Dear R-users,
My question is how to get right F tests for random effects in random effect models (I hope this
question has not been answered too many times yet - I didn't find an answer in rhelp archives).
My data are in mca2 (enc.) :
names(mca2)
[1] LigneePollinisateur Rendement
First a general comment on posting style, could you please be more specific
about where the error occurs as without this it is very difficult to
identify what the problem is.
Now concerning your problem. When I tried the code I posted yesterday I
thought it worked fine. I've tried it again now
Hi
quite near
using aggregate it is possible to reach what you want
TAB3 - with(TAB1, aggregate(Number,
list(Name_singular=Name), sum, na.rm=TRUE))
see
str(TAB3)
`data.frame': 3 obs. of 2 variables:
$ Name_singular: Factor w/ 3 levels A,B,C: 1 2 3
$ x: num 3 5 0
HTH
Petr
dear community,
I am a beginer in R , and can't predict with logistic model in package
logistf,
could anyone help me ? thanks !
the following is my command and result :
library(logistf)
data(sex2)
fit-logistf(case ~ age+oc+vic+vicl+vis+dia, data=sex2)
predict(fit,newdata=sex2)
Error in
Sorry,
Actually I gave my data in an image file (.RData) - I've just checked my send
emails.
Am I to give data in another format, such as text ? Here are they in text
(.txt).
The output are :
summary(aov1 - aov(Rendement ~ Error(Pollinisateur * Lignee), data = mca2)
Error: Pollinisateur
Hi
I figured it out.
if I use install.packages(..., method=wget) it works
but if I use the default method, it doesn't.
Rainer
Rainer M. Krug wrote:
Hi
I installed R 2.2.0 from source and want to use install.packages but it
doesn't work.
http_proxy is set to http://proxy.sun.ac.za:3128
Thanks to everyone for your help.
Yuup, this is my stupid word secs which I put there.
Usually I get to run simulation on my machine only a few seconds.
Now, I recode my timestamp, but still I don't know how to make
x days, x hours, x minutes, x seconds.
Best wishes, Muhammad Subianto
On this
Sorry for reposting, but even after extensive search I still did not
find any answers.
using:
summary(aov(pointErrorAbs~noOfSegments*turnAngle+Error(subj/(noOfSegments+turnAngle)),
data=anovaAllData ))
with subj being a random factor and noOfSegments and turnAngle being
fixed factors, I get
Hi
I installed R 2.2.0 from source and I have the packages for tcl and tk
installed on my system, but the package tcltk says, when I try to load
the library tcltk: Tcl/Tk support is not available on this system.
Are there any settings / variables which I have to set so that R
recognises that
Does p-value on Box.test(data,lag=l) returns probability, that
H0: cor(1)=cor(2)=..=cor(l)=0 holds?
Thanks.
[[alternative HTML version deleted]]
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PLEASE do
Hi,
Give a look to the help page:
? Box.test
Compute the Box-Pierce or Ljung-Box test statistic for
examining the null hypothesis of independence in a
given time series.
See also:
http://finzi.psych.upenn.edu/R/Rhelp02a/archive/27265.html
Regards.
Vito
You wrote:
Does p-value on
It's probably toadally elementary (and, like, duh) but
I can't figure out why the following doesn't work:
curve(function(x){qnorm(x,4,25)},from=0,to=1)
I get the error:
Error in xy.coords(x, y, xlabel, ylabel, log) :
'x' and 'y' lengths differ
But if I do
Hi,
I cannot seem to change the default binning settings for the x axis
successfully using hist(). I have tried using axis() in conjunction with
xaxt=n, but I keep getting the error message
Warning message:
parameter vect could not be set in high-level plot() function
can anyone help please?
On 10/27/2005 9:50 AM, Rolf Turner wrote:
It's probably toadally elementary (and, like, duh) but
I can't figure out why the following doesn't work:
curve(function(x){qnorm(x,4,25)},from=0,to=1)
I get the error:
Error in xy.coords(x, y, xlabel, ylabel, log) :
Hi All,
In R, can one comment out a block of code at once instead of using # one line
at a time? Say, in SAS, one can use /**/ to comment out many lines.
Thanks,
Johnny
[[alternative HTML version deleted]]
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R-help@stat.math.ethz.ch
On Thu, 27 Oct 2005, Li,Qinghong,ST.LOUIS,Molecular Biology wrote:
In R, can one comment out a block of code at once instead of using #
one line at a time? Say, in SAS, one can use /**/ to comment out
many lines.
Try RSiteSearch(comment multiple lines).
Note that R-aware editors can do
hi,
i have a vector like :
x-c(1,15,30,45,60,90,115)
i know that step by step i have always more than 10
min(diff(x)) =11
i want to add for each value a sequence of value:value+9
result should be :
1 2 3 4 5 6 7 8 9 10 15 16 17 18 19 20 21 22 23 24 30 31 (...) 39 45 46
(...) 54 60 61
Here's one way:
unlist(lapply(x, function(x) x:(x+9)))
[1] 1 2 3 4 5 6 7 8 9 10 15 16 17 18 19 20 21 22
23 24
[21] 30 31 32 33 34 35 36 37 38 39 45 46 47 48 49 50 51 52
53 54
[41] 60 61 62 63 64 65 66 67 68 69 90 91 92 93 94 95 96
Did you try fit$predict?
Elizabeth Lawson
jinlong li [EMAIL PROTECTED] wrote:
dear community,
I am a beginer in R , and can't predict with logistic model in package
logistf,
could anyone help me ? thanks !
the following is my command and result :
library(logistf)
data(sex2)
fit-logistf(case
On 27 Oct 2005 17:04:21 +0200, Yves Magliulo [EMAIL PROTECTED] wrote:
hi,
i have a vector like :
x-c(1,15,30,45,60,90,115)
i know that step by step i have always more than 10
min(diff(x)) =11
i want to add for each value a sequence of value:value+9
result should be :
1 2 3 4 5 6 7 8
Le 27.10.2005 17:04, Yves Magliulo a écrit :
hi,
i have a vector like :
x-c(1,15,30,45,60,90,115)
i know that step by step i have always more than 10
min(diff(x)) =11
i want to add for each value a sequence of value:value+9
result should be :
1 2 3 4 5 6 7 8 9 10 15 16 17 18 19 20 21
I built R 2.2.0 from source on my debian machine yesterday and updated
all packages. My problem is that dates function from its, that my
code heavely uses is now masked by dates from chron.
How can I specify tehat I want to use dates from its or how can I
prevent it from being masked?
I have read both the help files and that article... the article very nicely
evaluates the value of dealing with unbalanced data, and the help files show
that you can, but offer no guidance in terms of how the syntax should be
specified. The strata and classwt clearly can be specified, but it's not
Mike,
use ---
VarCorr(lme.object)
or for a user friendly output use varcomp from the 'ape' package--
require(ape)
varcomp(lme.object)
varcomp also allows scaling of components to unity (*100 gives %)
and also allows for cumulative sum of components.
Note. varcomp doesn't work for lmer
Dear Listers:
I have a question on handling large dataset. I searched R-Search and I
hope I can get more information as to my specific case.
First, my dataset has 1.7 billion observations and 350 variables,
among which, 300 are float and 50 are integers.
My system has 8 G memory, 64bit CPU, linux
Dear all,
This is a rather lengthy message, but I don't know what I made wrong in
my real example since the simple code works.
I have two variables a, b and a function f for which I would like to
calculate all possible combinations of the values of a and b.
If f is multiplication, I would simply
To redescribe the problem; I need to use dates from its
its depends on Hmisc
Hmisc depends chron
dates in chron masks dates in its
-- Forwarded message --
From: Omar Lakkis [EMAIL PROTECTED]
Date: Oct 27, 2005 11:47 AM
Subject: its dates masked by chron
To:
classwt in the current version of the randomForest package doesn't work
too well. (It's what was in version 3.x of the original Fortran code by
Breiman and Cutler, not the one in the new Fortran code.) I'd advise
against using it.
sampsize and strata can be use in conjunction. If strata is not
I think the general advice is that around 1/4 or 1/3 of your available
memory is about the largest data set that R can handle -- and often
considerably less depending upon what you do and how you do it (because R's
semantics require explicitly copying objects rather than passing pointers).
Fancy
Hi,
Apologies if the question is too simple
but I didn't find the answer by myself.
I'm able to create a 3-dimensionnal array A
and to write it with write.table()
... but, after that, I don't find how to read it
with read.table() getting the right 3 dimensions.
I tried to use as.array(), to
Omar Lakkis [EMAIL PROTECTED] writes:
To redescribe the problem; I need to use dates from its
its depends on Hmisc
Hmisc depends chron
dates in chron masks dates in its
So use its::dates ...
-- Forwarded message --
From: Omar Lakkis [EMAIL PROTECTED]
Date: Oct 27, 2005
Hi, I'm experimenting with using (R)SQLite to do data management. Here are
two little problems that I've encountered:
1. The presence of ',' in string values causes trouble since ',' is also the
delimiter used in the SQL statement.
2. A newline '\n' line attached to the last string value
I think what you're looking for is in anova()
fm1 - lmer(dv ~ IV ...)
anova(fm1)
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Jacques VESLOT
Sent: Thursday, October 27, 2005 2:22 AM
To: R-help@stat.math.ethz.ch
Subject: [R] F tests for random
It looks like you didn't vectorize the function you gave outer in your
longer example.
Consider your short example with a diagnostic printout:
a - 1:3
b - 1:4
f - function(a,b,d) {
+ cat(In f:, length(a), length(b), \n)
+ return(a*b+(sum(d)))
+ }
additional - runif(100)
If my calculation is correct (very doubtful, sometimes), that's
1.7e9 * (300 * 8 + 50 * 4) / 1024^3
[1] 4116.446
or over 4 terabytes, just to store the data in memory.
To sample rows and read that into R, Bert's suggestion of using connections,
perhaps along with seek() for skipping ahead,
On 27 Oct 2005, at 09:18, jinlong li wrote:
dear community,
I am a beginer in R , and can't predict with logistic model in
package
logistf,
Not exactly the answer to your question, but an alternative to the
logistf package, which purports to do similar things, is brlr (which
does
Hi, Jim:
Thanks for the calculation. I think you won't mind if I cc the reply
to r-help too so that I can get more info.
I assume you use 4 bytes for integer and 8 bytes for float, so
300x8+50x4=2600 bytes for each observation, right?
I wish I could have 500x8 G memory :) just kidding..
Dear Andy:
I think our emails crossed. But thanks as before.
Weiwei
On 10/27/05, Liaw, Andy [EMAIL PROTECTED] wrote:
If my calculation is correct (very doubtful, sometimes), that's
1.7e9 * (300 * 8 + 50 * 4) / 1024^3
[1] 4116.446
or over 4 terabytes, just to store the data in memory.
To
check ?dput and ?dget
Cheers
Francisco
From: [EMAIL PROTECTED]
To: r-help@stat.math.ethz.ch
Subject: [R] how to write and read an array ?
Date: Thu, 27 Oct 2005 19:00:10 +0200
Hi,
Apologies if the question is too simple
but I didn't find the answer by myself.
I'm able to create a
Hi, I wonder if there is interest/intention to allow for encrypted .RData
files? One can certainly do that outside R manually but that will leave a
decrypted RData file somewhere which one has to remember to delete.
Cheers,
Michael
__
Perfect! More useful than I was even hoping for. Great help, many thanks!
On 10/27/05, Liaw, Andy [EMAIL PROTECTED] wrote:
classwt in the current version of the randomForest package doesn't work
too well. (It's what was in version 3.x of the original Fortran code by
Breiman and Cutler, not
On 10/20/05, Mario Aigner-Torres [EMAIL PROTECTED] wrote:
[...]
I have right now a dataset that looks like this:
tail(partition, 3)
element run logfO2 TC buffer xAn sdXan Di Disigma
416 Al 36 -0.68 1180 AIR 0.734 0.007 2.10 0.02
417 Ca 36 -0.68 1180 AIR 0.734 0.007 1.29 0.02
418 Na 36
Hello list members!
I'm trying to enter some data in an R session using source() function
with an URL as argument. The data source is a PHP script located in an
apache web server and the data is a long list generated on-the-fly,
these are the initial lines:
groups-list()
On 10/26/05, Karin Lagesen [EMAIL PROTECTED] wrote:
I am trying to make horizontal violin plots. I have tried both vioplot
and simple.violinplot, but both of them seem to not be willing to take
the horizontal option. Is this correct, or am I just bungling it
somehow?
For instance, for
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Yes, it is of interest and was sitting on my todo list at
some time. If you want to go ahead and provide code to do it,
that would be terrific. There are other areas where encryption
would be good to have, so a general mechanism would be nice.
D.
I encountered this too, and my limited investigation (both on the web and in R)
was unable to find a work around.
-roger
Na Li wrote:
Hi, I'm experimenting with using (R)SQLite to do data management. Here are
two little problems that I've encountered:
1. The presence of ',' in string
I would be interested in that, particularly with certain kinds of confidential
data.
What was the approach you had in mind (if you in fact had one in mind)?
-roger
Na Li wrote:
Hi, I wonder if there is interest/intention to allow for encrypted .RData
files? One can certainly do that outside
David,
Sounds as if you're looking for cut.dendrogram().
My solution (with c. 250 cases) has been to color the terminals so
patterns can be seen even when there are too many terminals to label. I
don't think you can do that easily with plot.hclust() or plot.dendrogram()
so I posted a hacked
Raja Jayaraman rajnmsu79 at gmail.com writes:
Hello Everybody,
I am running R 2.2.0 with Windows XP
i am trying to fit nonlinear differential equation to data sets which looks
like this:
[SNIP]
and i need to fit these data to the following diff equation:
dNdt=a*N-b*N*C, dCdt=N^2,
Where
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Does
source(textConnection(readLines(url(http://...)))
give the correct answer. If not, what is being dropped
when you just use readLines() and look at the contents
of the download.
And how long is the longest line?
The RCurl package
Hello,
I've installed R on my RHEL3 cluster and I am trying to get Rmpi to
work properly.
R is installed using the following
./configure --prefix=/home/apps/R-2.2.0
I installed snow using
R CMD INSTALL /home/apps/snow
And finaly Rmpi
R CMD INSTALL /home/apps/Rmpi
Peter Dalgaard wrote:
Omar Lakkis [EMAIL PROTECTED] writes:
To redescribe the problem; I need to use dates from its
its depends on Hmisc
Hmisc depends chron
dates in chron masks dates in its
So use its::dates ...
... or ask the package maintainer (which might be a hard task: the
On Thu, 27 Oct 2005, Uwe Ligges wrote:
Peter Dalgaard wrote:
Omar Lakkis [EMAIL PROTECTED] writes:
To redescribe the problem; I need to use dates from its
its depends on Hmisc
Hmisc depends chron
dates in chron masks dates in its
So use its::dates ...
... or ask the package
Uwe,
It was unclear whether you were referring to chron or its as being
unmaintained.
I still maintain its, and I'm actually releasing a new version tonight
since Kurt has pointed out that the current version is failing package
checking.
It seems that both its and chron use namespaces. I
You probably need specify the repeated measures by using an Error term in aov
for repeated measures:
aov(trait ~ species + strain + Error(species/strain))
Take a look at Ripley's book.
Treat above with caution: I am no expert, but the answer is in that direction...
Michael Jerosch-Herold
I
I'm trying to create an app using TclTk and R
Can someone please explain how I bind a click event to the tree widget
(http://bioinf.wehi.edu.au/~wettenhall/RTclTkExamples/TreeWidget.html)
Ideally I'd like to bind to particular elements in the tree but tkbind
doesnt seem to work.
thanks
tom
This may appear too elementary to some on this list, but not to me. My
apologies if this is the case. I have mastered the lme function but the
nlme function has me stumped.
I am attempting to fit a nonlinear mixed model with 4 levels of nesting.
I am getting a cryptic error message and do
An alternative could be to store data in a MySql database and then select a
sample of the cases using the RODBC package.
Best
Søren
Fra: [EMAIL PROTECTED] på vegne af Liaw, Andy
Sendt: to 27-10-2005 19:21
Til: 'Berton Gunter'; 'Weiwei Shi'; 'r-help'
Emne: Re:
On 27 Oct 2005, Duncan Temple Lang wrote:
Yes, it is of interest and was sitting on my todo list at
some time. If you want to go ahead and provide code to do it,
that would be terrific. There are other areas where encryption
would be good to have, so a general mechanism would be nice.
D.
not sure if this message sent the first time, sorry :)
-- Forwarded message --
From: Jon Savian [EMAIL PROTECTED]
Date: Oct 27, 2005 1:04 PM
Subject: installing Rmpi
To: r-help@stat.math.ethz.ch
Hello,
I've installed R on my RHEL3 cluster and I am trying to get Rmpi to
work
You want FAQ 7.17 Why does outer() behave strangely with my function?
-thomas
On Thu, 27 Oct 2005, Rau, Roland wrote:
Dear all,
This is a rather lengthy message, but I don't know what I made wrong in
my real example since the simple code works.
I have two variables a, b and a
tom wright [EMAIL PROTECTED] writes:
I'm trying to create an app using TclTk and R
Can someone please explain how I bind a click event to the tree widget
(http://bioinf.wehi.edu.au/~wettenhall/RTclTkExamples/TreeWidget.html)
Ideally I'd like to bind to particular elements in the tree but
If I have an n1 x n1 x 2 array X I can calculate, say,
X[,,1]/X[,,2].
If it is a 4 dimensional array then I want to be able to calculate
X[,,,1]/X[,,,2], and similarly for higher dimensions.
How can I write a function to do this in a general way without having to
do a switch for each possible
On Thu, 2005-10-27 at 16:15 -0500, Na Li wrote:
On 27 Oct 2005, Duncan Temple Lang wrote:
Yes, it is of interest and was sitting on my todo list at
some time. If you want to go ahead and provide code to do it,
that would be terrific. There are other areas where encryption
would be
On 27 Oct 2005, Marc Schwartz uttered the following:
Seems to me that a better option would be to encrypt the full partition
such that (unless you write the files to a non-encrypted partition)
these issues are transparent.
I actually do that on a Mac via an encrypted sparse disk image. But
Why doesn't apply() already do what you want?
-- Bert Gunter
Genentech Non-Clinical Statistics
South San Francisco, CA
The business of the statistician is to catalyze the scientific learning
process. - George E. P. Box
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL
Thanks for the suggestion.
Perhaps I can see how to use apply to get the ratio, but say I also want
to return X[1] in a general way. Maybe I am being dense but I just
don't see it --- probably as a result of too much Perl/Python/Java
recently that is clouding my mind.
So can someone
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Na Li wrote:
On 27 Oct 2005, Duncan Temple Lang wrote:
Yes, it is of interest and was sitting on my todo list at
some time. If you want to go ahead and provide code to do it,
that would be terrific. There are other areas where encryption
Dear group,
I have a matrix with readings for ~180 variables
observed in 240 conditions.
I am doing a hierarchical clustering method (hclust)
by calculating eucledian distances among them.
When I plot the dendrogram from hclust, all my
variables at the end of the branches are cluttered. I
Not sure what you're after, but the kth dimension of an array y can be
obtained as:
apply(y,k,c). Each column of the resulting matrix can then be dimensioned,
if you like, via dim(y)[-k] .
-- Bert Gunter
Genentech Non-Clinical Statistics
South San Francisco, CA
The business of the statistician
On Thu, 27 Oct 2005 16:08:48 -0700 (PDT)
Srinivas Iyyer [EMAIL PROTECTED] wrote:
Dear group,
I have a matrix with readings for ~180 variables
observed in 240 conditions.
I am doing a hierarchical clustering method (hclust)
by calculating eucledian distances among them.
When I plot
fit$predict does print the fitted value for training data frame,
but what I want is to apply the fitted model to new coming data.
maybe I can form the equation manually .
thank you!
jinlong
From: Elizabeth Lawson [EMAIL PROTECTED]
To: jinlong li [EMAIL PROTECTED]
CC: [EMAIL PROTECTED]
How can I draw a 95% contour in sm.density?
For example,
y - cbind(rnorm(50), rnorm(50))
sm.density(y, display = slice)
will give 25%, 50% and 75% contours automatically, but
no reference on other values.
__
R-help@stat.math.ethz.ch mailing
Dear R-helpers,
Hi! All.
I'm doing a project which needs MCMC simulation.
I wonder whether there exists related packages in R.
The only one I know is a MCMCpack package.
What I want to do is implementing gibbs sampling and
Metropolis-Hastings Algorithm to get the posterior
of hierarchical
Hi,
Thanks for reporting the two problems. I'm attaching a simple update
to two functions that will allow you to specify a different separator,
e.g., using your example:
dbWriteTable(con, barley, barley, overwrite = TRUE, sep = ;)
This workaround still relies in dumping the data.frame into
On 27 October 2005 at 11:47, Omar Lakkis wrote:
| I built R 2.2.0 from source on my debian machine yesterday and updated
FYI, Debian had 2.2.0 package for you to download for over a week.
| all packages. My problem is that dates function from its, that my
| code heavely uses is now masked by
I feel a bit timid in asking this question: Why create the PS? Why not
create the pdf directly?
?pdf
You have lots of control over the size and other characteristics, and the
pdf can be used by MiKTeX to create a TeX - pdf document containing your
graphic.
I'm running R 2.2.0 on a DELL WinXP
On 27 Oct 2005, [EMAIL PROTECTED] wrote:
Rmpi version: 0.4-9 Rmpi is an interface (wrapper) to MPI APIs with
interactive R slave functionalities. See `library (help=Rmpi)' for
details. Error in dyn.load(x, as.logical(local), as.logical(now)) :
unable to load shared library
if solve(a,b) means to calculate an inverse matrix of
a with b, and i wonder why solve(a)%%b will get
different result?
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R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide!
Thanks a lot, but :
anova(lmer(Rendement ~ (1 | Pollinisateur) + (1 | Lignee) + (1 |
Pollinisateur : Lignee),
data = mca2))
Analysis of Variance Table
Erreur dans ok[, -nc] : nombre de dimensions incorrect
It looks like working with at least one fixed effect but not with random
On Thu, 27 Oct 2005, Cunningham Kerry wrote:
How can I draw a 95% contour in sm.density?
For example,
y - cbind(rnorm(50), rnorm(50))
sm.density(y, display = slice)
will give 25%, 50% and 75% contours automatically, but
no reference on other values.
See ?sm.options, the place to set
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