?polygon
Bert Gunter
Genentech Nonclinical Biostatisics
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Graves, Gregory
Sent: Thursday, August 13, 2009 11:17 AM
To: r-help@r-project.org
Subject: [R] shading between two smoothed
I hadn't checked this, I only had used the default.
The problem stems from the reassigned weighs during nls iterations,
where the psi.bisquare function can return some 0 weight values, which
then returns some NaN values in the resid vector that is calculated by
dividing residuals/weights.
I read the list in digest form which sometimes makes me late to respond.
Peter Dalgaard wrote:
In all fairness, it should probably be noted that quite a few people
swear BY S4 in addition to those who swear AT it.
Lest I give the impression of only dislike -- the coxme package (major
rewrite
Hello,
I have a question regarding estimation of the dispersion parameter (theta)
for generalized linear models with the negative binomial error structure. As
I understand, there are two main methods to fit glm's using the nb error
structure in R: glm.nb() or glm() with the
I found a work-around by just simply getting the sum of the
conditional values and dividing this by the mean. It's not elegant but
it works
On Aug 13, 3:11 pm, Dax rienk.doet...@gmail.com wrote:
Hello all,
I have a huge data set that I'm cleaning up a bit. I am extracted the
means per
When adding several logical vectors I expect each vector will be
coerced to integers and these vectors will then be added.
That doesn't always seem to be the case.
For example:
( f1 - as.factor ( sample ( x , 25 , rep = T ) ) )
[1] x x x x x x x x x x x x x x x x x x x x x x x x x
Hi,
solict excuese if I am reposting I am not sure I properly posted the
previous message
In the past I have used a DEA package known as FEAR on R platform. I could
not see that package any more. Instead a new package is there DEA. I kindly
apreciate comments or recomendations.
Ramilan
I am using the package tm for text-mining of abstracts and would like to
use it to find instances of gene names that may contain white space. For
instance gene regulatory protein 1. The default behavior of tm is to parse
this into 4 separate words, but I would like to use the class constructor
On 13-Aug-09 19:21:36, David Huffer wrote:
When adding several logical vectors I expect each vector will be
coerced to integers and these vectors will then be added.
That doesn't always seem to be the case.
For example:
( f1 - as.factor ( sample ( x , 25 , rep = T ) ) )
[1] x x x
Dear List,
I have a data frame of data taken every few seconds. I would like to subset
the data to retain only the data taken on the quarter hour, and as close to the
quarter hour as possible. So far I have figured out how to subset the data to
the quarter hour, but not how to keep only the
If I am on Windows and don't have GDB it does'nt look like it is possible. Any
tips?
Kevin
roger koenker rkoen...@uiuc.edu wrote:
At points of total desperation you can always consider
the time-honored, avuncular advice -- RTFM,
in this case Section 4.4 of Writing R Extensions.
Dear Sir/Madam,
Good Day!
How can we make output file in R?
In FORTRAN, we could do as follows:
WRITE (42, 107) x, y
107 FORMAT ( 2x, F9.3, 2x, F4.2)
What is equivalent to this in R?
With best regards,
Sarjinder
Updated web-page on Sept 6, 2004:
Thank you for all your suggestiona.
I tried to write a self-contained example which turned oiut to confuse people's
miind.
I realized also the formulation of my question was unclear. Sorry for that.
What I had in mind was something similar to Fortran Parameter declaration.
I spent some time
Hi all,
I have an issue with the lm() function regarding the listing of the
coefficients. My data are below, showing a list of hours (HR) relating to
the time spent resting (R) by an individual animal. Simply i want to run a
lm() to run in an anova() to see if there is a significant difference
Another dumb ggplot2 question:
a facet plot with free x scale, lots of
different ranges, want to specify that the
x axis ticks be sparse -- only 2 or 3. I was
about to say that I could figure out how to manually
set the ticks for each facet if necessary, but now
that I've looked around some
In order to ease my students into the R environment I am developing a package
which installs a variety of utility functions as well as slightly modified
versions of some standard R functions -- e.g. mean, hist, barplot, In my
versions of these standard R functions I either add options or
Are you sure you just don't want to tell them about the :: operator? It sounds
easier than what you're proposing.
E.g.,
base::mean(c(1:10, NA))
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Pitt, Joel
Sent: Thursday, August
Hi,
On Aug 13, 2009, at 3:43 PM, Sarjinder Singh wrote:
Dear Sir/Madam,
Good Day!
How can we make output file in R?
In FORTRAN, we could do as follows:
WRITE (42, 107) x, y
107 FORMAT ( 2x, F9.3, 2x, F4.2)
What is equivalent to this in R?
See:
?file
?cat
?sprintf
-steve
--
The Defaults package can be used to change the defaults of
functions and reset them back.
There is some question on whether all this is advisable.
It will invalidate any books, documentation, examples
in the help files that come with R and other
resources on R that they might have otherwise used
Thanks. It's a great solution to part of my problem. It provides the
functionally I want would be no harder for students to use than my approach.
I'm still interested in how to make what I was trying to do work -- simply to
add to my own R programming proficiency.
Joel
Hi!!
I need to draw a cylinder/tube joining two points. I am trying to make
something presentable, I have been able to do it using lines3d. But is it
possible to
increase the thickness of the lines? The size parameter does not work. Does any
one have any suggestions?
Thanks ../Murli
On 13-Aug-09 20:45:31, Ross Culloch wrote:
Hi all,
I have an issue with the lm() function regarding the listing of
the coefficients. My data are below, showing a list of hours (HR)
relating to the time spent resting (R) by an individual animal.
Simply i want to run a lm() to run in an
I have answered a similar question just hours ago. Your question either
indicates an unfamiliarity with R or, more generally, an unfamiliarity with
regression analysis, or both.
Your anova indicates that the overall model is significant. That is, your
model is an improvement over the null model
On Thu, Aug 13, 2009 at 03:36:22PM -0400, Mark Kimpel wrote:
I am using the package tm for text-mining of abstracts and would like to use
it to find instances of gene names that may contain white space. For instance
gene regulatory protein 1. The default behavior of tm is to parse this into
4
Your objections are quite cogent, but I believe they are misdirected. I'm not
at all interested in having my students ignore the existence of NA's and that's
precisely why I'm not using the Default package as someone else suggested. But
the mere existence of missing values in a data set doesn't
library(nlme)
m2 - gnls(conc ~ t1*(1-t2*exp(-k*time)),
data = df.Chloride,
start = list(
t1 = 35,
t2 = 0.91,
k = 0.22))
summary(m2)
plot(m2)
lag.plot(resid(m2), do.lines=FALSE)
acf(resid(m2))
m3 - update(m2, corr=corAR1(.67))
Hello,
My dataframe has new columns that start with the number 1 or 2 (resulting
from a reshape cast command).
Instead of having these columns automatically renamed by R so start with the
letter X, I would like to rename these columns to start with the characters
SURV_ (e.g., SURV_1, SURV_2).
I
You can add or remove elements from a list without affecting the
other elements. It is not necessary to update the list names when
adding or removing elements.
Since list elements can be referred to by name, you don't have to
worry about numbering them, or renumbering them, nor do you have to
Hi,
As I said in my original email, I'm sure that many of you will doubt the wisdom
of what I'm trying to do -- and I certainly share some of your misgivings. I
have misgivings too about the use of training wheels for bicycles, but they
are clearly useful for some people, and, in this
Hi Gregory,
I can plot out two nice curves using the following code, but I can't
figure out how to shade in the area lying between the two curves.
Use polygon.
?polygon
Graves, Gregory ggra...@sfwmd.gov 14/08/2009 4:17 am
I have a set of 52 weekly values, one is the desired high lake
Something like this. Create empty vector of correct length, paste values into
it and then use names(mydata) - myvector.
x - data.frame(aa=1:10, bb=letters[1:10])
myvector - c(rep(NA,length(x)))
for (i in 1:length(names(x))) {
myvector[i] - paste(SURV_,i, sep=)
}
--- On Thu, 8/13/09,
On Thu, 13 Aug 2009, hesicaia wrote:
Hello,
I have a question regarding estimation of the dispersion parameter (theta)
for generalized linear models with the negative binomial error structure. As
The theta is different from the dispersion. In the usual GLM notation:
E[y] = mu
VAR[y] =
willow1980 wrote:
Dear Professor Murdoch,
That is exactly the difficulty for me. I don't know how to make a prediction
with lmer using expand.grid; at the moment, I can use
“mo...@x%*%fixef(model)” to get predicted values for existing observational
data, but not data by expand.grid. Actually, if
rkevinbur...@charter.net wrote:
If I am on Windows and don't have GDB it does'nt look like it is possible. Any
tips?
For debugging without a debugger, you can always use the old-fashioned
method of inserting print statements (Rprintf in C). But you want to do
this without a debugger
Nair, Murlidharan T wrote:
Hi!!
I need to draw a cylinder/tube joining two points. I am trying to make something presentable, I have been able to do it using lines3d. But is it possible to
increase the thickness of the lines? The size parameter does not work. Does any one have any suggestions?
Hi Joel,
On Aug 13, 2009, at 6:10 PM, Pitt, Joel wrote:
Your objections are quite cogent, but I believe they are
misdirected. I'm not at all interested in having my students ignore
the existence of NA's and that's precisely why I'm not using the
Default package as someone else suggested.
Whoa! Just hang on a minute.
theta is NOT the dispersion parameter. Under the NB model, the variance of an
observation is mu+mu^2/theta, so that's how theta enters the picture. The
smaller theta is the larger the variance.
glm(..., family = negative.binomial(theta = something), ...)
Hi
Jonathan R. Blaufuss wrote:
Paul, You solution worked out really well when I ran my code in R.
However, when I try to turn the plot into a pdf, the unicode string
no longer seems to function and instead of the sigma symbol there are
just two periods (See example code below).
The following
Hello,
I have a data frame str(dat)'data.frame': 2 obs. of 30 variables
it contains two information-two types of cancers:stage A(A1 to A10) and stage
B(B1 to B20) ##totally 30 patients-2 sets of gene expression
I'd like to find the lists for top 20 differentially expressed genes using
You could do the following:
y - apply(dat,1,function(a) t.test(a[1:10],a[11:30])$p.value)
This will produce an array of 2 p-values.
--- On Fri, 14/8/09, Gina Liao yi...@hotmail.com wrote:
From: Gina Liao yi...@hotmail.com
Subject: [R] problem about t test
To: r-h...@stat.math.ethz.ch
Hi Cliff,
Excellent, just what I needed -- wish I had thought of that myself.
Thanks a lot!
Jacob
On 13 Aug 2009, at 01:49, Clifford Long wrote:
Hi Jacob,
At the risk of embarrassing myself, I gave it a shot. I'll throw this
out on the list, if for no other reason than perhaps someone
Is your system of equations linear?
--- On Fri, 14/8/09, Moreno Mancosu nom...@tiscali.it wrote:
From: Moreno Mancosu nom...@tiscali.it
Subject: [R] Solutions of equation systems
To: r-help@r-project.org
Received: Friday, 14 August, 2009, 2:29 AM
Hello all!
Maybe it's a newbie
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