text
  aax  =1.3770E-03 bbx =3.4644E-07
  aay  =1.9412E-04 bby =4.8840E-08))

## this is what I want
results - c(as.numeric(strsplit(grep(ax, input,val=T),  )[[1]][8]),
 as.numeric(strsplit(grep(ay, input,val=T),  )[[1]][8]),
 as.numeric(strsplit(grep(aax, input,val=T),  )[[1]][9]),
 as.numeric(strsplit(grep(aay, input,val=T),  )[[1]][9])
 )

## [1] 0.00137700 0.00019412 0.00137700 0.00019412

The use of strsplit is not ideal here as there is a different number
of space characters in the lines containing ax and aax for
instance (hence the indices 8 and 9 respectively).

I tried to use gsubfn for a cleaner construct,

strapply(input, ax += +([0-9.]+), c, simplify=rbind,combine=as.numeric)

but I can't seem to find the correct regular expression to deal with
the exponent.


Any tips are welcome!


Best regards,

baptiste

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Re: [R] boxplot

I believe
drawBoxplot doesn't exist.

Are you looking for
?boxplot

?

Tal

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E-mail: tal.gal...@gmail.com
Phone number: 972-52-7275845
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My Blogs:
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http://www.r-statistics.com/ (Statistics,R, English)




On Wed, Nov 18, 2009 at 1:41 PM, Sukhbir Rattan sukhbir.rat...@gmail.comwrote:

 Hi,

 I have simple query

 In which package drawBoxplot function is available?


 Regards,
 Sukhbir Singh Rattan

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Re: [R] Plotting Histogram using histogram() and for loop and Iwant to save the histogram individually ... HELP

Change the factor names of var in:
y~x | var 

Tal



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E-mail: tal.gal...@gmail.com
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On Wed, Nov 18, 2009 at 3:17 AM, ychu066 ychu...@aucklanduni.ac.nz wrote:


 Hi again, do you know how can I use the main function to change the title
 for
 eac h histogram. i.e that first graph show have a title Index 1 but
 because the variable name column starts the 8th the title shows up as
 Index
 8 , i have tried use main = colnames(data)[i-1] but it result errors




 Colin Millar wrote:
 
  Or alternatively store as a list and export later if you want
 
  ... after some tidying ...
 
 
  library(lattice)
 
  columns - 8:153
  plots - vector(list, length(columns))
  j - 0
  for (i in columns)
  {
plots[[ j - j+1 ]] -
  histogram( ~ data[,i] | data[,2],
ylab = Frequency, xlab = Score,
xlim = c(1,5), ylim = c(0,100),
main = colnames(data)[i]
  )
  }
 
  print(plots[[1]])
 
  # or export
 
  for (i in seq_along(plots))
  {
png(paste(hist, i, .png, sep = ))
print(plots[[i]])
dev.off()
  }
 
  HTH
  Colin.
 
  Incidentally,
 
  You put what you want to export between png(..) and dev.off()
 
  If you supply the data explicitly it doesn't make any sense to pass the
  data through the data argument.
 
  No need for paste(x) if is x is already a character vector.
 
 
  -Original Message-
  From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
  On Behalf Of Tal Galili
  Sent: 17 November 2009 12:15
  To: ychu066
  Cc: r-help@r-project.org
  Subject: Re: [R] Plotting Histogram using histogram() and for loop and
  Iwant to save the histogram individually ... HELP
 
  I know how you feel,
  I came a cross the same problem once, which took sometime to find a
  solution
  for.
 
  What you need to do is put the hist into a variable and then plot it,
  for
  example:
 
 
 
  library(lattice)
  for(i in 8:153){
 
  hist.to.plot - histogram(~ data[,i] | data[,2],
  data=data,,ylab=Frequency,xlim=c(1,5),xlab=Score,ylim=c(0,100)),main
  =paste(colnames(data)[i],sep=)
  plot(hist.to.plot)
  }
 
 
  Cheers,
  Tal
 
 
  --
 
 
  My contact information:
  Tal Galili
  E-mail: tal.gal...@gmail.com
  Phone number: 972-52-7275845
  FaceBook: Tal Galili
  My Blogs:
  http://www.talgalili.com (Web and general, Hebrew)
  http://www.biostatistics.co.il (Statistics, Hebrew)
  http://www.r-statistics.com/ (Statistics,R, English)
 
 
 
 
  On Tue, Nov 17, 2009 at 7:09 AM, ychu066 ychu...@aucklanduni.ac.nz
  wrote:
 
 
  tried but still doesnt work ...
 
  very weird ...
 
  ychu066 wrote:
  
   here is the codes that i tried.
  
   png(paste(hist,i,.png,sep=)
   + library(lattice)
   Error: unexpected symbol in:
   png(paste(hist,i,.png,sep=)
   library
   for(i in 8:153){
   + histogram(~ data[,i] | data[,2],
   data=data,ylab=Frequency,xlim=c(1,5),xlab=Score,ylim=c(0,100)))
   Error: unexpected ')' in:
   for(i in 8:153){
   histogram(~ data[,i] | data[,2],
   data=data,ylab=Frequency,xlim=c(1,5),xlab=Score,ylim=c(0,100)))
   }
   Error: unexpected '}' in }
   dev.off()
   Error in dev.off() : cannot shut down device 1 (the null device)
  
  
   ychu066 wrote:
  
   still doesnt work ...
  
  
   Karl Ove Hufthammer wrote:
  
   On Thu, 12 Nov 2009 19:10:52 -0800 (PST) ychu066 ychu066
   @aucklanduni.ac.nz wrote:
   And I also want to save each histogram in each separate pdf file
  using
   the
   following codes ?.
   png(hist.png[i])
   dev.off()
  
   Try png(paste(hist,i,.png,sep=) instead.
  
   --
   Karl Ove Hufthammer
  
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  View this message in context:
 
  http://old.nabble.com/Plotting-Histogram-using-histogram%28%29-and-for-l
  oop-and-I-want-to-save-the-histogram-individually-...-HELP-tp26328734p26
  384489.html
  Sent from the R help mailing list archive at Nabble.com.
 
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[R] reduce matrix

2009-11-18 Thread lloyd barcza

I am trying to reduce the dimension of matrix by removing zero elements and 
creating a sub-matrix.

For example:

A= [1,0,0,3;  0,1,2,0; 0,0,3,5]

then the new matrix B would be:

B= [1,3;1,2;3,5]

There are the same number of zero elements in each row of A so dimension of B 
will not be a problem. Is there a straightforward way to do this in R without 
writing a function using loops etc?

Any help or suggestions would be appreciated!

Thanks

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Re: [R] reduce matrix

2009-11-18 Thread Dimitris Rizopoulos


one way is the following:

A - rbind(c(1,0,0,3), c(0,1,2,0), c(0,0,3,5))
t(apply(A, 1, function (x) x[x != 0]))


I hope it helps.

Best,
Dimitris


lloyd barcza wrote:

I am trying to reduce the dimension of matrix by removing zero elements and 
creating a sub-matrix.

For example:

A= [1,0,0,3;  0,1,2,0; 0,0,3,5]

then the new matrix B would be:

B= [1,3;1,2;3,5]

There are the same number of zero elements in each row of A so dimension of B 
will not be a problem. Is there a straightforward way to do this in R without 
writing a function using loops etc?

Any help or suggestions would be appreciated!

Thanks

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

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

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Re: [R] parsing numeric values

Try this:

strapply(input, ([0-9]+\\.[0-9]+E-[0-9]+), c, simplify = rbind,
combine = as.numeric)

On Wed, Nov 18, 2009 at 9:57 AM, baptiste auguie
baptiste.aug...@googlemail.com wrote:
 Dear list,

 I'm seeking advice to extract some numeric values from a log file
 created by an external program. Consider the following example,

 input -
 readLines(textConnection(
 some text
  ax =    1.3770E-03     bx =    3.4644E-07
  ay =    1.9412E-04     by =    4.8840E-08

 other text
  aax  =    1.3770E-03     bbx =    3.4644E-07
  aay  =    1.9412E-04     bby =    4.8840E-08))

 ## this is what I want
 results - c(as.numeric(strsplit(grep(ax, input,val=T),  )[[1]][8]),
             as.numeric(strsplit(grep(ay, input,val=T),  )[[1]][8]),
             as.numeric(strsplit(grep(aax, input,val=T),  )[[1]][9]),
             as.numeric(strsplit(grep(aay, input,val=T),  )[[1]][9])
             )

 ## [1] 0.00137700 0.00019412 0.00137700 0.00019412

 The use of strsplit is not ideal here as there is a different number
 of space characters in the lines containing ax and aax for
 instance (hence the indices 8 and 9 respectively).

 I tried to use gsubfn for a cleaner construct,

 strapply(input, ax += +([0-9.]+), c, simplify=rbind,combine=as.numeric)

 but I can't seem to find the correct regular expression to deal with
 the exponent.


 Any tips are welcome!


 Best regards,

 baptiste

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-- 
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O

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[R] Optimal parameters for Savitzky-Golay smoothing filter (loop)

2009-11-18 Thread Ismail, Riyad

Hi 

I am running a Savitzky-Golay smoothing filter
(http://tolstoy.newcastle.edu.au/R/help/04/02/0385.html) for variables
in my dataset, dim (272:90). I managed to run the code for individual
variables in the dataset and then combine the results into a single
dataset. My novice attempt at this task is shown below
 
csg-NULL
for (i in 1:ncol(data.all))  {
sg-sav.gol(data.all[,i],1,forder=2,dorder=0)
csg[i]-data.frame(sg)
dat-do.call(cbind,(csg))

}

I eventually plan to test whether there is a significant difference
between the original noisy dataset (data.all) and the Savitzky-Golay
datasets(dat 1,dat2, ...). To create the  Savitzky-Golay datasets I plan
to change the size of the filter (j) so how would I create the new
datasets with the changing filter size ? 

csg-NULL
for (i in 1:ncol(data.all)) for(j in 1:10)  {
sg-sav.gol(data.all[,i],j,forder=2,dorder=0)
csg[i]-data.frame(sg)
dat-do.call(cbind,(csg))

}

And Is there anyway that I can combine the results into a single dataset
(data frame) or store them as separate objects in the workspace ?

Regards
Riyad

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Re: [R] re placing the dates format in R for exporting the data set...

2009-11-18 Thread jim holtman

?write.table

If you read the help file, and do a little experimenting, you will see
that there is a parameter 'rownames=FALSE' that may answer your
question.

Also since you did not have column names on your input, you get V1,
V2,... You can put your own column names. It helps again to read the
help file on 'read.table' and look at the parameter 'col.names'.
There is also the colnames function. It also might help to (re)read
the Intro to R.

On Tue, Nov 17, 2009 at 8:27 PM, ychu066 ychu...@aucklanduni.ac.nz wrote:

Moreover, I want to rename the column name V1,V2,V3,V4.V146. how do i
write the code in R ???

thanks everyone that look at the thread/

ychu066 wrote:

hi everyone, i am having difficulties with replacing the dates format in R
for exporting the data set...

eg: the code that i used was
toms_dat- replace(toms_dat, toms_dat ==2009-08-06, 2)
toms_dat- replace(toms_dat, toms_dat ==2009-08-04, 1)

but when i export the data as into txt file or excel file the dates come
up with very large numbers .:drunk:

please help me ...=)

http://old.nabble.com/file/p26400792/what.csv what.csv
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--
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+1 513 646 9390

What is the problem that you are trying to solve?

Re: [R] Presentation of data in Graphical format

Thanx

but I am not able to find a graph that wud suit my data

Regards

Our Thoughts have the Power to Change our Destiny.
Sunita


On Sun, Nov 15, 2009 at 8:54 PM, milton ruser milton.ru...@gmail.comwrote:

 Google R graph grallery
 Google R ggplot2
 Google R lattice

 and good luck

 milton
 On Sun, Nov 15, 2009 at 7:48 AM, Sunita22 sunita...@gmail.com wrote:


 Hello

 My data contains following columns:

 1st column: Posts (GM, Secretary, AM, Office Boy)
 2nd Column: Dept (Finance, HR, ...)
 3rd column: Tasks (Open the door, Fix an appointment, Fill the register,
 etc.) depending on the post
 4th column: Average Time required to do the task

 So the sample data would look like
 PostsDeptTask   Average time
 Office Boy  HR   Open the door  00:00:09
 Secretary   FinanceFix an appointment00.00.30
 .  ..

 I am trying to represent this data in Graphical format, I tried graphs
 like
 Mosaic plot, etc. But it does not represent the data correctly. My aim is
 to
 check the amount of time and its variability for groups of tasks

 Thank you in advance
 Regards
 Sunita

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Re: [R] parsing numeric values

A minor variant might be the following:

   library(gsubfn)
   strapply(input, \\d+\\.\\d+E[-+]?\\d+, as.numeric, simplify = rbind)

where:

- as.numeric is used in place of c in which case we do not need combine
- \\d+ matches one or more digits
- \\. matches a decimal point
- [-+]? matches -, + or nothing (i.e. an optional sign).
- parentheses around the regular expression not needed

On Wed, Nov 18, 2009 at 7:28 AM, Henrique Dallazuanna www...@gmail.com wrote:
 Try this:

 strapply(input, ([0-9]+\\.[0-9]+E-[0-9]+), c, simplify = rbind,
 combine = as.numeric)

 On Wed, Nov 18, 2009 at 9:57 AM, baptiste auguie
 baptiste.aug...@googlemail.com wrote:
 Dear list,

 I'm seeking advice to extract some numeric values from a log file
 created by an external program. Consider the following example,

 input -
 readLines(textConnection(
 some text
  ax =    1.3770E-03     bx =    3.4644E-07
  ay =    1.9412E-04     by =    4.8840E-08

 other text
  aax  =    1.3770E-03     bbx =    3.4644E-07
  aay  =    1.9412E-04     bby =    4.8840E-08))

 ## this is what I want
 results - c(as.numeric(strsplit(grep(ax, input,val=T),  )[[1]][8]),
             as.numeric(strsplit(grep(ay, input,val=T),  )[[1]][8]),
             as.numeric(strsplit(grep(aax, input,val=T),  )[[1]][9]),
             as.numeric(strsplit(grep(aay, input,val=T),  )[[1]][9])
             )

 ## [1] 0.00137700 0.00019412 0.00137700 0.00019412

 The use of strsplit is not ideal here as there is a different number
 of space characters in the lines containing ax and aax for
 instance (hence the indices 8 and 9 respectively).

 I tried to use gsubfn for a cleaner construct,

 strapply(input, ax += +([0-9.]+), c, simplify=rbind,combine=as.numeric)

 but I can't seem to find the correct regular expression to deal with
 the exponent.


 Any tips are welcome!


 Best regards,

 baptiste

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 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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 --
 Henrique Dallazuanna
 Curitiba-Paraná-Brasil
 25° 25' 40 S 49° 16' 22 O

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Re: [R] Importing tRNA data into R ?

2009-11-18 Thread Benilton Carvalho


readFASTA in the BioConductor Biostrings package.

b

On Nov 18, 2009, at 8:14 AM, Tal Galili wrote:


Hello dear R help group,
I would like to download the tRNA data on:
http://gtrnadb.ucsc.edu/download.html

And then import it into R.

Can anyone direct me as to how to do so?


Thanks,
Tal




--


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Tal Galili
E-mail: tal.gal...@gmail.com
Phone number: 972-52-7275845
FaceBook: Tal Galili
My Blogs:
http://www.talgalili.com (Web and general, Hebrew)
http://www.biostatistics.co.il (Statistics, Hebrew)
http://www.r-statistics.com/ (Statistics,R, English)


--


My contact information:
Tal Galili
E-mail: tal.gal...@gmail.com
Phone number: 972-52-7275845
FaceBook: Tal Galili
My Blogs:
http://www.talgalili.com (Web and general, Hebrew)
http://www.biostatistics.co.il (Statistics, Hebrew)
http://www.r-statistics.com/ (Statistics,R, English)

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Re: [R] SVM Param Tuning with using SNOW package

2009-11-18 Thread raluca


Hi Charlie,


Yes, you are perfectly right, when I make the clusters I should put 2, not
10 (it remained 10 from previous trials with 10 slaves).

cl- makeCluster(2, type=SOCK ) 

To tell the truth I do not understand very well what the 2nd parameter for
clusterApplyLB() has to be.

If the function sv.lin has just 1 parameter, sv.lin(c), where c is the cost,
how should I call clusterApplyLB?


 ? clusterApply LB(cl, ?,sv.lin, c=cost1)  ?



Below, I am providing a working example, using the gasoline data that comes
in the pls package.

Thank you for your time! 


library(e1071)
library(snow)
library(pls)

data(gasoline)

X=gasoline$NIR
Y=gasoline$octane

NR=10
cost1=seq(0.5,30, length=NR)


sv.lin- function(c) {

for (i in 1:NR) {

ind=sample(1:60,50)
gTest-  data.frame(Y=I(Y[-ind]),X=I(X[-ind,])) 
gTrain- data.frame(Y=I(Y[ind]),X=I(X[ind,])) 

svm.lin   - svm(gTrain$X,gTrain$Y, kernel=linear,cost=c[i], cross=5)
results.lin   - predict(svm.lin, gTest$X)

e.test.lin - sqrt(sum((results.lin-gTest$Y)^2)/length(gTest$Y))

return(e.test.lin)
}
}


cl- makeCluster(2, type=SOCK ) 


clusterEvalQ(cl,library(e1071))


clusterExport(cl,c(NR,Y,X)) 


RMSEP-clusterApplyLB(cl,?,sv.lin,c=cost1)

stopCluster(cl)





cls59 wrote:
 
 
 raluca wrote:
 
 Hello,
 
 Is the first time I am using SNOW package and I am trying to tune the
 cost parameter for a linear SVM, where the cost (variable cost1) takes 10
 values between 0.5 and 30.
 
 I have a large dataset and a pc which is not very powerful, so I need to
 tune the parameters using both CPUs of the pc.
 
 Somehow I cannot manage to do it. It seems that both CPUs are fitting the
 model for the same values of cost1, I guess the first 5, but not for the
 last 5.
 
 Please, can anyone help me!
 
 Here is the code:  
 
 data - data.frame(Y=I(Y),X=I(X))
 data.X-data$X
 data.Y-data$Y
 
 
 
 
 Helping you will be difficult as we're only three lines into your example
 and already I have no idea what the data you are using looks like. 
 Example code needs to be fully reproducible-- that means a small slice of
 representative data needs to be provided or faked using an appropriate
 random number generator.  
 
 Some things did jump out at me about your approach and I've made some
 notes below.
 
 
 
 raluca wrote:
 
 NR=10
 cost1=seq(0.5,30, length=NR)
 
 sv.lin- function(cl,c) {
 
 for (i in 1:NR) {
 
 ind=sample(1:414,276)
 
 hogTest-  data.frame(Y=I(data.Y[-ind]),X=I(data.X[-ind,])) 
 hogTrain- data.frame(Y=I(data.Y[ind]),X=I(data.X[ind,])) 
 
 svm.lin- svm(hogTrain$X,hogTrain$Y, kernel=linear,cost=c[i],
 cross=5)
 results.lin   - predict(svm.lin, hogTest$X)
 
 e.test.lin - sqrt(sum((results.lin-hogTest$Y)^2)/length(hogTest$Y))
 
 return(e.test.lin)
 }
 }
 
 cl- makeCluster(10, type=SOCK ) 
 
 
 
 If your machine has two cores, why are you setting up a cluster with 10
 nodes?  Usually the number of nodes should equal the number of cores on
 your machine in order to keep things efficient.
 
 
 
 raluca wrote:
 
 
 clusterEvalQ(cl,library(e1071))
 
 clusterExport(cl,c(data.X,data.Y,NR,cost1)) 
 
 RMSEP-clusterApplyLB(cl,cost1,sv.lin)
 
 
 
 Are you sure this evaluation even produces results? sv.lin() is a function
 you defined above that takes two parameters-- cl and c.
 clusterApplyLB() will feed values of cost1 into sv.lin() for the argument
 cl, but it has nothing to give for c.  At the very least, it seems
 like you would need something like:
 
   RMSEP - clusterApplyLB( cl, cost1, sv.lin, c = someVector )
 
 
 
 raluca wrote:
 
 
 stopCluster(cl)
 
 
 
 
 Sorry I can't be very helpful, but with no data and no apparent way to
 legally call sv.lin() the way you have it set up, I can't investigate the
 problem to see if I get the same results you described.  If you could
 provide a complete working example, then there's a better chance that
 someone on this list will be able to help you.
 
 Good luck!
 
 -Charlie
 

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[R] where can I download package svIO?

2009-11-18 Thread Dagmar Orlikowski

Hello,

today I upgraded R to 2.10 and Tinn-R to 2.3.3.1.
Tinn-R needs the package svIO, but it is not available anymore on the
package lists.
Every session I start R and chose the CRAN-Mirror I receive the following
warning: 


Bitte einen CRAN Spiegel für diese Sitzung auswählen ---
Warnmeldung:
In getDependencies(pkgs, dependencies, available, lib) :
  package svIO is not available
Lade Tcl/Tk Interface ... fertig
Fehler in library(svIO) : es gibt kein Paket 'svIO'


I found a similar problem for svMisc a few weeks ago
(http://www.mail-archive.com/r-help@r-project.org/msg74057.html). 
Will there be a new svIO-package the next weeks or is it included anywhere
elso now?

Thanks for your help,
dagmar

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[R] Spectrum confidence interval

2009-11-18 Thread Clément Poirier


Dear useRs,

I'd like to plot a confidence interval on a periodogram. My problem is 
that spec.pgram(sunspots,ci=0.95,log=yes) gives me a blue error bar on 
the plot, but spec.pgram(sunspots,ci=0.95,log=no) does not. My 
questions are:

1. how should I plot the confidence interval with log=no?
2. how should I get the min and max values of the confidence interval?
Many thanks for your help!
Clement Poirier

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[R] Effective measurement of point-polygon distance

2009-11-18 Thread titten tei

Dear list
I have two datasets, one with a large number of point coordinates, the other
with spatial polygons. I want to measure
the shortest distance from each point to the border of all polygons, and
then store the results as a column in a data frame.
(Or a vector that can be turned into a column in a data frame).

The points and polygons represent different types of events, happening at
different times. My next step will therefore be to
add dates to each event pair in order to measure the distance in space and
time. Both are stored in datasets, so that each row
represents one event.

I have (i think) the distance measurement in order, the problem is to get
the results into the data frame in an efficient manner.
I am thinking of something like a double for-loop, but can't get it to work.

I am also having problems reproducing my list of spatial polygons in a
simple way here, but hope that my explanation is sufficient.

# Making two test areas:
library(sp)
w1 - SpatialLines(list(Lines(list(Line(cbind(
c(80,85,87,90,85,80),
c(10,15,17,15,10,10)
))

w2 - SpatialLines(list(Lines(list(Line(cbind(
c(65,67,76,68,65),
c(30,29,24,22,30)
))

# Test points:
x = c(5, 7, 35, 28)
y = c(60, 70, 90, 85)
xy - SpatialPoints(cbind(y,x))

distance - rep(NA, 4)
for (i in 1:4){distance[i] - min(spDistsN1(coordinates(spsample((w1), n=50,
type = regular)), coordinates(xy[i,]), longlat=T))}
for (i in 1:4){distance[i] - min(spDistsN1(coordinates(spsample((w2), n=50,
type = regular)), coordinates(xy[i,]), longlat=T))}
distance

# What I need, is a for-loop (or something similar) that goes through the
list of polygons, checks the minimum
# distance to each point for each polygon, and stores the results as a
vector/variable of length (number of polygons * number of points.),
# so that the final result after going through all the events of both types
look somewhat like wanted.

wanted - c(2066.438, 1671.135, 1829.517, 1013.759, 2290.192, 1150.286,
2013.819, 1247.204)
wanted

# It sounds, and probably is, quite simple - yet I'm completely stuck...

- Neru

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Re: [R] Switch Help

2009-11-18 Thread oscar linares

Thanks for the Rxpert advice! I am up and running again...

Oscar

On Wed, Nov 18, 2009 at 5:57 AM, Colin Millar c.mil...@marlab.ac.uk wrote:

 I think you just missed some commas out...

 aar -
 function(command = c(scrn, dx, df))
 {
  command - match.arg(command)
   switch(command,
scrn = cat(scrn  :Screening,\n),
dx   = cat(dx:Diagnosis,\n),
df   = cat(df:Don't Forget,\n)
  )
 }

 Colin.


 Ps you don't need the curly brackets here if theres only one expresion,
 and sometimes its good to restrict the inputs to only those you want
 So that

 aar(something wrong)

 # Error in match.arg(command) : 'arg' should be one of scrn, dx,
 df


 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
 On Behalf Of oscar linares
 Sent: 18 November 2009 10:40
 To: r-help@r-project.org
 Subject: [R] Switch Help

 Dear Rexperts,

 Given,

 aar -function(command) {

 switch(command,
  {scrn = cat(scrn  :Screening,\n)}
  {dx   = cat(dx:Diagnosis,\n)}
  {df   = cat(df:Don't Forget,\n)}
 )
 }

 I want to be able to do:

 aar(dx) # function does cat(dx:Diagnosis,\n)

 aar(c(dx,df))  # function does cat(dx:Diagnosis,\n)
# function does df   = cat(df:Don't
 Forget,\n)

 BUT IT IS NOT WORKING FOR ME.

 Please help:-)

 --
 Oscar
 Oscar A. Linares, MD
 Translational Medicine Unit
 LaPlaisance Bay, Bolles Harbor
 Monroe, Michigan

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-- 
Oscar
Oscar A. Linares, MD
Translational Medicine Unit
LaPlaisance Bay, Bolles Harbor
Monroe, Michigan

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Re: [R] parsing numeric values

Thanks a lot, both of you.

Incidentally, I made R crash when I forgot the X argument to strapply,

library(gsubfn)
Loading required package: tcltk
Loading Tcl/Tk interface ... done
strapply(test, as.numeric)

 *** caught bus error ***
address 0x13c, cause 'non-existent physical address'

Traceback:
 1: .External(dotTclcallback, ..., PACKAGE = tcltk)
 2: .Tcl.callback(x, e)
 3: makeAtomicCallback(x, e)
 4: makeCallback(get(value, envir = ref), get(envir, envir = ref))
 5: FUN(X[[3L]], ...)
 6: lapply(val, val2obj)
 7: .Tcl.args.objv(...)
 8: structure(.External(dotTclObjv, objv, PACKAGE = tcltk), class
= tclObj)
 9: .Tcl.objv(.Tcl.args.objv(...))
10: tcl(set, e, e)
11: strapply1(x, pattern, backref, ignore.case)
12: FUN(test[[1L]], ...)
13: lapply(X, FUN, ...)
14: sapply(X, ff, simplify = is.logical(simplify)  simplify,
USE.NAMES = USE.NAMES)
15: strapply(test, as.numeric)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

sessionInfo()
R version 2.10.0 (2009-10-26)
i386-apple-darwin9.8.0

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

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

other attached packages:
[1] ggplot2_0.8.3  reshape_0.8.3  plyr_0.1.9 proto_0.3-8fortunes_1.3-6

2009/11/18 Gabor Grothendieck ggrothendi...@gmail.com:
 A minor variant might be the following:

   library(gsubfn)
   strapply(input, \\d+\\.\\d+E[-+]?\\d+, as.numeric, simplify = rbind)

 where:

 - as.numeric is used in place of c in which case we do not need combine
 - \\d+ matches one or more digits
 - \\. matches a decimal point
 - [-+]? matches -, + or nothing (i.e. an optional sign).
 - parentheses around the regular expression not needed

 On Wed, Nov 18, 2009 at 7:28 AM, Henrique Dallazuanna www...@gmail.com 
 wrote:
 Try this:

 strapply(input, ([0-9]+\\.[0-9]+E-[0-9]+), c, simplify = rbind,
 combine = as.numeric)

 On Wed, Nov 18, 2009 at 9:57 AM, baptiste auguie
 baptiste.aug...@googlemail.com wrote:
 Dear list,

 I'm seeking advice to extract some numeric values from a log file
 created by an external program. Consider the following example,

 input -
 readLines(textConnection(
 some text
  ax =    1.3770E-03     bx =    3.4644E-07
  ay =    1.9412E-04     by =    4.8840E-08

 other text
  aax  =    1.3770E-03     bbx =    3.4644E-07
  aay  =    1.9412E-04     bby =    4.8840E-08))

 ## this is what I want
 results - c(as.numeric(strsplit(grep(ax, input,val=T),  )[[1]][8]),
             as.numeric(strsplit(grep(ay, input,val=T),  )[[1]][8]),
             as.numeric(strsplit(grep(aax, input,val=T),  )[[1]][9]),
             as.numeric(strsplit(grep(aay, input,val=T),  )[[1]][9])
             )

 ## [1] 0.00137700 0.00019412 0.00137700 0.00019412

 The use of strsplit is not ideal here as there is a different number
 of space characters in the lines containing ax and aax for
 instance (hence the indices 8 and 9 respectively).

 I tried to use gsubfn for a cleaner construct,

 strapply(input, ax += +([0-9.]+), c, simplify=rbind,combine=as.numeric)

 but I can't seem to find the correct regular expression to deal with
 the exponent.


 Any tips are welcome!


 Best regards,

 baptiste

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 --
 Henrique Dallazuanna
 Curitiba-Paraná-Brasil
 25° 25' 40 S 49° 16' 22 O

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Re: [R] Presentation of data in Graphical format

I would start with
?boxplot


--


My contact information:
Tal Galili
E-mail: tal.gal...@gmail.com
Phone number: 972-52-7275845
FaceBook: Tal Galili
My Blogs:
http://www.talgalili.com (Web and general, Hebrew)
http://www.biostatistics.co.il (Statistics, Hebrew)
http://www.r-statistics.com/ (Statistics,R, English)




On Wed, Nov 18, 2009 at 2:47 PM, Sunita Patil sunita...@gmail.com wrote:

 Thanx

 but I am not able to find a graph that wud suit my data

 Regards

 Our Thoughts have the Power to Change our Destiny.
 Sunita


 On Sun, Nov 15, 2009 at 8:54 PM, milton ruser milton.ru...@gmail.com
 wrote:

  Google R graph grallery
  Google R ggplot2
  Google R lattice
 
  and good luck
 
  milton
  On Sun, Nov 15, 2009 at 7:48 AM, Sunita22 sunita...@gmail.com wrote:
 
 
  Hello
 
  My data contains following columns:
 
  1st column: Posts (GM, Secretary, AM, Office Boy)
  2nd Column: Dept (Finance, HR, ...)
  3rd column: Tasks (Open the door, Fix an appointment, Fill the register,
  etc.) depending on the post
  4th column: Average Time required to do the task
 
  So the sample data would look like
  PostsDeptTask   Average time
  Office Boy  HR   Open the door  00:00:09
  Secretary   FinanceFix an appointment00.00.30
  .  ..
 
  I am trying to represent this data in Graphical format, I tried graphs
  like
  Mosaic plot, etc. But it does not represent the data correctly. My aim
 is
  to
  check the amount of time and its variability for groups of tasks
 
  Thank you in advance
  Regards
  Sunita
 
  --
  View this message in context:
 
 http://old.nabble.com/Presentation-of-data-in-Graphical-format-tp26358857p26358857.html
  Sent from the R help mailing list archive at Nabble.com.
 
  __
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 http://www.r-project.org/posting-guide.html
  and provide commented, minimal, self-contained, reproducible code.
 
 
 

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Re: [R] where can I download package svIO?

2009-11-18 Thread Philippe Grosjean


Hello,

All sv packages are undergoing a major revision that makes them 
incompatible for some functions with the previous ones (among them, 
functions that were used by Tinn-R. However, Tinn-R is now supposed to 
use its own TinnR packages that uses its own version of the old 
functions, so that refarctoring of new ones is possible.


On CRAN, you find this description:

TinnR: Resources of Tinn-R GUI/Editor for R Environment

Implements a set of customized functions, adapted from svIDE, svMisc and 
svIO packages of Philippe Grosjean, necessary to Tinn-R GUI/Editor for R 
environment

Version:1.0.3
Depends:R (? 2.6.0), utils, tcltk, Hmisc, R2HTML
Published:  2009-02-10
Author: Jose Claudio Faria, based on the sources of Philippe Grosjean
Maintainer: Jose Claudio Faria joseclaudio.faria at gmail.com
License:GPL (? 2)
Citation:   TinnR citation info
CRAN checks:TinnR results

So, you are better to contact Jose Claudio Faria, because you should not 
have a dependecy on svIO any more for Tinn-R.

Abest,

Philippe Grosjean


..°}))
 ) ) ) ) )
( ( ( ( (Prof. Philippe Grosjean
 ) ) ) ) )
( ( ( ( (Numerical Ecology of Aquatic Systems
 ) ) ) ) )   Mons University, Belgium
( ( ( ( (
..

Dagmar Orlikowski wrote:

Hello,

today I upgraded R to 2.10 and Tinn-R to 2.3.3.1.
Tinn-R needs the package svIO, but it is not available anymore on the
package lists.
Every session I start R and chose the CRAN-Mirror I receive the following
warning: 



Bitte einen CRAN Spiegel für diese Sitzung auswählen ---
Warnmeldung:
In getDependencies(pkgs, dependencies, available, lib) :
  package ‘svIO’ is not available
Lade Tcl/Tk Interface ... fertig
Fehler in library(svIO) : es gibt kein Paket 'svIO'


I found a similar problem for svMisc a few weeks ago
(http://www.mail-archive.com/r-help@r-project.org/msg74057.html). 
Will there be a new svIO-package the next weeks or is it included anywhere

elso now?

Thanks for your help,
dagmar

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Re: [R] reduce matrix

2009-11-18 Thread Karl Ove Hufthammer

On Wed, 18 Nov 2009 04:18:08 -0800 (PST) lloyd barcza 
floyd...@yahoo.com wrote:
 I am trying to reduce the dimension of matrix by removing 
 zero elements and creating a sub-matrix.
 
 For example:
 
 A= [1,0,0,3;  0,1,2,0; 0,0,3,5]
 
 then the new matrix B would be:
 
 B= [1,3;1,2;3,5]
 
 There are the same number of zero elements in each row of A 
 so dimension of B will not be a problem.

This should work:

B=matrix(t(A)[t(A)!=0], nrow=nrow(A), byrow=TRUE)

-- 
Karl Ove Hufthammer

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Re: [R] Importing tRNA data into R ?

2009-11-18 Thread James W. MacDonald


Hi Tal,

Tal Galili wrote:

Hello dear R help group,
I would like to download the tRNA data on:
http://gtrnadb.ucsc.edu/download.html

And then import it into R.

Can anyone direct me as to how to do so?


You probably want the readFASTA() function in Biostrings, which is part 
of Bioconductor.


There are several packages in BioC that are useful for doing things with 
sequence data once read in, depending on what your purpose is. Further 
questions should probably be directed to the BioC listserv 
bioconduc...@stat.math.ethz.ch.


Best,

Jim







Thanks,
Tal




--


My contact information:
Tal Galili
E-mail: tal.gal...@gmail.com
Phone number: 972-52-7275845
FaceBook: Tal Galili
My Blogs:
http://www.talgalili.com (Web and general, Hebrew)
http://www.biostatistics.co.il (Statistics, Hebrew)
http://www.r-statistics.com/ (Statistics,R, English)


--


My contact information:
Tal Galili
E-mail: tal.gal...@gmail.com
Phone number: 972-52-7275845
FaceBook: Tal Galili
My Blogs:
http://www.talgalili.com (Web and general, Hebrew)
http://www.biostatistics.co.il (Statistics, Hebrew)
http://www.r-statistics.com/ (Statistics,R, English)

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--
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826

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[R] Error system is computationally singular by using function dmvnorm

2009-11-18 Thread Alla Bulashevska


Dear R users,
i try to use function dmvnorm(x, mean, sigma, log=FALSE)
from R package mvtnorm to calculate the probability of x
under the multivariate normal distribution with mean equal
to mean and covariance matrix sigma.
I become the following 
Error in solve.default(cov, ...) :
  system is computationally singular: reciprocal condition
number = 1.81093e-19

What could be the reason of it?
Thank you in Advance,
Alla.

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[R] xts timeseries

2009-11-18 Thread Jan Daniel Semrau

Hi,

I try to calculate the correlation between macroeconomic data from  
FRED vs Market Data
However, since the timeseries are not in synch, the correlation fails.

require(quantmod)

USPBS =get(getSymbols(USPBS, src=FRED ))
USPBS = USPBS['1983-1-1::']
monDMANEMP = Cl(to.monthly(USPBS))

  length(monDMANEMP)
[1] 312

  head(monDMANEMP)
  USPBS.Close
Oct 19838192
Nov 19838231
Dec 19838265
Jan 19848309
Feb 19848344
Mar 19848382

symbol = getSymbols(^DJA,from = 1983-01-01,to=Sys.Date())
market = Cl(get(symbol))
monMarket = Cl(to.monthly(market))

  length(monMarket)
[1] 314
  head(monMarket)
  market.Close
Oct 1983   494.18
Nov 1983   510.77
Dec 1983   502.94
Jan 1984   483.46
Feb 1984   454.97
Mar 1984   456.65


Now I try to calculate the correlation

  cor(monMarket, monDMANEMP)
Error in cor.default(monMarket, monDMANEMP) : incompatible dimensions

#This makes sense since my Market data is two data points longer.
#However if I try to merge them to get them aligned on one time axis,  
I get this

  head(merge.xts(monMarket, monDMANEMP))
  market.Close USPBS.Close
Oct 1983   494.18  NA
Nov 1983   NA8192
Nov 1983   510.77  NA
Dec 1983   NA8231
Dec 1983   502.94  NA
Jan 1984   NA8265

#If I try cbind the same happens
  head(cbind(monMarket, monDMANEMP))
  market.Close USPBS.Close
Oct 1983   494.18  NA
Nov 1983   NA8192
Nov 1983   510.77  NA
Dec 1983   NA8231
Dec 1983   502.94  NA
Jan 1984   NA8265

#If I then continue to align both of the timeseries on one standard axis

l= (round(Sys.Date()-as.Date(01JAN1983, %d%b%Y)))
timeline = to.monthly(xts(1:l, as.Date(01JAN1983, %d%b%Y)+1:l))
alignbar = xts(, index(timeline))

alMonMarket = merge.xts(alignbar, monMarket)
almonDMANEMP = merge.xts(alignbar, monDMANEMP)
x = merge.xts(alMonMarket, almonDMANEMP)

  head(x)
  market.Close USPBS.Close
Jan 1983   NA  NA
Feb 1983   NA  NA
Mar 1983   NA  NA
Apr 1983   NA  NA
May 1983   NA  NA
Jun 1983   NA  NA

Any pointer towards the error is highly appreciated

Jan
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Re: [R] A combinatorial optimization problem: finding the best permutation of a complex vector

2009-11-18 Thread Ravi Varadhan

Hi Erwin,

Thank you for the information about Cplex.  It seems quite impressive.  Is
it a proprietary software?  I saw that there is a Matlab interface to it.
Is there an R interface?


Thanks,
Ravi.


---

Ravi Varadhan, Ph.D.

Assistant Professor, The Center on Aging and Health

Division of Geriatric Medicine and Gerontology 

Johns Hopkins University

Ph: (410) 502-2619

Fax: (410) 614-9625

Email: rvarad...@jhmi.edu

Webpage:
http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.h
tml

 





-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Erwin Kalvelagen
Sent: Wednesday, November 18, 2009 12:20 AM
To: r-h...@stat.math.ethz.ch
Subject: Re: [R] A combinatorial optimization problem: finding the best
permutation of a complex vector

Ravi Varadhan rvaradhan at jhmi.edu writes:
 
 
 When I increased N = 1000, the time was about 1400 seconds!  
 

Not sure of this is important for you: This can be solved much faster. A
good 
solver can solve the n=1000 problem in less than 2 seconds. The Cplex
network 
code shows:

Network - Optimal:  Objective =   1.6173194067e+003
Network time =1.58 sec.  Iterations = 209126 (102313)

Even solved as an LP this takes about 150 seconds.

(The solutions are the same as reported by solve_LSAP).



Erwin Kalvelagen
Amsterdam Optimization Modeling Group
er...@amsterdamoptimization.com
http://amsterdamoptimization.com

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

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Re: [R] Importing tRNA data into R ?

A warm thank you to both James and Benilton.

James, I will go on that list and start looking around.

Best,
Tal


--


My contact information:
Tal Galili
E-mail: tal.gal...@gmail.com
Phone number: 972-52-7275845
FaceBook: Tal Galili
My Blogs:
http://www.talgalili.com (Web and general, Hebrew)
http://www.biostatistics.co.il (Statistics, Hebrew)
http://www.r-statistics.com/ (Statistics,R, English)




On Wed, Nov 18, 2009 at 4:27 PM, James W. MacDonald
jmac...@med.umich.eduwrote:

 Hi Tal,


 Tal Galili wrote:

 Hello dear R help group,
 I would like to download the tRNA data on:
 http://gtrnadb.ucsc.edu/download.html

 And then import it into R.

 Can anyone direct me as to how to do so?


 You probably want the readFASTA() function in Biostrings, which is part of
 Bioconductor.

 There are several packages in BioC that are useful for doing things with
 sequence data once read in, depending on what your purpose is. Further
 questions should probably be directed to the BioC listserv 
 bioconduc...@stat.math.ethz.ch.

 Best,

 Jim






 Thanks,
 Tal




 --


 My contact information:
 Tal Galili
 E-mail: tal.gal...@gmail.com
 Phone number: 972-52-7275845
 FaceBook: Tal Galili
 My Blogs:
 http://www.talgalili.com (Web and general, Hebrew)
 http://www.biostatistics.co.il (Statistics, Hebrew)
 http://www.r-statistics.com/ (Statistics,R, English)


 --


 My contact information:
 Tal Galili
 E-mail: tal.gal...@gmail.com
 Phone number: 972-52-7275845
 FaceBook: Tal Galili
 My Blogs:
 http://www.talgalili.com (Web and general, Hebrew)
 http://www.biostatistics.co.il (Statistics, Hebrew)
 http://www.r-statistics.com/ (Statistics,R, English)

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 __
 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.


 --
 James W. MacDonald, M.S.
 Biostatistician
 Douglas Lab
 University of Michigan
 Department of Human Genetics
 5912 Buhl
 1241 E. Catherine St.
 Ann Arbor MI 48109-5618
 734-615-7826


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Re: [R] SVM Param Tuning with using SNOW package

2009-11-18 Thread David Winsemius

I cannot really be sure what you are trying to do,  but doing a bit of  
surgery on your code lets it run on a multicore Mac:


library(e1071)
library(snow)
library(pls)

data(gasoline)

X=gasoline$NIR
Y=gasoline$octane

NR=10
cost1=seq(0.5,30, length=NR)

sv.lin- function(c) {

for (i in 1:NR) {

ind=sample(1:60,50)
gTest-  data.frame(Y=I(Y[-ind]),X=I(X[-ind,]))
gTrain- data.frame(Y=I(Y[ind]),X=I(X[ind,]))

svm.lin   	  - svm(gTrain$X,gTrain$Y, kernel=linear,cost=c[i],  
cross=5)

results.lin   - predict(svm.lin, gTest$X)

e.test.lin - sqrt(sum((results.lin-gTest$Y)^2)/length(gTest$Y))

return(e.test.lin)
}
}

cl- makeCluster(2, type=SOCK )

clusterEvalQ(cl, library(e1071))
cost1=seq(0.5,30, length=NR)

clusterExport(cl,c(NR,Y,X,  cost1))
# Pretty sure you need a copy of cost1 on each node.


RMSEP-clusterApply(cl, cost1, sv.lin)
# I thought the second argument was the matrix or vector over which to  
iterate.


stopCluster(cl)

# Since I don't know what the model meant, I cannot determine whehter  
this result is interpretable

 RMSEP
[[1]]
[1] 0.1921887

[[2]]
[1] 0.1924917

[[3]]
[1] 0.1885066

[[4]]
[1] 0.1871466

[[5]]
[1] 0.3550932

[[6]]
[1] 0.1226460

[[7]]
[1] 0.2426345

[[8]]
[1] 0.2126299

[[9]]
[1] 0.2276286

[[10]]
[1] 0.2064534

--
David Winsemius, MD

On Nov 18, 2009, at 7:09 AM, raluca wrote:



Hi Charlie,


Yes, you are perfectly right, when I make the clusters I should put  
2, not

10 (it remained 10 from previous trials with 10 slaves).

cl- makeCluster(2, type=SOCK )

To tell the truth I do not understand very well what the 2nd  
parameter for

clusterApplyLB() has to be.

If the function sv.lin has just 1 parameter, sv.lin(c), where c is  
the cost,

how should I call clusterApplyLB?


? clusterApply LB(cl, ?,sv.lin, c=cost1)  ?



Below, I am providing a working example, using the gasoline data  
that comes

in the pls package.

Thank you for your time!


library(e1071)
library(snow)
library(pls)

data(gasoline)

X=gasoline$NIR
Y=gasoline$octane

NR=10
cost1=seq(0.5,30, length=NR)


sv.lin- function(c) {

for (i in 1:NR) {

ind=sample(1:60,50)
gTest-  data.frame(Y=I(Y[-ind]),X=I(X[-ind,]))
gTrain- data.frame(Y=I(Y[ind]),X=I(X[ind,]))

svm.lin   	  - svm(gTrain$X,gTrain$Y, kernel=linear,cost=c[i],  
cross=5)

results.lin   - predict(svm.lin, gTest$X)

e.test.lin - sqrt(sum((results.lin-gTest$Y)^2)/length(gTest$Y))

return(e.test.lin)
}
}


cl- makeCluster(2, type=SOCK )


clusterEvalQ(cl,library(e1071))


clusterExport(cl,c(NR,Y,X))


RMSEP-clusterApplyLB(cl,?,sv.lin,c=cost1)

stopCluster(cl)





cls59 wrote:



raluca wrote:


Hello,

Is the first time I am using SNOW package and I am trying to tune  
the
cost parameter for a linear SVM, where the cost (variable cost1)  
takes 10

values between 0.5 and 30.

I have a large dataset and a pc which is not very powerful, so I  
need to

tune the parameters using both CPUs of the pc.

Somehow I cannot manage to do it. It seems that both CPUs are  
fitting the
model for the same values of cost1, I guess the first 5, but not  
for the

last 5.

Please, can anyone help me!

Here is the code:

data - data.frame(Y=I(Y),X=I(X))
data.X-data$X
data.Y-data$Y





Helping you will be difficult as we're only three lines into your  
example

and already I have no idea what the data you are using looks like.
Example code needs to be fully reproducible-- that means a small  
slice of
representative data needs to be provided or faked using an  
appropriate

random number generator.

Some things did jump out at me about your approach and I've made some
notes below.



raluca wrote:


NR=10
cost1=seq(0.5,30, length=NR)

sv.lin- function(cl,c) {

for (i in 1:NR) {

ind=sample(1:414,276)

hogTest-  data.frame(Y=I(data.Y[-ind]),X=I(data.X[-ind,]))
hogTrain- data.frame(Y=I(data.Y[ind]),X=I(data.X[ind,]))

svm.lin   	  - svm(hogTrain$X,hogTrain$Y,  
kernel=linear,cost=c[i],

cross=5)
results.lin   - predict(svm.lin, hogTest$X)

e.test.lin - sqrt(sum((results.lin-hogTest$Y)^2)/ 
length(hogTest$Y))


return(e.test.lin)
}
}

cl- makeCluster(10, type=SOCK )




If your machine has two cores, why are you setting up a cluster  
with 10
nodes?  Usually the number of nodes should equal the number of  
cores on

your machine in order to keep things efficient.



raluca wrote:



clusterEvalQ(cl,library(e1071))

clusterExport(cl,c(data.X,data.Y,NR,cost1))

RMSEP-clusterApplyLB(cl,cost1,sv.lin)




Are you sure this evaluation even produces results? sv.lin() is a  
function

you defined above that takes two parameters-- cl and c.
clusterApplyLB() will feed values of cost1 into sv.lin() for the  
argument
cl, but it has nothing to give for c.  At the very least, it  
seems

like you would need something like:

 RMSEP - clusterApplyLB( cl, cost1, sv.lin, c = someVector )



raluca wrote:



stopCluster(cl)





Sorry I can't be very helpful, but with no data and no apparent way  
to
legally call sv.lin() the way you have it set up, I can't  
investigate the

Re: [R] A combinatorial optimization problem: finding the best permutation of a complex vector

2009-11-18 Thread Ravi Varadhan

I just saw that Cplex is a commercial software from ILOG/IBM, and that there
is an R interface, Rcplex, for it.  While this is bad news, it is still
encouraging to know that the LSAP problem can be solved faster.  I will keep
looking for better/faster open source algorithms.

Ravi.


---

Ravi Varadhan, Ph.D.

Assistant Professor, The Center on Aging and Health

Division of Geriatric Medicine and Gerontology 

Johns Hopkins University

Ph: (410) 502-2619

Fax: (410) 614-9625

Email: rvarad...@jhmi.edu

Webpage:
http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.h
tml

 





-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Ravi Varadhan
Sent: Wednesday, November 18, 2009 9:39 AM
To: 'Erwin Kalvelagen'; r-h...@stat.math.ethz.ch
Subject: Re: [R] A combinatorial optimization problem: finding the best
permutation of a complex vector

Hi Erwin,

Thank you for the information about Cplex.  It seems quite impressive.  Is
it a proprietary software?  I saw that there is a Matlab interface to it.
Is there an R interface?


Thanks,
Ravi.


---

Ravi Varadhan, Ph.D.

Assistant Professor, The Center on Aging and Health

Division of Geriatric Medicine and Gerontology 

Johns Hopkins University

Ph: (410) 502-2619

Fax: (410) 614-9625

Email: rvarad...@jhmi.edu

Webpage:
http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.h
tml

 





-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Erwin Kalvelagen
Sent: Wednesday, November 18, 2009 12:20 AM
To: r-h...@stat.math.ethz.ch
Subject: Re: [R] A combinatorial optimization problem: finding the best
permutation of a complex vector

Ravi Varadhan rvaradhan at jhmi.edu writes:
 
 
 When I increased N = 1000, the time was about 1400 seconds!  
 

Not sure of this is important for you: This can be solved much faster. A
good 
solver can solve the n=1000 problem in less than 2 seconds. The Cplex
network 
code shows:

Network - Optimal:  Objective =   1.6173194067e+003
Network time =1.58 sec.  Iterations = 209126 (102313)

Even solved as an LP this takes about 150 seconds.

(The solutions are the same as reported by solve_LSAP).



Erwin Kalvelagen
Amsterdam Optimization Modeling Group
er...@amsterdamoptimization.com
http://amsterdamoptimization.com

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

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

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

Re: [R] Error system is computationally singular by using function dmvnorm

2009-11-18 Thread Ravi Varadhan

It means that your covariance matrix sigma is numerically singular.

Ravi.

---

Ravi Varadhan, Ph.D.

Assistant Professor, The Center on Aging and Health

Division of Geriatric Medicine and Gerontology 

Johns Hopkins University

Ph: (410) 502-2619

Fax: (410) 614-9625

Email: rvarad...@jhmi.edu

Webpage:
http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.h
tml

 





-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Alla Bulashevska
Sent: Wednesday, November 18, 2009 9:11 AM
To: r-help@r-project.org
Subject: [R] Error system is computationally singular by using function
dmvnorm


Dear R users,
i try to use function dmvnorm(x, mean, sigma, log=FALSE)
from R package mvtnorm to calculate the probability of x
under the multivariate normal distribution with mean equal
to mean and covariance matrix sigma.
I become the following 
Error in solve.default(cov, ...) :
  system is computationally singular: reciprocal condition
number = 1.81093e-19

What could be the reason of it?
Thank you in Advance,
Alla.

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

[R] levelplot

2009-11-18 Thread wenjun zheng

Hi, R Users
When I use the default package lattice, I found a problem about adjusting
the Figure Margin that can be changed by par(mai or mar) in traditional
plots.
So it's hard for me to add top and right axis.
Any suggestions will be appreciated.
-- 
Wenjun

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

[R] foor loop - undefined columns selected error

2009-11-18 Thread Michela Leonardi

Dear R-Help Members,

I am trying to read and analyse a set of 100 csv files.
I need work only on some columns in each of those, so I decided to use
a for loop, isolate the
column in each file to work on, but then an error mesage appear:
undefined columns selected

Here is my code:

setwd(F:/Data/)
a-list.files()
for (x in a) {
  u-read.csv(x, header=T, sep=,, check.names=FALSE)
#it give me the same problem using read.table
  h-u[,2]
}

Error in `[.data.frame`(u, , 2) : undefined columns selected

It does not give me any problem selecting ane entire row (e.g. u[2,])
or a single value (e.g. [5,2])
If I try to select a column after the for loop I does not show any
problem, e.g.:

a-list.files()
for (x in a) {
  u-read.csv(x, header=T, sep=,, check.names=FALSE)
}
  h-u[,2]

I would appreciate any suggestion or pointer to solve the problem or
to do the same thing in a different way.

Thanks for your consideration

--
Michela Leonardi

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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] Presentation of data in Graphical format

Yes I tried all the basic ones like box plot, pie chart, etc but the data
representation isnt that clear.


Regards

Our Thoughts have the Power to Change our Destiny.
Sunita


On Wed, Nov 18, 2009 at 7:20 PM, Tal Galili tal.gal...@gmail.com wrote:

 I would start with
 ?boxplot


 --


 My contact information:
 Tal Galili
 E-mail: tal.gal...@gmail.com
 Phone number: 972-52-7275845
 FaceBook: Tal Galili
 My Blogs:
 http://www.talgalili.com (Web and general, Hebrew)
 http://www.biostatistics.co.il (Statistics, Hebrew)
 http://www.r-statistics.com/ (Statistics,R, English)




 On Wed, Nov 18, 2009 at 2:47 PM, Sunita Patil sunita...@gmail.com wrote:

 Thanx

 but I am not able to find a graph that wud suit my data

 Regards

 Our Thoughts have the Power to Change our Destiny.
 Sunita


 On Sun, Nov 15, 2009 at 8:54 PM, milton ruser milton.ru...@gmail.com
 wrote:

  Google R graph grallery
  Google R ggplot2
  Google R lattice
 
  and good luck
 
  milton
  On Sun, Nov 15, 2009 at 7:48 AM, Sunita22 sunita...@gmail.com wrote:
 
 
  Hello
 
  My data contains following columns:
 
  1st column: Posts (GM, Secretary, AM, Office Boy)
  2nd Column: Dept (Finance, HR, ...)
  3rd column: Tasks (Open the door, Fix an appointment, Fill the
 register,
  etc.) depending on the post
  4th column: Average Time required to do the task
 
  So the sample data would look like
  PostsDeptTask   Average time
  Office Boy  HR   Open the door  00:00:09
  Secretary   FinanceFix an appointment00.00.30
  .  ..
 
  I am trying to represent this data in Graphical format, I tried graphs
  like
  Mosaic plot, etc. But it does not represent the data correctly. My aim
 is
  to
  check the amount of time and its variability for groups of tasks
 
  Thank you in advance
  Regards
  Sunita
 
  --
  View this message in context:
 
 http://old.nabble.com/Presentation-of-data-in-Graphical-format-tp26358857p26358857.html
  Sent from the R help mailing list archive at Nabble.com.
 
  __
  R-help@r-project.org mailing list
  https://stat.ethz.ch/mailman/listinfo/r-help
  PLEASE do read the posting guide
  http://www.R-project.org/posting-guide.html
 http://www.r-project.org/posting-guide.html

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

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




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

Re: [R] Problems by saving Rprofile.site under vista

Hello, I found a solution to the problem, quite easy. The R paste was on
read-only, so I went to the properties/security. Apparently he considers me
as a user and not an administrator when I open the files so I just gave the
users ( me) the authorization to modificate and it worked.

anna_l wrote:

Hi Charles, I´ve already been running it as an administrator this is why I
don´t understand it.

Charles Annis, P.E. wrote:

You may have to run R as Administrator (right-click, choose run as
administrator) to make these kinds of changes. After you have things the
way you like them, run R in the usual way by clicking on the icon.

Charles Annis, P.E.

charles.an...@statisticalengineering.com
561-352-9699
http://www.StatisticalEngineering.com

-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf Of anna_l
Sent: Friday, November 13, 2009 11:46 AM
To: r-help@r-project.org
Subject: [R] Problems by saving Rprofile.site under vista

Hello, I am trying to save some changes I have done on the Rprofile.site
under vista and it doesn´t let me save the file saying that it can´t
create
the following file (Rprofile.site) and that I should check the pathfile
or
the file name.

--
View this message in context:
http://old.nabble.com/Problems-by-saving-Rprofile.site-under-vista-tp26339605p26339605.html
Sent from the R help mailing list archive at Nabble.com.

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

-
Anna Lippel
new in R so be careful I should be asking a lt of questions!:teeth:
--
View this message in context:
http://old.nabble.com/Problems-by-saving-Rprofile.site-under-vista-tp26339605p26408392.html
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Re: [R] vignettes: .png graphics or pre-compiled .pdf

2009-11-18 Thread Michael Friendly


Achim Zeileis wrote:

On Fri, 13 Nov 2009, Michael Friendly wrote:

Alternatively, is there a way to generate .png graphs from the .Rnw 
file so that those are used in building
the .pdf for the package?  AFAICS, \SweaveOpts{} offers only the 
choices of eps/pdf = {TRUE/FALSE}.


Yes, but you can call the png() device yourself within the code chunk

=
png(file = fig1.png, ...)
...
dev.off()
@

and then put

\includegraphics{fig1}

manually into the LaTeX. It's certainly not as nice as Sweave's 
automatic handling of figures but will work and still keep the file 
self-contained.

Z


Thanks, Achim

This works, but has the infelicitous effect that both the png() call and 
dev.off(), with its output appear in the vignette (with echo=TRUE)


% do .png manually ...
fig1cpng, fig=TRUE, pdf=FALSE, eval=TRUE, echo=TRUE, debug=TRUE, 
results=verbatim, include=FALSE=

png(file=figs/fig-fig1c.png, width=4, height=4, units=in, res=72)
# plot stuff ...
dev.off()
@

I suppose I could break this up into 3 chunks as follows, but is there 
some other way, either with R or LaTeX constructs?


echo=FALSE=
png(file=figs/fig-fig1c.png, width=4, height=4, units=in, res=72)
@
fig1cpng, fig=TRUE, pdf=FALSE, eval=TRUE, echo=TRUE, debug=TRUE, 
results=verbatim, include=FALSE=

# plot stuff  ...
@
echo=FALSE=
dev.off()
@


--
Michael Friendly Email: friendly AT yorku DOT ca 
Professor, Psychology Dept.

York University  Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Streethttp://www.math.yorku.ca/SCS/friendly.html
Toronto, ONT  M3J 1P3 CANADA

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

Re: [R] A combinatorial optimization problem: finding the best permutation of a complex vector

2009-11-18 Thread Gottlieb, Neil

Ravi:


Cplex use to be an independent firm. Was acquired by Ilog which was acquired by 
IBM.
It has a nice callable API which is written in C++. It is a very good product.

The other optimizer you might want to look at that performs fast is FortMP 
which might
provide source code also. I last re-call it was written in Fortran
And they had some kind of academic pricing.

http://www.optirisk-systems.com/default.asp

Cplex and FortMp performance was very close both are good. I have
used both as standalone program and via the API calls.

Another less expensive Optimizer is Loqo from Princeton.

http://www.princeton.edu/~rvdb/loqo/LOQO.html

The optimizer to select depends on the model trying to solve.
I suggest you look at Optimization Software Guide by Jorge J. Moré and Stephen 
J. Wright
Available from SIAM:
http://www.ec-securehost.com/SIAM/FR14.html

Hope this detail helps!

Neil Gottlieb


-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On 
Behalf Of Ravi Varadhan
Sent: Wednesday, November 18, 2009 9:39 AM
To: 'Erwin Kalvelagen'; r-h...@stat.math.ethz.ch
Subject: Re: [R] A combinatorial optimization problem: finding the best 
permutation of a complex vector

Hi Erwin,

Thank you for the information about Cplex.  It seems quite impressive.  Is
it a proprietary software?  I saw that there is a Matlab interface to it.
Is there an R interface?


Thanks,
Ravi.


---

Ravi Varadhan, Ph.D.

Assistant Professor, The Center on Aging and Health

Division of Geriatric Medicine and Gerontology 

Johns Hopkins University

Ph: (410) 502-2619

Fax: (410) 614-9625

Email: rvarad...@jhmi.edu

Webpage:
http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.h
tml







-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Erwin Kalvelagen
Sent: Wednesday, November 18, 2009 12:20 AM
To: r-h...@stat.math.ethz.ch
Subject: Re: [R] A combinatorial optimization problem: finding the best
permutation of a complex vector

Ravi Varadhan rvaradhan at jhmi.edu writes:
 
 
 When I increased N = 1000, the time was about 1400 seconds!  
 

Not sure of this is important for you: This can be solved much faster. A
good 
solver can solve the n=1000 problem in less than 2 seconds. The Cplex
network 
code shows:

Network - Optimal:  Objective =   1.6173194067e+003
Network time =1.58 sec.  Iterations = 209126 (102313)

Even solved as an LP this takes about 150 seconds.

(The solutions are the same as reported by solve_LSAP).



Erwin Kalvelagen
Amsterdam Optimization Modeling Group
er...@amsterdamoptimization.com
http://amsterdamoptimization.com

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

__
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.

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

Re: [R] Presentation of data in Graphical format

2009-11-18 Thread Petr PIKAL

Hi

r-help-boun...@r-project.org napsal dne 18.11.2009 16:01:27:

 Yes I tried all the basic ones like box plot, pie chart, etc but the 
data
 representation isnt that clear.
 

I agree with Tal. But it partly depends on your data. If you have many 
levels and only few time values in each boxplot would not look well. Maybe 
you could check also ?xtabs or ?table and/or R graph gallery 
http://addictedtor.free.fr/graphiques/ if you find suitable graph.

Regards
Petr

 

 
 Regards
 
 Our Thoughts have the Power to Change our Destiny.
 Sunita
 
 
 On Wed, Nov 18, 2009 at 7:20 PM, Tal Galili tal.gal...@gmail.com 
wrote:
 
  I would start with
  ?boxplot
 
 
  --
 
 
  My contact information:
  Tal Galili
  E-mail: tal.gal...@gmail.com
  Phone number: 972-52-7275845
  FaceBook: Tal Galili
  My Blogs:
  http://www.talgalili.com (Web and general, Hebrew)
  http://www.biostatistics.co.il (Statistics, Hebrew)
  http://www.r-statistics.com/ (Statistics,R, English)
 
 
 
 
  On Wed, Nov 18, 2009 at 2:47 PM, Sunita Patil sunita...@gmail.com 
wrote:
 
  Thanx
 
  but I am not able to find a graph that wud suit my data
 
  Regards
 
  Our Thoughts have the Power to Change our Destiny.
  Sunita
 
 
  On Sun, Nov 15, 2009 at 8:54 PM, milton ruser milton.ru...@gmail.com
  wrote:
 
   Google R graph grallery
   Google R ggplot2
   Google R lattice
  
   and good luck
  
   milton
   On Sun, Nov 15, 2009 at 7:48 AM, Sunita22 sunita...@gmail.com 
wrote:
  
  
   Hello
  
   My data contains following columns:
  
   1st column: Posts (GM, Secretary, AM, Office Boy)
   2nd Column: Dept (Finance, HR, ...)
   3rd column: Tasks (Open the door, Fix an appointment, Fill the
  register,
   etc.) depending on the post
   4th column: Average Time required to do the task
  
   So the sample data would look like
   PostsDeptTask   Average 
time
   Office Boy  HR   Open the door  00:00:09
   Secretary   FinanceFix an appointment00.00.30
   .  . .
  
   I am trying to represent this data in Graphical format, I tried 
graphs
   like
   Mosaic plot, etc. But it does not represent the data correctly. My 
aim
  is
   to
   check the amount of time and its variability for groups of tasks
  
   Thank you in advance
   Regards
   Sunita
  
   --
   View this message in context:
  
  http://old.nabble.com/Presentation-of-data-in-Graphical-format-
 tp26358857p26358857.html
   Sent from the R help mailing list archive at Nabble.com.
  
   __
   R-help@r-project.org mailing list
   https://stat.ethz.ch/mailman/listinfo/r-help
   PLEASE do read the posting guide
   http://www.R-project.org/posting-guide.html
  http://www.r-project.org/posting-guide.html
 
   and provide commented, minimal, self-contained, reproducible code.
  
  
  
 
 [[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.
 
 
 
 
[[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.

Re: [R] vignettes: .png graphics or pre-compiled .pdf

2009-11-18 Thread Achim Zeileis


On Wed, 18 Nov 2009, Michael Friendly wrote:


Achim Zeileis wrote:

On Fri, 13 Nov 2009, Michael Friendly wrote:

Alternatively, is there a way to generate .png graphs from the .Rnw file 
so that those are used in building
the .pdf for the package?  AFAICS, \SweaveOpts{} offers only the choices 
of eps/pdf = {TRUE/FALSE}.


Yes, but you can call the png() device yourself within the code chunk

=
png(file = fig1.png, ...)
...
dev.off()
@

and then put

\includegraphics{fig1}

manually into the LaTeX. It's certainly not as nice as Sweave's automatic 
handling of figures but will work and still keep the file self-contained.

Z


Thanks, Achim

This works, but has the infelicitous effect that both the png() call and 
dev.off(), with its output appear in the vignette (with echo=TRUE)


% do .png manually ...
fig1cpng, fig=TRUE, pdf=FALSE, eval=TRUE, echo=TRUE, debug=TRUE, 
results=verbatim, include=FALSE=

png(file=figs/fig-fig1c.png, width=4, height=4, units=in, res=72)
# plot stuff ...
dev.off()
@

I suppose I could break this up into 3 chunks as follows, but is there some 
other way, either with R or LaTeX constructs?


echo=FALSE=
png(file=figs/fig-fig1c.png, width=4, height=4, units=in, res=72)
@
fig1cpng, fig=TRUE, pdf=FALSE, eval=TRUE, echo=TRUE, debug=TRUE, 
results=verbatim, include=FALSE=

# plot stuff  ...
@
echo=FALSE=
dev.off()
@


I typically re-use the code chunks, e.g.:

myplot, echo=TRUE, eval=FALSE=
plot(...)
@

myplot-png, echo=FALSE, eval=TRUE=
png(...)
myplot
dev.off()
@

which is also convenient if you want to add par() settings (e.g., 
mfrow/mfcol) and have the code somewhere in the text but the resulting 
figure in a floating environment.

Z



--
Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology 
Dept.

York University  Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Streethttp://www.math.yorku.ca/SCS/friendly.html
Toronto, ONT  M3J 1P3 CANADA






__
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] converting a vector of bytes to a PNG/JPEG image

2009-11-18 Thread Rajarshi Guha

Hi, I have some code that uses rJava. One of the Java side methods returns a
byte[] representing the bytes from a PNG image.

What I'd like to do is to be able to bring up the PNG on the R side (I can
bring up a Swing window to show the PNG but I want to avoid that). I have
looked at the pixmap and rimage packages but don't seem to be able to work
out how I'd go about this (or if it's at all possible).

Does anybody have any pointers?

Thanks,

-- 
Rajarshi Guha
NIH Chemical Genomics Center

[[alternative HTML version deleted]]

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

Re: [R] Presentation of data in Graphical format

I have been using R just very recently, I have gone through this
http://addictedtor.free.fr/graphiques/
a few weeks back but I am not able to understand as to how to choose the
graph amongst them? Can anyone guide me regarding this?

Thanks in advance
Regards

Our Thoughts have the Power to Change our Destiny.
Sunita


On Wed, Nov 18, 2009 at 8:42 PM, Petr PIKAL petr.pi...@precheza.cz wrote:

 Hi

 r-help-boun...@r-project.org napsal dne 18.11.2009 16:01:27:

  Yes I tried all the basic ones like box plot, pie chart, etc but the
 data
  representation isnt that clear.
 

 I agree with Tal. But it partly depends on your data. If you have many
 levels and only few time values in each boxplot would not look well. Maybe
 you could check also ?xtabs or ?table and/or R graph gallery
 http://addictedtor.free.fr/graphiques/ if you find suitable graph.

 Regards
 Petr



 
  Regards
 
  Our Thoughts have the Power to Change our Destiny.
  Sunita
 
 
  On Wed, Nov 18, 2009 at 7:20 PM, Tal Galili tal.gal...@gmail.com
 wrote:
 
   I would start with
   ?boxplot
  
  
   --
  
  
   My contact information:
   Tal Galili
   E-mail: tal.gal...@gmail.com
   Phone number: 972-52-7275845
   FaceBook: Tal Galili
   My Blogs:
   http://www.talgalili.com (Web and general, Hebrew)
   http://www.biostatistics.co.il (Statistics, Hebrew)
   http://www.r-statistics.com/ (Statistics,R, English)
  
  
  
  
   On Wed, Nov 18, 2009 at 2:47 PM, Sunita Patil sunita...@gmail.com
 wrote:
  
   Thanx
  
   but I am not able to find a graph that wud suit my data
  
   Regards
  
   Our Thoughts have the Power to Change our Destiny.
   Sunita
  
  
   On Sun, Nov 15, 2009 at 8:54 PM, milton ruser milton.ru...@gmail.com
   wrote:
  
Google R graph grallery
Google R ggplot2
Google R lattice
   
and good luck
   
milton
On Sun, Nov 15, 2009 at 7:48 AM, Sunita22 sunita...@gmail.com
 wrote:
   
   
Hello
   
My data contains following columns:
   
1st column: Posts (GM, Secretary, AM, Office Boy)
2nd Column: Dept (Finance, HR, ...)
3rd column: Tasks (Open the door, Fix an appointment, Fill the
   register,
etc.) depending on the post
4th column: Average Time required to do the task
   
So the sample data would look like
PostsDeptTask   Average
 time
Office Boy  HR   Open the door  00:00:09
Secretary   FinanceFix an appointment00.00.30
.  . .
   
I am trying to represent this data in Graphical format, I tried
 graphs
like
Mosaic plot, etc. But it does not represent the data correctly. My
 aim
   is
to
check the amount of time and its variability for groups of tasks
   
Thank you in advance
Regards
Sunita
   
--
View this message in context:
   
   http://old.nabble.com/Presentation-of-data-in-Graphical-format-
  tp26358857p26358857.html
Sent from the R help mailing list archive at Nabble.com.
   
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
   http://www.r-project.org/posting-guide.html
  
and provide commented, minimal, self-contained, reproducible code.
   
   
   
  
  [[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.
  
  
  
 
 [[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.



[[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.

Re: [R] A combinatorial optimization problem: finding the best permutation of a complex vector

2009-11-18 Thread Erwin Kalvelagen

See also:
http://yetanothermathprogrammingconsultant.blogspot.com/2009/11/assignment-problem.html
http://yetanothermathprogrammingconsultant.blogspot.com/2009/11/assignment-problem.html

Erwin Kalvelagen
Amsterdam Optimization Modeling Group
er...@amsterdamoptimization.com
http://amsterdamoptimization.com



On Wed, Nov 18, 2009 at 9:49 AM, Ravi Varadhan rvarad...@jhmi.edu wrote:

 I just saw that Cplex is a commercial software from ILOG/IBM, and that
 there
 is an R interface, Rcplex, for it.  While this is bad news, it is still
 encouraging to know that the LSAP problem can be solved faster.  I will
 keep
 looking for better/faster open source algorithms.

 Ravi.


 
 ---

 Ravi Varadhan, Ph.D.

 Assistant Professor, The Center on Aging and Health

 Division of Geriatric Medicine and Gerontology

 Johns Hopkins University

 Ph: (410) 502-2619

 Fax: (410) 614-9625

 Email: rvarad...@jhmi.edu

 Webpage:

 http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.h
 tml




 
 


 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
 On
 Behalf Of Ravi Varadhan
 Sent: Wednesday, November 18, 2009 9:39 AM
 To: 'Erwin Kalvelagen'; r-h...@stat.math.ethz.ch
 Subject: Re: [R] A combinatorial optimization problem: finding the best
 permutation of a complex vector

 Hi Erwin,

 Thank you for the information about Cplex.  It seems quite impressive.  Is
 it a proprietary software?  I saw that there is a Matlab interface to it.
 Is there an R interface?


 Thanks,
 Ravi.


 
 ---

 Ravi Varadhan, Ph.D.

 Assistant Professor, The Center on Aging and Health

 Division of Geriatric Medicine and Gerontology

 Johns Hopkins University

 Ph: (410) 502-2619

 Fax: (410) 614-9625

 Email: rvarad...@jhmi.edu

 Webpage:

 http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.h
 tml




 
 


 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
 On
 Behalf Of Erwin Kalvelagen
 Sent: Wednesday, November 18, 2009 12:20 AM
 To: r-h...@stat.math.ethz.ch
 Subject: Re: [R] A combinatorial optimization problem: finding the best
 permutation of a complex vector

 Ravi Varadhan rvaradhan at jhmi.edu writes:
 
 
  When I increased N = 1000, the time was about 1400 seconds!
 

 Not sure of this is important for you: This can be solved much faster. A
 good
 solver can solve the n=1000 problem in less than 2 seconds. The Cplex
 network
 code shows:

 Network - Optimal:  Objective =   1.6173194067e+003
 Network time =1.58 sec.  Iterations = 209126 (102313)

 Even solved as an LP this takes about 150 seconds.

 (The solutions are the same as reported by solve_LSAP).


 
 Erwin Kalvelagen
 Amsterdam Optimization Modeling Group
 er...@amsterdamoptimization.com
 http://amsterdamoptimization.com

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

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



[[alternative HTML version deleted]]

__
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.

[R] Creating an excel file and manipulating it from R


Hello everybody, I´ve been looking for a function that would create an excel
file in my working directory where I would write my dataframe but I only
found the functions to write or read in an existing file that you gave me on
my former post or on some websites. I can´t find either functions to
manipulate those datas: for example, I would like some lines to be red or
green according to their value. Thank you in advance!


-
Anna Lippel
new in R so be careful I should be asking a lt of questions!:teeth:
-- 
View this message in context: 
http://old.nabble.com/Creating-an-excel-file-and-manipulating-it-from-R-tp26408408p26408408.html
Sent from the R help mailing list archive at Nabble.com.

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

Re: [R] Presentation of data in Graphical format

yes in my data the 1st column is the main category say suppose Secretary
the second column is the sub category HR Dept the 3rd column is the list
of duties performed by the Secretary from HR dept and 4th column is time
required to perform the duty

so there are many such posts and dept with varied duties and times resp.

Regards

Our Thoughts have the Power to Change our Destiny.
Sunita


On Wed, Nov 18, 2009 at 8:42 PM, Petr PIKAL petr.pi...@precheza.cz wrote:

 Hi

 r-help-boun...@r-project.org napsal dne 18.11.2009 16:01:27:

  Yes I tried all the basic ones like box plot, pie chart, etc but the
 data
  representation isnt that clear.
 

 I agree with Tal. But it partly depends on your data. If you have many
 levels and only few time values in each boxplot would not look well. Maybe
 you could check also ?xtabs or ?table and/or R graph gallery
 http://addictedtor.free.fr/graphiques/ if you find suitable graph.

 Regards
 Petr



 
  Regards
 
  Our Thoughts have the Power to Change our Destiny.
  Sunita
 
 
  On Wed, Nov 18, 2009 at 7:20 PM, Tal Galili tal.gal...@gmail.com
 wrote:
 
   I would start with
   ?boxplot
  
  
   --
  
  
   My contact information:
   Tal Galili
   E-mail: tal.gal...@gmail.com
   Phone number: 972-52-7275845
   FaceBook: Tal Galili
   My Blogs:
   http://www.talgalili.com (Web and general, Hebrew)
   http://www.biostatistics.co.il (Statistics, Hebrew)
   http://www.r-statistics.com/ (Statistics,R, English)
  
  
  
  
   On Wed, Nov 18, 2009 at 2:47 PM, Sunita Patil sunita...@gmail.com
 wrote:
  
   Thanx
  
   but I am not able to find a graph that wud suit my data
  
   Regards
  
   Our Thoughts have the Power to Change our Destiny.
   Sunita
  
  
   On Sun, Nov 15, 2009 at 8:54 PM, milton ruser milton.ru...@gmail.com
   wrote:
  
Google R graph grallery
Google R ggplot2
Google R lattice
   
and good luck
   
milton
On Sun, Nov 15, 2009 at 7:48 AM, Sunita22 sunita...@gmail.com
 wrote:
   
   
Hello
   
My data contains following columns:
   
1st column: Posts (GM, Secretary, AM, Office Boy)
2nd Column: Dept (Finance, HR, ...)
3rd column: Tasks (Open the door, Fix an appointment, Fill the
   register,
etc.) depending on the post
4th column: Average Time required to do the task
   
So the sample data would look like
PostsDeptTask   Average
 time
Office Boy  HR   Open the door  00:00:09
Secretary   FinanceFix an appointment00.00.30
.  . .
   
I am trying to represent this data in Graphical format, I tried
 graphs
like
Mosaic plot, etc. But it does not represent the data correctly. My
 aim
   is
to
check the amount of time and its variability for groups of tasks
   
Thank you in advance
Regards
Sunita
   
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Re: [R] Writing a data frame in an excel file


Hi Charlie, I´ve been trying to use the sqlSave the way you showed me but it
would give me this error message which I couldn´t solve:
Erro em sqlSave(xlsFile, strategy, tablename = Result, rownames = FALSE) : 
  table ‘Result’ already exists

I would like to save the data frame in a specified worksheet but I couldn´t
find in the help on sqlSave how to do it. 


cls59 wrote:
 
 
 anna_l wrote:
 
 Hello, I am having trouble by using the write.table function to write a
 data frame of 4 columns and 7530 rows. I don´t  know if I should just use
 a sep=\n and change the .xls file into a .csv file. Thanks in advance
 
 
 
 Base R cannot write .xls files by it's self.  You should output CSV using
 write.csv():
 
   write.csv( dataFrame, file = 'results.csv' )
 
 If you are using R on windows, then the RODBC package provides a mechanism
 for dumping data frames directly to Excel files, possibly with multiple
 sheets:
 
   require( RODBC )
 
   xlsFile - odbcConnectExcel( 'results.xls', readOnly = F )
 
   sqlSave( xlsFile, dataFrame, tablename = 'R Results', rownames = F )
 
   odbcCloseAll()
 
 
 The tablename argument to sqlSave allows you to assign a name to the excel
 sheet that will contain the data.frame.
 
 
 -Charlie
 


-
Anna Lippel
new in R so be careful I should be asking a lt of questions!:teeth:
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[R] mann-whitney test with more groups

2009-11-18 Thread Kim Vanselow

Dear r-helpers,
I want to test groups of samples for significant differences.
Question: Does Group1 differ significantly from group2.
This is a question to be answered by mann-whitney-u-test.

I know that I can use wilcox.test with 2 samples.

My problem: How can r perform the test automatically if there are more than 2 
groups in my data frame.
Test group1 vs. 2, 1 vs. 3, 1 vs. 4, etc.


This is my skript:
Deckung - read.table(Gesamtdeckung.csv, sep=;, header=TRUE, dec=,, 
row.names=1)

x - Deckung$Gesamtdeckung
y - Deckung$Klasse

#U-Test
wilcox.test(x ~ y, paired = FALSE, subset = y %in% c(1, 2))
wilcox.test(x ~ y, paired = FALSE, subset = y %in% c(1, 3))
wilcox.test(x ~ y, paired = FALSE, subset = y %in% c(2, 3))

Any help would be greatly appreciated!

Thanks
Kim 
-- 
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Re: [R] Presentation of data in Graphical format

2009-11-18 Thread hadley wickham

 Yes I tried all the basic ones like box plot, pie chart, etc but the data
 representation isnt that clear.

Given that you have neither provided your data, nor explained what you
are trying to uncover from it, what sort of advice do you expect to
get?

Hadley

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

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Re: [R] parsing numeric values

Thanks. This is now fixed in the development version so that it gives
an error rather than crashing:

 library(gsubfn)
Loading required package: proto
Loading required package: tcltk
Loading Tcl/Tk interface ... done
 source(http://gsubfn.googlecode.com/svn/trunk/R/gsubfn.R;)
 strapply(test, as.numeric)
Error in as.character(pattern) :
  cannot coerce type 'builtin' to vector of type 'character'


On Wed, Nov 18, 2009 at 8:49 AM, baptiste auguie
baptiste.aug...@googlemail.com wrote:
 Thanks a lot, both of you.

 Incidentally, I made R crash when I forgot the X argument to strapply,

 library(gsubfn)
 Loading required package: tcltk
 Loading Tcl/Tk interface ... done
 strapply(test, as.numeric)

  *** caught bus error ***
 address 0x13c, cause 'non-existent physical address'

 Traceback:
  1: .External(dotTclcallback, ..., PACKAGE = tcltk)
  2: .Tcl.callback(x, e)
  3: makeAtomicCallback(x, e)
  4: makeCallback(get(value, envir = ref), get(envir, envir = ref))
  5: FUN(X[[3L]], ...)
  6: lapply(val, val2obj)
  7: .Tcl.args.objv(...)
  8: structure(.External(dotTclObjv, objv, PACKAGE = tcltk), class
 = tclObj)
  9: .Tcl.objv(.Tcl.args.objv(...))
 10: tcl(set, e, e)
 11: strapply1(x, pattern, backref, ignore.case)
 12: FUN(test[[1L]], ...)
 13: lapply(X, FUN, ...)
 14: sapply(X, ff, simplify = is.logical(simplify)  simplify,
 USE.NAMES = USE.NAMES)
 15: strapply(test, as.numeric)

 Possible actions:
 1: abort (with core dump, if enabled)
 2: normal R exit
 3: exit R without saving workspace
 4: exit R saving workspace

 sessionInfo()
 R version 2.10.0 (2009-10-26)
 i386-apple-darwin9.8.0

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

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

 other attached packages:
 [1] ggplot2_0.8.3  reshape_0.8.3  plyr_0.1.9     proto_0.3-8    fortunes_1.3-6

 2009/11/18 Gabor Grothendieck ggrothendi...@gmail.com:
 A minor variant might be the following:

   library(gsubfn)
   strapply(input, \\d+\\.\\d+E[-+]?\\d+, as.numeric, simplify = rbind)

 where:

 - as.numeric is used in place of c in which case we do not need combine
 - \\d+ matches one or more digits
 - \\. matches a decimal point
 - [-+]? matches -, + or nothing (i.e. an optional sign).
 - parentheses around the regular expression not needed

 On Wed, Nov 18, 2009 at 7:28 AM, Henrique Dallazuanna www...@gmail.com 
 wrote:
 Try this:

 strapply(input, ([0-9]+\\.[0-9]+E-[0-9]+), c, simplify = rbind,
 combine = as.numeric)

 On Wed, Nov 18, 2009 at 9:57 AM, baptiste auguie
 baptiste.aug...@googlemail.com wrote:
 Dear list,

 I'm seeking advice to extract some numeric values from a log file
 created by an external program. Consider the following example,

 input -
 readLines(textConnection(
 some text
  ax =    1.3770E-03     bx =    3.4644E-07
  ay =    1.9412E-04     by =    4.8840E-08

 other text
  aax  =    1.3770E-03     bbx =    3.4644E-07
  aay  =    1.9412E-04     bby =    4.8840E-08))

 ## this is what I want
 results - c(as.numeric(strsplit(grep(ax, input,val=T),  )[[1]][8]),
             as.numeric(strsplit(grep(ay, input,val=T),  )[[1]][8]),
             as.numeric(strsplit(grep(aax, input,val=T),  )[[1]][9]),
             as.numeric(strsplit(grep(aay, input,val=T),  )[[1]][9])
             )

 ## [1] 0.00137700 0.00019412 0.00137700 0.00019412

 The use of strsplit is not ideal here as there is a different number
 of space characters in the lines containing ax and aax for
 instance (hence the indices 8 and 9 respectively).

 I tried to use gsubfn for a cleaner construct,

 strapply(input, ax += +([0-9.]+), c, simplify=rbind,combine=as.numeric)

 but I can't seem to find the correct regular expression to deal with
 the exponent.


 Any tips are welcome!


 Best regards,

 baptiste

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 --
 Henrique Dallazuanna
 Curitiba-Paraná-Brasil
 25° 25' 40 S 49° 16' 22 O

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Re: [R] Presentation of data in Graphical format

Hello Sir

I had given a sample of my data, As I cannot disclose whole of my data this
is just a sample given

1st column: Posts (GM, Secretary, AM, Office Boy)
2nd Column: Dept (Finance, HR, ...)
3rd column: Tasks (Open the door, Fix an appointment, Fill the register,
etc.) depending on the post
4th column: Average Time required to do the task

So the sample data would look like
*PostsDeptTask Average time*
Office Boy  HR   Open the door  00:00:09
Office Boy  HR   Switch on the lights  00:00:10
Secretary   FinanceFix an appointment   00.00.30
    . .

    . .
    . .

in my data the 1st column is the main category say suppose Secretary the
second column is the sub category HR Dept the 3rd column is the list of
duties performed by the Secretary from HR dept and 4th column is time
required to perform the duty

so there are many such posts and dept with varied duties and times resp


Regards

Our Thoughts have the Power to Change our Destiny.
Sunita


On Wed, Nov 18, 2009 at 9:15 PM, hadley wickham h.wick...@gmail.com wrote:

  Yes I tried all the basic ones like box plot, pie chart, etc but the data
  representation isnt that clear.

 Given that you have neither provided your data, nor explained what you
 are trying to uncover from it, what sort of advice do you expect to
 get?

 Hadley

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


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Re: [R] Creating an excel file and manipulating it from R

Try the RDCOMClient [1] package.

[1]http://www.omegahat.org/RDCOMClient/

On Wed, Nov 18, 2009 at 1:31 PM, anna_l lippelann...@hotmail.com wrote:

 Hello everybody, I´ve been looking for a function that would create an excel
 file in my working directory where I would write my dataframe but I only
 found the functions to write or read in an existing file that you gave me on
 my former post or on some websites. I can´t find either functions to
 manipulate those datas: for example, I would like some lines to be red or
 green according to their value. Thank you in advance!


 -
 Anna Lippel
 new in R so be careful I should be asking a lt of questions!:teeth:
 --
 View this message in context: 
 http://old.nabble.com/Creating-an-excel-file-and-manipulating-it-from-R-tp26408408p26408408.html
 Sent from the R help mailing list archive at Nabble.com.

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-- 
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O

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Re: [R] foor loop - undefined columns selected error




Michela Leonardi wrote:

Dear R-Help Members,

I am trying to read and analyse a set of 100 csv files.
I need work only on some columns in each of those, so I decided to use
a for loop, isolate the
column in each file to work on, but then an error mesage appear:
undefined columns selected

Here is my code:

setwd(F:/Data/)
a-list.files()
for (x in a) {
  u-read.csv(x, header=T, sep=,, check.names=FALSE)
#it give me the same problem using read.table
  h-u[,2]
}

Error in `[.data.frame`(u, , 2) : undefined columns selected

It does not give me any problem selecting ane entire row (e.g. u[2,])
or a single value (e.g. [5,2])
If I try to select a column after the for loop I does not show any
problem, e.g.:

a-list.files()
for (x in a) {
  u-read.csv(x, header=T, sep=,, check.names=FALSE)
}
  h-u[,2]

I would appreciate any suggestion or pointer to solve the problem or
to do the same thing in a different way.

Thanks for your consideration



Michela,

What are your loops supposed to accomplish? They
just give you the last file in 'a'.
When you get the error, that indicates that at least
one of your files has only one column.
You don't get the error when you take h-u[,2] out
of the loop because the last file in 'a' does happen
to have 2 or more columns.
You need to rethink the loop with regard to what
you will do with 'h'. And you need to check what's
in those files.

 -Peter Ehlers


--
Michela Leonardi

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Re: [R] Presentation of data in Graphical format

2009-11-18 Thread hadley wickham

That is not enough information for anyone to suggest a useful plot.
For a start:

 * How many observations do you have?
 * How many difference posts/departments/tasks?
 * Are the variables nested or crossed?
 * Have you successfully parsed the time representation into something
R can work with?  Is the representation inconsistent as in your
example?
 * What is the purpose of the study?  What do you want to find out?

Maybe you should meet with a local statistical consultant to discuss
these issues in person. WARNING: you might have to pay - good advice
is not always/seldom/ever free.

Hadley

On Wed, Nov 18, 2009 at 9:53 AM, Sunita Patil sunita...@gmail.com wrote:
 Hello Sir

 I had given a sample of my data, As I cannot disclose whole of my data this
 is just a sample given

 1st column: Posts (GM, Secretary, AM, Office Boy)
 2nd Column: Dept (Finance, HR, ...)
 3rd column: Tasks (Open the door, Fix an appointment, Fill the register,
 etc.) depending on the post
 4th column: Average Time required to do the task

 So the sample data would look like
 Posts            Dept        Task                     Average time
 Office Boy      HR           Open the door          00:00:09
 Office Boy  HR   Switch on the lights  00:00:10
 Secretary       Finance    Fix an appointment   00.00.30
                             .                             .

                             .                             .
                             .                             .

 in my data the 1st column is the main category say suppose Secretary the
 second column is the sub category HR Dept the 3rd column is the list of
 duties performed by the Secretary from HR dept and 4th column is time
 required to perform the duty

 so there are many such posts and dept with varied duties and times resp


 Regards

 Our Thoughts have the Power to Change our Destiny.
 Sunita


 On Wed, Nov 18, 2009 at 9:15 PM, hadley wickham h.wick...@gmail.com wrote:

  Yes I tried all the basic ones like box plot, pie chart, etc but the
  data
  representation isnt that clear.

 Given that you have neither provided your data, nor explained what you
 are trying to uncover from it, what sort of advice do you expect to
 get?

 Hadley

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





-- 
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Re: [R] Presentation of data in Graphical format

2009-11-18 Thread Steve Lianoglou


Hi,

(Sorry, I didn't cc the r-help list)

On Nov 18, 2009, at 10:22 AM, Sunita Patil wrote:


I have been using R just very recently, I have gone through this
http://addictedtor.free.fr/graphiques/
a few weeks back but I am not able to understand as to how to choose  
the

graph amongst them? Can anyone guide me regarding this?


I'm not sure what you mean, exactly.

Many of those graphs there aren't just normal R functions. They are  
put together using several commands in order to build the final  
picture you see there.


For instance, say you like this graph:

http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=145

At the bottom left of the page, you'll find a Source Code section  
under Requirements.


Click the view link there:
http://addictedtor.free.fr/graphiques/graphcode.php?graph=145

And that's the code you need to make the graph (it's quite complex,  
but there are simpler ones.


-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] Writing a data frame in an excel file


Sorry Charlie, I didn´t understand that tablename=R Results was creating a
worksheet. But the thing now is that it works very well when I write for the
first time on the excel file but when I want to rewrite on it it gives the
error i wrote before saying that Results already exists, is there a way to
avoid that?


-
Anna Lippel
new in R so be careful I should be asking a lt of questions!:teeth:
-- 
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Re: [R] Presentation of data in Graphical format

2009-11-18 Thread Steve Lianoglou


Hi (again),

On Nov 18, 2009, at 10:53 AM, Sunita Patil wrote:


Hello Sir

I had given a sample of my data, As I cannot disclose whole of my  
data this

is just a sample given

1st column: Posts (GM, Secretary, AM, Office Boy)
2nd Column: Dept (Finance, HR, ...)
3rd column: Tasks (Open the door, Fix an appointment, Fill the  
register,

etc.) depending on the post
4th column: Average Time required to do the task

So the sample data would look like
*PostsDeptTask Average time*
Office Boy  HR   Open the door  00:00:09
Office Boy  HR   Switch on the lights  00:00:10
Secretary   FinanceFix an appointment   00.00.30
    . .

    . .
    . .

in my data the 1st column is the main category say suppose  
Secretary the
second column is the sub category HR Dept the 3rd column is the  
list of

duties performed by the Secretary from HR dept and 4th column is time
required to perform the duty

so there are many such posts and dept with varied duties and times  
resp


Fine, we see what your data looks like, but what are you trying to  
plot?! What do you want to show people about this data?


-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] Presentation of data in Graphical format

Hello Sir

I have got 150 observations, got 10 posts/ 6 departments/ tasks vary from 5
to 10,

A few of the variables are crossed specially in case of Office boy, where
the tasks are like open the door, put on the lights,

Yes time variable I have used Chron package, so that it works well

My aim for this study is to check the amount of time and its variability
for groups of tasks

Its my project work so need to work this out myself if it doesnt work then I
will have to consult a statistician

Thanks for guiding me to put up the question in more clearer way, I will
sure take care next time

Regards

Our Thoughts have the Power to Change our Destiny.
Sunita


On Wed, Nov 18, 2009 at 9:29 PM, hadley wickham h.wick...@gmail.com wrote:

 That is not enough information for anyone to suggest a useful plot.
 For a start:

  * How many observations do you have?
  * How many difference posts/departments/tasks?
  * Are the variables nested or crossed?
  * Have you successfully parsed the time representation into something
 R can work with?  Is the representation inconsistent as in your
 example?
  * What is the purpose of the study?  What do you want to find out?

 Maybe you should meet with a local statistical consultant to discuss
 these issues in person. WARNING: you might have to pay - good advice
 is not always/seldom/ever free.

 Hadley

 On Wed, Nov 18, 2009 at 9:53 AM, Sunita Patil sunita...@gmail.com wrote:
  Hello Sir
 
  I had given a sample of my data, As I cannot disclose whole of my data
 this
  is just a sample given
 
  1st column: Posts (GM, Secretary, AM, Office Boy)
  2nd Column: Dept (Finance, HR, ...)
  3rd column: Tasks (Open the door, Fix an appointment, Fill the register,
  etc.) depending on the post
  4th column: Average Time required to do the task
 
  So the sample data would look like
  PostsDeptTask Average time
  Office Boy  HR   Open the door  00:00:09
  Office Boy  HR   Switch on the lights  00:00:10
  Secretary   FinanceFix an appointment   00.00.30
      .
 .
 
      .
 .
      .
 .
 
  in my data the 1st column is the main category say suppose Secretary
 the
  second column is the sub category HR Dept the 3rd column is the list of
  duties performed by the Secretary from HR dept and 4th column is time
  required to perform the duty
 
  so there are many such posts and dept with varied duties and times resp
 
 
  Regards
 
  Our Thoughts have the Power to Change our Destiny.
  Sunita
 
 
  On Wed, Nov 18, 2009 at 9:15 PM, hadley wickham h.wick...@gmail.com
 wrote:
 
   Yes I tried all the basic ones like box plot, pie chart, etc but the
   data
   representation isnt that clear.
 
  Given that you have neither provided your data, nor explained what you
  are trying to uncover from it, what sort of advice do you expect to
  get?
 
  Hadley
 
  --
  http://had.co.nz/
 
 



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


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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] mann-whitney test with more groups



Kim Vanselow wrote:

Dear r-helpers,
I want to test groups of samples for significant differences.
Question: Does Group1 differ significantly from group2.
This is a question to be answered by mann-whitney-u-test.

I know that I can use wilcox.test with 2 samples.

My problem: How can r perform the test automatically if there are more than 2 
groups in my data frame.
Test group1 vs. 2, 1 vs. 3, 1 vs. 4, etc.


This is my skript:
Deckung - read.table(Gesamtdeckung.csv, sep=;, header=TRUE, dec=,, 
row.names=1)

x - Deckung$Gesamtdeckung
y - Deckung$Klasse

#U-Test
wilcox.test(x ~ y, paired = FALSE, subset = y %in% c(1, 2))
wilcox.test(x ~ y, paired = FALSE, subset = y %in% c(1, 3))
wilcox.test(x ~ y, paired = FALSE, subset = y %in% c(2, 3))

Any help would be greatly appreciated!

Thanks
Kim 


This sounds like serious data dredging, but if you're
sure that it's what you want, try the combn() function:

 y - gl(4, 5)
 x - rnorm(20)
 m - cbind(t(combn(4, 2)), NA)
 for(i in 1:nrow(idx))
m[i, 3] -
  wilcox.test(x ~ y, subset = y %in% idx[i,])$p.value
 m

 -Peter Ehlers

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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] mann-whitney test with more groups


Sorry, correction below.

Peter Ehlers wrote:


Kim Vanselow wrote:

Dear r-helpers,
I want to test groups of samples for significant differences.
Question: Does Group1 differ significantly from group2.
This is a question to be answered by mann-whitney-u-test.

I know that I can use wilcox.test with 2 samples.

My problem: How can r perform the test automatically if there are more 
than 2 groups in my data frame.

Test group1 vs. 2, 1 vs. 3, 1 vs. 4, etc.


This is my skript:
Deckung - read.table(Gesamtdeckung.csv, sep=;, header=TRUE, 
dec=,, row.names=1)


x - Deckung$Gesamtdeckung
y - Deckung$Klasse

#U-Test
wilcox.test(x ~ y, paired = FALSE, subset = y %in% c(1, 2))
wilcox.test(x ~ y, paired = FALSE, subset = y %in% c(1, 3))
wilcox.test(x ~ y, paired = FALSE, subset = y %in% c(2, 3))

Any help would be greatly appreciated!

Thanks
Kim 


This sounds like serious data dredging, but if you're
sure that it's what you want, try the combn() function:

 y - gl(4, 5)
 x - rnorm(20)
 m - cbind(t(combn(4, 2)), NA)
 for(i in 1:nrow(idx))
m[i, 3] -
  wilcox.test(x ~ y, subset = y %in% idx[i,])$p.value
 m

 -Peter Ehlers


  y - gl(4, 5)
  x - rnorm(20)
  m - cbind(t(combn(4, 2)), NA)
  for(i in 1:nrow(m))  # change 'idx' to 'm'
 m[i, 3] -
   wilcox.test(x ~ y, subset = y %in% m[i,])$p.value  # ditto


 -Peter Ehlers

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[R] How to install older version of R?

2009-11-18 Thread Pan,

Dear list

This is much like a linux problem, but I can't find any
reference for it. My OS is ubuntu 9.04 and a version of 2.9.2 of R has
been already installed in. Now, I need to install the version of 2.7.1.
I google a lot of websites and it seems like without a painless way
provided me to do it.
If any one offers me some suggestions/reference, I will
appreciate.

 Jia-Chiun Pan

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Re: [R] Writing a data frame in an excel file

2009-11-18 Thread Karl Ove Hufthammer

On Wed, 18 Nov 2009 08:02:47 -0800 (PST) anna_l lippelanna21
@hotmail.com wrote:
 Sorry Charlie, I didn?t understand that tablename=R Results was creating a
 worksheet. But the thing now is that it works very well when I write for the
 first time on the excel file but when I want to rewrite on it it gives the
 error i wrote before saying that Results already exists, is there a way to
 avoid that?

See the help page for 'sqlSave':
?sqlSave

More specifically, take a look at the 'append' and 'safer' arguments.

-- 
Karl Ove Hufthammer

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Re: [R] SVM Param Tuning with using SNOW package

2009-11-18 Thread Max Kuhn

On Tue, Nov 17, 2009 at 6:01 PM, raluca uca...@hotmail.com wrote:

 Hello,

 Is the first time I am using SNOW package and I am trying to tune the cost
 parameter for a linear SVM, where the cost (variable cost1) takes 10 values
 between 0.5 and 30.

 I have a large dataset and a pc which is not very powerful, so I need to
 tune the parameters using both CPUs of the pc.

 Somehow I cannot manage to do it. It seems that both CPUs are fitting the
 model for the same values of cost1, I guess the first 5, but not for the
 last 5.

 Please, can anyone help me! :-((

This is pretty easy to do with the train() funciton in the caret
package. From ?train, here is an example for a different data set

 library(caret)
 library(snow)
 library(mlbench)

 data(BostonHousing)

 mpiCalcs - function(X, FUN, ...)
+   {
+ theDots - list(...)
+ parLapply(theDots$cl, X, FUN)
+   }

 library(snow)
 cl - makeCluster(5, MPI)

 ## 50 bootstrap models distributed across 5 workers
 mpiControl - trainControl(workers = 5,
+number = 50,
+computeFunction = mpiCalcs,
+computeArgs = list(cl = cl))
 set.seed(1)
 usingMPI -  train(medv ~ .,
+data = BostonHousing,
+svmLinear,
+tuneGrid = data.frame(.C = seq(.5, 30, length = 10)),
+trControl = mpiControl)

 stopCluster(cl)
[1] 1


-- 

Max

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[R] Method dispatch for function

2009-11-18 Thread Stavros Macrakis

How can I determine what S3 method will be called for a particular
first-argument class?

I was imagining something like functionDispatch('str','numeric') =
utils:::str.default , but I can't find anything like this.

For that matter, I was wondering if anyone had written a version of
`methods` which gave their fully qualified names if they were not visible,
e.g.

methods('str') =
utils:::str.data.frameutils:::str.default
stats:::str.dendrogramstats:::str.logLikutils:::str.POSIXt

or

methods('str') =
 $utils
   str.data.frame str.defaultstr.POSIXt
 $stats
   str.dendrogram str.logLik

Thank you,

 -s

[[alternative HTML version deleted]]

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Re: [R] parsing numeric values

2009-11-18 Thread Bert Gunter

The previous elegant solutions required the use of the gsubfn package.
Nothing wrong with that, of course, but I'm always curious whether still
relatively simple base R solutions can be found, as they are often (but not
always!) much faster. And anyway, it seems to be in the spirit of your query
to try such a solution. So here is one base R approach that I believe works.
I'll break it up into 2 lines so you can see what's going on.

## Using your example...
## First replace everything but the number with spaces

 z - gsub([^[:digit:]E.+-], ,input)
 z
[1]   
[2] 1.3770E-03   3.4644E-07   
[3] 1.9412E-04   4.8840E-08   
[4]   
[5]   
[6]   1.3770E-033.4644E-07
[7]   1.9412E-044.8840E-08

## Now it can be scanned to a numeric via

 z-scan(textConnection(z),what=0)
Read 8 items
 z
[1] 1.3770e-03 3.4644e-07 1.9412e-04 4.8840e-08 1.3770e-03 3.4644e-07
1.9412e-04 4.8840e-08


I believe this strategy is reasonably general, but I haven't checked it
carefully and would appreciate folks pointing out where it trips up (e.g.
perhaps with NA's).

Best,

Bert Gunter
Genentech Nonclinical Biostatistics
 
 -Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of baptiste auguie
Sent: Wednesday, November 18, 2009 3:57 AM
To: r-help
Subject: [R] parsing numeric values

Dear list,

I'm seeking advice to extract some numeric values from a log file
created by an external program. Consider the following example,

input -
readLines(textConnection(
some text
  ax =1.3770E-03 bx =3.4644E-07
  ay =1.9412E-04 by =4.8840E-08

other text
  aax  =1.3770E-03 bbx =3.4644E-07
  aay  =1.9412E-04 bby =4.8840E-08))

## this is what I want
results - c(as.numeric(strsplit(grep(ax, input,val=T),  )[[1]][8]),
 as.numeric(strsplit(grep(ay, input,val=T),  )[[1]][8]),
 as.numeric(strsplit(grep(aax, input,val=T),  )[[1]][9]),
 as.numeric(strsplit(grep(aay, input,val=T),  )[[1]][9])
 )

## [1] 0.00137700 0.00019412 0.00137700 0.00019412

The use of strsplit is not ideal here as there is a different number
of space characters in the lines containing ax and aax for
instance (hence the indices 8 and 9 respectively).

I tried to use gsubfn for a cleaner construct,

strapply(input, ax += +([0-9.]+), c, simplify=rbind,combine=as.numeric)

but I can't seem to find the correct regular expression to deal with
the exponent.


Any tips are welcome!


Best regards,

baptiste

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

Re: [R] Writing a data frame in an excel file


Thanks Karl, well I am getting an error now after the following sqlSave
command:
sqlSave( xlsFile, datas, tablename = 'Datas_and_coefficients', rownames =
FALSE )

--  [RODBC] Failed exec in Update
22018 39 [Microsoft][Driver ODBC for Excel]invalid character value for the
diffusion specification (null) (null)


More specifically, take a look at the 'append' and 'safer' arguments.

-- 
Karl Ove Hufthammer

__
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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.




-
Anna Lippel
new in R so be careful I should be asking a lt of questions!:teeth:
-- 
View this message in context: 
http://old.nabble.com/Writing-a-data-frame-in-an-excel-file-tp26378240p26412410.html
Sent from the R help mailing list archive at Nabble.com.

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

Re: [R] mann-whitney test with more groups

2009-11-18 Thread Peter Dalgaard


Peter Ehlers wrote:

Sorry, correction below.

Peter Ehlers wrote:


Kim Vanselow wrote:

Dear r-helpers,
I want to test groups of samples for significant differences.
Question: Does Group1 differ significantly from group2.
This is a question to be answered by mann-whitney-u-test.

I know that I can use wilcox.test with 2 samples.

My problem: How can r perform the test automatically if there are 
more than 2 groups in my data frame.

Test group1 vs. 2, 1 vs. 3, 1 vs. 4, etc.


This is my skript:
Deckung - read.table(Gesamtdeckung.csv, sep=;, header=TRUE, 
dec=,, row.names=1)


x - Deckung$Gesamtdeckung
y - Deckung$Klasse

#U-Test
wilcox.test(x ~ y, paired = FALSE, subset = y %in% c(1, 2))
wilcox.test(x ~ y, paired = FALSE, subset = y %in% c(1, 3))
wilcox.test(x ~ y, paired = FALSE, subset = y %in% c(2, 3))

Any help would be greatly appreciated!

Thanks
Kim 


This sounds like serious data dredging, but if you're
sure that it's what you want, try the combn() function:

 y - gl(4, 5)
 x - rnorm(20)
 m - cbind(t(combn(4, 2)), NA)
 for(i in 1:nrow(idx))
m[i, 3] -
  wilcox.test(x ~ y, subset = y %in% idx[i,])$p.value
 m

 -Peter Ehlers


  y - gl(4, 5)
  x - rnorm(20)
  m - cbind(t(combn(4, 2)), NA)
  for(i in 1:nrow(m))  # change 'idx' to 'm'
 m[i, 3] -
   wilcox.test(x ~ y, subset = y %in% m[i,])$p.value  # ditto


There's also pairwise.wilcox.test, with multiple testing correction and 
all. (But someone called Lumley may chime in and remind you of the lack 
of guaranteed transitivity of rank tests.)



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

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[R] Data linkage functions for probabilistic linkage using person identifiers

2009-11-18 Thread Dagan A WRIGHT

I am somewhat new to R although using and liking already.  I am curious if 
there are any probabilistic packages similar in function to others such and 
Link King (http://www.the-link-king.com/).  I am looking for functions in SSN, 
First/Last name, date of birth, and a couple other indicators for matching.

Thanks

Dagan Wright, Ph.D., M.S.P.H.
Lead Addictions Research Analyst, Analysis  Evaluation Unit
Addictions  Mental Health Division (AMH)
500 Summer St. NE E86
Salem, Oregon 97301-1118

Office number: 503-945-5726
Fax number: 503-378-8467
dagan.a.wri...@state.or.us

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[R] border/box/frame around plot

2009-11-18 Thread brbell01


Hello I need to know how to put a closed frame around my plot.  I am plotting
using the igraph package, and I have been able to use box() with limited
success. Box() puts a border around only the upper and right edges of the
plot area, but misses the axes. By default, setting the axes=TRUE in igraph
does not produce closed axes (ie axes that run through the origin and up to
the limits of the plot window).  Any ideas?
-- 
View this message in context: 
http://old.nabble.com/border-box-frame-around-plot-tp26410451p26410451.html
Sent from the R help mailing list archive at Nabble.com.

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

[R] Y axis of 1-D Linear Discriminant Histograms

2009-11-18 Thread Bob Farmer

Hi all.
I would like to understand what are the units defined on the y-axis
when you plot the one-dimensional predictions (histograms) from lda()
(MASS) discriminant function objects?

While the helpfile suggests that a histogram is returned by default,
the presumably proportion-like values for each group seem to add up to
more than 1, and I'm not sure how to interpret the code from
ldahist(), which, I believe, defines the heights of each bin as

est1/(diff(breaks) * length(data[g == grp]))

where est1 is (as far as I can tell) the frequency within the bin, and
the denominator is apparently the bin width multiplied by the total
sample size for that panel.   It seems to be that a far more logical
result would be returned for each bin if the diff(breaks) component
was removed entirely.

While I don't think my concern affects the shape of each group's
histogram, I'd much prefer to display a more intuitive y-axis.

Example:
library(MASS)
ld1-lda(Species ~ Sepal.Length + Sepal.Width, iris)
plot(ld1, type = histogram, dimen = 1)
#(eyeballing it suggests that the sum of the frequencies reported on
the y-axis for each group exceeds 1)

Thanks very much.
--Bob Farmer
Dalhousie University

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

Re: [R] parsing numeric values

Hi,

Thanks for the alternative approach. However, I should have made my
example more complete in that other lines may also have numeric
values, which I'm not interested in. Below is an updated problem, with
my current solution,

tc - textConnection(
some text
 ax =1.3770E-03 bx =3.4644E-07
 ay =1.9412E-04 by =4.8840E-08

other text
 aax  =1.3770E-03 bbx =3.4644E-07
 aay  =1.9412E-04 bby =4.8840E-08

lots of other material,  including numeric values
 1.23E-4 123E5 12.3E-4 123E5 123E-4 123E5
 12.3E-4 123E5 12.3E-4 123E5 123E-4 123E5
etc...)

input -
readLines(tc)
close(tc)

## I want to retrieve the values for
## ax, ay, aax and aay only

results - c(
strapply(input, ax += +(\\d+\\.\\d+E[-+]?\\d+), as.numeric,
simplify = rbind),
strapply(input, ay += +(\\d+\\.\\d+E[-+]?\\d+), as.numeric,
simplify = rbind),
strapply(input, aax += +(\\d+\\.\\d+E[-+]?\\d+), as.numeric,
simplify = rbind),
strapply(input, aay += +(\\d+\\.\\d+E[-+]?\\d+), as.numeric,
simplify = rbind))

results

Using the suggested base R solution, I've come up with this variation,

z - gsub([^[:digit:]E.+-], , grep(ax|ay|aax|aay, input,
value=TRUE))

test - scan(textConnection(z),what=0)
test[seq(1, length(test), by=2)]


Thanks again,

baptiste

2009/11/18 Bert Gunter gunter.ber...@gene.com:
 The previous elegant solutions required the use of the gsubfn package.
 Nothing wrong with that, of course, but I'm always curious whether still
 relatively simple base R solutions can be found, as they are often (but not
 always!) much faster. And anyway, it seems to be in the spirit of your query
 to try such a solution. So here is one base R approach that I believe works.
 I'll break it up into 2 lines so you can see what's going on.

 ## Using your example...
 ## First replace everything but the number with spaces

 z - gsub([^[:digit:]E.+-], ,input)
 z
 [1]          
 [2]             1.3770E-03               3.4644E-07
 [3]             1.9412E-04               4.8840E-08
 [4] 
 [5]           
 [6]               1.3770E-03                3.4644E-07
 [7]               1.9412E-04                4.8840E-08

 ## Now it can be scanned to a numeric via

 z-scan(textConnection(z),what=0)
 Read 8 items
 z
 [1] 1.3770e-03 3.4644e-07 1.9412e-04 4.8840e-08 1.3770e-03 3.4644e-07
 1.9412e-04 4.8840e-08

 
 I believe this strategy is reasonably general, but I haven't checked it
 carefully and would appreciate folks pointing out where it trips up (e.g.
 perhaps with NA's).

 Best,

 Bert Gunter
 Genentech Nonclinical Biostatistics

  -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
 Behalf Of baptiste auguie
 Sent: Wednesday, November 18, 2009 3:57 AM
 To: r-help
 Subject: [R] parsing numeric values

 Dear list,

 I'm seeking advice to extract some numeric values from a log file
 created by an external program. Consider the following example,

 input -
 readLines(textConnection(
 some text
  ax =    1.3770E-03     bx =    3.4644E-07
  ay =    1.9412E-04     by =    4.8840E-08

 other text
  aax  =    1.3770E-03     bbx =    3.4644E-07
  aay  =    1.9412E-04     bby =    4.8840E-08))

 ## this is what I want
 results - c(as.numeric(strsplit(grep(ax, input,val=T),  )[[1]][8]),
             as.numeric(strsplit(grep(ay, input,val=T),  )[[1]][8]),
             as.numeric(strsplit(grep(aax, input,val=T),  )[[1]][9]),
             as.numeric(strsplit(grep(aay, input,val=T),  )[[1]][9])
             )

 ## [1] 0.00137700 0.00019412 0.00137700 0.00019412

 The use of strsplit is not ideal here as there is a different number
 of space characters in the lines containing ax and aax for
 instance (hence the indices 8 and 9 respectively).

 I tried to use gsubfn for a cleaner construct,

 strapply(input, ax += +([0-9.]+), c, simplify=rbind,combine=as.numeric)

 but I can't seem to find the correct regular expression to deal with
 the exponent.


 Any tips are welcome!


 Best regards,

 baptiste

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



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

Re: [R] Writing a data frame in an excel file

2009-11-18 Thread Orvalho Augusto

Why don't try the fabulous WRITEXLS package?

Caveman


On Wed, Nov 18, 2009 at 7:45 PM, anna_l lippelann...@hotmail.com wrote:

 Thanks Karl, well I am getting an error now after the following sqlSave
 command:
 sqlSave( xlsFile, datas, tablename = 'Datas_and_coefficients', rownames =
 FALSE )

 --  [RODBC] Failed exec in Update
 22018 39 [Microsoft][Driver ODBC for Excel]invalid character value for the
 diffusion specification (null) (null)


 More specifically, take a look at the 'append' and 'safer' arguments.

 --
 Karl Ove Hufthammer

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

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




 -
 Anna Lippel
 new in R so be careful I should be asking a lt of questions!:teeth:
 --
 View this message in context: 
 http://old.nabble.com/Writing-a-data-frame-in-an-excel-file-tp26378240p26412410.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
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Re: [R] parsing numeric values

It only works if some text at the beginning has no digits, dots, E
characters or sign characters.

On Wed, Nov 18, 2009 at 12:44 PM, Bert Gunter gunter.ber...@gene.com wrote:
 The previous elegant solutions required the use of the gsubfn package.
 Nothing wrong with that, of course, but I'm always curious whether still
 relatively simple base R solutions can be found, as they are often (but not
 always!) much faster. And anyway, it seems to be in the spirit of your query
 to try such a solution. So here is one base R approach that I believe works.
 I'll break it up into 2 lines so you can see what's going on.

 ## Using your example...
 ## First replace everything but the number with spaces

 z - gsub([^[:digit:]E.+-], ,input)
 z
 [1]          
 [2]             1.3770E-03               3.4644E-07
 [3]             1.9412E-04               4.8840E-08
 [4] 
 [5]           
 [6]               1.3770E-03                3.4644E-07
 [7]               1.9412E-04                4.8840E-08

 ## Now it can be scanned to a numeric via

 z-scan(textConnection(z),what=0)
 Read 8 items
 z
 [1] 1.3770e-03 3.4644e-07 1.9412e-04 4.8840e-08 1.3770e-03 3.4644e-07
 1.9412e-04 4.8840e-08

 
 I believe this strategy is reasonably general, but I haven't checked it
 carefully and would appreciate folks pointing out where it trips up (e.g.
 perhaps with NA's).

 Best,

 Bert Gunter
 Genentech Nonclinical Biostatistics

  -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
 Behalf Of baptiste auguie
 Sent: Wednesday, November 18, 2009 3:57 AM
 To: r-help
 Subject: [R] parsing numeric values

 Dear list,

 I'm seeking advice to extract some numeric values from a log file
 created by an external program. Consider the following example,

 input -
 readLines(textConnection(
 some text
  ax =    1.3770E-03     bx =    3.4644E-07
  ay =    1.9412E-04     by =    4.8840E-08

 other text
  aax  =    1.3770E-03     bbx =    3.4644E-07
  aay  =    1.9412E-04     bby =    4.8840E-08))

 ## this is what I want
 results - c(as.numeric(strsplit(grep(ax, input,val=T),  )[[1]][8]),
             as.numeric(strsplit(grep(ay, input,val=T),  )[[1]][8]),
             as.numeric(strsplit(grep(aax, input,val=T),  )[[1]][9]),
             as.numeric(strsplit(grep(aay, input,val=T),  )[[1]][9])
             )

 ## [1] 0.00137700 0.00019412 0.00137700 0.00019412

 The use of strsplit is not ideal here as there is a different number
 of space characters in the lines containing ax and aax for
 instance (hence the indices 8 and 9 respectively).

 I tried to use gsubfn for a cleaner construct,

 strapply(input, ax += +([0-9.]+), c, simplify=rbind,combine=as.numeric)

 but I can't seem to find the correct regular expression to deal with
 the exponent.


 Any tips are welcome!


 Best regards,

 baptiste

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Re: [R] parsing numeric values

Here is a slight variation:

 read.table(textConnection(grep(aa?[xy], input, value = TRUE)),
+colClasses = c(NULL, NULL, numeric))
  V3 V6
1 0.00137700 3.4644e-07
2 0.00019412 4.8840e-08
3 0.00137700 3.4644e-07
4 0.00019412 4.8840e-08



On Wed, Nov 18, 2009 at 1:54 PM, baptiste auguie
baptiste.aug...@googlemail.com wrote:
 Hi,

 Thanks for the alternative approach. However, I should have made my
 example more complete in that other lines may also have numeric
 values, which I'm not interested in. Below is an updated problem, with
 my current solution,

 tc - textConnection(
 some text
  ax =    1.3770E-03     bx =    3.4644E-07
  ay =    1.9412E-04     by =    4.8840E-08

 other text
  aax  =    1.3770E-03     bbx =    3.4644E-07
  aay  =    1.9412E-04     bby =    4.8840E-08

 lots of other material,  including numeric values
  1.23E-4 123E5 12.3E-4 123E5 123E-4 123E5
  12.3E-4 123E5 12.3E-4 123E5 123E-4 123E5
 etc...)

 input -
 readLines(tc)
 close(tc)

 ## I want to retrieve the values for
 ## ax, ay, aax and aay only

 results - c(
 strapply(input, ax += +(\\d+\\.\\d+E[-+]?\\d+), as.numeric,
 simplify = rbind),
 strapply(input, ay += +(\\d+\\.\\d+E[-+]?\\d+), as.numeric,
 simplify = rbind),
 strapply(input, aax += +(\\d+\\.\\d+E[-+]?\\d+), as.numeric,
 simplify = rbind),
 strapply(input, aay += +(\\d+\\.\\d+E[-+]?\\d+), as.numeric,
 simplify = rbind))

 results

 Using the suggested base R solution, I've come up with this variation,

 z - `, grep(ax|ay|aax|aay, input,
 value=TRUE))

 test - scan(textConnection(z),what=0)
 test[seq(1, length(test), by=2)]


 Thanks again,

 baptiste

 2009/11/18 Bert Gunter gunter.ber...@gene.com:
 The previous elegant solutions required the use of the gsubfn package.
 Nothing wrong with that, of course, but I'm always curious whether still
 relatively simple base R solutions can be found, as they are often (but not
 always!) much faster. And anyway, it seems to be in the spirit of your query
 to try such a solution. So here is one base R approach that I believe works.
 I'll break it up into 2 lines so you can see what's going on.

 ## Using your example...
 ## First replace everything but the number with spaces

 z - gsub([^[:digit:]E.+-], ,input)
 z
 [1]          
 [2]             1.3770E-03               3.4644E-07
 [3]             1.9412E-04               4.8840E-08
 [4] 
 [5]           
 [6]               1.3770E-03                3.4644E-07
 [7]               1.9412E-04                4.8840E-08

 ## Now it can be scanned to a numeric via

 z-scan(textConnection(z),what=0)
 Read 8 items
 z
 [1] 1.3770e-03 3.4644e-07 1.9412e-04 4.8840e-08 1.3770e-03 3.4644e-07
 1.9412e-04 4.8840e-08

 
 I believe this strategy is reasonably general, but I haven't checked it
 carefully and would appreciate folks pointing out where it trips up (e.g.
 perhaps with NA's).

 Best,

 Bert Gunter
 Genentech Nonclinical Biostatistics

  -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
 Behalf Of baptiste auguie
 Sent: Wednesday, November 18, 2009 3:57 AM
 To: r-help
 Subject: [R] parsing numeric values

 Dear list,

 I'm seeking advice to extract some numeric values from a log file
 created by an external program. Consider the following example,

 input -
 readLines(textConnection(
 some text
  ax =    1.3770E-03     bx =    3.4644E-07
  ay =    1.9412E-04     by =    4.8840E-08

 other text
  aax  =    1.3770E-03     bbx =    3.4644E-07
  aay  =    1.9412E-04     bby =    4.8840E-08))

 ## this is what I want
 results - c(as.numeric(strsplit(grep(ax, input,val=T),  )[[1]][8]),
             as.numeric(strsplit(grep(ay, input,val=T),  )[[1]][8]),
             as.numeric(strsplit(grep(aax, input,val=T),  )[[1]][9]),
             as.numeric(strsplit(grep(aay, input,val=T),  )[[1]][9])
             )

 ## [1] 0.00137700 0.00019412 0.00137700 0.00019412

 The use of strsplit is not ideal here as there is a different number
 of space characters in the lines containing ax and aax for
 instance (hence the indices 8 and 9 respectively).

 I tried to use gsubfn for a cleaner construct,

 strapply(input, ax += +([0-9.]+), c, simplify=rbind,combine=as.numeric)

 but I can't seem to find the correct regular expression to deal with
 the exponent.


 Any tips are welcome!


 Best regards,

 baptiste

 __
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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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 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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[R] (no subject)

2009-11-18 Thread Karen Federico

How do you perform a multicollinearity test using R. Also how do you perform
a selection stepwise to carry out a multiple regression analysis?


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[R] How to choose appropriate linear model? (ANOVA)

2009-11-18 Thread Peng Yu

I'm wondering how to choose an appropriate linear model for a given
problem. I have been reading Applied Linear Regression Models by John
Neter, Michael H Kutner, William Wasserman and Christopher J.
Nachtsheim. I'm still not clear how to choose an appropriate linear
model.

For multi-factor ANOVA, shall I start with all the interaction terms
and do an F-test to see with interaction terms are not significant,
then do a linear regression on a model without the non-significant
iteration term?

Could somebody point me some good book or chapters on this topic?

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Re: [R] (no subject)

2009-11-18 Thread Moritz Fromwald


http://www.lmgtfy.com/?q=multicollinearity+test+using+R
http://www.lmgtfy.com/?q=selection+stepwise+multiple+regression+analysis+using+R

Moritz

Karen Federico schrieb:

How do you perform a multicollinearity test using R. Also how do you perform
a selection stepwise to carry out a multiple regression analysis?


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[R] standard error for the estimated value (lmer fitted model)

2009-11-18 Thread willow1980


Dear R users,
I want to draw standard error lines for the predicted regression line
estimated by logistic regression using lmer. I have two predictors: cafr and
its quadratic form I(cafr^2), where cafr is a variable centered around the
mean of original variable. Now, the estimated value from the fitted model
will be,
(mo...@x)%*%fixef(model)
In the logit scale, the mean sum of square from fitted model will be, 
sesample=sqrt(sum(resid(model)^2)/(n-p-1)), where p is the degrees of
freedom used for fitting.
Could someone make a judgement if it is reasonable to calculate standard
error of the estimated value by
sesample*sqrt(vector%*%ginv(t(mo...@x)%*%mo...@x)%*%t(vector))
, where vector is the (1,cafr,I(cafr^2)) which representing empirical data
vector at considered point.
If this is correct, I think I can use this method to draw standard error
line. Otherwise, would you please suggest a reasonable one?
Thank you very much for your attention!
Yours sincerely, Jianghua
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[R] Re ading multiple Excel 2007 files with a loop

2009-11-18 Thread Mark W. Miller



I have several hundred Excel 2007 data files in a folder.  I would like to
read every file in a single given folder using a loop.

I have searched the FAQ, the forum archives here, other or older R boards
and the R Import / Export documentation, and have asked some very
knowledgeable R users without learning of a solution.  I hope someone here
can help.

I understand that the most common suggestion is to convert the files to csv
format.  However, there are so many files in my case (ultimately  1000) I
would rather avoid doing that.

I have also found many solutions to this problem for txt files and files in
additional formats other than Excel 2007.

I can read three Excel 2007 files one at a time with the following example
code using R 2.10.0 on a computer running Windows (XP, I think):




library(RODBC)


channel - odbcDriverConnect(DRIVER=Microsoft Excel Driver (*.xls, *.xlsx,
*.xlsm, *.xlsb); 
DBQ=U:\\test folder\\testA.xlsx; ReadOnly=False)
 
sqlTables(channel)

my.data.A - sqlFetch(channel, Sheet1)

odbcClose(channel)



channel - odbcDriverConnect(DRIVER=Microsoft Excel Driver (*.xls, *.xlsx,
*.xlsm, *.xlsb); 
DBQ=U:\\test folder\\testB.xlsx; ReadOnly=False)
 
sqlTables(channel)

my.data.B - sqlFetch(channel, Sheet1)

odbcClose(channel)



channel - odbcDriverConnect(DRIVER=Microsoft Excel Driver (*.xls, *.xlsx,
*.xlsm, *.xlsb); 
DBQ=U:\\test folder\\testC.xlsx; ReadOnly=False)
 
sqlTables(channel)

my.data.C - sqlFetch(channel, Sheet1)

odbcClose(channel)





# However, when I attempt to read the same three files with the loop below I
receive an error:




library(RODBC)


setwd(U:/test folder)


fname - list.files(pattern=.\\.xlsx, full.names = FALSE, recursive =
TRUE, ignore.case = TRUE)

z - length(fname)

print(z)


for (sp in 1:z) {

channel - odbcDriverConnect(DRIVER=Microsoft Excel Driver (*.xls, *.xlsx,
*.xlsm, *.xlsb); 

DBQ=U:\\test folder\\fname[sp]; ReadOnly=False)
 
sqlTables(channel)

my.data - sqlFetch(channel, Sheet1)

print(my.data)

odbcClose(channel)
}




# The error I receive states:

Error in odbcTableExists(channel, sqtable) : 
  ‘Sheet1’: table not found on channel


# Thank you sincerely in advance for any help with this problem.

Mark Miller

Gainesville, Florida


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Re: [R] How to choose appropriate linear model? (ANOVA)

Hello Peng,
What you are talking about is model selection process.
Although it also sound like you are referring to the more general subject of
regression model strategies, consider finding this book:
http://www.amazon.com/Regression-Modeling-Strategies-Frank-Harrell/dp/0387952322

Frank Harrell is a very insightful lecturer, I heard his writing is also
good.

I would love to read recommendation from other R members regarding your
question.

Best,
Tal




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E-mail: tal.gal...@gmail.com
Phone number: 972-52-7275845
FaceBook: Tal Galili
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On Wed, Nov 18, 2009 at 9:48 PM, Peng Yu pengyu...@gmail.com wrote:

 I'm wondering how to choose an appropriate linear model for a given
 problem. I have been reading Applied Linear Regression Models by John
 Neter, Michael H Kutner, William Wasserman and Christopher J.
 Nachtsheim. I'm still not clear how to choose an appropriate linear
 model.

 For multi-factor ANOVA, shall I start with all the interaction terms
 and do an F-test to see with interaction terms are not significant,
 then do a linear regression on a model without the non-significant
 iteration term?

 Could somebody point me some good book or chapters on this topic?

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


[[alternative HTML version deleted]]

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Re: [R] parsing numeric values