michael watson (IAH-C michael.watson at bbsrc.ac.uk writes:
The data is counts of a particular
molecule in different cell types taken from the same 5 subjects. The
data are paired as they come from the same subject. The aim is to
determine whether the cell types differ in terms of the
ArunPrasad agurubar at uark.edu writes:
I am looking for a package in R which can help me in using the
imputation technique to find the missing values for my regression analysis.
The recommended search for imputation in r-project gave me 400 citations. I
assume you have tried
Dear Rglers,
when using a callback in rgl (Windows, if it matters)
http://finzi.psych.upenn.edu/R/library/rgl/html/callbacks.html
I would like to get the Asynchronous keyboard status (as least
Shift/Control, but preferably other key) to set markers in a plot.
getGraphicsEvents seems to be
Patrick Giraudoux patrick.giraudoux at univ-fcomte.fr writes:
Dear listers,
Here we have a strange result we can hardly cope with. We want to
compare a null mixed model with a mixed model with one independent
variable.
lmmedt1-lme(mediane~1, random=~1|site, na.action=na.omit,
Werner Wernersen pensterfuzzer at yahoo.de writes:
I am very happy that I have Sweave and R to write my
papers. But I still have to do some tables by hand
since I have not found out how I can customize the
latex tables produced by R further (I mainly use
xtable()). Like for instance, I have
Ben Bolker bolker at ufl.edu writes:
Perhaps read.fwf is what you want? (fwf stands for
fixed width format). You would have to work out the
field widths, but it would seem to be pretty straightforward).
[A little bit of extra verbiage will make gmane happier ...]
Ben Bolker
Christopher Hatherly Christopher.Hatherly at anu.edu.au writes:
I am trying to fit an ellipse equation to some spatial human factors data,
varying the major and minor axes randomly and specifying an exp~ variogram
for errors. Using normally-distributed random effects produces some -ve
Gallego Liberman, Matias m.gallego at isofoton.com writes:
When using grid.edit inside a pdf device it applies the changes on a
second plot, not erasing the first one.
..
DF-data.frame(A=c(1:12),B=c(1:12)*c(rnorm(12,mean=1)),C=2*c(1:12),D=re
p(c(1:4),each=3))
Irene Mantzouni ima at difres.dk writes:
I am trying to run a regression where the predictor values are not real
data but each is estimated from a different model. So, for each value I
have a mean and variance.
Which package/function should I use in this case?
See the Dobson example in
Eleni Christodoulou elenichri at gmail.com writes:
I am trying to draw a Kaplan-Meier curve and I found online that Kaplan -
Meier estimates are computed with a function called km in the event package.
Is there an update for that because when I choose to download packages in
R,. there is no
[Ricardo Rodriguez] Your XEN ICT Team webmaster at xen.net writes:
Please, is it possible to pass an username and a password to source() to
access code stored in restricted access web server?
I know I can use commands like...
[Ricardo Rodriguez] Your XEN ICT Team webmaster at xen.net writes:
But considering I am just newbie, could you point me to any example to
get this working? Thanks!
I was thinking of something like this (note: you must store PassEnv2.r on disk
as a file).
# File PassEnv.r
Steven Vamosi smvamosi at gmail.com writes:
In a nutshell, the experiment involved presenting females from two
groups (treatment, control) with an opportunity to mate with a virgin
male every 6 hours for 48 hours. Every female was presented this
opportunity at every time step (i.e., whether
Carla Rebelo crebelo at liaad.up.pt writes:
May you help me? I need to understand the function predict. I need to
understand the algorithm implemented, the calculations associated. Where
can I find this information?
In the documentation:
predict is a generic function for predictions from
Alexander Ovodenko alexander.ovodenko at gmail.com writes:
I have recently started learning R. I converted a Stata datafile into an R
image file, but I am unable to do anything with the data.
You probably forgot to read in the data; converting alone does not help.
Try ls() to get a list
Lassana TOURE lassana.toure at ier.ml writes:
Can someone help me how to set up a directory and load additional packages
at the startup than I do not have to do it each time I go to R session.
It depends on your system and the type of installation, but searching for
.Rprofile in the manuals
sich at gmx.de writes:
I am interested in using R for machine learning (supervised classification).
Currently, I have been investigating especially the rpart, tree, and
randomForest package, and have
achieved first results.
are there any experiences, how the learned classificators could
Ng Stanley stanleyngkl at gmail.com writes:
I am faced with a strange problem. My picture file is empty when the
following statements were run from R script. But the picture file shows up
correctly, when the commands are individually run from Rgui.
png(file=histogram_correlation.png, bg =
Ben Fairbank BEN at SSANET.COM writes:
When preparing a series of histograms I found that hist was combining
the two lowest categories or bins, 1 and 2. Specifying breaks, as
illustrated below, resulted in the correct histogram:
values - sample(10,500,replace=TRUE)
hist(values)
Martin Maechler maechler at stat.math.ethz.ch writes:
The consequence of this will be that .. before the weekend ..
only __e-mail addresses__ subscribed to R-help will be allowed to post to
R-help without any moderation, and we are even considering outright
rejection all non-subscribers,
Duncan Murdoch murdoch at stats.uwo.ca writes:
It's worth mentioning that you can be subscribed and have no mail
delivered: just check Disabled in the mail delivery options on the
subscription page. That's what anyone using gmane should do, so that
they can still post without requiring
hadley wickham h.wickham at gmail.com writes:
Unless nabble/gmane have hefty anti-spam protection in place, spammers
will misuse those services. A centralised target is just too
tempting.
Works well for gmane. You must be subscribed, and you have to enter a word from
a blurbed
Falco tinnunculus kestrel78 at gmail.com writes:
How do I run interaction between to categoric variables in lme()?
I tried this:
lmefit1- lme(Handling ~Mass+factor(Prey)+factor (Decap)+
factor(Prey)*factor(Decap), random = ~ 1 |Place, data=nestling1)
Error in MEEM(object, conLin,
Rick DeShon deshon at msu.edu writes:
..
When I use nlsList code that is virtually identical to the example in
the doc file I get the following error.
..
Error in nlsList.formula(RT ~ SSasymp(trial, Asym, R0, lrc),
data = df.group, :
Data must be a groupedData object if
Nuno Prista nmprista at fc.ul.pt writes:
Is there on R a package containing Maximum entropy spectral analysis
function?
Burg and Yule-Walker are in spec.ar(stats)
Dieter
__
R-help@r-project.org mailing list
Daniel S. Ott dott at uvm.edu writes:
I have been working with a mixed effects model in R where I have
a lot of fixed effects with a lot of variables. When I use the
summary command I can only view the end of the output with the
intraclass correlations and distribution of
Dan Ott ott at unbc.ca writes:
My name is Dan Ott and I recently learned R mainly for the purposing
of running ANOVA's and linear regression. I just started using a data
set where I want to run a repeated measures anova as well as a
split-plot anova. My question is: What is the syntax
hadley wickham h.wickham at gmail.com writes:
qplot(vals, ..density.., data = data.frame.A, geom=histogram, facets
= factor.1 ~ factor.2, binwidth = 1) + geom_density(data=data.frame.B)
uhh.. how should I understand y (?)=..density..
Dieter
__
array chip arrayprofile at yahoo.com writes:
(Real names are prefered here)
I am trying to test some contrasts, using glht() in
multcomp package on fixed effects in a linear mixed
model fitted with lme() in nlme package. The command I
used is:
data=dat)
glht(dat.lme, linfct = mcp(type
Dear baseRs,
I recently made a mistake when renaming data frame columns, accidentally
creating an NA column. I found the following strange behavior when negative
indexes are used.
Can anyone explain what happens here. No workarounds required, just curious.
Dieter
Version: Windows, R version
Delphine Fontaine delphine.fontaine at genexion.com writes:
I would like to create a new data frame composed of 2 columns of another
data frame. But it does not give me what I want...
casesCNST[1:10,]
case X1 X2 X3 X4 expected
1A1 0 0 0 0E
2A2 0 0 0 1C
Dear R2008,
In Windows 2000, I used the following shell extension to allow right-click
rgui start in a directory (assuming rgui.exe is on the path:
-
REGEDIT4
[HKEY_CLASSES_ROOT\Directory\shell\Run R]
[HKEY_CLASSES_ROOT\Directory\shell\Run R\command]
@=Rgui.exe --no-restore --no-save
Gabor Grothendieck ggrothendieck at gmail.com writes:
How are you starting up the command line? If I position myself to the right
side of the Windows Explorer window in Vista and press Shift-RightClick and
then choose Open Command Window Here then the command window
comes up instantaneously
Nicolas Ris Nicolas.Ris at sophia.inra.fr writes:
I am trying to analyse the data of the box 10.5 in the Biometry from
Sokal and Rohlf (2001) using R. This is a three-level nested anova with
equal sample size : 3 different treatments are compared ; 2 rats (coded
1 or 2) / treatment are
Milton Cezar Ribeiro milton_ruser at yahoo.com.br writes:
I would like to test if are there some significant orientation of frequencies
on a polar analysis.
Check packages CircStats and circular.
Dieter
__
R-help@r-project.org mailing list
Deepayan Sarkar deepayan.sarkar at gmail.com writes:
Try looking at the first example in
http://dsarkar.fhcrc.org/lattice/book/Chapter12-Interaction/edited.R
for inspiration.
May I suggest to use
http://dsarkar.fhcrc.org/lattice/book/figures.html
instead. Nice.
Dieter
Tony zeng xh.along at gmail.com writes:
I am meetting one problem.I am estimating the variability of a
population using one sample.I must do two-side and one-side hypothesis
test,and estimate the confidence interval,But I don't know which
function I can use !
You should describe
Ptit_Bleu ptit_bleu at yahoo.fr writes:
...
Is there a way to pass arguments to Sweave like Sweave(myfile.rnw,
namevar=Device2) and it will change namevar by Device2 into the file
myfile.rnw before creating the .tex file ?
Or is it possible to do it via another language, that is: loading the
Bin Yue leffgh at 163.com writes:
After reading the following two links:
http://luna.cas.usf.edu/~mbrannic/files/regression/Logistic.html
http://www.tufts.edu/~gdallal/logistic.htm
I've known the mathematical basis for logistic regression.However I am
still not so sure about the
Mark Wardle mark at wardle.org writes:
I'm having difficulty getting access to data generated by survfit and
print.survfit when they are using with a Cox model (survfit.coxph).
I would like to programmatically access the median survival time for
each strata together with the 95% confidence
Todd Remund tkremund98 at hotmail.com writes:
I know that there is a function, (spectro3D), that produces the Power
Spectrogram. Are there R functions
that produce the Frequency Spectrogram and the Phase Spectrogram? Thank you
for your time.
fft in stats gives you all you need, possibly
Michael Kubovy kubovy at virginia.edu writes:
This is one of the cases where I wish there were a function that
exercised all the arguments of a graphics function by visualizing
the effect of changing two or three levels of each argument (one by
one, of course). This might have the
정 태훈 hoontaechung at gmail.com writes:
I got a reply for my previous several postings saying that I was
spamming the r-help mailing list.
I am very sorry to all subscribers if I did that.
But I've been reposting my message to the mailing list several times
because I didn't know whether
Michael Kubovy kubovy at virginia.edu writes:
Dear r-helpers,
How do I tell xYplot() and Key() that I want the labels in italic?
Key(x = 0.667, y = 0.833, other = list(title = expression(italic(v)),
cex.title = 1,
labels = c(expression(italic(b)), expression(italic(c)),
Stéphane CRUVEILLER scruveil at genoscope.cns.fr writes:
I would like to know whether it is possible to draw several
stacked barplots (i.e. side by side on the same sheet)...
my data look like :
Cond1 Cond1' Cond2 Cond2'
Compartment 111,812,05
Douglas Bates bates at stat.wisc.edu writes:
(lmer)
The default is PQL, to refine the
starting estimates, followed by optimization of the Laplace
approximation. In some cases it is an advantage to suppress the PQL
iterations which can be done with one of the settings for the control
Michael Hoffman b3i4old02 at sneakemail.com writes:
I would like to be able to do something like this:
echo=F,fig=T,width=mywidth=
...
@
with mywidth set in a previous code chunk. Is there a way to do this in
Sweave?
Not in the , but you could set a hook for fig:
From
Richard M. Heiberger rmh at temple.edu writes:
I think this does what you are asking for. It should be
relatively easy to write a method
latex.ftable()
based on this. One or two row.vars and one or two col.vars
should be straightforward (with n.rgroup and n.cgroup used
for the
cathelf cathelf at hotmail.com writes:
Sorry for bothering your guys again. I am trying to use par to put 6
figures into 3 rows and 2 columns. My code is:
op - par(mfrow = c(1, 2))
xyplot(x1+x2+x3 ~ y, data=resulta, type=l, pch=LETTERS[1:3], lty=c(1:3),
main=For k=3, theata1=1)
Catherine A. Holt caholt at u.washington.edu writes:
I am modeling the effects of an environmental variable (X) on fish recruitment
(Y) for several,
ecologically related species (i) using a mixed-effects model. The linear
relationship between X and Y
includes a fixed effect that is common
Felipe Carrillo mazatlanmexico at yahoo.com writes:
Hi:I recently started using the melt function and
found that it is very useful and powerful,however I
can't seem to find the way to change the default
column header value to my custom column name.
melted data are data frames. You can
Dieter Menne wrote:
I tried to create an ftable lookalike of the following data set in
LaTeX/Sweave
with summary(formula,..), but I could not get it to work for count tables;
numeric tables work fine.
summary(formula,...,fun=table) does not give the full cross breakdown.
Frank E
Tyler Smith tyler.smith at mail.mcgill.ca writes:
I'm trying to figure out how anova works in R by translating the
examples in Sokal And Rohlf's (1995 3rd edition) Biometry. I've hit a
snag with planned comparisons, their box 9.4 and section 9.6. It's a
basic anova design:
how to do
Petr PIKAL petr.pikal at precheza.cz writes:
I just encountered a strange behaviour trying to plot lattice xyplot with
dates on x axis
xyplot(rnorm(10)~seq(as.Date(2000/1/1), by=month,
length=10)|sample(1:2, 10, replace=T))
Warning message:
is.na() applied to non-(list or vector)
Caio Azevedo cnaberdl at gmail.com writes:
When I try to save a plot in a PDF format, using R 2.6.0 for windows, it
appears the following message
Error: Invalid font type
Warning messages:
1: font family not found in PostScript font database
2: font family not found in PostScript font
Benjamin Zuckerberg bzuckerb at syr.edu writes:
After having produced a cumulative distribution using ecdf, I would
like to extract the exact x-value for a given percentile. For example
I can ascertain the 1st and 3rd quartile using the summary function:
cawa.cdp - ecdf(cawaocc$LEFF80)
Vlad Skvortsov vss at 73rus.com writes:
Let's say I have vector x with positive integer values ranging from 1 to
N. I need to obtain another vector y of size N where y[i] contains the
number of times value i occurs in x. It is in a sense similar to hist()
(with appropriate number of breaks)
apsawant apsawant at yahoo.com writes:
I am trying to run a simple example script to calculate AOV.
Below is the script file (aov.R) I am trying to execute:
aov.R
--
aov(rt - shape * color + Error(subj/(shape * color)), data=Hays.df)
summary(aov(rt - shape * color +
Heidemeier Dr, Joachim joachim.heidemeier at uba.de writes:
...
For the analyses of the data I want to group one column (like the
classes in a histogram).
So I'd like to add one column with the center of each group with width=2
for an x value in the interval of the class.
So the output
Dimitri Liakhovitski ld7631 at gmail.com writes:
I just installed R 2.6.0 (had R 2.5 before).
Here is my problem. Usually, when I work with R I first go to
File-Change dir and browse to a folder that seats OUTSIDE of the
folder C:\Program Files\R\R-2.6.0 and then create my script there
Pedro Mardones mardones.p at gmail.com writes:
I would like to try to implement a big series of nested loops in a C
code and then call it from R; however I'm not familiar with C
programming. Does anyone know about some sort of reference I can use
that help me to translate my code to C? (I'm
Charles C. Berry cberry at tajo.ucsd.edu writes:
As the posting guide suggests, you could perform a search using
RSiteSearch(repeated measures, restric=functions)
say.
That generates an inventory of functions that pertain to repeated
measures designs.
The problem I noted in practice
Chung-hong Chan chainsawtiney at gmail.com writes:
I have plot the PDF of t distribution with df = 74.
curve(dt(x,df=74),from=-4, to=4)
how can I shade the area under curve (for example, col=red) from t=+- 1.996?
If you could used lattice plots instead, below is a modified version of the
Gang Chen gangchen at mail.nih.gov writes:
Suppose I have a mixed-effects model where yij is the jth sample for
the ith subject:
yij= beta0 + beta1(age) + beta2(age^2) + beta3(age^3) + beta4(IQ) +
beta5(IQ^2) + beta6(age*IQ) + beta7(age^2*IQ) + beta8(age^3 *IQ)
+random
Dieter Menne dieter.menne at menne-biomed.de writes:
Trying again with a minimal example. When I run the following batch file under
Windows 2000, R 2.6.0, I get the error message below. Rtools are installed and
at the front of the path.
rem Begin test package; File test.cmd
rem Check
Dear List,
After having installed R 2.6.0/Windows 2000, my trusted command script to build
and install my package fails with an error message I do not understand. I have
installed a fresh copy of Rtools, and made sure that these are the first on the
path.
For testing, I am using a package version
Gabor Grothendieck ggrothendieck at gmail.com writes:
Look at the xtable package and latex in the Hmisc package.
On 10/21/07, Jesse D Lecy jdlecy at maxwell.syr.edu wrote:
..
I am new to R and I am trying to figure out how to print text output from an
operation like table() to a pdf file.
Irene Mantzouni ima at difres.dk writes:
I am trying to fit a 2-level hierarchical lme().
I can extract ranef() and coef() without problems for levels=1:2.
However, when it comes to resid() at level=2, the resulting list has some
unnamed entries (label=NA). I
checked with my data (NAs have
hadley wickham h.wickham at gmail.com writes:
On 10/10/07, Christoph Krammer ck at altaica.de wrote:
is there a possibility to set default options to qplot?
Sure. It's a bit of hack, but:
GeomPoint$default_aes - function(x) aes(shape=19, colour=red, size=5)
will do what you want.
azadeh sadeghian a.sadeghian1386 at yahoo.com writes:
I am student M.S. statistics in department statistics . I am working in the
function nls in the [R 2.3.1]
You should update to a more recent version of R (2.6.0 is current)
with 246 data and want to fit the exp model to vectors( v and
Tom Sgouros tomfool at as220.org writes:
What I have is twelve bins of data, and the population
in each bin. The top bin is open-ended, and the whole distribution is
more or less poisson-ish.
I can think of a couple of ways to fake this ok, but is there a real R
way to do it?
sun flyhyena at yahoo.com.cn writes:
Another question is, I want to measure the main effects and at least two
interactions, variables are factors, how do I ensure this in formula,
~.+v1:v2 +v3:v4 ?
I would give something like the following a try (since you did not tell use
where
as expected under Windows. The
path is correct, and Rblas.dll is present
I made a copy of Rblas.dll in \bin naming it Rblas, and got it to work.
I post this here since I don't know if this a problem of lme4 or rather the
Windows-R-build.
Dieter Menne
__
R
On 9/28/07, Anouk Simard Anouk.Simard at bio.ulaval.ca wrote:
I would like to extract the fitted values from a model using LMER but
only for the fix portion of the model and not for the fix and random
portion (e.g it is the procedure outpm or outp in SAS).
..
Quoting Douglas Bates bates at
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