I am fitting models to the responses to a questionnaire that has
seven yes/no questions (Item). For each combination of Subject and
Item, the variable Response is coded as 0 or 1.
I want to include random effects for both Subject and Item. While I
understand that the datasets are fairly
Daniel Ezra Johnson johnson4 at babel.ling.upenn.edu writes:
...
If one compares the random effect estimates, in fact, one sees that
they are in the correct proportion, with the expected signs. They are
just approximately eight orders of magnitude too small. Is this a bug?
...
BLUPs are
Responding to the original post, which I did not save.
On 31/12/06, John Kornak [EMAIL PROTECTED] wrote:
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
nr.attempts
-aggregate(RawSeq$GENOTYPE_ID,list(sample=RawSeq$SAMPLE_ID,assay=RawSeq$ASSAY_ID),length)
This was simply to figure out how many times the same piece of information
had been obtained. I ran out of patience. It took beyond forever and tapply
did not perform much better. The reshape
I'm a bit new with python, but have found it extremely easy to learn and
use. I have been using it to pre-process some text files that we often
deal with and need to be formatted in a certain way before they can be
used for statistical analysis in another software program.
I suppose there is one
Hi wizards, I have a question. Which programming paradigm does R
handle? . Iam looking for this information but I didn't found nothing.
Thanks in advance.
personal web site:
http://www.geocities.com/ricardo_rios_sv/index.html
--
personal web site:
Its object oriented inspired by the Dylan language and Scheme. Some additional
information is available in this thread:
https://stat.ethz.ch/pipermail/r-help/2003-July/036437.html
There are also a number of packages which layer other programming
language models on top of R:
- R.oo provides for
If one compares the random effect estimates, in fact, one sees that
they are in the correct proportion, with the expected signs. They are
just approximately eight orders of magnitude too small. Is this a bug?
BLUPs are essentially shrinkage estimates, where shrinkage is
determined with
If one compares the random effect estimates, in fact, one sees that
they are in the correct proportion, with the expected signs. They are
just approximately eight orders of magnitude too small. Is this a bug?
BLUPs are essentially shrinkage estimates, where shrinkage is
determined with
Hi all,
Please, is there any way of controlling factors in row/columns when using
ftable/xtabs? As far as I can see, the last cross-clasifing variable in the
formula will appear in columns. The previous ones, in rows. For instance, is it
possible to make tension and replicate appear in
Hi Ricardo,
Please, is there any way of controlling factors in row/columns when using
ftable/xtabs? As far as I can see, the last cross-clasifing variable in the
formula will appear in columns. The previous ones, in rows. For instance, is
it possible to make tension and replicate appear
hadley wickham[EMAIL PROTECTED] 31/12/2006 19:33
Hi Ricardo,
You might want to have a look at the reshape package,
http://had.co.nz/reshape, which provides a more general and flexible
framework for reshaping data in R.
The version of warpbreaks I have doesn't have the replicate variable,
so
Add the argument col.vars = 2:3 to your ftable call. See ?ftable
On 12/31/06, Ricardo Rodríguez [EMAIL PROTECTED] wrote:
Hi all,
Please, is there any way of controlling factors in row/columns when using
ftable/xtabs? As far as I can see, the last cross-clasifing variable in the
formula
I've found a way to make this problem, if it's not a bug, more clear.
I've taken my original data set A and simply doubled it with
AA-rbind(A,A).
Doing so, instead of this:
Random effects: # A
Groups NameVariance Std.Dev.
Subject (Intercept) 1.63e+00 1.28e+00
Item(Intercept)
Thanks, Hadley,
My fault: I've not provided the line concerning replicate variable. It is
included in ?xtabs:
warpbreaks$replicate - rep(1:9, len = 54)
It will be great to have an example with these given data. Anyway, I will
have a look to reshape at the given site. Thanks a lot!
I'm not sure that shrinkage is the answer, in this case. I observed a
similar problem with the gamma distribution, which I mentioned here:
http://tolstoy.newcastle.edu.au/R/e2/help/06/12/6903.html
Since there hasn't been any discussion, I'm starting to think that it
is a bug.
Andrew
On Sun,
I converted the whole data frame to character by using
as.matrix
And then using a posting that explained how to get the naming conventions
back (which had been lost when converting to matrix)
Anything that I did not list with the id's it insisted in including them
with the measured variables.
Daniel Ezra Johnson johnson4 at babel.ling.upenn.edu writes:
...
More broadly, is it hopeless to analyze this data in this manner, or
else, what should I try doing differently? It would be very useful to
be able to have reliable estimates of random effect sizes, even when
they are rather
Daniel Ezra Johnson johnson4 at babel.ling.upenn.edu writes:
If one compares the random effect estimates, in fact, one sees that
they are in the correct proportion, with the expected signs. They are
just approximately eight orders of magnitude too small. Is this a bug?
BLUPs are
Gregor,
Thanks for your replies.
1) Yes, I have tweaked the data to show as clearly as I can that this is a
bug, that a tiny change in initial conditions causes the collapse of a
reasonable 'parameter' estimate.
2) mcmcsamp() does not work (currently) for binomial fitted models.
3) This is
I converted the whole data frame to character by using
as.matrix
You shouldn't need to do that.
And then using a posting that explained how to get the naming conventions
back (which had been lost when converting to matrix)
Anything that I did not list with the id's it insisted in including
The reason that I used the as.matrix is because I understood that everything
in the data.frame had to be either numeric or character. Most of mine were
factors.
Thank you so much for finding my elusive spelling mistake. I removed the
offending d from measured and now it works. However, I have run
I have a vector containg about 20 unique values. It is called rejectrs$rs.
It is a factor
I have a data frame with about 10 rows.
I want to exclude all rows where in variable rs the value is one of the 20
on the exclude list. I thought this would work but none did.
I found a solution to my problem. I thought I would post it here. That will
help me in 3 months when I have forgotten it or some other poor soul who
stumbles across the same problem.
RawSeqBig-RawSeqBig[RawSeqBig$ASSAY_ID %in% rejectrs$rs==FALSE,]
Farrel Buchinsky [EMAIL PROTECTED] wrote in
On Sun, 31 Dec 2006, Farrel Buchinsky wrote:
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
I am having problems with the 'if' syntax.
I have an n x 4 matrix, X say. The first two columns hold x, y values and
I am attempting to fill the second two columns with the quadrant in which
the datapoint (x, y) is and with the heading angle.
So I have two problems
1) how to do this elegantly
On 12/31/2006 9:35 PM, Richard Rowe wrote:
I am having problems with the 'if' syntax.
I have an n x 4 matrix, X say. The first two columns hold x, y values and
I am attempting to fill the second two columns with the quadrant in which
the datapoint (x, y) is and with the heading angle.
Hey, I am very new to R and I need to use it (and the ACEPACK
package) to do some statistical analysis.
I have installed acepack but efforts to get started has been
unsuccessful. I can't seem to be able to load my data files because I
am yet to figure the syntax to use. Is there a work
what is the format of your data files, txt/csv/mdb/xls? the syntax is
very different.
could you please give more info?
thanks.
On 12/31/06, Obinna Duru [EMAIL PROTECTED] wrote:
Hey, I am very new to R and I need to use it (and the ACEPACK
package) to do some statistical analysis.
I have
On Sun, 31 Dec 2006, Charles C. Berry wrote:
On Sun, 31 Dec 2006, Farrel Buchinsky wrote:
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
Step 1:
quadrant - 1 + (X[, 1] 0) + 2*(X[, 2] 0)
This is not the usual labelling of the quadrants as '3' and '4' are
interchanged. If you want to be picky about it
quadrant - ifelse(quadrant 2, 7 - quadrant, quadrant)
Step 2:
angle - atan2(X[,2], X[,1]) %% (2*pi) # I think this is what
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