Dear List,
Must be a silly question, but I was wondering whether there is a direct way of
calculating "standard error of a HR or exp(coef)" from coxph objects
x <- coxph(Surv(time, status) ~ age + inst, lung)> xcoef exp(coef)
se(coef) zpage 0.0190 1.02 0.00925 2.06 0.04i
Check the *apply() series of functions. tapply() will do what you want.
attach(mtcars)
tapply(hp,list(cyl,gear),mean)
HTH,
Daniel
Mark Alen wrote:
>
> I know commands like xtabs and table allow a user to do cross-tabulation
> For example the following command generates a pivot table that sh
I know commands like xtabs and table allow a user to do cross-tabulation
For example the following command generates a pivot table that shows the number
of cars that have the same number of gears and cylinders.
>xtabs(~cyl+gear,data =mtcars)
gear
cyl 3 4 5
4 1 8 2
6 2 4 1
812 0 2
>
We
I am trying to make this transition from a casual R programmer to a
professional programmer (trying to make money with R)
What tools should a professional R developer have?
what are the good utilities that can help R developers to code and debug more
efficiently? what type of tools are missing?
Typically not, unless the device has not closed properly. Does the second
plot show up in the pdf?
Daniel
cherron wrote:
>
> Hello,
>
>>I am currently working on a script and I output plots to pdf using
>
> pdf(...)
> plot(...)
> dev.off()
>
>>then later I was trying to plot something and w
For the first part, use the col and pch arguments:
id<-rep(c(0,2),each=50)
e<-rnorm(100)
x<-rnorm(100)
y<-id+x+e
xyplot(y~x,groups=id,col=c(3,4),pch=c(12,13))
For the second part, I do not know what exactly mean by superimpose the mean
level? Should the mean for each group be displayed as a horiz
Hello
I do not think I have fully grasped how to use Amelia to deal with missing
data.
For instance, suppose I have a data.frame variable with 4 columns (year,
mon, ssn, dev) = (year, month, measurements, standard deviation of the
measurement). Of course, there are some random missing val
library(multicore)
options(cores=10)
getOption("cores")
On Fri, Jul 22, 2011 at 11:35 AM, Madana_Babu wrote:
> Hi,
>
> Can you please explain me that how can i perform this on a multicore
> processor? since i have a machine with 16-cores. I can do this much faster
> if i use all cores.
>
> Tha
On Fri, Jul 22, 2011 at 12:30 PM, Bansal, Vikas wrote:
> Thanks for your reply.That is why I wrote in the message that I have sent
> this message before but did not get any help (first line of my message).
> can you please tell me that if user will input 50 files or 100 how my code
> will work.D
Hello again R-folks,
I'm trying to apply a loop to multiple data frames and then organize the data
in a manageable form. I have the code for my loop figured out (thanks to help
from this list)...it runs up to 2000 iterations of a "while" loop until it
finds a 40-row "d2p" column sum >5
n<-nrow(
Sarath,
Maybe someone can show a direct access to the statistic. One way to
get around is to access 't' component of the boot object which
contains individual estimates. so you can extract standard error by
sqrt(var(bootObj$t))
Weidong Gu
On Fri, Jul 22, 2011 at 11:36 AM, Sarath Gamini Bannehek
Thanks for your reply.That is why I wrote in the message that I have sent this
message before but did not get any help (first line of my message).
can you please tell me that if user will input 50 files or 100 how my code will
work.Do I need to write file1,file2 till file 100 in this code?
lappl
On Fri, Jul 22, 2011 at 12:15 PM, Bansal, Vikas wrote:
> Dear all,
>
> I need your help as I was not able to find out the solution.I sent this
> message before but did not get any help.Please help me.
You only sent the message yesterday!!! (then again a few hours ago,
and *again* just now)
rath
Dear all,
I need your help as I was not able to find out the solution.I sent this message
before but did not get any help.Please help me.
The thing is-
I am having a code which is reading file with this code-
df=read.table("Case2.pileup",fill=T,sep="\t",colClasses="character")
but as am making
Does the following do what you want? The singletons()
function identifies the entries that appear only once
in a vector and we use its output to eliminate the singleton
entries.
> singletons <- function(x) !(duplicated(x) | duplicated(x,fromLast=TRUE))
> d <- data.frame(x=c(101, 102, 101, 105
Dear R users!
I have a problem using tune() from e1071 package. I need to to tune a neural
network where response variable is a vector. I've used this function as it
shown below and I got the error:
tune.netWhole <- tune("nnet", x, y, ranges = list(...), tunecontrol = ...)
# weights: 28
initial
Hi all,
I am hoping to keep certain rows of my data set. These are rows whose value
in column X is equal to the value in column X for another row. For example:
1 1
2 1
3 2
4 3
5 4
6 4
>From this I would want the following:
1 1
2 1
5 4
6 4
I am struggling with the for loop. Here is wh
Hi,
For the last few days I have tried utilise your package "pegas" in order
to obtain some values for indices like the nuclear diversity and tajimas
d value.
I have modified my dataset (a text file containing dna sequences) in
order to be able to read it in with the tools provided by pegas. H
Dear R user,
I used the following to do a bootstrap.
>bootObj<-boot(data=DAT, statistic=Lp.est,
R=1000,x0=3)
I have the following output from the above bootstrap. How
can I extract components of the output.
For example, how can I extract the std.error?
> bootObj
ORDINARY NONPARAMETRIC BOOT
I suspect that a few s/def/bind def/ on that prologue might improve
things a bit.
The ps R creates freely switches between the sRGB ABC space and
setgray. That is a good thing; it helps ensure that black will
be just black when sent to a CMYK device. Without that you can
get CMY black from some
Hi,
Can you please explain me that how can i perform this on a multicore
processor? since i have a machine with 16-cores. I can do this much faster
if i use all cores.
Thanks in advance...
Regards,
Madana
--
View this message in context:
http://r.789695.n4.nabble.com/R-on-Multicore-for-Linux-t
Thank you David, the useRaster=T does the trick! But, unfortunately, it
doesn't work for persp.
Is there any way to avoid the sRGB colors at the beginning of the R session?
I tried to edit my Rprofile:
.First <- function() {
a<-system("ls /dati/software/R_lib/*.r",intern=T)
for (i in a)
Hi,
Look at ?combn
t(combn(Vector, 2))
gives:
[,1] [,2]
[1,] "a" "b"
[2,] "a" "c"
[3,] "b" "c"
No idea how it is speed-wise.
HTH,
Josh
On Fri, Jul 22, 2011 at 10:09 AM, Megh Dal wrote:
> Let say, I have a character vector of arbitrary length:
>
> Vector <- c("a", "b", "c")
>
> Usin
I suspect that a few s/def/bind def/ on that prologue might improve
things a bit.
The ps R creates freely switches between the sRGB ABC space and
setgray. That is a good thing; it helps ensure that black will
be just black when sent to a CMYK device. Without that you can
get CMY black from some
Another option in this specific case is to use the new useRaster=TRUE
option, which makes the image function generate much more compact and
faster-rendering image plots. This code:
setEPS()
postscript (file="volc.eps",width=5,height=4)
image(volcano,useRaster=TRUE)
dev.off()
in R 2.13 generates a
Let say, I have a character vector of arbitrary length:
Vector <- c("a", "b", "c")
Using that vector I would like to create a matrix (with number of columns as 2)
with all pairwise combinations of those elements, like:
Vector <- c("a", "b", "c")
Mat <- rbind(c("a", "b"), c("a", "c"), c("b",
On 2011-07-22 07:33, marcel wrote:
Basic question: I looked around quite a bit, still having a little trouble
manipulating the distance between the Y-axis label and the plot. In this
case, I would like to move the Y axis title closer to the plot.
# Data
tC<- textConnection("
Time Type1 Type2 Ty
Thanks Joshua and Berton for your pointers. Yes it was typo as I wanted to mean
to select few columns.
-Original Message-
From: Joshua Wiley [mailto:jwiley.ps...@gmail.com]
Sent: 22 July 2011 22:02
To: Bogaso Christofer
Cc: r-help@r-project.org
Subject: Re: [R] Indexing problem with matr
Hi:
On Fri, Jul 22, 2011 at 2:28 AM, Marko wrote:
> Hello,
> i have following problem and I hope you can help me a little bit
>
>
> My dataframe looks like:
>
> df
> a m d typ value
> 1950 1 1 5 -4.1
> 1950 1 2 9 2.7
> 1950 1 3 3 -1.3
> 1950 1 4 5
See the "drop" argument (and link) in ?"["
-- Bert
On Fri, Jul 22, 2011 at 9:46 AM, Bogaso Christofer
wrote:
> Dear all, assume I have a matrix with just 1 row. Now suppose I want to
> fetch 1st few rows from that matrix, however resulting object becomes
> vector. Here is 1 such example:
>
>
>
On Fri, Jul 22, 2011 at 9:46 AM, Bogaso Christofer
wrote:
> Dear all, assume I have a matrix with just 1 row. Now suppose I want to
> fetch 1st few rows from that matrix, however resulting object becomes
I'm assuming you mean the first few columns. The place to look is
?"[" where you would find
Dear all, assume I have a matrix with just 1 row. Now suppose I want to
fetch 1st few rows from that matrix, however resulting object becomes
vector. Here is 1 such example:
> matrix(1:5, 1)
[,1] [,2] [,3] [,4] [,5]
[1,]12345
>
> matrix(1:5, 1)[,-1]
[1] 2 3 4 5
The tkexamp function in the TeachingDemos package can help with creating tcltk
dialog boxes. There are also several other functions in that package that use
tcltk dialogs that you could use as examples to build your own if tkexamp is
not enough for you.
--
Gregory (Greg) L. Snow Ph.D.
Statist
On 2011-07-22 07:42, Bert Gunter wrote:
See the "alternating" parameter in the "scales" parameter list of
?xyplot. Presumably, something like:
xyplot( ...,
scales = list(..., alternating = 1),... )
I would just use tck=c(1,0):
xyplot(...,
scales = list(tck = c(1,0), x = list(draw = F
Jeff,
Thanks for the hint. It is a good solution.
Thanks!
From: Jeff Newmiller [mailto:jdnew...@dcn.davis.ca.us]
Sent: Thursday, July 21, 2011 7:00 PM
To: Hu, Yinghua; r-help@r-project.org
Subject: Re: [R] Summing daily values by weekday and weekend
Clue: make a column representing the desired
Hello, I am trying to build some dialog boxes but I am having problems. I'm
using R-2.13.1 in Windows 7
I want to have 4 numerical entry boxes and 3 radiobuttons in a row ( 4 rows)
for entry data
and 2 rows for output with a button for 'compute' and another for ;quit'
Can somebody indicate a tut
On 2011-07-28 12:14:32, Cleber N.Borges wrote:
I am tring make a simple surface plot ( 2 by 2 terms of a MARS model
(with earth package) but I get the follow error message:
> library( earth )
> data( gasoline, package='pls' )
> nir <- gasoline$NIR
> class( nir )
[1] "AsIs"
> oct <- gasol
On 22.07.2011 15:45, Mitra, Sumona wrote:
Dear all,
Apologies for not being specific earlier.
The R version I am using is 2.12.2.
Everytime I try installing XMLRPC using the following command:-
install.packages(repos = "http://www.omegahat.org/XMLRPC/XMLRPC_0.2-4.tar.gz";)
What you speci
Hi, Kim-
For starters you might have a look at
?by
?tapply
?aggregate
Ken
On 07/22/11, kimberly sels wrote:
> Hi,
>
> I need to calculate the average length of a trait per individual. I am not
> used to working with R so I could use some help.
> The table goes like this:
>
> indtrait
> 1
Hello!
It's a shoot in the dark, but I'll try. If one has a total of 100
(e.g., %), and three components of the total, e.g.,
mytotal=data.frame(x=50,y=30,z=20), - one could build a pie chart with
3 sectors representing x, y, and z according to their proportions in
the total.
I am wondering if it's
Hi,
I need to calculate the average length of a trait per individual. I am not
used to working with R so I could use some help.
The table goes like this:
indtrait
1 3.6
1 3.8
1 3.9
1 3.6
2 5.5
2 5.2
3 4.8
3 4.5
and so on...
If I type mean(trai
Basic question: I looked around quite a bit, still having a little trouble
manipulating the distance between the Y-axis label and the plot. In this
case, I would like to move the Y axis title closer to the plot.
# Data
tC <- textConnection("
Time Type1 Type2 Type3
1.3 .50 .10 .40
4.5 .45 .20 .35
This kind of problem can be addressed with branch and cut or similar
Operations Research methods.
Get a look at the CRAN task view "Optimization and Mathematical
Programming" specially the packages for Integer Programming and Mixed
Integer Programming.
Depending on the demands you have in yo
See the "alternating" parameter in the "scales" parameter list of
?xyplot. Presumably, something like:
xyplot( ...,
scales = list(..., alternating = 1),... )
is what you want.
-- Bert
On Fri, Jul 22, 2011 at 6:07 AM, marcel wrote:
> I notice that with this solution there are still y-axis tick
That's great! Thank you all!!
Final question: how can I edit permanently the .ps.prolog? Is the .First()
function an option?
Please, tell me every detail as I am a total dumb!
Many thanks
Gaetano
On Fri, Jul 22, 2011 at 11:27 AM, Ted Harding wrote:
> On 22-Jul-11 09:20:23, peter dalgaard wrot
Dear all,
Apologies for not being specific earlier.
The R version I am using is 2.12.2.
Everytime I try installing XMLRPC using the following command:-
> install.packages(repos = "http://www.omegahat.org/XMLRPC/XMLRPC_0.2-4.tar.gz";)
I get the following error
Warning: unable to access index
I notice that with this solution there are still y-axis tick marks on both
sides of the plot. Is there a way to remove the ones on the right side?
--
View this message in context:
http://r.789695.n4.nabble.com/Lattice-place-ticks-only-on-y-axis-tp3684094p3686638.html
Sent from the R help mailing
Dear all,
I need your help as I was not able to find out the solution.
The thing is-
I am having a code which is reading file with this code-
df=read.table("Case2.pileup",fill=T,sep="\t",colClasses="character")
but as am making a tool so that user can use it and can do analysis on his
file.But
> From: thern...@mayo.edu
> To: abouesl...@gmail.com
> Date: Fri, 22 Jul 2011 07:04:15 -0500
> CC: r-help@r-project.org
> Subject: Re: [R] Cox model approximaions (was "comparing SAS and R
> survival)
>
> For time scale that are truly discret
On Fri, 22 Jul 2011, Mitra, Sumona wrote:
Dear R users,
I am trying to download the XMLRPC package for R from
www.omegahat.org without any success. Any pointers?
The posting guide (see the footer of this message).
We have absolutely no idea what problems you encountered, what
platform you
Dear all,
randomisation or resampling is viewed by some as an alternative to
correction for multiple testing such as Bonferroni or Holm.
Is there any package implementing such an approach in microarray analysis?
Cheers,
j.
--
Dr. January Weiner 3 -
For time scale that are truly discrete Cox proposed the "exact partial
likelihood". I call that the "exact" method and SAS calls it the
"discrete" method. What we compute is precisely the same, however they
use a clever algorithm which is faster. To make things even more
confusing, Prentice int
On 07/22/2011 07:16 AM, David Winsemius wrote:
Context added back in:
SamiC wrote:
Hi,
So I am trying to plot my results of a model. what i have is the
majority
of the data between the values of 0 and 30, then one outlier at 80 and
another at 130. the model plots a nice line through the data
On 07/22/2011 01:42 AM, Youcheng Lin wrote:
Hello, everyone.
I am trying to show the correlation matrix using
color2D.matplot(). And I want to map (0,1) to (dark red to dark green).
But by default color2D.matplot() will map(min element of given matrix,
max element of given matrix) to (dark r
Dear R users,
I am trying to download the XMLRPC package for R from www.omegahat.org without
any success. Any pointers?
Sumona
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www
On 2011-07-21 17:29, askantik wrote:
Hi,
I've done some searching where others have had trouble with this error (or
"warning" actually), but I'm unable to solve my problem. I have a data
sheet with 13 columns and 36 rows. Each column has exactly the same number
of rows. I've created glms and
Dear all
I have the following code that works in paraller (and is pretty fast actually)
The only problem I still have is that every core just prints only once.
dimz<-1000
Shadowlist<-mclapply(1:dimz, function(i) {
print(sprintf('Creating the %d map',i));
Thank you guys for all the help. I appreciate!
--
View this message in context:
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Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
Hello,
i have following problem and I hope you can help me a little bit
My dataframe looks like:
df
a m d typvalue
1950 1 15 -4.1
1950 1 29 2.7
1950 1 33 -1.3
1950 1 45 -1.9
1950 1 52 0.2
1950 1 68 0.5
1951 1 1
Hello,
i have following problem and I hope you can help me a little bit
My dataframe looks like:
df
a m d typvalue
1950 1 15 -4.1
1950 1 29 2.7
1950 1 33 -1.3
1950 1 45 -1.9
1950 1 52 0.2
1950 1 68 0.5
1951 1 1
I tried with the option sRGB=F in the postscript() command, but I got the
error message "unused argument(s) (sRGB = F)"
I think that Peter's solution is the best one, as it consists, as far as I
understand, in changing the default content of .ps.postscript.
The problem is that I don't know how to
Dear all,
randomisation or resampling is viewed by some as an alternative to
correction for multiple testing such as Bonferroni or Holm.
Is there any package implementing such an approach in microarray analysis?
Cheers,
j.
--
Dr. January Weiner 3 -
On Fri, Jul 22, 2011 at 9:55 AM, pilchat wrote:
> I tried with the option sRGB=F in the postscript() command, but I got the
> error message "unused argument(s) (sRGB = F)"
>
True - because that option is not there, but to include one wopuld be an
option.
>
> I think that Peter's solution is th
On Jul 22, 2011, at 11:08 , (Ted Harding) wrote:
> On 22-Jul-11 08:02:40, peter dalgaard wrote:
>> [much snip]
>>
>> The .ps.prolog is not in C code but in an R character vector.
>
> While '?postscript' says (uder "Details:"):
>
>
> Most of the PostScript prologue used is taken from the
> R
On 22-Jul-11 09:20:23, peter dalgaard wrote:
>
> On Jul 22, 2011, at 11:08 , (Ted Harding) wrote:
>
>> On 22-Jul-11 08:02:40, peter dalgaard wrote:
>>> [much snip]
>>>
>>> The .ps.prolog is not in C code but in an R character vector.
>>
>> While '?postscript' says (uder "Details:"):
>>
>>
>>
On Fri, Jul 22, 2011 at 10:02 AM, peter dalgaard wrote:
>
> On Jul 22, 2011, at 09:04 , Rainer M Krug wrote:
>
> > On Fri, Jul 22, 2011 at 12:44 AM, Duncan Murdoch
> > wrote:
> >
> >> On 11-07-21 5:17 PM, pilchat wrote:
> >>
> >>> thank you guys for your reply.
> >>>
> >>> i was sure that it was
On 22-Jul-11 08:02:40, peter dalgaard wrote:
> [much snip]
>
> The .ps.prolog is not in C code but in an R character vector.
While '?postscript' says (uder "Details:"):
Most of the PostScript prologue used is taken from the
R character vector '.ps.prolog'. This is marked in the
output, a
Wonjae Lee wrote:
>
>> strptime('20110101 0900',"%Y%m%d %H%M")
> [1] "2011-01-01 09:00:00"
>> strptime('20110101 900',"%Y%m%d %H%M")
> [1] NA
>
> If I have a 3-digit hour like '900', please show me how to convert it to
> 09:00:00.
>
d = c('20110101 900', '20110101 1900')
d1= gsub(" (\\d\\d
2011/7/21 Abdullah OUESLATI :
>
> [...]
> I do not understand why you expect to get comparable results with SAS
> "discrete" and coxph "exact". They are two different approaches to
> handling ties (as Terry explained; of course, some comparability
> should be expected in "normal" cases).
> [...]
>
On Jul 22, 2011, at 09:04 , Rainer M Krug wrote:
> On Fri, Jul 22, 2011 at 12:44 AM, Duncan Murdoch
> wrote:
>
>> On 11-07-21 5:17 PM, pilchat wrote:
>>
>>> thank you guys for your reply.
>>>
>>> i was sure that it was related to changes in the generation of ps
>>> files with the latest R rele
On Jul 21, 2011, at 23:11 , David Winsemius wrote:
>
> On Jul 21, 2011, at 3:38 PM, zlu wrote:
>
>> Hi Peter,
>
> I'm not sure how many people still have 9 month old postings on their mail
> client and will know that Peter Dalgaard is the intended recipient.
>
>> Do you have any idea or code
On Fri, Jul 22, 2011 at 12:44 AM, Duncan Murdoch
wrote:
> On 11-07-21 5:17 PM, pilchat wrote:
>
>> thank you guys for your reply.
>>
>> i was sure that it was related to changes in the generation of ps
>> files with the latest R release.
>>
>> now the question is: how can i restore the old behavio
Dear All,
Sorry to bother. I'd like to estimate GARCH-M( GARCH IN THE MEAN) model. And
find that a package called rgarch could help. But I always can't instal
rgarch package successfully. I posted my problems and got some suggestions
but still failed. Does any one knows other method that could do G
Dear Dennins,
Many thanks for you reply. Sorry for the convoluted loops, but I am starting to
learn some programming and the loops are a bit complicated for me. Finally, a
collegue help me with the code, and one code that works is like follow:
Pma<-rep (1:40)
P<-seq(1,4, 1)
Plot<-rep(P,10)
dbh
> -Original Message-
> From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
> On Behalf Of Dennis Murphy
> Sent: Thursday, July 21, 2011 8:55 PM
> To: karena
> Cc: r-help@r-project.org
> Subject: Re: [R] Random number generation
>
> Hi:
>
> Here's one way using uniform
On Wed, Jul 20, 2011 at 10:43 PM, David Winsemius
wrote:
>
> On Jul 21, 2011, at 1:04 AM, Daniel Malter wrote:
>
>> http://mlg.eng.cam.ac.uk/dave/rmbenchmark.php
>>
>> I haven't ever tried it myself, but online sources suggest that Matlab
>> possibly gains speed by internally avoiding loops rather
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