On Tue, 27 May 2008, T.D.Rudolph wrote:
In the following example:
x - rnorm(1:100)
y - seq(from=-2.5, to=3.5, by=0.5)
z - as.matrix(table(cut(x,c(-Inf, y, +Inf
## I wish to transform the values in z
j - log(z)
## Yet retain the row names
row.names(j)-row.names(z)
Hmm. The rownames
Hi Marcus!
On Wednesday 28 May 2008 05:56, Marcus Vinicius wrote:
Dear all,
May anyone explain to me how I run a linear programming or Data
Envelopment Analysis (DEA models) into R?
Package DEA (on CRAN):
http://cran.r-project.org/web/packages/DEA/index.html
Package FEAR (NOT on CRAN):
Hi everyone,
I run the R loops on window XP and vista. Both are Intel core 2 Duo
2.2 GHz with 2 GB ram and XP is significantly faster than vista. Dose
anyone know how speed up R loops in vista?
Thank you in advance.
Chunhao Tu
__
Ullrich Ecker ullrich.ecker at uwa.edu.au writes:
I am fairly new to R, and I am aware that others have had this
problem before, but I have failed to solve the problem from previous
replies I found in the archives.
Now, I want to calculate a post-hoc test following up a within-subjects
Dear R users,
The May 2008 issue of `R News' is now available on CRAN under the
Documentation/Newsletter link.
John
(on behalf of the R News Editorial Board)
John Fox, Professor
Department of Sociology
McMaster University
Hamilton ON Canada L8S 4M4
Hello,
I am just about to install R and was wondering about a few things.
I have only worked in Matlab because I wanted to do a logistic
regression. However Matlab does not do logistic regression with
stepwiseforward method. Therefore I thought about testing R. So my
question is
can I do
Hi Duncan,
Duncan Murdoch wrote:
Duncan Murdoch wrote:
Esmail Bonakdarian wrote:
Hello all,
I have a matrix of bit values.
I compute certain values based on the bits in each row. There may be
*duplicate* entries in the matrix, ie several rows may be identical.
These rows change over time,
From the NEWS file for R-patched:
o A field containing just a sign is no longer regarded as numeric
(it was on all platforms in 2.7.0, but not on most in earlier
versions of R).
So the default behaviour has already been changed. The right way to
overcome this was (as
Muhammad Azam wrote:
Respected R helpers/ users
I am one of the new R user. I have a problem regarding to know which of the
integer in each column of the following matrix is in majority. I want to know
that integer e.g. in the first column 1 is in majority. Similarly in the third
column 4
I don't know if this helps, but recently I tried to use rmeta to make
a forest plot and gave up because the data I had were not in the right
format, so I simulated a forest plot using gplots. I did it all
sideways and then rotated the PostScript. See
Great R people,
I have noticed a strange behaviour in read.delim() and friends in the R
2.7.0 version. I will describe you the problem and also the solution I
already found, just to be sure it is an expected behaviour and also to
tell people, who may experience the same difficulty, a way to
Hi everyone,
I am fairly new to R, and I am aware that others have had this
problem before, but I have failed to solve the problem from previous
replies I found in the archives.
As this is such a standard procedure in psychological science, there
must be an elegant solution to this...I think.
Hello all,
I've come across an online posting
http://www.biostat.wustl.edu/archives/html/s-news/2001-10/msg00119.html
that described how to get confidence intervals for predicted values from
predict.glm. These instructions were meant for S-Plus. Yet, it generally seems
to work with R too,
Hi,
Is there an R function or package that computes
p-value?
-GV
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented,
[EMAIL PROTECTED] wrote:
This is somewhat subtle.
Rolf's solution (here corrected to...)
a - list()
for(i in 0:1) a[[i+1]] - i
is the best of the loop solutions (or at least the best I know of). The
But Bill does know a better way -- it just slipped his mind.
system.time({ a -
Respected R helpers/ users
I am one of the new R user. I have a problem regarding to know which of the
integer in each column of the following matrix is in majority. I want to know
that integer e.g. in the first column 1 is in majority. Similarly in the third
column 4 is in majority. So what is
Muhammad Azam:
I am one of the new R user. I have a problem regarding to know which of
the integer in each column of the following matrix is in majority. I want
to know that integer e.g. in the first column 1 is in majority.
x=matrix(c(1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,4,1,2,3,3),ncol=4)
x
I feel the discussion about ease of installation on Linux (/*NIX type
systems) isn't really relevant to the Pros and Cons of R.
The problems encountered by people are often a consequence of their lack of
knowledge/understanding of the operating system, and not a deficiency of R
itself.
Just my
Hallo!
I found a question exactly as mine, but I did not found an answer. Therefore I
post this again - hopefully there will be an answer!
Thanks in advance!
karl
From: Berta ibanez
Date: Tue, 27 Feb 2007 18:58:48 +0100
Hi R-users,
I want to calculate the sample size needed to carry out a
Hi,
I wish to extract a subset of the information of given by
summary(lmer.object) as a dataframe. In particular, I wish to extract
just a table listing the Estimate, Std Error, and t-values rounded to
3 decimal places. I have learned how to extract the coefficients with
Hello,
well, I searched list-archive, cran and the references, but found
nothing. Thus:
Does anybody around here know anything about Dempster-Shafer Theory,
Evidence Theory or Hints in R? Has anybody stumbled about a package that
I overlooked or implemented something in this area? I really would
I am working on a project to find a model for the concentration of dissolved
oxygen in the river clyde. Ive fitted a linear mixed model as
lme(DOW~Temperature+Salinity+Year+factor(Station)*factor(Depth),
random~1|id), where id is an identifier of the day over 20 years defined as
Day*1 +
Ardia David [EMAIL PROTECTED] writes:
Great, thanks a lot! It works properly now.
By the way, how can I get rid of the warning message :
* checking line endings in C/C++/Fortran sources/headers ... WARNING
Found the following sources/headers with CR or CRLF line endings:
Should I open an
Jen,
try
na.action = na.exclude
Andrew
On Wed, May 28, 2008 9:26 pm, Jen_mp3 wrote:
I am working on a project to find a model for the concentration of
dissolved
oxygen in the river clyde. Ive fitted a linear mixed model as
lme(DOW~Temperature+Salinity+Year+factor(Station)*factor(Depth),
Dear Brian and Bill,
Here's an interesting contrasting example (taken from this month's Help Desk
column in R News, which Bill has already seen), first verifying the relative
timings for Brian's example:
system.time({
+ a - vector(list, 10001)
+ for(i in 0:1) a[[i+1]] - i
+ })
user
Christoph,
I see two problems:
(1) use plot(x,y,pch=16,xlim=c(0,10),asp=1), as the default has the x/y scales
different.
(2) It looks to me that the expression srt=180/pi*atan(slope) should be
srt=180*atan(slope)/pi
Regards,
Tom
Dr. Christoph Scherber wrote:
Dear all,
I stumbled over a
Dear Chunhao Tu,
There is, coincidentally, a discussion of loops and related issues in the
Help Desk column in the current issue of R News (see the newsletter link on
CRAN).
Regards,
John
--
John Fox, Professor
Department of Sociology
McMaster University
Hamilton,
On Wed, May 28, 2008 at 02:29:10PM +0200, Martin Maechler wrote:
EH == Erin Hodgess [EMAIL PROTECTED]
on Sun, 25 May 2008 13:27:04 -0500 writes:
EH Try: ./configure --with-x=no
well.. no! really don't.
Seconded.
At best this qualified for the 'then do not do it' school
I am trying to simulate a series of ones and zeros (1 or 0) and I am using
rbinom but realizing that the number of successes expected is not accurate.
Any advice out there.
This is the example:
N-500
status-rbinom(N, 1, prob = 0.15)
count-sum(status)
15 percent of 500 should be 75 but what I
A google search for logistic regression with stepwise forward in r
returns the following post:
https://stat.ethz.ch/pipermail/r-help/2003-December/043645.html
Haris Skiadas
Department of Mathematics and Computer Science
Hanover College
On May 28, 2008, at 7:01 AM, Maria wrote:
Hello,
I am
Kim,
Is is what you want?
tmp - readLines(textConnection(
TGCATACACCGACAACATCCTCGACGACTACACCTACTACG
CGCCTACACCAACGATGTCCTGGACGACTTCTGCTACTACG
CGCCTACACCAACGATGTCCTGGACGACTTCTGCTACTACG
CGCCTACACCAACGATGTCCTGGACGACTTCTGCTACTACG
CGCCTACACCAACGATGTCCTGGACGACTTCTGCTACTACG
On Wed, 28 May 2008, John Fox wrote:
Dear Brian and Bill,
Here's an interesting contrasting example (taken from this month's Help Desk
column in R News, which Bill has already seen), first verifying the relative
timings for Brian's example:
system.time({
+ a - vector(list, 10001)
+
You asked for each of 500 to be included with probability 0.15, not for
15% of 500. If you want the latter, use sample, e.g.
sample(c(rep(1,75), rep(0,425)))
And to see if your 77 is reasonable for binomial sampling:
binom.test(77, 500, 0.15)
Exact binomial test
data: 77 and 500
On 28-May-08 12:53:26, Philip Twumasi-Ankrah wrote:
I am trying to simulate a series of ones and zeros (1 or 0) and I am
using rbinom but realizing that the number of successes expected is
not accurate. Any advice out there.
This is the example:
N-500
status-rbinom(N, 1, prob = 0.15)
Do it again. What did you get this time? Then do it another time. Do you
see what is happening?
Charles Annis, P.E.
[EMAIL PROTECTED]
phone: 561-352-9699
eFax: 614-455-3265
http://www.StatisticalEngineering.com
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
I remember reading the colSum and colMean were better, when you need
sums and means
On Wed, May 28, 2008 at 8:26 AM, Esmail Bonakdarian [EMAIL PROTECTED] wrote:
Neil Shephard wrote:
Loops are not massively efficient within R.
Look into using the apply() family of functions
Teds reply is a bit comforting and as indicated in my post, I am resorting to
using sample but as an academic issue, does randomness preclude precision?
Randomness should be in the sequence of zeros and ones and how they are
simulated at each iteration of the process but not in the eventual
Neil Shephard wrote:
Loops are not massively efficient within R.
Look into using the apply() family of functions
(eapply()/lapply()/mapply/rapply()/tapply()).
Didn't someone post not too long ago that apply is
internally represented as a for-loop? Or am I not
remembering this correctly?
The
Dear Ben,
Given a set of words
('foo', 'bar', 'bar', 'bar', quux . foo) this can be in 10.000 items.
I would like to compute the significance of the word occurrence with P-Value.
Is there a simple way to do it?
- GV
On Wed, May 28, 2008 at 11:46 PM, Ben Bolker [EMAIL PROTECTED] wrote:
Philip Twumasi-Ankrah nana_kwadwo_derkyi at yahoo.com writes:
Teds reply is a bit comforting and as indicated in my post,
I am resorting to
using sample but as an academic
issue, does randomness preclude precision?
Randomness should be in the sequence of zeros and ones and
how they
What do you mean by ... *eventual* nature of the distribution? If you
simulated 100 samples, would you expect to see 1.5 successes? Or 1? Or 2?
How many, in your thinking, is eventual?
Charles Annis, P.E.
[EMAIL PROTECTED]
phone: 561-352-9699
eFax: 614-455-3265
Dear all --
I want to compute weighted.mean() for grouped rows.
Data frame extract is just below. For each Key, I want the mean of
IAC weighted by Wt.
DP0[1:20,]
Key
IACWt
2 C3-PD030020050.PD030020050.3.12.3.0 0.765
Dear R-community,
I'm looking forward to analyse the results statistically
for a new medical diagnostic tool. The aim is to know whether a given
subject is different from the mean or distribution of a population of
controls for one continuous variable (a neuro-imaging results which
can be
Thanks, that worked!
Andrew Robinson-6 wrote:
Jen,
try
na.action = na.exclude
Andrew
On Wed, May 28, 2008 9:26 pm, Jen_mp3 wrote:
I am working on a project to find a model for the concentration of
dissolved
oxygen in the river clyde. Ive fitted a linear mixed model as
Dear R users,
I want to estimate a Cox PH model with time-dependent covariates so I am
using a counting process format with the following formula:
Surv(data$start, data$stop, data$event.time) ~ cluster(data$id) + G1 +
G2 + G3 + G4 + G5 +G6
Gs represent a B-spline basis functions so they
I think I see the rub: You would like to see the distribution of a sample
be identical to the distribution from which it was sampled. But if it is
random then that can happen only in the long run, not on every sample. That
is why samples from a normal density are *not* themselves normal -
Hi Maria,
But why do you want to use forwards or backwards
methods? These all are 'backward' methods of modeling.
Try using AIC or BIC. BIC is much better than AIC.
And, you do not have to believe me or any one else on
this.
Just make a small data set with a few variables with
known
Hallo,
i tried writing a function to extract
all the odds ratio's from a ftable:
(+ p.adjust needs to build in)
So i tried the following:
ORCalcul - function(m) {
or-matrix(1:(length(m[,1])-1)*(length(m[1,])-1)*5,length(m[,1])-1,length(m[1,])-1)
for(i in 1:length(m[,1])-1) {
Hello -
Chip Barnaby wrote:
Dear all --
I want to compute weighted.mean() for grouped rows.
Data frame extract is just below. For each Key, I want the mean of IAC
weighted by Wt.
DP0[1:20,]
Key
IACWt
2
Hi there,
I would like to know if it is possible to modify a text file with a R function.
In fact I would like to know if a function Search Replace exists.
My problem is to create config files from a Base file in which I have to modify
values of parameters.
My Base File:
#...
#...
Param1=
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Gundala Viswanath wrote:
| Dear Ben,
|
| Given a set of words
| ('foo', 'bar', 'bar', 'bar', quux . foo) this can be in 10.000
items.
| I would like to compute the significance of the word occurrence with
P-Value.
|
| Is there a simple way to
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf
Of Philip Twumasi-Ankrah
Sent: Wednesday, May 28, 2008 6:52 AM
To: [EMAIL PROTECTED]
Cc: r-help@r-project.org
Subject: Re: [R] rbinom : Does randomness preclude precision?
Teds reply is a bit
Hello R Freaks,
I calculate the difference in days between two events with the following
litte R expresseion:
T1a - strptime(T1,%m/%d/%y %H:%M:%S);
T2a - strptime(T2,%m/%d/%y %H:%M:%S);
T1b - as.Date(T1a);
T2b - as.Date(T2a);
days - T2b-T1b;
time - T2a - T1a;
In the project I would like to
Hello. I know how to make a bar plot in which a numeric y variable is
plotted against some grouping variable X (say, groups A, B, C) when this
grouping variable is subdivided into each of two subgroups; so the bars
would be: (group A subgroup 1) beside (group A subgroup 2), then (group B
subgroup
At 10:25 AM 5/28/2008, Esmail Bonakdarian wrote:
Erin Hodgess wrote:
I remember reading the colSum and colMean were better, when you need
sums and means
Well .. I'm waiting for the experts to jump in and give us the
straight story on this :-)
All of the algorithms are represented internally
See ?is.holiday in chron. You need to supply
a .Holidays vector and then do this:
library(chron)
d1 - Sys.Date()
d2 - Sys.Date() + 100
sq - sq(d1, d2, by = day)
sum(!is.holiday(sq) !is.weekend(sq)) # endpoints included
The fCalendar package also has functionality in this area.
On Wed, May
Lars Fischer lars at sec.informatik.tu-darmstadt.de writes:
Hello,
well, I searched list-archive, cran and the references, but found
nothing. Thus:
Does anybody around here know anything about Dempster-Shafer Theory,
Evidence Theory or Hints in R? Has anybody stumbled about a package
alicia.senauer at yale.edu writes:
I am trying to use R lm() with quantitative and qualitative predictors, but am
getting different results than those that I get in SAS.
In the R ANOVA table documentation I see that Type-II tests corresponds to
the
tests produced by SAS for
Bill Shipley bill.shipley at usherbrooke.ca writes:
Hello. I know how to make a bar plot in which a numeric y variable is
plotted against some grouping variable X (say, groups A, B, C) when this
grouping variable is subdivided into each of two subgroups; so the bars
would be: (group A
I did have the problem of not having two continuous variables and this
approach circumvents this, allowing me in fact to plot the rownames.
Prof Brian Ripley wrote:
On Tue, 27 May 2008, T.D.Rudolph wrote:
In the following example:
x - rnorm(1:100)
y - seq(from=-2.5, to=3.5, by=0.5)
Hi folks,
I have five imputed data sets and would like to apply the same
recoding routines to each. I could do this sort of thing pretty
easily in Stata using MIM, but I've decided to go cold turkey on other
stats packages as a incentive for learning more about R. Most of the
recoding is for
Dear all
nbsp;
I wish to carry out sigma- and beta-convergence analysis in respect of panel
data [wherein current value of one of the variables needs be regressed upon
suitably transformed lagged values of another variable(s)]. I am quite new to
the R-language and am not very much aware of the
Hi I am still fairly new to R but picking it up quickly. I have some
problems manipulating data in tables. I was wondering if anyone new any good
resources such as an R manual. Some of the intro pdfs I viewed do not show
how...much appreciated.
[[alternative HTML version deleted]]
Dear Donald,
I can't guarantee that there aren't other problems, but your call to
update() is in error; you need
allmis - update(allmis, white = recode(RACE, '1=1; else=0; '))
not
allmis - update(allmis, white - recode(RACE, '1=1; else=0; '))
[The last ; in the recode specification is
Dear R Community,
I have a dataframe like this
dat product1 product2 ... productn
01.1.2008 1 1 1
02.1.2008 1 1 2
.
15.2.2008 2 2 NA
.
04.4.2008 2 2 1
05.4.2008 NA 2
Hi, I've seen in the NestCohort package that one can do a hazard model with a
binary outcome using covariates. I am interested in multistate hazard models
with time-varying covariates, but can't seem to find this already implemented
in an R package. Is this included somewhere but called
There is a very good book called Data Manipulation with R by Phil
Spector that just became available. It is brief and concise. I would
recommend that book for learning about manipulating data in tables.
For anyone interested in data exploration and graphics I would also
recommend Deepayan
Hi,
I'm trying to produce a plot of an image of a Matrix, but I don't get
other colors than the default grey scale:
image(Matrix(topo.matrix.2),col.regions=topo.colors(100),colorkey=FALSE)
this still is plotted in grey.
Is there any mistake in my syntax?
Thanks and regards,
Javier
--
Greetings helpRs --
I would like to use plot() to plot two cumulative distribution curves so
that a user of the plot can compare the distributions of the two
variables. The following code draws two distributions separately, but I
cannot find the instruction necessary to add a second
On 5/28/08, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote:
Hi,
I'm trying to produce a plot of an image of a Matrix, but I don't get
other colors than the default grey scale:
image(Matrix(topo.matrix.2),col.regions=topo.colors(100),colorkey=FALSE)
this still is plotted in grey.
Is there
step or stepAIC functions do the job. You can opt to use BIC by changing
the mulplication of penalty.
I think AIC and BIC are not only limited to compare two pre-defined
models, they can be used as model search criteria. You could enumerate
the information criteria for all possible models if
Hi,
I am reading the source code of rpart. I have problems understand the following
code and would appreciate for any helps. In rpart.s, there is a line:
rpfit lt;- .C(C_s_to_rp,
nbsp;nbsp;nbsp; nbsp;nbsp;nbsp; nbsp;nbsp;nbsp; n = as.integer(nobs),
nbsp;nbsp;nbsp; nbsp;nbsp;nbsp;
Xiaohui Chen wrote:
step or stepAIC functions do the job. You can opt to use BIC by changing
the mulplication of penalty.
I think AIC and BIC are not only limited to compare two pre-defined
models, they can be used as model search criteria. You could enumerate
the information criteria for
Frank E Harrell Jr 写道:
Xiaohui Chen wrote:
step or stepAIC functions do the job. You can opt to use BIC by
changing the mulplication of penalty.
I think AIC and BIC are not only limited to compare two pre-defined
models, they can be used as model search criteria. You could
enumerate the
[EMAIL PROTECTED] wrote:
Hi everyone,
I run the R loops on window XP and vista. Both are Intel core 2 Duo
2.2 GHz with 2 GB ram and XP is significantly faster than vista. Dose
anyone know how speed up R loops in vista?
Thank you in advance.
Chunhao Tu
On Wed, May 28, 2008 at 03:47:49PM -0700, Xiaohui Chen wrote:
Frank E Harrell Jr ??:
Xiaohui Chen wrote:
step or stepAIC functions do the job. You can opt to use BIC by
changing the mulplication of penalty.
I think AIC and BIC are not only limited to compare two pre-defined
models,
Try gantt.chart in the plotrix package.
On Wed, May 28, 2008 at 1:54 PM, kljosc [EMAIL PROTECTED] wrote:
Dear R Community,
I have a dataframe like this
dat product1 product2 ... productn
01.1.2008 1 1 1
02.1.2008 1 1 2
.
Hi Stephen,
Have you looked at 'save' and 'load'?
As far as I understand, to really release the memory
you need to close R, so you may try to write a script
(shell script on Unix, batch file on Windows) which
invokes Rcmd to load the data, make an iteration and
save the result, so that R dies
Dear Brian and list members,
Thanks very much for your response Brian!
I applied the adjusted calculation that you advised me to use
[1/(1+exp(-upperlogit))] and as a result I don't get any more NA values in my
upper confidence interval values.
Yet, some outcomes are very akward, since for
Hi,
Suppose I have the following tabular data:
1729_at | TRADD | TNFRSF1A-associated via death domain | protein-coding
1773_at | FNTB | farnesyltransferase, CAAX box, beta | protein-coding
177_at | PLD1 | phospholipase D1, phosphatidylcholine-specific | protein-coding
What is the right
Using any 'significance level', I think is the main
problem in the stepwise variable selection method. As
such in 'normal' circumstances the interpretation of
p-value is topsy-turvy. Then you can only imagine as
to what happens to this p-value interpretation in this
process of variable
Hi all,
After running this code:
__BEGIN__
dat - read.table(gene_prob.txt, sep = \t)
n - length(dat$V1)
print(n)
print(dat$V1)
__END__
With this input in gene_prob.txt
__INPUT__
HFE 0.00107517988586552
NF1 0.000744355305599206
PML 0.000661649160532628
TCF30.000661649160532628
NF2
I would like to be able to extract the names of the variables in a formula that
specifies random effects. For example, given:
random = ~ 1+year | st_name
I'd like to be able to get year and st_name out of random. Neither
terms(random) nor random[2] seems to work. Is there a way to get
83 matches
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