On Fri, 8 Jul 2005, Florian Hahne wrote:
Dear listers,
I am trying to compute the exact conditional test given strata margins
of a 2 by 2 by K array using the mantelhaen.test function to get a
common odds ratio estimate.
The estimate for the test on the following data is 0, which in my
On Mon, 11 Jul 2005, Adaikalavan Ramasamy wrote:
I am not sure if there is an easy way around this. An ugly hack is to
make a copy the function survival:::plot.cox.zph and make your
modified function. But there are others in the list who might know
neater solutions.
If you then send a patch
On Wed, 13 Jul 2005, EJ Nikelski wrote:
Your suggestion that the unprintable characters represent UTF-8 encoded
Unicode left and right double quotes also appears correct. Now, although
the suggested work-around may well help, the foreign package does seem
to be creating a corrupted file. That
On Thu, 14 Jul 2005, Duncan Murdoch wrote:
On 7/14/2005 7:19 AM, Ginters wrote:
Why does memory need so much (1.6 GB) space? How can I enlarge it? Is it
possible to allocate a part of memory used to the hard drive? Or, is the
trouble only with my script?
This sounds like a problem with the
/dsc2005/program.html
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle
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PLEASE
On Fri, 15 Jul 2005, Kylie-Anne Richards wrote:
FIRST Q: The default uses the mean of 'vo' and mean of 'po', but what is it
using for the factors?? Is it the sum of the coef of the factors divided by
the number of factors??
It uses the mean of each factor variable. The $means component of
On Fri, 15 Jul 2005, David Groos wrote:
Thank you-all very much for your help, your responses and help has been
very encouraging. The following doesn't close the case but it tables
it...
First I copied Ken's code into my R Console and...it worked great!
That was baffling as it looked
On Sat, 16 Jul 2005, Kylie-Anne Richards wrote:
Thank you for your help.
In any case, to specify f.pom You need it to be a factor with the same set
of levels. You don't say what the lowest level of pom is, but if it is,
say, -3.
On Sat, 16 Jul 2005, Bernardo Rangel Tura wrote:
At 10:11 12/7/2005, [EMAIL PROTECTED] wrote:
hi all
why does R do this:
(-8)^(1/3)=NaN
the answer should be : -2
Yes and no.
The problem is that the reciprocal of 3 is not exactly representable as a
floating point number (it has an
On Sat, 16 Jul 2005, Thomas Lumley wrote:
Yes, but you don't need to go via the baseline. The survival curves for
any two covariate vectors z1 and z2 are related by
S(t; z1)= S(t; z2)^(z1-z2)
Actually
S(t; z1)=S(t;z2) ^(beta'(z1-z2))
of course.
-thomas
On Mon, 18 Jul 2005, Weiwei Shi wrote:
Hi,
I have a dataset with 2194651x135, in which all the numbers are 0,1,2,
and is bar-delimited.
I used the following approach which can handle 100,000 lines:
t-scan('fv', sep='|', nlines=10)
t1-matrix(t, nrow=135, ncol=10)
t2-t(t1)
one do this?
legend(-5, .3, substitute(hat(phi) == PHI, list(PHI = PHI)))
or
legend(-5, .3, bquote(hat(phi) == .(PHI)))
-thomas
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On Thu, 21 Jul 2005 [EMAIL PROTECTED] wrote:
Hi,
I have a question about the output for variance of random effect from a gamma
frailty model using coxph in R. Is it the vairance of frailties themselves or
variance of log frailties? Thanks.
For a Gamma frailty model it is the variance of
On Fri, 22 Jul 2005, Dan Bolser wrote:
On Fri, 22 Jul 2005, Gabor Grothendieck wrote:
Try as.expression(bquote(...whatever...))
Sob, wimper, etc.
a-7
plot(1)
legend(topleft,legend=do.call(expression,
list(bquote(alpha==.(a)),bquote(alpha^2+1==.(a^2+1)
On Fri, 22 Jul 2005, Gabor Grothendieck wrote:
I think legend accepts a list argument directly so that could be
simplified to just:
a-7
plot(1)
L - list(bquote(alpha==.(a)),bquote(alpha^2+1==.(a^2+1)))
legend(topleft,legend=L)
Except that it wouldn't then work: the mathematical stuff
On Mon, 25 Jul 2005, Petr Mandys wrote:
Thank you!
I'm using this:
require(NADA)
var_sf=survfit(Surv(a, !b))
var_result=new(cenfit, survfit=var_sf)
Class cenfit has methods to get mean a variance from survfit result. Is
this correct?
NADA is designed for left censoring. I don't know
On Mon, 25 Jul 2005, Wladimir Eremeev wrote:
Hello, all
Please, consider the following pieces of code.
1.
v-0.5
text(x=2,y=2,eval(substitute(expression(bold(S==V)),list(V=formatC(v,format=f,digits=2)
This plots S=0.5 in bold. Both S and 0.5 are bold.
2.
v-0.5
On Tue, 26 Jul 2005, Garrett Fox wrote:
I am trying to do logistic regression with a categorical predictor variable
with the glm() function, family=binomial. Using glm() I would like to be
able to calculate the confidence intervals of all three possible odds ratios
for a factor (the factor
On Wed, 27 Jul 2005, Peter Dalgaard wrote:
Adaikalavan Ramasamy [EMAIL PROTECTED] writes:
I think it is doing what is supposed to do but I never used read.spss,
so take this with a pinch of salt.
In R when you use as.integer on a factor, the one with the lowest level
gets a value of 1 and
On Wed, 27 Jul 2005, McGehee, Robert wrote:
However, the sink() does not seem to be capturing the error messages as
I would have hoped. That is, if the R-script is {print(abc);
stop(def)}, the print output is captured to the file, the stop error
message is not, and instead sent to the
-guide.html
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On Fri, 29 Jul 2005, John Sorkin wrote:
I am trying to model data in which subjects are followed through time to
determine if they fall, or do not fall. Some of the subjects fall once,
some fall several times. Follow-up time varies from subject to subject.
I know how to model time to the
On Fri, 29 Jul 2005, Dieter Menne wrote:
John Sorkin jsorkin at grecc.umaryland.edu writes:
I am trying to model data in which subjects are followed through time to
determine if they fall, or do not fall. Some of the subjects fall once,
some fall several times. Follow-up time varies from
On Mon, 1 Aug 2005, Chris Wallace wrote:
I am struggling with migrating some stata code to R. I have a data
frame containing, sometimes, repeat observations (rows) of the same
family. I want to keep only one observation per family, selecting
that observation according to some other
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On Wed, 3 Aug 2005, Vicky Landsman wrote:
Dear all,
I have a list containing 150 simulated datasets in R. Is there a way to
convert it to the Stata format such that I will be able to apply some Stata
functions on each dataset in the list?
For Stata your best best is probably to stack all
On Wed, 3 Aug 2005, array chip wrote:
Hi, I have a matrix with both positive and negative
numbers, I would like to use image() to draw a
heatmap. How can I can design a palette (or is there a
function already available) that treat negative
numbers in a blue gradient and positive numbers in a
On Thu, 4 Aug 2005, Jose Claudio Faria wrote:
I would like to suggest that all R functions/etc like:
codes-deprecated
grid-internal
ns-alt
ns-dblcolon
ns-hooks
ns-internals
ns-lowlev
ns-reflect.Rd
tools-internal
ts-defunct
utils-deprecated
utils-internal
... and another
On Thu, 4 Aug 2005, Matt Crawford wrote:
I understand that in R, for loops are not used as often as other
languages, and am trying to learn how to avoid them. I am wondering
if there is a more efficient way to write a certain piece of code,
which right now I can only envision as a for loop.
On Mon, 8 Aug 2005, Jake Michaelson wrote:
I use Mac OS X at home and Linux at work, so the R Aqua GUI has spoiled
me. I have not seen its equal so far (on Windows or Linux). The most
important thing to me is how easily accessible the help and
documentation is. I like how when I begin
On Tue, 9 Aug 2005 [EMAIL PROTECTED] wrote:
dear R wizards:
plot( 1, 1, ylim=(2,10), xlim=(2,10), type=n);
rect( -1, -1, 12, 12, col=gray(0.99) );
unfortunately wipes out the border axes around the plot. how do I keep
this?
I think you meant
plot( 1, 1, ylim=c(2,10), xlim=c(2,10),
On Wed, 10 Aug 2005, Gorjanc Gregor wrote:
Dear R-users!
I would like to fit exponential, Weibull and log-logistic via glm() like
functions. Does anyone know a way to do this? Bellow is a bit longer
description of my problem.
I think you want to use survreg(). It will still work when there
On Thu, 11 Aug 2005, Clark Allan wrote:
hi all
is there a package that undertakes subset selection but BASED ON AIC or
any other information criteria.
i've seen the subselect and the leaps package but i have not played
around with them yet.
The leaps package finds a best model of each
--
---
David L. Van Brunt, Ph.D.
mailto:[EMAIL PROTECTED]
[[alternative HTML version deleted]]
Thomas Lumley Assoc. Professor, Biostatistics
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On Sat, 13 Aug 2005, Prof Brian Ripley wrote:
I suspect you want
AdjForBase2 - function (data, inds)
and to refer to data[inds, 1] and data[inds, 2], but since your code is
completely devoid of spaces and indentation, I have paid it little
attention.
On Mon, 15 Aug 2005 [EMAIL PROTECTED] wrote:
Dear R wizards:
under R-2.1.0:
eargs - 3:5;
line - paste(c(echo A B, eargs));
cat(executing from R: ', line, '\n);
system(line);
Oddly, only A and B are echoed, not the eargs. I had hoped that
line would be one string at this point, and
On Fri, 19 Aug 2005, Fredrik Thuring wrote:
I have a few questions concerning reading of tables from R to
other programs. My main question is if it???s even possible to read a table
created in R (with the functions data.frame and save) to Excel (or
maybe SAS) and if so how does one do
On Fri, 19 Aug 2005, [iso-8859-1] G?ran Brostr?m wrote:
Similar strange results appear in other date-related functions. I plan to
write functions that converts, eg, 1977-01-31 to the real number 1977.084
and back. What function in R does what 'mdy.date' claims to do?
Well, mdy.date does
On Thu, 25 Aug 2005, Devarajan, Karthik wrote:
Hello
I am fitting a Cox PH model using the function coxph(). Does anyone know how
to obtain the estimate of the covariance matrix under the null hypothesis.
The function coxph.detail() does not seem to be useful for this purpose.
You can
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On Mon, 29 Aug 2005 [EMAIL PROTECTED] wrote:
Hello,
I'm interested in LaTeX notations in R graphs. For example, I would like to
know
the R code to obtain the graph here,
http://www.r-project.org/screenshots/power.png
Here is the code:
x-seq(-10,10,length=400)
y1-dnorm(x)
y2-dnorm(x,m=3)
On Fri, 2 Sep 2005, Brahm, David wrote:
In a clean environment under R-2.1.0 on Linux:
x - 1:5
x[3] - 9
Error: Object x not found
Isn't that odd? (Note x - 9 works just fine.)
Well, yes and no.
It is the result of a bug fix a version or two ago that dealt with the
case where there was
On Fri, 2 Sep 2005, Spencer Graves wrote:
Permit a mild protest on the word appropriate in this context. The
global assignment operator - provides, for my tastes, excessive
opportunities for problems. If I define x someplace else and then
call your function, it may change my x in
On Sat, 3 Sep 2005, John Sorkin wrote:
A question for R (and perhaps S and SPlus) historians.
Does anyone know the reason for the inconsistency in the way that the
action that should be taken when data are missing is specified? There
are several variants, na.action, na.omit, T, TRUE, etc. I
On Sat, 3 Sep 2005, A Das wrote:
Hi all, I've been trying to get a large (12mb) Stata
survey database into R. I managed that, but when I
attach survey weights, something goes wrong. The error
message is: object dchina not found. Here's the
script:
If that is the *first* message then
On Sun, 4 Sep 2005, A Das wrote:
Thanks, Thomas.
Yes, that's exactly what happened: the warnings
came first after data(China), and then after
dchina-svydesign... So the design object isn't
being produced? The dataset is very large, and the
weights were already set in Stata before
obsChina - subset(China, !is.na(psu) !is.na(strata) !is.na(weight0x))
and then use obsChina rather than China in the svydesign() function.
-thomas
-Bobby
--- Thomas Lumley [EMAIL PROTECTED] wrote:
On Sun, 4 Sep 2005, A Das wrote:
Thanks, Thomas.
Yes
On Mon, 5 Sep 2005, [EMAIL PROTECTED] wrote:
A trap easy to fall into!
So easy, in fact, that it's a FAQ.
-thomas
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On Tue, 6 Sep 2005, [EMAIL PROTECTED] wrote:
However, a related method available for 'optim' is L-BFGS-B
which allows _box constraints_, that is each variable can be
given a lower and/or upper bound. The initial value must satisfy
the constraints. This can be set in a parameter for 'mle'.
On Wed, 7 Sep 2005, Chris Buddenhagen wrote:
1) I have been really pleased with R as a means of doing and learning
statistics. I work in a Spanish speaking country- and I wanted to pass on
the benefits of R to my Spanish speaking colleagues. There are a couple of
introductions to R in Spanish
are known. I wouldn't use them except when I was
actually interested in the variance components, and I haven't worked on
any problems like that, so I haven't investigated the issue.
[I don't write the survival package, I just port it]
-thomas
Thomas Lumley Assoc
On Thu, 8 Sep 2005, John Sorkin wrote:
I have a batch of data in each line of data contains three values,
calcium score, age, and sex. I would like to predict calcium scores as a
function of age and sex, i.e. calcium=f(age,sex). Unfortunately the
calcium scorers have a very ugly distribution.
On Thu, 8 Sep 2005, Shige Song wrote:
Dear All,
The coxph function in the survival package allows multiple frailty
terms.
Um, no, it doesn't.
In all the examples I saw, however, the frailty terms are nested.
What will happen if I have non-nested (that is, cross-classified) frailties
in
On Thu, 8 Sep 2005, Erich Neuwirth wrote:
sapply(1:length(xxx),function(x)b[xxx[x],yyy[x]])
does what I need and produces
[1] 1 2 1 2 1 4 3 4 3 4
Is there a function taking xxx,yyy, and b as arguments
producing the same result?
b[cbind(xxx,yyy)]
Essentially, I am asking for a version of
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that this is
always true since the file format is undocumented).
However I could not find a description of this supposed change.
It's in the ChangeLog file in the foreign package.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University
On Fri, 9 Sep 2005, Heinz Tuechler wrote:
Dear Martin,
Thank you for your answer. As I said, I appreciate this change. The
documentation does not explain precisely, how variables with labels are
treated now. It only tells If SPSS value labels are converted to factors
the underlying numerical
://faculty.washington.edu/tlumley/survey/NEWS
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle
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On Sun, 11 Sep 2005, Arkady Sherman wrote:
c:\Program Files\R\rw2011\bin\R.exe --no-save test out.txt
the file c:/temp/foo.txt will contain nothing.
But I'd like it should contain the warning message Foo warning.
Is the behavior a bug of R or there is another way to get it working.
The
list
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On Mon, 12 Sep 2005, Chris Buddenhagen wrote:
Is there a simple means of doing this multiple comparison test in R?
p.adjust()
-thomas
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On Tue, 13 Sep 2005, [EMAIL PROTECTED] wrote:
A recent exchange on the 'octave' list led to the following
paper being cited, which I had not met before:
What Every Computer Scientist Should Know About
Floating-Point Arithmetic, by David Goldberg,
snip
So I'm writing to bring it to the
On Tue, 13 Sep 2005, Zhen Zhang wrote:
Hello everyone,
I tried to use coxph.detail() to get the hazard function. But a warning
messge always returns to me, even in the example provided by its help
document:
?coxph.detail
fit - coxph(Surv(futime,fustat) ~ age + rx + ecog.ps, ovarian,
On Thu, 22 Sep 2005, Anne wrote:
DeaR list
I would like to know if there is a direct method to compute the
expected remaining survival time for a subject having survived up to
time t. survexp gives me the probabilty for subject S to survive up to
day D
You can't estimate expected survival
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On Mon, 26 Sep 2005, Denis Chabot wrote:
But the mgcv manual warns that p-level for the smooth can be
underestimated when df are estimated by the model. Most of the time
my p-levels are so small that even doubling them would not result in
a value close to the P=0.05 threshold, but I have one
On Tue, 27 Sep 2005, Simon.Bond wrote:
Does anyone have any suggestions for a way round this problem for the
future (I had to resort to using Stata), or maybe more realistically, how
much work it would take to build an extendible version of the gee
algorithm?
I don't think it would take
On Tue, 27 Sep 2005, Ferran Carrascosa wrote:
Hi everyone,
I would like some package of R or any help to solve the next problem
with a weighting fatcors:
Giving a data matrix with dichotomous (2 or more) variables in columns
and individuals in rows, and also a theorical distribution of the
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On Wed, 28 Sep 2005, Denis Chabot wrote:
But what about another analogy, that of polynomials? You may not be sure what
degree polynomial to use, and you have not decided before analysing your
data. You fit different polynomials to your data, checking if added degrees
increase r2
On Thu, 29 Sep 2005, Karin Lagesen wrote:
I have a file like this:
a 0.1
a 0.2
a 0.9
b 0.5
b 0.9
b 0.7
c 0.6
c 0.99
c 0.88
Which I would like to get to be the following matrix:
0.1 0.20.30.4 ...
a 1
On Thu, 29 Sep 2005, Spencer Graves wrote:
Questions like this are best directed to the package maintainer(s).
From help(package=leaps), I learned that Thomas Lumley is the author and
maintainer for leaps; I'm including him as a 'cc', so he can correct or
add to my comments if he
On Fri, 30 Sep 2005, Mike Prager wrote:
Recent R function names seem to be using CaseOfTheLetters to mark words
rather than dots as was done previously. Is the use of dots in function
names deprecated, or is that simply a style choice? Will function names
with dots cause problems in future
On Fri, 30 Sep 2005, Erin Hodgess wrote:
Dear R People:
I have R Version 2.1.1. for Windows in binary form.
I would like to look at the C code for massdist. It is part
of the density function.
The .C() call shows that massdist is in the base package. This means that
it is likely to be
On Tue, 4 Oct 2005, Karin Lagesen wrote:
First, how does boxplot determine the size of the box? And is the line
inside the box the mean or the median (or something completely
different?) And how does it determine how long out the whiskers should
go?
Part of the problem is that there are lots
On Sat, 1 Oct 2005, Jim Hurd wrote:
Which provides data in DTA (STATA), XPT (SAS), and POR (SPSS) formats all
of which I have tried to read with the foreign package but I am not able to
load any of them. I have 2 gb of RAM, but R crashes when the memory gets
just over 1 GB. I am using
On Tue, 4 Oct 2005, David L. Van Brunt, Ph.D. wrote:
Hello, all.
I wanted to use the survey package to analyze data from the National
Ambulatory Medical Care Survey, and am having some difficulty translating
the analysis keywords from one package (Stata) to the other (R). The data
were
guide! http://www.R-project.org/posting-guide.html
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On Thu, 6 Oct 2005, Pyy-Martikainen Marjo wrote:
I specify a model with strata by covariate interactions. I would like to
conduct a Wald test
for the null hypothesis no differences between any covariate effects in the 3
groups.
The survey package has a function regTermTest (which isn't
On Fri, 7 Oct 2005, Peter Muhlberger wrote:
Does anyone know how -log(x) can equal 743 but -log(x+0)=Inf? That's what
the following stream of calculations suggest:
Browse[2] -log ( 1e-323+yMat2 - yMat1 * logitShape(matrix(parsList$Xs,
nrow = numXs, ncol=numOfCurves), matrix(means, nrow =
On Fri, 7 Oct 2005, Peter Muhlberger wrote:
The max function won't do the trick because I need the entire matrix. I
could do one cell at a time, but this is part of a ML routine that needs to
be evaluated hundreds of thousands of times, so I can't afford to slow it
down that much.
pmax,
svyratio(~as.numeric(y1*(id21)), ~as.numeric(id21), design=dmu284)
All three give the same mean estimator and standard error.
-thomas
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On Tue, 11 Oct 2005, joerg van den hoff wrote:
many thanks to thomas and gabor for their help. both solutions solve my
problem perfectly.
but just as an attempt to improve my understanding of the inner workings of R
(similar problems are sure to come up ...) two more question:
1.
why
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On Fri, 14 Oct 2005, Ido M. Tamir wrote:
Hello,
i am trying to subset a dataframe multiple times:
something like:
stats - by(df, list(items), ttestData)
ttestData - function(df){
t.test( df[,c(2,3,4), df[,c(5,6,7)]
}
While this works for small data, it is to slow for my
actual
the problem?
You can specify Hess=TRUE in the original polr() call so that refitting
would not be necessary. This is sensible anyway if you know you are going
to be computing standard errors.
-thomas
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and provide commented, minimal, self-contained, reproducible code.
Thomas Lumley
-allGenerics()@.Data
sigs-lapply(gens, function(g) linearizeMlist(getMethods(g))@classes)
names(sigs)[EMAIL PROTECTED]
sigs-lapply(sigs, function(gen){ gen[unlist(sapply(gen, function(sig)
any(sig %in% classes)))]})
sigs[sapply(sigs,length)0]
}
Thomas Lumley Assoc. Professor
in this discussion is probably the better route.
The main remaining problem in my code is that with super=TRUE it will
report all inherited methods, even where more specific methods override
them. That should be fixable.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL
, minimal, self-contained, reproducible code.
Thomas Lumley Assoc. Professor, Biostatistics
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. New York: John Wiley and Sons.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle
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On Fri, 21 Jul 2006, Valentin Dimitrov wrote:
Dear Leaf,
I modified your code as follows:
gamma.fun - function(mu,sd,start=100)
{
f.fn - function(alpha)
{abs(sd^2-mu^2/(gamma(1+1/alpha))^2*(gamma(1+2/alpha)-(gamma(1+1/alpha))^2))}
alpha - optim(start, f.fn)
beta -
as the input, and reducing functions, which
return a vector of length 1.
The == operator is vectorized, but if() requires a condition of length 1,
so they don't match. The solution is to apply some reducing function.
Two possible options are length() and (as you found) any().
-thomas
Thomas
point may
come close (there was a message yesterday from someone trying to interface
pari/gp, which does this, with R).
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle
On Fri, 28 Jul 2006, johan Faux wrote:
hello everybody,
I have some code which looks like:
dyn.load(lpSolve.so)
res - lp(some.parameters)
and everything runs fine.
What lp() does, it's just calling a C function which is in lpSolve.so
If I call lp() a large number of times:
for(1 in
of the scale.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle__
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PLEASE do read
On Tue, 1 Aug 2006, Swidan, Firas wrote:
Hi,
R is having the following weird behavior and I am not sure if that is a
feature or a bug:
It's a feature. And a very old FAQ (#7.5)
I am working on the following 3D array:
bIm
, , 1
[,1]
[1,] TRUE
[2,] TRUE
[3,] TRUE
[4,] TRUE
[5,]
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