Dear Users,
In case of ridge logistic regression, i want to calculate the optimum
penalty using aic and bic criteria. Here is the sample code:
fit - lrm(RES ~CAT01+NUM01+NUM02+CAT02+CAT03+CAT04+NUM03+CAT05+CAT06+NUM04+
CAT07+CAT08+NUM05+NUM06, data = train.data, x = TRUE, y =
Dear Users,
In case of ridge logistic regression, i want to calculate the optimum
penalty using aic and bic criteria. Here is the sample code:
fit - lrm(RES ~CAT01+NUM01+NUM02+CAT02+CAT03+CAT04+NUM03+CAT05+CAT06+NUM04+
CAT07+CAT08+NUM05+NUM06, data = train.data, x = TRUE, y =
Hi
I am looking for a function which is executing some code repeatedly,
exactly like lapply() and sappl() are doing, but do not return anything
as I am not interested in the return values.
An example would be:
p - data.frame(runif(10), runif(10), runif(10))
lapply( p, function(ps) {x11();
Tobias Teichert wrote:
Hi Everybody,
I need to install the R-package 'foreign'. However, when I try the
standard install.packages('foreign') I get the following error
message:
package 'foreign' is not available in: install.packages(foreign)
The funny thing is, that I am using an Ubuntu
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Hello,
I want to compute OR from a simulation,
I simulate outcome-y and binary covariate, and I repeat it 1000 times.
I built a logistic model, and want to compute OR for every sample
At the end I'm looking for the mean(OR) of the 1000 repetitions.
Can I use cc (from epicalc)?
example: if yall is
G'day Rainer,
On Fri, 25 Jan 2008 10:34:32 +0200
Rainer M Krug [EMAIL PROTECTED] wrote:
[...]
p - data.frame(runif(10), runif(10), runif(10))
lapply( p, function(ps) {x11(); plot(ps)} )
which results in three graphs and a printout:
[...]
How can I avoid this printout without using
Juan Pablo Fededa wrote:
Dear Contributors:
I have two vectors x and z, and I want to display the histograms of both
vectors in the same graph, x in red bars, z in blue bars.
If you have any clue on how to do that, I will be very glad to hear it!!
Thanks in advance again,
Hi Juan,
The
Berwin A Turlach wrote:
G'day Rainer,
On Fri, 25 Jan 2008 10:34:32 +0200
Rainer M Krug [EMAIL PROTECTED] wrote:
[...]
p - data.frame(runif(10), runif(10), runif(10))
lapply( p, function(ps) {x11(); plot(ps)} )
which results in three graphs and a printout:
[...]
How can I avoid
Asche auf mein Haupt.
Yours,
Mag. Ferri Leberl
Am Donnerstag, den 24.01.2008, 17:12 + schrieb Prof Brian Ripley:
I suspect you have ignored
'If you are using an old version of R and think it does not work
properly, upgrade to the latest version and try that, before posting.'
[EMAIL PROTECTED] wrote:
Hi,
i'm very new to R, so sorry for what i'm sure is a very basic question. I'm
producing a boxplot with the data below:
df3-data.frame(
x=c(10,11,115,12,13,14,16,17,18,21,22,23,24,26,27,28,29,3,30,32,33,34,35,4,4
Berwin A Turlach wrote:
Of course, you could always do something like:
ilapply - function(...) invisible(lapply(...))
## perhaps better:
## ilapply - function(X, FUN, ...) invisible(lapply(X, FUN, ...))
ilapply(p, function(ps) {x11(); plot(ps)})
lapply just a for loop
Dear members of R forum,
Say I have a list:
L - list(1:3, 1:3, 1:3)
that I want to turn into a matrix.
I wonder why if I do:
do.call(cbind, L)
I get the matrix I want, but if I do
cbind(L)
I get something different from what I want. Why is that? How does
do.call() actually work?
I've read
Perhaps there are other opinions, but from my point
of view R is spectacularly similar in Linux and Windows
(and will be virtually identical in Linux and Unix). As
long as you are doing R things, you should be in home
territory.
I regularly transfer R objects between 64-bit Linux and
Windows,
Use Rprof on your code to see where time is being spend and then focus
on those areas for improvement.
On Jan 25, 2008 2:21 AM, Juliet Hannah [EMAIL PROTECTED] wrote:
Dear R Programmers,
I am trying to run a Poisson regression on all pairs of variables in a data
set and
obtain the permutation
Thanjavur,
I'm new to R, so it is possible I'm interpreting you syntax
incorrectly, but it looks like in the second equation you are only
including the interaction of age*race, the main effect of age, but
not the main effect of race which is what came out significant in your
first model.
In
On Jan 25, 2008 11:27 AM, Sergey Goriatchev [EMAIL PROTECTED] wrote:
Dear members of R forum,
Say I have a list:
L - list(1:3, 1:3, 1:3)
that I want to turn into a matrix.
I wonder why if I do:
do.call(cbind, L)
I get the matrix I want, but if I do
cbind(L)
I get something
I have one graph with two linear plots, one where the points are marked with
a triangle and the others marked with a dot. How do I label them in a legend
for example, comparable to what you automatically get in Excel (sorry for
the comparison people), so you know which type of point corresponds
Sergey Goriatchev wrote:
Dear members of R forum,
Say I have a list:
L - list(1:3, 1:3, 1:3)
that I want to turn into a matrix.
I wonder why if I do:
do.call(cbind, L)
I get the matrix I want, but if I do
cbind(L)
I get something different from what I want. Why is that? How does
Hi
I am carrying out some logit regressions and want to (a) make sure I'm
taking the right approach and (b) work out how to carry out some additional
analysis. So, to carry out a logit regression where the dependent variable
is a factor db, I use something like:
res1_l - glm(formula = db ~ y1 +
Hi
I am trying to carry out some maximum likelihood estimation and I'm not
making much headway, and I'm hoping that someone will be able to point me in
the right direction.
I am modelling mortality statistics. One way to do this is to model the
mortality rate (or, more accurately, log of the
Dear R-Users,
I am working on an Hierarchical Bayes model and tried to replace the inner
for-loop (which loops over a list with n.observations elements) with truely
vectorized code (where I calculated everything based on ONE dataset over all
respondents).
However, when comparing the
I have had a strange problem with rgl. I am currently switching from a
desktop computer to a workstation. When I get a very large data set and
run spectro3D, the computations run then the window with the 3d plot
appears it doesn't show the data inside and immediately shuts down R.
The computers
Hi All,
Thanjuvar wrote:
model2-lm(lavi~age+sex+age*race+diabetes+hypertension, data=tb1)
David wrote:
in the second equation you are only including the interaction of
age*race,
the main effect of age, but not the main effect of race which is what
came out significant
in your first
Hi,
one possibility is to start R in a terminal window by entering
R
then R should be started.
now simply enter:
source(exmaple.r)
and everything should be fine.
Hope this helps,
Roland
Prateek Singh wrote:
Hi,
I have 'R' code in file. saved it as exmaple.r
here is the code...
Take a look at ?reshape - it is used to convert between 'long' and 'wide'
formats of data tables (frames).
-Christos
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of
[EMAIL PROTECTED]
Sent: Friday, January 25, 2008 4:30 PM
To:
On 26/01/2008, at 10:54 AM, Carson Farmer wrote:
Dear List,
I am attempting to perform a harmonic analysis on a time series of
snow
depth, in which the annual curve is essentially asymmetric (i.e. snow
accumulates slowly over time, and the subsequent melt occurs
relatively
rapidly).
This is a text part of the message.
It is shown for the users of old-style e-mail clients
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide
Hi, The following code, from Angelo Canty article on line
Resampling Methods in R: the boot Package, 2002, works fine for Angelo Canty
using R 2.6.0 on Windows XP.
It also works for me using R 1.2.1 and S-PLUS 2000 on Windows XP after
installing the S-PLUS bootstrap
I have everything in the data frame now. The calculations I need to
preform for each round are slightly different. How do I specify to make
one calculation for one round and one for the other? (One round is
called C, and the other is F)
Thomas Levine
On Thu, 2008-01-24 at 18:23 -0500, Thomas
Dear List,
I am attempting to perform a harmonic analysis on a time series of snow
depth, in which the annual curve is essentially asymmetric (i.e. snow
accumulates slowly over time, and the subsequent melt occurs relatively
rapidly). I am trying to fit a curve to the data, however, the
Hi, I'm trying to set up AR(1) as a correlation structure in modeling some
data (attached file data.txt in text format) with lme, but have trouble
getting it to work.
Incent, Correctness, and Oppor are 3 categorical variables, Beta is a
response variable, and Time is an equally-spaced variable
On Jan 25, 2008 2:04 PM, Domenico Vistocco [EMAIL PROTECTED] wrote:
You could use ggplot2:
library(ggplot2)
x=rnorm(100)
y=rnorm(100)
df=melt(data.frame(x,y))
#for vertical histogram
ggplot(data=df,aes(x=value))+geom_histogram()+facet_grid(.~variable)
#for horizontal histogram
Benilton Carvalho wrote:
I'm afraid others might have some other recommendations regarding your
message... but the first one is that the bioconductor mailing list is
more appropriate to this...
1. We all three should note that we should use sensible subject lines.
2. You, Benilton, should
Prateek Singh wrote:
Hi,
I got command to execute R code from Mark.
but it was showing error..
Error in library(hopach) : there is no package called 'hopach'
Does it mean this library hopach
hopach is a package.
is not installed. But I have installed complete Bioconductor
You might look at the method histbackback (back-to-back histograms) in
package Hmisc. At the time I looked at this package about a year ago,
I could not get it working on my Mac, so I don't actually know what
the results look like, but I have created them before in XLispStat and
found
http://cran.r-project.org/src/contrib/Descriptions/popbio.html
On Jan 25, 2008, at 10:51 AM, Michelle DePrenger-Levin wrote:
Hello,
I'm in need of running a PVA and want to load {popbio}. However, I
can't find
it. I can't see where or how to load it. I have added repositories and
http://cran.r-project.org/src/contrib/Descriptions/popbio.html
On 25/01/2008, Michelle DePrenger-Levin [EMAIL PROTECTED] wrote:
Hello,
I'm in need of running a PVA and want to load {popbio}. However, I can't find
it. I can't see where or how to load it. I have added repositories and
On 1/25/2008 12:55 PM, Remund, Todd wrote:
I have had a strange problem with rgl. I am currently switching from a
desktop computer to a workstation. When I get a very large data set and
run spectro3D, the computations run then the window with the 3d plot
appears it doesn't show the data
On 1/25/2008 11:39 AM, Karin Lagesen wrote:
I have a data frame containing columns which are factors. I use this
to make boxplots for the data, with one box per factor. I would now
like to get at the data in the data frame which corresponds to the
outliers. I have so far found the $out, which
Hi, I'm trying to set up AR(1) as a correlation structure in modeling some
data (attached file data.txt in text format) with lme, but have trouble
getting it to work.
Incent, Correctness, and Oppor are 3 categorical variables, Beta is a
response variable, and Time is an equally-spaced variable
What about reading the last four lines of this email?
G.
On Fri, Jan 25, 2008 at 04:45:04PM +0100, [EMAIL PROTECTED] wrote:
How can I join two lists? I have q1 and q2 and I want to merge them. I
[...]
__
R-help@r-project.org mailing list
Try c(q1,q2)
Nael
On Jan 25, 2008 4:45 PM, [EMAIL PROTECTED] wrote:
How can I join two lists? I have q1 and q2 and I want to merge them. I
have tried to use the comand merge, but not work. Any solutions? Thanks!
q1
$Input1
7.84615384615385
0.5
$Input2
8.92307692307692
On 1/25/2008 9:46 AM, Luis Ridao Cruz wrote:
R-help,
Sorry for this question (I guess it has been addressed before but
I could not find it in the archives)
but how can I see a function code
when the following comes up:
svymean
function (x, design, na.rm = FALSE, ...)
{
hits=-2.6 tests�YES_00
X-USF-Spam-Flag: NO
On Fri, 2008-01-25 at 14:46 +, Luis Ridao Cruz wrote:
R-help,
Sorry for this question (I guess it has been addressed before but
I could not find it in the archives)
but how can I see a function code
when the following comes up:
svymean
a*b is not an interaction term. An interaction term looks like a:b.
y~age*race means
y~age+race+age:race.
For
TB model1-lm(lavi~age+sex+race+diabetes+hypertension, data=tb1)
TB model2-lm(lavi~age+sex+age*race+diabetes+hypertension, data=tb1)
both main effects are present in model 2 (below) as
From: Bill Vorias
Is there an Interaction function in the Random Forest
algorithm in the current version of R?
No (at least not in the randomForest package). Prof. Breiman regarded
that feature as experimental, and said he wouldn't mind not having it
in the R version. I don't know if Prof.
Paul Sweeting [EMAIL PROTECTED] wrote in
news:[EMAIL PROTECTED]:
Hi
I am trying to carry out some maximum likelihood estimation and I'm
not making much headway, and I'm hoping that someone will be able to
point me in the right direction.
I am modelling mortality statistics. One way to
Tirthadeep wrote:
Dear Users,
In case of ridge logistic regression, i want to calculate the optimum
penalty using aic and bic criteria. Here is the sample code:
fit - lrm(RES ~CAT01+NUM01+NUM02+CAT02+CAT03+CAT04+NUM03+CAT05+CAT06+NUM04+
CAT07+CAT08+NUM05+NUM06, data =
hits=-2.6 tests=BAYES_00
X-USF-Spam-Flag: NO
See ?grid though read the Note section of that page, which says that
more fine tuning can be achieved through the use of abline directly.
Also, note that abline is vectorized so you don't need the loop. Here is
you example, adjusted to avoid the large
Hi,
I have been trying to run R programs on the XGrid but without any
sucess...it would be great help if somebody could give me an
indication/steps as to how to get this running...am using a Mac OSX Leopard
and the xgrid is on a tiger cluster...
thanks very much in advance!
[[alternative
I think you can do this fairly easily with the reshape
package. Is this basically what you want?
x - Plot1 Species1Abundance1
Plot1 Species2Abundance2
Plot2 Species1Abundance1
Plot2 Species3Abundance3
xx - read.table(textConnection(x), header=TRUE,
as.is=TRUE); xx
dear all,
I have a very simple question but I could not figure out.
I need to make plots with grid in the background.
something like I old retrive like this
a=runif(100)*10
b=runif(100)*10
plot(a,b, pch=20, xlim=c(0, round(max(a))), ylim=c(0, round(max(b
vs=seq(0, max(a), 0.5)
for(i in
You could use ggplot2:
library(ggplot2)
x=rnorm(100)
y=rnorm(100)
df=melt(data.frame(x,y))
#for vertical histogram
ggplot(data=df,aes(x=value))+geom_histogram()+facet_grid(.~variable)
#for horizontal histogram
ggplot(data=df,aes(x=value))+geom_histogram()+facet_grid(.~variable) +
coord_flip()
Hello, I would like to make my R script more interactive. Well, I want the
script to work like this:
I run the script from R Console and it offers me some options (press 1 for
something, or press 2 for something else). After pressing 1 or 2, do
corresponding procedure.
I am not able to find out
Hi
[EMAIL PROTECTED] napsal dne 24.01.2008 23:21:05:
I need to group some subjects according to two
variables (var1, var2)
I have a data frame that looks something like this:
Subject var1 var2
1 400150
2 320100
3 580600
4 145
I'm afraid others might have some other recommendations regarding your
message... but the first one is that the bioconductor mailing list is
more appropriate to this...
Apparently you didn't install all the BioConductor packages (and I'm
glad you didn't :-) ).
Just install the package
On 1/25/2008 8:14 AM, John Lande wrote:
dear all,
I have a very simple question but I could not figure out.
I need to make plots with grid in the background.
something like I old retrive like this
a=runif(100)*10
b=runif(100)*10
plot(a,b, pch=20, xlim=c(0, round(max(a))), ylim=c(0,
Visit this site for free classifieds http://www.a2z-4-sale.com, have nice week
end
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and
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
Hi All.
I'm trying to run nlsList an getting an error that makes no sense to
me. I have accuracy and reaction time data over many trials for each
person (id)
When I use nlsList code that is virtually identical to the example in
the doc file I get the following error. I've tried everything I
I need to write a C# program to create and display Cusum chart from any
of the packages,
spc, qcc or strucchange.
Issues:
1-The data resides in a MS SQL Database. The C# program will handle
obtaining the data for the requisite types of samples.
Assistance needed on:
1-How can I call the cusum
R-help,
Sorry for this question (I guess it has been addressed before but
I could not find it in the archives)
but how can I see a function code
when the following comes up:
svymean
function (x, design, na.rm = FALSE, ...)
{
.svycheck(design)
UseMethod(svymean, design)
}
environment:
How can I test whether a plot I'm about to call will be within a layout or
not? I need to fix some par options based on that ...
Thanks, Joh
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting
Hi,
This IS the code of the function. It is a generic function, the actual method
used depends on the class of the object.
You will find methods for this function by doing:
R methods(svymean)
[1] svymean.survey.design* svymean.survey.design2* svymean.svyrep.design*
[4] svymean.twophase*
I have a data frame containing columns which are factors. I use this
to make boxplots for the data, with one box per factor. I would now
like to get at the data in the data frame which corresponds to the
outliers. I have so far found the $out, which gives the values of any
data points which lie
hits=-2.6 tests=BAYES_00
X-USF-Spam-Flag: NO
On Fri, 2008-01-25 at 14:21 +, David Winsemius wrote:
Paul Sweeting [EMAIL PROTECTED] wrote in
news:[EMAIL PROTECTED]:
snip /
The most straightforward approach would be to use glm() with
family=poisson, a.k.a Poisson regression. Don't ask me
Dear Svempa,
See ?legend.
In this case, you could have discovered the legend function via
apropos(legend) or help.search(legend).
I hope this helps,
John
John Fox, Professor
Department of Sociology
McMaster University
Hamilton, Ontario, Canada L8S 4M4
How can I join two lists? I have q1 and q2 and I want to merge them. I
have tried to use the comand merge, but not work. Any solutions? Thanks!
q1
$Input1
7.84615384615385
0.5
$Input2
8.92307692307692
-3.2
$Input3
4.53846153846154
-5
q2
$Input1
With thanks to all who responded, especially Charles Berry and
Don MacQueen, my student has everything working. The final
solution was:
1. Install X11 and X11SDK (or make sure they are installed).
2. There is a button for starting X11 within the R GUI.
3. Sys.setenv(
Hi,
I have 'R' code in file. saved it as exmaple.r
here is the code...
library(hopach)
GSE - read.table(gene_expression_data,sep=\t,header=TRUE,row.names=TRUE)
gene.dist - distancematrix(t(GSE),d=euclid)
gene.hobj - hopach(t(GSE), dmat=gene.dist, mss=med)
?grid
--- John Lande [EMAIL PROTECTED] wrote:
dear all,
I have a very simple question but I could not figure
out.
I need to make plots with grid in the background.
something like I old retrive like this
a=runif(100)*10
b=runif(100)*10
plot(a,b, pch=20, xlim=c(0, round(max(a))),
Or you can use lattice's xyplot(..., type = c(p,g))
?panel.xyplot provides details
-- Bert Gunter
Genentech
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of John Kane
Sent: Friday, January 25, 2008 9:49 AM
To: John Lande; r-help@r-project.org
Subject:
Hello,
I'm in need of running a PVA and want to load {popbio}. However, I can't find
it. I can't see where or how to load it. I have added repositories and
changed the CRAN mirror site. I see {polynom} and {popgen} but no {popbio}
between.
What am I doing wrong?
Thanks,
Michelle
Hi,
I got command to execute R code from Mark.
but it was showing error..
Error in library(hopach) : there is no package called 'hopach'
Does it mean this library hopach is not installed. But I have
installed complete Bioconductor package.
I am confused.
can you help me in this
thanks
YAHOO.Shortcuts.hasSensitiveText = false; YAHOO.Shortcuts.sensitivityType =
[]; YAHOO.Shortcuts.doUlt = false; YAHOO.Shortcuts.location = us;
YAHOO.Shortcuts.lang = us; YAHOO.Shortcuts.document_id = 0;
YAHOO.Shortcuts.document_type = ; YAHOO.Shortcuts.document_title = ;
Hi Jarek,
an alternative approach is to provide more precise starting values!
It pays off to realise that it's possible to find quite good guesses
for some of the parameters in your model function:
t ~ tr+(ts-tr)/((1+(a*h)^n)^(1-(1/n)))
The parameters tr and ts correspond to the
Hello.
Does anyone know of an existing function that takes a list in the form of:
Plot1 Species1Abundance1
Plot1 Species2Abundance2
Plot2 Species1Abundance1
Plot2 Species3Abundance3
.
.
.
PlotN SpeciesNAbundanceN
and translates into a matrix in the form of
Species1
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