But if the multicollinearity is so strong, then I am wondering why it
worked in the data frame as opposed to 4 seprate vectors? It should
not make any difference...
Dimitri
On Tue, Apr 21, 2009 at 12:21 PM, Vemuri, Aparna avem...@epri.com wrote:
Thanks Dimitri! Following exactly what you did, I
Probably better asked on the BioC list.
On Apr 21, 2009, at 11:40 AM, Selena Niu wrote:
Has anyone analyzed Illumina 550K data using DNAcopy package? I have
around
2300 samples. According to
Venkatraman and Olshen 2007 paper, it needs about 25 min to run a
single
sample for Affymetrix
These are all field measured values.
For a little background here, I have field measurements of SO4, NO3 and NH4. I
used these variables in an atmospheric chemistry model to calculate PBW on a
line-by-line basis.
To bypass the use of the complex atmospheric chemistry model in the future, I
On Apr 21, 2009, at 12:37 PM, Vemuri, Aparna wrote:
These are all field measured values.
For a little background here, I have field measurements of SO4, NO3
and NH4. I used these variables in an atmospheric chemistry model to
calculate PBW on a line-by-line basis.
To bypass the use of
I'd be happy if everyone made a minimal effort to solve their problems
before posting. There may be 130 pages of printed FAQs, but the
html file is fully searchable. It would be easier to browse with a good ToC,
but it's not that overwhelming to _look to see if there's a FAQ related to
your
Redhat's Security Enhanced Linux (in some modes)
generates messages like that when code in a shared library
is not compiled to have position independent code.
I.e., the -fpic or -fPIC flag was not supplied when
compiling. Your build log showed that -fpic was used
when compiling your code, but the
Is there a way of listing the variables contained in a file created
with the save() command other than load()ing the file?
I have a couple of rather larger files that I would rather not load ...
Benno Pütz
MPI of Psychiatry Tel: +49+(0)89-30622 222
Kraepelinstr. 2
Can't you just read in the very first line of the file (that contains names)?
Dimitri
2009/4/21 Benno Pütz pu...@mpipsykl.mpg.de:
Is there a way of listing the variables contained in a file created
with the save() command other than load()ing the file?
I have a couple of rather larger files
Jason:
Thanks for posting this ... interesting.
A guess: Depends on the problem, the hardware, the matrix libraries,...
e.g. in relatively small problems, Revolution's overhead may consume more
time and resources than the problem warrants. In others, you may see many
fold improvements. Very
Dear All,
Apologies if this is too simple for this list.
Let us assume that you have an instrument measuring particle distributions.
The output is a set of counts {n_i} corresponding to a set of average
sizes {d_i}.
The set of {d_i} ranges from d_i_min to d_i_max either linearly of
Thank you all. Warnings well-taken.
My question arose in the context of my Applied Categorical Data
Analysis course. We're mainly using SAS. Recent homework questions have
been of the form, The file provides data on 4 variables A, B, C, and D.
Find a good-fitting model . . . [more questions about
That's our guess too. We're running some tests now on the code to see
what's going on, and it's entirely possible the performance gains are
a function of the problem size, so we're testing that too. Changes in
R between 2.7.2 (upon which REvolution R is currently based) and 2.9.0
are also a
Hi Lorenzo,
I think it would be better if you provided a few example
datasets/tables. Right now, I can't exactly circumscribe your problem.
When binning data, the cut() function tends to be very useful. To fit
common univariate distributions to a given dataset, you should take a
look at the
Hello,
I wrote the function below to integrate polysplines and thought that
it may be useful to others. Please consider this code released under
the GPL2 or later.
Thanks,
Bill
integrate.polySpline.txt
Notice: This e-mail message, together with any attachments, contains
Hi, I was looking for the fisher test to use on my data (no normal, non
symetrical and because is median what i'm looking for I don't what to
made bootstraping) to test the median Ho=1, but I'm not sure if
Fisher.test in R is what I need or I just don't know how to use it.
Here is the example
Have also a look at package bootStepAIC.
Best,
Dimitris
Christopher W. Ryan wrote:
Thank you all. Warnings well-taken.
My question arose in the context of my Applied Categorical Data
Analysis course. We're mainly using SAS. Recent homework questions have
been of the form, The file provides
Hi,
I'm trying to make multiple plots in a same graph window in R.
The multiple graphs are showing up in the right positions on the window, but
I'm having the problem that the graphic window is being refreshed every time a
new plot is drawn, so that I end up with only the last graph coming
On Apr 21, 2009, at 12:58 PM, BARRES-DE-ALMEIDA U. wrote:
Hi,
I'm trying to make multiple plots in a same graph window in R.
The multiple graphs are showing up in the right positions on the
window, but I'm having the problem that the graphic window is being
refreshed every time a new
Dear R People:
Is there a Quality Control in R book that would be accessible for
undergraduates, please?
I'm teaching a QC course in the fall semester and would be happy to
have a Use R book or something like that, please.
Thanks in advance,
Erin
--
Erin Hodgess
Associate Professor
I finally found the problem within my site_data object...
this works well:
snip
site_data - sqlQuery(channel, select site_no from [biomass_data$]
group by site_no)$site_no
for(i in site_data) {
assign(paste(site,i,_data,sep=), sqlQuery(channel,
paste(select * from [biomass_data$] where
Hi all,
I would like to know how to do a plot with 2 y axes in R. With google,
I found this topic has been discussed twice in the past:
- http://tolstoy.newcastle.edu.au/R/e2/help/06/11/6049.html
- https://stat.ethz.ch/pipermail/r-help/2000-September/008182.html
Those links provide quite a
If you call
par(new=TRUE)
after each call to par(fig=c(xmin,xmax,ymin,ymax))
then a subsequent call to plot() will not erase
the page.
In S+ the par(new=TRUE) is not needed, but it does
no harm.
Bill Dunlap
TIBCO Software Inc - Spotfire Division
wdunlap tibco.com
How can I delete both rows and columns that do not meet a particular cut off
value.
Example:
d - rbind(c(0,1,6,4),
+ c(2,5, 7,5),
+ c(3,6,1,6),
+ c(4,4,4,4))
f - as.matrix(d)
f
[,1] [,2] [,3] [,4]
[1,]0164
[2,]257
When I remake those variables and try ccf(do1,dr1), the plot appears
reasonable. What problem were you experiencing? It looks as though
your method of differencing (whatever it was) offset the date
registration of the zoo series in dr2, but ccf(do1, dr2) still does
not appear to choke on
f[rowSums(f=1)0,colSums(f=1)0]
Judging from your result, you want less than or equal to 1.
HTH,
Stephan
Crosby, Jacy R schrieb:
How can I delete both rows and columns that do not meet a particular cut off
value.
Example:
d - rbind(c(0,1,6,4),
+ c(2,5, 7,5),
+ c(3,
On 22/04/2009, at 8:34 AM, Crosby, Jacy R wrote:
How can I delete both rows and columns that do not meet a
particular cut off value.
Example:
d - rbind(c(0,1,6,4),
+ c(2,5, 7,5),
+ c(3,6,1,6),
+ c(4,4,4,4))
f - as.matrix(d)
f
[,1] [,2]
Christophe Dutang1 wrote:
I would like to know how to do a plot with 2 y axes in R. With google,
I found this topic has been discussed twice in the past:
- http://tolstoy.newcastle.edu.au/R/e2/help/06/11/6049.html
- https://stat.ethz.ch/pipermail/r-help/2000-September/008182.html
Those
This is what I get.
ccf(do1,dr1)
Errore in na.fail.default(ts.intersect(as.ts(x), as.ts(y))) :
valore mancante nell'oggetto #italian translation of 'missing values in
object'
ccf(do1,dr2)
Errore in na.fail.default(ts.intersect(as.ts(x), as.ts(y))) :
valore mancante nell'oggetto #italian
I thought of testing the difference in deviance between the null model
and the fitted model, assuming it is distributed as chi-sq. However,
Faraway writes that if the outcome is binary, the deviance
distribution is far from chisq.
I've done a permutation test:
N-5000; # Towards the upper limit,
If you were doing that with the full sized do1 and dr1, then my guess
would be different data as the root cause. If you were doing this on
the tiny sample objects that I created from your dput output, then I
don't have an answer, since there were no missing values in those
objects.
--
Rolf Turner wrote:
On 22/04/2009, at 8:34 AM, Crosby, Jacy R wrote:
How can I delete both rows and columns that do not meet a particular
cut off value.
Example:
d - rbind(c(0,1,6,4),
+ c(2,5, 7,5),
+ c(3,6,1,6),
+ c(4,4,4,4))
f -
The problem is that I was doing that for the tiny sample objects.
So I really have no clue about
David Winsemius wrote:
If you were doing that with the full sized do1 and dr1, then my guess
would be different data as the root cause. If you were doing this on
the tiny sample objects
Wacek Kusnierczyk wrote:
Rolf Turner wrote:
d[apply(d,1,function(x){any(x=1)}),apply(d,2,function(x){any(x=1)})]
... or gain a bit on performance by doing the threshold comparison on
the whole matrix just once at once:
dd = d = 1
d[apply(d, 1, any), apply(d, 2, any)]
Hi Wacek,
Wacek Kusnierczyk schrieb:
... or gain a bit on performance by doing the threshold comparison on
the whole matrix just once at once:
dd = d = 1
d[apply(d, 1, any), apply(d, 2, any)]
d[apply(dd, 1, any), apply(dd, 2, any)]
Or not?
Cheers,
Stephan
When I get such unexpected behavior, I generally reinstall software. I
am currently using the Urbanek prepared MacOSX 2.8.1 binary under
Leopard with the 64 bit GUI. The stats package is part of the core
distribution, so reinstalling the stats package would mean
reinstalling R. Other
Hello,
I am trying to import SAS files into R using sas.get() in Hmisc. I am
running both SAS and R on a UNIX server. I've pasted my command and
ensuing errors below:
sas.get(lib=EOG, mem=eog3pub00_1)
Error in if (status != 0) { : argument is of length zero
In addition: Warning message:
In
Here you are
dput(do1[1:10])
structure(c(0.0818, 0.008, 0.172,
-0.0311, 0, 0.629, -0.317,
-0.433, -0.469, -0.359), index =
structure(c(9497,
9498, 9499, 9500, 9503, 9504, 9505, 9506,
Surely Faraway does not suggest using the Wald statistic in preference
to the deviance?
Even if the distribution of deviance is not exactly chi-square, it
appears generally accepted that a comparison of the difference in
deviance to the chi-square statistic is better than using the ratio
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Nirav Mehta
Sent: Tuesday, April 21, 2009 3:46 PM
To: r-help@r-project.org
Subject: [R] sas.get() exit
Hello,
I am trying to import SAS files into R using sas.get() in
Hi, I'm actually running Linux - is Hmisc broken for that as well? I
saw the previous discussion, but had assumed it was only for Windows
machines.
On Tue, Apr 21, 2009 at 7:04 PM, Nordlund, Dan (DSHS/RDA)
nord...@dshs.wa.gov wrote:
-Original Message-
From: r-help-boun...@r-project.org
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Nirav Mehta
Sent: Tuesday, April 21, 2009 4:11 PM
Cc: r-help@r-project.org
Subject: Re: [R] sas.get() exit
Hi, I'm actually running Linux - is Hmisc broken for that as well? I
Someone pointed out that Hmisc, version 3.4-4 works just great with
R-2.8.1 on Linux. I downgraded the package version from 5 and it now
works wonderfully.
Thanks for looking, and your help!
On Tue, Apr 21, 2009 at 7:04 PM, Nordlund, Dan (DSHS/RDA)
nord...@dshs.wa.gov wrote:
-Original
Hi everyone,
I am wandering if someone was able to get an anova table using the function lmer
in lme4 package with an other distribution than gaussian (ex: poisson). In fact,
I am using a GLMM with a poisson distribution where I have 2 independant fixed
variables (coded as factors with
Dear all,
I have a data frame that looks like this:
dat
V1 V2 V3
1 0.000 2 554889
2 2.001 09978
3 0.342 35263
4 123.000 03209
5 0.004 02434
I want to get a subset of that data
Dear R users,
I meet with an unsolved error when using the function vcovHC() in package
sandwich().
I have a balanced panel dataset, and I run the following codes:
library(plm)
data-plm.data(data, c(state,year))
fn-plm(y~x1+x2, data=data, method=within, effect=individual)
library(lmtest)
On Apr 21, 2009, at 7:52 PM, Gundala Viswanath wrote:
Dear all,
I have a data frame that looks like this:
dat
V1 V2 V3
1 0.000 2 554889
2 2.001 09978
3 0.342 35263
4 123.000 03209
5 0.004
On 21/04/2009 8:52 PM, Gundala Viswanath wrote:
Dear all,
I have a data frame that looks like this:
dat
V1 V2 V3
1 0.000 2 554889
2 2.001 09978
3 0.342 35263
4 123.000 03209
5 0.004
Is your first model a special case of the second with eta1 = 0?
If yes, what about using 2*log(likelihood ratio) being approximately
chi-square?
Can you recast the problem to use nls? If yes, might the 'nls'
methods for 'anova' or 'profile' give you what you want?
Hope
Dear all,
We have created an R package and submitted it to C-RAN. The package
includes several C functions that use Rmath library. The package cannot
be installed on a computer where -lRmath is not found. We were
suggested to do a configure test for this but I am not really sure how
to do this
On 21/04/2009 9:39 PM, Volodymyr Melnykov wrote:
Dear all,
We have created an R package and submitted it to C-RAN. The package
includes several C functions that use Rmath library. The package cannot
be installed on a computer where -lRmath is not found. We were
suggested to do a configure test
You may refer to the R News article on qcc package by Scrucca.
http://cran.r-project.org/doc/Rnews/Rnews_2004-1.pdf
On Wed, Apr 22, 2009 at 4:00 AM, Erin Hodgess erinm.hodg...@gmail.com wrote:
Dear R People:
Is there a Quality Control in R book that would be accessible for
undergraduates,
In addition to the refs already provided, I have read both R Graphics by Paul
Murrell and Lattice by Deepayan Sarkar, and can highly recommend both of them.
Bala subramanian wrote:
Friends,
i) I am new to R. Kindly suggest some resources that has examples of
plotting with R.
ii) How to set
I ran the memory limit function in R 2.9.0 and received the 'error'
below. The memory appears to update correctly, so there's probably no
implication beyond cosmetic; however, thought I would make sure since the
function as written did not generate the same error in my 2.8.0 version of
R.
Thanks
Hi!
I'm at the very beggining of my R experience and I'm hoping someone can
point me in the right direction. I want to create a script that locates all
files within a directory tree that have certain keywords in their file
names, checks these against files in another location, then copies files
On Tue, 21 Apr 2009 21:49:36 -0400
Duncan Murdoch murd...@stats.uwo.ca wrote:
On 21/04/2009 9:39 PM, Volodymyr Melnykov wrote:
Dear all,
We have created an R package and submitted it to C-RAN. The package
includes several C functions that use Rmath library. The package
cannot be
R is certainly not the natural tool you would use for this, but with effort it
could be done, I think.
dir(..., recursive = TRUE)
will list files descending down a directory tree. You may then need to use
things like basename() to strip off the directory names, grep() to search for
the
I wonder whether it is possible in R to generate color-coded 3D plots, like
the attached example.
Basically a function f(x,y) (the 3rd dimension) is rendered through colors
intensities. The side color-bar is a guide to the
interpretation of the plot.
Thank you very much,
Maura
e tutti i
David,
Faraway suggests using the Hosmer Lemeshow test in the case of a
binary response, and discusses the inadequacy of Wald statistics.
However, I'm not sure it applies here due to the limited number of
cases.
Thanks, Ehud.
On Wed, Apr 22, 2009 at 2:04 AM, David Winsemius
set.seed(999)
abs(rnorm(20))
[1] 0.28174016 1.31255963 0.79518398 0.27007049 0.27730642 0.56602374
1.87865826 1.26679114 0.96774968 1.12100936 1.32546371 0.13397739
0.93874945
[14] 0.17253810 0.95765045 1.36268625 0.06833513 0.10065765 0.90134475
2.07435711
v - abs(rnorm(20))
v
[1] 1.2285633
The attachment didn't come through, but try:
example(filled.countour)
#or
library(lattice)
example(levelplot)
hth,
Kingsford Jones
On Tue, Apr 21, 2009 at 9:46 PM, mau...@alice.it wrote:
I wonder whether it is possible in R to generate color-coded 3D plots, like
the attached example.
I changed the condition to:
highlyCor-cbind(rownames(x)[row(x)[((x 0.9)|(x(-.9)))]],
colnames(x)[col(x)[((x 0.9)|(x(-.9)))]])
Actually what I am trying to do is run factor analysis on this 923 by 925 x
matrix but many of the variables where too highly correlated and so I got
some message
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