[R] Elegant Code
Hi, Can anyone help to write a more elegant version of my code? I am sure this can be put into a loop but I am having trouble creating the objects b1,b2,b3,...,etc. b1 - rigamma(50,1,1) theta1 - rgamma(50,0.5,(1/b1)) sim1 - rpois(50,theta1) b2 - rigamma(50,1,1) theta2 - rgamma(50,0.5,(1/b2)) sim2 - rpois(50,theta2) b3 - rigamma(50,1,1) theta3 - rgamma(50,0.5,(1/b3)) sim3 - rpois(50,theta3) b4 - rigamma(50,1,1) theta4 - rgamma(50,0.5,(1/b4)) sim4 - rpois(50,theta4) b5 - rigamma(50,1,1) theta5 - rgamma(50,0.5,(1/b5)) sim5 - rpois(50,theta5) par(mfrow=c(1,5)) boxplot(sim1) boxplot(sim2) boxplot(sim3) boxplot(sim4) boxplot(sim5); Thanks, Raphael __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to interpret glmnet lasso error
I get an error when I try to use glmnet to fit a lasso model on some data. My code: lasso - glmnet(predictorPartitionTrainingM, targetPartitionTraining, alpha=1) The error that is returned: Error in elnet(x, is.sparse, ix, jx, y, weights, offset, type.gaussian, : NA/NaN/Inf in foreign function call (arg 5) Some potentially important details: - 50 predictor variables - 300 observations - everthing is numeric - predictorPartitionTrainingM is a matrix - targetPartitionTraining is a vector Thanks in advance, Ryan Zotti [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Generation of correlated variables
On Thu, Mar 15, 2012 at 11:23:28PM -, Ted Harding wrote: On 15-Mar-2012 Filoche wrote: Hi everyone. Based on a dependent variable (y), I'm trying to generate some independent variables with a specified correlation. For this there's no problems. However, I would like that have all my regressors to be orthogonal (i.e. no correlation among them). For example, y = x1 + x2 + x3 where the correlation between y x1 = 0.7, x2 = 0.4 and x3 = 0.8. However, x1, x2 and x3 should not be correlated to each other. Anyone can help me? Regards, Phil Your fundamental problem here (with the correlations you specify) is the following. Your desired correlation matrix can be constructed by C - cbind( c(1.0,0.7,0.4,0.8),c(0.7,1.0,0.0,0.0), c(0.4,0.0,1.0,0.0),c(0.8,0.0,0.0,1.0) ) rownames(C) - c(y,x1,x2,x3) colnames(C) - c(y,x1,x2,x3) C # y x1 x2 x3 # y 1.0 0.7 0.4 0.8 # x1 0.7 1.0 0.0 0.0 # x2 0.4 0.0 1.0 0.0 # x3 0.8 0.0 0.0 1.0 And now: det(C) # [1] -0.29 and it is impossible for the determinant of a correlation matrix to have a negative determinant: a correlation matyrix must be positive-semidefinite, and therefore have a non-negative determinant. An alternative check is to look at the eigen-structure of C: eigen(C) # $values # [1] 2.1357817 1.000 1.000 -0.1357817 # # $vectors # [,1] [,2] [,3] [,4] # [1,] 0.7071068 0.00e+00 0.000 0.7071068 # [2,] 0.4358010 -1.172802e-16 0.7874992 -0.4358010 # [3,] 0.2490291 -8.944272e-01 -0.2756247 -0.2490291 # [4,] 0.4980582 4.472136e-01 -0.5512495 -0.4980582 so one of the eigenvalues (-0.1357817) is negative, again impossible for a correlation matrix. Thank you for this analysis. For general correlations, say, s1, s2, s3, the matrix is y x1 x2 x3 y 1 s1 s2 s3 x1 s1 1 0 0 x2 s2 0 1 0 x3 s3 0 0 1 and its determinant is 1 - s1^2 - s2^2 - s3^2. Since there was also a requirement that y = x1 + x2 + x3, the correlation matrix should be singular. Hence, the required correlation structure implies s1^2 + s2^2 + s3^2 = 1. If this condition is satisfied, then a multivariate distribution obtained by multiplying a vector from three-dimensional N(0, I) by the matrix (s1 s2 s3) (s100) ( 0 s20) ( 00 s3) has the required correlation structure. However, this is still not a solution of the original question, since the original requirement was to find x1, x2, x3, when y is given. I do not know, whether a solution for an arbitrary y exists, even if the above condition on the correlations is satisfied. Petr Savicky. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Elegant Code
On 16-03-2012, at 08:09, Raphael Fraser wrote:
Hi,
Can anyone help to write a more elegant version of my code? I am sure
this can be put into a loop but I am having trouble creating the
objects b1,b2,b3,...,etc.
b1 - rigamma(50,1,1)
theta1 - rgamma(50,0.5,(1/b1))
sim1 - rpois(50,theta1)
b2 - rigamma(50,1,1)
theta2 - rgamma(50,0.5,(1/b2))
sim2 - rpois(50,theta2)
b3 - rigamma(50,1,1)
theta3 - rgamma(50,0.5,(1/b3))
sim3 - rpois(50,theta3)
b4 - rigamma(50,1,1)
theta4 - rgamma(50,0.5,(1/b4))
sim4 - rpois(50,theta4)
b5 - rigamma(50,1,1)
theta5 - rgamma(50,0.5,(1/b5))
sim5 - rpois(50,theta5)
par(mfrow=c(1,5))
boxplot(sim1)
boxplot(sim2)
boxplot(sim3)
boxplot(sim4)
boxplot(sim5);
Not reproducible since rigamma is not a standard function.
What package?
Why store results in separate variables?
Use matrices then it become much easier.
Like this
N - 5
Nsample - 50
# temporary
rigamma - function(n,a,b) runif(n)
b - matrix(0,N*Nsample,nrow=N)
theta - matrix(0,N*Nsample,nrow=N)
sim - matrix(0,N*Nsample,nrow=N)
for( k in 1:N ) {
b[k, ]- rigamma(Nsample, 1, 1)
theta[k,] - rgamma(Nsample,0.5,(1/b[k,]))
sim[k,] - rpois(Nsample,theta[k,])
}
par(mfrow=c(1,N))
for( k in 1:N) boxplot(sim[k,])
Berend
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Re : Elegant Code
Hi Raphael,
Something like that?
require(pscl)sim - numeric()
for(i in 1:5){
eval(parse(text=paste('b',i,' - rigamma(50,1,1)',sep='')))
eval(parse(text=paste('theta',i,' - rgamma(50,0.5,(1/b',i,'))',sep='')))
eval(parse(text=paste('sim',i,' - rpois(50,theta',1,')',sep='')))
eval(parse(text=paste('sim - cbind(sim, sim',i,')',sep='')))
}
x11()
par(mfrow=c(1,5))
boxplot(c(sim1,sim2,sim3,sim4,sim5))
x11()
boxplot(sim)
Regards,
Pascal
- Mail original -
De : Raphael Fraser raphael.fra...@gmail.com
À : r-help@r-project.org
Cc :
Envoyé le : Vendredi 16 mars 2012 16h09
Objet : [R] Elegant Code
Hi,
Can anyone help to write a more elegant version of my code? I am sure
this can be put into a loop but I am having trouble creating the
objects b1,b2,b3,...,etc.
b1 - rigamma(50,1,1)
theta1 - rgamma(50,0.5,(1/b1))
sim1 - rpois(50,theta1)
b2 - rigamma(50,1,1)
theta2 - rgamma(50,0.5,(1/b2))
sim2 - rpois(50,theta2)
b3 - rigamma(50,1,1)
theta3 - rgamma(50,0.5,(1/b3))
sim3 - rpois(50,theta3)
b4 - rigamma(50,1,1)
theta4 - rgamma(50,0.5,(1/b4))
sim4 - rpois(50,theta4)
b5 - rigamma(50,1,1)
theta5 - rgamma(50,0.5,(1/b5))
sim5 - rpois(50,theta5)
par(mfrow=c(1,5))
boxplot(sim1)
boxplot(sim2)
boxplot(sim3)
boxplot(sim4)
boxplot(sim5);
Thanks,
Raphael
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to change the number of axis?
On 03/16/2012 01:28 AM, qiao xue wrote: Hi, I use R to plot a graph with 2 frames. Because the limit of pixel or others, the screen fail to show the graph. So I have to draw a point every 10 frames. So the total of x axis becomes 2000. So when imaging the picture, I still hope that the total of x-axis is 2. I need to find a way to modify the number of axis. How could I do this? Hi Qiao, Let's assume that you want a scatterplot: # first let's indulge our secret desire to make up data x-rnorm(2)+5*sin(seq(0.001,20,by=0.001)) # now plot this data plot(x) # Wow! Pretty messy. Now take the mean of every ten # values to get a vector of 2000 values x10-mean(x[1:10]) for(i in 2:2000) x10-c(x10,mean(x[(i*10):(i*10+9)])) # when plotting this, add the x values, which were # previously just made up from the length of the vector plot(seq(1,2,by=10),x10) Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Bar graph with 2 Y axis
On 03/16/2012 09:24 AM, KAYIS Seyit Ali wrote: Dear R users, I need to draw a barplot with 2 Y axis. I have 3 days each of wich having 2 groups (and error bar for each of them). The height of the 3rd day is too tall compared to others. That's why I have to use a second Y axis for that. I am using barplot2 function of gplots library (to be able to add error bars as well). Data and codes currently I am using is below. ... Any help regarding adding second Y axis is deeply apprecited. Hi Seyit, It is fairly easy to get the bars like this: library(plotrix) barpos-barp(means,ylim=range(means+SEM)+c(0,4),col=2:3) dispersion(barpos$x,barpos$y,CIU,CIL,interval=FALSE) or even more simply: dispersion(barpos$x,barpos$y,SEM) I am not sure that you need an extra y axis here. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] ncd4 package
Hi I am using windows. I cant install ncdf4 package but it didn't work . any suggestions!! -- View this message in context: http://r.789695.n4.nabble.com/ncd4-package-tp4477496p4477496.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Ggplot barchart drops factor levels: how to show them with zero counts?
To visualize my problem a little; see this screenshot http://i40.tinypic.com/fodsm0.png http://i40.tinypic.com/fodsm0.png . So I would like factor level 4 to show up but without a bar (zero counts). Thanks -- View this message in context: http://r.789695.n4.nabble.com/Ggplot-barchart-drops-factor-levels-how-to-show-them-with-zero-counts-tp4475417p4477563.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] line plot over a barplot
Hi Dear all, I have data in the following format : X-axisY-axis 010% 0-20 20% 20-4030% 40-6040% . and so on. I want to plot a bar graph of the above. Also I would want to add a trendline passing either through the center of each bar or through the top. x-letters[1:5] y-1:5 bb-barplot(y, names.arg=x) lines(bb, y) lines(bb, y/2) Is it also possible to get the r-squared and p-values for this trendline? summary(fit-lm(y~bb)) Regards Petr How do I all of the above? I would be extremely indebted by your help. Thanks in advance Regards, Anupam -- Graduate Student, Laboratory of Computational Biology, Center For DNA Fingerprinting And Diagnostics, 4-1-714 to 725/2, Tuljaguda complex Mozamzahi Road, Nampally, Hyderabad-51 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ncd4 package
This one is for windows. http://cran.r-project.org/web/packages/RNetCDF/index.html but you need netcdf libraries and udunits libraries installed. http://cran.r-project.org/web/packages/RNetCDF/INSTALL Cheers See the On Fri, 2012-03-16 at 00:39 -0700, Amen wrote: Hi I am using windows. I cant install ncdf4 package but it didn't work . any suggestions!! -- View this message in context: http://r.789695.n4.nabble.com/ncd4-package-tp4477496p4477496.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Re : Elegant Code
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf Of Pascal Oettli
Sent: Friday, March 16, 2012 12:36 AM
To: Raphael Fraser
Cc: r-help@r-project.org
Subject: [R] Re : Elegant Code
Hi Raphael,
Something like that?
require(pscl)sim - numeric()
for(i in 1:5){
eval(parse(text=paste('b',i,' - rigamma(50,1,1)',sep='')))
eval(parse(text=paste('theta',i,' -
rgamma(50,0.5,(1/b',i,'))',sep='')))
eval(parse(text=paste('sim',i,' - rpois(50,theta',1,')',sep='')))
eval(parse(text=paste('sim - cbind(sim, sim',i,')',sep='')))
}
x11()
par(mfrow=c(1,5))
boxplot(c(sim1,sim2,sim3,sim4,sim5))
x11()
boxplot(sim)
Regards,
Pascal
- Mail original -
De : Raphael Fraser raphael.fra...@gmail.com
À : r-help@r-project.org
Cc :
Envoyé le : Vendredi 16 mars 2012 16h09
Objet : [R] Elegant Code
Hi,
Can anyone help to write a more elegant version of my code? I am sure
this can be put into a loop but I am having trouble creating the
objects b1,b2,b3,...,etc.
b1 - rigamma(50,1,1)
theta1 - rgamma(50,0.5,(1/b1))
sim1 - rpois(50,theta1)
b2 - rigamma(50,1,1)
theta2 - rgamma(50,0.5,(1/b2))
sim2 - rpois(50,theta2)
b3 - rigamma(50,1,1)
theta3 - rgamma(50,0.5,(1/b3))
sim3 - rpois(50,theta3)
b4 - rigamma(50,1,1)
theta4 - rgamma(50,0.5,(1/b4))
sim4 - rpois(50,theta4)
b5 - rigamma(50,1,1)
theta5 - rgamma(50,0.5,(1/b5))
sim5 - rpois(50,theta5)
par(mfrow=c(1,5))
boxplot(sim1)
boxplot(sim2)
boxplot(sim3)
boxplot(sim4)
boxplot(sim5);
Thanks,
Raphael
Or, just get rid of the for loops altogether, something like this
trials -5
N - 50
b- rigamma(N*trials, 1, 1)
theta - rgamma(N*trials,0.5,1/b)
sim - rpois(N*trials,theta)
dim(sim) - c(N,trials)
boxplot(sim)
Hope this is helpful,
Dan
Daniel Nordlund
Bothell, WA USA
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Ggplot barchart drops factor levels: how to show them with zero counts?
I can reproduce the OP's problem with ggplot 0.9.0 but I don't know how to solve it: perhaps you should take this to the ggplot2 mailing list: https://groups.google.com/group/ggplot2?pli=1 Michael On Fri, Mar 16, 2012 at 4:17 AM, Bart6114 bartsmeet...@gmail.com wrote: To visualize my problem a little; see this screenshot http://i40.tinypic.com/fodsm0.png http://i40.tinypic.com/fodsm0.png . So I would like factor level 4 to show up but without a bar (zero counts). Thanks -- View this message in context: http://r.789695.n4.nabble.com/Ggplot-barchart-drops-factor-levels-how-to-show-them-with-zero-counts-tp4475417p4477563.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Change in behavior of update.views()?
I haven't seen this cryptic warning before:
update.views('Robust')
Warning message:
In update.views(Robust) :
The following packages are not available: covRobust, distr, FRB, MASS, mblm,
multinomRob, mvoutlier, quantreg, RandVar, rgam, RobAStBase, robfilter, RobLox,
RobRex, robust, RobustAFT, robustbase, ROptEst, ROptRegTS, rrcov, sandwich, wle
library(covRobust)
It is puzzling because as the second command shows the package covRobust is
installed.
Here is my
sessionInfo()
R version 2.14.2 (2012-02-29)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] datasets splines utils stats graphics grDevices methods base
other attached packages:
[1] covRobust_1.0 ade4_1.4-17 BiocInstaller_1.2.1 ctv_0.7-4
sos_1.3-1 brew_1.0-6 Hmisc_3.9-2
survival_2.36-12
[9] MASS_7.3-17
loaded via a namespace (and not attached):
[1] cluster_1.14.2 grid_2.14.2lattice_0.20-0 tools_2.14.2
__
Professor Michael Kubovy
University of Virginia
Department of Psychology
for mail add: for FedEx or UPS add:
P.O.Box 400400 Gilmer Hall, Room 102
Charlottesville, VA 22904-4400 485 McCormick Road
USA Charlottesville, VA
22903
roomphone
Office:B011 +1-434-982-4729
Lab:B019+1-434-982-4751
WWW:http://www.people.virginia.edu/~mk9y/
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] substituting own test statistics in a built-in function
So then you need to find the code for those functions inside the source package you downloaded, and use it to make your own functions. The authors can't prevent you from seeing the code. Sarah On Mar 15, 2012 10:43 PM, Aparna Sampath aparna.sampat...@gmail.com wrote: Hi Sarah Goslee Thanking you for replying to my doubt. I downloaded the multtest package from CRAN and also went through the package specific PDF file, they have given a list of functions which includes the mt.transformV, mt.checkothers etc, that I am trying to access which they call as the internal functions and say that these set of functions cannot be called by the user. and these functions perform the permutation part, so I need to somehow access them. Regards Ap On Thu, Mar 15, 2012 at 6:40 PM, Sarah Goslee sarah.gos...@gmail.comwrote: Hi, On Mar 15, 2012 4:28 AM, Aparna Sampath aparna.sampat...@gmail.com wrote: Hi All I would like to compute the raw p-value from permutation tests and I found mt.sample.rawp() from the package multtest almost similar to what I want to do. But in the function definition: mt.sample.rawp(V,classlabel,test=t,side=abs,fixed.seed.sampling=y,B=1,na=.mt.naNUM,nonpara=n) I would like to choose my own t-test which is designed using my model parameters, so it is like a modification of t-test. I would like to use this t-test instead of the ones in the list. I am not sure if this can be done. Can anyone tell me how to do it, if it is possible. the other way I tried is to copy the function and and modify it. Indeed, that's the way to customize functions. But it uses internal functions from the package like mt.checkothers() which I do not know perform what kind of function. I tried to access its function definition, but I was not able to do so. is there some other way I could see what these internal functions do, so that I could possibly try to use the same logic and write the code. If you download the package source from CRAN, you'll have all of it, including any comments that have been stripped out. Appreciate all help. Thanks a lot :) Regards Ap Sarah -- Aparna Sampath Master of Science (Bioinformatics) Nanyang Technological University Mob no : +65 91601854 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Urgente: retiro de la lista
JB == Jaime Bernal-Hadad jaib...@yahoo.com on Thu, 15 Mar 2012 19:11:19 -0700 writes: JB Urgente JB Dedido al gran n�mero de correos recibidos que afectan seriamente mi trabajo, es urgente que me reitren de esta lista. JB Alguien me puede decir que debo hacer JB � JB Gracias Por favor, hace lo Ustedes mismo: -- https://stat.ethz.ch/mailman/listinfo/r-help __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Timer on a function
On Thu, 15 Mar 2012, Bert Gunter wrote:
Bill et. al:
1. This is new to me. Thanks.
2. As I read the man page, this is not guaranteed to work if the model
fitting function does not contain sufficient interrupts. Is that
correct?
Yes. If someone wrote a model fitting package in Fortran with no
callbacks then it is not interruptible, including not by timers. In
that case all you can do is to kill the R session.
The author of setTimeLimit()
-- Bert
On Thu, Mar 15, 2012 at 4:14 PM, William Dunlap wdun...@tibco.com wrote:
There is a setTimeLimit function in base. It could be encapsulated into
the following to limit the time spent on an expression:
timeOut - function (expr, ...) {
on.exit(setTimeLimit())
setTimeLimit(...)
expr
}
Using setTimeLimit(transient = TRUE) is slightly simpler here.
E.g., with the following slow way to compute Euler's phi
f - function(n) sum(sapply(seq_len(n), function(i)1/i)) - log(n)
I get
timeOut(f(1e5), elapsed=1)
[1] 0.5772207
timeOut(f(1e6), elapsed=1)
Error in FUN(1:100[[711624L]], ...) : reached elapsed time limit
Use try() or tryCatch() to check for the error. E.g.,
sapply(1:7, function(n)tryCatch(timeOut(f(10^n), elapsed=1),
error=function(e)-1))
[1] 0.6263832 0.5822073 0.5777156 0.5772657 0.5772207 -1.000
-1.000
You could look at 'e' in the error handler to see if it is a time out problem.
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf
Of Bert Gunter
Sent: Thursday, March 15, 2012 3:05 PM
To: Ramiro Barrantes
Cc: r-help@r-project.org
Subject: Re: [R] Timer on a function
On Thu, Mar 15, 2012 at 2:24 PM, Ramiro Barrantes
ram...@precisionbioassay.com wrote:
Hello,
I have a program that consists of a loop fitting a function over many
models. Sometimes the fitting on a particular model takes minutes to converge.
Is there
a way that I can limit the amount of time that R spends on a given model:
AFAIK, no -- this is an OS level issue.
Of course, most iterative fitting procedures have controls for the
number of iterations, convergence criteria, etc. , but there is no
awareness of timing except when the OS is interrogated, e.g. by
?proc.time or ?system.time . Such calls would have to be built into
the fitting function or OS level services would have to be invoked to
run the R process with timing limitations built in. See e.g. ?Rscript
for one possible approach.
Corrections or clever tricks to get around these perceived limitations
welcomed, of course.
-- Bert
Cheers,
Bert
say if my line is:
fittingFunction( func, model.1)
can I have some function:
stopIfUnderTime( fittingFunction( func, model.1) , 5 )
where stopIfUnderTime will return the result if it finishes under 5 seconds, or
NA
otherwise.
Is there anything like this? (just looked through the web but did not find
anything)
Thanks,
Ramiro
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Bert Gunter
Genentech Nonclinical Biostatistics
Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-
biostatistics/pdb-ncb-home.htm
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Bert Gunter
Genentech Nonclinical Biostatistics
Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Brian D. Ripley, rip...@stats.ox.ac.uk
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@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] multivariate regression and lm()
Hello, I would like to perform a multivariate regression analysis to model the relationship between m responses Y1, ... Ym and a single set of predictor variables X1, ..., Xr. Each response is assumed to follow its own regression model, and the error terms in each model can be correlated. Based on my readings of the R help archives and R documentation, the function lm() should be able to perform this analysis. However my tests of lm() show that it really just fits m separate regression models (without accounting for any possible correlation between the response variables). I have attached an example below that demonstrates that the multivariate analysis result produced by lm() is identical to running separate regression analyses on each of the Y1, ... Ym response variables, which is not the desired objective. Can anyone confirm if lm() is indeed capable of performing multivariate regression analysis, and if so how? Thanks very much, Ernest PS my post is based on an earlier 2005 post where the same question was asked ... the conclusion at that time was that the function lm() is capable of handling the multivariate analysis. However my tests (shown below) indicate that lm() actually seems to perform separate regressions for each of the response variables without accounting for their possible correlation. ### multivariate analysis using lm() ### ex7.8 - data.frame(z1 = c(0, 1, 2, 3, 4), y1 = c(1, 4, 3, 8, 9), y2 = c(-1, -1, 2, 3, 2)) f.mlm - lm(cbind(y1, y2) ~ z1, data = ex7.8) summary(f.mlm) Response y1 : Call: lm(formula = y1 ~ z1, data = ex7.8) Residuals: 1 2 3 4 5 0 1 -2 1 0 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) 1. 1.0954 0.913 0.4286 z12. 0.4472 4.472 0.0208 * --- Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 Residual standard error: 1.414 on 3 degrees of freedom Multiple R-squared: 0.8696, Adjusted R-squared: 0.8261 F-statistic:20 on 1 and 3 DF, p-value: 0.02084 Response y2 : Call: lm(formula = y2 ~ z1, data = ex7.8) Residuals: 1 2 3 4 5 -1.110e-16 -1.000e+00 1.000e+00 1.000e+00 -1.000e+00 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) -1. 0.8944 -1.118 0.3450 z11. 0.3651 2.739 0.0714 . --- Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 Residual standard error: 1.155 on 3 degrees of freedom Multiple R-squared: 0.7143, Adjusted R-squared: 0.619 F-statistic: 7.5 on 1 and 3 DF, p-value: 0.07142 ### separate linear regressions on y1 and y2 ### f.mlm1 = lm(y1 ~ z1, data=ex7.8); summary(f.mlm1) Call: lm(formula = y1 ~ z1, data = ex7.8) Residuals: 1 2 3 4 5 0 1 -2 1 0 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) 1. 1.0954 0.913 0.4286 z12. 0.4472 4.472 0.0208 * --- Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 Residual standard error: 1.414 on 3 degrees of freedom Multiple R-squared: 0.8696, Adjusted R-squared: 0.8261 F-statistic:20 on 1 and 3 DF, p-value: 0.02084 f.mlm2 = lm(y2 ~ z1, data=ex7.8); summary(f.mlm2) Call: lm(formula = y2 ~ z1, data = ex7.8) Residuals: 1 2 3 4 5 -1.110e-16 -1.000e+00 1.000e+00 1.000e+00 -1.000e+00 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) -1. 0.8944 -1.118 0.3450 z11. 0.3651 2.739 0.0714 . --- Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 Residual standard error: 1.155 on 3 degrees of freedom Multiple R-squared: 0.7143, Adjusted R-squared: 0.619 F-statistic: 7.5 on 1 and 3 DF, p-value: 0.07142 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ncd4 package (really ncdf4)
On Fri, 16 Mar 2012, Stefan Luedtke wrote: This one is for windows. http://cran.r-project.org/web/packages/RNetCDF/index.html but you need netcdf libraries and udunits libraries installed. http://cran.r-project.org/web/packages/RNetCDF/INSTALL Which are the non-Windows instructions. On Windows the libraries are statically linked into the binary package (and BTW, it is udunits2, not udunits, these days). ncdf4 is available for Windows from the author: see http://cirrus.ucsd.edu/~pierce/ncdf/ . However, the author does not make clear that is a non-standard 32-bit-only build. The main reason that there is no Windows binary on CRAN is the lack of 64-bit support. And ncdf is also available for Windows. Cheers See the On Fri, 2012-03-16 at 00:39 -0700, Amen wrote: Hi I am using windows. I cant install ncdf4 package but it didn't work . any suggestions!! -- Brian D. Ripley, rip...@stats.ox.ac.uk 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] multivariate regression and lm()
Dear Ernest, The ML estimator for the mulitvariate linear model assuming multinormal errors is the same as equation-by-equation LS, but multivariate tests performed for all of the responses on the resulting multivariate linear model object (e.g., by anova() or Anova() in the car package) will take the correlations of the responses into account. I hope that this helps, John John Fox Sen. William McMaster Prof. of Social Statistics Department of Sociology McMaster University Hamilton, Ontario, Canada http://socserv.mcmaster.ca/jfox/ On Fri, 16 Mar 2012 07:32:02 -0400 Ernest Lo treem...@gmail.com wrote: Hello, I would like to perform a multivariate regression analysis to model the relationship between m responses Y1, ... Ym and a single set of predictor variables X1, ..., Xr. Each response is assumed to follow its own regression model, and the error terms in each model can be correlated. Based on my readings of the R help archives and R documentation, the function lm() should be able to perform this analysis. However my tests of lm() show that it really just fits m separate regression models (without accounting for any possible correlation between the response variables). I have attached an example below that demonstrates that the multivariate analysis result produced by lm() is identical to running separate regression analyses on each of the Y1, ... Ym response variables, which is not the desired objective. Can anyone confirm if lm() is indeed capable of performing multivariate regression analysis, and if so how? Thanks very much, Ernest PS my post is based on an earlier 2005 post where the same question was asked ... the conclusion at that time was that the function lm() is capable of handling the multivariate analysis. However my tests (shown below) indicate that lm() actually seems to perform separate regressions for each of the response variables without accounting for their possible correlation. ### multivariate analysis using lm() ### ex7.8 - data.frame(z1 = c(0, 1, 2, 3, 4), y1 = c(1, 4, 3, 8, 9), y2 = c(-1, -1, 2, 3, 2)) f.mlm - lm(cbind(y1, y2) ~ z1, data = ex7.8) summary(f.mlm) Response y1 : Call: lm(formula = y1 ~ z1, data = ex7.8) Residuals: 1 2 3 4 5 0 1 -2 1 0 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) 1. 1.0954 0.913 0.4286 z12. 0.4472 4.472 0.0208 * --- Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 Residual standard error: 1.414 on 3 degrees of freedom Multiple R-squared: 0.8696, Adjusted R-squared: 0.8261 F-statistic:20 on 1 and 3 DF, p-value: 0.02084 Response y2 : Call: lm(formula = y2 ~ z1, data = ex7.8) Residuals: 1 2 3 4 5 -1.110e-16 -1.000e+00 1.000e+00 1.000e+00 -1.000e+00 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) -1. 0.8944 -1.118 0.3450 z11. 0.3651 2.739 0.0714 . --- Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 Residual standard error: 1.155 on 3 degrees of freedom Multiple R-squared: 0.7143, Adjusted R-squared: 0.619 F-statistic: 7.5 on 1 and 3 DF, p-value: 0.07142 ### separate linear regressions on y1 and y2 ### f.mlm1 = lm(y1 ~ z1, data=ex7.8); summary(f.mlm1) Call: lm(formula = y1 ~ z1, data = ex7.8) Residuals: 1 2 3 4 5 0 1 -2 1 0 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) 1. 1.0954 0.913 0.4286 z12. 0.4472 4.472 0.0208 * --- Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 Residual standard error: 1.414 on 3 degrees of freedom Multiple R-squared: 0.8696, Adjusted R-squared: 0.8261 F-statistic:20 on 1 and 3 DF, p-value: 0.02084 f.mlm2 = lm(y2 ~ z1, data=ex7.8); summary(f.mlm2) Call: lm(formula = y2 ~ z1, data = ex7.8) Residuals: 1 2 3 4 5 -1.110e-16 -1.000e+00 1.000e+00 1.000e+00 -1.000e+00 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) -1. 0.8944 -1.118 0.3450 z11. 0.3651 2.739 0.0714 . --- Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 Residual standard error: 1.155 on 3 degrees of freedom Multiple R-squared: 0.7143, Adjusted R-squared: 0.619 F-statistic: 7.5 on 1 and 3 DF, p-value: 0.07142 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible
Re: [R] Ggplot barchart drops factor levels: how to show them with zero counts?
You can tell that levels must not be dropped with scale_x_discrete(): library(ggplot2) mtcars$cyl-factor(mtcars$cyl) plot1 - ggplot(mtcars[!mtcars$cyl==4,], aes(cyl))+geom_bar() plot1 + scale_x_discrete(drop=FALSE) Or explicitly set the values you want in the x axis with the argument limits: plot1 + scale_x_discrete(limits=levels(mtcars$cyl)) Regards, Helios El día 15/03/2012 a las 16:47, Bart6114 bartsmeet...@gmail.com escribió: Hello, When plotting a barchart with ggplot it drops the levels of the factor for which no counts are available. For example: library(ggplot) mtcars$cyl-factor(mtcars$cyl) ggplot(mtcars[!mtcars$cyl==4,], aes(cyl))+geom_bar() levels(mtcars[!mtcars$cyl==4,]) This shows my problem. Because no counts are available for factorlevel '4', the label 4 dissapears from the plot. However, I would still like it to show up, but without a bar (zero observations). I would like to use this for the presentation of data with a Likert-like scale. Thanks in advance! Bart -- View this message in context: http://r.789695.n4.nabble.com/Ggplot-barchart-drops-factor-levels-how-to-show-the m-with-zero-counts-tp4475417p4475417.html Sent from the R help mailing list archive at Nabble.com. INSTITUTO DE BIOMECÁNICA DE VALENCIA Universidad Politécnica de Valencia • Edificio 9C Camino de Vera s/n • 46022 VALENCIA (ESPAÑA) Tel. +34 96 387 91 60 • Fax +34 96 387 91 69 www.ibv.org Antes de imprimir este e-mail piense bien si es necesario hacerlo. En cumplimiento de la Ley Orgánica 15/1999 reguladora de la Protección de Datos de Carácter Personal, le informamos de que el presente mensaje contiene información confidencial, siendo para uso exclusivo del destinatario arriba indicado. En caso de no ser usted el destinatario del mismo le informamos que su recepción no le autoriza a su divulgación o reproducción por cualquier medio, debiendo destruirlo de inmediato, rogándole lo notifique al remitente. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ncd4 package (really ncdf4)
sorry, I did not know that, thanks! On Fri, 2012-03-16 at 11:35 +, Prof Brian Ripley wrote: On Fri, 16 Mar 2012, Stefan Luedtke wrote: This one is for windows. http://cran.r-project.org/web/packages/RNetCDF/index.html but you need netcdf libraries and udunits libraries installed. http://cran.r-project.org/web/packages/RNetCDF/INSTALL Which are the non-Windows instructions. On Windows the libraries are statically linked into the binary package (and BTW, it is udunits2, not udunits, these days). ncdf4 is available for Windows from the author: see http://cirrus.ucsd.edu/~pierce/ncdf/ . However, the author does not make clear that is a non-standard 32-bit-only build. The main reason that there is no Windows binary on CRAN is the lack of 64-bit support. And ncdf is also available for Windows. Cheers See the On Fri, 2012-03-16 at 00:39 -0700, Amen wrote: Hi I am using windows. I cant install ncdf4 package but it didn't work . any suggestions!! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Singleton pattern
Hi all, I know it may not have much sense thinking about a Singleton Pattern in an R application which doesn't use any OOP facilities, however I'm curious to know if anybody faced the same issue. I've been googling but using singleton pattern as a key word leads to typical OOP languages like Java or C++ among others. So my problem is that I'd like to ensure some very big objects aren't copied again and again in some other variables. In the worst case I'll check all code by myself to ensure it but in this case the application won't force programmers to take it in consideration which is what I am really looking for. Any advice will be highly appreciated :P Thanks! -- *David Cassany Viladomat Software Developer Transmural Biote**ch S.L* [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Change in behavior of update.views()?
On Fri, 16 Mar 2012, Michael Kubovy wrote:
I haven't seen this cryptic warning before:
update.views('Robust')
Warning message:
In update.views(Robust) :
The following packages are not available: covRobust, distr, FRB, MASS,
mblm, multinomRob, mvoutlier, quantreg, RandVar, rgam, RobAStBase,
robfilter, RobLox, RobRex, robust, RobustAFT, robustbase, ROptEst,
ROptRegTS, rrcov, sandwich, wle
library(covRobust)
It is puzzling because ? as the second command shows ? the package
covRobust is installed.
Even though it is installed, update.views() tries to find out whether the
installed version is the most current version.
Essentially, it does the following:
(1) Query names of packages in the task view.
(2) Query names/versions of all available.packages() in the repository.
(3) Query names/versions of all installed.packages() on the local machine.
(4) install.packages() that are either not yet installed or not current.
The error message above occurs in step (2). The available.packages() found
with your setup include _none_ of the packages in the task view. Possibly
this is due to the repos used or the getOption(pkgType) requested.
On my machine:
R getOption(repos)
[1] http://CRAN.R-project.org/;
R getOption(pkgType)
[1] source
And then the following works:
Step (1)
R pkgs - ctv:::.get_pkgs_from_ctv_or_repos(Robust)
R pkgs
$`http://CRAN.R-project.org/`
[1] covRobust distr FRB MASSmblm
[6] multinomRob mvoutlier quantregRandVar rgam
[11] RobAStBase robfilter RobLox RobRex robust
[16] RobustAFT robustbase ROptEst ROptRegTS rrcov
[21] sandwichwle
Step (2)
R apkgs - available.packages(contriburl = contrib.url(names(pkgs)))
R dim(apkgs)
[1] 3661 13
And for the error message ctv looks essentially at
R pkgs[[1]][ !(pkgs[[1]] %in% apkgs[,1]) ]
character(0)
I suspect that with your settings the apkgs object does not include all
CRAN packages yet. Setting a different repos and/or a different pkgType
should solve the problem.
hth,
Z
Here is my
sessionInfo()
R version 2.14.2 (2012-02-29)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] datasets splines utils stats graphics grDevices methods base
other attached packages:
[1] covRobust_1.0 ade4_1.4-17 BiocInstaller_1.2.1 ctv_0.7-4
sos_1.3-1 brew_1.0-6 Hmisc_3.9-2 survival_2.36-12
[9] MASS_7.3-17
loaded via a namespace (and not attached):
[1] cluster_1.14.2 grid_2.14.2lattice_0.20-0 tools_2.14.2
__
Professor Michael Kubovy
University of Virginia
Department of Psychology
for mail add: for FedEx or UPS add:
P.O.Box 400400 Gilmer Hall, Room 102
Charlottesville, VA 22904-4400 485 McCormick Road
USA Charlottesville, VA
22903
roomphone
Office:B011 +1-434-982-4729
Lab:B019+1-434-982-4751
WWW:http://www.people.virginia.edu/~mk9y/
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] help to split a ID column in a data.frame and create a new ID column
Dear Researchers, I have a data.frame with 2 columns like this: mydf - data.frame(value=c(1,2,3,4,5),ID=c(Area_1,Area_2,Area_3,Area_4,Area_5)) mydf value ID 1 1 Area_1 2 2 Area_2 3 3 Area_3 4 4 Area_4 5 5 Area_5 I need to convert the *ID *in the following version mydf value ID newID 1 1 Area_1 AreaSample1 2 2 Area_2 AreaSample2 3 3 Area_3 AreaSample3 4 4 Area_4 AreaSample4 5 5 Area_5 AreaSample5 some people know the right function to split ID and create a new column Thanks in advance Gianni [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Generation of correlated variables
On Thu, Mar 15, 2012 at 10:48:48AM -0700, Filoche wrote:
Hi everyone.
Based on a dependent variable (y), I'm trying to generate some independent
variables with a specified correlation. For this there's no problems.
However, I would like that have all my regressors to be orthogonal (i.e.
no correlation among them.
For example,
y = x1 + x2 + x3 where the correlation between y x1 = 0.7, x2 = 0.4 and x3 =
0.8. However, x1, x2 and x3 should not be correlated to each other.
Hi.
The previous discussion shows that the required correlations
should have sum of squares 1. It is not clear, whether your
expected application allows to normalize the correlations to
satisfy this condition. If this normalization is possible, then
try the following approach.
It creates a matrix trans, which satisfies the following.
If Z is a matrix whose columns have zero mean and the identity covariance
matrix, then Z %*% trans has the required correlation structure.
This may be checked by looking at cov2cor(t(trans) %*% trans).
Moreover, trans should have the first column c(1, 0, 0) so that
the first column of Z is not changed by the transformation.
# normalize the correlations (see the discussion above)
rho - c(0.7, 0.4, 0.8)
rho - rho/sqrt(sum(rho^2))
(required - cbind(c(1, rho), rbind(c(rho), diag(3
trans - cbind(
y=rho,
x1=c(rho[1], 0, 0),
x2=c(0, rho[2], 0),
x3=c(0, 0, rho[3]))
# check that trans generates the required correlations
max(abs(cov2cor(t(trans) %*% trans) - required)) # [1] 1.110223e-16
# get orthonormal columns
gram.schmidt - function(a)
{
n - ncol(a)
for (i in seq.int(length=n)) {
for (j in seq.int(length=i-1)) {
a[, i] - a[, i] - sum(a[, j]*a[, i])*a[, j]
}
a[, i] - a[, i]/sqrt(sum(a[, i]^2))
}
a
}
# multiply trans by a unitary matrix, so that the first column becomes (1, 0,
0)
U - gram.schmidt(trans[, 1:3])
trans - t(U) %*% trans
# check that trans still generates the required correlations
max(abs(cov2cor(t(trans) %*% trans) - required)) # [1] 1.110223e-16
# choose an example of the real vector y and normalize
y - rnorm(100)
ynorm - y - mean(y)
ynorm - ynorm/sqrt(sum(ynorm^2))
# find two more normalized vectors orthogonal to ynorm
u - gram.schmidt(cbind(1, ynorm, rnorm(length(y)), rnorm(length(y[, 3:4]
Z - cbind(ynorm, u)
# get the solution as suggested at the beginning
S - Z %*% trans
# check that S is a solution for the normalized y (ynorm)
max(abs(cor(S) - required)) # [1] 1.110223e-16
max(abs(S[, 1] - ynorm)) # [1] 8.326673e-17
max(abs(S[, 2] + S[, 3] + S[, 4] - ynorm)) # [1] 1.110223e-16
This solution contains ynorm. In order to get y as required, a
linear transformation, which is inverse to the normalization, should
be done. Since it is linear, it does not change the correlations.
Hope this helps.
Petr Savicky.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] var
ex.nc [1] file cruncep_tair_2010.nc has 4 dimensions: [1] longitude Size: 720 [1] latitude Size: 360 [1] time Size: 1460 [1] points_terre Size: 62482 [1] [1] file cruncep_tair_2010.nc has 4 variables: [1] int mask[longitude,latitude] Longname:mask Missval:NA [1] short indice_ligne[points_terre] Longname:indice_ligne Missval:NA [1] short indice_col[points_terre] Longname:indice_col Missval:NA [1] float Temperature[longitude,latitude,time] Longname:Temperature Missval:1e+30 these are the information of my file. How can I display the temperature variable and manipulation it;I wanna convert from hourly to daily.any help!!! -- View this message in context: http://r.789695.n4.nabble.com/var-tp4477613p4477613.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Spatstat - coordinates in observation window
Dear R users, I wish to run spatial point pattern analysis (e.g. pair correlation function, mark correlation function) for which I need to create an observation window (window=owin) from which the spatial analysis is generated. The command I used to create this observation window as follows: X1- ppp(x, y, window=owin(c(80.58,144.96),c(101.06,165.13)), unitname=c(metres,metres), marks=dbh) I managed to create the observation window with this command. However, my data (x,y coordinates of objects in a square plot) didn't fit into this observation window's frame. It seems like I need to 'move or twist' my data by a certain angle so that they fit within the border of the observation window's frame. I'm not sure how to do that. Is there a command of function for that? I would be very grateful for any help or suggestions. I hope I described my problem so that it is understandable. Thank you, L. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to Group Categorical data in R?
Hi, I am newbie to R and working on result presentation? My Input table is in following format A B CD X TCK Z U ZM E VZR Z U ZM E VPR I need to present my result in the following way. Colum3 C ABD XT K Column3 Z Z U M E VR Z U M Column3 P E VR How can i implement it? Thanks -- View this message in context: http://r.789695.n4.nabble.com/How-to-Group-Categorical-data-in-R-tp4477622p4477622.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Extending a group of S4 classes by setClassUnion ?
Martin Morgan wrote
On 03/15/2012 09:51 AM, Alexander wrote:
Hi Martin,
thanks for your quick answer. I didn't know that '.' could be
missleading.
Is there any standard way to name function for S4 objects? get,set
etc..?
Hi Alexander -- it's usually better to include the original email in the
reply, to provide context especially for those joining the thread later.
I think 'get' and 'set' are implicit in the action of the 'getter'
fun(x) and 'setter' fun(x) - value function. I would have written (I
wouldn't have used par, which is an existing function unrelated to what
you're trying to do).
In fact, I have several getter and setter. For example gettermean and
gettervariance are less clear then getter.mean and getter.variance. The
names mean.getter, variance.getter have the disadvantage to have getter
and setter not in first place... (Ok, these are very minor problems...)
Martin Morgan wrote
setGeneric(parent,
function(object, ...) standardGeneric(parent'))
setMethod(parent, Father, function(object, ...) object@name)
setGeneric(parent-,
function(object, ..., value) standardGeneric(parent-))
setReplaceMethod(parent, c(Father, Son1),
function(object, ..., value) {
object@name - value
object
})
and used as
parent(obj)
parent(obj) - son
I realize I'm confused about Father / Son and 'parent' here, maybe you
meant something else by 'par'.
Yes indeed, par means parameter. But you're right, it is to close to
parent and very misleading in this example
Martin Morgan wrote
I saw your example, and I was wondering, why get.par(ext) put out Son1,
and not the same as get.par(new(Son1, name=Son1, par=3))
the setIs established a relationship between Extension and Father; you
could have established a relationship between Extension and Son1
setIs(Extension, Son1, ...)
and then you would get your expected result. I have to say that I have
rarely used setIs, so the complexity of inheritance may hold some
surprises, e.g., when there are setIs defined, from Extension to Father,
Son1, and Son2.
Martin
If I define a function just like setMethod(get.par, Father,
function(object) object@name) , for example
setMethod(get.par, Father, function(object) object@par)
then it would work, for all objects, which are either Son1 or Son2, but
not
all object, which are Father, contains also the variable par
get.par(new(Father))
Alexander
--
View this message in context:
http://r.789695.n4.nabble.com/Extending-a-group-of-S4-classes-by-setClassUnion-tp4475251p4475650.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@ mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
Location: M1-B861
Telephone: 206 667-2793
__
R-help@ mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
I rewrote the example and I think if will have to write some setIs methods.
Do you know, how this is done? Here is a little example which shows, that
the order of initialization for setIs determins the results !!
setClass(Father,representation(name=character))
setClass(Son1,contains=Father,representation(parameter=numeric))
setClass(Son2,contains=Father,representation(parameter=logical))
Son1-new(Son1,name=Son1,parameter=3)
Son2-new(Son2,name=Son2,parameter=TRUE)
setGeneric(get.parameter,function(object){standardGeneric
(get.parameter)})
setMethod(get.parameter,Son1,function(object){return(object@parameter+3)})
setMethod(get.parameter,Son2,function(object){return(object@parameter==TRUE)})
get.parameter(Son1)
get.parameter(Son2)
setClass(Extension,representation(person=Father,text=character))
ext1 - new(Extension,person=Son1,text=new try)
ext2 - new(Extension,person=Son2,text=yesyes)
setIs(Extension, Son1,test=function(from){print(setIsSon1)
return(class(from@person)==Son1)
},
coerce=function(from) as(from@person,Son1,strict=FALSE),
replace=function(from, value) {from@person - value
from
}
)
setIs(Extension, Son2,test=function(from){print(setIsSon2)
return(class(from@person)==Son2)
},
coerce=function(from) as(from@person,Son2,strict=FALSE),
replace=function(from, value) {from@person - value
from
}
)
get.parameter(ext1) #setIsSon1, 6 correct result
get.parameter(ext2)# setIsSon1, Error in as(object, Son1, strict =
FALSE) :
Re: [R] ncd4 package
Thanks a lot
I installed it but the interface did not show up
I got this message
Local ({pkg - select.list (sort (. Packages (all.available = TRUE)),
graphics = TRUE)
+ If (nchar (pkg)) library (pkg, character.only = TRUE)})
Notification message:
package 'RNetCDF has been compiled with version 2.14.2 R
--
View this message in context:
http://r.789695.n4.nabble.com/ncd4-package-tp4477496p4477713.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] ncd4 package
I got theses but no interface
library(udunits2)
library(ncdf)
local({pkg - select.list(sort(.packages(all.available =
TRUE)),graphics=TRUE)
+ if(nchar(pkg)) library(pkg, character.only=TRUE)})
--
View this message in context:
http://r.789695.n4.nabble.com/ncd4-package-tp4477496p4477732.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] R merge two dataframes with different row?
Hi everyone, I have a question for R code to merge. Say I have two dataframes: File1 is: V1V2V3V4 1100101name1 2200201name2 2300301name3 3400401name4 3500501name5 4600601name6 4700701name7 File2 is: V1V2V3V4 15055p1 3402449p2 4550650p3 4651660p4 2150250p5 2250350p6 3450499p7 2100250p8 I hope to have the merged file3 meet the following three criteria: (1) File1$V1==File2$V1, and (2) File1V2=File2$V2, and (3) File1V3=File2$V3. In this case, we can see that there should be four records meet these three criteria. So the final merge file should looks like: File1$V1 File1$V2 File1$V3 File1$V4 File2$V1 File2$V2 File2$V3 File2$V4 2200 201 name2 2150 250p5 2200 201 name2 2 100 250p8 2300 301 name3 2 250 350p6 4600 601 name6 4 550 650 p3 Is there any one know how to make R code to achieve this? I thought out a way to use for loop to read for each row in the file1 to compare the whole data frame in file2 to find the mathcing rows but for loop takes so much time. I would like to have a vectorized code to make it faster but I don't know how to manage this. Thanks, [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Rolling regressions with sample extended one period at a time
hey, thanks for the hint. I too figured I'd have to write a for-loop. I have the problem now of how to extract the single element of the fitted values vector. For example, run 1 of the regression generates 80 fitted values, run 2 generates 81 fitted values, run 3 produces 82 fitted values and so on. I need to extract the 80th, 81st, 82nd (all the last values generated at every run) value into a separate vector. I know that lm (and glm) provides a specific function for extracting the predicted values but I don't know how to use it inside a loop. Can you suggest anything? P. -- View this message in context: http://r.789695.n4.nabble.com/Rolling-regressions-with-sample-extended-one-period-at-a-time-tp4470316p4478016.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Problem reading mixed CSV file
I am having trouble reading this CSV file in R. There are six attributes that I need to read - CVar1, CVar2, Location, Year, Nvar3, Nvar4. Can somebody help in reading this file? On line 10 it has city and state separated by comma. I had been a user of SAS where I can use different format to read in for this line. Can I do this in R too? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] how to speed up the inefficient code
hi,
i'm really in trouble to simulate some experiment.
that is, it takes too much time to process the following code.
following is short example,
---
p-data.frame(a=rnorm(10),b=rnorm(10),c=rnorm(10),d=rnorm(10))
test-data.frame(a=rnorm(1),b=rnorm(1),c=rnorm(1),d=rnorm(1))
result-list()
for(i in 1:nrow(p)){
result[[i]]-sum((p[i,]-test)^2)
}
result_1-unlist(result)
p_1-cbind(p,result_1)
---
is there any efficient way to shorten the time and make same output?
--
View this message in context:
http://r.789695.n4.nabble.com/how-to-speed-up-the-inefficient-code-tp4478046p4478046.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Re : ncd4 package
Hi, Package ncdf4 is not available for Windows. Regards, Pascal - Mail original - De : Amen amen.alya...@bordeaux.inra.fr À : r-help@r-project.org Cc : Envoyé le : Vendredi 16 mars 2012 16h39 Objet : [R] ncd4 package Hi I am using windows. I cant install ncdf4 package but it didn't work . any suggestions!! -- View this message in context: http://r.789695.n4.nabble.com/ncd4-package-tp4477496p4477496.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] replacing values in Array
Hey Gerrit , Thanks your solution works -- View this message in context: http://r.789695.n4.nabble.com/replacing-values-in-Array-tp4468739p4477758.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Adding mean values to boxplots
That works great by the way. Thanks very much for your help! -- View this message in context: http://r.789695.n4.nabble.com/Adding-mean-values-to-boxplots-tp4474700p4478031.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to Group Categorical data in R?
Hi Manish, Try # data set x - structure(list(V1 = structure(c(1L, 3L, 4L, 2L, 4L, 2L), .Label = c(A, E, X, Z), class = factor), V2 = structure(c(1L, 2L, 3L, 4L, 3L, 4L), .Label = c(B, T, U, V), class = factor), V3 = structure(c(1L, 1L, 3L, 3L, 3L, 2L), .Label = c(C, P, Z), class = factor), V4 = structure(c(1L, 2L, 3L, 4L, 3L, 4L), .Label = c(D, K, M, R), class = factor)), .Names = c(V1, V2, V3, V4), class = data.frame, row.names = c(NA, -6L )) # result lapply(split(x, x$V3), [, c(1, 2, 4)) See ?lapply, ?split and ?[ for more information. HTH, Jorge.- On Fri, Mar 16, 2012 at 4:43 AM, Manish Gupta wrote: Hi, I am newbie to R and working on result presentation? My Input table is in following format A B CD X TCK Z U ZM E VZR Z U ZM E VPR I need to present my result in the following way. Colum3 C ABD XT K Column3 Z Z U M E VR Z U M Column3 P E VR How can i implement it? Thanks -- View this message in context: http://r.789695.n4.nabble.com/How-to-Group-Categorical-data-in-R-tp4477622p4477622.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to extend a slot of a class?
i think if you do: coord$time-YOURTIMEVECTOR should work and the new vector is put correctly in the data slot. Maybe also coord@data$time-YOURTIMEVECTOR On Wed, Mar 14, 2012 at 01:39:20PM +0100, Marco Smolla wrote: Hej hej, is there a way to extend the SpatialPointsDataFrame data slot?This is the structure of an object of it: str(coord) Formal class 'SpatialPointsDataFrame' [package sp] with 5 slots ..@ data :'data.frame': 214 obs. of 2 variables: .. ..$ location.long: num [1:214] -79.8 -79.8 -79.8 -79.8 -79.8 ... .. ..$ location.lat : num [1:214] 9.16 9.16 9.16 9.16 9.16 ... ..@ coords.nrs : num(0) ..@ coords : num [1:214, 1:2] -79.8 -79.8 -79.8 -79.8 -79.8 ... .. ..- attr(*, dimnames)=List of 2 .. .. ..$ : NULL .. .. ..$ : chr [1:2] location.long location.lat ..@ bbox : num [1:2, 1:2] -79.84 9.16 -79.84 9.17 .. ..- attr(*, dimnames)=List of 2 .. .. ..$ : chr [1:2] location.long location.lat .. .. ..$ : chr [1:2] min max ..@ proj4string:Formal class 'CRS' [package sp] with 1 slots .. .. ..@ projargs: chr NA data is a data.frame including the information of long and lat location. I would like to have there a third information: time (but as POSIXct). Is there an elegant way to do this? Best, marco [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- :: Igor Sosa Mayor :: joseleopoldo1...@gmail.com :: :: GnuPG: 0x1C1E2890 :: http://www.gnupg.org/ :: __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to speed up the inefficient code
Hi mrzung46,
Try
cbind(p, result_1 = rowSums((p-c(test))^2))
HTH,
Jorge.-
On Fri, Mar 16, 2012 at 8:32 AM, mrzung wrote:
hi,
i'm really in trouble to simulate some experiment.
that is, it takes too much time to process the following code.
following is short example,
---
p-data.frame(a=rnorm(10),b=rnorm(10),c=rnorm(10),d=rnorm(10))
test-data.frame(a=rnorm(1),b=rnorm(1),c=rnorm(1),d=rnorm(1))
result-list()
for(i in 1:nrow(p)){
result[[i]]-sum((p[i,]-test)^2)
}
result_1-unlist(result)
p_1-cbind(p,result_1)
---
is there any efficient way to shorten the time and make same output?
--
View this message in context:
http://r.789695.n4.nabble.com/how-to-speed-up-the-inefficient-code-tp4478046p4478046.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] help to split a ID column in a data.frame and create a new ID column
Hi Gianni, Thank you for the reproducible example! Try mydf$newID - with(mydf, gsub(_, Sample, ID)) mydf HTH, Jorge.- On Fri, Mar 16, 2012 at 7:54 AM, gianni lavaredo wrote: Dear Researchers, I have a data.frame with 2 columns like this: mydf - data.frame(value=c(1,2,3,4,5),ID=c(Area_1,Area_2,Area_3,Area_4,Area_5)) mydf value ID 1 1 Area_1 2 2 Area_2 3 3 Area_3 4 4 Area_4 5 5 Area_5 I need to convert the *ID *in the following version mydf value ID newID 1 1 Area_1 AreaSample1 2 2 Area_2 AreaSample2 3 3 Area_3 AreaSample3 4 4 Area_4 AreaSample4 5 5 Area_5 AreaSample5 some people know the right function to split ID and create a new column Thanks in advance Gianni [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to speed up the inefficient code
Try this -- use matrices instead of dataframes if you want speed:
p-data.frame(a=rnorm(10),b=rnorm(10),c=rnorm(10),d=rnorm(10))
test-data.frame(a=rnorm(1),b=rnorm(1),c=rnorm(1),d=rnorm(1))
result-list()
for(i in 1:nrow(p)){
+ result[[i]]-sum((p[i,]-test)^2)
+ }
result_1-unlist(result)
p_1-cbind(p,result_1)
# don't use dataframes; use matrices
pm - as.matrix(p)
testm - unlist(test)
result_2 - colSums((t(pm) - testm)^2)
p_2 - cbind(pm, result_2)
p_1
a b c d result_1
1 1.4580819 0.03351271 -0.6414914 -0.4448870 2.464525
2 -0.7603889 -0.41833604 -1.3576672 -0.1230215 6.270578
3 1.3343855 -1.35613207 2.0560362 -1.0356030 3.592794
4 0.5974293 0.88175552 -1.4756855 0.1634320 6.707364
5 -0.8008295 0.37385864 -0.7822124 -0.4896094 4.712335
6 -0.5550789 0.07063761 0.9432475 1.0785456 4.868218
7 1.0641638 -1.52241836 0.3912154 0.1071740 2.165140
8 1.5619793 -0.30982169 1.2756762 -0.8522361 1.266879
9 -0.1049558 -1.0559 0.5425563 0.3232156 3.279428
10 -0.1565198 0.59954267 -1.3878649 1.8615366 12.132722
p_2
a b c d result_2
[1,] 1.4580819 0.03351271 -0.6414914 -0.4448870 2.464525
[2,] -0.7603889 -0.41833604 -1.3576672 -0.1230215 6.270578
[3,] 1.3343855 -1.35613207 2.0560362 -1.0356030 3.592794
[4,] 0.5974293 0.88175552 -1.4756855 0.1634320 6.707364
[5,] -0.8008295 0.37385864 -0.7822124 -0.4896094 4.712335
[6,] -0.5550789 0.07063761 0.9432475 1.0785456 4.868218
[7,] 1.0641638 -1.52241836 0.3912154 0.1071740 2.165140
[8,] 1.5619793 -0.30982169 1.2756762 -0.8522361 1.266879
[9,] -0.1049558 -1.0559 0.5425563 0.3232156 3.279428
[10,] -0.1565198 0.59954267 -1.3878649 1.8615366 12.132722
On Fri, Mar 16, 2012 at 8:32 AM, mrzung mrzun...@gmail.com wrote:
hi,
i'm really in trouble to simulate some experiment.
that is, it takes too much time to process the following code.
following is short example,
---
p-data.frame(a=rnorm(10),b=rnorm(10),c=rnorm(10),d=rnorm(10))
test-data.frame(a=rnorm(1),b=rnorm(1),c=rnorm(1),d=rnorm(1))
result-list()
for(i in 1:nrow(p)){
result[[i]]-sum((p[i,]-test)^2)
}
result_1-unlist(result)
p_1-cbind(p,result_1)
---
is there any efficient way to shorten the time and make same output?
--
View this message in context:
http://r.789695.n4.nabble.com/how-to-speed-up-the-inefficient-code-tp4478046p4478046.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Data Munger Guru
What is the problem that you are trying to solve?
Tell me what you want to do, not how you want to do it.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Ggplot barchart drops factor levels: how to show them with zero counts?
R. Michael Weylandt michael.weylandt at gmail.com writes: I can reproduce the OP's problem with ggplot 0.9.0 but I don't know how to solve it: perhaps you should take this to the ggplot2 mailing list: https://groups.google.com/group/ggplot2?pli=1 Michael On Fri, Mar 16, 2012 at 4:17 AM, Bart6114 bartsmeets86 at gmail.com wrote: To visualize my problem a little; see this screenshot http://i40.tinypic.com/fodsm0.png http://i40.tinypic.com/fodsm0.png . So I would like factor level 4 to show up but without a bar (zero counts). Thanks Supposedly ggplot(subset(mtcars,cyl!=4),aes(cyl))+stat_bin(drop=FALSE) *should* work (see ?stat_bin) -- maybe a bug? I would second the advice to put this on the ggplot mailing list ... __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Partial matching when using $ ? Feature or bug?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi I have the following code: x - data.frame(x1=1, x2=2, y1=3) x$y [1] 3 x$x NULL I was surprised (and definitely irritated?) when I realised that partial matching also works for the $. Is this intended? I assume the reason is that $ is internally a function? Rainer - -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Stellenbosch University South Africa Tel : +33 - (0)9 53 10 27 44 Cell: +33 - (0)6 85 62 59 98 Fax : +33 - (0)9 58 10 27 44 Fax (D):+49 - (0)3 21 21 25 22 44 email: rai...@krugs.de Skype: RMkrug -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAk9jQ+YACgkQoYgNqgF2egpe7QCeL2us46r9NVtJsXteUhEaBcwe disAn2eY5Ci5/QNgRLOwOs8HVTcF3KHn =Qgnt -END PGP SIGNATURE- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] contingency tables
Ok, before I definetly give up, and throw the laptop out of the window, or fill my data.frame manually, I'll ask for some help. I have a data.frame named MyTable with 3 columns, that looks like this: V1 V2 V3 red-jappearanceblood-n 105.032 red-j appearanceground-n 93.749 red-j appearancesea-n 102.167 red-j appearancesky-n 10.898 orange-jappearanceobject-n 109.354 orange-jas_adj_aspainting-n 93.248 orange-jcolorbanknote-n 159.167 orange-jcolorcar-n 117.985 yellow-jappearanceskin-n109.527 yellow-jareacircle-n87.064 yellow-jareainfarction-n120.759 yellow-jas_adj_ascorn-n 219.739 yellow-jas_adj_asflax-n 122.576 yellow-jas_adj_asgold-n 90.814 green-j appearancewater-n 91.477 green-j architecturebuilding-n 103.582 green-j architecturecourse-n103.325 green-j areaRio-n 106.614 green-j areaauditorium-n102.505 green-j areacity-n 150.005 blue-j appearancecypress-n 145.133 blue-j appearancefirmament-n 148.655 blue-j appearanceman-n 85.731 blue-j appearancerange-n 90.706 blue-j appearancesurface-n 100.991 blue-j areagraph-n 92.708 blue-j arealibrary-n 77.135 purple-jappearanceleave-n 119.423 purple-jappearancelesion-n 134.287 purple-jcolorViking-n 145.516 purple-jcoloramethyst-n 175.619 purple-jcolorbanknote-n 158.045 purple-jcolorbottle-n 132.395 purple-jcolorchocolate-n141.833 The elements on the first column can be: red-j, orange-j, yellow-j, green-j, blue-j or purple-j. Elements on column 2 are contexts in which the color appears. And in column 3 there is a kind of frequency measurement between color and context. I am trying to build a new data.frame where the 6 colors in column 1 are placed as column names, all the unique contexts in column 2 are placed as row names and the values on column 3 are in the correspondent cells (or 0 if an intersection color-context is empty). Easy to prepare the empty data.frame, but I cant find out how to fill it up with the frequencies. Ideas? Anybody has a ready script for this? Thank you!!! Marianna -- View this message in context: http://r.789695.n4.nabble.com/contingency-tables-tp4478204p4478204.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Partial matching when using $ ? Feature or bug?
Hi Rainer, On Fri, Mar 16, 2012 at 9:45 AM, Rainer M Krug r.m.k...@gmail.com wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi I have the following code: x - data.frame(x1=1, x2=2, y1=3) x$y [1] 3 x$x NULL I was surprised (and definitely irritated?) when I realised that partial matching also works for the $. Is this intended? This is documented behavior, which by definition makes it a feature, right? Both ‘[[’ and ‘$’ select a single element of the list. The main difference is that ‘$’ does not allow computed indices, whereas ‘[[’ does. ‘x$name’ is equivalent to ‘x[[name, exact = FALSE]]’. Also, the partial matching behavior of ‘[[’ can be controlled using the ‘exact’ argument. It's also a really good reason to use [[ in functions or anywhere there might be a chance of confusion. Sarah -- Sarah Goslee http://www.functionaldiversity.org __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Re : Elegant Code
Thank you all. Your responses were very helpful.
Raphael
On Fri, Mar 16, 2012 at 5:04 AM, Daniel Nordlund
djnordl...@frontier.com wrote:
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf Of Pascal Oettli
Sent: Friday, March 16, 2012 12:36 AM
To: Raphael Fraser
Cc: r-help@r-project.org
Subject: [R] Re : Elegant Code
Hi Raphael,
Something like that?
require(pscl)sim - numeric()
for(i in 1:5){
eval(parse(text=paste('b',i,' - rigamma(50,1,1)',sep='')))
eval(parse(text=paste('theta',i,' -
rgamma(50,0.5,(1/b',i,'))',sep='')))
eval(parse(text=paste('sim',i,' - rpois(50,theta',1,')',sep='')))
eval(parse(text=paste('sim - cbind(sim, sim',i,')',sep='')))
}
x11()
par(mfrow=c(1,5))
boxplot(c(sim1,sim2,sim3,sim4,sim5))
x11()
boxplot(sim)
Regards,
Pascal
- Mail original -
De : Raphael Fraser raphael.fra...@gmail.com
À : r-help@r-project.org
Cc :
Envoyé le : Vendredi 16 mars 2012 16h09
Objet : [R] Elegant Code
Hi,
Can anyone help to write a more elegant version of my code? I am sure
this can be put into a loop but I am having trouble creating the
objects b1,b2,b3,...,etc.
b1 - rigamma(50,1,1)
theta1 - rgamma(50,0.5,(1/b1))
sim1 - rpois(50,theta1)
b2 - rigamma(50,1,1)
theta2 - rgamma(50,0.5,(1/b2))
sim2 - rpois(50,theta2)
b3 - rigamma(50,1,1)
theta3 - rgamma(50,0.5,(1/b3))
sim3 - rpois(50,theta3)
b4 - rigamma(50,1,1)
theta4 - rgamma(50,0.5,(1/b4))
sim4 - rpois(50,theta4)
b5 - rigamma(50,1,1)
theta5 - rgamma(50,0.5,(1/b5))
sim5 - rpois(50,theta5)
par(mfrow=c(1,5))
boxplot(sim1)
boxplot(sim2)
boxplot(sim3)
boxplot(sim4)
boxplot(sim5);
Thanks,
Raphael
Or, just get rid of the for loops altogether, something like this
trials -5
N - 50
b - rigamma(N*trials, 1, 1)
theta - rgamma(N*trials,0.5,1/b)
sim - rpois(N*trials,theta)
dim(sim) - c(N,trials)
boxplot(sim)
Hope this is helpful,
Dan
Daniel Nordlund
Bothell, WA USA
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Partial matching when using $ ? Feature or bug?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 16/03/12 14:54, Sarah Goslee wrote: Hi Rainer, On Fri, Mar 16, 2012 at 9:45 AM, Rainer M Krug r.m.k...@gmail.com wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi I have the following code: x - data.frame(x1=1, x2=2, y1=3) x$y [1] 3 x$x NULL I was surprised (and definitely irritated?) when I realised that partial matching also works for the $. Is this intended? This is documented behavior, which by definition makes it a feature, right? Not necessary - one can also document bugs. But I agree - this has to be considered a feature. Both ‘[[’ and ‘$’ select a single element of the list. The main difference is that ‘$’ does not allow computed indices, whereas ‘[[’ does. ‘x$name’ is equivalent to ‘x[[name, exact = FALSE]]’. Also, the partial matching behavior of ‘[[’ can be controlled using the ‘exact’ argument. It's also a really good reason to use [[ in functions or anywhere there might be a chance of confusion. Absolutely - I think I have to change my habit. I always prefered using $ as it seemed to me more logical. Thanks, Rainer Sarah - -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Stellenbosch University South Africa Tel : +33 - (0)9 53 10 27 44 Cell: +33 - (0)6 85 62 59 98 Fax : +33 - (0)9 58 10 27 44 Fax (D):+49 - (0)3 21 21 25 22 44 email: rai...@krugs.de Skype: RMkrug -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAk9jR6AACgkQoYgNqgF2egqfdwCdGOhe5jk/xgaxpISf9GGMA+Yk 68IAn1RA9N7vJnytAliFszXJxt3/3tJC =hIXq -END PGP SIGNATURE- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Partial matching when using $ ? Feature or bug?
It's also a really good reason to use [[ in functions or anywhere there might be a chance of confusion. Absolutely - I think I have to change my habit. I always prefered using $ as it seemed to me more logical. I started out that way because it's shorter and nicer-looking code, but it can cause partial-matching problems, and also LaTeX annoyances in Sweave code. Someday I'll go back through my packages and get rid of all the lingering $. R: lots of ways to do the same thing, but some of them are booby-trapped. Sarah -- Sarah Goslee http://www.functionaldiversity.org __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R merge two dataframes with different row?
On Mar 16, 2012, at 5:51 AM, zhu free wrote: Hi everyone, I have a question for R code to merge. Say I have two dataframes: File1 is: V1V2V3V4 1100101name1 2200201name2 2300301name3 3400401name4 3500501name5 4600601name6 4700701name7 File2 is: V1V2V3V4 15055p1 3402449p2 4550650p3 4651660p4 2150250p5 2250350p6 3450499p7 2100250p8 I hope to have the merged file3 meet the following three criteria: (1) File1$V1==File2$V1, and (2) File1V2=File2$V2, and (3) File1V3=File2$V3. In this case, we can see that there should be four records meet these three criteria. So the final merge file should looks like: File1$V1 File1$V2 File1$V3 File1$V4 File2$V1 File2$V2 File2$V3 File2$V4 2200 201 name2 2150 250p5 2200 201 name2 2 100 250p8 2300 301 name3 2 250 350p6 4600 601 name6 4 550 650 p3 Is there any one know how to make R code to achieve this? I thought out a way to use for loop to read for each row in the file1 to compare the whole data frame in file2 to find the mathcing rows but for loop takes so much time. I would like to have a vectorized code to make it faster but I don't know how to manage this. Why not merge on the exact criterion and then subset out the rows that qualify on the logical tests? dfm - merge(File1, File2, 1) subset(dfm, V2.x = V2.y V3.x = V3.y) V1 V2.x V3.x V4.x V2.y V3.y V4.y 2 2 200 201 name2 150 250 p5 4 2 200 201 name2 100 250 p8 6 2 300 301 name3 250 350 p6 12 4 600 601 name6 550 650 p3 -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] contingency tables
Le vendredi 16 mars 2012 à 06:46 -0700, mari681 a écrit : Ok, before I definetly give up, and throw the laptop out of the window, or fill my data.frame manually, I'll ask for some help. I have a data.frame named MyTable with 3 columns, that looks like this: snip The elements on the first column can be: red-j, orange-j, yellow-j, green-j, blue-j or purple-j. Elements on column 2 are contexts in which the color appears. And in column 3 there is a kind of frequency measurement between color and context. I am trying to build a new data.frame where the 6 colors in column 1 are placed as column names, all the unique contexts in column 2 are placed as row names and the values on column 3 are in the correspondent cells (or 0 if an intersection color-context is empty). Easy to prepare the empty data.frame, but I cant find out how to fill it up with the frequencies. Ideas? Anybody has a ready script for this? If I understand correctly, this is very simple using xtabs(). dat - structure(list(V1 = structure(c(5L, 5L, 5L, 5L, 3L, 3L, 3L, 3L, 6L, 6L, 6L, 6L, 6L, 6L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 4L, 4L, 4L, 4L, 4L, 4L, 4L), .Label = c(blue-j, green-j, orange-j, purple-j, red-j, yellow-j), class = factor), V2 = structure(c(1L, 4L, 10L, 12L, 8L, 27L, 29L, 31L, 11L, 18L, 21L, 24L, 25L, 26L, 14L, 15L, 16L, 23L, 17L, 19L, 2L, 3L, 7L, 9L, 13L, 20L, 22L, 5L, 6L, 33L, 28L, 29L, 30L, 32L ), .Label = c(appearanceblood-n, appearancecypress-n, appearancefirmament-n, appearanceground-n, appearanceleave-n, appearancelesion-n, appearanceman-n, appearanceobject-n, appearancerange-n, appearancesea-n, appearanceskin-n, appearancesky-n, appearancesurface-n, appearancewater-n, architecturebuilding-n, architecturecourse-n, areaauditorium-n, areacircle-n, areacity-n, areagraph-n, areainfarction-n, arealibrary-n, areaRio-n, as_adj_ascorn-n, as_adj_asflax-n, as_adj_asgold-n, as_adj_aspainting-n, coloramethyst-n, colorbanknote-n, colorbottle-n, colorcar-n, colorchocolate-n, colorViking-n), class = factor), V3 = c(105.032, 93.749, 102.167, 10.898, 109.354, 93.248, 159.167, 117.985, 109.527, 87.064, 120.759, 219.739, 122.576, 90.814, 91.477, 103.582, 103.325, 106.614, 102.505, 150.005, 145.133, 148.655, 85.731, 90.706, 100.991, 92.708, 77.135, 119.423, 134.287, 145.516, 175.619, 158.045, 132.395, 141.833)), .Names = c(V1, V2, V3), class = data.frame) xtabs(V3 ~ V2 + V1, data=dat) BTW, creating the data frame took me the most time, so please provide a working data set using dput() next time. Regards __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] contingency tables
On Mar 16, 2012, at 9:46 AM, mari681 wrote: Ok, before I definetly give up, and throw the laptop out of the window, or fill my data.frame manually, I'll ask for some help. I have a data.frame named MyTable with 3 columns, that looks like this: V1 V2 V3 red-jappearanceblood-n 105.032 red-j appearanceground-n 93.749 red-j appearancesea-n 102.167 red-j appearancesky-n 10.898 orange-jappearanceobject-n 109.354 orange-jas_adj_aspainting-n 93.248 orange-jcolorbanknote-n 159.167 orange-jcolorcar-n 117.985 yellow-jappearanceskin-n109.527 yellow-jareacircle-n87.064 yellow-jareainfarction-n120.759 yellow-jas_adj_ascorn-n 219.739 yellow-jas_adj_asflax-n 122.576 yellow-jas_adj_asgold-n 90.814 green-j appearancewater-n 91.477 green-j architecturebuilding-n 103.582 green-j architecturecourse-n103.325 green-j areaRio-n 106.614 green-j areaauditorium-n102.505 green-j areacity-n 150.005 blue-j appearancecypress-n 145.133 blue-j appearancefirmament-n 148.655 blue-j appearanceman-n 85.731 blue-j appearancerange-n 90.706 blue-j appearancesurface-n 100.991 blue-j areagraph-n 92.708 blue-j arealibrary-n 77.135 purple-jappearanceleave-n 119.423 purple-jappearancelesion-n 134.287 purple-jcolorViking-n 145.516 purple-jcoloramethyst-n 175.619 purple-jcolorbanknote-n 158.045 purple-jcolorbottle-n 132.395 purple-jcolorchocolate-n141.833 The elements on the first column can be: red-j, orange-j, yellow-j, green-j, blue-j or purple-j. Elements on column 2 are contexts in which the color appears. And in column 3 there is a kind of frequency measurement between color and context. I am trying to build a new data.frame where the 6 colors in column 1 are placed as column names, all the unique contexts in column 2 are placed as row names and the values on column 3 are in the correspondent cells (or 0 if an intersection color-context is empty). Easy to prepare the empty data.frame, but I cant find out how to fill it up with the frequencies. Ideas? Anybody has a ready script for this? ?xtabs aRealTable - xtabs(V3 ~ V1+V2, data=MyTable) -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ROC Analysis
Hi everybody, Pascal, your script works again but I want to calculate the LR otherwise. I know the likelihood ratio is linked at the roc curve and so there are different ways to calculate the LR. The slope of an ROC curve can be defined in three ways: (1) as the tangent at a particular point on the ROC curve corresponding to a test value x (2) as the slope between the origin 0 and the point on the ROC curve corresponding to a test value x (3) as the slope between two points on the ROC curve corresponding to the test values x and y http://r.789695.n4.nabble.com/file/n4478233/LR.png But in my case, I want calculated the LR with the third way. So, LR (x,y) =(sensitivity (x)-sensitivity (y))/(specificity (y)-specificity (x)) = (TPR(x)-TPR (y))/(FPR (x)-FPR (y)) It is possible ?! All the best, Camille - -- Camille Leclerc, Master student Lab ESE, UMR CNRS 8079 Univ Paris-Sud Bat 362 F-91405 Orsay Cedex FRANCE -- View this message in context: http://r.789695.n4.nabble.com/ROC-Analysis-tp4469203p4478233.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] multiple density plot
Hello I am looking for a special plot. Let's suppose I have *100 days and *each day I have a (1D) distribution of the same variable. I would like to plot *dates on x axis and *one distribution per date on the y axe. Do you know a way of doing it ? Cheers -- View this message in context: http://r.789695.n4.nabble.com/multiple-density-plot-tp4478196p4478196.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to start R in maximized size???
Dear all, when I start R, I want that the console window should be in the Maximized size automatically. Can somebody help me how to achieve that? Thanks and regards, __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to start R in maximized size???
On 16/03/2012 10:23 AM, Christofer Bogaso wrote: Dear all, when I start R, I want that the console window should be in the Maximized size automatically. Can somebody help me how to achieve that? If you are working in Windows and starting R by clicking on the shortcut, just change the Run: property of the shortcut. (Right click it, choose properties...) Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] plot columns
Hey guys, can anyone help? i have a sample table: table - structure(c(4, 7, 0.2, 3, .1, 7, 222, 3, 10, 5, 11, 8, 8, 10, 7), .Dim = c(5L, 3L), .Dimnames = list(c(gene1, gene2, gene3, gene4, gene5), c(codon1, codon2, codon3))) table codon1 codon2 codon3 gene14.0 7 11 gene27.0222 8 gene30.2 3 8 gene43.0 10 10 gene50.1 5 7 i want to plot column 1 versus column 3. Does anyone know how to read in particular columns and plot? i was looking at this: https://stat.ethz.ch/pipermail/r-help/2007-July/137638.html but i can't seem to alter it to my needs Thank you Aoife [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] where I can find more color names or color definition?
I found this useful: http://research.stowers-institute.org/efg/R/Color/Chart/ColorChart.pdf HTH, -- David -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of FJ M Sent: Wednesday, March 14, 2012 3:39 PM To: totang...@gmail.com; R Subject: Re: [R] where I can find more color names or color definition? Load package fBasics library(fBasics) colors() should give you what you want. Also helpful are colorTable() colorLocator() Which I found by searching for colors from the R console help menu. Date: Wed, 14 Mar 2012 22:55:39 +0800 From: totang...@gmail.com To: r-help@r-project.org Subject: [R] where I can find more color names or color definition? hi everyone . Now I want to draw several lines in one frame.And it seems needs more colors except for blue red,black .Where can i found these color name or define some new color ?thank you . -- TANG Jie Email: totang...@gmail.com Tel: 0086-2154896104 Shanghai Typhoon Institute,China [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. This e-mail and any materials attached hereto, including, without limitation, all content hereof and thereof (collectively, XR Content) are confidential and proprietary to XR Trading, LLC (XR) and/or its affiliates, and are protected by intellectual property laws. Without the prior written consent of XR, the XR Content may not (i) be disclosed to any third party or (ii) be reproduced or otherwise used by anyone other than current employees of XR or its affiliates, on behalf of XR or its affiliates. THE XR CONTENT IS PROVIDED AS IS, WITHOUT REPRESENTATIONS OR WARRANTIES OF ANY KIND. TO THE MAXIMUM EXTENT PERMISSIBLE UNDER APPLICABLE LAW, XR HEREBY DISCLAIMS ANY AND ALL WARRANTIES, EXPRESS AND IMPLIED, RELATING TO THE XR CONTENT, AND NEITHER XR NOR ANY OF ITS AFFILIATES SHALL IN ANY EVENT BE LIABLE FOR ANY DAMAGES OF ANY NATURE WHATSOEVER, INCLUDING, BUT NOT LIMITED TO, DIRECT, INDIRECT, CONSEQUENTIAL, SPECIAL AND PUNITIVE DAMAGES, LOSS OF PROFITS AND TRADING LOSSES, RESULTING FROM ANY PERSON'S USE OR RELIANCE UPON, OR INABILITY TO USE, ANY XR CONTENT, EVEN IF XR IS ADVISED OF THE POSSIBILITY OF SUCH DAMAGES OR IF SUCH DAMAGES WERE FORESEEABLE. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to start R in maximized size???
No no, I meant to say the console window, where we type the syntax etc. BTW, what is the official name of this window? Thanks, On Fri, Mar 16, 2012 at 8:15 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 16/03/2012 10:23 AM, Christofer Bogaso wrote: Dear all, when I start R, I want that the console window should be in the Maximized size automatically. Can somebody help me how to achieve that? If you are working in Windows and starting R by clicking on the shortcut, just change the Run: property of the shortcut. (Right click it, choose properties...) Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Partial matching when using $ ? Feature or bug?
Sarah Goslee sarah.goslee at gmail.com writes: R: lots of ways to do the same thing, but some of them are booby-trapped. Fortune candidate! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Partial matching when using $ ? Feature or bug?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 16/03/12 15:05, Sarah Goslee wrote: It's also a really good reason to use [[ in functions or anywhere there might be a chance of confusion. Absolutely - I think I have to change my habit. I always prefered using $ as it seemed to me more logical. I started out that way because it's shorter and nicer-looking code, absolutely. but it can cause partial-matching problems, It did just for me... and also LaTeX annoyances in Sweave code. Good to know - I'll keep that in mind. Someday I'll go back through my packages and get rid of all the lingering $. R: lots of ways to do the same thing, but some of them are booby-trapped. Absolutely - but isn't that the fun part of R? Rainer Sarah - -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Stellenbosch University South Africa Tel : +33 - (0)9 53 10 27 44 Cell: +33 - (0)6 85 62 59 98 Fax : +33 - (0)9 58 10 27 44 Fax (D):+49 - (0)3 21 21 25 22 44 email: rai...@krugs.de Skype: RMkrug -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAk9jTCoACgkQoYgNqgF2egp7yQCeJOSxxKSeFjYtCxucxYSj8MtU bbAAni6vsxE7Rm14luVg41tUT34/LcZ+ =Tw5l -END PGP SIGNATURE- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to start R in maximized size???
Duncan's suggestion worked for me. What about it didn't work for you? Kevin On Fri, Mar 16, 2012 at 9:35 AM, Christofer Bogaso bogaso.christo...@gmail.com wrote: No no, I meant to say the console window, where we type the syntax etc. BTW, what is the official name of this window? Thanks, On Fri, Mar 16, 2012 at 8:15 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 16/03/2012 10:23 AM, Christofer Bogaso wrote: Dear all, when I start R, I want that the console window should be in the Maximized size automatically. Can somebody help me how to achieve that? If you are working in Windows and starting R by clicking on the shortcut, just change the Run: property of the shortcut. (Right click it, choose properties...) Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Kevin Wright [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to start R in maximized size???
On 16/03/2012 10:35 AM, Christofer Bogaso wrote: No no, I meant to say the console window, where we type the syntax etc. BTW, what is the official name of this window? I think console window is good enough. Duncan Murdoch Thanks, On Fri, Mar 16, 2012 at 8:15 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 16/03/2012 10:23 AM, Christofer Bogaso wrote: Dear all, when I start R, I want that the console window should be in the Maximized size automatically. Can somebody help me how to achieve that? If you are working in Windows and starting R by clicking on the shortcut, just change the Run: property of the shortcut. (Right click it, choose properties...) Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to start R in maximized size???
But unfortunately it did not work for me. I am using R-2.14.2 with windows 7 home basic Thanks, On Fri, Mar 16, 2012 at 8:26 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 16/03/2012 10:35 AM, Christofer Bogaso wrote: No no, I meant to say the console window, where we type the syntax etc. BTW, what is the official name of this window? I think console window is good enough. Duncan Murdoch Thanks, On Fri, Mar 16, 2012 at 8:15 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 16/03/2012 10:23 AM, Christofer Bogaso wrote: Dear all, when I start R, I want that the console window should be in the Maximized size automatically. Can somebody help me how to achieve that? If you are working in Windows and starting R by clicking on the shortcut, just change the Run: property of the shortcut. (Right click it, choose properties...) Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plot columns
plot(codon3 ~ codon1, data = table) should work but I'm not in a position to verify. If for some reason it doesn't does plot(codon3 ~ codon1, data = as.data.frame(table)) get it? Michael On Mar 16, 2012, at 10:32 AM, aoife doherty aoife.m.dohe...@gmail.com wrote: Hey guys, can anyone help? i have a sample table: table - structure(c(4, 7, 0.2, 3, .1, 7, 222, 3, 10, 5, 11, 8, 8, 10, 7), .Dim = c(5L, 3L), .Dimnames = list(c(gene1, gene2, gene3, gene4, gene5), c(codon1, codon2, codon3))) table codon1 codon2 codon3 gene14.0 7 11 gene27.0222 8 gene30.2 3 8 gene43.0 10 10 gene50.1 5 7 i want to plot column 1 versus column 3. Does anyone know how to read in particular columns and plot? i was looking at this: https://stat.ethz.ch/pipermail/r-help/2007-July/137638.html but i can't seem to alter it to my needs Thank you Aoife [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Timer on a function
From: Prof Brian Ripley [mailto:rip...@stats.ox.ac.uk]
Using setTimeLimit(transient = TRUE) is slightly simpler here.
Brian,
I thought I should have been able to use transient=TRUE instead of the
on.exit(setTimeLimit()) but that gave me an unwanted error report after
the top-level expression finished (if there was no timeout). E.g.,
to - function(expr, ...) {
+ setTimeLimit(..., transient=TRUE)
+ expr
+ }
f - function(n) sum(sapply(seq_len(n), function(i)1/i)) - log(n)
to(f(1e7), elapsed=1)
Error in FUN(1:1000[[371022L]], ...) : reached elapsed time limit
to(f(1e2), elapsed=1)
[1] 0.5822073
Error: reached elapsed time limit
sessionInfo()
R version 2.14.2 (2012-02-29)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
(On a new 64-bit Windows 7 PC)
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-Original Message-
From: Prof Brian Ripley [mailto:rip...@stats.ox.ac.uk]
Sent: Friday, March 16, 2012 4:28 AM
To: Bert Gunter
Cc: William Dunlap; r-help@r-project.org; Ramiro Barrantes
Subject: Re: [R] Timer on a function
On Thu, 15 Mar 2012, Bert Gunter wrote:
Bill et. al:
1. This is new to me. Thanks.
2. As I read the man page, this is not guaranteed to work if the model
fitting function does not contain sufficient interrupts. Is that
correct?
Yes. If someone wrote a model fitting package in Fortran with no
callbacks then it is not interruptible, including not by timers. In
that case all you can do is to kill the R session.
The author of setTimeLimit()
-- Bert
On Thu, Mar 15, 2012 at 4:14 PM, William Dunlap wdun...@tibco.com wrote:
There is a setTimeLimit function in base. It could be encapsulated into
the following to limit the time spent on an expression:
timeOut - function (expr, ...) {
on.exit(setTimeLimit())
setTimeLimit(...)
expr
}
Using setTimeLimit(transient = TRUE) is slightly simpler here.
E.g., with the following slow way to compute Euler's phi
f - function(n) sum(sapply(seq_len(n), function(i)1/i)) - log(n)
I get
timeOut(f(1e5), elapsed=1)
[1] 0.5772207
timeOut(f(1e6), elapsed=1)
Error in FUN(1:100[[711624L]], ...) : reached elapsed time limit
Use try() or tryCatch() to check for the error. E.g.,
sapply(1:7, function(n)tryCatch(timeOut(f(10^n), elapsed=1),
error=function(e)-1))
[1] 0.6263832 0.5822073 0.5777156 0.5772657 0.5772207 -1.000
-1.000
You could look at 'e' in the error handler to see if it is a time out
problem.
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On
Behalf
Of Bert Gunter
Sent: Thursday, March 15, 2012 3:05 PM
To: Ramiro Barrantes
Cc: r-help@r-project.org
Subject: Re: [R] Timer on a function
On Thu, Mar 15, 2012 at 2:24 PM, Ramiro Barrantes
ram...@precisionbioassay.com wrote:
Hello,
I have a program that consists of a loop fitting a function over many
models. Sometimes the fitting on a particular model takes minutes to
converge. Is
there
a way that I can limit the amount of time that R spends on a given model:
AFAIK, no -- this is an OS level issue.
Of course, most iterative fitting procedures have controls for the
number of iterations, convergence criteria, etc. , but there is no
awareness of timing except when the OS is interrogated, e.g. by
?proc.time or ?system.time . Such calls would have to be built into
the fitting function or OS level services would have to be invoked to
run the R process with timing limitations built in. See e.g. ?Rscript
for one possible approach.
Corrections or clever tricks to get around these perceived limitations
welcomed, of course.
-- Bert
Cheers,
Bert
say if my line is:
fittingFunction( func, model.1)
can I have some function:
stopIfUnderTime( fittingFunction( func, model.1) , 5 )
where stopIfUnderTime will return the result if it finishes under 5
seconds, or NA
otherwise.
Is there anything like this? (just looked through the web but did not
find anything)
Thanks,
Ramiro
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Bert Gunter
Genentech Nonclinical Biostatistics
Internal Contact Info:
Phone: 467-7374
Website:
Re: [R] Re : Elegant Code
Wonder if this is part of some assignment with points on elegance
of code. Sort of when I teach a class..
On Fri, 16 Mar 2012 10:02:48 -0400 Raphael Fraser
raphael.fra...@gmail.com wrote:
Thank you all. Your responses were very helpful.
Raphael
On Fri, Mar 16, 2012 at 5:04 AM, Daniel Nordlund
djnordl...@frontier.com wrote:
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf Of Pascal Oettli
Sent: Friday, March 16, 2012 12:36 AM
To: Raphael Fraser
Cc: r-help@r-project.org
Subject: [R] Re : Elegant Code
Hi Raphael,
Something like that?
require(pscl)sim - numeric()
for(i in 1:5){
eval(parse(text=paste('b',i,' - rigamma(50,1,1)',sep='')))
eval(parse(text=paste('theta',i,' -
rgamma(50,0.5,(1/b',i,'))',sep='')))
eval(parse(text=paste('sim',i,' - rpois(50,theta',1,')',sep='')))
eval(parse(text=paste('sim - cbind(sim, sim',i,')',sep='')))
}
x11()
par(mfrow=c(1,5))
boxplot(c(sim1,sim2,sim3,sim4,sim5))
x11()
boxplot(sim)
Regards,
Pascal
- Mail original -
De : Raphael Fraser raphael.fra...@gmail.com
À : r-help@r-project.org
Cc :
Envoyé le : Vendredi 16 mars 2012 16h09
Objet : [R] Elegant Code
Hi,
Can anyone help to write a more elegant version of my code? I am sure
this can be put into a loop but I am having trouble creating the
objects b1,b2,b3,...,etc.
b1 - rigamma(50,1,1)
theta1 - rgamma(50,0.5,(1/b1))
sim1 - rpois(50,theta1)
b2 - rigamma(50,1,1)
theta2 - rgamma(50,0.5,(1/b2))
sim2 - rpois(50,theta2)
b3 - rigamma(50,1,1)
theta3 - rgamma(50,0.5,(1/b3))
sim3 - rpois(50,theta3)
b4 - rigamma(50,1,1)
theta4 - rgamma(50,0.5,(1/b4))
sim4 - rpois(50,theta4)
b5 - rigamma(50,1,1)
theta5 - rgamma(50,0.5,(1/b5))
sim5 - rpois(50,theta5)
par(mfrow=c(1,5))
boxplot(sim1)
boxplot(sim2)
boxplot(sim3)
boxplot(sim4)
boxplot(sim5);
Thanks,
Raphael
Or, just get rid of the for loops altogether, something like this
trials -5
N - 50
b - rigamma(N*trials, 1, 1)
theta - rgamma(N*trials,0.5,1/b)
sim - rpois(N*trials,theta)
dim(sim) - c(N,trials)
boxplot(sim)
Hope this is helpful,
Dan
Daniel Nordlund
Bothell, WA USA
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Singleton pattern
Since no one else has bit, I'll take a stab. I'm an experienced R person, but I've recently been teaching myself objective-c and I've been using singletons quite a bit (and mis-using them quite a bit!). Not a computer scientist at all. You've been warned. I don't think there is a comparable concept in R. You do have a choice of S3 or S4 classes for your object orientation in R. S3 is very loose in that you can add to S3 objects readily and abuse them a lot. There really is no checking of them unless you implement it manually. S4 objects are much tighter and they are less readily modified and are self-checking (I know some will complain about this characterization but it's approximately correct). So perhaps you want an S4 object so it's less likely to get mangled, but I doubt there is a way to prevent users from copying it, which would be more along the lines of a singleton. You can google the archives for some great discussions of S3 vs S4 if that sounds interesting. Bryan *** Bryan Hanson Professor of Chemistry Biochemistry DePauw University On Mar 16, 2012, at 7:47 AM, David Cassany wrote: Hi all, I know it may not have much sense thinking about a Singleton Pattern in an R application which doesn't use any OOP facilities, however I'm curious to know if anybody faced the same issue. I've been googling but using singleton pattern as a key word leads to typical OOP languages like Java or C++ among others. So my problem is that I'd like to ensure some very big objects aren't copied again and again in some other variables. In the worst case I'll check all code by myself to ensure it but in this case the application won't force programmers to take it in consideration which is what I am really looking for. Any advice will be highly appreciated :P Thanks! -- *David Cassany Viladomat Software Developer Transmural Biote**ch S.L* [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem reading mixed CSV file
What do you mean by Mixed? If a field has a comma, then it is supposed be to enclosed in quotes. You could preprocess the file looking for cases where there are more fields than there there are supposed to be, and if they are always in the same place, you could enclose them in quotes and then reprocess. You would really have to show what the file looks like for the different mixed cases to get a good answer to your question. And of course, R can do it, if we knew what it was we are supposed to do. So at least provide commented, minimal, self-contained, reproducible code and data. On Fri, Mar 16, 2012 at 7:03 AM, Ashish Agarwal ashish.agarw...@gmail.com wrote: I am having trouble reading this CSV file in R. There are six attributes that I need to read - CVar1, CVar2, Location, Year, Nvar3, Nvar4. Can somebody help in reading this file? On line 10 it has city and state separated by comma. I had been a user of SAS where I can use different format to read in for this line. Can I do this in R too? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Data Munger Guru What is the problem that you are trying to solve? Tell me what you want to do, not how you want to do it. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Faster way to implement this search?
I am working on a simulation where I need to count the number of matches for an arbitrary pattern in a large sequence of binomial factors. My current code is for(indx in 1:(length(bin.05)-3)) if ((bin.05[indx] == test.pattern[1]) (bin.05[indx+1] == test.pattern[2]) (bin.05[indx+2] == test.pattern[3])) return.values$count.match.pattern[1] = return.values$count.match.pattern[1] + 1 Since I am running the above code for each simulation multiple times on sequences of 10,000,000 factors the code is taking longer than I would like. Is there a better (more R way of achieving the same answer? Walter Anderson __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] quadprog error?
I forgot to attach the problem data, 'quadprog.Rdata' file, in my prior email. I want to report a following error with quadprog. The solve.QP function finds a solution to the problem below that violates the last equality constraint. I tried to solve the same problem using ipop from kernlab package and get the solution in which all equality constraints are enforced. I also tried an old version of quadprog, Version: 1.4-11, Date: 2007-07-12 and my problem is solved correctly. I have tried to contact Berwin A. Turlach berwin.turl...@gmail.com (maintainer for quadprog package) a week ago, with no success. ## load(file='quadprog.Rdata') # solve QP using quadprog require(quadprog) sol = solve.QP(Dmat, dvec, Amat, bvec, meq) x = sol$solution check = x %*% Amat - bvec # for some reason last equality constraint is violated round(check[1:meq], 4) # solve QP using kernlab require(kernlab) n = nrow(Amat) sv = ipop(c = matrix(dvec), H = Dmat, A = t(Amat[,1:meq]), b = bvec[1:meq], l = rep(-1000, n), u = rep(1000, n), r = rep(0,meq)) x = primal(sv) check = x %*% Amat - bvec # all constraints are ok round(check[1:meq], 4) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Singleton pattern
David Cassany david.cassany at transmuralbiotech.com writes: Hi all, I know it may not have much sense thinking about a Singleton Pattern in an R application which doesn't use any OOP facilities, however I'm curious to know if anybody faced the same issue. I've been googling but using singleton pattern as a key word leads to typical OOP languages like Java or C++ among others. While it isn't too hard to implement the Singleton pattern using reference classes, I would think for what you want to do the memoise package can be used. Create a wrapper function to return the objects and the cached value will be returned each time. So my problem is that I'd like to ensure some very big objects aren't copied again and again in some other variables. In the worst case I'll check all code by myself to ensure it but in this case the application won't force programmers to take it in consideration which is what I am really looking for. Any advice will be highly appreciated :P Thanks! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Singleton pattern
Using the singleton pattern in R has never occurred to me so far, as I think it applies to languages that support multiple references to one instance. R doesn't do that, at least not in ways that would be required for applying the singleton pattern as described in the GoF book, anyway. One would have to use closures and / or environments to approximate references, I suppose. When passed around as parameters, R objects don't get copied unless the called function starts modifying them, so if the primary concern is to prevent unnecessary / costly copying of bulky objects, creating the thing once and then passing it around as necessary, taking care that called functions don't change it, is perhaps good enough. Best regards, Jan On Fri, Mar 16, 2012 at 12:15:27PM -0400, Bryan Hanson wrote: Since no one else has bit, I'll take a stab. I'm an experienced R person, but I've recently been teaching myself objective-c and I've been using singletons quite a bit (and mis-using them quite a bit!). Not a computer scientist at all. You've been warned. I don't think there is a comparable concept in R. You do have a choice of S3 or S4 classes for your object orientation in R. S3 is very loose in that you can add to S3 objects readily and abuse them a lot. There really is no checking of them unless you implement it manually. S4 objects are much tighter and they are less readily modified and are self-checking (I know some will complain about this characterization but it's approximately correct). So perhaps you want an S4 object so it's less likely to get mangled, but I doubt there is a way to prevent users from copying it, which would be more along the lines of a singleton. You can google the archives for some great discussions of S3 vs S4 if that sounds interesting. Bryan *** Bryan Hanson Professor of Chemistry Biochemistry DePauw University On Mar 16, 2012, at 7:47 AM, David Cassany wrote: Hi all, I know it may not have much sense thinking about a Singleton Pattern in an R application which doesn't use any OOP facilities, however I'm curious to know if anybody faced the same issue. I've been googling but using singleton pattern as a key word leads to typical OOP languages like Java or C++ among others. So my problem is that I'd like to ensure some very big objects aren't copied again and again in some other variables. In the worst case I'll check all code by myself to ensure it but in this case the application won't force programmers to take it in consideration which is what I am really looking for. Any advice will be highly appreciated :P Thanks! -- *David Cassany Viladomat Software Developer Transmural Biote**ch S.L* [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- +- Jan T. Kim ---+ | email: jtt...@gmail.com| | WWW: http://www.jtkim.dreamhosters.com/ | *-= hierarchical systems are for files, not for humans =-* __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] a question about writing C extensions to functions
Dear R People: I'm not sure if I should ask this here or in Rcpp, but I thought I'd start here first. If I'm writing a C program, when do I know to use SEXP vs. int or float, please? Thanks, Erin -- Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: erinm.hodg...@gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] bias sampling
hi i want to analyze Right Censore-Length bias data under cox model with covariate. what is the package ? tank you. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem reading mixed CSV file
I want to import this CSV file into R. The CSV file is ,,,1968,21,0 ,,Boston,1968,13,0 ,,Boston,1968,18,0 ,,Chicago,1967,44,0 ,,Providence,1968,17,0 ,,Providence,1969,48,0 ,,Binky,1968,24,0 ,,Chicago,1968,23,0 ,,Dally,1968,7,0 ,,Raleigh, North Carol,1968,25,0 Addy ABC-Dogs Stars-W8.1,,Providence,1968,38,0 DEF_REQPRF/,,Dartmouth,1967,31,1 PL,,,1967,38,1 XY,PopatLal,,1967,5,1 XY,PopatLal,,1967,6,8 XY,PopatLal,,1967,7,7 XY,PopatLal,,1967,9,1 XY,PopatLal,,1967,10,1 XY,PopatLal,,1967,13,1 XY,PopatLal,Boston,1967,6,1 XY,PopatLal,Boston,1967,7,11 XY,PopatLal,Boston,1967,9,2 XY,PopatLal,Boston,1967,10,3 XY,PopatLal,Boston,1967,7,2 I tried using scan and read.table but results are not visible :( scan(D:/data/temp.csv,list(,,,0,0,0),sep=,) -x Read 51 records x [[1]] [1] ÿþ [16] [31] [46] read.table(D:/data/temp.csv,header=F,sep=,) -x x V1 V2 1 ÿþ NA 2 NA 3 NA 4 NA Can somebody please help in importing this CSV file? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] quadprog error?
On Mar 16, 2012, at 12:20 PM, none wrote: I forgot to attach the problem data, 'quadprog.Rdata' file, in my prior email. Please read the Posting Guide's description of what kind of attachments the mail-server will accept. -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Faster way to implement this search?
There's almost certainly a better way, but I'd be more inclined to look for it if you'd provide a small reproducible example so I could actually try it. Without knowing the structure of your data, it's very hard to offer alternatives. Sarah On Fri, Mar 16, 2012 at 12:59 PM, Walter Anderson wandrso...@gmail.com wrote: I am working on a simulation where I need to count the number of matches for an arbitrary pattern in a large sequence of binomial factors. My current code is for(indx in 1:(length(bin.05)-3)) if ((bin.05[indx] == test.pattern[1]) (bin.05[indx+1] == test.pattern[2]) (bin.05[indx+2] == test.pattern[3])) return.values$count.match.pattern[1] = return.values$count.match.pattern[1] + 1 Since I am running the above code for each simulation multiple times on sequences of 10,000,000 factors the code is taking longer than I would like. Is there a better (more R way of achieving the same answer? Walter Anderson -- Sarah Goslee http://www.functionaldiversity.org __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem reading mixed CSV file
On Mar 16, 2012, at 1:11 PM, Ashish Agarwal wrote: I want to import this CSV file into R. The CSV file is ,,,1968,21,0 ,,Boston,1968,13,0 ,,Boston,1968,18,0 ,,Chicago,1967,44,0 ,,Providence,1968,17,0 ,,Providence,1969,48,0 ,,Binky,1968,24,0 ,,Chicago,1968,23,0 ,,Dally,1968,7,0 ,,Raleigh, North Carol,1968,25,0 Addy ABC-Dogs Stars-W8.1,,Providence,1968,38,0 DEF_REQPRF/,,Dartmouth,1967,31,1 PL,,,1967,38,1 XY,PopatLal,,1967,5,1 XY,PopatLal,,1967,6,8 XY,PopatLal,,1967,7,7 XY,PopatLal,,1967,9,1 XY,PopatLal,,1967,10,1 XY,PopatLal,,1967,13,1 XY,PopatLal,Boston,1967,6,1 XY,PopatLal,Boston,1967,7,11 XY,PopatLal,Boston,1967,9,2 XY,PopatLal,Boston,1967,10,3 XY,PopatLal,Boston,1967,7,2 I tried using scan and read.table but results are not visible :( scan(D:/data/temp.csv,list(,,,0,0,0),sep=,) -x Read 51 records x [[1]] [1] ÿþ [16] [31] [46] read.table(D:/data/temp.csv,header=F,sep=,) -x x V1 V2 1 ÿþ NA 2 NA 3 NA 4 NA Can somebody please help in importing this CSV file? Looks like an encoding mismatch. You have not offered the requested information about you setup so further comment would all be guesswork. But you can perhaps educate yourself by reading: ?Encoding And line ten has 7 elements. count.fields(textConnection(,,,1968,21,0 + ,,Boston,1968,13,0 + ,,Boston,1968,18,0 + ,,Chicago,1967,44,0 + ,,Providence,1968,17,0 + ,,Providence,1969,48,0 + ,,Binky,1968,24,0 + ,,Chicago,1968,23,0 + ,,Dally,1968,7,0 + ,,Raleigh, North Carol,1968,25,0 + Addy ABC-Dogs Stars-W8.1,,Providence,1968,38,0 + DEF_REQPRF/,,Dartmouth,1967,31,1 + PL,,,1967,38,1 + XY,PopatLal,,1967,5,1 + XY,PopatLal,,1967,6,8 + XY,PopatLal,,1967,7,7 + XY,PopatLal,,1967,9,1 + XY,PopatLal,,1967,10,1 + XY,PopatLal,,1967,13,1 + XY,PopatLal,Boston,1967,6,1 + XY,PopatLal,Boston,1967,7,11 + XY,PopatLal,Boston,1967,9,2 + XY,PopatLal,Boston,1967,10,3 + XY,PopatLal,Boston,1967,7,2),sep=,) [1] 6 6 6 6 6 6 6 6 6 7 6 6 6 6 6 6 6 6 6 6 6 6 6 6 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Faster way to implement this search?
You didn't show your complete code but the following may help you speed things
up.
Compare a function, f0, structured like your code and one, f1, that calls sum
once
instead of counting length(x)-3 times.
f0 - function(x, test.pattern) {
count - 0
for(indx in seq_len(length(x)-3)) {
if ((x[indx] == test.pattern[1]) (x[indx+1] == test.pattern[2])
(x[indx+2] == test.pattern[3])) {
count - count + 1
}
}
count
}
f1 - function(x, test.pattern) {
indx - seq_len(length(x)-3)
sum((x[indx] == test.pattern[1]) (x[indx+1] == test.pattern[2])
(x[indx+2] == test.pattern[3]))
}
bin.05 - round((log10(1:1000)%%1e-3 - log10(1:1000)%%1e-4) * 1e4) #
quasi-random sample of 10^7 from {0,...,9}
system.time(print(f0(bin.05, c(2,3,3
[1] 3194
user system elapsed
14.350.00 14.35
system.time(print(f1(bin.05, c(2,3,3
[1] 3194
user system elapsed
0.700.210.90
You are probably also slowing things down by doing
yourList$yourCounts[1] - yourList$yourCounts[1] + 1
many times instead of
count - yourList$yourCounts[1]
once and
count - count + 1
many times. The former evaluates $, [, $-, and [- many
times and the $- and [- in particular may use a fair bit of time.
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf
Of Walter Anderson
Sent: Friday, March 16, 2012 10:00 AM
To: R Help
Subject: [R] Faster way to implement this search?
I am working on a simulation where I need to count the number of matches
for an arbitrary pattern in a large sequence of binomial factors. My
current code is
for(indx in 1:(length(bin.05)-3))
if ((bin.05[indx] == test.pattern[1]) (bin.05[indx+1] ==
test.pattern[2]) (bin.05[indx+2] == test.pattern[3]))
return.values$count.match.pattern[1] =
return.values$count.match.pattern[1] + 1
Since I am running the above code for each simulation multiple times on
sequences of 10,000,000 factors the code is taking longer than I would
like. Is there a better (more R way of achieving the same answer?
Walter Anderson
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Changing axis labels depending on panel in lattice
Hello,
I am lattice scatterplot that has 2 panels (could be a few more). Both
panels have a y-axis label that is different on the
left and right sides. However the right hand side axis labelling depends on
which panel i'm in .
(I am plotting two curves in one panel, the left y-axis has the scale for
the red line and the right y-axis has the scale for the blue line
I need to convert the y-lims for blue to the scales of the red line. Since
the scales depend on the panel, all i need to know
is which panel i'm in.)
Im using ,axis=axis.PCT in xyplot and right now
axis.PCT-
function(side, ...)
{
ylim - current.panel.limits()$ylim
switch(side,
left = {
prettyF - pretty(ylim)
panel.axis(side = side, outside = TRUE,text.cex=0.5,rot=0,
at = prettyF, labels = prettyF)
},
axis.default(side = side, ...))
Is there anything i can do get the information regarding the panel i'm in?
Regards
Saptarshi
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Changing axis labels depending on panel in lattice
On Mar 16, 2012, at 1:34 PM, Saptarshi Guha wrote:
Hello,
I am lattice scatterplot that has 2 panels (could be a few more). Both
panels have a y-axis label that is different on the
left and right sides. However the right hand side axis labelling
depends on
which panel i'm in .
(I am plotting two curves in one panel, the left y-axis has the
scale for
the red line and the right y-axis has the scale for the blue line
I need to convert the y-lims for blue to the scales of the red line.
Since
the scales depend on the panel, all i need to know
is which panel i'm in.)
Im using ,axis=axis.PCT in xyplot and right now
axis.PCT-
function(side, ...)
{
ylim - current.panel.limits()$ylim
switch(side,
left = {
prettyF - pretty(ylim)
panel.axis(side = side, outside =
TRUE,text.cex=0.5,rot=0,
at = prettyF, labels = prettyF)
},
axis.default(side = side, ...))
Is there anything i can do get the information regarding the panel
i'm in?
?panel.number
--
David Winsemius, MD
West Hartford, CT
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem reading mixed CSV file
Line 10 has City and State that too separated by comma. For line 10 how can I read differently as compared to the other lines? On Fri, Mar 16, 2012 at 10:59 PM, David Winsemius dwinsem...@comcast.net wrote: On Mar 16, 2012, at 1:11 PM, Ashish Agarwal wrote: I want to import this CSV file into R. The CSV file is ,,,1968,21,0 ,,Boston,1968,13,0 ,,Boston,1968,18,0 ,,Chicago,1967,44,0 ,,Providence,1968,17,0 ,,Providence,1969,48,0 ,,Binky,1968,24,0 ,,Chicago,1968,23,0 ,,Dally,1968,7,0 ,,Raleigh, North Carol,1968,25,0 Addy ABC-Dogs Stars-W8.1,,Providence,1968,38,0 DEF_REQPRF/,,Dartmouth,1967,31,1 PL,,,1967,38,1 XY,PopatLal,,1967,5,1 XY,PopatLal,,1967,6,8 XY,PopatLal,,1967,7,7 XY,PopatLal,,1967,9,1 XY,PopatLal,,1967,10,1 XY,PopatLal,,1967,13,1 XY,PopatLal,Boston,1967,6,1 XY,PopatLal,Boston,1967,7,11 XY,PopatLal,Boston,1967,9,2 XY,PopatLal,Boston,1967,10,3 XY,PopatLal,Boston,1967,7,2 I tried using scan and read.table but results are not visible :( scan(D:/data/temp.csv,list(,,,0,0,0),sep=,) -x Read 51 records x [[1]] [1] ÿþ [16] [31] [46] read.table(D:/data/temp.csv,header=F,sep=,) -x x V1 V2 1 ÿþ NA 2 NA 3 NA 4 NA Can somebody please help in importing this CSV file? Looks like an encoding mismatch. You have not offered the requested information about you setup so further comment would all be guesswork. But you can perhaps educate yourself by reading: ?Encoding And line ten has 7 elements. count.fields(textConnection(,,,1968,21,0 + ,,Boston,1968,13,0 + ,,Boston,1968,18,0 + ,,Chicago,1967,44,0 + ,,Providence,1968,17,0 + ,,Providence,1969,48,0 + ,,Binky,1968,24,0 + ,,Chicago,1968,23,0 + ,,Dally,1968,7,0 + ,,Raleigh, North Carol,1968,25,0 + Addy ABC-Dogs Stars-W8.1,,Providence,1968,38,0 + DEF_REQPRF/,,Dartmouth,1967,31,1 + PL,,,1967,38,1 + XY,PopatLal,,1967,5,1 + XY,PopatLal,,1967,6,8 + XY,PopatLal,,1967,7,7 + XY,PopatLal,,1967,9,1 + XY,PopatLal,,1967,10,1 + XY,PopatLal,,1967,13,1 + XY,PopatLal,Boston,1967,6,1 + XY,PopatLal,Boston,1967,7,11 + XY,PopatLal,Boston,1967,9,2 + XY,PopatLal,Boston,1967,10,3 + XY,PopatLal,Boston,1967,7,2),sep=,) [1] 6 6 6 6 6 6 6 6 6 7 6 6 6 6 6 6 6 6 6 6 6 6 6 6 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] summing transfers
I just want the weighted sum of all the cases where either route is found in VEHx and the other is found in the previous or subsequent variable. The only examples I can think of producing are the following: # OBDataSumm - read.spss(P:/Data/OBSurveys/OBSurvey-2010-2011/Final Delivery, Metro On-Board O-D Survey/LAMTA_OD_WEIGHTED_DATA_SETS_012512/LAMTA_OD_SUMMARY_WEIGHTED_012512.SAV, use.value.labels=TRUE, trim_values = TRUE, trim.factor.names = TRUE, max.value.labels=Inf, to.data.frame=TRUE) Warning message: In read.spss(P:/Data/OBSurveys/OBSurvey-2010-2011/Final Delivery, Metro On-Board O-D Survey/LAMTA_OD_WEIGHTED_DATA_SETS_012512/LAMTA_OD_SUMMARY_WEIGHTED_012512.SAV, : P:/Data/OBSurveys/OBSurvey-2010-2011/Final Delivery, Metro On-Board O-D Survey/LAMTA_OD_WEIGHTED_DATA_SETS_012512/LAMTA_OD_SUMMARY_WEIGHTED_012512.SAV: Unrecognized record type 7, subtype 18 encountered in system file describe(OBDataSumm,num.desc=c(mean,median,var,sd,valid.n),xname=NA,maxfac=10,show.pc=TRUE) Description of OBDataSumm Numeric meanmedian varsd valid.n SAMPN2.155e+05 1.733e+05 1.151e+10 1.073e+05 3.378e+04 ~snip~ expfactor1.168 1.0890.19750. 3.378e+04 expwgt 41.93 22.22 7720 87.87 3.378e+04 ltfactor0.6339 0.5 0.081280.2851 3.378e+04 ltweight 26.7 12.42 4473 66.88 3.378e+04 Factor ~snip~ VEH1 Value Count Percent MT-802 1645 4.87 MT-801 1211 3.58 MT-804 975 2.89 MT-803 568 1.68 MT-.51 510 1.51 MT-720 460 1.36 MT-.60 433 1.28 MT-.18 409 1.21 MT-.81 396 1.17 MT-805 396 1.17 mode = MT-802 Valid n = 33782 467 categories - only first 10 shown VEH2 Value Count Percent 1214235.94 MT-802 2304 6.82 MT-801 1375 4.07 MT-803 874 2.59 MT-804 598 1.77 MT-901 527 1.56 MT-805 461 1.36 MT-720 323 0.96 MT-910 268 0.79 MT-207 260 0.77 mode = Valid n = 33782 379 categories - only first 10 shown VEH3 Value Count Percent 2579576.36 MT-802 883 2.61 MT-801 600 1.78 MT-901 256 0.76 MT-803 251 0.74 MT-804 227 0.67 MT-805 126 0.37 MT-224 114 0.34 MT-720 113 0.33 MT-204 105 0.31 mode = Valid n = 33782 378 categories - only first 10 shown VEH4 Value Count Percent 3153293.34 MT-801 126 0.37 MT-802 111 0.33 MT-901 89 0.26 MT-804 74 0.22 MT-803 71 0.21 MT-224 38 0.11 MT-741 36 0.11 MT-.60 34 0.1 MT-207 33 0.1 mode = Valid n = 33782 321 categories - only first 10 shown VEH5 Value Count Percent ...3327098.48 MT-803 ... 18 0.05 MT-802 ... 13 0.04 MT-233 ... 11 0.03 MT-741 ... 11 0.03 MT-804 ... 11 0.03 MT-234 ... 10 0.03 MT-801 ...9 0.03 MT-901 ...9 0.03 MT-.60 ...8 0.02 mode = Valid n = 33782 187 categories - only first 10 shown VEH6 Value Count Percent ...3370099.76 MT-232 ...3 0.01 MT-741 ...3 0.01 MT-802
Re: [R] Problem reading mixed CSV file
On 2012-03-16 10:48, Ashish Agarwal wrote: Line 10 has City and State that too separated by comma. For line 10 how can I read differently as compared to the other lines? Edit the file and put quotes around the city-state combination: Raleigh, North Carol Also: always run count.fields() on your files before importing. Peter Ehlers On Fri, Mar 16, 2012 at 10:59 PM, David Winsemius dwinsem...@comcast.net wrote: On Mar 16, 2012, at 1:11 PM, Ashish Agarwal wrote: I want to import this CSV file into R. The CSV file is ,,,1968,21,0 ,,Boston,1968,13,0 ,,Boston,1968,18,0 ,,Chicago,1967,44,0 ,,Providence,1968,17,0 ,,Providence,1969,48,0 ,,Binky,1968,24,0 ,,Chicago,1968,23,0 ,,Dally,1968,7,0 ,,Raleigh, North Carol,1968,25,0 Addy ABC-Dogs Stars-W8.1,,Providence,1968,38,0 DEF_REQPRF/,,Dartmouth,1967,31,1 PL,,,1967,38,1 XY,PopatLal,,1967,5,1 XY,PopatLal,,1967,6,8 XY,PopatLal,,1967,7,7 XY,PopatLal,,1967,9,1 XY,PopatLal,,1967,10,1 XY,PopatLal,,1967,13,1 XY,PopatLal,Boston,1967,6,1 XY,PopatLal,Boston,1967,7,11 XY,PopatLal,Boston,1967,9,2 XY,PopatLal,Boston,1967,10,3 XY,PopatLal,Boston,1967,7,2 I tried using scan and read.table but results are not visible :( scan(D:/data/temp.csv,list(,,,0,0,0),sep=,) -x Read 51 records x [[1]] [1] ÿþ [16] [31] [46] read.table(D:/data/temp.csv,header=F,sep=,) -x x V1 V2 1 ÿþ NA 2 NA 3 NA 4 NA Can somebody please help in importing this CSV file? Looks like an encoding mismatch. You have not offered the requested information about you setup so further comment would all be guesswork. But you can perhaps educate yourself by reading: ?Encoding And line ten has 7 elements. count.fields(textConnection(,,,1968,21,0 + ,,Boston,1968,13,0 + ,,Boston,1968,18,0 + ,,Chicago,1967,44,0 + ,,Providence,1968,17,0 + ,,Providence,1969,48,0 + ,,Binky,1968,24,0 + ,,Chicago,1968,23,0 + ,,Dally,1968,7,0 + ,,Raleigh, North Carol,1968,25,0 + Addy ABC-Dogs Stars-W8.1,,Providence,1968,38,0 + DEF_REQPRF/,,Dartmouth,1967,31,1 + PL,,,1967,38,1 + XY,PopatLal,,1967,5,1 + XY,PopatLal,,1967,6,8 + XY,PopatLal,,1967,7,7 + XY,PopatLal,,1967,9,1 + XY,PopatLal,,1967,10,1 + XY,PopatLal,,1967,13,1 + XY,PopatLal,Boston,1967,6,1 + XY,PopatLal,Boston,1967,7,11 + XY,PopatLal,Boston,1967,9,2 + XY,PopatLal,Boston,1967,10,3 + XY,PopatLal,Boston,1967,7,2),sep=,) [1] 6 6 6 6 6 6 6 6 6 7 6 6 6 6 6 6 6 6 6 6 6 6 6 6 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] eigenvalues of matrices of partial derivatives with ryacas
Dear Gabor,
Thank you so much for your help! Your suggested code worked!
I have a couple of questions. I'm trying to understand your code so I
can use it in future programming needs. First, my understanding of the
first line of your code is that it creates an R function EigenValues
that corresponds to the Yacas function of the same name:
EigenValues - function(x) Sym(EigenValues(, x, ))
The x variable is kind of a place holder for the product of the
matrices for which I want the eigenvalues, correct? Can you explain the
use of the two sets of quotes in the Sym function? Why does the x have
to be outside quotes and why did you include the commas on either side
of the x?
Second, the term xx^2 appears in the result of the eigenvalue call.
If I ignore this term, this answer is equivalent to the answer I get in
Mathematica. How should I interpret this term, since x only appears in
the EigenValue R function and is not part of my model?
Finally, I am using TinnR 2.3.6.3 as an R-GUI. When I'm using Ryacas
functions, I can send single lines of code to R via TinnR, but I get the
following error message when I send multiple lines of code:
source(.trPaths[4], echo=TRUE, max.deparse.length=150)
Error in srcfilecopy(filename, lines, file.info(filename)[1, mtime]) :
unused argument(s) (file.info(filename)[1, mtime])
Any thoughts on what the problem might be and how to troubleshoot it?
Thanks again for your help!
Adam
On 3/15/2012 5:16 PM, Gabor Grothendieck wrote:
On Thu, Mar 15, 2012 at 7:51 PM, Adam Zeilingerzeil0...@umn.edu wrote:
Hello,
I am trying to construct two matrices, F and V, composed of partial
derivatives and then find the eigenvalues of F*Inverse(V). I have the
following equations in ryacas notation:
library(Ryacas)
FIh- Expr(betah*Sh*Iv)
FIv- Expr(betav*Sv*Ih)
VIh- Expr((muh + gamma)*Ih)
VIv- Expr(muv*Iv)
I successfully found the partial derivatives:
f11- deriv(FIh, Ih)
f12- deriv(FIh, Iv)
f21- deriv(FIv, Ih)
f22- deriv(FIv, Iv)
v11- deriv(VIh, Ih)
v12- deriv(VIh, Iv)
v21- deriv(VIv, Ih)
v22- deriv(VIv, Iv)
Next I would like to put these partial derivatives into two matrices, F and
V:
F- Expr({{f11, f12}, {f21, f22}})
V- Expr({{v11, v12}, {v21, v22}})
Finally, I would like to find the eigenvalues of F*Inverse(V). Something
like:
yacas(EigenValues(F*Inverse(V)))
However, this does not work. I get the following error message:
In function While : bad argument number 1 (counting from 1)The offending
argument $ii49= $nr49 evaluated to Not Length-10CommandLine(1) : Invalid
argument
According to Mathematica, the correct eigenvalues are:
{-((Sqrt[betah] Sqrt[betav] Sqrt[Sh] Sqrt[Sv])/Sqrt[gamma muv + muh muv]),
(Sqrt[betah] Sqrt[betav] Sqrt[Sh] Sqrt[Sv])/Sqrt[gamma muv + muh muv]}
I don't understand the error message. Any suggestions on how to get the
correct eigenvalues using R would be greatly appreciated. I'm using R
2.14.0.
Try doing it this way instead:
library(Ryacas)
EigenValues- function(x) Sym(EigenValues(, x, ))
Iv- Sym(Iv); Ih- Sym(Ih)
Sv- Sym(Sv); Sh- Sym(Sh)
betav- Sym(betav); betah- Sym(betah)
muv- Sym(muv); muh- Sym(muh)
gamma- Sym(gamma)
FIh- betah*Sh*Iv
FIv- betav*Sv*Ih
VIh- (muh + gamma)*Ih
VIv- muv*Iv
f11- deriv(FIh, Ih)
f12- deriv(FIh, Iv)
f21- deriv(FIv, Ih)
f22- deriv(FIv, Iv)
v11- deriv(VIh, Ih)
v12- deriv(VIh, Iv)
v21- deriv(VIv, Ih)
v22- deriv(VIv, Iv)
F- List(List(f11, f12), List(f21, f22))
V- List(List(v11, v12), List(v21, v22))
EigenValues(F * Inverse(V))
For the last line I get:
EigenValues(F*Inverse(V))
expression(Roots(xx^2 - betav * Sv * muv * (betah * Sh * (muh +
gamma))/((muh + gamma) * muv)^2))
--
Adam Zeilinger
Post Doctoral Scholar
Department of Entomology
University of California Riverside
www.linkedin.com/in/adamzeilinger
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Y-axis label on the right hand side in lattice?
Hello, Is there a way to add ylab on the right hand side also (in lattice)? Different from the left hand side? Cheers Saptarshi [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem reading mixed CSV file
I have a file that is 5000 records and to edit that file is not easy. Is there any way to line 10 differently to account for changes in the third field? On Fri, Mar 16, 2012 at 11:35 PM, Peter Ehlers ehl...@ucalgary.ca wrote: On 2012-03-16 10:48, Ashish Agarwal wrote: Line 10 has City and State that too separated by comma. For line 10 how can I read differently as compared to the other lines? Edit the file and put quotes around the city-state combination: Raleigh, North Carol __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Y-axis label on the right hand side in lattice?
from ?xyplot use the ylab.right argument On Fri, Mar 16, 2012 at 2:11 PM, Saptarshi Guha saptarshi.g...@gmail.comwrote: Hello, Is there a way to add ylab on the right hand side also (in lattice)? Different from the left hand side? Cheers Saptarshi [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Y-axis label on the right hand side in lattice?
On Mar 16, 2012, at 2:53 PM, Richard M. Heiberger wrote: from ?xyplot use the ylab.right argument On Fri, Mar 16, 2012 at 2:11 PM, Saptarshi Guha saptarshi.g...@gmail.com wrote: Hello, Is there a way to add ylab on the right hand side also (in lattice)? Different from the left hand side? I thought he wanted facilities provided by doubleYScale in latticExtra package -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Y-axis label on the right hand side in lattice?
On Mar 16, 2012, at 3:03 PM, David Winsemius wrote: On Mar 16, 2012, at 2:53 PM, Richard M. Heiberger wrote: from ?xyplot use the ylab.right argument On Fri, Mar 16, 2012 at 2:11 PM, Saptarshi Guha saptarshi.g...@gmail.com wrote: Hello, Is there a way to add ylab on the right hand side also (in lattice)? Different from the left hand side? I thought he wanted facilities provided by doubleYScale in latticExtra package ^latticeExtra^ -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Spatstat - coordinates in observation window
On 16/03/12 23:02, Lucie V wrote: Dear R users, I wish to run spatial point pattern analysis (e.g. pair correlation function, mark correlation function) for which I need to create an observation window (window=owin) from which the spatial analysis is generated. The command I used to create this observation window as follows: X1- ppp(x, y, window=owin(c(80.58,144.96),c(101.06,165.13)), unitname=c(metres,metres), marks=dbh) Surely this should read unitname=c(metre,metres) i.e. singular then plural. I managed to create the observation window with this command. However, my data (x,y coordinates of objects in a square plot) didn't fit into this observation window's frame. It seems like I need to 'move or twist' my data by a certain angle so that they fit within the border of the observation window's frame. I'm not sure how to do that. Is there a command of function for that? I would be very grateful for any help or suggestions. I hope I described my problem so that it is understandable. Thank you, L. Why did you choose to use the window owin(c(80.58,144.96),c(101.06,165.13)) if that is not the window containing your points? In any analysis of spatial point patterns a window should be specified (a priori) and this window should consist of the region in which points were observed or looked for. Remember that there is information in *where the points aren't* as well as in where they *are*. You can't tell where points aren't unless you know where they've been looked for. So your analysis would appear to be on a shaky foundation from the start. That being said, it is very easy (though unsound and misleading) to construct a window containing all your points in an a posteriori fashion. Tools to do this include the functions ripras() and clickpoly(). Note that a window need *not* necessarily be a rectangle! There are also tools for adjusting and transforming existing windows. See affine(), rotate(), shift(), erosion(), dilation(), and expand.owin(). Transforming the observed points so that they fit into a given window makes no sense at all, as far as I can discern. cheers, Rolf Turner __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ggplot2: goem_smooth and suppress messages
On 3/15/2012 4:11 PM, tibaker wrote: Hi When I run my script using ggplot and geom_smooth I get messages that I would like to suppress: p- ggplot(dataSubset) p- p + aes(x = as.Date(factor(key),format=%Y%m%d)) + geom_line() p- p + geom_smooth(span=0.2,se=FALSE,size=0.7) The messages look like this: geom_smooth: method=auto and size of largest group is1000, so using loess. Use 'method = x' to change the smoothing method. There were 15 warnings (use warnings() to see them) The warning is printed not when p is assigned, but when it is plotted (printed). I have tried p- p + suppressMessages(geom_smooth(span=0.2,se=FALSE,size=0.7)) but this does not work. I would like to keep using method=auto but without any messages. Any ideas on how to suppress the messages when using geom_smooth? Thank you! Use suppressWarnings when printing. p - ggplot(mtcars, aes(wt, mpg)) + geom_smooth() suppressMessages(print(p)) If you are getting display by implicit printing of the plot, then this won't work. -- Brian S. Diggs, PhD Senior Research Associate, Department of Surgery Oregon Health Science University __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R-help Digest, Vol 109, Issue 16
Q #1: yesterday: A: 1. Restructure your database with NoSQL. See MongoDB.org. 2. Choose application language with which to work (and get Driver) and write your code. 3. R package - rmongodb. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Apt-get
Ok. When I type in sudo add-apt-repository ppa:marutter/rrutter I get a prompt for a password. I enter my domain password and get some print about adding the ppa and requeting that I press enter. I press enter and this is followed by print stating that the key B04C661B is being requested from hkp sevrer keyserverubuntu.com followed by connection refused HTTP fetch error 7: couldn't connect no valid Open GPG found. I'm not sure what next but I think I need to configure the keyserver. Tried this via the command line and it failed. Maybe creating a key.txt file will work but when I search http://keyserver.ubuntu.com:11371/ for E084DAB9 that fails as well. What next? From: Tyler Ritchie tyler.ritc...@gmail.com @r-project.org Sent: Thursday, March 15, 2012 1:36 PM Subject: Re: [R] Apt-get Beltrand was also on the mark, suggesting you add Michael Rutter's ppa to your repository sources. In both cases (adding the CRAN Ubuntu repositories or Michael Rutter's ppa), an additional package repository is added to your system's packages. apt then checks that repository along with the other Ubuntu repositories and exposes the relevant binary R packages that Michael Rutter is curating. So, your IS people are correct in saying that the latest version of R available through the Ubuntu packages is 2.13.1, but there are more up to date R repositories to use. If you don't have the system rights to add any additional repositories, you'll need your IS folks to add them for you. -Tyler [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] ggplot axis limit
Hi, This is probably an easy one, but I am new to ggplot2 and cannot find an answer online. I am bar plotting values of 10 groups. These values are all within a 90-100 range, so I would like leave out the area of the bars below 90. If I say graph + scale_y_continuous(limit=c(90, 100)), it does limit the axis but the bars disappear completely. Any solution here? Thanks a lot! Mathijs -- View this message in context: http://r.789695.n4.nabble.com/ggplot-axis-limit-tp4478835p4478835.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] plotting border over map
I am using following codes to plot map
library(sp)
library(rgdal)
library(maps)
library(gplots)
library(clim.pact)
library(fields)
source(/R/PlotGridded2DMap.R)
source(/R/image.plot.fix.R)
source(/R/image.plot.plt.fix.r)
seasonal_plot-function(input,lonll=-180,latll=-90,lonres=5.,latres=3.75,write_file=TRUE,The_title=NULL){
if(is.null(The_title)){
for (ki in 1:length(input)){
The_title[[ki]]-sprintf(XCH4 CH4 (ppb),ki)
}
}
if(!is.list(input)){input=list(input)}
lon.ll - lonll #lower left corner of grid
lat.ll - latll#lower left corner of grid
lon.res- lonres #resolution in degrees longitude
lat.res- latres#resolution in degrees latitude
for (ki in 1:length(input)){
# plot for whole world
sh-dim(input[[ki]]$avg)
numpix.x - sh[1] #number of pixels in x directions in
grid
numpix.y - sh[2] #number of pixels in y directions in
grid
#print(ki)
#print(input[[ki]]$avg)
mat- t(input[[ki]]$avg)# length
xs - seq(lon.ll,by=lon.res,length=dim(mat)[2])+0.5*lon.res
#centers of cells
ys - seq(lat.ll,by=lat.res,length=dim(mat)[1])+0.5*lat.res
#centers of cells
col=rich.colors(32)
xlims -c(-180,180)
ylims -c(-90,90)
old.par- par(no.readonly = TRUE)
par(mar=c(par()$mar[1:3],4))
cex.set- 1.2
par(cex=cex.set)
par(mgp=c(2.0,0.3,0))
par(tcl=-0.1)
opath - (/Result/scitm3/) # path to save image
if(write_file){png(file=paste(opath,The_title[[ki]],.png,sep=
),width=1000,height=800,pointsize=23)}
if(!write_file){x11()}
image.plot.fix(x=xs,y=ys,z=input[[ki]]$avg,zlim=c(1600,2000),nlevel=64,col=col,xlab=Longitude,ylab=Latitude,legend.width=0.03,
offset=0.05,legend.only=F,lg=F)
map(database = world, add=TRUE,col=black)
title(paste(The_title[[ki]]))
if(write_file){dev.off()}
}
}
when I try to use map(database = world, add=TRUE,col=black)
I get error
Error in map(database = world, add = TRUE, col = black) :
unused argument(s) (database = world)
if I comment this line then I get plot but it does not have world border.
I really got stuck at this point and I do not know how to fix it.
--
View this message in context:
http://r.789695.n4.nabble.com/plotting-border-over-map-tp4479163p4479163.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] ggmap crash
Not sure if this is the right place to report this, but:
Am using ggmap to generate a map of a bounding box from 161
latitude/longitude pairs and the code crashes R (in ess). Data is at
http://analysis.d8u.us/~hdiwan/plotSource.csv and the code to read it
is below. I'm not sure if ess, emacs, ggmap, R, or my laptop is to
blame. Here's the code:
rmc - read.csv('http://analysis.d8u.us/~hdiwan/rmc.csv', header=TRUE)
siteLat = c(as.numeric(rmc$latitude))
siteLon = c(as.numeric(rmc$longitude))
sites - as.data.frame(cbind(siteLat, siteLon, ''))
lats - c(floor(min(siteLat))-10, ceiling(max(siteLat))+10)
lons - c(floor(min(siteLon))-10, ceiling(max(siteLon))+10)
map - GetMap.bbox(c(min(siteLon)-5, max(siteLon)+5), c(min(siteLat)-5,
max(siteLat)+5), maptype='satellite')
[1]
http://maps.google.com/maps/api/staticmap?center=53.277508,-9.011888zoom=5size=640x640maptype=satelliteformat=png32sensor=true;
lonr - c(map$BBOX$ll[2], map$BBOX$ur[2])
latr - c(map$BBOX$ll[1], map$BBOX$ur[1])
lonr - c(map$BBOX$ll[2], map$BBOX$ur[2])
latr - c(map$BBOX$ll[1], map$BBOX$ur[1])
ggplot(sites, aes(siteLon, siteLat)) + annotation_raster(h_raster, lonr[1],
lonr[2], latr[1], latr[2]) + geom_point(aes(x=siteLon, y=siteLat),
colour='red', data = sites)
*** caught segfault ***
address 0x196188000, cause 'memory not mapped'
Traceback:
1: grid.Call.graphics(L_raster, x$raster, x$x, x$y, x$width,
x$height, resolveHJust(x$just, x$hjust), resolveVJust(x$just,
x$vjust), x$interpolate)
2: drawDetails.rastergrob(x, recording = FALSE)
3: drawDetails(x, recording = FALSE)
4: drawGrob(x)
5: recordGraphics(drawGrob(x), list(x = x), getNamespace(grid))
6: grid.draw.grob(x$children[[i]], recording = FALSE)
7: grid.draw(x$children[[i]], recording = FALSE)
8: drawGTree(x)
9: recordGraphics(drawGTree(x), list(x = x), getNamespace(grid))
10: grid.draw.gTree(x$children[[i]], recording = FALSE)
11: grid.draw(x$children[[i]], recording = FALSE)
12: drawGTree(x)
13: recordGraphics(drawGTree(x), list(x = x), getNamespace(grid))
14: grid.draw.gTree(gtable_gTree(x), recording)
15: grid.draw(gtable_gTree(x), recording)
16: grid.draw.gtable(gtable)
17: grid.draw(gtable)
18: print.ggplot(list(data = list(siteLat = c(53.277465, 53.277482,
53.277533, 53.277608, 53.277657, 53.277673, 53.277658, 53.277643,
53.27763, 53.27763, 53.277642, 53.277645, 53.277642, 53.277637,
53.277637, 53.277645, 53.277648, 53.277645, 53.27764, 53.277637,
53.277628, 53.27762, 53.277612, 53.277598, 53.277593, 53.277607,
53.277603, 53.277605, 53.27761, 53.277617, 53.277623, 53.277632,
53.277632, 53.277632, 53.27763, 53.277628, 53.277628, 53.277628,
53.277628, 53.277638, 53.277643, 53.277653, 53.277663, 53.277665,
53.277667, 53.277668, 53.27767, 53.277688, 53.277688, 53.277692,
53.2777, 53.277703, 53.277705, 53.277707, 53.277708, 53.277708,
53.277707, 53.277705, 53.277703, 53.277703, 53.277702, 53.277702,
53.2777, 53.277698, 53.277697, 53.277695, 53.27769, 53.277702,
53.27771, 53.277712, 53.277715, 53.277725, 53.277725, 53.277725,
53.277723, 53.277723, 53.277723, 53.277722, 53.27772, 53.277718,
53.27772, 53.277715, 53.277707, 53.277688, 53.27769, 53.27769,
53.277685, 53.277677, 53.277673, 53.277678, 53.277687, 53.277695,
53.277702, 53.277702, 53.277703, 53.2777, 53.277695, 53.277707,
53.277718, 53.277728, 53.277742, 53.277753, 53.277748, 53.277742,
53.277747, 53.27774, 53.277748, 53.277742, 53.277735, 53.277728,
53.277743, 53.277735, 53.27773, 53.277727, 53.277718, 53.27771,
53.277713, 53.277707, 53.277692, 53.277688, 53.277682, 53.27767,
53.277662, 53.277652, 53.277645, 53.277645, 53.277632, 53.277617,
53.277603, 53.277597, 53.277593, 53.277585, 53.277575, 53.277567,
53.277555, 53.277548, 53.277535, 53.277535, 53.277528, 53.277522,
53.277513, 53.277503, 53.277493, 53.277482, 53.277472, 53.277457,
53.277458, 53.277448, 53.277453, 53.277445, 53.277438, 53.27743,
53.277435, 53.277427, 53.277435, 53.277427, 53.277418, 53.277423,
53.277417, 53.27741, 53.277413, 53.277415, 53.277428, 53.277433,
53.277438, 53.277438, 53.277435, 53.27744, 53.277435, 53.277433,
53.277448, 53.277442, 53.277445, 53.27744, 53.27744, 53.277438,
53.277438, 53.277437, 53.277433, 53.277428, 53.277415, 53.277403,
53.27739, 53.277382, 53.277372, 53.277357, 53.27734, 53.277322,
53.2773, 53.27728, 53.277263), siteLon = c(-9.01199, -9.011975,
-9.011978, -9.01198, -9.011932, -9.011922, -9.011915, -9.011912,
-9.011907, -9.011923, -9.011932, -9.011945, -9.011958, -9.01197,
-9.011977, -9.011977, -9.01196, -9.01194, -9.011913, -9.011905,
-9.011907, -9.0119, -9.011903, -9.011903, -9.011905, -9.011912,
-9.011895, -9.011903, -9.011908, -9.011903, -9.011898, -9.011887,
-9.011885, -9.011885, -9.011883, -9.011883, -9.011885, -9.011885,
-9.011887, -9.011892, -9.011897, -9.011895, -9.011903, -9.011907,
-9.011908, -9.011912, -9.011915, -9.011922, -9.011915, -9.011918,
-9.011927, -9.011932, -9.011932, -9.011933, -9.011932, -9.011932,
-9.011932, -9.01193, -9.011928, -9.011928, -9.011928, -9.011928,
