Michael Papenfus mmpapenf at wisc.edu writes:
I have defined the following function:
fr-function(x) {
u-x[1]
v-x[2]
sqrt(sum((plnorm(c(3,6),u,v)-c(.55,.85))^2))
}
which I then solve using optim
y-optim(c(1,1),fr)
y$par
[1] 1.0029771 0.7610545
This works fine.
Now
Spencer,
Thank you for the kind and elaborate reply to my previous post.
I did consider the option you suggested and many variations. Depending on the
order of the random factors, lme will either give the same output as the aov
model for soiltype or for habitat, but not both in the same model.
On 7/30/06, Kartik Pappu [EMAIL PROTECTED] wrote:
Hello All,
I have a device that spews out experimental data as a series of text
files each of which contains one column with several rows of numeric
data. My problem is that for each trial it gives me one text file
(and I run between 30 to
OK, I see how the standardized random effects are calculated. Here is
what I now see
library(nlme)
fm2 - lme(distance~age, Orthodont)
# unstandardized
age_ranef - ranef(fm2)[,2]
#standardized
age_Sranef - ranef(fm2, standard=TRUE)[,2]
# We can use these to solve for the standard error,
Nurza,
Try running a while loop steping out until you have a start and finish
thats the function is opposite in sign. You need a start and finish
where F is + and - on either side of the loop. Graphing F might help.
step-10
checkme-F(start)*F(finish+step)
while(checkme0){
b1-3
plot(1,1, main= bquote(paste(Results for , beta==.(b1
seems to work.
Stuart
Dr Stuart J Leask DM MRCPsych MA BChir
Senior Lecturer and Honorary Consultant in Clinical Psychiatry
University Dept of Psychiatry, Duncan Macmillan House
Porchester Road. Nottingham. NG3 6AA.
See
?aov
?lm
something like
lm(result~yourfactor1+yourfactor2+yourfactor3+yourfactor5,
data=yourdataframe)
or
aov(result~yourfactor1+yourfactor2+yourfactor3+yourfactor5,
data=yourdataframe)
but the exact structure of lm or aov construction depends on what you
want to test.
HTH
Petr
On
Dear R Users,
Suppose I have a dataset like this:
a b
39700 485.00
39300 485.00
39100 480.00
38800 487.00
38800 492.00
39300 507.00
39500 493.00
39400 494.00
39500 494.00
39100 494.00
39200 490.00
Now I want get a-b for all possible combinations of a and b. Using
Now I want get a-b for all possible combinations of a and b.
outer(a,b,-)
hth
ido
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and
diffs - do.call(expand.grid, dt)
diffs$delta - rowSums(expand.grid(dt$a, -dt$b))
---
Jacques VESLOT
CNRS UMR 8090
I.B.L (2ème étage)
1 rue du Professeur Calmette
B.P. 245
59019 Lille Cedex
Tel : 33 (0)3.20.87.10.44
Fax : 33
Dear all,
I'm trying to improve the documentation I provide my R packages, and
to that end I'd like to find out what you think is great R
documentation. I'm particularly interested in function documentation,
but great vignettes, websites or book are also of interest.
What is your favourite bit
Dear R users,
Two questions:
1) Is there a way to simplify the mtext() line below ?
beta=c(1,-1)
m=5
plot(1)
mtext( bquote(paste( beta == .(paste( (, paste(beta, collapse=, ), ) ))
)), outer=TRUE,line=-3)
2) How do I get the embedded carriage return \n below to work, i.e for the
text that
Rainer M Krug [EMAIL PROTECTED] writes:
Hi
is it possible to subscribe to RNews that it get's emailed as soon as it
is released or is there an announcement list for new issues?
It is announced on R-announce, along with a few other selected items.
See, e.g.
Juan Lewinger [EMAIL PROTECTED] writes:
Dear R users,
Two questions:
1) Is there a way to simplify the mtext() line below ?
beta=c(1,-1)
m=5
plot(1)
mtext( bquote(paste( beta == .(paste( (, paste(beta, collapse=, ), ) ))
)), outer=TRUE,line=-3)
The outer paste() is superfluous,
hadley wickham skreiv:
I'm trying to improve the documentation I provide my R packages, and
to that end I'd like to find out what you think is great R
documentation. I'm particularly interested in function documentation,
but great vignettes, websites or book are also of interest.
What is
Hi all,
I have a large set of descriptors, which are stored as the vectors, each one
containing about 450 elements. Now I have to perform some algebraical
operations on this set to eliminate the redundant ones. The problem is, that
not all vales in the vectors are known.
Are there any norm
Hello
I've just realised attachments are not allowed, so the data for the example in
my previous message is:
pos.df=read.table(http://www.savefile.com/projects3.php?fid=6240314pid=847249key=119090;,
header=T)
Hello,
I am trying to run a makeConstrasts() function to compute eBayes t-
test with the following design list (six hybridizations and three
samples -in duplicates):
A BC
1 1 00
2 1 00
3 0 10
4 0 10
50 01
6
Hi
see
?complete.cases and/or ?is.na for evaluating non missing entries.
However in any operation in which you use NA value, result shall be
NA as you do not know what actually is NA.
HTH
Petr
On 31 Jul 2006 at 11:44, Joanna Procelewska wrote:
Date sent: Mon, 31 Jul 2006
Greetings,
I am unable to successfully BUILD due to a file that apears to be too
long.
I know it it due to the length of a particular R program because if I
remove a line, even a comment line,
from the file it then successfully builds. However, if I add the line
back in, the build fails.
The
At 10:09 31/07/2006, hadley wickham wrote:
Dear all,
I'm trying to improve the documentation I provide my R packages, and
to that end I'd like to find out what you think is great R
documentation. I'm particularly interested in function documentation,
Hadley, I do not think any bit of function
Hi!
Can anyone let me know where is the function glmmNQ? It's said that it is in
the MASS library but I can not find it.
Thanks
Salomé
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the
As we have said to you before, we need a reproducible example, and it is
very likely that you are speculating.
There is no 'BUILD' command in R: do you mean 'R CMD build'? If so,
that does not parse any `R program'.
On Mon, 31 Jul 2006, Zajd, John wrote:
Greetings,
I am unable to
On Mon, 31 Jul 2006, Maria Salomé Esteves Cabral wrote:
Hi!
Can anyone let me know where is the function glmmNQ? It's said that it
is in the MASS library but I can not find it.
Where is it said to be in the MASS *package*? Not in MASS the book, for
sure. The function of that name used in
Zajd, John wrote:
Greetings,
I am unable to successfully BUILD due to a file that apears to be too
long.
I know it it due to the length of a particular R program because if I
remove a line, even a comment line,
from the file it then successfully builds. However, if I add the line
back
Hi dear R community,
I have up to 12 measures of a protein for each of 6 patients, taken
every two or three days. The pattern of the protein looks periodic,
but the height of the peaks is highly variable. It's something like
this:
patient - data.frame(
day = c(1, 3, 5, 8, 10, 12, 15,
Thanks for the answer.
The problem is I have to perform a forward selection on the set and in every
step construct an orthonormal base for the subspace spanned on the selected
vectors. This means that I can use only the full vectors for the constructing
a base, or?
Joanna
--- Petr Pikal [EMAIL
Hi
I have been asked by a colleague to perform a statistical analysis
which uses random effects - but I am struggling to get this to work
with nlme in R. Help would be very much appreciated!
Essentially, the data consists of:
10 patients. Each patient has been given three different treatments
As suggested I try another post.
First I give a reproducible example. The example data set has been
provided by I. Plewis (1997), Statistics in Education. London: Arnold (I
include the residuals obtained by MLWin):
# -
library(nlme)
# Example data
Is there a way of using monospaced fonts in legends in a plot,
but still using standard proportionally spaced fonts for all the titles?
--
Erich Neuwirth, University of Vienna
Faculty of Computer Science
Computer Supported Didactics Working Group
Visit our SunSITE at http://sunsite.univie.ac.at
boxcox from MASS and bct from TeachingDemos do different things. The boxcox
function does not return the transformed y values, it returns log-likelihood
values for various values of lambda, these values can be used to decide which
value of lambda to use (generally it is used by giving a
I am writing as I am still having trouble trying to define my own covariance
matrix. My code is displayed below. I am defining the covariance matrix in
the form of an AR1 process so it can be easily checked if working correctly.
Another question I have is if it is possible to define the
--- hadley wickham [EMAIL PROTECTED] wrote:
Dear all,
I'm trying to improve the documentation I provide my
I am a new user and at moment I am finding An
Introduction to S and the Hmisc and Design Libraries
by Carlos Alzola and Frank E. Harrell is very helpful
as it explains some simple
On Mon, 31 Jul 2006, Erich Neuwirth wrote:
Is there a way of using monospaced fonts in legends in a plot,
but still using standard proportionally spaced fonts for all the titles?
Yes, just use the family= argument as appropriate, e.g. par(family=mono)
before calling legend.
--
Brian D.
One thing you could try (probably as last resort, if someone comes up with a
better idea, use that) is to plot to an xfig device, then use xfig (or jfig) to
move the rectangle to the back, then convert it to whatever final graphics
format you want.
-Original Message-
From: [EMAIL
On Sun, 30 Jul 2006, Uwe Ligges wrote:
[EMAIL PROTECTED] wrote:
Kartik Pappu a écrit :
However I need to plot my data in a log transformed color scale. Is
this possible? I will be happy to explain further, but basically I
need to do this because there are large variations in the max and
It looks like the pwr.p.test function from the pwr package would do what you
want.
-Original Message-
From: [EMAIL PROTECTED] on behalf of Chris Evans
Sent: Sun 7/30/2006 12:53 PM
To: r-help@stat.math.ethz.ch
Subject: [R] Power of a single sample binomial test
The only references to
To sum up, I can't figure out how MLWin calculates the
standardized residuals. But I understand that this is not a
question for the R list.
Nevertheless, it would help if someone could point me to some
arguments why not to use them and stick to the results
obtainable by ranef().
Hi
Hi, Andy:
What's the Jerry Friedman's ISLE? I googled it and did not find the paper on
it. Could you give me a link, please?
Thanks,
Weiwei
On 7/31/06, Eleni Rapsomaniki [EMAIL PROTECTED] wrote:
Hello
I've just realised attachments are not allowed, so the data for the
example in
my
Hi:
I am trying to add a data set in my package but get the following error
when the package is checked:
Undocumented data sets:
seacarb_test
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in
Hi Andy,
I get different order of importance for my variables depending on their
order in the training data.
Perhaps answering my own question, the change in importance rankings could be
attributed to the fact that before passing my data to randomForest I impute the
missing values randomly
I have a cut-and-paste error in this message that I sent a few minutes
ago. I show the evaluation of rr as
rr - ranef(model.4b, postVar = TRUE)
when it was
rr - ranef(fm1, postVar = TRUE)
I also omitted the evaluation of rr1, which is
rr1 - rr$class
On 7/31/06, Douglas Bates [EMAIL
Thank you for providing the reproducible example and the explanation
of what you are seeking to calculate.
On 7/31/06, Dirk Enzmann [EMAIL PROTECTED] wrote:
As suggested I try another post.
First I give a reproducible example. The example data set has been
provided by I. Plewis (1997),
It's the 5th paper on his web page.
http://www-stat.stanford.edu/~jhf/ftp/isle.pdf
http://www-stat.stanford.edu/~jhf/ftp/isle.pdf
Cheers,
Andy
_
From: Weiwei Shi [mailto:[EMAIL PROTECTED]
Sent: Monday, July 31, 2006 11:38 AM
To: Eleni Rapsomaniki
Cc: Liaw, Andy;
I think I need to clarify a little further on my original question.
I have the following two rows of data:
mydat-data.frame(d1=c(3,5),d2=c(6,10),p1=c(.55,.05),p2=c(.85,.35))
mydat
d1 d2 p1 p2
1 3 6 0.55 0.85
2 5 10 0.05 0.35
I need to optimize the following function using optim for each row
Hi.. I am running R version 2.3.1 on a Windows XP machine with the latest
Miktex 2.5 installed. I get no errors from R when running the Sweave example,
testfile - system.file(Sweave, Sweave-test-1.Rnw, package = utils)
However, when I tex the resulting .tex file (after installing a4.sty) I get
On 7/31/06, Dov Stekel [EMAIL PROTECTED] wrote:
Hi
I have been asked by a colleague to perform a statistical analysis
which uses random effects - but I am struggling to get this to work
with nlme in R. Help would be very much appreciated!
Essentially, the data consists of:
10 patients.
Supply your additional arguments to optim() and they will get passed to
your function:
mydat-data.frame(d1=c(3,5),d2=c(6,10),p1=c(.55,.05),p2=c(.85,.35))
fr-function(x, d) {
+ # d is a vector of d1, d2, p1 p2
+ u - x[1]
+ v - x[2]
+ d1 - d[1]
+ d2 - d[2]
+ p1 -
LL wrote:
Hi.. I am running R version 2.3.1 on a Windows XP machine with the latest
Miktex 2.5 installed. I get no errors from R when running the Sweave example,
testfile - system.file(Sweave, Sweave-test-1.Rnw, package = utils)
However, when I tex the resulting .tex file (after
Douglas
That's very helpful! It's just a syntax error in my use of lme (I find
the documentation hard to figure!). I'm actually also using the formula
lme(Measurement~Treatment/When etc)
as this gives the right contrasts to look at the interactions between
each of the treatments and
Ooh,
lme(Measurement~Treatment/When etc)
and
lm(Measurement ~ Treat/When + Patient)
give exactly the same results! How interesting!
Dov
which seems unsatisfactory for independence
reasons. (I'm not really a statistician - just the most stats-savvy
person in my department!)
Found it from another paper:
importance sample learning ensemble (ISLE)
which originates from Friedman and Popescu (2003).
On 7/31/06, Weiwei Shi [EMAIL PROTECTED] wrote:
Hi, Andy:
What's the Jerry Friedman's ISLE? I googled it and did not find the paper
on it. Could you give me a link,
I added an example of passing additional arguments through optim() to
the objective and gradient functions to the Discussion section of the
Wiki-fied R documentation. See it at
http://wiki.r-project.org/rwiki/doku.php?id=rdoc:stats:optim
-- Tony Plate
PS. I had to add purge=true to the end
When I try to import an spss sav file with read.spss() I am getting the
following error
'Error in read.spss(X:\\.sav) : error reading system-file header'
and the import process is aborted.
I have tried in v. 2.3.0 and 2.3.1
The sav-file loads without problems in spss v14 I have tried saving
Dr. Bates,
Thanks for the notes! It helps. So now I see consistent resluts from
both lme and lmer. Since I have several response variables to look at, I
will reduce the model separately.
Speaking of the model reduction, it is clear in this example that the
trivial variance of Operator:Run could
On Mon, 31 Jul 2006, Sundar Dorai-Raj wrote:
LL wrote:
Hi.. I am running R version 2.3.1 on a Windows XP machine with the latest
Miktex 2.5 installed. I get no errors from R when running the Sweave
example,
testfile - system.file(Sweave, Sweave-test-1.Rnw, package = utils)
Hi, does anybody know where I might the RCurl package - the omegahat.org
server seems to be down
Thanks,
---
Rajarshi Guha [EMAIL PROTECTED]
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
Hi all,
I am trying to generate a distribution for the mean euclidean
distance between a group of n elements in a given surface (the
elements are randomly picked). Fo doing so I've written the
following code:
sampling- function(x,size) {
x- x[sample(1:nrow(x),size),]
mat-
hi,
i am a new member.
i am using R in finding correlation between two variables of unequal length.
when i use
cor(x,y,na.rm=T,use=complete)
where x has observations from 1928 to 2006 y has observations from 1950 to
2006. I used na.rm=T to use the complete observations. So missing values
hi,
i am a new member.
i am using R in finding correlation between two variables of unequal length.
when i use
cor(x,y,na.rm=T,use=complete)
where x has observations from 1928 to 2006 y has observations from 1950 to
2006. I used na.rm=T to use the complete observations. So missing values
Rajarshi Guha [EMAIL PROTECTED] writes:
Hi, does anybody know where I might the RCurl package - the omegahat.org
server seems to be down
The Bioconductor project hosts a mirror of a subset of Omegahat
packages (RCurl is included). You can find the listing here:
I'm attempting to modify how biplot draws its red vectors (among other
things). This is how I've started:
Biplot - function(xx, comps = c(1, 2), cex = c(.6, .4))
{
## Purpose: Makes a biplot with princomp() object to not show arrows
##
Runninn R.2.3.1 Windows XP
I have a dataset just imported from SPSS. It has any
number of 99's as missing data and it looks like the
next dataset will have custom missing codes. I have
abouat 120 variables and an N of 2000.
I think thatI would like to apply a function to the
data.frame (or to
You test matrix did not have any 99 in it, so I replaced all '3's with NAs
mat
cat dog rat
[1,] 3 3 5
[2,] 5 5 NA
[3,] 6 3 4
[4,] 8 6 9
mat[mat == 3] - NA
mat
cat dog rat
[1,] NA NA 5
[2,] 5 5 NA
[3,] 6 NA 4
[4,] 8 6 9
You can not do
Its easiest to just check the source. biplot is a generic which calls
biplot.princomp which calls biplot.default which in turn calls plot so
try this and examine the source:
stats:::biplot.default
On 7/31/06, Patrick Connolly [EMAIL PROTECTED] wrote:
I'm attempting to modify how biplot draws
On 7/29/06, Nantachai Kantanantha [EMAIL PROTECTED] wrote:
Hi everyone,
I would like to ask a question regarding to the data used to fit the mixed
model.
I wonder that, for the response variable data used to fit the mixed model
(either via spm or lme), we must have several observations per
In writing about the star data from package mlmRev I was reminded of
a comment in the New York Times obituary, C. Frederick Mosteller, a
Pioneer of Statistics, Dies at 89, that appeared on July 27. In part
it stated
In the 1980's, he was instrumental in persuading Tennessee to conduct
a
Greetings,
A couple general questions regarding the use of splines to interpolate depth
profile data.
Here is an example of a set of depths, with associated attributes for a given
soil profile, along with a function for calculating midpoints from a set of
soil horizon boundaries:
#calculate
Dear all,
I am trying to apply Ridge regression to my dataset, and then I would like
to predict the Y responses using the Ridge model (of certain lambda) for
new data point. The only Ridge regression functions I found is in MASS
library. However, there are very few functions available:
Hi!
Can anyone let me know how can I get the stdDev of the random intercept from
the output of glmmPQL?
Thanks
Salomé
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PLEASE do read the posting guide
I want to get a lighter shade of a color...I have a lot of colored objects and
want each one printed as a foreground against a slightly lighter background.
I thought I could try something like changing the alpha channel by first
converting it to rgb.
But prior to trying that, I'm stuck with how
If I want to display a few polynomial regression fits I can do something
like
for (i in 1:6) {
mod - lm(y ~ poly(x,i))
print(summary(mod))
}
Suppose that I don't want to over-write the fitted model objects,
though. How do I create a list of blank fitted model objects
This is an automated message from the
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Murray,
Here is a general paradigm I tend to use for such problems. It extends
to fairly general model sequences, including different responses, c
First a couple of tiny, tricky but useful functions:
subst - function(Command, ...) do.call(substitute, list(Command,
list(...)))
abut -
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