Re: [R] Simulate phi-coefficient (correlation between dichotomous vars)
Newsgroup members,
I appreciate the help on this topic.
David Duffy provided a solution (below) that was quite helpful, and came
close to what I needed. It did a great job creating two vectors of
dichotomous variables with a known correlation (what I referred to as a
phi-coefficient).
My situation is a bit more complicated and I'm not sure it is easily
solved. The problem is that I must assume one of the vectors is
constant and generate one or more vectors that covary with the constant
vector.
In a continuous example I could use the following code that I got from
the S-PLUS newsgroup year ago:
sample.cor-function (x, rho)
{
y - (rho * (x - mean(x)))/sqrt(var(x)) + sqrt(1 - rho^2) *
rnorm(length(x))
cat(Sample corr = , cor(x, y), \n)
return(y)
}
X-rnorm(100) #a constant vector
Y1-sample.cor(X,.30) # a new vector that correlates with X .30
Y2-sample.cor(X,.45) # a second vector that correlates with X .45
I can, of course, have X be a vector of zeros and ones, and I can
dichotomize Y1 and Y2, but the program always returns a phi-coefficient
correlation lower than the continuous correlation. Mathematically, I
guess this is expected because the phi-coefficient is partially a
function of the percentage of positive responses. This, in turn,
explains Pearson's (1900) interest in the whole area of tetrachoric
correlations -- a tetrachoric correlation being the Pearson product
moment correlation that would have been observed had two dichotomously
scored variables been measured on a continuous scale (Pearson, 1900).
Appreciate any additional input or possible solutions.
Paul
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of David Duffy
Sent: Monday, September 12, 2005 1:34 AM
To: r-help@stat.math.ethz.ch
Subject: [R] Simulate phi-coefficient
From: Bliese, Paul D LTC USAMH [EMAIL PROTECTED]
Given a sample of zeros and ones, for example:
VECTOR1-rep(c(1,0),c(15,10))
How would I create a new sample (VECTOR2) also containing zeros and
ones, in which the phi-coefficient between the two sample vectors was
drawn from a population with a known phi-coefficient value?
I know there are ways to do this with normally distributed numbers
(for
example the mvrnorm function in MASS), but am stumped when dealing
with
dichotomous variables.
Paul
One way is to sample from the 2x2 table with the specified means and
pearson
correlation (phi):
for a fourfold table, a b
c d
with marginal proportions p1 and p2
cov - phi * sqrt(p1*(1-p1)*p2*(1-p2))
a - p1*p2 + cov
b - p1*(1-p2) - cov
c - (1-p1)*p2 - cov
d - (1-p1)*(1-p2) + cov
expand.grid(0:1,0:1)[sample(1:4, size=25, replace=TRUE,
prob=c(a,b,c,d)),]
David.
| David Duffy (MBBS PhD) ,-_|\
| email: [EMAIL PROTECTED] ph: INT+61+7+3362-0217 fax: -0101 / *
| Epidemiology Unit, Queensland Institute of Medical Research \_,-._/
| 300 Herston Rd, Brisbane, Queensland 4029, Australia GPG 4D0B994A v
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Re: [R] Make check fails on d-p-q-r-tests.R...
You will have to show us the error! It will be shown in d-p-q-r-tests.Rout.fail (unless this was a segfault or similar). It is not OK to skip the test, but note that this test is random and does fail about 1 in 50 times, so you could just try rerunning it. On Mon, 26 Sep 2005, Jeff Ross wrote: Hi, R-2.1.1 OS: OpenBSD-current (3.8) on i386 Compiler:gcc version 3.3.5 (propolice) Thread model: single configure \ --with-readline \ --with-tcltk \ --with-tcl-config=/usr/local/lib/tcl8.4/tclConfig.sh \ --with-tk-config=/usr/local/lib/tk8.4/tkConfig.sh \ --with-libpng \ --with-jpeglib \ --with-zlib \ --with-bzlib \ --with-pcre \ --with-libiconv-prefix=/usr/local/ Please do NOT use unrecommended flags like --with-zlib, especially not on your first build. None of those flags should have been needed. I'm brand new to R so I don't know how critical this error is. Here's the last bit what make check FORCE=FORCE outputs: running code in 'grDevices-Ex.R' ... OK comparing 'grDevices-Ex.Rout' to 'grDevices-Ex.Rout.prev' ... OK running code in 'graphics-Ex.R' ... OK comparing 'graphics-Ex.Rout' to 'graphics-Ex.Rout.prev' ... OK running code in 'stats-Ex.R' ... OK comparing 'stats-Ex.Rout' to 'stats-Ex.Rout.prev' ... OK running code in 'datasets-Ex.R' ... OK comparing 'datasets-Ex.Rout' to 'datasets-Ex.Rout.prev' ... OK running code in 'methods-Ex.R' ... OK comparing 'methods-Ex.Rout' to 'methods-Ex.Rout.prev' ... OK running code in 'grid-Ex.R' ... OK comparing 'grid-Ex.Rout' to 'grid-Ex.Rout.prev' ... OK running code in 'splines-Ex.R' ... OK comparing 'splines-Ex.Rout' to 'splines-Ex.Rout.prev' ... OK running code in 'stats4-Ex.R' ... OK comparing 'stats4-Ex.Rout' to 'stats4-Ex.Rout.prev' ... OK running code in 'tcltk-Ex.R' ... OK comparing 'tcltk-Ex.Rout' to 'tcltk-Ex.Rout.prev' ... OK updating test dependencies `Makedeps' is up to date. running strict specific tests running code in 'eval-etc.R' ... OK comparing 'eval-etc.Rout' to './eval-etc.Rout.save' ... OK running code in 'simple-true.R' ... OK comparing 'simple-true.Rout' to './simple-true.Rout.save' ... OK running code in 'arith-true.R' ... OK comparing 'arith-true.Rout' to './arith-true.Rout.save' ... OK running code in 'arith.R' ... OK comparing 'arith.Rout' to './arith.Rout.save' ... OK running code in 'lm-tests.R' ... OK comparing 'lm-tests.Rout' to './lm-tests.Rout.save' ... OK running code in 'primitive-funs.R' ... OK comparing 'primitive-funs.Rout' to './primitive-funs.Rout.save' ... OK running code in 'ok-errors.R' ... OK comparing 'ok-errors.Rout' to './ok-errors.Rout.save' ... OK running code in 'method-dispatch.R' ... OK comparing 'method-dispatch.Rout' to './method-dispatch.Rout.save' ... OK running code in 'd-p-q-r-tests.R' ...*** Error code 1 Stop in /usr/local/src/R-2.1.1/tests. *** Error code 1 Stop in /usr/local/src/R-2.1.1/tests (line 206 of Makefile). *** Error code 1 Stop in /usr/local/src/R-2.1.1/tests (line 191 of Makefile). Tried finding this error in the archives to no avail. If it is okay to ignore this error, how can I skip this test? Thanks for any input! Jeff Ross __ 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] create trend variable in a regression using R
Dear Giacomo, what you mean precisely saying to create a Trend variable in a regression? If it concerns about time series analysis you could give a look to my contribute: http://cran.r-project.org/doc/contrib/Ricci-ts-italian.pdf Best Regards Vito Hi, my name is Giacomo. I would like to know how to create a Trend variable in a regression using R. Thank you for your help. My best regards, Giacomo Diventare costruttori di soluzioni Became solutions' constructors The business of the statistician is to catalyze the scientific learning process. George E. P. Box Statistical thinking will one day be as necessary for efficient citizenship as the ability to read and write H. G. Wells Top 10 reasons to become a Statistician 1. Deviation is considered normal 2. We feel complete and sufficient 3. We are 'mean' lovers 4. Statisticians do it discretely and continuously 5. We are right 95% of the time 6. We can legally comment on someone's posterior distribution 7. We may not be normal, but we are transformable 8. We never have to say we are certain 9. We are honestly significantly different 10. No one wants our jobs Visitate il portale http://www.modugno.it/ e in particolare la sezione su Palese http://www.modugno.it/archivio/palesesanto_spirito/ __ 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] calculating distances using Gower's coefficient on mixed variables.
nikonia == nikonia [EMAIL PROTECTED] on Mon, 26 Sep 2005 12:15:55 +0200 writes: nikonia I want to compute the distances in a mixed variable nikonia matrix using the Gower coefficient. I understand it nikonia is possible to calculate distances in a matrix with nikonia mixed variables using the dudi.pco command. How nikonia would this work? No need for esoteric functions. The recommended(*) package 'cluster' has daisy() for computing dissimilarities. One of its major features has always been the ability to work with mixed variables (continuous, nominal, ordinal, .. (a)symmetric binary,...) implementing a slight generalization of Gower's proposal. Even though the help for daisy starts its 'Details' section with 'daisy' is fully described in chapter 1 of Kaufman and Rousseeuw (1990). I think I should add some more details to the help page when I get time.. Martin Maechler, ETH Zurich (*) recommended packages are always available by library(pkg) in a normal R installation. __ 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] hist(x, ...) with normal distribution curve
Knut Krueger wrote: . I am looking for a histogram or box plot with the adding normal distribution curve I think that must be possible, but I am not able to find out how to do. Regards Knut __ 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 *There are a lot of answers to add a histogram. Here is a simple way to add a tiny boxplot to a plot / histogram x-rexp(100) hist(x) boxplot(x,axes=F,add=T,horizontal=T, at=par()$usr[3]+diff(par()$usr[3:4])*.017, boxwex=0.02*diff(par()$usr[3:4]),pch=8) Peter Wolf * __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] questions about boxplots
concerning question 1: -- labeling of outliers -- you can get the outliers by boxplot(...)$out try: set.seed(17) x-rexp(99) names(x)-paste(x,1:99) out-boxplot(x)$out text(rep(1.1,length(out)), out, names(out)) Peter Wolf Stephen D. Weigand wrote: Dear Yulei, On Sep 26, 2005, at 6:56 PM, Yulei He wrote: Hi, there. I have two questions about using R to create boxplots. 1. The function boxplot() plots the outliers. How can I label the exact values arount these outlier points? Does R have an option allow me to do that? You can use identify(). Here's a toy example set.seed(1) y - rt(30, 3) boxplot(y) identify(x = rep(1,30), y = y, label = format(y, digits = 2)) ### now click on the outlier in the plot and you should see -7.398 ### beside the outlier 2. How can I put two boxplots in one x-y axis? x - rnorm(10) y - rnorm(20, 3, 5) z - runif(30) boxplot(x, y, z, labels = c(x, y, z)) ### - or - boxplot(list(x = x, y = y, z = z)) Thanks. Yulei Stephen Weigand Rochester, Minnesota, USA __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] hist(x, ...) with normal distribution curve
Le 27.09.2005 10:32, Peter Wolf a écrit : Knut Krueger wrote: I am looking for a histogram or box plot with the adding normal distribution curve I think that must be possible, but I am not able to find out how to do. Regards Knut *There are a lot of answers to add a histogram. Here is a simple way to add a tiny boxplot to a plot / histogram x-rexp(100) hist(x) boxplot(x,axes=F,add=T,horizontal=T, at=par()$usr[3]+diff(par()$usr[3:4])*.017, boxwex=0.02*diff(par()$usr[3:4]),pch=8) Peter Wolf The tufte axes, described there : http://www.cl.cam.ac.uk/users/sjm217/projects/graphics/ may be of interrest here. What about making it a possibility for all plots ? For example using : R par(xaxt='tufte') R plot(rnorm(200), rnorm(200)) would produce a scatterplot with the tufte axes Romain. -- visit the R Graph Gallery : http://addictedtor.free.fr/graphiques ~ ~~ Romain FRANCOIS - http://addictedtor.free.fr ~~ Etudiant ISUP - CS3 - Industrie et Services ~~http://www.isup.cicrp.jussieu.fr/ ~~ Stagiaire INRIA Futurs - Equipe SELECT ~~ http://www.inria.fr/recherche/equipes/select.fr.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] Wrong signature
I've got a comlaint about the signature in the last post. I answered form another computer and there is the automatic signature of our second business. On this place is also a part of the equine resarch program in progress. I did not realize that there was the siganture below. Sorry for that. Regards Knut __ 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] regression methods for circular(?) data.
I retract the siggestion I proposed last night -- it was based on a bad hunch! Sorry for wasting time. Best wishes, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 27-Sep-05 Time: 09:59:29 -- XFMail -- __ 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] About Coda Package
Dear R users: I am using the package coda (the last verison in CRAN) to analyse the output from a MCMC Bayesian analysis. And I get unconsitented results. I have export the chain using the read.table function and after I have transformed this data frame to an mcmc object using the mcmc function. I am interested in three variables, when I use the function effectiveSize I have these figures: 403.37301854.4534 369.8643. But when I run the function codamenu to perform same convergence test I get this warning mensage: Checking effective sample size ... *** WARNING !!! Some variables in your chain have an effective sample size of less than 200 This is too small, and may cause errors in the diagnostic tests HINT: Look at plots first to identify variables with slow mixing. (Choose menu Output Analysis then Plots) Re-run your chain with a larger sample size and thinning interval. If possible, reparameterize your model to improve mixing *** Some thing is wrong. Could someone explain to me what is happening? Thanks, Juan Pablo. === Juan Pablo Sánchez Serrano Dep. Ciencia Animal, UPV. C/ Camino de Vera s/n 46022 Valencia (Spain) Telf. 963877007 Ext.74382 __ 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] plotting multiple plots on a single graph
Hi ***PLEASE do read the posting guide!*** see ?par ?points ?lines ?split.screen ?layout ?matplot ?lattice HTH Petr On 26 Sep 2005 at 18:08, C Tate wrote: __ 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 Petr Pikal [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] About Coda Package
Dear Juan Pablo,
It is best to send package-specific queries the package maintainer (me
in this case) which you can find out by typeing library(help=coda)
The inconsistency comes from two different ways of estimating the
spectral density at frequency 0: spectrum0() adapted from Heidelberger
Welch, fits a generalized linear model to the periodogram. This function
is called by the effectiveSize() function. Unfortunately it crashes
when there is very high autocorrelation. The alternative function
spectrum0.ar does the same thing by fitting an autoregressive model to
the data, and won't crash even on highly autocorrelated data. The latter
function is called by codamenu().
The two functions are giving different results here, but to be honest,
an effective sample size of 370 isn't sufficient for serious inference
from an MCMC sample either. I can only reiterate the advice given by
the warning message.
Martyn
On Tue, 2005-09-27 at 11:11 +0200, Juan Pablo Sanchez Serrano wrote:
Dear R users:
I am using the package coda (the last verison in CRAN) to analyse the
output from a MCMC Bayesian analysis. And I get unconsitented
results. I have export the chain using the read.table function and
after I have transformed this data frame to an mcmc object using the
mcmc function. I am interested in three variables, when I use the
function effectiveSize I have these figures: 403.37301854.4534
369.8643. But when I run the function codamenu to perform same
convergence test I get this warning mensage:
Checking effective sample size ...
***
WARNING !!!
Some variables in your chain have an
effective sample size of less than 200
This is too small, and may cause errors
in the diagnostic tests
HINT:
Look at plots first to identify variables
with slow mixing. (Choose menu Output
Analysis then Plots)
Re-run your chain with a larger sample
size and thinning interval. If possible,
reparameterize your model to improve mixing
***
Some thing is wrong. Could someone explain to me what is happening?
Thanks,
Juan Pablo.
---
This message and its attachments are strictly confidential. ...{{dropped}}
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Re: [R] dates are shown as X15.Feb.03
This is a good example of where you did not give us enough information to answer your question. as.Date has a lot of formatting options for working with dates. If you are still having problems, please provide a short example (i.e. reproducable code). Thanks, Roger On 9/26/05, Chris Buddenhagen [EMAIL PROTECTED] wrote: Why is R recognizing dates like this? Chris Buddenhagen, Botany Department, Charles Darwin Research Station, Santa Cruz,Galapagos. Mail: Charles Darwin Foundation, Casilla 17-01-3891 Avenida 6 de Diciembre N36-109 y Pasaje California Quito, ECUADOR __ EL CONTENIDO DE ESTE MENSAJE ES DE ABSOLUTA RESPONSABILIDAD DEL AUTOR. FUNDACION CHARLES DARWIN WWW.DARWINFOUNDATION.ORG http://WWW.DARWINFOUNDATION.ORG [[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] Producing empirical bayes estimates in disease mapping for lognormal model
I'm trying to produce empirical bayes estimates based on the lognormal model in disease mapping Is there a way this can be done in R? thanks Oarabile __ 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] regsubsets selection criterion
Hello, I am using the 'regsubsets' function (from leaps package) to get the best linear models to explain 1 variable from 1 to 5 explanatory variables (exhaustive search). Is there anyone who can tell me on which criterion is based the 'regsubsets' function ? Thank you. samuel Samuel BERTRAND Doctorant Laboratoire de Biomecanique LBM - ENSAM - CNRS UMR 8005 http://bio-web.paris.ensam.fr 151, bd de l'Hopital 75013 PARIS Tel. +33 (0) 1 44 24 64 53 Fax +33 (0) 1 44 24 63 66 [[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] regsubsets selection criterion
Is there anyone who can tell me on which criterion is based the 'regsubsets' function ? the leaps help page says: cp or adjr2 or r2 is the value of the chosen model selection statistic for each model so each of these can be chosen as the selection statistic using the method argument hth, ingmar __ 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] getting variable length numerical gradient
2005/9/26, Dimitris Rizopoulos [EMAIL PROTECTED]:
AFAIK the deriv() is for symbolic derivatives, so I don't know if it
will work in your case.
numericDeriv surely computes numerical gradient. The problem here is
its interface, which requires the vector of symbols involved in the
expression to differenziate.
Best,
Dimitris
- Original Message -
From: Antonio, Fabio Di Narzo [EMAIL PROTECTED]
To: Dimitris Rizopoulos [EMAIL PROTECTED]
Cc: R-help@stat.math.ethz.ch
Sent: Monday, September 26, 2005 10:58 AM
Subject: Re: getting variable length numerical gradient
Tnx very much Dimitris,
your code does what I need. I've just adapted it to my needs (e.g., I
don't deal with scalar functions), and so solved my problem.
Given this, is there a way to use the deriv function in the base
package, within this context (variable length vector of indipendent
variables)?
Best,
Antonio, Fabio Di Narzo.
On 9/25/05, Dimitris Rizopoulos [EMAIL PROTECTED]
wrote:
maybe you can find the following function useful (any comments are
greatly appreciated):
fd - function(x, f, scalar = TRUE, ..., eps =
sqrt(.Machine$double.neg.eps)){
f - match.fun(f)
out - if(scalar){
if(length(f0 - f(x, ...)) != length(x))
stop('f' must be vectorized)
x. - x + eps * pmax(abs(x), 1)
c(f(x., ...) - f0) / (x. - x)
} else{
n - length(x)
res - array(0, c(n, n))
f0 - f(x, ...)
ex - pmax(abs(x), 1)
for(i in 1:n){
x. - x
x.[i] - x[i] + eps * ex[i]
res[, i] - c(f(x., ...) - f0) / (x.[i] - x[i])
}
res
}
out
}
## Examples
x - seq(-3.3, 3.3, 0.1)
all.equal(fd(x, pnorm, mean = 0.5), dnorm(x, mean = 0.5))
# Approximate the Hessian matrix for a logistic regression
# the score vector function
gn - function(b, y, X){
p - as.vector(plogis(X %*% b))
-colSums(X * (y - p))
}
# We simulate some data and fit the logistic regression
n - 800
x1 - runif(n,-3, 3); x2 - runif(n, -3, 3)
pr - plogis(0.8 + 0.4 * x1 - 0.3 * x2)
y - rbinom(n, 1, pr)
fm - glm(y ~ x1 + x2, binomial)
## The Hessian using forward difference approximation
fd(fm$coef, gn, scalar = FALSE, y = y, X = cbind(1, x1, x2))
## The true Hessian
solve(summary(fm)$cov.unscaled)
I hope it helps.
Best,
Dimitris
Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven
Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/(0)16/336899
Fax: +32/(0)16/337015
Web: http://www.med.kuleuven.be/biostat/
http://www.student.kuleuven.be/~m0390867/dimitris.htm
- Original Message -
From: Antonio, Fabio Di Narzo [EMAIL PROTECTED]
To: R-help@stat.math.ethz.ch
Sent: Sunday, September 25, 2005 11:37 AM
Subject: [R] getting variable length numerical gradient
Hi all.
I have a numerical function f(x), with x being a vector of generic
size (say k=4), and I wanna take the numerically computed
gradient,
using deriv or numericDeriv (or something else).
My difficulties here are that in deriv and numericDeric the
function
is passed as an expression, and one have to pass the list of
variables
involved as a char vector... So, it's a pure R programming
question.
Have a nice sunday,
Antonio, Fabio Di Narzo.
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[R] graphics guide?
I am trying to create some graphs with R and it seems to be able to do what I need. However, I have so far not been able to find any sort of explanation of how the graphics system works. I am for instance trying to create a multiple figure, and I seem to have to call plot.new() before every new plot command, I have however not found any explanation of what this actually does. ?plot.new does give an explanation, but it is explained in R, so to speak. Where do I find out what for instance a graphics frame is? Thanks, Karin -- Karin Lagesen, PhD student [EMAIL PROTECTED] http://www.cmbn.no/rognes/ __ 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] graphics guide?
Hi, Karin Lagesen wrote: I am trying to create some graphs with R and it seems to be able to do what I need. However, I have so far not been able to find any sort of explanation of how the graphics system works. I am for instance trying to create a multiple figure, and I seem to have to call plot.new() before every new plot command, I have however not found any Do you mean several graphs in the same window? If so, you want something like, e.g.: par(mfrow = c(2, 2)) Take a look at ?par and the mfrow or mfcol options. Cheers and HTH, Kev -- Ko-Kang Kevin Wang PhD Student Centre for Bioinformation Science Building 27, Room 1004 Mathematical Sciences Institute (MSI) Australian National University Canberra, ACT 2601 Australia Homepage: http://wwwmaths.anu.edu.au/~wangk/ Ph (W): +61-2-6125-2431 Ph (H): +61-2-6125-7488 Ph (M): +61-40-451-8301 __ 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] graphics guide?
Karin Lagesen [EMAIL PROTECTED] 9/27/2005 9:27:29 AM I am trying to create some graphs with R and it seems to be able to do what I need. However, I have so far not been able to find any sort of explanation of how the graphics system works. I am for instance trying to create a multiple figure, and I seem to have to call plot.new() before every new plot command, I have however not found any explanation of what this actually does. ?plot.new does give an explanation, but it is explained in R, so to speak. Where do I find out what for instance a graphics frame is? If you'd like a more comprehensive reference in book form, I recommend Paul Murrell's book R Graphics. HTH Peter Peter L. Flom, PhD Assistant Director, Statistics and Data Analysis Core Center for Drug Use and HIV Research National Development and Research Institutes 71 W. 23rd St http://cduhr.ndri.org www.peterflom.com New York, NY 10010 (212) 845-4485 (voice) (917) 438-0894 (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] multiple plots on same x axis
Hi. I have two vectors of gene expression for each of several days. I want to plot both vectors on the same plot for a visual representation of up versus down regulation. I've tried using add=T but that doesn't work. eg plot(Day, gene1) plot(Day, gene2, add=T) Any help would be appreciated. Iain __ 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] Make check fails on d-p-q-r-tests.R...
On 1:03:39 am 09/27/05 Prof Brian Ripley [EMAIL PROTECTED] wrote: You will have to show us the error! It will be shown in d-p-q-r-tests.Rout.fail (unless this was a segfault or similar). It is not OK to skip the test, but note that this test is random and does fail about 1 in 50 times, so you could just try rerunning it. I am so sorry. I didn't even think to look for a .fail file. Here is the last bit of it: ## for PR#7902: ex - -c(rev(1/x), ex) All.eq(-x, qcauchy(pcauchy(-x))) [1] TRUE All.eq(+x, qcauchy(pcauchy(+x, log=TRUE), log=TRUE)) [1] TRUE All.eq(1/x, pcauchy(qcauchy(1/x))) [1] TRUE All.eq(ex, pcauchy(qcauchy(ex, log=TRUE), log=TRUE)) [1] `is.NA' value mismatches: 1 in current, 0 in target Warning message: NaNs produced in: qcauchy(p, location, scale, lower.tail, log.p) II - c(-Inf,Inf) stopifnot(pcauchy(II) == 0:1, ## qcauchy(0:1) == II, + pcauchy(II, log=TRUE) == c(-Inf,0), + qcauchy(c(-Inf,0), log=TRUE) == II) Error in if (!(is.logical(r - eval(ll[[i]])) all(r))) stop(paste(deparse(mc[[i + : missing value where TRUE/FALSE needed In addition: Warning message: NaNs produced in: qcauchy(p, location, scale, lower.tail, log.p) Execution halted This is from the latest R-patched source tar ball, and it is the identical error as R-2.1.1. I've consistently gotten the same error, even with configuration file tweaks and making clean between runs. Thanks! Jeff Ross __ 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] quick points question
Hi Just one of those niggles... I've just been trying to plot a filled circle. I thought that this would do it plot(1,1,type=n) points(1,1,pch=1,bg=blue,cex=5) #bg: background (fill) color for open plot symbols But I need to do this instead points(1.2,1,pch=19,col=blue,cex=5) Am I misunderstanding the bg option in the points function? Richard -- Dr. Richard Nixon, MRC Biostatistics Unit, Cambridge, UK http://www.mrc-bsu.cam.ac.uk/personal/richard __ 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] quick points question
Richard Nixon wrote: Hi Just one of those niggles... I've just been trying to plot a filled circle. I thought that this would do it plot(1,1,type=n) points(1,1,pch=1,bg=blue,cex=5) #bg: background (fill) color for open plot symbols But I need to do this instead points(1.2,1,pch=19,col=blue,cex=5) Am I misunderstanding the bg option in the points function? Richard Please read ?points and it's paragraph on te argument pch with quite some information regarding filled symbols... Uwe Ligges __ 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] quick points question
Richard Nixon [EMAIL PROTECTED] writes: Hi Just one of those niggles... I've just been trying to plot a filled circle. I thought that this would do it plot(1,1,type=n) points(1,1,pch=1,bg=blue,cex=5) #bg: background (fill) color for open plot symbols But I need to do this instead points(1.2,1,pch=19,col=blue,cex=5) Am I misunderstanding the bg option in the points function? Sort of. The quick answer is: example(points). I think you'll get the point. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ 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] negative binomial in GEE
Dear R-help, I was recently wanting to use GEE with the negative binomial family. It seems that this is lacking in the otherwise excellent implementations of the GEE methodology ( packages: gee, yags, geepack). I would have thought it a simple step to allow the creation of a family, i.e providing the link function (log mu) and the variance function (mu + mu^2/theta) , assuming theta is specified; and then to let the gee code do the business in a similar fashion to glm. However the gee codes all seem to rely a set of C routines with either the normal, poisson, or binomial, hardwired in. Does anyone have any suggestions for a way round this problem for the future (I had to resort to using Stata), or maybe more realistically, how much work it would take to build an extendible version of the gee algorithm? thanks Simon Bond. __ 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] time series: smooth and aggregate?
I am working on automatic optimization of ARIMA parameters. That takes a lot of computing power, which I would like to reduce by aggregating and smoothing. Any thoughts on the subject? Suggested algorithms? What is the best order? aggregate then smooth or smooth then aggregate? Many thanks in advance, -- Jean-Luc __ 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] Error in make check-all
Dear R-users, i'm a very newbie in linux, but decided to build R from source. Following the R Installation and Administration manual, i did this: ./configure --enable-R-shlib # this option is here because i intend to build the GNOME console after... make make check no problems in make check, but: make check-devel #and also make check-all indicated some WARNINGs in the log file: /usr/local/R-2.1.1/tests/tcltk.Rcheck/00check.Rcheck Right below is the content of this log file (I translated some words): [start log file] * using log directory '/usr/local/R-2.1.1/tests/tcltk.Rcheck' * using R version 2.1.1, 2005-06-20 * looks like 'tcltk' is a base package * skipping installation test * checking package directory ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking DESCRIPTION meta-information ... OK * checking package dependencies ... OK * checking index information ... OK * checking package subdirectories ... OK * checking S3 generic/method consistency ... WARNING Erro: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution See section 'Generic functions and methods' of the 'Writing R Extensions' manual. * checking replacement functions ... WARNING Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution In R, the argument of a replacement function which corresponds to the right hand side must be named 'value'. * checking foreign function calls ... WARNING Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution See section 'System and foreign language interfaces' of the 'Writing R Extensions' manual. * checking Rd files ... OK * checking for missing documentation entries ... WARNING Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution All user-level objects in a package should have documentation entries. See chapter 'Writing R documentation files' in manual 'Writing R Extensions'. * checking for code/documentation mismatches ... WARNING Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution * checking Rd \usage sections ... OK * checking DVI version of manual ... OK [end log file] The problem is in the tcltk package. I have searched in the archives, but didin't find anything similar to this problem (maybe there is, but i was not able to identify it). I really don't know what all the warnings means. What i need to know is what am i missing, and if there is something i can fix it. Also, are there any problems if i continue the installation without fix something? P.S.: actually R is running already from where it was buit, but i want to install it. So i want to avoid future problems, if this warnings really make some. Any help is appreciated. Thanks! Fernando Mayer. version _ platform i686-pc-linux-gnu arch i686 os linux-gnu [SuSE 9.3] system i686, linux-gnu status major2 minor1.1 year 2005 month06 day 20 language R [[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] Error in make check-all
This is what happens if you don't have a usable X11 display. Did you perhaps use a root account on a console owned by a normal user? On Tue, 27 Sep 2005, Fernando Mayer wrote: Dear R-users, i'm a very newbie in linux, but decided to build R from source. Following the R Installation and Administration manual, i did this: ./configure --enable-R-shlib # this option is here because i intend to build the GNOME console after... make make check no problems in make check, but: make check-devel #and also make check-all indicated some WARNINGs in the log file: /usr/local/R-2.1.1/tests/tcltk.Rcheck/00check.Rcheck Right below is the content of this log file (I translated some words): [start log file] * using log directory '/usr/local/R-2.1.1/tests/tcltk.Rcheck' * using R version 2.1.1, 2005-06-20 * looks like 'tcltk' is a base package * skipping installation test * checking package directory ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking DESCRIPTION meta-information ... OK * checking package dependencies ... OK * checking index information ... OK * checking package subdirectories ... OK * checking S3 generic/method consistency ... WARNING Erro: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution See section 'Generic functions and methods' of the 'Writing R Extensions' manual. * checking replacement functions ... WARNING Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution In R, the argument of a replacement function which corresponds to the right hand side must be named 'value'. * checking foreign function calls ... WARNING Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution See section 'System and foreign language interfaces' of the 'Writing R Extensions' manual. * checking Rd files ... OK * checking for missing documentation entries ... WARNING Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution All user-level objects in a package should have documentation entries. See chapter 'Writing R documentation files' in manual 'Writing R Extensions'. * checking for code/documentation mismatches ... WARNING Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution * checking Rd \usage sections ... OK * checking DVI version of manual ... OK [end log file] The problem is in the tcltk package. I have searched in the archives, but didin't find anything similar to this problem (maybe there is, but i was not able to identify it). I really don't know what all the warnings means. What i need to know is what am i missing, and if there is something i can fix it. Also, are there any problems if i continue the installation without fix something? P.S.: actually R is running already from where it was buit, but i want to install it. So i want to avoid future problems, if this warnings really make some. Any help is appreciated. Thanks! Fernando Mayer. version _ platform i686-pc-linux-gnu arch i686 os linux-gnu [SuSE 9.3] system i686, linux-gnu status major2 minor1.1 year 2005 month06 day 20 language R [[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 -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of
Re: [R] Error in make check-all
Fernando Mayer [EMAIL PROTECTED] writes: Dear R-users, .. Erro: .First.lib failed for 'tcltk' ... The problem is in the tcltk package. I have searched in the archives, but didin't find anything similar to this problem (maybe there is, but i was not able to identify it). I really don't know what all the warnings means. What i need to know is what am i missing, and if there is something i can fix it. Also, are there any problems if i continue the installation without fix something? Well, tcl/tk isn't working... P.S.: actually R is running already from where it was buit, but i want to install it. So i want to avoid future problems, if this warnings really make some. Any help is appreciated. Thanks! Fernando Mayer. version _ platform i686-pc-linux-gnu arch i686 os linux-gnu [SuSE 9.3] Installing the tk-devel and tcl-devel packages should help. system i686, linux-gnu status major2 minor1.1 year 2005 month06 day 20 language R [[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 -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ 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] quick points question
On Tue, 27 Sep 2005, Richard Nixon wrote: Hi Just one of those niggles... I've just been trying to plot a filled circle. I thought that this would do it plot(1,1,type=n) points(1,1,pch=1,bg=blue,cex=5) #bg: background (fill) color for open plot symbols But I need to do this instead points(1.2,1,pch=19,col=blue,cex=5) Am I misunderstanding the bg option in the points function? Yes. See the examples. pch=1 is not an `open plot symbol': 21-25 are. So in your case points(1.3, 1, pch=21, col=blue, bg=red, cex=5) may be illuminating. -- 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
[R] make check in ~/fem outputs only 1 test, huh ?
fem-4.0.1 [and all the other modules, except post] compiles OK, AFAIK, but when I do a make check only 1 test is reported, as follows: making checksrc making checkview3d making checkviewaxis making checktests make check-TESTS $ELMER_HOME undefined, setting it to ../src CC: no input files specified test: unexpected operator Tests completed, passed: 0 out of total 0 tests PASS: runtests === All 1 tests passed === As I understand it, about 50 tests should have been run. What's wrong and how do I fix it, please ? Gratefully, Courtney __ 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] Error in make check-all
Prof Brian Ripley [EMAIL PROTECTED] writes: This is what happens if you don't have a usable X11 display. Did you perhaps use a root account on a console owned by a normal user? More likely on SUSE is to get done in by a lack of -devel packages. I've already mentioned tcl-devel and tk-devel but you also need xorg-x11-devel, readline-devel, and libjpeg-devel. The latter two are not going to cause that particular error though. On Tue, 27 Sep 2005, Fernando Mayer wrote: Dear R-users, i'm a very newbie in linux, but decided to build R from source. Following the R Installation and Administration manual, i did this: ./configure --enable-R-shlib # this option is here because i intend to build the GNOME console after... make make check no problems in make check, but: make check-devel #and also make check-all indicated some WARNINGs in the log file: /usr/local/R-2.1.1/tests/tcltk.Rcheck/00check.Rcheck Right below is the content of this log file (I translated some words): [start log file] * using log directory '/usr/local/R-2.1.1/tests/tcltk.Rcheck' * using R version 2.1.1, 2005-06-20 * looks like 'tcltk' is a base package * skipping installation test * checking package directory ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking DESCRIPTION meta-information ... OK * checking package dependencies ... OK * checking index information ... OK * checking package subdirectories ... OK * checking S3 generic/method consistency ... WARNING Erro: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution See section 'Generic functions and methods' of the 'Writing R Extensions' manual. * checking replacement functions ... WARNING Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution In R, the argument of a replacement function which corresponds to the right hand side must be named 'value'. * checking foreign function calls ... WARNING Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution See section 'System and foreign language interfaces' of the 'Writing R Extensions' manual. * checking Rd files ... OK * checking for missing documentation entries ... WARNING Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution All user-level objects in a package should have documentation entries. See chapter 'Writing R documentation files' in manual 'Writing R Extensions'. * checking for code/documentation mismatches ... WARNING Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution * checking Rd \usage sections ... OK * checking DVI version of manual ... OK [end log file] The problem is in the tcltk package. I have searched in the archives, but didin't find anything similar to this problem (maybe there is, but i was not able to identify it). I really don't know what all the warnings means. What i need to know is what am i missing, and if there is something i can fix it. Also, are there any problems if i continue the installation without fix something? P.S.: actually R is running already from where it was buit, but i want to install it. So i want to avoid future problems, if this warnings really make some. Any help is appreciated. Thanks! Fernando Mayer. version _ platform i686-pc-linux-gnu arch i686 os linux-gnu [SuSE 9.3] system i686, linux-gnu status major2 minor1.1 year 2005 month
Re: [R] Error in make check-all
Dear Prof. Ripley, that was exactly what i did. Should i login on the system as root, instead of login as user and became root via console? What should i do to have X11 usable? Thanks, Fernando Mayer. Prof Brian Ripley escreveu: This is what happens if you don't have a usable X11 display. Did you perhaps use a root account on a console owned by a normal user? On Tue, 27 Sep 2005, Fernando Mayer wrote: Dear R-users, i'm a very newbie in linux, but decided to build R from source. Following the R Installation and Administration manual, i did this: ./configure --enable-R-shlib # this option is here because i intend to build the GNOME console after... make make check no problems in make check, but: make check-devel #and also make check-all indicated some WARNINGs in the log file: /usr/local/R-2.1.1/tests/tcltk.Rcheck/00check.Rcheck Right below is the content of this log file (I translated some words): [start log file] * using log directory '/usr/local/R-2.1.1/tests/tcltk.Rcheck' * using R version 2.1.1, 2005-06-20 * looks like 'tcltk' is a base package * skipping installation test * checking package directory ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking DESCRIPTION meta-information ... OK * checking package dependencies ... OK * checking index information ... OK * checking package subdirectories ... OK * checking S3 generic/method consistency ... WARNING Erro: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution See section 'Generic functions and methods' of the 'Writing R Extensions' manual. * checking replacement functions ... WARNING Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution In R, the argument of a replacement function which corresponds to the right hand side must be named 'value'. * checking foreign function calls ... WARNING Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution See section 'System and foreign language interfaces' of the 'Writing R Extensions' manual. * checking Rd files ... OK * checking for missing documentation entries ... WARNING Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution All user-level objects in a package should have documentation entries. See chapter 'Writing R documentation files' in manual 'Writing R Extensions'. * checking for code/documentation mismatches ... WARNING Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution * checking Rd \usage sections ... OK * checking DVI version of manual ... OK [end log file] The problem is in the tcltk package. I have searched in the archives, but didin't find anything similar to this problem (maybe there is, but i was not able to identify it). I really don't know what all the warnings means. What i need to know is what am i missing, and if there is something i can fix it. Also, are there any problems if i continue the installation without fix something? P.S.: actually R is running already from where it was buit, but i want to install it. So i want to avoid future problems, if this warnings really make some. Any help is appreciated. Thanks! Fernando Mayer. version _ platform i686-pc-linux-gnu arch i686 os linux-gnu [SuSE 9.3] system i686, linux-gnu status major2 minor1.1 year 2005 month06 day 20 language R [[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] Error in make check-all
On Tue, 27 Sep 2005, Fernando Mayer wrote: Dear Prof. Ripley, that was exactly what i did. Should i login on the system as root, instead of login as user and became root via console? What should i do to have X11 usable? Well, I don't worry about this, but it you want to do a complete test you need the console running the user that is going to be running R. (I see this when running tests remotely, as then I have no X11 display set to save bandwidth. I just ignore it.) Thanks, Fernando Mayer. Prof Brian Ripley escreveu: This is what happens if you don't have a usable X11 display. Did you perhaps use a root account on a console owned by a normal user? On Tue, 27 Sep 2005, Fernando Mayer wrote: Dear R-users, i'm a very newbie in linux, but decided to build R from source. Following the R Installation and Administration manual, i did this: ./configure --enable-R-shlib # this option is here because i intend to build the GNOME console after... make make check no problems in make check, but: make check-devel #and also make check-all indicated some WARNINGs in the log file: /usr/local/R-2.1.1/tests/tcltk.Rcheck/00check.Rcheck Right below is the content of this log file (I translated some words): [start log file] * using log directory '/usr/local/R-2.1.1/tests/tcltk.Rcheck' * using R version 2.1.1, 2005-06-20 * looks like 'tcltk' is a base package * skipping installation test * checking package directory ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking DESCRIPTION meta-information ... OK * checking package dependencies ... OK * checking index information ... OK * checking package subdirectories ... OK * checking S3 generic/method consistency ... WARNING Erro: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution See section 'Generic functions and methods' of the 'Writing R Extensions' manual. * checking replacement functions ... WARNING Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution In R, the argument of a replacement function which corresponds to the right hand side must be named 'value'. * checking foreign function calls ... WARNING Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution See section 'System and foreign language interfaces' of the 'Writing R Extensions' manual. * checking Rd files ... OK * checking for missing documentation entries ... WARNING Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution All user-level objects in a package should have documentation entries. See chapter 'Writing R documentation files' in manual 'Writing R Extensions'. * checking for code/documentation mismatches ... WARNING Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution * checking Rd \usage sections ... OK * checking DVI version of manual ... OK [end log file] The problem is in the tcltk package. I have searched in the archives, but didin't find anything similar to this problem (maybe there is, but i was not able to identify it). I really don't know what all the warnings means. What i need to know is what am i missing, and if there is something i can fix it. Also, are there any problems if i continue the installation without fix something? P.S.: actually R is running already from where it was buit, but i want to install it. So i want to avoid future problems, if this warnings really make some. Any help is appreciated. Thanks! Fernando Mayer. version _ platform i686-pc-linux-gnu arch
[R] Weighting factor
Hi everyone, I would like some package of R or any help to solve the next problem with a weighting fatcors: Giving a data matrix with dichotomous (2 or more) variables in columns and individuals in rows, and also a theorical distribution of the dichotomous variables I would like a row weight (one per individual) that transform the real distribution of variables to the theorical distribution. Thanks in advance and best regards, -- Ferran Carrascosa __ 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] negative binomial in GEE
On Tue, 27 Sep 2005, Simon.Bond wrote: Does anyone have any suggestions for a way round this problem for the future (I had to resort to using Stata), or maybe more realistically, how much work it would take to build an extendible version of the gee algorithm? I don't think it would take that much work [and I've done it a couple of times, once in XLISP-Stat and once in SPIDA]. An entirely interpreted implementation will be relatively slow, though it might be possible to improve that quite a bit with sparse matrix techniques. -thomas __ 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] dates are shown as X15.Feb.03
On 9/27/2005 12:13 PM, Chris Buddenhagen wrote: Dear Duncan Murdoch Thanks for responding. I will provide more complete info with future questions. The data for a small pilot study are below. The values for each month are the percentage cover of an invasive plant here in the Galapagos (TT=treatment) type = immediately herbicide applied or applied to regrowth later. I called the data glyphosate.txt. The code is glyp-read.delim(C:\\Chris\\active projects\\Aristolochia\\glyphosate.txt, header=T) list(names(glyp)) This is the output that mystified me: [1] TT type CUADRANTES X15dec02 X15jan03 [6] X15feb03 X15apr03 X15jun03 X15aug03 X15oct03 It looks as though you have column headings like 15dec02. That's not a legal R variable name, so it prepends the X to make it into one. That way you can do things like glyp$X15dec02 to extract that column. glyp$15dec02 would give a syntax error. While I have an expert on hand I have another question, how do I produce a graph of time against percentage cover with error bars. I wanted to only present months on the x axis. I start by reorganizing the data using this: Various functions implement error bars, but I haven't used them in a long time, so I'll leave this question for someone else to answer. Duncan Murdoch glyp2-reshape(glyp, direction=long, idvar=c(TT, type, CUADRANTES),varying=list(names(glyp)[4:10]),v.names=cover) but couldn't get month names to appear in the column time. TTtypeCUADRANTES 15dec02 15jan03 15feb03 15apr03 15jun03 15aug03 15oct03 T1immediate 1 63 59 60 55 4.5 1 2 T1immediate 2 75 75 75 75 6.5 1 2 T1immediate 22 72 70 70 65 35 2 3.5 T1immediate 26 90 80 80 75 17.52 4 T1immediate 33 75 80 85 85 40 1 2 T2immediate 18 85 80 80 22.52.5 2 5 T2immediate 21 90 85 85 60 16.50 1 T2immediate 23 85 80 80 75 17.51 2 T2immediate 28 90 85 85 27.527.50 1 T2immediate 31 90 85 85 9 12.51 2 T3immediate 3 50 58 60 65 35 1 2 T3immediate 10 63 60 60 15 2.5 0 10 T3immediate 12 90 85 85 17.515 0 5 T3immediate 16 85 82 80 78 9 1 1.5 T3immediate 34 75 80 85 85 35 1.5 2.5 T4wait4 75 75 75 7.5 2.5 0 0 T4wait11 63 60 60 12.52.5 1 2 T4wait24 90 85 80 3.5 5.5 1 2 T4wait29 85 80 80 1.5 4.5 1 2 T4wait32 85 80 80 3.5 4.5 2 3.5 T5wait6 50 50 50 1 1 0.5 2 T5wait14 80 75 75 15 5.5 1 2 T5wait15 90 80 80 1 5.5 1 3 T5wait20 85 80 80 22.58.5 0 0 T5wait25 85 80 80 22.58.5 1 1.5 T6wait8 75 75 75 1.5 4.5 0 1.5 T6wait9 90 85 85 1.5 3.5 1 2 T6wait13 80 75 75 1 3.5 1 1.5 T6wait19 90 85 80 1 2.5 1 2 T6wait27 85 80 75 1 3.5 1 2 Tccontrol 5 50 45 45 40 23 20 25 Tccontrol 7 50 53 54 55 55 50 55 Tccontrol 17 90 80 70 22.59 15 20 Tccontrol 30 75 75 70 75 45 60 70 Tccontrol 35 90 85 80 85 65 60 70 Chris Buddenhagen, Botany Department, Charles Darwin Research Station, Santa Cruz,Galapagos. Mail: Charles Darwin Foundation, Casilla 17-01-3891 Avenida 6 de Diciembre N36-109 y Pasaje California Quito, ECUADOR __ EL CONTENIDO DE ESTE MENSAJE ES DE ABSOLUTA RESPONSABILIDAD DEL AUTOR. FUNDACION CHARLES DARWIN WWW.DARWINFOUNDATION.ORG __ 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 unsplit - unsplit does not seem to reverse the effect of split
In data OME in MASS I would like to extract the first 5 observations per subject (=ID). So I do library(MASS) OMEsub - split(OME, OME$ID) OMEsub - lapply(OMEsub,function(x)x[1:5,]) unsplit(OMEsub, OME$ID) - which results in [[1]] [1] 1 1 1 1 1 [[2]] [1] 30 30 30 30 30 [[3]] [1] low low low low low Levels: N/A high low [[4]] [1] 35 35 40 40 45 [[5]] [1] coherent incoherent coherent incoherent coherent Levels: coherent incoherent [[6]] [1] 1 4 0 1 2 [[1094]] [1] 4 5 5 5 2 [[1095]] [1] 100 100 100 100 100 [[1096]] [1] 18 18 18 18 18 [[1097]] [1] N/A N/A N/A N/A N/A Levels: N/A high low There were 50 or more warnings (use warnings() to see the first 50) warnings() Warning messages: 1: number of items to replace is not a multiple of replacement length 2: number of items to replace is not a multiple of replacement length 3: number of items to replace is not a multiple of replacement length According to documentation unsplit is the reverse of split, but I must be missing a point somewhere... Can anyone help? Thanks in advance. Søren __ 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 plots on same x axis
Try plot(Day, gene1) lines(Day, gene2) see ?lines for more details. Charles Annis, P.E. [EMAIL PROTECTED] phone: 561-352-9699 eFax: 614-455-3265 http://www.StatisticalEngineering.com -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of IAIN GALLAGHER Sent: Tuesday, September 27, 2005 10:35 AM To: r-help@stat.math.ethz.ch Subject: [R] multiple plots on same x axis Hi. I have two vectors of gene expression for each of several days. I want to plot both vectors on the same plot for a visual representation of up versus down regulation. I've tried using add=T but that doesn't work. eg plot(Day, gene1) plot(Day, gene2, add=T) Any help would be appreciated. Iain __ 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] Using unsplit - unsplit does not seem to reverse the effect of split
Søren Højsgaard [EMAIL PROTECTED] writes: In data OME in MASS I would like to extract the first 5 observations per subject (=ID). So I do library(MASS) OMEsub - split(OME, OME$ID) OMEsub - lapply(OMEsub,function(x)x[1:5,]) unsplit(OMEsub, OME$ID) - which results in [[1]] [1] 1 1 1 1 1 [[2]] [1] 30 30 30 30 30 [[3]] [1] low low low low low Levels: N/A high low [[4]] [1] 35 35 40 40 45 [[5]] [1] coherent incoherent coherent incoherent coherent Levels: coherent incoherent [[6]] [1] 1 4 0 1 2 [[1094]] [1] 4 5 5 5 2 [[1095]] [1] 100 100 100 100 100 [[1096]] [1] 18 18 18 18 18 [[1097]] [1] N/A N/A N/A N/A N/A Levels: N/A high low There were 50 or more warnings (use warnings() to see the first 50) warnings() Warning messages: 1: number of items to replace is not a multiple of replacement length 2: number of items to replace is not a multiple of replacement length 3: number of items to replace is not a multiple of replacement length According to documentation unsplit is the reverse of split, but I must be missing a point somewhere... Can anyone help? Thanks in advance. Søren It only works if the first argument is or could have resulted from a split on the second argument. That is clearly not the case when you are creating subvectors. I have on occasion wanted an unsplit that worked without the 2nd argument as in unsplit(l, rep(seq(along=l), sapply(l,length)) ) but if you think about it, it's not really doing anything that do.call(c,l) or do.call(rbind,l) won't do. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ 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] Using unsplit - unsplit does not seem to reverse the effect of split
On Tue, 2005-09-27 at 19:12 +0200, Søren Højsgaard wrote: In data OME in MASS I would like to extract the first 5 observations per subject (=ID). So I do library(MASS) OMEsub - split(OME, OME$ID) OMEsub - lapply(OMEsub,function(x)x[1:5,]) unsplit(OMEsub, OME$ID) - which results in [[1]] [1] 1 1 1 1 1 [[2]] [1] 30 30 30 30 30 [[3]] [1] low low low low low Levels: N/A high low [[4]] [1] 35 35 40 40 45 [[5]] [1] coherent incoherent coherent incoherent coherent Levels: coherent incoherent [[6]] [1] 1 4 0 1 2 [[1094]] [1] 4 5 5 5 2 [[1095]] [1] 100 100 100 100 100 [[1096]] [1] 18 18 18 18 18 [[1097]] [1] N/A N/A N/A N/A N/A Levels: N/A high low There were 50 or more warnings (use warnings() to see the first 50) warnings() Warning messages: 1: number of items to replace is not a multiple of replacement length 2: number of items to replace is not a multiple of replacement length 3: number of items to replace is not a multiple of replacement length According to documentation unsplit is the reverse of split, but I must be missing a point somewhere... Can anyone help? Thanks in advance. Søren If you read the documentation for split/unsplit, you will also note that in the Details section it says: 'unsplit' works only with lists of vectors as opposed to lists of data frames, which is the result of your split() operation. Also note that in the Value section, it indicates: 'unsplit' returns a vector for which 'split(x, f)' equals 'value' as opposed to unsplit returning a data frame. Thus, use: OME1 - do.call(rbind, OMEsub) where OME1 will be the result of rbind()'ing the data frames in the OMEsub list. See ?do.call for more information. HTH, Marc Schwartz __ 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] Weighting factor
On Tue, 27 Sep 2005, Ferran Carrascosa wrote: Hi everyone, I would like some package of R or any help to solve the next problem with a weighting fatcors: Giving a data matrix with dichotomous (2 or more) variables in columns and individuals in rows, and also a theorical distribution of the dichotomous variables I would like a row weight (one per individual) that transform the real distribution of variables to the theorical distribution. You should be able to do this with postStratify() in the survey package (if you have joint distributions for the variables) or calibrate() if you have only marginal distributions. You would need to create a survey design object, use postStratify() or calibrate() on it, then use weights() to extract the weights. -thomas __ 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] missing handling
Hi,
I have the following codes to replace missing using median, assuming missing
only occurs on continuous variables:
trn1-read.table('trn1.fv', header=F, na.string='.', sep='|')
# median
m.trn1-sapply(1:ncol(trn1), function(i) median(trn1[,i], na.rm=T))
#replace
trn2-trn1
for (each in 1:nrow(trn1)){
index.missing=which(is.na(trn1[each,]))
trn2[each,]-replace(trn1[each,], index.missing, m.trn1[index.missing])
}
Anyone can suggest some ways to improve it since replacing 10 takes 1.5 sec:
system.time(for (each in 1:10){index.missing=which(is.na(trn1[each,]));
trn2[each,]-replace(trn1[each,], index.missing, m.trn1[index.missing]);})
[1] 1.53 0.00 1.53 0.00 0.00
Another general question is
are there some packages in R doing missing handling?
Thanks,
--
Weiwei Shi, Ph.D
Did you always know?
No, I did not. But I believed...
---Matrix III
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[R] dynamic lists (data frames?)
Can someone please show me what I need to get something like this to
work
for(a in c(1:5)){
data$a-c(a:10)
}
so that i end up with a structure
data$1-[1,2,3,4,5,6,7,8,9,10]
data$2-[2,3,4,5,67,8,9,10]
data$3-[3,4,5,67,8,9,10]
data$4-[4,5,67,8,9,10]
data$5-[5,67,8,9,10]
thanks loads
Tom
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[R] Listing object sizes without RODBC objects: contributed function
I include my workaround for object.size failing on RODBC objects.
Code adapted from Petr Pikal's code
(http://tolstoy.newcastle.edu.au/R/help/04/06/1228.html).
ls.objects-function (pos = 1, order.by,...)
{
napply - function(names, fn) sapply(names, function(x) fn(get(x,pos=pos)))
names - ls(pos = pos,...)
obj.class - napply(names, function(x) as.character(class(x))[1])
obj.drop - match(RODBC,obj.class)
obj.class - obj.class[-obj.drop]
names - names[-obj.drop]
obj.mode - napply(names, mode)
obj.type - ifelse(is.na(obj.class), obj.mode, obj.class)
obj.size - napply(names, object.size)
obj.dim - t(napply(names, function(x) as.numeric(dim(x))[1:2]))
vec - is.na(obj.dim)[, 1] (obj.type != function)
obj.dim[vec, 1] - napply(names, length)[vec]
out - data.frame(obj.type, obj.size, obj.dim)
names(out) - c(Type, Size, Rows, Columns)
if (!missing(order.by)) out - out[order(out[[order.by]]), ]
out
}
Leif S. Kirschenbaum, Ph.D.
Senior Yield Engineer
Reflectivity, Inc.
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Re: [R] dynamic lists (data frames?)
Le 27 Septembre 2005 10:39, tom wright a écrit :
Can someone please show me what I need to get something like this to
work
for(a in c(1:5)){
data$a-c(a:10)
}
so that i end up with a structure
data$1-[1,2,3,4,5,6,7,8,9,10]
data$2-[2,3,4,5,67,8,9,10]
data$3-[3,4,5,67,8,9,10]
data$4-[4,5,67,8,9,10]
data$5-[5,67,8,9,10]
thanks loads
Tom
That's an exercise I give to my students! This will create the sequences:
data - lapply(1:5, seq, 10)
You can then assign the names with
names(data) - as.character(1:5)
but 'data$1' will not work. You will need either 'data$1' or 'data[[1]]'.
I'd use different names...
HTH.
--
Vincent Goulet, Associate Professor
École d'actuariat
Université Laval, Québec
[EMAIL PROTECTED] http://vgoulet.act.ulaval.ca
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Re: [R] missing handling
Use 'which(...arr.ind=T)'
x.1
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 6 10 3 4 10 7 9 8 4 10
[2,] 8 7 4 7 4 8 3 NA 3 4
[3,] 7 7 10 10 3 5 3 2 2 2
[4,] 3 4 5 10 10 2 6 9 4 5
[5,] 3 5 9 5 6 NA 3 NA 6 7
[6,] 9 6 10 5 10 4 2 10 NA 5
[7,] 5 2 5 10 3 7 6 4 6 8
[8,] 2 6 1 8 9 2 7 8 3 8
[9,] 9 1 4 9 8 10 2 NA 1 7
[10,] 2 4 8 7 NA 4 3 NA 5 5
x.4
[1] 5.5 5.5 5.0 7.5 8.0 5.0 3.0 8.0 4.0 6.0
Med - apply(x.1, 2, median, na.rm=T) # get median
Ind - which(is.na(x.1), arr.ind=T) # determine which are NA
x.1[Ind] - Med[Ind[,'col']] # replace with median
x.1
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 6 10 3 4 10 7 9 8 4 10
[2,] 8 7 4 7 4 8 3 8 3 4
[3,] 7 7 10 10 3 5 3 2 2 2
[4,] 3 4 5 10 10 2 6 9 4 5
[5,] 3 5 9 5 6 5 3 8 6 7
[6,] 9 6 10 5 10 4 2 10 4 5
[7,] 5 2 5 10 3 7 6 4 6 8
[8,] 2 6 1 8 9 2 7 8 3 8
[9,] 9 1 4 9 8 10 2 8 1 7
[10,] 2 4 8 7 8 4 3 8 5 5
On 9/27/05, Weiwei Shi [EMAIL PROTECTED] wrote:
Hi,
I have the following codes to replace missing using median, assuming
missing
only occurs on continuous variables:
trn1-read.table('trn1.fv', header=F, na.string='.', sep='|')
# median
m.trn1-sapply(1:ncol(trn1), function(i) median(trn1[,i], na.rm=T))
#replace
trn2-trn1
for (each in 1:nrow(trn1)){
index.missing=which(is.na(trn1[each,]))
trn2[each,]-replace(trn1[each,], index.missing, m.trn1[index.missing])
}
Anyone can suggest some ways to improve it since replacing 10 takes 1.5sec:
system.time(for (each in 1:10){index.missing=which(is.na(trn1[each,]));
trn2[each,]-replace(trn1[each,], index.missing, m.trn1[index.missing]);})
[1] 1.53 0.00 1.53 0.00 0.00
Another general question is
are there some packages in R doing missing handling?
Thanks,
--
Weiwei Shi, Ph.D
Did you always know?
No, I did not. But I believed...
---Matrix III
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What the problem you are trying to solve?
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Re: [R] dynamic lists (data frames?)
When sapply is used on a character vector it will use those
as the names so:
data - sapply(as.character(1:5), function(x) seq(as.numeric(x),10))
will give data with the required names.
On 9/27/05, tom wright [EMAIL PROTECTED] wrote:
Can someone please show me what I need to get something like this to
work
for(a in c(1:5)){
data$a-c(a:10)
}
so that i end up with a structure
data$1-[1,2,3,4,5,6,7,8,9,10]
data$2-[2,3,4,5,67,8,9,10]
data$3-[3,4,5,67,8,9,10]
data$4-[4,5,67,8,9,10]
data$5-[5,67,8,9,10]
thanks loads
Tom
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[R] Binding dataframe with different length in rows and columns
Dear all, I'm trying to combine in R the two following datasets. I'm would be very grateful if someone could help me with this problem. Dataset 1: X Y Z 1 27 48 2 25 50 3 27 40 4 28 56 Where X is a unique number and Y and Z some variables Dataset 2: X I J 1 10 12 1 12 12 1 23 30 1 40 46 2 7 8 2 8 9 2 9 8 3 2 0 4 98 87 4 78 89 Where X IS NOT this time a unique number. I and J are some variables. Thank you by advance Jérôme Lemaître Étudiant au doctorat Université Laval Québec, QC __ 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] Binding dataframe with different length in rows and columns
Hi Jerome, look at the merge() function Nolwenn On Tue, 27 Sep 2005, Jérôme Lemaître wrote: Dear all, I'm trying to combine in R the two following datasets. I'm would be very grateful if someone could help me with this problem. Dataset 1: X Y Z 1 27 48 2 25 50 3 27 40 4 28 56 Where X is a unique number and Y and Z some variables Dataset 2: X I J 1 10 12 1 12 12 1 23 30 1 40 46 2 7 8 2 8 9 2 9 8 3 2 0 4 98 87 4 78 89 Where X IS NOT this time a unique number. I and J are some variables. Thank you by advance Jérôme Lemaître Étudiant au doctorat Université Laval Québec, QC __ 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] dynamic lists (data frames?)
Hmm my bad,
Thanks for your replies but I think my example was a little to simple
the actual code I'm using is:
f_haardisolve-function(v_dataset){
#pad data to make length a power of 2
v_dataset-f_paddata(v_dataset)
l_cooef-list() #holder for cooefficents
i_count-1 #identity counter
while(length(v_dataset)0){
#seperate odd and even points
v_dataset-f_splitpoints(v_dataset)
v_dataset-f_haarpredict(v_dataset)
v_dataset-f_haaruplift(v_dataset)
str_idx-paste('c',i_count,sep='')
l_cooef
$str_idx-v_dataset[c((length(v_dataset)/2)+1:(length(v_dataset)/2))]
#should be no wrap on the previous line
v_dataset-v_dataset[c(1:length(v_dataset)/2)]
i_count-i_count+1
}
l_cooef
}
In this particular case I could probably calculate the number of
iterations and use l_cooef-names() but more is there a more generic
method for adding another column of data?
On Tue, 2005-27-09 at 10:39 -0400, tom wright wrote:
Can someone please show me what I need to get something like this to
work
for(a in c(1:5)){
data$a-c(a:10)
}
so that i end up with a structure
data$1-[1,2,3,4,5,6,7,8,9,10]
data$2-[2,3,4,5,67,8,9,10]
data$3-[3,4,5,67,8,9,10]
data$4-[4,5,67,8,9,10]
data$5-[5,67,8,9,10]
thanks loads
Tom
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Re: [R] [ESS] Indentation in R code
On Mon, Sep 26, 2005 at 07:05:33PM +0200, Göran Broström wrote:
On Mon, Sep 26, 2005 at 09:27:56AM +0200, Martin Maechler wrote:
I'm crossposting to the ESS-help mailing list which is slightly
more appropriate here. [This may be a rare case where
crossposting seems to make much sense.]
PD == Peter Dalgaard [EMAIL PROTECTED]
on 25 Sep 2005 19:40:45 +0200 writes:
PD Seth Falcon [EMAIL PROTECTED] writes:
On 24 Sep 2005, [EMAIL PROTECTED] wrote:
I am using emacs-21.3 when writing R functions on Linux debian, and
I am trying to follow the advice i R-exts.pdf (2.1.1) regarding
indentation. That is, I set 'c-default-style' to bsd and
'c-basic-offset' to 4. However, while this gives me the intended
indentation in C code, it doesn't change the behavior in R code; I
still get an indentation of size 2. This is my .emacs file after
customization:
(require 'ess-site)
(custom-set-variables
;; custom-set-variables was added by Custom -- don't edit or
;; cut/paste it! Your init file should contain only one such
;; instance.
'(c-basic-offset 4)
'(c-default-style bsd))
(custom-set-faces
;; custom-set-faces was added by Custom -- don't edit or
cut/paste it!
;; Your init file should contain only one such instance.
)
Not sure if this is the best way, but I have the following after
loading ess-site:
(setq ess-indent-level 4)
PD I have (I believe it stems from Martin M. originally):
yes, most probably {IIRC, Kurt Hornik was involved too}.
PD (add-hook 'c-mode-hook '(lambda()
PD(c-set-style stroustrup)))
the above is not quite what I have or did recommend,
which is rather bsd + offset 4 as Göran has above
In fact, Göran mentions the R-exts manual and that has
the following *before* giving the emacs-lisp statements:
(For GNU Emacs 20: for GNU Emacs 21 use
customization to set the `c-default-style' to `bsd' and
`c-basic-offset' to `4'.)
and indeed, that's what Göran did and you should do with a
current emacs, either customize via GUI or,
in your ~/.emacs file, find the section '(custom-set-variables ...)' and
add
'(c-basic-offset 4)
'(c-default-style bsd)
to the lines already there, or if there's no such section, add
(custom-set-variables
;; custom-set-variables was added by Custom -- don't edit or cut/paste it!
;; Your init file should contain only one such instance.
'(c-basic-offset 4)
'(c-default-style bsd)
to the end of your ~/.emacs file
[...]
but this is not sufficient to get correct (4) indentation (ess) in R
functions. We need some reference to ess as well, right? Maybe another
reference to the ESS manual is in order in 'R-exts'?
Martin, I realize that it was stupid of me to cut here; I only refer to C
indentation, and forget that the lines of lisp code referring to ESS of
course is necessary to get indentation working in R functions.
Once again, thanks for your good help.
Göran
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Re: [R] dynamic lists (data frames?)
Got it thanks
the trick was to create a variable with the new name
str_idx-paste('c',i,sep='')
then use double square brackets
l_cooef[str_idx]]-whatever()
f_haardisolve-function(v_dataset){
#pad data to make length a power of 2
v_dataset-f_paddata(v_dataset)
l_cooef-list() #holder for cooefficents
i_count-1 #identity counter
while(length(v_dataset)0){
#seperate odd and even points
v_dataset-f_splitpoints(v_dataset)
v_dataset-f_haarpredict(v_dataset)
v_dataset-f_haaruplift(v_dataset)
str_idx-paste('c',i_count,sep='')
l_cooef[[str_idx]]-list()
l_cooef[[str_idx]]-v_dataset[c((length(v_dataset)/2)+1:(length(v_dataset)/2))]
v_dataset-v_dataset[c(1:length(v_dataset)/2)]
i_count-i_count+1
}
l_cooef
}
On Tue, 2005-27-09 at 10:39 -0400, tom wright wrote:
Can someone please show me what I need to get something like this to
work
for(a in c(1:5)){
data$a-c(a:10)
}
so that i end up with a structure
data$1-[1,2,3,4,5,6,7,8,9,10]
data$2-[2,3,4,5,67,8,9,10]
data$3-[3,4,5,67,8,9,10]
data$4-[4,5,67,8,9,10]
data$5-[5,67,8,9,10]
thanks loads
Tom
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Re: [R] Binding dataframe with different length in rows and columns
Hello , How about cbind or rbind? You could create a new data frame and push yours into it. Greetz Jérôme Lemaître schrieb: Dear all, I'm trying to combine in R the two following datasets. I'm would be very grateful if someone could help me with this problem. Dataset 1: X Y Z 1 27 48 2 25 50 3 27 40 4 28 56 Where X is a unique number and Y and Z some variables Dataset 2: X I J 1 10 12 1 12 12 1 23 30 1 40 46 2 7 8 2 8 9 2 9 8 3 2 0 4 98 87 4 78 89 Where X IS NOT this time a unique number. I and J are some variables. Thank you by advance Jérôme Lemaître Étudiant au doctorat Université Laval Québec, QC __ 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] suggest some books or materials for matrices basics , its partitions, iterations, clusturing
Your question seems almost too broad, but I will attempt a brief response. Have you reviewed the material on matrices in An Introduction to R, avaliable via, e.g., help.start()? Also, have you reviewed LAPACK (http://www.netlib.org/lapack/)? If the answer to both is yes, submit another post (after reading the posting guide, www.R-project.org/posting-guide.html, which should increase the chances that you will get a quick, useful reply). spencer graves booop booop wrote: Dear sir, Could anybody kindly suggest me some good e-books(which are available in the internet),or other materials in the web sites to refer examples ... in the following area matrices its basics partitioning of matrices... iterations of matrices Clusturing in matrices... thank you sir.. with kind regards, boopathy. __ 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 -- Spencer Graves, PhD Senior Development Engineer PDF Solutions, Inc. 333 West San Carlos Street Suite 700 San Jose, CA 95110, USA [EMAIL PROTECTED] www.pdf.com http://www.pdf.com Tel: 408-938-4420 Fax: 408-280-7915 __ 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] Dummy quesion about environment
Hi,
I'm trying to understand environment object in R.
I used the example:
f - function(x) {
y - 10
g - function(x) x + y
return(g)
}
h - f()
h(3)
then i saw that f return an environment
h
function(x) x + y
environment: 01B28570
but I coudn't access to x and y object in that environment:
I tried
get(x,env=h)
I tried
h$y
can I access y and x?
how can I see an environment tree? oes search does it?
Thanks,
Ron
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Re: [R] Dummy quesion about environment
Try 'get(x, env = environment(h))'
-roger
Ron Ophir wrote:
Hi,
I'm trying to understand environment object in R.
I used the example:
f - function(x) {
y - 10
g - function(x) x + y
return(g)
}
h - f()
h(3)
then i saw that f return an environment
h
function(x) x + y
environment: 01B28570
but I coudn't access to x and y object in that environment:
I tried
get(x,env=h)
I tried
h$y
can I access y and x?
how can I see an environment tree? oes search does it?
Thanks,
Ron
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http://www.biostat.jhsph.edu/~rpeng/
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Re: [R] Dummy quesion about environment
Ron Ophir [EMAIL PROTECTED] writes:
Hi,
I'm trying to understand environment object in R.
I used the example:
f - function(x) {
y - 10
g - function(x) x + y
return(g)
}
h - f()
h(3)
then i saw that f return an environment
h
function(x) x + y
environment: 01B28570
but I coudn't access to x and y object in that environment:
I tried
get(x,env=h)
I tried
h$y
can I access y and x?
Well, there are special issues with x above, but the basic thing is to
take environment(h). Notice that h _is_ a function that _has_ an
associated environment.
get(y,env=environment(h))
[1] 10
As I said, x is stranger, which is because you used f() in the call:
get(x,env=environment(h))
str(get(x,env=environment(h)))
symbol
a - get(x,env=environment(h))
missing(a)
[1] TRUE
evalq(x,environment(h))
Error in eval(expr, envir, enclos) : argument x is missing, with no
default
evalq(missing(x),environment(h))
[1] TRUE
You'll get the point if you look long and hard enough...
how can I see an environment tree?
You can't. You can see the parent of an environment, the grandparent,
etc., but there is no way to see which children a given environment
has.
oes search does it?
Huh?
Thanks,
Ron
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(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
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Re: [R] Dummy quesion about environment
Hej,
but in your function you add x and y to 10 and 3, so your values are
merged to one value available in g variable.
And now you want to see what was your y and your x?
I guess I do not get the idea of your question.
Well, then you could return y and x as well as g.
Greetz n god luck.
Roger D. Peng schrieb:
Try 'get(x, env = environment(h))'
-roger
Ron Ophir wrote:
Hi,
I'm trying to understand environment object in R.
I used the example:
f - function(x) {
y - 10
g - function(x) x + y
return(g)
}
h - f()
h(3)
then i saw that f return an environment
h
function(x) x + y
environment: 01B28570
but I coudn't access to x and y object in that environment:
I tried
get(x,env=h)
I tried
h$y
can I access y and x?
how can I see an environment tree? oes search does it?
Thanks,
Ron
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Re: [R] Weighting factor
Uau! This package is very interesting, very thank you Thomas. Thanks to all! 2005/9/27, Thomas Lumley [EMAIL PROTECTED]: On Tue, 27 Sep 2005, Ferran Carrascosa wrote: Hi everyone, I would like some package of R or any help to solve the next problem with a weighting fatcors: Giving a data matrix with dichotomous (2 or more) variables in columns and individuals in rows, and also a theorical distribution of the dichotomous variables I would like a row weight (one per individual) that transform the real distribution of variables to the theorical distribution. You should be able to do this with postStratify() in the survey package (if you have joint distributions for the variables) or calibrate() if you have only marginal distributions. You would need to create a survey design object, use postStratify() or calibrate() on it, then use weights() to extract the weights. -thomas -- Ferran Carrascosa __ 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] Make check fails on d-p-q-r-tests.R...
I am afraid this does look like a real problem, if a minor one. We have for the first problem x - 10^(ex - c(1,2,5*(1:5),50,100,200,300,Inf)) ex - -c(rev(1/x), ex) qcauchy(ex, log=TRUE) The first entry of the result should be Inf and the last -Inf. From the output you have shown us I would guess the last is NaN. If this is what is going on, it is a problem but a somewhat esoteric one that probably reflects a lack of IEC60559 (aka IEEE754) conformance. It needs more hands-on debugging than we can provide on a help list. On Tue, 27 Sep 2005, Jeff Ross wrote: On 1:03:39 am 09/27/05 Prof Brian Ripley [EMAIL PROTECTED] wrote: You will have to show us the error! It will be shown in d-p-q-r-tests.Rout.fail (unless this was a segfault or similar). It is not OK to skip the test, but note that this test is random and does fail about 1 in 50 times, so you could just try rerunning it. I am so sorry. I didn't even think to look for a .fail file. Here is the last bit of it: ## for PR#7902: ex - -c(rev(1/x), ex) All.eq(-x, qcauchy(pcauchy(-x))) [1] TRUE All.eq(+x, qcauchy(pcauchy(+x, log=TRUE), log=TRUE)) [1] TRUE All.eq(1/x, pcauchy(qcauchy(1/x))) [1] TRUE All.eq(ex, pcauchy(qcauchy(ex, log=TRUE), log=TRUE)) [1] `is.NA' value mismatches: 1 in current, 0 in target Warning message: NaNs produced in: qcauchy(p, location, scale, lower.tail, log.p) II - c(-Inf,Inf) stopifnot(pcauchy(II) == 0:1, ## qcauchy(0:1) == II, + pcauchy(II, log=TRUE) == c(-Inf,0), + qcauchy(c(-Inf,0), log=TRUE) == II) Error in if (!(is.logical(r - eval(ll[[i]])) all(r))) stop(paste(deparse(mc[[i + : missing value where TRUE/FALSE needed In addition: Warning message: NaNs produced in: qcauchy(p, location, scale, lower.tail, log.p) Execution halted This is from the latest R-patched source tar ball, and it is the identical error as R-2.1.1. I've consistently gotten the same error, even with configuration file tweaks and making clean between runs. Thanks! Jeff Ross -- 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] Simulate phi-coefficient (correlation between dichotomous vars)
On Tue, 27 Sep 2005, Bliese, Paul D LTC USAMH wrote:
My situation is a bit more complicated and I'm not sure it is easily
solved. The problem is that I must assume one of the vectors is
constant and generate one or more vectors that covary with the constant
vector.
One way is to sample from the 2x2 table with the specified means and
pearson correlation (phi):
for a fourfold table, a b
c d
with marginal proportions p1 and p2
cov - phi * sqrt(p1*(1-p1)*p2*(1-p2))
a - p1*p2 + cov
b - p1*(1-p2) - cov
c - (1-p1)*p2 - cov
d - (1-p1)*(1-p2) + cov
Calculate the conditional probabilities from the above
P(X2=1|X1=1)= a/(a+b) = p2 + cov/p1
P(X2=1|X1=0)= c/(c+d) = p2 - cov/(1-p1)
condsim - function(X, phi, p2, p1=NULL) {
if (!all(X %in% c(0,1))) stop(expecting 1's and 0's)
if (is.null(p1)) p1 - mean(X)
covar - phi * sqrt(p1*(1-p1)*p2*(1-p2))
if (covar0 covar(min(p1,p2)-p1*p2)) {
warning(Specified correlation too large for given marginal proportions)
covar - min(p1,p2)-p1*p2
}else if (covar0 covar -min(p1*p2,(1-p1)*(1-p2))) {
warning(Specified correlation too small for given marginal proportions)
covar - -min(p1*p2,(1-p1)*(1-p2))
}
Y - X
i1 - X==1
i0 - X==0
Y[i1] - rbinom(sum(i1),1, p2 + covar/p1)
Y[i0] - rbinom(sum(i0),1, p2 - covar/(1-p1))
data.frame(X,Y)
}
David Duffy.
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Re: [R] R CMD build produces tar error under FreeBSD 5.4
On Sun, Sep 25, 2005 at 12:07:02PM +0100, Prof Brian Ripley wrote: On Sun, 25 Sep 2005, Andrew Robinson wrote: Hi R-helpers, I am trying to build a package under FreeBSD 5.4-RELEASE #0 using R Version 2.1.1. I have constructed a package using package.skeleton(), when I try $ R CMD build foo * checking for file 'foo/DESCRIPTION' ... OK * preparing 'foo': * checking DESCRIPTION meta-information ... OK * cleaning src * removing junk files tar: Option -L is not permitted in mode -x Error: cannot open file 'foo/DESCRIPTION' for reading foo/DESCRIPTION exists and the permissions are correct. The same command works under Linux Fedora 2. The man pages on each OS imply that tar differs across the two platforms. Does anyone have any thoughts on a work-around? No, because R does not use tar -L (which is to do with tape lengths on GNU tar). It does use tar chf and tar xhf. The h modifier would appear to be applicable only to dumps, so at a wild guess the error message means -h is not permitted. Try replacing xhf by xf. FreeBSD = 5.3 uses bsdtar. Previous versions used GNU tar. In bsdtar, -h is a synonym for -L, and -L means: -L (c and r mode only) All symbolic links will be followed. Nor- mally, symbolic links are archived as such. With this option, the target of the link will be archived instead. The man page for bsdtar doesn't indicate an option to dereference symlinks during extraction. :( Eric __ 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] different models
Hi I have a largish dataset (26 columns 35000 rows) which I have been subjecting to logistic regression and support vector machine analysis. I have noticed that R easily copes with using the data in either technique. Now I have to try and see what the best modeling technique to use is. I only have limited time (who doesnt) so I thought it would be best to try the data with any other techniques on R that can handle that data set and then use predict() and so on. I have identified the following techniques (you may know of more) and think the packages indicated will support them: Neural networks - AMORE Genetic/evolutionary - ? Bayes - deal Decision trees - knnTree Gaussian processes - predict Are these the right packages where I can go model = etc, predict(model,etc using my dataset? Have I missed some techniques? Does anyone know the package I couldnt find for genetic. All help/comments welcome. Thanks Stephen -- 27/09/2005 [[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: x11 position in the Unix environment
Shengzhe Wu [EMAIL PROTECTED] wrote: In the Unix environment, I open a window by x11(). May I specify the position of this window by specifying the position of the top left of the window as in Windows environment? I use xwit (version 3.4), a system command which manipulates existing X windows. My R code for initiating a graphics window contains: system(paste(xwit -move 2045 0 -names 'R Graphics: Device , dev.cur(), ', sep=), ignore.stderr=TRUE) See, e.g, http://www.x.org/contrib/utilities/xwit-3.4.tar.gz. (I'm pretty sure I got the idea from another kind soul on R-help.) -- David Brahm ([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] Make check fails on d-p-q-r-tests.R...
On Tue, 27 Sep 2005, Prof Brian Ripley wrote: I am afraid this does look like a real problem, if a minor one. We have for the first problem x - 10^(ex - c(1,2,5*(1:5),50,100,200,300,Inf)) ex - -c(rev(1/x), ex) qcauchy(ex, log=TRUE) The first entry of the result should be Inf and the last -Inf. From the output you have shown us I would guess the last is NaN. If this is what is going on, it is a problem but a somewhat esoteric one that probably reflects a lack of IEC60559 (aka IEEE754) conformance. It needs more hands-on debugging than we can provide on a help list. Thanks for the analysis. I'll move this over to r-devel. Jeff __ 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] Plot Data Points in boxplots
Hello, I would like to plot my data in a fashion similar to a boxplot, but plot the true data points without a box, just overlay lines of the summary generated by the boxplot. I have less than 10 observations within each group, so I think showing the actual data would be more effective than the box of the boxplot. I have been unable to find a way to do this. Here is example data: d168teni d168dh10i d168hb10i d168icc10i d168rcs10i d168t410i d168tb410i 17252 29 8039 68 27647 28 6849 21 3 12385 87 71 164137 45847 50 7018 1 boxplot(d168teni) works to describe the data (each column a column in the plot). However, instead of the boxes, I want the data plotted (in a column) with the 5 summary lines drawn over the points. I have tried using functions from Design and have been unable to find a solution. I think I am missing the point. Any suggestions on where to look or how to approach this differently? thanks, aric __ 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] Plot Data Points in boxplots
Try this: boxplot(Sepal.Length ~ Species, iris) with(iris, stripchart(Sepal.Length ~ Species, vertical = TRUE, add = TRUE)) On 9/27/05, Aric Gregson [EMAIL PROTECTED] wrote: Hello, I would like to plot my data in a fashion similar to a boxplot, but plot the true data points without a box, just overlay lines of the summary generated by the boxplot. I have less than 10 observations within each group, so I think showing the actual data would be more effective than the box of the boxplot. I have been unable to find a way to do this. Here is example data: d168teni d168dh10i d168hb10i d168icc10i d168rcs10i d168t410i d168tb410i 17252 29 8039 68 27647 28 6849 21 3 12385 87 71 164137 45847 50 7018 1 boxplot(d168teni) works to describe the data (each column a column in the plot). However, instead of the boxes, I want the data plotted (in a column) with the 5 summary lines drawn over the points. I have tried using functions from Design and have been unable to find a solution. I think I am missing the point. Any suggestions on where to look or how to approach this differently? thanks, aric __ 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] scatterplot3d + density() + polygon(color)
Hi R Users, How to use the function polygon() together with the package scatterplot3d? I am trying to color below of the curves defined for the function density(). I tried to use the site: R GRAPH GALLERY as tutorial. I tried to adapt the example of this page: [figure]: http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=30 [code]: http://addictedtor.free.fr/graphiques/sources/source_30.R to my case but I do not obtain success. Somebody could give a tip to me, please? I am thankful anticipatedly. Cleber Borges #My code test ## library(scatterplot3d) x=c(0.4, -1.2, .8, -.7, 0) d1 = density(x[1],bw=1.2, from=-3.0, to=3.0 ) d2 = density(x[2],bw=0.8, from=-3.0, to=3.0 ) d3 = density(x[3],bw=0.6, from=-2.5, to=2.5 ) d4 = density(x[4],bw=0.5, from=-2.0, to=2.0 ) d5 = density(x[5],bw=0.3, from=-1.5, to=1.5 ) sx = c(d1$x,d2$x,d3$x,d4$x,d5$x) sy = c(d1$y,d2$y,d3$y,d4$y,d5$y) sz = c(rep(0.1,512),rep(0.2,512),rep(0.3,512),rep(0.4,512),rep(0.5,512)) scatterplot3d(x=sx,y=sz,z=sy,type='l') ## __ 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
