On 19 December 2008 at 19:53, Bill Harris wrote:
| That did sound promising. I ran
|
| ,
| | sudo R CMD REMOVE -l /usr/lib/R/site-library/ lme4
| `
|
| and the files disappeared.
Still not a good idea. See /etc/R/Renviron -- the directory
/usr/lib/R/site-library is used by your Ubunt
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Bill Harris writes:
>> This shows you how you can get current R binaries with just one apt-get
>> command. With that, you then get to decide if you want the prebuild r-cran-*
>> packages (as e.g. r-cran-lme4) or whether you want to built them yourse
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Dirk Eddelbuettel writes:
> First off, see the R FAQ and the Ubuntu README on CRAN:
>http://cran.r-project.org/bin/linux/ubuntu/
Dirk,
Thanks; that looks promising!
> This shows you how you can get current R binaries with just one apt-get
> co
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"Steven McKinney" writes:
> This may just be version incompatibilities.
>
> A similar discussion recently transpired on
> r-sig-mixed-models, see e.g.
>
> https://stat.ethz.ch/pipermail/r-sig-mixed-models/2008q4/001526.html
Steven,
That did sound
On 19 December 2008 at 17:13, Bill Harris wrote:
| While I'm not an R expert, I have used R on Windows XP. Now I've moved
| to Ubuntu (Intrepid), and I'm trying to configure R to work with the
| Gelman and Hill _Data Analysis Using Regression and
| Multilevel/Hierarchical Models_. So far, it's n
Write a panel= function:
dataM <- structure(list(ID = c(1L, 1L, 1L, 1L, 45L, 46L, 46L, 46L, 46L
), Dose = c(0L, 0L, 0L, 0L, 30L, 30L, 30L, 30L, 30L), Visit = c(0.5,
1, 1.5, 2, 3, 0.5, 1, 1.5, 2), Value = c(-0.065802, 0.24085,
-0.22907, 0.24074, -0.81316, -0.20786, -0.29336, -0.55657, -0.21659
)),
This may just be version incompatibilities.
A similar discussion recently transpired on
r-sig-mixed-models, see e.g.
https://stat.ethz.ch/pipermail/r-sig-mixed-models/2008q4/001526.html
HTH
Steven McKinney
Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer R
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While I'm not an R expert, I have used R on Windows XP. Now I've moved
to Ubuntu (Intrepid), and I'm trying to configure R to work with the
Gelman and Hill _Data Analysis Using Regression and
Multilevel/Hierarchical Models_. So far, it's not working.
Hi -
How can I add different notes in different panels?
My data looks like
ID Dose Visit Value
110 0.5 -6.5802e-02
210 1.0 2.4085e-01
310 1.5 -2.2907e-01
410 2.0 2.4074e-01
... ... ... ... ...
270 45 30 3.0 -8.1316e-01
271 46 30 0.5 -
solved:
There was indeed a problem with exec rights in the /tmp dir as they were set
by my VPS host. I fixed it by creating a dir 'tempdir' in my homedir, and
giving it 777 rights. Then set the environment variable TMPDIR in R:
Sys.setenv(TMPDIR="/home/jeroen/tempdir");
install.packages("Cairo")
Try this:
> L <- list(data.frame(A=2, B=3, C=4),
+ data.frame(A=2, B=1, C=3, D=2, E=4, F=5),
+ data.frame(A=1, B=2, C=4, D=3, E=2, F=4, G=5, H=4, I=2))
> library(plyr)
> do.call(rbind.fill, L)
A B C D E F G H I
1 2 3 4 NA NA NA NA NA NA
2 2 1 3 2 4 5 NA NA NA
3 1 2 4 3 2 4 5 4 2
Hi Dimitri,
Not exceptionally elegant, but this should do it:
alldata <- as.data.frame(matrix(as.numeric(NA),nrow=99,ncol=9))
colnames(alldata) <- colnames(L[[?]])
( where ? is a 9-column data frame with the correct names )
foreach (i in 1:99) {
alldata[i,colnames(L[[i]])] <- L[[i]]
}
Hello, everyone!
I have list L that contains 99 data frames. All data frames have only
one row, but a different number of columns. Some data frames have 3
columns, some - 6 columns, and some - 9 columns. The names of the
first 3 columns are identical in all 99 data frames (e.g., A, B, and
C). The
On Fri, 19 Dec 2008, Heinz Tuechler wrote:
Dear David!
Thank you for your response. I like csv files, because in that case I can
easily compare different versions of similar data.frames. Similar in this
case means that I may add a column or change some transformation command for
one column.
Dear David!
Thank you for your response. I like csv files,
because in that case I can easily compare
different versions of similar data.frames.
Similar in this case means that I may add a
column or change some transformation command for
one column. With dput it's rather difficult, and
when
On Dec 19, 2008, at 2:04 PM, Heinz Tuechler wrote:
Dear All,
trying to write a data.frame, containing Surv objects to a csv-file
I get
"Error in dimnames(X) <- list(dn[[1L]], unlist(collabs, use.names =
FALSE)) :
length of 'dimnames' [2] not equal to array extent".
See example below.
M
On Fri, Dec 19, 2008 at 05:44:47AM -0800, kdebusk wrote:
> I have data sets from three different sites. None of the data sets are
> normally distributed and can not be log-transformed to a normal
> distribution. I would like to compare the data sets to see if any of
> the sites are similar to each
Call for Papers
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I use a CentOS 5.2 VPS to generate graphs through an R web-application. I
generate generate both pdf() and png() formats of the graphs. The pdf works
just fine and generates perfect pictures. However, the figures generated by
the png() (and also the jpg) device are messed up.
The weird thing is
Dear colleagues,
I have two questions about R that I cannot answer via google
searching:
1) Is there any way to speed up tab completion? This is near-instant in
bash, and occasionally takes upwards of 10 seconds in R. When I hit tab,
I've usually typed dataframe$ab or lst$ab or somethin
Dear All,
trying to write a data.frame, containing Surv objects to a csv-file I get
"Error in dimnames(X) <- list(dn[[1L]], unlist(collabs, use.names = FALSE)) :
length of 'dimnames' [2] not equal to array extent".
See example below.
May be, I overlooked something, but I expected
that also d
> -Original Message-
> From: r-help-boun...@r-project.org
> [mailto:r-help-boun...@r-project.org] On Behalf Of
> joseph.g.bo...@gsk.com
> Sent: Friday, December 19, 2008 7:41 AM
> To: Thomas Lumley
> Cc: r-help@r-project.org
> Subject: Re: [R] understanding lexical scope
>
> Thomas, Jeff
Check that your data partitions have the 'exec' flag set in /etc/fstab,
particulary the /tmp partition:
http://www.centos.org/modules/newbb/viewtopic.php?topic_id=1687&forum=31
Jeff
Jeroen Ooms wrote:
I am trying to install package "Cairo" on CentOS 5.2, but I keep getting this
error:
* Inst
I am trying to install package "Cairo" on CentOS 5.2, but I keep getting this
error:
* Installing *source* package 'Cairo' ...
/usr/lib64/R/bin/INSTALL: ./configure: /bin/sh: bad interpreter: Permission
denied
ERROR: configuration failed for package 'Cairo'
** Removing '/usr/lib64/R/library/Cairo
Thanks, Dirk.
I had read your very long conversation on the openMPI list but wasn't
sure if there was a resolution.
I had overlooked the fact that there is an hpc list, will post there
from now on.
Cheers,
Whit
On Fri, Dec 19, 2008 at 11:52 AM, Dirk Eddelbuettel wrote:
>
> Whit,
>
> On 19 Dec
Whit,
On 19 December 2008 at 10:17, Whit Armstrong wrote:
| Does anyone know if these errors can be safely ignored?
|
| [linuxsvr.kls.corp:16242] mca: base: component_find: unable to open
| osc pt2pt: file not found (ignored)
|
| this is on RHEL5 w/ openMPI 1.2.7
Yes. Hao (of Rmpi fame) and I
Thanks to all who replied! This is great! I am going to dig into this over
the holidays. I will post what I end up with...
Thanks again,
James Planey
Graduate Research Assistant
Department of Animal Biology
University of Illinois @ Urbana-Champaign
--
View this message in context:
http://www.
The plotrix package does this (). However, maybe only for lines.
The code below will plot as many graphs of different types one on another,
and it contains a plot with a different axis. The graphs are self scaling
for y axis and date axis.
I have included background code for setting up date data
How can I specify formula using nlme to estimate y=exp(X'B)/(1+exp(X'B)) ?
Justin BEM
BP 1917 Yaoundé
Tél (237) 99597295
(237) 22040246
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yes I did, sorry. obviously good for stats rather than general code but
still good bed time reading :-)
Simon.
- Original Message -
From: "June Kim"
To: "Simon Pickett"
Sent: Friday, December 19, 2008 3:28 PM
Subject: Re: [R] I need course in R
On Fri, Dec 19, 2008 at 7:50 PM, Si
Thomas, Jeff, Mark, Antonio,
Thank you for your answers. They have helped me clarify how R functions
work. They work differently from SAS functions (which SAS calls macros.)
If you know SAS, consider the following code:
*
%macro q(y);
data one;
outvar = &y. + &x.; output;
c
Does anyone know if these errors can be safely ignored?
[linuxsvr.kls.corp:16242] mca: base: component_find: unable to open
osc pt2pt: file not found (ignored)
this is on RHEL5 w/ openMPI 1.2.7
-Whit
On Mon, Dec 15, 2008 at 6:31 PM, Dirk Eddelbuettel wrote:
> On Mon, Dec 15, 2008 at 01:16:4
Hi Erich,
Can you explain why you don't want them? The philosophy behind the
legend code is to attempt to match the appearance of the geoms in the
plot as closely as possible. There are a few exceptions, like this
diagonal line, where the legends are slightly different to make it
easier to see c
On Fri, 19 Dec 2008, Dieter Menne wrote:
Jack Bowden mrc-bsu.cam.ac.uk> writes:
> dU1dtheta <- deriv(~ xi-(alpha0+alpha1*gi), c("alpha0","alpha1"))
> eval(dU1dtheta)
(Intercept)
-0.2547153
attr(,"gradient")
alpha0 alpha1
[1,] -1 0
I want to extract the output gradient values
Hi, I have the following problem with ggplot2: When I specify black contours
for bars in a barplot, ggplot automatically shows diagonal lines in the
legend boxes. Is there a way, to remove these diagonal lines?
Here's a simple example:
library(ggplot2)
df<-data.frame(x=gl(6,1),y=rnorm(6,10
Jack Bowden mrc-bsu.cam.ac.uk> writes:
> > dU1dtheta <- deriv(~ xi-(alpha0+alpha1*gi), c("alpha0","alpha1"))
> > eval(dU1dtheta)
> (Intercept)
> -0.2547153
> attr(,"gradient")
> alpha0 alpha1
> [1,] -1 0
>
> I want to extract the output gradient values of -1 and 0 but I don'
I have data sets from three different sites. None of the data sets are
normally distributed and can not be log-transformed to a normal
distribution. I would like to compare the data sets to see if any of
the sites are similar to each other, and would like something more
powerful than a non-parametr
Charlotte Bell sheffield.ac.uk> writes:
>
> Hi,
>
> I have spatially autocorrelated data (with a binary response variable and
> continuous predictor variables). I believe I need to do an autologistic
> model, does anyone know a method for doing this in R?
There are several approaches that you
Try AICtab in the bbmle package
> - Original Message -
> From: "Odette Gaston"
> To:
> Sent: Friday, December 19, 2008 11:26 AM
> Subject: [R] Akaike weight in R
>
>
>> Hi folks,
>>
>> Wondering how can I generate "Akaike weight" with R? I know the
>> description,
>> but is t
probably best just to change each variable one by one to the correct
classification after you have read the data frame in.
variable<-as.character(variable)
- Original Message -
From: "threshold"
To:
Sent: Friday, December 19, 2008 12:35 PM
Subject: [R] re ad.table
Hi , I want t
Hi,
I would like to estimate coefficients using poisson regression and then get
standard errors that are adjusted for heteroskedasticity, using a complex
sample survey data. Then I will calculate prevalence ratio and confidence
intervals.
Can sandwich estimator of variance be used when observa
Seems to work for me:
> x <- read.table(textConnection("a b c d e f
+ SPX LSZ 100 C 0 34.4
+ SPX LSZ 100 P 0 1.3
+ SPX LSZ 105 C 0 30.3
+ SPX LSZ 105 P 0 1.85
+ SPX LSZ
Hi , I want to use the read.table to the following example 'data.txt' format:
a b c d e f
SPX LSZ 100 C 0 34.4
SPX LSZ 100 P 0 1.3
SPX LSZ 105 C 0 30.3
SPX LSZ 105 P 0 1.85
SPX
You can also try the R for SAS and SPSS users at
http://rforsasandspssusers.com/
in case you are an existing user of analytics software...its quite user
friendly.
Regards,
Ajay
www.decisionstats.com
Douglas MacArthur - "We are not retreating - we are advancing in another
direction."
On Fri,
Hi
I am trying to use the deriv and eval functions to obtain the value of a
function , say "xi-(alpha0+alpha1*gi)" , differentiated with respect to
alpha0 and alpha1, in the following way
# for gi = 0
> dU1dtheta <- deriv(~ xi-(alpha0+alpha1*gi), c("alpha0","alpha1"))
> eval(dU1dtheta)
(I
Dear R users,
The nnet package includes the multinom method for the confint function.
The R Help file (?confint) for the generic function in the stats package
and the help files for the glm and nls methods in the MASS package
indicate that one can use the "parm" argument as "a specification of
I'm pretty sure you have to work it out yourself. Here is an example of how
you would tabulate the AIC weights from three models (check that my
calculations are correct before using this yourself!).
Basically model.name$aic will cut out the AIC values then write a formula to
calculate the weig
Odette
> Wondering how can I generate "Akaike weight" with R? I know the description,
> but is there any function to generate by R on the web-site or R library?
> I am using GLM or GLMM (family=binomial), so would be appreciated if you
> help me.
You could have a look at this.
http://bm2.genes.n
Hi folks,
Wondering how can I generate "Akaike weight" with R? I know the description,
but is there any function to generate by R on the web-site or R library?
I am using GLM or GLMM (family=binomial), so would be appreciated if you
help me.
Thanks for your contributions in advance,
Regards,
Odet
Ricardo L Gómez educ.umass.edu> writes:
> lm(formula = outcom ~ vari1 + vari2 + dummy1 + dummy2)
..
> but now, using this model, I need to calculate the predicted value of
> OUTCOM (only for one observation) , when vari1=8 and vari 2 =64, and
> also the confidence interval(the data set has
R is not as daunting as it first seems and you might get by without having
to get formal training.
Speaking as someone who taught themselves to use R for statistics, graphics
and data manipulation, I found that the "Introduction to R" book (the small
yellow one) and the numerous pdfs available
Dan Kelley wrote:
Is there a way a function ('parent', say) can manipulate the ...
argument, and then pass the manipulated value into another function
('child', say) that it calls?
What I'm trying to do is to use some plotting defaults within 'parent'
that are not part of parent's argument
xavier ordoñez wrote:
I am interested to take a course in R. Someone know of some course in europe
for the first semester of the next year?.
Yes, some, but hard to suggest commercial companies or universities and
certain courses, because it depends on so many facts:
- the languages you un
I am interested to take a course in R. Someone know of some course in europe
for the first semester of the next year?.
Happy Year
Thank you,
Xavier
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This really is a topic for R-devel ... see the posting guide.
On Fri, 19 Dec 2008, Graham Williams wrote:
(R 2.8.0 on Debian GNU/Linux sid)
?file.info contains:
mtime, ctime, atime: integer of class '"POSIXct"': file modification,
creation and last access times.
This implies that ct
(R 2.8.0 on Debian GNU/Linux sid)
?file.info contains:
mtime, ctime, atime: integer of class '"POSIXct"': file modification,
creation and last access times.
This implies that ctime is "file [...] creation [...] time"
Has R implemented ctime differently to Unix?
I understand, on Linu
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