Dear listers,
I am working since a while with the sp package and still wonder how the
plot methods are managed with sp spatial objects. For instance,
SpatialPolygonsDataFrame objects have obviously a plot method. However
it cannot be found in the list provided by methods(plot) . Furthermore
Hi,
In Splus7 this statement
xlrmN1 - sample(c(0,1,2),400 ,prob=c(0.02 ,0.93 ,0.05 ))
worked fine, but in R the interpreter reports that the length of the
vector to chose c(0,1,2) is shorter than the size of many times I want
to be selected from the vector c(0,1,2).
Any good reason?
See below
This is called 'rounding error', and has been discussed here previously.
If it matters to you (why?) use pmax(0, kde$y).
When doing numerical calculations you should always be aware that the
numerical results will differ from algebraic ones, and that is all that is
happening here.
On Sat, 30
Dear Mr. Bengtsson,
I worked on the code you sent. But, I dont think it is responding either.
Kindly verify.
evaluate(matlab, pwd=cd(););
Sending expression on the Matlab server to be evaluated...: 'pwd=cd();'
Received an 'MatlabException' reply (-1) from the Matlab server: 'Error:
Expected
This is very odd, but maybe 'cd' is not a command on your Windows
Matlab installation. I tried the same code on a Unix installation (I
don't have access to Matlab for Windows but others have been using
R.matlab there successfully). Find out what the command for getting
the current directory in
Aldi Kraja wrote:
Hi,
In Splus7 this statement
xlrmN1 - sample(c(0,1,2),400 ,prob=c(0.02 ,0.93 ,0.05 ))
worked fine, but in R the interpreter reports that the length of the
vector to chose c(0,1,2) is shorter than the size of many times I want
to be selected from the vector c(0,1,2).
Any
Talbot Katz wrote:
Hi Uwe.
Thank you so much for responding! I guess I wasn't entirely clear about
the problem. If I make the mistake of trying to install a package from
CRAN in a second session after I've already installed it in a previous
session, it won't install in the second
sj wrote:
I am fitting a coxph model on a large dataset (approx 100,000 patients), and
then trying to estimate the survival curves for several new patients based
on the coxph object using survfit. When I run coxph I get the coxph object
back fairly quickly however when I try to run survfit
Hello all,,
Im looking for a simple function to produce a crosstab from a dumped
sql query result. Its very hard to produce crosstabs with most
databases (Access being the exception), so with the vast array of R
packages, Im sure this has to have already been implemented somewhere.
Examples are
On Sat, 30 Dec 2006 07:41:48 + (GMT),
Prof Brian Ripley [EMAIL PROTECTED] wrote:
[...]
You need to set the environment of ll to that containing your data
objects. This would happen automatically if you defined ll in the
function fit.mle. A brutal solution would be
fit.mle -
Partial Summary and discussion:
=
Thank you to Chao Gai, Chuck Cleland, and Jim Lemon for their suggestion
to use replace=T in R.
There is a problem though (see below)
In the Splus7, sample is defined as
-
sample(x, size = n, replace = F, prob = NULL, n = NULL,
Alan Gibson alan.gibson at gmail.com writes:
Im looking for a simple function to produce a crosstab from a dumped
sql query result.
xtabs in stats is a simple solution, but package reshape is much more flexible
and comes with a good introduction.pdf.
Dieter
Aldi,
Your concept of sample is different from mine.
I would expect with replacement to be equivalent for a for loop of sampling
without replacement.
samples - 1:400
for (i in 1:400) samples[i] - sample(c(0,1,2),1 ,prob=c(0.02 ,0.93 ,0.05 ))
Sampling without replacement:
first :
If it matters to you (why?) use pmax(0, kde$y).
Actually, it bothers me because I need sufficient precision of numerical
calculation in this case, where the density estimate is around zero. To
illustrate why I concern about it, I'd like to introduce the problem I am
working with.
The problem is
Aldi Kraja wrote:
Partial Summary and discussion:
=
Thank you to Chao Gai, Chuck Cleland, and Jim Lemon for their suggestion
to use replace=T in R.
There is a problem though (see below)
In the Splus7, sample is defined as
-
sample(x, size = n, replace =
It is much cleaner to do this sort of thing with lexical scope. For
example,
mkll - function(x, y) {
function(ymax=15, xhalf=6) {
-sum(stats::dpois(y, lambda=ymax/(1+x/xhalf), log=TRUE))
}
}
creates a log-likelihood likelyhood function for data x,y that can
On Sat, 30 Dec 2006 15:46:01 -0600 (CST),
Luke Tierney [EMAIL PROTECTED] wrote:
It is much cleaner to do this sort of thing with lexical scope. For
example,
mkll - function(x, y) {
function(ymax=15, xhalf=6) {
-sum(stats::dpois(y, lambda=ymax/(1+x/xhalf), log=TRUE))
Hi all,
Given a data frame as...
head(veg)
genus species trophia type geo zone importance
1 Sphagnum subsecundum MA En100
2 Sphagnum denticulatum MA En200
3 Molinia caerulea MA En300
4 Sphagnumflexuosum
Dear Experts,
Thank you so much for your opinions. I probably will go with python.
Following your suggestion, I started reading some tutorials but have a
quick question. In the sense of statistical computing, is there
anything that can be easily done with python but not with SAS/R? Could
you
tmp - data.frame(G=factor(letters[c(1,2,3,1,2,3)]),
+ S=factor(LETTERS[c(1,1,1,2,2,2)]))
tmp
G S
1 a A
2 b A
3 c A
4 a B
5 b B
6 c B
tmp$G.S - with(tmp, interaction(G, S))
tmp
G S G.S
1 a A a.A
2 b A b.A
3 c A c.A
4 a B a.B
5 b B b.B
6 c B c.B
thanks for all the tips.
using 'unstack(read.table('/tmp/codes', header=TRUE))' gets me
user1 user2
1 100 100
2 200 200
3 300 300
where /tmp/codes contains
code name
100 user1
200 user1
300 user1
100 user2
200 user2
300 user2
so unstack is exactly what i was looking for. for the
On 12/30/06, Wensui Liu [EMAIL PROTECTED] wrote:
Dear Experts,
Thank you so much for your opinions. I probably will go with python.
Following your suggestion, I started reading some tutorials but have a
quick question. In the sense of statistical computing, is there
anything that can be
That has two disadvantages:
(1) it only works if the user is defining ll himself; however, if the
user is getting
ll from somewhere else then its not applicable since the user no
longer controls its
scope whereas resetting the environment method still works
(2) its cleaner for the developer but
Its easier to write command line filters using perl/python/gawk than R.
Its possible in R but awkward as there is no good way (platform
independent,easy to use) of referring to stdin data.
Something as simple as
gawk 1
which just copies its input to its output is pretty awkward in R. What
R
Dear R list members
I would be grateful if anyone could guide me to a solution for fixing my
rimage package problem described below.
I recently upgraded my machine from fedora core 3 to fedora core 6 and
then upgraded R from version 2.3.1 from version 2.4.1.
I then fired up R, tried to load
On Sun, 2006-12-31 at 00:25 +0100, Ricardo Rodríguez wrote:
Hi all,
Given a data frame as...
head(veg)
genus species trophia type geo zone importance
1 Sphagnum subsecundum MA En100
2 Sphagnum denticulatum MA En200
3 Molinia
http://bioconductor.org/packages/2.0/bioc/html/EBImage.html
This will read/write about 95 image formats into R, all those supported by
ImageMagick and provide many image processing filters. If Windows is your
platform, this version will work on Windows as well (the version release in
Bioconductor
Cannot help you much with that as the thing seems to compile normally. As
you use a global R installation, try giving yourself write permissions in
/usr/lib/R/library, this might help. Otherwise, try installing R from source
in your home or elsewhere where you have all write permissions and check
Sequenom has an odd format of calling a SNP genotype
gg
[1] C GA A C C AG C C T G
homozygous A is called A and heterozygous is called AT
The genetics package cannot handle the fact that some genotypes are declared
with 2 letter while other are declared with only 1. Consequently the
Farrel Buchinsky wrote:
Sequenom has an odd format of calling a SNP genotype
gg
[1] C GA A C C AG C C T G
homozygous A is called A and heterozygous is called AT
The genetics package cannot handle the fact that some genotypes are declared
with 2 letter while other are declared
Thanks. I stumbled upon another way that is quite similar. I like it since I
can manipulate the entire vector in the same way.
RawSeqG-paste(RawSeq$GENOTYPE_ID,RawSeq$GENOTYPE_ID,sep=)
#this duplicates heterozygotes to become ATAT or CGCG which makes no sense,
so now we use substr
I have hundreds of humans who have undergone SNP genotyping at hundreds of
loci. Some have even undergone the procedure twice or thrice (kind of an
internal control).
So obviously I need to find those replications, and confirm that the results
are the same. If there is discordance then I need to
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