I am writing a little abstraction for a series of tests. For example,
I am running an anova and kruskal.test on a one-factor model. That
isn't a particular problem, I have an interface like:
my.function <- function(model,data) {
print(deparse(substitute(data)))
a <- anova(lm(formula,data
> "Pascal" == Pascal A Niklaus <[EMAIL PROTECTED]> writes:
Pascal> lme should do the job (r1,r2,r3 are your random factors):
Pascal> library(nlme) y.lme <- lme(y ~ 1,random = ~ 1 | r1/r2/r3)
Pascal> summary(y.lme)
Pascal> This is equivalent to a call to varcomp in S-Plus
Thanks! This was th
I'm pulling my hair (and there's not much left!) on this one. Basically I'm
not getting the same result t when I "step" through the program and evaluate
each element separately than when I use the outer() function in the
FindLikelihood() function below.
Here's the functions:
Dk<- function(x
The hist() function expects to be given data, not the counts in the bins.
It sounded like you are giving hist() the counts.
One thing you may try is by constructing an object of class "histogram" by
hand (see the "Value" section of ?hist), and just plot() it. However,
beware that by default hist(
Hi,
I have a set of observations which are divided into two sets A and B.
I have some code that bins the dataset into 10 bins based on the max and
min of the observed values.
I would like to make a histogram of A & B using my calculated bins but
plot the distribution of B on top of A (like a st
Hi,
I was using the affy package in R for sometime. I reinstalled the R
environment lately due to some other issues and now I get errors when I use
the function ReadAffy. The error is reproduced here:
Error in validityMethod(object): No slot of name "phenoLabels" for this
object of class "pheno
The book by Borcher's et al Estimating Animal Abundance provides R/S+
code that you may find useful for your work.
Jeff Laake
Bret Collier wrote:
>
> >R-Users,
>
> Everyone, I am a new user of R and I was wondering if anyone could point me
> to a reference (book or article) that discusses writi
R-Users,
Everyone, I am a new user of R and I was wondering if anyone could point me
to a reference (book or article) that discusses writing population
simulations in R (or S).
Thanks in advance,
Bret A. Collier
Arkansas Cooperative Fish and Wildlife Research Unit
Department of Biological Scie
One way:
x<-c(1,3,-1,0,4)
> x[x>0]<-NA
> x
[1] NA NA -1 0 NA
>
bob
-Original Message-
From: Yulei He [mailto:[EMAIL PROTECTED]
Sent: Monday, October 27, 2003 4:05 PM
To: [EMAIL PROTECTED]
Subject: [R] how to set missing values in R
Hi, there.
Can I ask how to set up missing values i
x[x>0] <- NA
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
>>> Yulei He <[EMAIL PROTECTED]> 10/27/03 04:05PM >>>
Hi, there.
Can I ask how to set up missing values in R? Suppose
See the recent discussion about is.na() on this list. You can do what
you want as
> x<-c(1,3,-1,0,4)
> is.na(x) = x > 0
> x
[1] NA NA -1 0 NA
Yulei He <[EMAIL PROTECTED]> writes:
> Hi, there.
>
> Can I ask how to set up missing values in R? Suppose I want to assign the
> missing value to the
Hi, there.
Can I ask how to set up missing values in R? Suppose I want to assign the
missing value to the elements in vector which is greater than zero like
this:
x<-c(1,3,-1,0,4);
after the missing value assignment, x becomes (NA,NA,-1,0,NA).
Thanks!
Yulei
$$
Hi
Michael Grottke wrote:
Hello,
Some time ago, I discovered the possibility of using mathematical
symbols for axis labels etc. In order ensure consistency between text
and graphics of some paper, I would like to include the calligraphic H
(obtained in LaTeX via \mathcal{H}) in several diagram
I received a lot of good advice how to remove NaN columns - thank you all
!!!
The simplest mechanism to center/scale and remove NaN columns seems to be
> xdata <- data.frame(A = 3:1, B = 1:3, rep(9, 3))
> xs <- scale(xdata)
> mask <- sapply(as.data.frame(xs), function(x) all(is.nan(x)))
> scaled.
On Mon, 27 Oct 2003, Liaw, Andy wrote:
> [OK, it's not so strange: na.action is not a documented argument for
> model.matrix, and the call to model.frame in model.matrix.default does not
> have ..., but shouldn't it?]
o, as it documented as for arguments to other methods.
--
Brian D. Ripley,
Strangely (to me), just passing na.action=na.pass to model.matrix doesn't
work:
> f <- factor(rep(letters[1:3], 5))
> is.na(f[sample(15, 3)]) <- TRUE
> model.matrix(~f, data=model.frame(~f, na.action=na.pass))
(Intercept) fb fc
11 0 0
21 1 0
31 0 1
4
Perhaps a much simpler method (just thought of it) would be to set
options(na.action="na.pass")
before you start. Or use na.action=na.pass() as an argument in
the call to model.frame(), since that's where the problem begins.
See help("na.omit"), help("model.frame").
- tom blackwell - u
I would re-expand the model matrix by indexing its (nobs) rows
with a longer vector (of length n) containing the correspondence.
If there is only one term (say "Z") in the formula which contains
the problematic NAs, I would do (roughly)
ff <- Y ~ Z# following the example in ?model.m
Dear Thomas,
Thank you for you reply and solution - it works perfectly! It hadn't
occurred to me that a 1 column subset of a data frame was still a data
frame and that therefore I didn't need to use data.frame() at all!
To the list as well, please ignore my second mail on this thread. I was
tr
Dear List,
I think I have found the source of my problem in a reply from Thomas
Lumley to a previous question on R-Help:
http://www.r-project.org/nocvs/mail/r-help/2002/0586.html
My code is not working because substitute() does not substitute formal
arguments to functions, and I guess the firs
On Mon, 27 Oct 2003, Gavin Simpson wrote:
>
> But R throws up the following error:
>
> Error in poly(Alk1, degree = 2, coefs = structure(list(alpha =
> c(37.7515662650602, :
> Object "Alk1" not found
>
> When trying to evaluate the following code:
>
> pAsgn <- paste("predList[[i]][[n]] <
I have a factor (with "n" observations and "k" levels), with only
"nobs" < n of the observations not missing. I would like to produce a
(n x k) model matrix with treatment contrasts for this factor, with
rows of NAs placeholding the missing observations. If I use
model.matrix() I get back a (nobs
Hi again
Thanks all for your fast! reply
regards
Ulisses
Debian GNU/Linux: a dream come true
-
"Computers are useless. They can only give answers."Pablo Picasso
--->Visita http:
m[1:5 + nrow(m)*c(2,3,1,2,1)] <- 0 if m is a matrix. Remember you can
index a matrix as a vector.
If m is a data frame (you didn't say what it is) I would loop over
columns (not rows) explicitly, since the code is going to do that
implicitly.
On Mon, 27 Oct 2003 [EMAIL PROTECTED] wrote:
>
[EMAIL PROTECTED] wrote:
Hi all
I want to assign a constant to a different column for each row
eg:
m[1,2] <- 0;
m[2,3] <- 0;
m[3,1] <- 0;
m[4,2] <- 0;
m[5,1] <- 0;
...
etc...
i've tried apply/tapply with no luck
and also the following
coefs <- rtt.abs[,5:8];
coefs.i <- coefs[] == 1;
Hi all
I want to assign a constant to a different column for each row
eg:
m[1,2] <- 0;
m[2,3] <- 0;
m[3,1] <- 0;
m[4,2] <- 0;
m[5,1] <- 0;
...
etc...
i've tried apply/tapply with no luck
and also the following
coefs <- rtt.abs[,5:8];
coefs.i <- coefs[] == 1;
coefs[coefs.i] <- 0;
rowIdx <- sample(nrow(a), size=nbrOfSamples)
a[rowIdx,]
and/or
colIdx <- sample(ncol(a), size=nbrOfSamples)
a[,colIdx]
/Henrik Bengtsson
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of
> [EMAIL PROTECTED]
> Sent: den 27 oktober 2003 16:26
> To:
Thanks so much, Martin and Andy for your help. I understand it now.
Pauline
At 03:00 PM 10/25/2003 +0200, Martin Maechler wrote:
> "Pauline" == Pauline Gu <[EMAIL PROTECTED]>
> on Fri, 24 Oct 2003 10:03:23 -0700 writes:
Pauline> Hello, experts, Does the number of input for
Pa
Hi
I am having a particular problem with some glm models I am running. I
have been adapting code from Bill Venables 'Programmers niche' in RNews
Vol 2/2 to fit ca. 1000 glm models to a combination of species 0/1 data
(as Y) and related physicochemical data (X), to automate the process of
fitti
Like this:
a.subset <- a[sample(nrow(a), how.many.I.want), ]
HTH,
Andy
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED]
> Sent: Monday, October 27, 2003 10:26 AM
> To: [EMAIL PROTECTED]
> Subject: [R] how to select random rows ?
>
>
> How can I select random
How can I select random subsets (rows!) from a data set ?
If I generate simple data set
> a <- data.frame(x=1:2, y = NaN, z = 2:1)
> a
x y z
1 1 NaN 2
2 2 NaN 1
I can select random subsets (colums) very easily using sample function:
> sample(a, 2)
z y
1 2 NaN
2 1 NaN
I expected that us
On Mon, Oct 27, 2003 at 06:57:08AM -0800, Brett Magill wrote:
> I am trying to install Rpy to test it out as an R
> interface for a project that I am working on.
> However, I get the following error. Any clues as to
> what might be going on? I have alo tried RSPython, but
> I gave up due to error
On Monday 27 October 2003 03:50, Wolfram Fischer wrote:
> If I have drawn a string with ``ltext( x, y, labels="first string" )''
> how can a draw a second string just one line (or strheight("X")
> below the first string regardless of the size and scales of the panel?
No reliable (that is, documen
Hello,
I would like to know if there is a possibility to open an R session via Java
(using the SJava package), then to terminate it, and re-run another.
It seems not to be possible. If this is the case, I would like to understand
where is the problem or the limitation (is it due to the SJava
imple
On Monday 27 October 2003 04:19, Prof Brian Ripley wrote:
> On Mon, 27 Oct 2003, Edzer J. Pebesma wrote:
> > The following now occurs to me when I try to
> >
> > load lattice (R 1.7.1, debian stable):
> > > library(lattice)
> >
> > Error in loadNamespace(i, c(lib.loc, .libPaths()), keep.source) :
>
I am trying to install Rpy to test it out as an R
interface for a project that I am working on.
However, I get the following error. Any clues as to
what might be going on? I have alo tried RSPython, but
I gave up due to errors. RSPython segfaults when
started from R and gives an error message I
On Mon, 27 Oct 2003, Ing. Michael Rost wrote:
> Dear all, I'm trying reproduce an example of bioassays Yielding
> Concentration-Mortality Data particularly control - adjustment model
> from book Bioassay of Entomopathogenic Microbes and Nematodes chapter 7
> with R.
>
> I used glm with family=bino
Could one use "cat" for comments, as:
cat("this is a comment that may survive 'source'\n")
??
hope this helps. spencer graves
Martin Maechler wrote:
"Olivia" == Olivia Lau <[EMAIL PROTECTED]>
on Sun, 26 Oct 2003 00:49:45 -0400 writes:
Olivia> Hi, Is there a way to make
> "Olivia" == Olivia Lau <[EMAIL PROTECTED]>
> on Sun, 26 Oct 2003 00:49:45 -0400 writes:
Olivia> Hi, Is there a way to make demo() print comments
Olivia> along with the code and output?
not so easily. The same applies to example(.).
Both demo(.) and example(.) end up callin
Dear all,
I'm trying reproduce an example of bioassays Yielding Concentration-Mortality Data
particularly control - adjustment model from book Bioassay of Entomopathogenic
Microbes and Nematodes chapter 7 with R.
I used glm with family=binomial and link=probit, but I do not know how to implement
Hi Cristian,
I don't know about a R routine for exact CIs, but I found a function called
"ageadjust" using a gamma distribution approximation some time ago -take a
look at http://medepi.org/epitools/rfunctions/index.html.
That Webpage seems a bit outdated now, but the calculations given in the
age
Does anybody know a R routine to calculate exact Confidence Intervals for
Incidence Rate Ratio?
Thanks
Cristian
-
Biometria - biometria.univr.it
__
[EMAIL PROTECTED] mailing list
https://www.stat.math.e
Dear R-helpers,
if someone is interested in (last night I dreamed):
...
SH <- -3.8
fn.2 <- function(p){
for (i1 in ilong){
ex[i1] <- (1E-19*p[1]*n*L*voigt(u,v,f[i1],foN,p[2],p[3])[[1]])
}
sum((log(tt)-ex)^2)
}
out.2 <-nlm(fn.2, p = c(SH,GG,GL), hessian = TRUE,
steptol = 1e-6,
__
[EMAIL PROTECTED] mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Could you at least tell us which R package(s) and versions you are using
here?
You can access Oracle databases by ROracle and RODBC and perhaps other
ways. If this is ROracle, it would be better to use the R-sig-DB list
(see https://www.stat.math.ethz.ch/mailman/listinfo) or talk directly to
the
Model frames do not contain interactions, they contain variables.
`a:b' is not the name of a variable whereas A is.
On Mon, 27 Oct 2003, Vito Muggeo wrote:
> dear all,
> for some reason I am intersted in updating a glm taking variables from its
> model argument, namely:
>
> > dati<-data.frame(y=
relating to my former messages concerning the strange fetch problems I
have, I found out that 'fetch' fetches only every second row of the
'native' SQL-results and fills up the rest of the rows with zeros.
Here a draft for the native SQL-query:
12:43:07 SQL> SELECT OBS_DAY, OBS_YEAR, STAT_ID FR
Dear List,
I would like to know if there exist some R implementation of John
Whitehead's procedures for the planning and analysis of group sequential
clinical trials. His book is enlightenig but somewhat frustrating : it
has a good basic exposition of his framework, but the technical details
a
dear all,
for some reason I am intersted in updating a glm taking variables from its
model argument, namely:
> dati<-data.frame(y=runif(10),x=1:10)
> obj<-glm(y~x,data=dati)
> obj$model[,c("A","a:b")]<-cbind(rnorm(10),runif(10))
> names(obj$model)
[1] "y" "x" "A" "a:b"
> update(obj,.~.+A,dat
> "Edzer" == Edzer J Pebesma <[EMAIL PROTECTED]>
> on Mon, 27 Oct 2003 10:56:57 +0100 writes:
Edzer> The following now occurs to me when I try to load
Edzer> lattice (R 1.7.1, debian stable):
>> library(lattice)
Edzer> Error in loadNamespace(i, c(lib.loc, .libPaths()),
On Mon, 27 Oct 2003, Edzer J. Pebesma wrote:
> The following now occurs to me when I try to
> load lattice (R 1.7.1, debian stable):
>
> > library(lattice)
> Error in loadNamespace(i, c(lib.loc, .libPaths()), keep.source) :
> package `grid' does not have a name space
> Error in library(la
Edzer J. Pebesma wrote:
The following now occurs to me when I try to
load lattice (R 1.7.1, debian stable):
library(lattice)
Error in loadNamespace(i, c(lib.loc, .libPaths()), keep.source) :
package `grid' does not have a name space
Error in library(lattice) : package/namespace load failed
The following now occurs to me when I try to
load lattice (R 1.7.1, debian stable):
library(lattice)
Error in loadNamespace(i, c(lib.loc, .libPaths()), keep.source) :
package `grid' does not have a name space
Error in library(lattice) : package/namespace load failed
I did an update.packages(
If I have drawn a string with ``ltext( x, y, labels="first string" )''
how can a draw a second string just one line (or strheight("X")
below the first string regardless of the size and scales of the panel?
Thanks
Wolfram
__
[EMAIL PROTECTED] mailing lis
On 26 Oct 2003, Russell Senior wrote:
>
> Given a set of data:
>
> > names(data)
> [1] "city" "house" "visit""value"
>
> I am looking for a way to compute the variance components of the
> nested model (ie, visit 1 at house 2 at city 3 isn't related to visit
> 1 and house 2 at city 4
lme should do the job (r1,r2,r3 are your random factors):
library(nlme)
y.lme <- lme(y ~ 1,random = ~ 1 | r1/r2/r3)
summary(y.lme)
This is equivalent to a call to varcomp in S-Plus
Pascal
--
Dr. Pascal A. Niklaus
Institute of Botany
University of Basel
Schönbeinstrasse 6
CH-4056 Basel
This is not really an rhelp question. I'll get back to you later today
with answers related to R.oo.
Henrik Bengtsson
The R.oo author
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of
> Gabriel Baud-Bovy
> Sent: den 27 oktober 2003 01:56
> To: [EMAI
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