Hi,
I am new to R and AIC scores but what I get from coxme seems wrong. The AIC
score increases as p-values decrease.
Since lower AIC scores mean better models and lower p-values mean stronger
effects or differences then shouldn't they change in the same direction? I
found this happens with the da
Hello
I'm trying to make boxplots
However I'm having issues because my x axis is distance downstream on a
river. The boxplots function in r assumes the x axis are categorical
variables but I would like my boxplots to show true distance downstream just
as it would if I used the plots function. H
Hi,
I wanted to compute the value of the function ifn at certain values of n. But I
am receiving the following error when I was using the following code(given at
the end).
Error: evaluation nested too deeply: infinite recursion / options(expressions=)?
I feel that since the function Grx is
I've now tried Babtiste's code and my reaction is WOW! it shows me how to
do just what I need to do. I know enough to follow all the code but it
would have taken me a LOOO time to generate it. thank you Babtiste!
gary
On Sat, Aug 21, 2010 at 2:15 PM, baptiste auguie <
baptiste.aug...@g
Hi all,
I have searched for a long time to find out R program about V ariable S
election for GLMM (Generalized Linear Mixed Model).
I saw several great R packages for V ariable S election. IÂ also found several
R packages for GLMM. But, I did not find yet R package about V ariable S
e
Thanks.
On Aug 21, 2010, at 4:01 PM, RICHARD M. HEIBERGER wrote:
cbind(A=x, B=y)
On Sat, Aug 21, 2010 at 6:53 PM, r.ookie wrote:
Is there a way to rename the columns to something like A and B in the cbind
function?
x <- rnorm(n = 10, mean = 0, sd = 1)
y <- rnorm(n = 10, mean = 0, sd = 1)
cb
On 2010-08-21 16:53, r.ookie wrote:
Is there a way to rename the columns to something like A and B in the cbind
function?
x<- rnorm(n = 10, mean = 0, sd = 1)
y<- rnorm(n = 10, mean = 0, sd = 1)
cbind(x,y)
Unless I completely misunderstand your query, ?cbind tells you:
"... vectors or matri
cbind(A=x, B=y)
On Sat, Aug 21, 2010 at 6:53 PM, r.ookie wrote:
> Is there a way to rename the columns to something like A and B in the cbind
> function?
>
> x <- rnorm(n = 10, mean = 0, sd = 1)
> y <- rnorm(n = 10, mean = 0, sd = 1)
> cbind(x,y)
>
> ___
Is there a way to rename the columns to something like A and B in the cbind
function?
x <- rnorm(n = 10, mean = 0, sd = 1)
y <- rnorm(n = 10, mean = 0, sd = 1)
cbind(x,y)
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R-help@r-project.org mailing list
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many useful suggestions that I'll work on, especially babtiste's detailed
code. yes, I want something like Fig 1.7, or 7.18, or 7.22, but where the
x,y values are characteristics of the mini-histogram that is plotted.
attached (if it makes it through) is what i'm trying to do in R.
On Sat, Aug
Once you load
library(grid)
the rest works. Nice job :)
Dennis
On Sat, Aug 21, 2010 at 1:15 PM, baptiste auguie <
baptiste.aug...@googlemail.com> wrote:
> Hi,
>
>
> I think you could do it quite easily with lattice,
>
> library(lattice)
>
> latticeGrob <- function(p, ...){
> grob(p=p, ..., c
On Sat, 21 Aug 2010, Laura S wrote:
Dear all:
Any suggestions are much appreciated. I am looking for a way to make a
series of similar, but slightly modified, .r files.
My issue is automating making 320 .r files that change the for(i in 1:x) in
my base .r file (as well as other elements, e.g.,
I'm glad he asked that question, I found Barry's and your suggestion useful for
myself. Thanks! (R surprises me every day).
On Aug 21, 2010, at 1:12 PM, RICHARD M. HEIBERGER wrote:
The question isn't completely clear. I am guessing you want something
like Figure 1.7 or Figure 7.18 in Paul Murre
Hi,
I think you could do it quite easily with lattice,
library(lattice)
latticeGrob <- function(p, ...){
grob(p=p, ..., cl="lattice")
}
drawDetails.lattice <- function(x, recording=FALSE){
lattice:::plot.trellis(x$p, newpage=FALSE)
}
plots <- replicate(4, xyplot(rnorm(10)~rnorm(10),xlab=
The question isn't completely clear. I am guessing you want something
like Figure 1.7 or Figure 7.18 in Paul Murrell's book.
library(party)
example(ctree)
Rich
On Sat, Aug 21, 2010 at 3:40 PM, Bernard Leemon wrote:
> I want to make a graph where each element plotted is itself a graph. I can
On Sat, Aug 21, 2010 at 8:48 PM, r.ookie wrote:
> I'm trying to understand your question because when I think of a graph, I
> think of one canvas, on which, various functions are plotted (a function can
> be one point for example).
>
> So, when you say each 'element' do you mean each function?
>
We need a little bit of clarification. If you mean making a layout
elements that are themselves graphs (i.e.a page with four graphs) then
I like using ggplot2 for these types of things.
hth
Stephen Sefick
On Sat, Aug 21, 2010 at 2:40 PM, Bernard Leemon wrote:
> I want to make a graph where each
I'm trying to understand your question because when I think of a graph, I think
of one canvas, on which, various functions are plotted (a function can be one
point for example).
So, when you say each 'element' do you mean each function?
If so, then that seems to be asking how to plot a function
On Sat, Aug 21, 2010 at 3:01 AM, Gabor Grothendieck
wrote:
> On Fri, Aug 20, 2010 at 3:47 PM, Hall, Ken (CDC/OSELS/NCPHI)
> wrote:
I have also added some slightly simpler sqldf solutions here:
http://code.google.com/p/sqldf/#Example_16._Moving_Average
___
I want to make a graph where each element plotted is itself a graph. I can
see how to use par(fig=) and viewport to do that, but they require (i think)
me to do my own scaling as they are scaled to the graphics window. any
advice on which approach I should take (just bite the bullet and do my own
Just in case anyone might stumble across a similar question:
I am grateful to Claudio Agostinelli (one of the developers of the circular
package) who pointed me out to the arrows.circular function (which started me
learning a lot more about decorating plots).
Cheers, Tim
On Thu, Aug 12, 2010 at 0
I have personal experience with SAS and R people.
Agreed, there is a huge cultural gap between of SAS (and SAS users) and open
source / R users and projects.
In my experience frequently the closed source companies and users of their
expensive products who reside in their small, comfortable gh
On 08/21/2010 08:08 PM, Nick Torenvliet wrote:
> Hi all,
>
> I'm trying to do a simple curve fit and coming up with some interesting
> results I would like to get comment on.
> So as shown below, tsR is my explanatory and response is... well... my
> response.
>
> This same data in gnumeric gets f
I agree, instead of burning this guy, why not convert him? He may forever
resent R because of the hostility he's experienced here.
Some people have had negative comments towards me simply because I've asked an
obvious question but it has not affected me whatsoever. However, the negativity
could
If I may quote Rodney King, "Why Can't We All Just Get Along?"
I suggest the time is long past to end this thread and its vitriol.
John
John Sorkin
Chief Biostatistics and Informatics
Univ. of Maryland School of Medicine
Division of Gerontology and Geriatric Medicine
jsor...@grecc.umaryland.edu
--
On Sat, Aug 21, 2010 at 6:48 PM, Laura S wrote:
> Dear all:
>
> Any suggestions are much appreciated. I am looking for a way to make a
> series of similar, but slightly modified, .r files.
>
> My issue is automating making 320 .r files that change the for(i in 1:x) in
> my base .r file (as well as
Hi all,
I'm trying to do a simple curve fit and coming up with some interesting
results I would like to get comment on.
So as shown below, tsR is my explanatory and response is... well... my
response.
This same data in gnumeric gets fitted with the curve "response=10078.4 +
1358.67 * ln (explanat
Wow, it works! Thanks Erik. Your suggestion worked.
MikTek is indeed in the path, so I just modified the lines to:
junk <- system(paste("pdflatex ",latexFiles[i1]),
intern=TRUE)
On Sat, Aug 21, 2010 at 12:07 PM, Erik Iverson wrote:
> On 08/21/2010 11:02 AM, Juliet Hannah wrot
Dear all:
Any suggestions are much appreciated. I am looking for a way to make a
series of similar, but slightly modified, .r files.
My issue is automating making 320 .r files that change the for(i in 1:x) in
my base .r file (as well as other elements, e.g., the load(...),
setwd(...)). For smalle
Dear Prof. Ripley,
Thank you for the authoritative information. I will implement my own
file numbering scheme, but I'm surprised it was never asked for in all
those years. It seems like a useful feature, to know what your output
filename will be.
Thanks again,
baptiste
On 21 August 2010 18:27,
On Sat, Aug 21, 2010 at 3:32 PM, Donald Paul Winston
wrote:
> Good grief. Adding a report function is not going to make R less flexible.
> Don't
> you want to use a tool that's relevant to the rest of the world? That world is
> much bigger then your world. This is ridiculous.
>
> Looks like some
Hi:
On Sat, Aug 21, 2010 at 9:29 AM, Xiyan Lon wrote:
> Dear All,
>
> I have a model to predict time series data for example:
>
> data(LakeHuron)
> Lake.fit <- arima(LakeHuron,order=c(1,0,1))
>
This is what Lake.fit contains (an object of class Arima):
> names(Lake.fit)
[1] "coef" "sigm
On Sat, Aug 21, 2010 at 5:58 AM, Dennis Murphy wrote:
> Hi:
>
> In lattice, how does one handle separate graphical behavior for two
> different factors? In the xyplot below, the objective is to use the levels
> of one factor to distinguish corresponding shapes and colors, and the levels
> of the o
Dear All,
I have a model to predict time series data for example:
data(LakeHuron)
Lake.fit <- arima(LakeHuron,order=c(1,0,1))
then the function predict() can be used for predicting future data
with the model:
LakeH.pred <- predict(Lake.fit,n.ahead=5)
I can see the result LakeH.pred$pred and La
Just so this thread is complete on the record:
Filenames such as "Rplot%03d.png" are used in C code as format strings
when opening a file. Nothing in R subsequently knows the file name --
the file is accessed through the FILE* pointer.
Despite what baptiste 'assumes', it is clearly documente
Hi:
Henrique's solution is elegant, but if you want to summarize certain
features of the test (e.g., the value of the test statistic and its
p-value), then here's a different approach using packages reshape and plyr.
# Since your data in group C had a sample size of 2, I redid the data frame
usin
I believe this is specific to Windows, which you have nowhere
mentioned. And the preferred way to make a binary package there (see
'Writing R Extensions') has long been R CMD INSTALL --build and not R
CMD build --binary. So this is really a question about R CMD INSTALL
--build: --use-zip-data
On 08/21/2010 11:02 AM, Juliet Hannah wrote:
I have downloaded a file that I don't know how to describe correctly.
It contains R code and Latex, and I should be able to reproduce an
analysis by running an R script in this folder.
There is a line in the R script:
junk<- system(paste("/usr/tex
I have downloaded a file that I don't know how to describe correctly.
It contains R code and Latex, and I should be able to reproduce an
analysis by running an R script in this folder.
There is a line in the R script:
junk <- system(paste("/usr/texbin/pdflatex ",latexFiles[i1]),
You may find a close reading of ?merge helpful, particularly this
sentence: "If there is more than one match, all possible
matches contribute one row each" (so check that you don't have
multiple matches).
Hadley
On Sat, Aug 21, 2010 at 10:45 AM, Cecilia Carmo wrote:
> Hi everyone,
>
> I have be
Hi everyone,
I have been merging many big dataframes (about 8 rows
each) and I never had this problem, but now it happened to
me and I want to know if someone knows what could be
happening.
The final dataframe has many rows, an impossible number! I
have done edit(dataframe) and I saw that
I must repeat: "just show us what is the kind of report you want to
do, and you will perhaps
get a solution to reproduce it"
We still don't know what is the output of your report() function.
This, is ridiculous.
On Saturday, August 21, 2010, Frank Harrell wrote:
>
>
> On Sat, 21 Aug 2010, Donald
> Good grief. Adding a report function is not going to make R less flexible.
> Don't
> you want to use a tool that's relevant to the rest of the world? That world is
> much bigger then your world. This is ridiculous.
How big a world do you want , Google use R successfully , and it is
being used b
This would make a nice feature for the next R release---a parameter
that overrides the default choice for the number of ticks or labels on
the axes. since it has to be calculated already, this should not be
hard---spoken by someone without knowledge of the innards, of course.
/iaw
On Sat, Aug 21
Sweave/LaTeX is really not as bad as you think. I started using it and I'm
generating reports without a glitch. I'd consider giving it an honest effort.
On Aug 20, 2010, at 10:01 PM, Donald Paul Winston wrote:
Sweave and LaTex is way to much overhead to deal with. There should be a
built in sta
Yeah but, in considering Revolution, they do not offer a Mac version. Their Mac
version (community version) is just an older version of R---?? What was that
about? Their support is patchy and personally I would avoid them like the
plague (for other reasons not mentioned). I would however encoura
On Sat, 21 Aug 2010, Donald Paul Winston wrote:
Good grief. Adding a report function is not going to make R less flexible. Don't
you want to use a tool that's relevant to the rest of the world? That world is
much bigger then your world. This is ridiculous.
Looks like some people are complain
Try this:
lapply(split(x, x$site),
function(.x){
.xl <- split(.x[-(1:2)], .x$status)
mapply(t.test, .xl[[1]], .xl[[2]], SIMPLIFY = FALSE)
})
On Sat, Aug 21, 2010 at 11:15 AM, Alison Macalady wrote:
> I have a data.frame with ~250 observations (rows) in each of ~50 categories
> (columns). I wo
Good grief. Adding a report function is not going to make R less flexible.
Don't
you want to use a tool that's relevant to the rest of the world? That world is
much bigger then your world. This is ridiculous.
Looks like some people are complaining about me criticizing R and the people
who
de
thanks,
I'am not veru used with R!!
regards
2010/8/21 Henrique Dallazuanna
> Adel,
>
> read.table return a data.frame, Gavin showed, you need pass which column
> will be plotted to hist.
> scan return a vector.
>
>
> On Sat, Aug 21, 2010 at 10:59 AM, Adel ESSAFI wrote:
>
>> It works fine.
>>
>
-- Forwarded message --
From: Adel ESSAFI
Date: 2010/8/21
Subject: Re: [R] basic hist() question
To: Henrique Dallazuanna
It works fine.
Could you explain to me why it did not worked for read.table?
regards
Adel
2010/8/21 Henrique Dallazuanna
> Try this:
>
> a <- scan('dur
On Aug 20, 2010, at 1:53 PM, Laetitia Schmid wrote:
Hi Richard,
thank you very much. I got the results I needed. But I am still
interested to find out how it would work with a if-else function in
this context.
lapply(para, function(x) if (max(x) >= 4 ){1} else {0})
--
David
Best,
Laeti
Glad that I could help :)
Another thing that came to my mind ist that when you simply look at the values
of the different groups, they differ quite strongly in my opinion. They are
between two and three times higher in the second group than the ones from the
first group. Therefore it would be a
I have a data.frame with ~250 observations (rows) in each of ~50
categories (columns). I would like to perform t.tests on subsets of
observations within each column, with the subsets according to index
vectors contained in other columns of the data.frame.
My data.frame looks something like
On Sat, 21 Aug 2010, Donald Winston wrote:
The point is SAS has had simple reporting for 30 years. R apparently doesn't
have any. Why is it so hard to accept that a report function analogous to a
plot function would be a good thing?
R has had more advanced reporting features that SAS since
Hi Cedric,
Thanks a lot for your help, after calculating U value using the formula
from wikipedia I also found that the W given by R was in fact the U value
that I could directly compared to table of critical value.
Your advice were really good and useful. I would also be careful with the
conclusi
>michy har.mrc.ac.uk> writes:
>
> Hello,
> Im trying to create a heatmap with a dataset (38 x 15037) but get the
> error below:
>
> Error: protect(): protection stack overflow
> Execution halted
>
> or
>
> Error: C stack usage is too close to the limit
> Execution halted
>
> I tried to
Try this:
a <- scan('dureetasks.txt')
hist(a)
On Sat, Aug 21, 2010 at 10:32 AM, Adel ESSAFI wrote:
> Hi
> In fact, I searching for a simpler solution. I remember that I have done
> this without these functions (but I forgot)
> simply, is there any function that "force" R to take variable a as
Hi
In fact, I searching for a simpler solution. I remember that I have done
this without these functions (but I forgot)
simply, is there any function that "force" R to take variable a as table ?
Regards
Adel
> a=read.table("dureetasks.txt")
> summary(a)
V1
Min. : 1
1st Qu.:
You are correct. (I really should start using these reading glasses).
My apologies
On Sat, 21 Aug 2010 14:20:17 +0200, baptiste auguie
wrote:
I dunno, it doesn't seem to do it for me,
name = "Rplot%03d.png"
real.name = path.expand(name)
real.name
#[1] "Rplot%03d.png"
list.files(patt=".png
Hi:
In lattice, how does one handle separate graphical behavior for two
different factors? In the xyplot below, the objective is to use the levels
of one factor to distinguish corresponding shapes and colors, and the levels
of the other factor to perform level-wise loess smooths.
# Illustrative d
Donald Paul Winston wrote:
Sweave and LaTex is way to much overhead to deal with. There should be a
built in standard report() function analogous to plot().
Something like the following is necessary if you want real people to take R
seriously:
report(data=, vars=,
label=, by=,
sum=vectorOfColum
Your notes are not well thought out.
You'll find that r-help is a friendly place for new users that do not
come in with an attitude.
I once used SAS (for 23 years) and know it very well. I wrote the
first SAS procedures for a graphics device, percentiles,
logistic regression, and Cox regre
On Sat, Aug 21, 2010 at 3:35 AM, Tim Gruene wrote:
> On Fri, Aug 20, 2010 at 10:01:17PM -0700, Donald Paul Winston wrote:
>>
>> Sweave and LaTex is way to much overhead to deal with. There should be a
>> built in standard report() function analogous to plot().
>>
>> Something like the following is
I dunno, it doesn't seem to do it for me,
name = "Rplot%03d.png"
real.name = path.expand(name)
real.name
#[1] "Rplot%03d.png"
list.files(patt=".png")
#[1] "Rplot001.png"
sessionInfo()
R version 2.11.1 (2010-05-31)
i386-apple-darwin9.8.0
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.U
Frank E Harrell Jr Professor and ChairmanSchool of Medicine
Department of Biostatistics Vanderbilt University
On Sat, 21 Aug 2010, Donald Paul Winston wrote:
Sweave and LaTex is way to much overhead to deal with. There should be a
built in standard report() f
On Fri, Aug 20, 2010 at 10:01:17PM -0700, Donald Paul Winston wrote:
>
> Sweave and LaTex is way to much overhead to deal with. There should be a
> built in standard report() function analogous to plot().
>
> Something like the following is necessary if you want real people to take R
> seriously:
Now I understand. You need the name which png() does not return.
So I think you need to do (untested, I am struggling with the cat()):
makePlot = function(p, name="Rplot%03d", width=300)
{
real.name.png = path.expand(paste(name,'.png'sep='') # function needed here
real.name.pdf = path.expand(pas
On 08/21/2010 12:19 AM, josquint wrote:
>
> I am running and analysis of sequencing data uisng the EdgeR package. I have
> received the following error:
>
> Using grid search to estimate tagwise dispersion. Error: cannot allocate
> vector of size 307.3 Mb
>
> indicating the memory allocation is
My function needs to do two things with the filename:
First, create the plot file. For this, Rplot%03d is OK because it is
correctly interpreted by the graphics device.
Second, generate a text string referring to this filename. This is
where I need to convert Rplot%03d to, say, Rplot001. I am ass
Not sure what you want. Plot does that automatically. It seems to use
path.expand() to make the %03d expansion. Not that path.expand() is
documented to do this, but it seem to work.
Kees
On Sat, 21 Aug 2010 13:04:54 +0200, baptiste auguie
wrote:
Dear list,
I'm using the brew package t
Dear list,
I'm using the brew package to generate a report containing various
plots. I wrote a function that creates a plot in png and pdf formats,
and outputs a suitable text string to insert the file in the final
document using the asciidoc syntax,
<%
tmp <- 1
makePlot = function(p, name=paste(
On Sat, 2010-08-21 at 11:37 +0200, Adel ESSAFI wrote:
> Hi list
>
> I loaded the content of a file dureetasks.txt to variable a. This file
> contains an interger per line.
> when I print a vector, it displays correctly.
> however, when I try to print the histogram, I get this error message
>
>
On 08/21/2010 12:35 AM, ivo welch wrote:
...
(PS: Is there an easier way to tell R that I want a whole lot more
tick marks and/or labels than what it gives me by default?)
Hi Ivo,
I haven't been able to find a way to make the axis function print more
tick mark labels than it wants to. That's w
On 08/20/2010 09:42 PM, Barry Rowlingson wrote:
...
Client: “Time? Renaming files from *.jpg to *.eps takes time?!”
So _that's_ why Windows hides the file extensions.
Jim
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-h
Hi list
I loaded the content of a file dureetasks.txt to variable a. This file
contains an interger per line.
when I print a vector, it displays correctly.
however, when I try to print the histogram, I get this error message
> a=read.table("dureetasks.txt")
> hist(a)
Error in hist.default(a) :
On Sat, Aug 21, 2010 at 4:09 AM, Donald Paul Winston
wrote:
> The ability to generate standard detail, summary, cross-tabs, and control
> break reports is very important in government and corporate enterprises.
The great thing about standards, as a wise man once said, is that
there are so many
Just show us what is the kind of report you want to do, and you will perhaps
get a solution to reproduce it. Then, if you don't like the way to do that,
write your own code or don't use R, noone force you. The majority of R users
are satisfied with the way to generate reports, because it is flexibl
On 21-Aug-10 08:33:50, Gavin Simpson wrote:
> [...]
> If that is too much trouble then I'm sure SAS will welcome you
> with open arms (and then have one of those arms in down payment ;-)
>
> HTH
> G
... And also leave you with only one leg to stand on ... ;-)
Ted.
> [...]
-
On Fri, 2010-08-20 at 22:13 -0700, Donald Paul Winston wrote:
> People have been generating reports with a computer for many years. R is
> supposed to be an analytical engine. Report writing is fundamental to any
> kind of analysis tool. SAS has had several report procedures/functions since
> the v
On Fri, 2010-08-20 at 20:09 -0700, Donald Paul Winston wrote:
> I should not have used the terms 4GL and 3GL. I'm just looking for a
> "simple" way to create a report in R. It appears the R way to generate
> a report is to "roll your own". There is no report() function
> analogous to plot() (which
This is mentioned on page 70 of 'The R Inferno'.
On 20/08/2010 22:38, ivo welch wrote:
Dear R experts: this is probably correct behavior, but I do want to
point out that it is unexpected to someone not too well versed:
test=factor("A","B","C","A")
ifelse(test=="A", as.factor("A"), test)
[1]
I am running and analysis of sequencing data uisng the EdgeR package. I have
received the following error:
Using grid search to estimate tagwise dispersion. Error: cannot allocate
vector of size 307.3 Mb
indicating the memory allocation is too small. How would I change this
confiuration in R so
People have been generating reports with a computer for many years. R is
supposed to be an analytical engine. Report writing is fundamental to any
kind of analysis tool. SAS has had several report procedures/functions since
the very beginning(1960's?). SAS stands for Statistical Analysis System. D
Sweave and LaTex is way to much overhead to deal with. There should be a
built in standard report() function analogous to plot().
Something like the following is necessary if you want real people to take R
seriously:
report(data=, vars=,
label=, by=,
sum=vectorOfColumnNames>, title=, footer=,
pa
I should not have used the terms 4GL and 3GL. I'm just looking for a "simple"
way to create a report in R. It appears the R way to generate a report is to
"roll your own". There is no report() function analogous to plot() (which is
very good) to generate a report from a table of data. I did no
On Fri, Aug 20, 2010 at 3:47 PM, Hall, Ken (CDC/OSELS/NCPHI)
wrote:
> I am working on a simple pilot project comparing the capability of SQL,
> SAS and R to perform a rolling mean per the following instructions. I
> have completed the SQL and SAS analysis, so now it's R's turn.
>
> Calculate mean
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