[R] dot diagram
Hi,
I am wondering whether there is a function that could plot
a dot diagram like the output of following code.
Thanks in advance!
Best wishes!
Jinsong
-my dirty code here-
mydata - c(26,26,27,27,27,27,28,28,28,28,28,28,28,28,28,
28,28,28,28,29,29,29,29,29,29,29,29,29,29,29,
30,30,30,30,30,30,30,30,31,31,31,31,32,33,33,
33,34,34,35,43)
my.dot.plot - function(x, ...) {
x.table - table(x)
x.x - as.numeric(names(x.table))
x.y - as.numeric(x.table)
n - length(x.x)
x.final - NULL
for (i in 1:n) {
tmp - data.frame(x=rep(x.x[i], x.y[i]), y=1:x.y[i])
x.final - rbind(x.final, tmp)
}
plot(x.final, yaxt=n, ylab=, pch=19, frame.plot=FALSE, ...)
}
my.dot.plot(mydata, xlab =speed, xlim=c(25,45))
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] copying and pasting to R in linux
Louis, OK, I don't use any GUI, just the command line. Everything works fine on the command line. I had the same problem with downloaded Suse 10. It doesn't contain all the same packages that the purchased version does. You have to do Yast / Installation Source and add installation sources. They are listed at http://en.opensuse.org/Package_Repositories Larry On Saturday 08 April 2006 23:49, you wrote: Here are the combinations I have tried: Standard R gui, kwrite cut and paste small files, source small files Standard R gui, kate same as above Standard R gui, office word processor same as above Tk R gui source works fine, but doesn't support cut and paste By the way I just installed suse 10.0 from the downloaded cd's and when I try to install the latest R rpm, I am told I am missing a couple of support files. Any suggestions here? On Saturday 08 April 2006 16:19, Larry Howe wrote: On Saturday 08 April 2006 16:27, louis homer wrote: When I use R, I am accustomed to developing programs in a text processor, and then copying from the text processor and pasting into R. This usually works fine, except that using the default text processor in Suse 9.0, long programs don't transfer completely. Using the 'source' program, also only works with small programs. Suggestions? Hmmm...I'm using Suse 9 and 10, and I don't have that problem. Can you give some more detail? By the default editor, do you mean KWrite? It's OK but Kate is somewhat better for programming. It's hidden way inside the start menu so I usually just go Start / Run command / kate. Are you saying that - create R script in editor - save script - start R - source(name of file) does not work? Larry Howe __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] (IT WAS) Aggregating an its series
Thanks for the brilliant solution. ***AGAIN*** Now - just to go deeper into the **same subject** on which I'm really supposed to work very soon - if I want to aggregate by date only data, say, before noon (12.00.00) what should I do? Ciao Vittorio Alle 16:13, venerdì 07 aprile 2006, Whit Armstrong ha scritto: aggregate(base,by=list(as.factor(format(dates(base),%Y%m%d))),mean,na. rm=T) -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Vittorio Sent: Friday, April 07, 2006 11:38 AM To: r-help@stat.math.ethz.ch Subject: [R] Aggregating an its series I'm using a very long irregular time-series of air temperature and relative humidity of this kind (this is an extract only) its.format(% Y%d%m %X) base T H 20020601 12.00.00 27.1 47 20020601 15.00.00 29.1 39 20020601 18.00.00 27.4 39 20020601 21.00.00 24.0 40 20020602 0.00.00 22.0 73 20020602 3.00.00 19.2 49 20020602 6.00.00 19.5 74 20020602 9.00.00 24.8 45 20020602 12.00.00 27.7 NA 20020602 15.00.00 29.2 39 20020602 18.00.00 27.2 44 20020602 21.00.00 23.9 50 20020603 0.00.00 21.0 75 20020603 3.00.00 19.6 65 20020603 6.00.00 19.8 71 20020603 9.00.00 23.2 67 20020603 12.00.00 24.9 65 20020603 15.00.00 21.7 74 20020603 18.00.00 22.8 63 20020603 21.00.00 21.2 75 20020604 0.00.00 18.0 91 I would like to aggregate T and H by day and produce another its of this kind aggr T H 20020601 NA NA 20020602 NA NA 20020603 NA NA 20020604 NA NA where the daily average of T and H (not counting the NA values) is is put in aggr. What is the quickest way to get this result? Thanks Vittorio __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] type converters not being saved to workspace
Any one can explain why this happens or any work arounds?
setClass('foo')
[1] foo
setAs('foo', 'character', function(from) from)
showMethods('coerce')
Function coerce:
from = ANY, to = array
from = ANY, to = call
from = ANY, to = character
from = ANY, to = complex
from = ANY, to = environment
from = ANY, to = expression
from = ANY, to = function
from = ANY, to = integer
from = ANY, to = list
from = ANY, to = logical
from = ANY, to = matrix
from = ANY, to = name
from = ANY, to = numeric
from = ANY, to = single
from = ANY, to = ts
from = ANY, to = vector
from = ANY, to = NULL
from = foo, to = character
q()
Save workspace image? [y/n/c]: y
(restart)
showMethods('coerce')
Function coerce:
from = ANY, to = array
from = ANY, to = call
from = ANY, to = character
from = ANY, to = complex
from = ANY, to = environment
from = ANY, to = expression
from = ANY, to = function
from = ANY, to = integer
from = ANY, to = list
from = ANY, to = logical
from = ANY, to = matrix
from = ANY, to = name
from = ANY, to = numeric
from = ANY, to = single
from = ANY, to = ts
from = ANY, to = vector
from = ANY, to = NULL
from = NULL, to = OptionalFunction
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Boxplot using Formula
Matt Goff goff at nawwal.org writes: The problem is that boxplot is displaying groups that are empty in the plot. Call factor() again on the groups, which will drop levels. You can do that in an extra line, or on-the-fly: data-data.frame(values=c(1:25), groups=rep(c(A,B,C,D,E), each=5)) data = subset(data,groups!=C) boxplot(values~factor(groups), data=data) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] dim(x) error message in lme (nlme package)
Andreas Svensson andreas.svensson at bio.ntnu.no writes: I had a suspicion that you can't have the lme4 package loaded when using lme (from the nlme package), and lo! I get the full summary of lme only if lme4 is NOT loaded. Yes, currently the two don't coexist well, so better make sure to use only on at a time. Dieter __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Multiple ablines
G. Alex Janevski galexski at umich.edu writes: points(y~x, pch=*, col=black) lm(y~x) fm=lm(y~x) abline(fm, col=red) This works. The problem arises in that I would like to run my simulation multiple times, to plot the data points together on the same plot, and more importantly the regression lines of the simulated data. Therefore, I have placed the code within the loop of the simulation. This works fine for points(), I can watch the additional points being added to the plot as the simulations run. However, when I include abline() it gives this error: Error in abline(a, b, h, v, untf, col, lty, lwd, ...) : 'a' and 'b' must be finite I can take the code as written and place it outside of the loop and it works fine, plotting the points and regression line for the data of the last run of the simulation. ... Just a guess: try to call plot(...) in each repetition of the loop once; points and lines require an existing plot, where scaling etc. is already defined. Dieter __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] type converters not being saved to workspace
It is recommended that you use a package for this sort of thing.
When a package is loaded, the S4 methods it contains are merged into the
metadata. When the global environment is loaded, they are not. Call
'cacheMetaData(1)' to do so.
[This looks like a bug: cacheMetaData is called on .GlobalEnv in the
startup code for package methods, but seems not to work when called from
there. I think this is because package methods is not at that point on
the search path (the call is from .onLoad) and hence the coerce() generic
is not visible to cacheMetaData. If you have S4 code in a package, it
will ensure that package methods is attached before your package is
loaded.]
On Sun, 9 Apr 2006, Joseph Wang wrote:
Any one can explain why this happens or any work arounds?
setClass('foo')
[1] foo
setAs('foo', 'character', function(from) from)
showMethods('coerce')
Function coerce:
from = ANY, to = array
from = ANY, to = call
from = ANY, to = character
from = ANY, to = complex
from = ANY, to = environment
from = ANY, to = expression
from = ANY, to = function
from = ANY, to = integer
from = ANY, to = list
from = ANY, to = logical
from = ANY, to = matrix
from = ANY, to = name
from = ANY, to = numeric
from = ANY, to = single
from = ANY, to = ts
from = ANY, to = vector
from = ANY, to = NULL
from = foo, to = character
q()
Save workspace image? [y/n/c]: y
(restart)
showMethods('coerce')
Function coerce:
from = ANY, to = array
from = ANY, to = call
from = ANY, to = character
from = ANY, to = complex
from = ANY, to = environment
from = ANY, to = expression
from = ANY, to = function
from = ANY, to = integer
from = ANY, to = list
from = ANY, to = logical
from = ANY, to = matrix
from = ANY, to = name
from = ANY, to = numeric
from = ANY, to = single
from = ANY, to = ts
from = ANY, to = vector
from = ANY, to = NULL
from = NULL, to = OptionalFunction
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Boxplot using Formula
Matt Goff wrote:
I am trying to use the formula interface for the boxplot.
Currently running R 2.2.1 on Windows XP.
The problem is that boxplot is displaying groups that are empty in the
plot.
The following example demonstrates what it is happening (though my actual
situation is a little more complicated):
data-data.frame(values=c(1:25), groups=rep(c(A,B,C,D,E),
each=5))
boxplot(data$values~data$groups, subset=data$groups!=C)
The plot includes a space for level C with no boxplot. I would like to
have only those levels with associated boxplots be shown in the figure.
So in this case, there should only be values A, B, D, and E evenly
spaced along the horizontal axis.
I am a little confused because I am reusing old code and I don't remember
having this issue before, so perhaps there have been some changes in the
behavior of the boxplot function since the last time I use the code.
It seems like there's probably a simple solution, but I'm not seeing it.
Thanks,
Matt Goff
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Hi, Matt,
I'm afraid you cannot do what you want with boxplot.formula. You have at
least two options:
1) Supply only data that has no empty levels.
2) Create a new function that does what you need:
## add `drop.unused.levels' argument to boxplot.formula
boxplot2 -
function (formula, data = NULL, ...,
subset, na.action = NULL,
drop.unused.levels = TRUE)
{
if (missing(formula) || (length(formula) != 3))
stop('formula' missing or incorrect)
m - match.call(expand.dots = FALSE)
if (is.matrix(eval(m$data, parent.frame(
m$data - as.data.frame(data)
m$... - NULL
m$na.action - na.action
m$drop.unused.levels - drop.unused.levels
m[[1]] - as.name(model.frame)
mf - eval(m, parent.frame())
response - attr(attr(mf, terms), response)
boxplot(split(mf[[response]], mf[-response]), ...)
}
values - 1:25
groups - factor(rep(c(A,B,C,D,E), each=5))
boxplot2(values ~ groups, subset = groups != C)
HTH,
--sundar
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Primitives
How one can make a list of all functions in R's base package which are given as Primitives like abs, sqrt cumsum (but not log) ? Thanks a lot Diethelm Wuertz __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 38, Issue 9
Mi nueva dirección de correo es: [EMAIL PROTECTED] New e-mail address: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Primitives
On 4/9/2006 5:46 AM, Diethelm Wuertz wrote: How one can make a list of all functions in R's base package which are given as Primitives like abs, sqrt cumsum (but not log) ? There's an is.primitive() test function; you just need to get all objects, and test them one by one. Duncan Murdoch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] cross product
2006/4/8, He, Yulei [EMAIL PROTECTED]:
Hi, there.
How do I calculate the cross-product in the form of
\sum_{i=1}^{n}X_{i}^{t} \Sigma X_{i} using R code without using do loop?
X_{i} is the covariate matrix for subject I, \Sigma is the covariance
matrix.
If I don't miss something in the matrix algebra, maybe you want the
following:
crossprod(crossprod(t(X),sigma),X)
where X is the 'n by d' matrix of covariates, and sigma the 'd by d' matrix
of assigned covariances.
Antonio, Fabio Di Narzo.
Thanks for your help.
Yulei
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] more documentation on lmer?
Dear Bill, You might check Faraway's 'Extending the Linear Model with R: Generalized Linear, Mixed Effects and Nonparametric Regression Models' (2006). Without having read the book properly, at least I noticed that package lme4 and the function lmer is used in the examples. Best regards, Henrik Hello. Is there any documentation on the lmer function in the lme4 package beyond what was published in the May 2005 R News (vol.5/1)? As well, has the nonlinear version of lmer appeared yet? Bill Shipley -- Henrik Pärn Department of Biology NTNU 7491 Trondheim Norway +47 735 96282 (office) +47 909 89 255 (mobile) +47 735 96100 (fax) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Calculation of r.squared for linear model with offset
R^2 for a model is usually defined as 1-RSS/TSS where TSS is the SS about the mean and RSS is the residual SS from the model. Consider the model in R z - runif(20) y - z+rnorm(20) my.model - lm(y~offset(z)) summary(my.model)$r.squared Here the RSS is equivalent to the TSS and gives 0 when it should (IMHO and a few others perhaps) be 1 - RSS/TSS(corrected for the mean only) RSS = sum(resid(my.model)^2) TSS = sum((y-mean(y))^2) Have I missed this somewhere in the FAQ's or elsewhere? Regards Ross Darnell __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] dot diagram
Don't know about a function but it can be done in one plot statement
like this:
plot(seq(x) - match(x, x) ~ x, list(x = sort(mydata)),
xlim=c(25,45), ylab =, yaxt=n, pch=19, frame.plot=FALSE)
On 4/9/06, Jinsong Zhao [EMAIL PROTECTED] wrote:
Hi,
I am wondering whether there is a function that could plot
a dot diagram like the output of following code.
Thanks in advance!
Best wishes!
Jinsong
-my dirty code here-
mydata - c(26,26,27,27,27,27,28,28,28,28,28,28,28,28,28,
28,28,28,28,29,29,29,29,29,29,29,29,29,29,29,
30,30,30,30,30,30,30,30,31,31,31,31,32,33,33,
33,34,34,35,43)
my.dot.plot - function(x, ...) {
x.table - table(x)
x.x - as.numeric(names(x.table))
x.y - as.numeric(x.table)
n - length(x.x)
x.final - NULL
for (i in 1:n) {
tmp - data.frame(x=rep(x.x[i], x.y[i]), y=1:x.y[i])
x.final - rbind(x.final, tmp)
}
plot(x.final, yaxt=n, ylab=, pch=19, frame.plot=FALSE, ...)
}
my.dot.plot(mydata, xlab =speed, xlim=c(25,45))
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] adding a row to a matrix
Hi All, This is probably a very simple question. I was trying to add a row to the rows in a matrix. For example: a - matrix(1:6,2,3) b - a[1,] print(a) [,1] [,2] [,3] [1,]135 [2,]246 print(b) [1] 1 3 5 I now want to add 'b' to every row of 'a', so the end result should look like: [,1] [,2] [,3] [1,]26 10 [2,]37 11 But if I do c = apply(a,1,+,b), I get: c [,1] [,2] [1,]23 [2,]67 [3,] 10 11 Now, I could easily transform this to get what I want, but I'd like to know how I could get the result without many intermediate steps ( I have large matrices, so transforming them at each step would not be efficient). If someone could point me in the right direction, that would be a great help. thanks. - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] RFC: default background on lattice plots (conclusion)
I haven't heard any more comments on this, and R 2.3.0 is almost here, so I'll bring this thread to a close. I have changed the default theme to the old PDF default for all devices (except postscript, which still defaults to color=FALSE) in the latest lattice (part of R-alpha now). It's easy enough to get the old defaults back, instructions are given in ?trellis.device. Deepayan __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] adding a row to a matrix
You can try sweep: sweep(a,2,b,+) -Christos -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Tim Smith Sent: Sunday, April 09, 2006 11:28 AM To: r-help@stat.math.ethz.ch Subject: [R] adding a row to a matrix Hi All, This is probably a very simple question. I was trying to add a row to the rows in a matrix. For example: a - matrix(1:6,2,3) b - a[1,] print(a) [,1] [,2] [,3] [1,]135 [2,]246 print(b) [1] 1 3 5 I now want to add 'b' to every row of 'a', so the end result should look like: [,1] [,2] [,3] [1,]26 10 [2,]37 11 But if I do c = apply(a,1,+,b), I get: c [,1] [,2] [1,]23 [2,]67 [3,] 10 11 Now, I could easily transform this to get what I want, but I'd like to know how I could get the result without many intermediate steps ( I have large matrices, so transforming them at each step would not be efficient). If someone could point me in the right direction, that would be a great help. thanks. - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] configure error
*I've been trying for several weeks to install R-2.2.1 on a PC with an AMD Athlon 64 2800*+* processor running Mandriva 2006_64. After unpacking R-2.2.1.tar.gz I ran ./configure. However, configure stopped prematurely with the message *configure:27295: WARNING: gfortran and gcc disagree on int and double configure:27297: error: Maybe change CFLAGS or FFLAGS?* Altough I've looked in both the R_Help archive and R Installation and Administration, I can't find any documentation which says what settings should be for CFLAGS or FFLAGS. I tried to mimic the settings shown on page 31 of R Installation and Administration but that failed too.* *Does anyone know what the settings should be for this case? Any advice would be greatly appreciated. Richard Carter * __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] lm$effects in lm()
Hi .. lm() returns an effects component in its output. I read the explanation in R but was not quite clear. say my response is Y and design matrix is X say X has QR decomposition X=QR is effects = Q (Q'Q)^-1 Q' Y ??? i am sure this is wrong as it did not match the output from lm() . what is the actual calculation. Harsh. - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] configure error
On Sunday 09 April 2006 11:41, R. A. L. Carter wrote: prematurely with the message *configure:27295: WARNING: gfortran and gcc disagree on int and double configure:27297: error: Maybe change CFLAGS or FFLAGS?* Altough I've looked in both the R_Help archive and This is primarily a guess, but it sounds like your version of gfortran isn't compatible with your version of gcc. Larry Howe __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] logistic regression model with non-integer weights
When fitting a logistic regression model using weights I get the following warning data.model.w - glm(ABN ~ TR, family=binomial(logit), weights=WEIGHT) Warning message: non-integer #successes in a binomial glm! in: eval(expr, envir, enclos) Details follow *** I have a binary dependent variable of abnormality ABN = T, F, T, T, F, F, F... and a continous predictor TR = 1.962752 1.871123 1.893543 1.685001 2.121500, ... As the number of abnormal cases (ABN==T) is only 14%, and there is large overlapping between abnormal and normal cases, the logistic regression found by glm is always much closer to the normal cases than for the abnormal cases. In particular, the probability of abnormal is at most 0.4. Coefficients: Estimate Std. Error z value Pr(|z|) (Intercept) 0.7607 0.7196 1.057 0.2905 TR2 -1.4853 0.4328 -3.432 0.0006 *** --- I would like to compensate for the fact that the a priori probability of abnormal cases is so low. I have created a weight vector WEIGHT - ABN WEIGHT[ ABN == TRUE ] - 1 / na / 2 WEIGHT[ ABN == FALSE ] - 1 / nn / 2 so that all weights add up to 1, where ``na'' is the number of abnormal cases, and ``nn'' is the number of normal cases. That is, normal cases have less weight in the model fitting because there are so many. But then I get the warning message at the beginning of this email, and I suspect that I'm doing something wrong. Must weights be integers, or at least greater than one? Regards, -- Ramón Casero Cañas http://www.robots.ox.ac.uk/~rcasero/wiki http://www.robots.ox.ac.uk/~rcasero/blog __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] adding a row to a matrix
Try this: t(t(a)+b) On 4/9/06, Tim Smith [EMAIL PROTECTED] wrote: Hi All, This is probably a very simple question. I was trying to add a row to the rows in a matrix. For example: a - matrix(1:6,2,3) b - a[1,] print(a) [,1] [,2] [,3] [1,]135 [2,]246 print(b) [1] 1 3 5 I now want to add 'b' to every row of 'a', so the end result should look like: [,1] [,2] [,3] [1,]26 10 [2,]37 11 But if I do c = apply(a,1,+,b), I get: c [,1] [,2] [1,]23 [2,]67 [3,] 10 11 Now, I could easily transform this to get what I want, but I'd like to know how I could get the result without many intermediate steps ( I have large matrices, so transforming them at each step would not be efficient). If someone could point me in the right direction, that would be a great help. thanks. - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] using latex() function with other .sty files
I am having some problems using the latex() function in the Hmisc package. When I turned on the ctable option in latex(), the LaTeX code produced by latex()somehow conflicts with the style back my unversity uses for theses. Has anyone on the list had a similar conflict and been able to fix it. One simple fix I know of is to have ctable=FALSE. The tables work fine then, but I prefer the look (and other options) of ctable=TRUE. This is by no means an urgent request, since I can simply turn of the ctable option, but if anyone does know of a fix, I'd certainly appreciate the help. Thanks Brian __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] (IT WAS) Aggregating an its series
Just strip off the hours component of the dates, then take a subset of the data where the hour is = 12. I did not execute this, so you might need to change it a bit: hours - as.integer(format(dates(base),%H)) new.data - base[hours = 12,] aggregate(new.data,by=list(as.factor(format(dates(new.data),%Y%m%d))),mean,na.rm=T) -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of vittorio Sent: Sunday, April 09, 2006 6:12 AM To: r-help@stat.math.ethz.ch Subject: Re: [R] (IT WAS) Aggregating an its series Thanks for the brilliant solution. ***AGAIN*** Now - just to go deeper into the **same subject** on which I'm really supposed to work very soon - if I want to aggregate by date only data, say, before noon (12.00.00) what should I do? Ciao Vittorio Alle 16:13, venerdì 07 aprile 2006, Whit Armstrong ha scritto: aggregate(base,by=list(as.factor(format(dates(base),%Y%m%d))),mean,na. rm=T) -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Vittorio Sent: Friday, April 07, 2006 11:38 AM To: r-help@stat.math.ethz.ch Subject: [R] Aggregating an its series I'm using a very long irregular time-series of air temperature and relative humidity of this kind (this is an extract only) its.format(% Y%d%m %X) base T H 20020601 12.00.00 27.1 47 20020601 15.00.00 29.1 39 20020601 18.00.00 27.4 39 20020601 21.00.00 24.0 40 20020602 0.00.00 22.0 73 20020602 3.00.00 19.2 49 20020602 6.00.00 19.5 74 20020602 9.00.00 24.8 45 20020602 12.00.00 27.7 NA 20020602 15.00.00 29.2 39 20020602 18.00.00 27.2 44 20020602 21.00.00 23.9 50 20020603 0.00.00 21.0 75 20020603 3.00.00 19.6 65 20020603 6.00.00 19.8 71 20020603 9.00.00 23.2 67 20020603 12.00.00 24.9 65 20020603 15.00.00 21.7 74 20020603 18.00.00 22.8 63 20020603 21.00.00 21.2 75 20020604 0.00.00 18.0 91 I would like to aggregate T and H by day and produce another its of this kind aggr T H 20020601 NA NA 20020602 NA NA 20020603 NA NA 20020604 NA NA where the daily average of T and H (not counting the NA values) is is put in aggr. What is the quickest way to get this result? Thanks Vittorio __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] adding a row to a matrix
Thanks Christosworked a treat! Christos Hatzis [EMAIL PROTECTED] wrote: You can try sweep: sweep(a,2,b,+) -Christos -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Tim Smith Sent: Sunday, April 09, 2006 11:28 AM To: r-help@stat.math.ethz.ch Subject: [R] adding a row to a matrix Hi All, This is probably a very simple question. I was trying to add a row to the rows in a matrix. For example: a - matrix(1:6,2,3) b - a[1,] print(a) [,1] [,2] [,3] [1,]135 [2,]246 print(b) [1] 1 3 5 I now want to add 'b' to every row of 'a', so the end result should look like: [,1] [,2] [,3] [1,]26 10 [2,]37 11 But if I do c = apply(a,1,+,b), I get: c [,1] [,2] [1,]23 [2,]67 [3,] 10 11 Now, I could easily transform this to get what I want, but I'd like to know how I could get the result without many intermediate steps ( I have large matrices, so transforming them at each step would not be efficient). If someone could point me in the right direction, that would be a great help. thanks. - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] help on using 'sum' in writng a function
Hi, I am writing a function that includes 'sum' function
such as:
f-function(x){
c-c(-1,0,1)
f-sum(c+x)
}
expecting f to be -1+x+0+x+1+x=3x. But I found out that f is
sum(x). So, f is always a scalar, which means that f(c(0,1))
is not a vector as c(0,3), but 3(0+1)=3. I would like to ask
you helping me in solving this problem. I would like to
thank you in advance.
Sungsu.
UC riverside.
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] help on using 'sum' in writng a function
If c is c(c1, c2, c3) and x is c(x1, x2, x3) then
c+x is (c1+x1, c2+x2, c3+x3)
so sum(c+x) is c1+x1+c2+x2+c3+x3 = sum(c) + sum(x)
What you were expecting is given by:
rowSums(outer(1:4, c(-1,0,1), +)) # gives c(3, 6, 9, 12)
Review the Introduction to R manual and also look at ?outer and ?rowSums
On 4/9/06, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote:
Hi, I am writing a function that includes 'sum' function
such as:
f-function(x){
c-c(-1,0,1)
f-sum(c+x)
}
expecting f to be -1+x+0+x+1+x=3x. But I found out that f is
sum(x). So, f is always a scalar, which means that f(c(0,1))
is not a vector as c(0,3), but 3(0+1)=3. I would like to ask
you helping me in solving this problem. I would like to
thank you in advance.
Sungsu.
UC riverside.
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] help on using 'sum' in writng a function
Or, of course, if you are willing to reduce it then its just
sum(c) + length(c) * x
On 4/9/06, Gabor Grothendieck [EMAIL PROTECTED] wrote:
If c is c(c1, c2, c3) and x is c(x1, x2, x3) then
c+x is (c1+x1, c2+x2, c3+x3)
so sum(c+x) is c1+x1+c2+x2+c3+x3 = sum(c) + sum(x)
What you were expecting is given by:
rowSums(outer(1:4, c(-1,0,1), +)) # gives c(3, 6, 9, 12)
Review the Introduction to R manual and also look at ?outer and ?rowSums
On 4/9/06, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote:
Hi, I am writing a function that includes 'sum' function
such as:
f-function(x){
c-c(-1,0,1)
f-sum(c+x)
}
expecting f to be -1+x+0+x+1+x=3x. But I found out that f is
sum(x). So, f is always a scalar, which means that f(c(0,1))
is not a vector as c(0,3), but 3(0+1)=3. I would like to ask
you helping me in solving this problem. I would like to
thank you in advance.
Sungsu.
UC riverside.
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Primitives
Duncan Murdoch wrote: On 4/9/2006 5:46 AM, Diethelm Wuertz wrote: How one can make a list of all functions in R's base package which are given as Primitives like abs, sqrt cumsum (but not log) ? There's an is.primitive() test function; you just need to Sorry when I ask again, how to list all functions in R's base installation? Thanks Diethelm Wuertz get all objects, and test them one by one. Duncan Murdoch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] calculation of r (corelation coefficient) from models
Dear R users This is a stats question rather than R question. For continuous predictors, we get estimates of slopes and their se and t values (slope/se) in R ouptput. If we have a model with more than one continuous variable (i.e., multiple regression), we get slope, se and t value for each continuous predictor. Here is my question - is there any way I can calculate r value or correlation (partial correlation?) between each continuous predicator and response, using these parameters in R output? If I just have one response and one predictor, I would use cor.test(x, y) or cor(x, y) function but I was wondering whether I could calculate correlation coefficient for each predictor from a statistical model. Cohens d (dimensionless effect size) is very easy to calculate from t values and sample size when I have categorical (dichotomous) predictors, but I could not get r (correlation coefficient; another dimensionless effect size) when I have continuous predictors using t values or related statistics from models. Thank you very much Shinichi __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Primitives
On 4/9/2006 5:57 PM, Diethelm Wuertz wrote:
Duncan Murdoch wrote:
On 4/9/2006 5:46 AM, Diethelm Wuertz wrote:
How one can make a list of all functions in R's base
package which are given as Primitives like abs, sqrt
cumsum (but not log) ?
There's an is.primitive() test function; you just need to
Sorry when I ask again, how to list all functions in R's
base installation?
ls(baseenv()) or ls(package:base)
will give you all their names. So you need to use something like
names - ls(baseenv())
result - rep(FALSE, length(names))
for (i in seq(along=names)) {
result[i] - is.primitive(get(names[i], envir=baseenv()))
}
names[result]
Duncan Murdoch
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Re : AUC under spline curve
Dear R list, I have fitted cubic regression spline with fixed degree of freedom to a set of data using package mgcv. Now I want to calculate the area under the spline curve. Someone has suggested me to use trapezoidal rule. Do you know if someone has written a package that will carry out that analysis, and where can I download it ? Thanks in advance. Stella __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] SE estimates for treatment groups from nlme
I am wondering how to obtain SE estimates for fixed effects from a nonlinear mixed effects model? I have fixed effects corresponding to three factors A, B and C with 2, 3 and 3 levels respectively. I have fit a model of the following general form: nlme1-nlme(y~ SasympOrig(x, Asym, lrc), data=df, fixed=list(Asym~A*B*C, lrc~A*B*C), start=c(fixef(ETR.nlme)[1], rep(0,17), fixef(ETR.nlme)[2], rep(0,17))) I am using the default (contr.treatment and contr.poly). The summary table (tTable) gives me the baseline coefficients and a list of differences and I have no trouble calculating the coefficients for any of my treatment groups by forming the correct linear combination of coefficients. However, I don't understand how to obtain the standard errors for these linear combinations from the summary report. What I want to obtain would be 18 parameter estimates with appropriate SEs for my 18 different groups (A*B*C=2*3*3=18). In response to a similar posting, it was recommended to use the function estimable in the package gregmisc. I have looked at this and cannot figure out how to apply it in my situation. Any help would be greatly appreciated. Thanks, Katie Katie Grieve Quantitative Ecology and Resource Management University of Washington __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] help on using sum in writng a function again
Hi, thanks for your reply.
Here I would like to ask you again more directly.
The following is what I had for now.
The function to begin with is
dnorm(theta+2*pi*j,0,1)*(pnorm(((2*pi*(k+1)-rho*
(theta+2*pi*j)).
Now, I wanted to sum it over k from -1 to 1. So, I
wrote the following.
f1-function(theta,j){
aa-seq(-1,1,lenght=20001)
sum(dnorm(theta+2*pi*j,0,1)*(pnorm(((2*pi*(aa+1)-rho*
(theta+2*pi*j))
}
Next, I would like sum over j as
(This is a way I thouhgt about computing a double sum)
f2-function(theta){
aa-c(-1,0,1)
sum(f(theta,aa))
}
expecting f2 be a function of theta.
Then, I wanted to plot f2 for theta from 0 to 2*pi. But, f2
(seq(0,2*pi,length=10)) is a scalar, not a vector with the
dimension of 10x1. I would like to ask you how I can use
rowSums with outer or some other method to correct my coding.
I would like to thank you in advance.
Sungsu.
UC riverside.
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] weighted kernel density estimate
Weighted spatial kernel density estimation is available in the function 'density.ppp' in the package 'spatstat'. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] passing known medoids to clara() in the cluster package
Greetings, I have had good success using the clara() function to perform a simple cluster analysis on a large dataset (1 million+ records with 9 variables). Since the clara function is a wrapper to pam(), which will accept known medoid data - I am wondering if this too is possible with clara() ... The documentation does not suggest that this is possible. Essentially I am trying to implement a supervised classification of numerous geographic data layers. The unsupervised approach using clara() works well, but I feel the output classes would be more meaningful if I were able to let clara() know about the classes that I have in mind. Is this at all feasible, or am I trying to accomplish something that is not possible? Cheers, -- Dylan Beaudette Soils and Biogeochemistry Graduate Group University of California at Davis 530.754.7341 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] [Help] a Correlation Problem
I encounter a statistic problem about correlation. I use R to test wether two variables are correlated or not. (pearson correlation) cor.test(x,y) give a p=5.87 Because the x, y is not normal distributed (qqplot indicate that) I also perform (spearman rank correlation) cor.test(x,y,method=spearman) give a very significant result p10e-4 I don't know how to explain this. Will this result tell us that x, y are correlated but not a linear one, and we can't use the coefficient estimated by spearman rank correlation because its interpretation is not quite clear. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] [Help] a Correlation Problem
Try this where g is f summed over j and k for given scalars theta and rho and gv is g vectorized over theta. I have not checked this carefully so be sure you do: f - function(theta = 0, rho = 0, j = 0, k = 0) dnorm(theta+2*pi*j,0,1)*pnorm(2*pi*(k+1)-rho*(theta+2*pi*j)) g - function(theta = 0, j = 0, k = 0) sum(sapply(k, function(k) sum(f(theta, j = j, k = k gv - function(theta = 0, ...) sapply(theta, g, ...) x - seq(0, pi, length = 100) plot(x, gv(x, j = -1:1, k = -1:1)) On 4/9/06, kenzy ken [EMAIL PROTECTED] wrote: I encounter a statistic problem about correlation. I use R to test wether two variables are correlated or not. (pearson correlation) cor.test(x,y) give a p=5.87 Because the x, y is not normal distributed (qqplot indicate that) I also perform (spearman rank correlation) cor.test(x,y,method=spearman) give a very significant result p10e-4 I don't know how to explain this. Will this result tell us that x, y are correlated but not a linear one, and we can't use the coefficient estimated by spearman rank correlation because its interpretation is not quite clear. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] help on using sum in writng a function again
Sorry, I replied to the wrong email. Here it is again:
Try this where g is f summed over j and k for given scalars
theta and rho and gv is g vectorized over theta. I have not
checked this carefully so be sure you do:
f - function(theta = 0, rho = 0, j = 0, k = 0)
dnorm(theta+2*pi*j,0,1)*pnorm(2*pi*(k+1)-rho*(theta+2*pi*j))
g - function(theta = 0, j = 0, k = 0)
sum(sapply(k, function(k) sum(f(theta, j = j, k = k
gv - function(theta = 0, ...) sapply(theta, g, ...)
x - seq(0, pi, length = 100)
plot(x, gv(x, j = -1:1, k = -1:1))
On 4/9/06, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote:
Hi, thanks for your reply.
Here I would like to ask you again more directly.
The following is what I had for now.
The function to begin with is
dnorm(theta+2*pi*j,0,1)*(pnorm(((2*pi*(k+1)-rho*
(theta+2*pi*j)).
Now, I wanted to sum it over k from -1 to 1. So, I
wrote the following.
f1-function(theta,j){
aa-seq(-1,1,lenght=20001)
sum(dnorm(theta+2*pi*j,0,1)*(pnorm(((2*pi*(aa+1)-rho*
(theta+2*pi*j))
}
Next, I would like sum over j as
(This is a way I thouhgt about computing a double sum)
f2-function(theta){
aa-c(-1,0,1)
sum(f(theta,aa))
}
expecting f2 be a function of theta.
Then, I wanted to plot f2 for theta from 0 to 2*pi. But, f2
(seq(0,2*pi,length=10)) is a scalar, not a vector with the
dimension of 10x1. I would like to ask you how I can use
rowSums with outer or some other method to correct my coding.
I would like to thank you in advance.
Sungsu.
UC riverside.
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Generic code for simulating from a distribution.
Hello all,
I have the code below to simulate samples of certain size from a
particular distribution (here,beta distribution) and compute some
statistics for the samples.
betasim2-function(nsim,n,alpha,beta)
{
sim-matrix(rbeta(nsim*n,alpha,beta),ncol=n)
xmean-apply(sim,1,mean)
xvar-apply(sim,1,var)
xmedian-apply(sim,1,median)
simset-data.frame(sampleno=seq1:nsim),means=xmean,vars=xvar,medians=xmedian)
return(simset)
}
I can write a similar coding for any distribution individually.
Now, I would like to have a generic code, say if I specify the
distribution with the parameters and simulation and sample size I would
like to have the simulations done for the mentioned distribution and the
statistics performed.
I would appreciate any help in doing so?
Thanks for your time.
Mathangi
Mathangi Gopalakrishnan
Graduate student
Dept of Mathematics and Statistics
University of Maryland, Baltimore County
Baltimore, MD
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] interlogistic regression-interactive parameters
hello I wonder if anyone can tell me the logic of using of interactive parameters in logistic regression ? (or direct me any link containing explaining it) kind regards Ahmet Temiz -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
