On Thu, 1 Jun 2017, POLWART, Calum (COUNTY DURHAM AND DARLINGTON NHS FOUNDATION
TRUST) via R-help wrote:
Before I go and do this another way - can I check if anyone has a way of
looping through data in odfWeave (or possibly sweave) to do a repeating
analysis on subsets of data?
For simplicit
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Charles C. Berry Dept of Family Medicine & Public Health
cberry at ucsd edu UC San Diego /
On Tue, 6 Jun 2017, Morway, Eric wrote:
Using the dataset below, I got close to what I'm after, but not quite all
the way there. Any suggestions appreciated:
Daily <- read.table(textConnection(" Date wyrQ
1911-04-01 1990 4.530695
1911-04-02 1990 4.700596
1911-04-03 1990 4.898814
1
On Tue, 20 Jun 2017, lily li wrote:
Hi R users,
I have a question about fitting a cosine curve. I don't know how to set the
approximate starting values.
See
Y.L. Tong (1976) Biometrics 32:85-94
The method is known as `cosinor' analysis. It takes advantage of the
*intrinsic* linear
what I'm calling amplitude, the d and f are what
I'm calling phase.
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On Fri, 1 Jul 2016, Mark Shanks wrote:
Hi,
Imagine the two problems:
1) You have an event that occurs repeatedly over time. You want to
identify periods when the event occurs more frequently than the base
rate of occurrence. Ideally, you don't want to have to specify the
perio
On Sat, 9 Jul 2016, Debasish Pai Mazumder wrote:
I have 4-dimension array x(lat,lon,time,var)
I am using "apply" to calculate over time
new = apply(x,c(1,2,4),FUN=function(y) {length(which(y>=70))})
This is very slow. Is there anyway make it faster?
If dim(x)[3] << prod(dim(x)[-3]),
new <-
On Mon, 8 Aug 2016, Ellis, Alicia M wrote:
I have a large dataset with ~500,000 columns and 1264 rows. Each column
represents the percent methylation at a given location in the genome.
I need to run 500,000 linear models for each of 4 predictors of interest
in the form of:
Methylation.stie
On Fri, 2 Sep 2016, Bert Gunter wrote:
[snip]
The "trick" is to use tapply() to select the necessary row indices of
your data frame and forget about all the do.call and rbind stuff. e.g.
I agree the way to go is "select the necessary row indices" but I get
there a different way. See below.
On Sat, 3 Sep 2016, Bert Gunter wrote:
Chuck et. al.:
As I said previously, my intuition about the relative efficiency of
tapply() and duplicated() in the context of this thread was wrong.
My `intuition' was wrong, too.
But tapply() uses split() which runs quite fast. So not a big surprise,
On Sat, 18 Apr 2015, Brant Inman wrote:
I have two large data frames with the following structure:
df1
id date test1.result
1 a 2009-08-28 1
2 a 2009-09-16 1
3 b 2008-08-06 0
4 c 2012-02-02 1
5 c 2010-08-03 1
6 c 2012-08-02 0
df2
id date te
On Sat, 11 Jul 2015, Bert Gunter wrote:
David/Jeff:
Thank you both.
You seem to confirm that my observation of an "infelicity" in
strsplit() is real. That is most helpful.
I found nothing in David's message 2 code that was surprising. That
is, the splits shown conform to what I would expect f
On Fri, 20 Feb 2015, Aron Lindberg wrote:
Hmm…Chuck’s solution may actually be problematic because there are several
entries which at the deepest level are called “sha”, but that should not be
included, such as:
input[[67]]$content[[1]]$commit$tree$sha
and
input[[67]]$content[[1]]
On Mon, 23 Feb 2015, Ramiro Barrantes wrote:
Thank you for pointing this out. I had no idea about the distinction
but there are some good references on the matter
(http://www.r-bloggers.com/packages-v-libraries-in-r/). I am pasting
the corrected version below, any suggestions appreciated:
On Sat, 7 Mar 2015, Rolf Turner wrote:
On 06/03/15 22:34, Namratha K wrote:
Dear Sir/Madam,
I am a student pursuing MCA .As i am doing an project using R language .I
want to implement A/B testing using R language.I am searching in google
from past few days and not able to implement .So i requ
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cberry at ucsd edu UC San Diego / La Jolla, CA 92093-0901
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On Sat, 29 Aug 2015, Shant Ch wrote:
Hello Dr. Berry,
I know the theoretical side but note we are not talking about
expectation of sums rather expectation of ABSOLUTE value of the function
(X1/3+X2/3+X3/3-X4), i.e. E|X1/3+X2/3+X3/3-X4| , I don't think this
can be handled for log normal distr
On Tue, 15 Sep 2015, Bert Gunter wrote:
Thanks to both Davids.
I realize that these things are often a matter of aesthetics -- and
hence have little rational justification -- but I agree with The Other
David: eval(parse) seems to me to violate R's soul( it makes R a macro
language instead of a
On Thu, 17 Sep 2015, Berend Hasselman wrote:
On 17 Sep 2015, at 01:42, Dénes Tóth wrote:
On 09/16/2015 04:41 PM, Bert Gunter wrote:
Yes! Chuck's use of mapply is exactly the split/combine strategy I was
looking for. In retrospect, exactly how one should think about it.
Many thanks to all
On Tue, 22 Sep 2015, John Sorkin wrote:
In any event, I still don't know how to fit a single normal distribution
and get a measure of fit e.g. log likelihood.
Gotta love R:
y <- rnorm(10)
logLik(glm(y~1))
'log Lik.' -17.36071 (df=2)
HTH,
Chuck
On Tue, 22 Sep 2015, John Sorkin wrote:
Charles,
I am not sure the answer to me question, given a dataset, how can one
compare the fit of a model of the fits the data to a mixture of two
normal distributions to the fit of a model that uses a single normal
distribution, can be based on the g
On Wed, 21 Oct 2015, Ravi Varadhan wrote:
Hi, I am dealing with a regression problem where the response variable,
time (second) to walk 15 ft, is rounded to the nearest integer. I do
not care for the regression coefficients per se, but my main interest is
in getting the prediction equation fo
t of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276
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On Sun, 17 Jan 2016, Lars Bishop wrote:
I’d appreciate your help on understanding the following.
It is not very clear to me from the model.matrix documentation, why
simply changing the order of terms in the formula may change the number
of resulting columns. Please note I’m purposely not in
On Mon, 3 Oct 2016, Frank S. wrote:
Dear R users,
[deleted]
I want to get a list of "k" data tables (or data frames) so that each
contains those individuals who for the first time are at least 65,
looping on each of the dates of vector "v". Let's consider the following
example with 5 ind
On Wed, 19 Oct 2016, g.maub...@weinwolf.de wrote:
Hi All,
I would like to store a long string with white space in a variable:
-- cut --
# Create README.md
readme <- "---
title: "Your project title here"
author: "Author(s) name(s) here"
date: "Current date here"
output: html_document
---
[s
On Mon, 31 Oct 2016, Jeff Newmiller wrote:
The help page describes the first argument x as a numeric... it is not
designed to accept character,
Actually it is so designed, but not advertised as such. See below.
so the fact that you get anything even close to right is just a bonus.
As the do
On Mon, 7 Nov 2016, Rolf Turner wrote:
On 07/11/16 13:07, William Dunlap wrote:
Have you tried reparameterizing, using logb (=log(b)) instead of b?
Uh, no. I don't think that that makes any sense in my context.
The "b" values are probabilities and must satisfy a "sum-to-1" constraint.
To a
On Tue, 8 Nov 2016, Doran, Harold wrote:
Without reaching out to another package in R, I wonder what the best way is to
speed enhance the following toy example? Over the years I have become very
comfortable with the family of apply functions and generally not good at
finding an improvement fo
On Mon, 14 Nov 2016, Bert Gunter wrote:
Yes, but it need some help, since nchar gives the length of the
*entire* string; e.g.
## to count "a" 's :
x <-(c("abbababba","bbabbabbaaaba"))
nchar(gsub("[^a]","",x))
[1] 4 6
This is one of about 8 zillion ways to do this in base R if you don't
wan
On Mon, 14 Nov 2016, Marc Schwartz wrote:
On Nov 14, 2016, at 11:26 AM, Charles C. Berry wrote:
On Mon, 14 Nov 2016, Bert Gunter wrote:
[stuff deleted]
Hi,
Both gsub() and strsplit() are using regex based pattern matching
internally. That being said, they are ultimately calling
On Wed, 7 Dec 2016, Marc Girondot via R-help wrote:
Hi,
From the documentation of ?options
Options set in package parallel
These will be set when package parallel (or its namespace) is loaded if not
already set.
mc.cores:
a integer giving the maximum allowed number of additional R processes
On Mon, 20 Feb 2017, stephen sefick wrote:
Hello,
I would like to add something to a data frame that is 1) invisible to the
user, 2) has no side effects, and 3) I can test for in a following
function. Is this possible? I am exploring classes and attributes and I
have thought about using a list
On Tue, 21 Feb 2017, stephen sefick wrote:
Sorry for not being clear. I have never used S3 methods before. Below is
some R code that sketches out my idea. Is this a sensible solution?
Sure. See comments (untested) inline.
Chuck
test_data <- data.frame(a=1:10, b=1:10, c=1:10)
functionA <-
ng-guide.html
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e. Any idea?
Thanks
--
Regards,
Anh Tran
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k to `a`
as would "is.na(a) <- 1", etc.)
HTH,
Chuck
thanks
Stephen Sefick
On Tue, Aug 12, 2008 at 6:32 PM, Charles C. Berry <[EMAIL PROTECTED]> wrote:
On Tue, 12 Aug 2008, Mike Prager wrote:
rcoder <[EMAIL PROTECTED]> wrote:
I have a matrix that has a combina
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ter_ startup to get behavior like you describe.
Perhaps, you have something later in your .Rprofile that specifically
load()'s your old .RData?
Chuck
p.s.
sessionInfo()
R version 2.7.1 (2008-06-23)
x86_64-unknown-linux-gnu
locale:
C
attached base packages:
[1] stats graphics gr
On Thu, 21 Aug 2008, Rolf Turner wrote:
On 21/08/2008, at 10:21 AM, Charles C. Berry wrote:
On Thu, 21 Aug 2008, Rolf Turner wrote:
>
>
> For reasons that are best known to myself [ ;-) ] I have a value of
> .Random.seed
> saved (via dput()) in a file ``.Random.seed.sav
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t;
HTH,
Chuck
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in that case.
HTH,
Chuck
>
Many thanks,
Chris
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each
of the above forms.
"[" merely tries to do something reasonable.
Why do you think k should have any attributes, and what names do you think
k should have???
HTH,
Chuck
?
YU
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t from the R help mailing list archive at Nabble.com.
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x )
fit <- coxph( clogit.response( winner ) ~ strata( heat ) + x )
new.preds <- ave(
predict( fit ,newdata=newdat, type = 'risk'),
newdat$heat, FUN=prop.table )
Ought to do it.
HTH,
Chuck
Thanks!!
-N
On 8/22/09 10:57
On Sun, 23 Aug 2009, Charles C. Berry wrote:
On Sat, 22 Aug 2009, Noah Silverman wrote:
And, of course that leads me to another question...
With svm {e1071} I can ask the predict function to give me probabilities
with lrm {Desigh} I can ask the predict function to give me probabilities
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http:
lit().
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p
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7;t store the values in a list to start with.
HTH,
Chuck
I think the question is really trivial, but I tried to work on it and couldn't
reach anythg.
Thanks.
Maram
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<
makeindex $<
cheers!
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Typo corrected below.
On Sat, 13 Mar 2010, Charles C. Berry wrote:
On Sat, 13 Mar 2010, Adrian Johnson wrote:
Hi:
I have a two large files (over 300K lines).
file 1:
NameX
UK 199
UK 230
UK 139
..
UAE194
UAE 94
File 2:
Name XY
UK
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ec,na.rm=T)"
X1 X2
X1 NA NA
X2 NA NA
[1] "sum(vec,na.rm=T)"
[1] 6
[1] "var(vec,na.rm=T)"
X1 X2
X1 NA NA
X2 NA NA
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http://famprevm
ces_2.9.1 methods_2.9.1
[5] splines_2.9.1 stats_2.9.1 utils_2.9.1
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On Mon, 13 Jul 2009, Heinz Tuechler wrote:
At 20:18 13.07.2009, Charles C. Berry wrote:
On Mon, 13 Jul 2009, Heinz Tuechler wrote:
> Dear All,
>
> since years I am struggling with Surv objects in data.frames. The
> following seems to have to do with it.
> See below the modifi
On Mon, 13 Jul 2009, Charles C. Berry wrote:
On Mon, 13 Jul 2009, Heinz Tuechler wrote:
At 20:18 13.07.2009, Charles C. Berry wrote:
> On Mon, 13 Jul 2009, Heinz Tuechler wrote:
>
> > Dear All,
> >
> > since years I am struggling with Surv objects in data.fra
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Charles C. Berry(8
0:54:18
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R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-proje
complete or doesn't do quite what you want it to do.
HTH,
Chuck
Charles C. Berry wrote:
I think you'll need to dig into sys.call() and match.call() and put
together your own matching scheme to force a function to first match by
position and then match all else by name.
If ma
around partial
matching issues when named args are used BEFORE ... in the formals of a
function and calls are constructed that rely on position taking precedence
over partial matches in ... .
HTH,
Chuck
Charles C. Berry wrote:
I did not follow that.
But I might guess that you do not gro
.
Charles C. Berry(858) 534-2098
Dept of Family/Preventive Medicine
E mailto:cbe...@tajo.ucsd.edu UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901
nformation:
Tal Galili
Phone number: 972-50-3373767
FaceBook: Tal Galili
My Blogs:
http://www.r-statistics.com/
http://www.talgalili.com
http://www.biostatistics.co.il
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Charles C. Berry(858) 534-2098
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