Please look at
http://biostat.mc.vanderbilt.edu/twiki/pub/Main/StatReport/latexFineControl.pdf
for ways to do fine control of tabular data formatting via Sweave.
Bill Cunliffe wrote:
Hi there,
I've spent a while searching for ways of outputting table data from R in
presentable formats, su
Hello,
Can summary.formula.reverse be customized to allow other summary
statistics to be reported rather than the quartiles and mean +/- sd? The
"fun" option apparently doesn't apply when method='reverse'
Thanks
--
Abhijit Dasgupta, PhD
Statistician | Clinical Sci
Hello,
I'm running R 2.8.1 on Ubuntu Hardy. I'm trying to install tkrplot.
Using r-cran-tkrplot from the repository, I'm getting the following error:
> library(tkrplot)
Loading required package: tcltk
Loading Tcl/Tk interface ... done
Error in structure(.External("dotTcl", ..., PACKAGE = "tcltk
> From: Abhijit Dasgupta
> Date: October 31, 2010 1:30:02 AM EDT
> To: Matt Shotwell
> Subject: Re: [R] ForestPlot or similar
>
> I just did something very similar using ggplot's pointrange geom. In the
> following, I'm plotting hazard ratios, for which the nom
from where you are,
year.plot+ylim(0,0.1)
Abhijit
On Nov 2, 2010, at 9:57 AM, Shige Song wrote:
> Dear All,
>
> I am trying to graph a simple scatter plot where the x axis is year
> and the y axis is a percentage (percentage of infant death). Instead
> of plotting the raw data, I want to plot
You need to use a print statement
print(forestplot())
Lattice and ggplot2 need to be explicitly printed to get output into
jpeg. I believe Matt's function only provides the graphics object and
not the printed version.
Abhijit
On 11/2/2010 4:32 PM, Mestat wrote:
> Thanks Matt,
> I am having
The other way (in the same spirit as par(mfrow = ...) in base graphics) is to
use the grid.arrange function in the gridExtra package. See it's documentation
for examples.
On Nov 4, 2010, at 9:36 AM, ashz wrote:
>
> Dear All,
>
> I have this script:
>
> dat <- data.frame(Month = hstat$Date,
Another solution is using grid.arrange in the gridExtra package. This works
like the par(mfrow=...) command, but for grid-based graphics like lattice and
ggplot2
On Nov 8, 2010, at 1:19 PM, Marcus Drescher wrote:
> Dear all,
>
> I am trying (!!!) to generate pdfs that have 8 plots on one page
Thanks
On 11/16/2010 12:41 PM, Seth Falcon wrote:
> Hi Abhijit,
>
> [I've cc'd R-help to keep the discussion on the list]
>
> On Tue, Nov 16, 2010 at 8:06 AM, Abhijit Dasgupta
> wrote:
>
>> Seth,
>>
>> I was looking for something like this to
Santanu,
I second Phil's suggestion. sas.get is actually quite nice.
Another current option is using a command-line utility called dsread
(http://www.oview.co.uk/dsread/) to convert the sas7bdat file to a csv or tsv
format, which can then easily be read into R using read.table and its
deriva
I would think that the following code should work:
newcodesM = reshape(codesM, id=1)
If other variables in the data.frame are factors, reshape thinks all of them
are ID variables and tries to use all of them as "keys". Specifying the id
variable you want to keep (I used id=1 since "key" is in t
As for your second question, you could certainly do
newcodesM = transform(newcodesM, variable1 =
unlist(strsplit(variable,'\\.'))[1], variable2 = unlist(strsplit(variable,
'\\.'))[2], variable3 = unlist(strsplit(variable,'\\.'))[3])
though I'm sure there is a more efficient use of strsplit in t
I bogged about 3 possible solutions recently (statbandit.wordpress.com).
Possibly the 2nd most recent post.
Abhijit
On Aug 9, 2010 8:28 AM, "W Eryk Wolski" wrote:
Hi,
ESS replaces "_" by "<-". How can I switch off this feature?
I need to be able to type the underscore
Thanks
Eryk
--
Witold
Please read the Sweave documentation. The default is set to 0.8\textwidth.
You have to change a \SweaveOpt.
On Aug 17, 2010 7:00 PM, "Randall Wrong" wrote:
Dear R users,
I am using Sweave.
I would like to use the width option for the graphics :
\begin{figure}[h!]
\centering
\includegraphics[w
No, the \setkeys statement should be in the main body of the Sweave file,
not in the R code part.
On Aug 18, 2010 9:20 AM, "Randall Wrong" wrote:
Thanks Karen and Abhijit.
I have read the section 4.1.2 of the Sweave user manual. Actually the manual
lacks example code.
I would like to change th
This is a problem a few of us have experienced with snow, and there is a
discussion on the R-hpc list about this. No solution yet, as far as I
can tell.
Abhijit
On 9/7/2010 9:18 AM, bfoubert wrote:
> I'm working with snow and created a local cluster. So far, the same code has
> always worked (pl
Hi,
Is there a function similar to the layout function in base graphics in
either lattice or ggplot? I'm hoping someone has written a function
wrapper to the appropriate commands in grid that would make this easier :)
Abhijit
[[alternative HTML version deleted]]
__
Hi,
All of the components in the grid.arrange statement are from ggplot2 and
lattice, which are both in turn based on the grid package. What
grid.arrange is able to do is use the grid framework to arrange the
individual plots on a page. The base graphics are not based on grid, and
so won't wor
One possibility is:
library(doBy)
summaryBy(Rate~Source+Bin, data=Df, FUN=sum)
On 5/17/2011 12:48 PM, LCOG1 wrote:
> Okay everyone heres a likely softball for someone.
>
> Consider the following data frame:
>
> #Create data
> x<-rep(c(1,15),10)
> y<-rnorm(20)
> z<-c(rep("auto",10),rep("bus",10))
(cl)
When I run the same code in Windows R-2.11 (either 32-bit or 64-bit), R
hangs at cl<-makeCluster(6, type='SOCK') and no R processes are spawned.
I was wondering if others have encountered this problem, and any
suggestions on solving this would be greatly appreciated.
--
Abhiji
The tikzDevice package can do this.
On 3/2/2011 6:48 AM, Jonas Stein wrote:
> Hi,
>
> i want to make my plots look uniform in LaTeX documents.
>
> - usage of the same font on axes and in legend like LaTeX uses
>(for example "Computer Modern")
>
> - put real LaTeX formulas on the axes
>
> Hav
Seconded. Go to the support forum at www.rstudio.org and post your
question/bug/suggestion. Those folks have been excellent in their
response times and feedback.
On 3/4/2011 9:14 AM, Shige Song wrote:
> Why don't you post the question to the RStudio support forum? The
> folks there are quite re
You need to read up on the Wilcoxon signed-rank test and the output from
wilcox.test!!!
The confidence interval is of the difference of medians, which can
certainly be negative. In fact, your estimate is -33, and the confidence
interval is (-68, 0) which is reasonable.
The value of W is a posi
You need to read up on the Wilcoxon signed-rank test and the output from
wilcox.test!!!
The confidence interval is of the difference of medians, which can
certainly be negative. In fact, your estimate is -33, and the confidence
interval is (-68, 0) which is reasonable.
The value of W is a posi
or,
gsub('V','',vn)
On 8/10/2011 2:23 PM, Peter Langfelder wrote:
> On Wed, Aug 10, 2011 at 11:22 AM, Soyeon Kim wrote:
>> Dear All,
>>
>> I have vn variable
>>> vn
>> [1] "V300" "V376"
>> What I want to get is
>> 300 376
> as.numeric(substring(vn, 2))
>
> HTH
>
> Peter
>
> _
There is a recent blog post by Dirk Eddelbeutel on how to do something
similar using his Rcpp package and C++, with massive time improvements.
http://dirk.eddelbuettel.com/blog/
On 9/2/2011 12:43 PM, Noah Silverman wrote:
> Hello,
>
> I need to calculate a moving average and an exponentially wei
Please see the R Machine Learning Task View
(http://cran.r-project.org/web/views/MachineLearning.html) for a
starting point on decision trees.
On 9/14/2011 7:11 PM, Lorenzo Isella wrote:
> Dear All,
> I am recycling a previous email of mine where I asked some questions
> about clustering mixed
On Jun 23, 2011, at 4:42 PM, elisheva corn wrote:
> hi all-
>
> I am doing some research, have never used R before until today and need to
> understand the following program for a project.
> if some one could PLEASE help me understand this program ASAP i would
> GREATLY appreciate it (any syntax
Gabor's answer explains the error perfectly. You might want to look at the xlsx
package as well as the RODBC package if you're on Windows. RODBC is really
fast, if you can use it.
Abhijit
On Jun 23, 2011, at 2:00 PM, wwreith wrote:
> library(xlsReadWrite)
> mydata<-read.xls("file path", head
;red')+...
On Jul 7, 2011, at 6:16 PM, Christopher Desjardins wrote:
> Thanks that worked perfectly. One thing if I may. Is it possible to make the
> center dot red and the lines connecting the dots black?
>
> Thanks,
> Chris
>
>
> On Jul 7, 2011, at 5:10 PM, Abhijit
Sarah Goslee might want to chime in, but using odfWeave and appropriate
LibreOffice templates, you can generate beautifully formatted tables,
possibly in the style you wish, in LibreOffice, as well as add R figures.
The R2wd package (which has a proprietary component) will also generate
tables
So, I was playing around a bit on my Mac
LyX can do Sweave (see http://wiki.lyx.org/LyX/LyxWithRThroughSweave), and will
actually output HTML or ODT. However, on a cursory pass, I couldn't get the
graphics to translate, since the Sweave driver translates the graphics as .ps
or .pdf files,
You need to use either the lme4 or nlme packages for mixed models.
(There are some other possibilities as well). See
http://glmm.wikidot.com/faq for MUCH more detail
On 10/27/2011 7:19 PM, Molly Hanlon wrote:
> Hi All,
>
> I'm working with some SAS code to analyze an experiment set up as follows
I've had R on an Ubuntu system for about 18 months now, and getting R
up and running was a breeze. (I didn't realize it earlier, but Dirk
certainly gets my vote of thanks for his efforts in making this process
as easy as it is). Specially in terms of dependencies and the like, the
Ubuntu packa
The two sets of packages I use a lot for their utility functions and for
making my day-to-day analysis and reporting easier are Hmisc and Design
by Frank Harrell and {gdata,gmodels,gplots} by Greg Warnes. Frank's
packages have good documentation and cover a pretty good range of
regression metho
Type ?scale in R for the answer :)
Gundala Viswanath wrote:
Hi all,
I found this snippet in a gene expression
clustering code.
__BEGIN__
temp <- readLines("GSE1110_series_matrix.txt");
cat(temp[-grep("^!|^\"$", temp)], file="GSE1110clean.txt", sep="\n");
mydata <- read.delim("GSE1110clean.txt"
I believe read.xls has a colClasses argument. If you import using
read.xls(filename, colClasses='character')
everything will be imported as a string, and you can re-convert after
importing
Alberto Monteiro wrote:
I found a curious bug in read.xls. I don't know if it's reproducible.
It's like
Yes, see ?system
samitj wrote:
Hi,
Can we execute a unix shell command from within R shell?
thanks,
Sam
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PLEASE do read the posting guide http://www.R-project.org/post
One issue you will have is that, if you're using the same cutpoints for
the binning for all three tables, you'll probably get different numbers
of values from each column in each bin, so you won't be able to form a
"matrix". Of course, I might be misunderstanding what you mean by
"binning" :)
preciated.
>
>
> Thanks,
> Patrick
>
> [[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
library(Hmisc) has latex and html functions to convert the output into
latex (then to pdf, if you wish), and into html. A useful link for this
is http://biostat.mc.vanderbilt.edu/twiki/bin/view/Main/SweaveConvert
Bunny, lautloscrew.com wrote:
Hi everybody,
I have a simple regression summary
Won't scale(x,center=F, scale=x[1,]) do the trick?
--
Abhijit
Quoting Gabor Grothendieck <[EMAIL PROTECTED]>:
> This should work whether your data, x, is a data frame or a matrix:
>
> x / x[rep(1, nrow(x)),]
>
>
> On Thu, Jul 3, 2008 at 6:04 PM, Greg Kettler <[EMAIL PROTECTED]>
wrote:
>> Hi,
>
Hi,
I would like to use odfWeave to output some contingency tables (the
output of "table") into OOo. I know I can do this in LaTex (using
"latex" in the Hmisc package), but I was wondering if it is possible in
OdfWeave. My documentation to odfTable says inputs can only be vector,
matrix or dat
Another suggestion is:
blah = as.character(aa)
blah=gsub('[a-z]','0',blah,ignore.case=T)
aa = as.factor(blah)
I've found changing factors to characters rather than numeric is
generally safer.
Abhijit
Doran, Harold wrote:
> Perfect. My headache is gone. Thanks.
>
>
>> -Original Message-
you haven't escaped the \ for the \n, I think. Your line should be
cat("\\hline \\n"). You did escape the \ for hline, though.
Abhijit Dasgupta, Ph.D
Assistant Professor | Division of Biostatistics
Dept of Pharmacology and Experimental Therapeutics | Thomas Jefferson
University
1
you'll love Flexicon, a game which
> comb[[elided Hotmail spam]]
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting g
Hi Ravi,
One thing I tend to do is, when using read.table, specify the option
'colClasses='character''. This forces everything to be read as a
character. From there, as.numeric works fine, and you don't have to deal
with factors and reconverting them.
Hope this helps
Abhijit
Ravi Varadhan wro
My naive understanding of this (I switched to Ubuntu a year ago from
WinXP for similar reasons) is that Ubuntu as an OS uses less memory than
WinXP, thus leaving more memory for computation, swap space, etc. In
other words, Ubuntu is "lighter" than XP on system resources.
Abhijit
Doran, Harold
Or you could use the read.xls program in the gdata library that uses a
perl script underneath.
Charles Danko wrote:
> try:
> var <- read.table("weekly.txt", sep="\t", header=TRUE)
>
> Charles
>
> On Thu, Apr 24, 2008 at 3:29 PM, tzsmile <[EMAIL PROTECTED]> wrote:
>
>> i just want to read data
perl function underneath.
Abhijit Dasgupta, Ph.D
Assistant Professor | Division of Biostatistics
Dept of Pharmacology and Experimental Therapeutics | Thomas Jefferson
University
1015 Chestnut St | Suite M100 | Philadelphia PA 19107
Ph: (215) 503-9201 | Fax: (215) 503-3804
adasgupt (at) mail (dot
Multiple linear regression is handled by the function lm() in the
default installation of R. This takes inputs as lm(y~x1+x2+x3).
If you're going to be using R regularly, there are several books which
cover the basic statistical analyses available in R (and then some),
including those by Peter
of"
> >>> attr(summary(pb), "Pr(>F)")
> >> NULL
> >>
> >> __
> >> 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.
--
Abhijit Dasgupta
__
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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.
I believe this is determined by how much memory your computer has, not
particularly by R itself.
Mingjun Huang wrote:
Hello,
I am new to R, can anyone give me an idea of how R handle a large dataset
(e.g. couple of Gbytes)? Thanks a lot!
Best,
Mingjun
___
Won't diag(w)%*%co%*%diag(w) do it?
Dan Stanger wrote:
Hello All,
I have a covariance matrix, generated by read.table, and cov:
co<-cov(read.table("c:/r.x"))
XYZ
X 0.0012517684 0.0002765438 0.0007887114
Y 0.0002765438 0.0002570286 0.0002117336
Z 0.00078
Another possibility:
# Generate the months in sequential order:
m <- months(seq(as.Date('2000/1/1'), by='month',length=12),abbreviate=T)
# Concatenate the data
est=rbind(est31,est30,est28)
# generate the right order
ind <- match(substr(rownames(est),1,3),m)
# reorder the rows
est <- est[ind,]
BTW,
The line in question randomly decides which of the two correlated
columns to drop. If C1 and C2 are correlated you could drop either one,
the code decides which randomly, which is a principled way to do this.
This does mean that repeated runs of this code will give you different
results, but th
ty 300x300 fig1.pdf fig1.png")
--
Abhijit Dasgupta, PhD
Director and Principal Statistician
ARAASTAT
Ph: 301.385.3067
E: adasgu...@araastat.com
W: http://www.araastat.com
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ermine how 'm' relates to
'x$y'. Any tips/guidance is appreciated.
Mark T. W. Ebbert
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and provide
____
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.
--
Abhijit Dasgupta, PhD
Director and Principal Statistician
A
Look at the "qvalue" package by Dabney and Storey, which might satisfy
your last query
On 09/30/2010 06:40 PM, Jim Silverton wrote:
Does anyone has the Rcode for Gilbert's 2005 paper on the discrete FDR and
Tarone's 1990 paper? And Storey's pFDR?
Reading Gilbert's paper and references, and going on the web, I see that
Gilbert provided Fortran source code for his method as well as Tarone's
method. It might be possible to wrap this in R
On 09/30/2010 06:40 PM, Jim Silverton wrote:
Does anyone has the Rcode for Gilbert's 2005 paper on th
On 10/1/10 9:18 AM, lord12 wrote:
How do you call R methods from Java? I want to create a GUI using Swing in
Jaa that calls R methods in Java.
Look in the documentation for the rJava package
--
Abhijit Dasgupta, PhD
Director and Principal Statistician
ARAASTAT
Ph: 301.385.3067
E: adasgu
gt;
> __
> 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.
--
Abhijit Dasgupta, PhD
Director and Principal Statistician
LEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Abhijit Dasgupta, PhD
Director and Principal Statistician
ARAASTAT
Ph: 301.385.3067
E: adasgu...@araastat.com
W: http://www
.
Many thanks,
Chris Beeley,
Institute of Mental Health, UK
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ed, minimal, self-contained, reproducible code.
David Winsemius, MD
West Hartford, CT
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and provide commented, minimal,
The paste-y argument is my usual trick in these situations. I forget
that tapply can take multiple ordering arguments :)
Abhijit
On 08/24/2010 02:17 PM, David Winsemius wrote:
On Aug 24, 2010, at 1:59 PM, Abhijit Dasgupta, PhD wrote:
The only problem with this is that Chris's u
You haven't wrapped p in the print command, which is one of the ways to
make sure the plot gets printed when we need it.
print(p+geom_point(aes(size=3))) does the trick
On 08/26/2010 06:08 AM, Petr PIKAL wrote:
Dear all
I want to save several ggplots in one pdf document. I tried this
for (i
not data.
~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of
data.
~ John Tukey
-Oorspronkelijk bericht-
Van: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.o
-
Van: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] Namens Abhijit Dasgupta
Verzonden: dinsdag 7 september 2010 16:38
Aan: r-help@r-project.org
Onderwerp: [R] Something similar to layout in lattice or ggplot
Hi,
Is there a function similar to the layout function in base
gra
uld be nice not to have to 'copy and
paste' it into R on every startup:
http://www.r-statistics.com/wp-content/uploads/2010/02/Friedman-Test-with-Post-Hoc.r.txt
This would be for Ubuntu, if that makes any difference.
Cheers
--
Abhijit Dasgupta, PhD
Director and Principal St
I'm sure the legal ground is tricky. However, OpenOffice and LibreOffice
and KWord have been able to open the (proprietary) MS Word doc format
for a while now, and they are open source (and Libre Office might even
be GPL'd), so the algorithm is in fact "published" in Jeremy's sense,
and has b
Seconded
On 03/16/2011 05:37 PM, Bert Gunter wrote:
Ha! -- A fortunes candidate?
-- Bert
If this is really a time series, then you will have serious validity
problems due to auto-correlation among non-independent units. (But if you
are just searching for a way to pull the wool over the eyes of
You can easily do this by:
qplot(x=as.factor(sch),y=est, geom='point', colour='red') +
geom_pointrange(aes(x=as.factor(sch), y=est, ymin=lower.95ci, ymax=upper.95ci))+
xlab('School') + ylab("Value-added")+theme_bw()
On 07/07/2011 05:55 PM, Christopher Desjardins wrote:
Hi,
I have the followi
I think most of us are in a similar situation. I've usually kept mine in
a file which is sourced when I start R. The main problem I have with
this is that it clutters up my environment with a lot of stuff I don't
need all the time. I'm in the process of creating a custom package which
will be l
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