Re: [R] Need help with error
As it says at the bottom of every post:
PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Without an example that fails, it is hard to help.
Allan
On 18/03/11 16:26, Savitri N Appana wrote:
Hi R users,
I am getting the following error when using the splsda function in R
v2.12.1:
Error in switch(classifier, logistic = { : EXPR must be a length 1
vector
What does this mean and how do I fix this?
Thank you in advance!
Best,
Savi
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Re: [R] How do I delete multiple blank variables from a data frame?
On 19/03/11 01:35, Joshua Wiley wrote:
Hi Rita,
This is far from the most efficient or elegant way, but:
## two column data frame, one all NAs
d- data.frame(1:10, NA)
## use apply to create logical vector and subset d
d[, apply(d, 2, function(x) !all(is.na(x)))]
This works, but apply converts d to a matrix which is not needed, so try
d[, sapply(d, function(x) !all(is.na(x)))]
if performance is an issue (apply is about 3x slower on your test data
frame d, more for larger data frames).
For the related problem of removing columns of constant-or-na values,
the best I could come up with is
zv.1 - function(x) {
## The literal approach
y - var(x, na.rm = TRUE)
return(is.na(y) || y == 0)
}
sapply(train, zv.1)
See
http://www.cybaea.net/Blogs/Data/R-Eliminating-observed-values-with-zero-variance.html
for the benchmarks.
Allan
I am just apply()ing to each column (the 2) of d, the function
!all(is.na(x)) which will return FALSE if all of x is missing and TRUE
otherwise. The result is a logical vector the same length as the
number of columns in d that is used to subset only the d columns with
at least some non-missing values. For documentation see:
?apply
?is.na
?all
?[
?Logic
HTH,
Josh
On Fri, Mar 18, 2011 at 3:35 PM, Rita Carreiraritacarre...@hotmail.com wrote:
Dear List Members,I have 55 data frames, each of which with 272 variables and
267 observations. Some of these variables are blanks but the blanks are not the
same for every data frame. I would like to write a procedure in which I import
a data frame, see which variables are blank, and delete those variables. My
data frames have variables named P1 to P136 and Q1 to Q136.
I have a couple of questions regarding this issue:
1) Is a loop an efficient way to address this problem? If not, what are my
alternatives and how do I implement them?2) I have been playing with a single data
frame to try to figure out a way of having R go through the columns and see which
ones it should delete. I have figured out how to delete rows with missing data
(newdata- na.omit(olddata)) but how do I do it for columns???
Thank you very much for your help and have a great weekend!
Rita If you think education is expensive,
try ignorance--Derek Bok
[[alternative HTML version deleted]]
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Re: [R] [R-sig-ME] lmm WITHOUT random factor (lme4)
On Mar 19, 2011; 01:39am Andrzej Galecki wrote: I agree with you that caution needs to be exercised. Simply because mathematically the same likelihood may be defined using different constant. Yes. But this is ensured by the implementation. If the call to anova() is made with the lm$obj first in the sequence then an error is thrown. If the call is correctly made, with the lme$obj placed first in the sequence, then the log of the likelihood of each object is calculate by nlme:::logLik.lme using the same formula [via lapply(object, logLik, REML), where logLik points to nlme:::logLik.lme]. You will note, as Andrzej Galecki has pointed out, that the logLik.lm of the lm$obj is different from logLik.lme. ## logLik(fm) 'log Lik.' -950.1465 (df=3) logLik(fm, REML=T) 'log Lik.' -946.8318 (df=3) Regards, Mark. -- View this message in context: http://r.789695.n4.nabble.com/lmm-WITHOUT-random-factor-lme4-tp3384054p3389249.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] [O/T] reference for regular expressions
On Fri, Mar 18, 2011 at 09:45:57PM -0500, Erin Hodgess wrote: Dear R People: Could someone recommend a good reference on regular expressions, please? ... Mastering Regular Expressions; Friedl, Jeffrey E. F.; ISBN 9780596528126. Many of the O'Reilly books (as this one) may be purchased in an electronic format , which is often slightly less expensive, can be faster to arrive, and is readily amenable (in the case of O'Reilly, at least) to low-cost (or free) electronic delivery of updates. That said, another approach would be to run Perl in debug mode against some (Perl) script, and use the debugger to see exactly what matches (and what happens when you change something). You might able to do this with R's browser() fiunction, at least to some extenr; I confess that I have a great deal more experience with Perl, so I'm more comfortable experimenting in that way using the Perl debugger. (And in any case, Perl is well-known for the facility with which one may use regular expressions in it.) The above are not (intended as) mutually exclusive. Peace, david -- David H. Wolfskill r...@catwhisker.org Depriving a girl or boy of an opportunity for education is evil. See http://www.catwhisker.org/~david/publickey.gpg for my public key. pgpiOFK7fTKGP.pgp Description: 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] Replace split with regex for speed ?
Thanks for your suggestions. Cheers, Chris -- View this message in context: http://r.789695.n4.nabble.com/Replace-split-with-regex-for-speed-tp3386098p3388958.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 do I delete multiple blank variables from a data frame?
I actually prefer to do this portion of the work (data prep) inside of excel. When you export the data as an cvs doc the NA's will be in the excel spreadsheet. Now the search and/or the search and replace option become very handy. Probably a better way in [R] though. Tyler Date: Fri, 18 Mar 2011 18:35:20 -0700 From: jwiley.ps...@gmail.com To: ritacarre...@hotmail.com CC: r-help@r-project.org Subject: Re: [R] How do I delete multiple blank variables from a data frame? Hi Rita, This is far from the most efficient or elegant way, but: ## two column data frame, one all NAs d - data.frame(1:10, NA) ## use apply to create logical vector and subset d d[, apply(d, 2, function(x) !all(is.na(x)))] I am just apply()ing to each column (the 2) of d, the function !all(is.na(x)) which will return FALSE if all of x is missing and TRUE otherwise. The result is a logical vector the same length as the number of columns in d that is used to subset only the d columns with at least some non-missing values. For documentation see: ?apply ?is.na ?all ?[ ?Logic HTH, Josh On Fri, Mar 18, 2011 at 3:35 PM, Rita Carreira ritacarre...@hotmail.com wrote: Dear List Members,I have 55 data frames, each of which with 272 variables and 267 observations. Some of these variables are blanks but the blanks are not the same for every data frame. I would like to write a procedure in which I import a data frame, see which variables are blank, and delete those variables. My data frames have variables named P1 to P136 and Q1 to Q136. I have a couple of questions regarding this issue: 1) Is a loop an efficient way to address this problem? If not, what are my alternatives and how do I implement them?2) I have been playing with a single data frame to try to figure out a way of having R go through the columns and see which ones it should delete. I have figured out how to delete rows with missing data (newdata - na.omit(olddata)) but how do I do it for columns??? Thank you very much for your help and have a great weekend! Rita If you think education is expensive, try ignorance--Derek Bok [[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. -- Joshua Wiley Ph.D. Student, Health Psychology University of California, Los Angeles http://www.joshuawiley.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] Performance Difference? Windows vs. Linux
On Fri, 18 Mar 2011, Shige Song wrote: One thing that Linux makes trivially easy is to interpolate R with C++ through the Rcpp package. The GCC compiler collection is part of all mainstream Linux distro. This is, however, not the case with Windows: you may be able to do it eventually (not sure about this point), but it takes quite some tweaks... Oh, come on: you admit don't know what you are talking about, but you then give advice on something unrelated to the command line. That forces other people to correct your erroneous advice for the record. You do not need Rcpp to use C++ with R, and only a very small minority of C++-using packages do whereas Rcpp leans very heavily on the work of the core team to support C++. There is a C++ compiler which is part of the Rtools collection which you need to use compiled code on Windows. But actually that is no different from Linux, where the person who installed Linux has to arrange to install the compilers from the distro. Shige On Fri, Mar 18, 2011 at 6:00 PM, Brigid Mooney bkmoo...@gmail.com wrote: I'm not trying to start a Windows vs. Linux debate, but I've been using R on a Windows machine for a while, and was recently wondering if R's performance would be faster on a Linux machine. And similarly, if any incremental increase in processing speed would be worth the time it would take me to migrate my entire system to Linux (including a database that I access via an R package.) I don't know how much it matters what R is doing - but I've got R pulling a large amount data from a database, performing many complex computations on that data, and then writing output data to a database. Thanks so much for the input, Brigid __ 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. -- 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] Performance Difference? Windows vs. Linux
To try to answer the actual question I run x86_64 Linux and both 32-bit Windows XP and x64 Windows 7 on my home desktop. So from years of experience of using the same hardware on those OSes: 1) Generally Linux will be a bit faster, mainly because I do not hobble it with --enable-R-shlib (the only way R can be built on Windows). But the difference is small (5-20%). 2) Linux handles large amounts of memory (and especially swapping) better, so the differences will be more if what you do is using nearly all the address space or physical RAM of your computer. 3) Linux's process launch and disc access is many times faster, which makes a big difference to R development work. From your described usage I would expect you to see a worthwhile performance gain -- it does matter what you are doing with R. It also matters which database system. On Fri, 18 Mar 2011, Brigid Mooney wrote: I'm not trying to start a Windows vs. Linux debate, but I've been using R on a Windows machine for a while, and was recently wondering if R's performance would be faster on a Linux machine. And similarly, if any incremental increase in processing speed would be worth the time it would take me to migrate my entire system to Linux (including a database that I access via an R package.) I don't know how much it matters what R is doing - but I've got R pulling a large amount data from a database, performing many complex computations on that data, and then writing output data to a database. Thanks so much for the input, Brigid __ 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.
Re: [R] [O/T] reference for regular expressions
On Fri, Mar 18, 2011 at 10:45 PM, Erin Hodgess erinm.hodg...@gmail.com wrote: Dear R People: Could someone recommend a good reference on regular expressions, please? There are links to a number of sites on the gsubfn home page: http://gsubfn.googlecode.com/#REGULAR_EXPRESSION_LINKS -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at 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] How to find position in bin-data?
Hi there, probably there is a very simple solution, but I cannot think of one... I have a vector with values: data - c(1,6,3,4,8,4,2,9) and I have a vector with bin breaks: bins - c(1,3,5,7,9,11) Now, I'd like to get for each data point the index of the bin-vector where the value falls in (or equals the lower bin break). In the example case, I'd like to get: c(1,3,2,2,4,1,5) How would you solve it? Antje __ 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 access the elements of a univariate results table with Anova (library car)
Dear R users, I use the excelent Anova function of the library car because the easy way to get sphericity correction. Unless I use the scan function. I have not been able to access the values ââof sum squares and degrees of freedom for each effect in the univariate summary table. Example of the car library for Anova function: library(car) phase - factor(rep(c(pretest, posttest, followup), c(5, 5, 5)), levels=c(pretest, posttest, followup)) hour - ordered(rep(1:5, 3)) idata - data.frame(phase, hour) mod.ok - lm(cbind(pre.1, pre.2, pre.3, pre.4, pre.5, post.1, post.2, post.3, post.4, post.5, fup.1, fup.2, fup.3, fup.4, fup.5) ~ treatment*gender, data=OBrienKaiser) av.ok - Anova(mod.ok, idata=idata, idesign=~phase*hour) summary(av.ok, multivariate=FALSE) If you assign the above line to a new object you will get a multivariate summary and not the univariate one. my.summary - summary(av.ok, multivariate=FALSE) my.summary Does anyone know how to assign the full univariate output to a new object or variable. The logical way does not produce the desired result. Than'ks in advance. Juan Hernández Cabrera Facultad de PsicologÃa Universidad de La Laguna Spain [[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 find position in bin-data?
On 11-03-19 8:18 AM, Antje Niederlein wrote: Hi there, probably there is a very simple solution, but I cannot think of one... I have a vector with values: data- c(1,6,3,4,8,4,2,9) and I have a vector with bin breaks: bins- c(1,3,5,7,9,11) Now, I'd like to get for each data point the index of the bin-vector where the value falls in (or equals the lower bin break). In the example case, I'd like to get: c(1,3,2,2,4,1,5) How would you solve it? Use cut. For example, data - c(1,6,3,4,8,4,2,9) bins - c(1,3,5,7,9,11) result - cut(data, breaks=bins, right=FALSE) as.numeric(result) 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 find position in bin-data?
Thanks a lot! That's what I was looking for :-) A On 19 March 2011 13:56, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 11-03-19 8:18 AM, Antje Niederlein wrote: Hi there, probably there is a very simple solution, but I cannot think of one... I have a vector with values: data- c(1,6,3,4,8,4,2,9) and I have a vector with bin breaks: bins- c(1,3,5,7,9,11) Now, I'd like to get for each data point the index of the bin-vector where the value falls in (or equals the lower bin break). In the example case, I'd like to get: c(1,3,2,2,4,1,5) How would you solve it? Use cut. For example, data - c(1,6,3,4,8,4,2,9) bins - c(1,3,5,7,9,11) result - cut(data, breaks=bins, right=FALSE) as.numeric(result) 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 find position in bin-data?
Am 19.03.2011 13:18, schrieb Antje Niederlein: Hi there, probably there is a very simple solution, but I cannot think of one... I have a vector with values: data- c(1,6,3,4,8,4,2,9) and I have a vector with bin breaks: bins- c(1,3,5,7,9,11) cut() does what you want: cut(data, bins) [1] NA (5,7] (1,3] (3,5] (7,9] (3,5] (1,3] (7,9] Levels: (1,3] (3,5] (5,7] (7,9] (9,11] as.numeric(cut(data,bins)) [1] NA 3 1 2 4 2 1 4 data[1] is NA because of the structure of the intervals. Grüsse, Alex __ 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] cross-validation in rpart
I am trying to find out what type of sampling scheme is used to select the 10 subsets in 10-fold cross-validation process used in rpart to choose the best tree. Is it simple random sampling? Is there any documentation available on this? Thanks, Penny. -- View this message in context: http://r.789695.n4.nabble.com/cross-validation-in-rpart-tp3389329p3389329.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] strange PREDICTIONS from a PIECEWISE LINEAR (mixed) MODEL
Hi Dears, When I introduce an interaciton in a piecewise model I obtain some quite unusual results. If that would't take u such a problem I'd really appreciate an advise from you. I've reproduced an example below... Many thanks x-rnorm(1000) y-exp(-x)+rnorm(1000) plot(x,y) abline(v=-1,col=2,lty=2) mod-lm(y~x+x*(x-1)) summary(mod) yy-predict(mod) lines(x[order(x)],yy[order(x)],col=2,lwd=2) #--lme #grouping factor, unbalanced g-as.character(c(1:200)) id-sample(g,size=1000,replace=T, prob=sample(0:1,200,rep=T)) table(id) #unbalanced mod2-lme(y~x+x*(x-1),random=~x|id, data=data.frame(x,y,id)) summary(mod2) newframe-data.frame( #fictious id id=fictious, x) newframe[1:5,] #predictions yy2-predict(mod2,level=0, newdata=newframe) lines(x[order(x)],yy2[order(x)],col=blue,lwd=2) # add variable in the model z-rgamma(1000,4,6) mod3-lme(y~x+x*(x-1)+z ,random=~x|id, data=data.frame(x,y,z,id)) summary(mod3) #new id newframe2-data.frame( #fictious id id=fictious, x, z) #predict yy3-predict(mod3,level=0, newdata=newframe2) lines(x[order(x)],yy3[order(x)],col=green,lwd=2) # ADD INTERACTION z:x mod4-lme(y~x+x*(x-1)+ z+ z:x+ z:x*(x-1) ,random=~x|id, data=data.frame(x,y,z,id)) #predict yy4-predict(mod4,level=0, newdata=newframe2) lines(x[order(x)],yy4[order(x)],col=violet,lwd=2) #something bizarre #starts to happen #in the predicted values # they begin to jiggle around the straight line -- *Little u can do against ignorance,it will always disarm u: is the 2nd principle of thermodinamics made manifest, ...entropy in expansion.**But setting order is the real quest 4 truth, ..and the mission of a (temporally) wise dude. * [[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] Plotting graph problem!!
http://r.789695.n4.nabble.com/file/n3389613/Life_Expectancies_2008.csv Life_Expectancies_2008.csv I am trying to plot a histogram base on the file i uploaded above. I am facing a trouble in sorting out the frequency of the life expectancies. I wanted to plot a graph of life expectancies at birth versus frequency,but i have no idea how to change the locations into frequencies taking the range of life expectancies at birth from 40 to 90. I tried using table(Life.Expectancies.at.Birth) to show the frequencies of each number and I do not know how to continue. -- View this message in context: http://r.789695.n4.nabble.com/Plotting-graph-problem-tp3389613p3389613.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] Generating repeated measures data
At 00:37 19/03/2011, John Sorkin wrote:
How would one generate data to be used in a simulation of a repeated
measures ANOVA given a known (1) within-person correlation with
known (2) mean and SD of data obtained at each of three times of observation?
You do not say which distribution you want them to have but for
normal the best choice seems to be to load MASS and use rmvtnorm.
Generating multivariate datasets from distributions
other than the normal
can be more challenging.
In \R contributed packages provide the following among others:
\begin{description}
\item[\pkg{corcount}]
Poisson, negative binomial, zero--inflated versions
\item[\pkg{binarySimCLF}]
Generates binary variables, see \citet{qaqish03}
for details
\item[\pkg{bindat}]
Generates binary by thresholding normal
\item[\pkg{mvtBinaryEP}]
Binary
\item[\pkg{sn}]
Skew normal and skew $t$
\end{description}
Apologies for all the LaTeX but I fear if I try to edit it I will
delete something crucial.
Thanks,
John
John Sorkin
Chief Biostatistics and Informatics
Univ. of Maryland School of Medicine
Division of Gerontology and Geriatric Medicine
jsor...@grecc.umaryland.edu
Confidentiality Statement:
This email message, including any attachments, is for t...{{dropped:6}}
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Extracting columns from a class
Hi, Here is the prcomp output. tom=prcomp(matrix(rnorm(25),5,5)) R functions often output lists. To see what's in this one, run names(tom) or type tom$ and use tab completion. Once you do that, the following is more obvious. pc1=tom$rotation[,1] sd1=tom$sdev[1] column=c(sd1,pc1) write.table(column,tom,row.names=F,col.names=F) This will send the column to the file tom. Tom On Thu, Mar 17, 2011 at 8:10 AM, nuncio m nunci...@gmail.com wrote: Hi list, I am not a frequent user of R. Recently I used R in principal component analysis and got the result as a class, which has information like standard deviation and principal components from 1 to 10. How is it possible to extract the column corresponding to first principal component and write it to a file the out from prcomp command is something like this Standard deviations: [1] 3.325801e+00 7.669837e-01 6.625773e-01 4.990732e-01 3.470071e-01 [6] 2.946679e-01 2.206289e-01 1.645828e-01 1.570887e-01 4.741294e-16 Rotation: PC1 PC2 PC3 PC4 PC5 [1,] -0.07900624 -0.0824864352 0.1208419434 0.1763425845 0.089545020 [2,] -0.09114708 -0.0901675110 0.1377608881 0.2224127252 0.076620976 [3,] -0.10510742 -0.0935434206 0.1113586044 0.2513993555 0.029783117 I want to extract PC1 and 1 value in the standard deviation Thanks -- Nuncio.M Research Scientist National Center for Antarctic and Ocean research Head land Sada Vasco da Gamma Goa-403804 [[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] how to access the elements of a univariate results table with Anova (library car)
On Mar 19, 2011, at 8:44 AM, Juan Andres Hernandez wrote: Dear R users, I use the excelent Anova function of the library car because the easy way to get sphericity correction. Unless I use the scan function. I have not been able to access the values of sum squares and degrees of freedom for each effect in the univariate summary table. Example of the car library for Anova function: library(car) phase - factor(rep(c(pretest, posttest, followup), c(5, 5, 5)), levels=c(pretest, posttest, followup)) hour - ordered(rep(1:5, 3)) idata - data.frame(phase, hour) mod.ok - lm(cbind(pre.1, pre.2, pre.3, pre.4, pre.5, post.1, post.2, post.3, post.4, post.5, fup.1, fup.2, fup.3, fup.4, fup.5) ~ treatment*gender, data=OBrienKaiser) av.ok - Anova(mod.ok, idata=idata, idesign=~phase*hour) summary(av.ok, multivariate=FALSE) If you assign the above line to a new object you will get a multivariate summary and not the univariate one. my.summary - summary(av.ok, multivariate=FALSE) my.summary Does anyone know how to assign the full univariate output to a new object or variable. The logical way does not produce the desired result. Than'ks in advance. summary,Anova.mlm appears to returns the object that was passed to it. How to I know this (despite never having used the function before and having tried unsuccessfully to access the answer with help(summary.Anova.mlm))? I looked at the code. You are getting console output that varies a bit with different parameters to summary, but the object av.ok being passed as the value of summary and is not changing. all.equal(av.ok, my.summary) [1] TRUE If you want to capture the text output that appears on the console display then you need to use either sink() or capture.output(). Juan Hernández Cabrera Facultad de Psicología Universidad de La Laguna Spain -- 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] Plotting graph problem!!
On Mar 19, 2011, at 9:10 AM, andrew456 wrote: http://r.789695.n4.nabble.com/file/n3389613/Life_Expectancies_2008.csv Life_Expectancies_2008.csv I am trying to plot a histogram base on the file i uploaded above. I am facing a trouble in sorting out the frequency of the life expectancies. I wanted to plot a graph of life expectancies at birth versus frequency,but i have no idea how to change the locations into frequencies taking the range of life expectancies at birth from 40 to 90. I tried using table(Life.Expectancies.at.Birth) to show the frequencies of each number and I do not know how to continue. You should show how you turned that data into an R object first. Then someone may offer a hint to take the next step in your homework. -- 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] cross-validation in rpart
I assume you mean rpart::xpred.rpart ? The beauty of R means that you can look at the source. For the simple case (where xval is a single number) the code does indeed do simple random sampling xgroups- sample(rep(1:xval, length = nobs), nobs, replace = FALSE) If you want another sampling, then you simply pass a vector as the xval parameter, as the documentation says: “This may also be an explicit list of integers that define the cross-validation groups”. Hope this helps a little. Allan On 19/03/11 09:21, Penny B wrote: I am trying to find out what type of sampling scheme is used to select the 10 subsets in 10-fold cross-validation process used in rpart to choose the best tree. Is it simple random sampling? Is there any documentation available on this? Thanks, Penny. __ 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] persuade tabulate function to count NAs in a data frame
Hi,
I'd like to ask you a question again. It is basically about data frames, NAs
and tabulate function.
I have this data frame. I already used this in one of the previous questions of
mine. It intentionally looks this simple, my real 'df' dataframe is much bigger
actually and again, I am not willing to annoy anyone with huge databases... So,
my database:
id -c(1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,3,3,3,3,3,3,3,3,3,3)
a -c(3,1,3,3,1,3,3,3,3,1,3,2,1,2,1,3,3,2,1,1,1,3,1,3,3,3,2,1,1,3)
b -c(3,2,1,1,1,1,1,1,1,1,1,2,1,3,2,1,1,1,2,1,3,1,2,2,1,3,3,2,3,2)
c -c(1,3,2,3,2,1,2,3,3,2,2,3,1,2,3,3,3,1,1,2,3,3,1,2,2,3,2,2,3,2)
d -c(3,3,3,1,3,2,2,1,2,3,2,2,2,1,3,1,2,2,3,2,3,2,3,2,1,1,1,1,1,2)
e -c(2,3,1,2,1,2,3,3,1,1,2,1,1,3,3,2,1,1,3,3,2,2,3,3,3,2,3,2,1,4)
df -data.frame(id,a,b,c,d,e)
df
I have managed to calculate the distributions of the numbers occurring in
columns 'b' to 'e' but considering the fact at the very same time that these
distributions should be 'groupped by' the id numbers in column 'id'. It works
fine, check it -
matrix(matrix(unlist(lapply(df[,(-(1))],function(x)
tapply(x,df$id,tabulate,nbins=nlevels(factor(df[,2]
[[1]])),ncol=3,nrow=3,byrow=TRUE)
matrix(matrix(unlist(lapply(df[,(-(1))],function(x)
tapply(x,df$id,tabulate,nbins=nlevels(factor(df[,3]
[[2]])),ncol=3,nrow=3,byrow=TRUE)
matrix(matrix(unlist(lapply(df[,(-(1))],function(x)
tapply(x,df$id,tabulate,nbins=nlevels(factor(df[,4]
[[3]])),ncol=3,nrow=3,byrow=TRUE)
matrix(matrix(unlist(lapply(df[,(-(1))],function(x)
tapply(x,df$id,tabulate,nbins=nlevels(factor(df[,5]
[[4]])),ncol=3,nrow=3,byrow=TRUE)
matrix(matrix(unlist(lapply(df[,(-(1))],function(x)
tapply(x,df$id,tabulate,nbins=nlevels(factor(df[,6]
[[5]])),ncol=4,nrow=3,byrow=TRUE)
Now my problem is: what if my data frame contains NA values here and there and
what if I want my in-built tabulate function to collect these NAs as well? So
what if I want it to count how many occurrences I have from these NAs?
Here's my modified data frame with the NAs:
id -c(1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,3,3,3,3,3,3,3,3,3,3)
a -c(NA,1,3,3,1,3,3,3,3,1,3,2,1,2,1,3,3,2,1,1,1,3,1,3,3,3,2,1,1,3)
b -c(3,2,1,1,1,1,1,1,1,1,1,2,1,3,2,1,1,1,2,1,3,1,2,2,1,3,3,2,3,2)
c -c(1,3,2,3,2,1,2,3,3,2,2,3,NA,2,3,3,3,1,1,2,3,3,1,2,2,3,2,2,3,2)
d -c(3,3,3,1,3,2,2,1,2,3,2,2,2,1,3,1,2,2,3,2,3,2,3,2,1,1,1,1,1,2)
e -c(2,3,1,2,1,2,3,3,1,1,2,1,1,3,3,2,1,1,3,3,2,2,3,3,3,2,3,NA,1,4)
df -data.frame(id,a,b,c,d,e)
df
At first I tried something like this (you see, the only thing I did was that I
tried to apply this exclude=NULL thing).
unlist(lapply(df[,(-(1))],function(x)
tapply(x,df$id,tabulate,nbins=nlevels(factor(df[,2],exclude=NULL [[1]])
At least my code realizes the fact that I have 4 different levels in column 'a'
(1,2,3,NA) and not only three (1,2,3). Check it here:
nlevels(factor(df[,2],exclude=NULL))
But you see in the result that somehow it could not calculate the NAs. It says
3 0 6 0(!) 4 3 3 0 4 1 5 0
Instead of the correct:
3 0 6 1(!) 4 3 3 0 4 1 5 0
Or in case of:
unlist(lapply(df[,(-(1))],function(x)
tapply(x,df$id,tabulate,nbins=nlevels(factor(df[,4],exclude=NULL [[3]])
It says
2 4 4 0 2 3 4 0(!) 1 5 4 0
Instead of the correct
2 4 4 0 2 3 4 1(!) 1 5 4 0
etc.
Does someone have any ideas how to persuade the function tabulate to count
NAs? Is it possible at all?
Thanks very much and have a pleasant weekend,
Laszlo
Ez az e-mail és az összes hozzá tartozó csatolt melléklet titkos és/vagy
jogilag, szakmailag vagy más módon védett információt tartalmazhat.
Amennyiben nem Ãn a levél cÃmzettje akkor a levél tartalmának közlése,
reprodukálása, másolása, vagy egyéb más úton történŠterjesztése,
felhasználása szigorúan tilos. Amennyiben tévedésbÅl kapta meg ezt az
üzenetet kérjük azonnal értesÃtse az üzenet küldÅjét. Az Erste Bank
Hungary Zrt. (EBH) nem vállal felelÅsséget az információ teljes és pontos
- cÃmzett(ek)hez történÅ - eljuttatásáért, valamint semmilyen
késésért, kapcsolat megszakadásból eredŠhibáért, vagy az információ
felhasználásából vagy annak megbÃzhatatlanságából eredÅ kárért.
Az üzenetek EBH-n kÃvüli küldÅje vagy cÃmzettje tudomásul veszi és
hozzájárul, hogy az üzenetekhez más banki alkalmazott is hozzáférhet az
EBH folytonos munkamenetének biztosÃtása érdekében.
This e-mail and any attached files are confidential and/...{{dropped:19}}
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Plotting graph problem!!
You should probably tell us which part of a- read.csv(http://r.789695.n4.nabble.com/file/n3389613/Life_Expectancies_2008.csv;) hist(a) doesn't do what you expect. (Though often when people say histogram they want something else - what's with that anyhow?) Allan On 19/03/11 13:10, andrew456 wrote: http://r.789695.n4.nabble.com/file/n3389613/Life_Expectancies_2008.csv Life_Expectancies_2008.csv I am trying to plot a histogram base on the file i uploaded above. I am facing a trouble in sorting out the frequency of the life expectancies. I wanted to plot a graph of life expectancies at birth versus frequency,but i have no idea how to change the locations into frequencies taking the range of life expectancies at birth from 40 to 90. I tried using table(Life.Expectancies.at.Birth) to show the frequencies of each number and I do not know how to continue. -- View this message in context: http://r.789695.n4.nabble.com/Plotting-graph-problem-tp3389613p3389613.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] cross-validation in rpart
On Sat, 19 Mar 2011, Penny B wrote: I am trying to find out what type of sampling scheme is used to select the 10 subsets in 10-fold cross-validation process used in rpart to choose the best tree. Is it simple random sampling? Is there any documentation available on this? Not SRS (and least in its conventional meaning), as it is partitioning: the 10 folds are disjoint. Note that this happens in two places, in rpart() and in xpred.rpart(), but the (default) method is the same. I presume you asked about the first, but it wasn't clear. There is a lot of documentation on the meaning of '10-fold cross-validation', e.g. in my 1996 book. There are a few slightly different ways to do it, and you can read the rpart sources if you want to know the details. -- 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] persuade tabulate function to count NAs in a data frame
On Sat, 2011-03-19 at 15:58 +0100, Bodnar Laszlo EB_HU wrote:
Hi,
I'll top-post as the original Q is very lengthy:
tabs -lapply(df[,2:6],
function(x, id){ t(table(addNA(x), id, useNA = ifany)) }, df$id)
is one way of doing what you want. More details are here:
http://stackoverflow.com/questions/5362702/persuading-tabulate-function-to-count-nas-in-a-data-frame-in-r
where you also posted your Q.
HTH
G
I'd like to ask you a question again. It is basically about data frames, NAs
and tabulate function.
I have this data frame. I already used this in one of the previous questions
of mine. It intentionally looks this simple, my real 'df' dataframe is much
bigger actually and again, I am not willing to annoy anyone with huge
databases... So, my database:
id -c(1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,3,3,3,3,3,3,3,3,3,3)
a -c(3,1,3,3,1,3,3,3,3,1,3,2,1,2,1,3,3,2,1,1,1,3,1,3,3,3,2,1,1,3)
b -c(3,2,1,1,1,1,1,1,1,1,1,2,1,3,2,1,1,1,2,1,3,1,2,2,1,3,3,2,3,2)
c -c(1,3,2,3,2,1,2,3,3,2,2,3,1,2,3,3,3,1,1,2,3,3,1,2,2,3,2,2,3,2)
d -c(3,3,3,1,3,2,2,1,2,3,2,2,2,1,3,1,2,2,3,2,3,2,3,2,1,1,1,1,1,2)
e -c(2,3,1,2,1,2,3,3,1,1,2,1,1,3,3,2,1,1,3,3,2,2,3,3,3,2,3,2,1,4)
df -data.frame(id,a,b,c,d,e)
df
I have managed to calculate the distributions of the numbers occurring in
columns 'b' to 'e' but considering the fact at the very same time that these
distributions should be 'groupped by' the id numbers in column 'id'. It works
fine, check it -
matrix(matrix(unlist(lapply(df[,(-(1))],function(x)
tapply(x,df$id,tabulate,nbins=nlevels(factor(df[,2]
[[1]])),ncol=3,nrow=3,byrow=TRUE)
matrix(matrix(unlist(lapply(df[,(-(1))],function(x)
tapply(x,df$id,tabulate,nbins=nlevels(factor(df[,3]
[[2]])),ncol=3,nrow=3,byrow=TRUE)
matrix(matrix(unlist(lapply(df[,(-(1))],function(x)
tapply(x,df$id,tabulate,nbins=nlevels(factor(df[,4]
[[3]])),ncol=3,nrow=3,byrow=TRUE)
matrix(matrix(unlist(lapply(df[,(-(1))],function(x)
tapply(x,df$id,tabulate,nbins=nlevels(factor(df[,5]
[[4]])),ncol=3,nrow=3,byrow=TRUE)
matrix(matrix(unlist(lapply(df[,(-(1))],function(x)
tapply(x,df$id,tabulate,nbins=nlevels(factor(df[,6]
[[5]])),ncol=4,nrow=3,byrow=TRUE)
Now my problem is: what if my data frame contains NA values here and there
and what if I want my in-built tabulate function to collect these NAs as
well? So what if I want it to count how many occurrences I have from these
NAs?
Here's my modified data frame with the NAs:
id -c(1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,3,3,3,3,3,3,3,3,3,3)
a -c(NA,1,3,3,1,3,3,3,3,1,3,2,1,2,1,3,3,2,1,1,1,3,1,3,3,3,2,1,1,3)
b -c(3,2,1,1,1,1,1,1,1,1,1,2,1,3,2,1,1,1,2,1,3,1,2,2,1,3,3,2,3,2)
c -c(1,3,2,3,2,1,2,3,3,2,2,3,NA,2,3,3,3,1,1,2,3,3,1,2,2,3,2,2,3,2)
d -c(3,3,3,1,3,2,2,1,2,3,2,2,2,1,3,1,2,2,3,2,3,2,3,2,1,1,1,1,1,2)
e -c(2,3,1,2,1,2,3,3,1,1,2,1,1,3,3,2,1,1,3,3,2,2,3,3,3,2,3,NA,1,4)
df -data.frame(id,a,b,c,d,e)
df
At first I tried something like this (you see, the only thing I did was that
I tried to apply this exclude=NULL thing).
unlist(lapply(df[,(-(1))],function(x)
tapply(x,df$id,tabulate,nbins=nlevels(factor(df[,2],exclude=NULL [[1]])
At least my code realizes the fact that I have 4 different levels in column
'a' (1,2,3,NA) and not only three (1,2,3). Check it here:
nlevels(factor(df[,2],exclude=NULL))
But you see in the result that somehow it could not calculate the NAs. It says
3 0 6 0(!) 4 3 3 0 4 1 5 0
Instead of the correct:
3 0 6 1(!) 4 3 3 0 4 1 5 0
Or in case of:
unlist(lapply(df[,(-(1))],function(x)
tapply(x,df$id,tabulate,nbins=nlevels(factor(df[,4],exclude=NULL [[3]])
It says
2 4 4 0 2 3 4 0(!) 1 5 4 0
Instead of the correct
2 4 4 0 2 3 4 1(!) 1 5 4 0
etc.
Does someone have any ideas how to persuade the function tabulate to count
NAs? Is it possible at all?
Thanks very much and have a pleasant weekend,
Laszlo
Ez az e-mail és az összes hozzá tartozó csatolt melléklet titkos és/vagy
jogilag, szakmailag vagy más módon védett információt tartalmazhat.
Amennyiben nem Ön a levél címzettje akkor a levél tartalmának közlése,
reprodukálása, másolása, vagy egyéb más úton történő terjesztése,
felhasználása szigorúan tilos. Amennyiben tévedésből kapta meg ezt az
üzenetet kérjük azonnal értesítse az üzenet küldőjét. Az Erste Bank Hungary
Zrt. (EBH) nem vállal felelősséget az információ teljes és pontos -
címzett(ek)hez történő - eljuttatásáért, valamint semmilyen késésért,
kapcsolat megszakadásból eredő hibáért, vagy az információ felhasználásából
vagy annak megbízhatatlanságából eredő kárért.
Az üzenetek EBH-n kívüli küldője vagy címzettje tudomásul veszi és
hozzájárul, hogy az üzenetekhez más banki alkalmazott is hozzáférhet az EBH
folytonos munkamenetének biztosítása érdekében.
This e-mail
Re: [R] Plotting graph problem!!
On 19/03/11 15:04, Allan Engelhardt wrote: You should probably tell us which part of a- read.csv(http://r.789695.n4.nabble.com/file/n3389613/Life_Expectancies_2008.csv;) hist(a) Should be hist(a$Life.Expectancies.at.Birth), of course. Sorry. doesn't do what you expect. (Though often when people say histogram they want something else - what's with that anyhow?) Allan On 19/03/11 13:10, andrew456 wrote: http://r.789695.n4.nabble.com/file/n3389613/Life_Expectancies_2008.csv Life_Expectancies_2008.csv I am trying to plot a histogram base on the file i uploaded above. I am facing a trouble in sorting out the frequency of the life expectancies. I wanted to plot a graph of life expectancies at birth versus frequency,but i have no idea how to change the locations into frequencies taking the range of life expectancies at birth from 40 to 90. I tried using table(Life.Expectancies.at.Birth) to show the frequencies of each number and I do not know how to continue. -- View this message in context: http://r.789695.n4.nabble.com/Plotting-graph-problem-tp3389613p3389613.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] Plotting graph problem!!
data1-read.delim(C:\\Users\\wenyin\\desktop\\Life_Expectancies_2008.txt,header=T) attach(data1) names(data1) table(Life.Expectancies.at.Birth) so this thing showed up: Life.Expectancies.at.Birth 42 46 47 48 49 50 51 52 53 54 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 2 2 1 4 4 1 2 2 5 5 1 2 3 5 3 2 6 6 3 3 1 5 6 7 8 6 72 73 74 75 76 77 78 79 80 81 82 83 13 11 14 9 8 2 5 3 12 8 5 2 -- View this message in context: http://r.789695.n4.nabble.com/Plotting-graph-problem-tp3389613p3389759.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] Plotting graph problem!!
I assigned the dataset to data1,then i tried typing hist(data1),it says: Error in hist.default(data1) : 'x' must be numeric how can I change the Locations to frequency so that it is in numeric form and I can plot the histogram? You should probably tell us which part of a- read.csv(http://r.789695.n4.nabble.com/file/n3389613/Life_Expectancies_2008.csv;) hist(a) doesn't do what you expect. (Though often when people say histogram they want something else - what's with that anyhow?) Allan -- View this message in context: http://r.789695.n4.nabble.com/Plotting-graph-problem-tp3389613p3389830.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] Could you share your R program to import US CDC mortality data?
Hello - I downloaded yearly mortality (all cause) data from CDC website. But have trouble to import them into R, have you worked with CDC mortality data before? I would appreciate it if you could share your R code on importing the data into R. Thanks, Renny [[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] Could you share your R program to import US CDC mortality data?
On Mar 19, 2011, at 12:03 PM, Renny Li wrote: Hello - I downloaded yearly mortality (all cause) data from CDC website. You should offer a specific URL. The CDC website is huge and there are undoubtedly many places where various forms of such data are available. But have trouble to import them into R, have you worked with CDC mortality data before? I would appreciate it if you could share your R code on importing the data into R. [[alternative HTML version deleted]] You should also learn how to submit plain text messages to rhelp. -- 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] Libraries issue
Hi, I've just discovered R keeps installing my packages into C:\Users\Ben instead of C:\\Users\\Ben;/R/win-library/2.12 which is what is returned by running Sys.getenv(R_LIBS_USER). I've tried setting environment variables in windows control panel of R_LIBS. But nothing seems to be working, it still wants to fill my user folder, I've tried uninstalling and re-installing but it still does the same thing. Does anybody know how I can fix this? Thanks, Ben W. [[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] quantmod Some Single Letter Tickers Not getFin
Hi John, The financial statement pages exist, but they require the exchange to be specified. For example: http://www.google.com/finance?fstype=iiq=NYSE:GE and http://www.google.com/finance?fstype=iiq=GE take you to the same page, but http://www.google.com/finance?fstype=iiq=NYSE:F works, while http://www.google.com/finance?fstype=iiq=F results in a 400 'Bad request' error. This seems to work for this one symbol, maybe it will work for others as well. getFin(NYSE:F) Best, -- Joshua Ulrich | FOSS Trading: www.fosstrading.com On Thu, Mar 17, 2011 at 10:48 PM, Sparks, John James jspa...@uic.edu wrote: Hi, I have been learning the quantmod package over the last several days. I went to check some of my data pulls against other sources and was surprised to find that a few tickers that have single characters do not successfully scrape from Google Finance using getFin(). Particularly require(quantmod) getFin(A) getFin(E) getFin(F) getFin(G) getFin(M) all result in a file not found error. I show the last one below. getFin(M) Error in download.file(paste(google.fin, Symbol, sep = ), quiet = TRUE, : cannot open URL 'http://finance.google.com/finance?fstype=iiq=M' In addition: Warning message: In download.file(paste(google.fin, Symbol, sep = ), quiet = TRUE, : cannot open: HTTP status was '400 Bad Request' I checked out the financial statement pages for all of these and they exist and are as expected: 5 quarters worth of quarterly figures (except for cash-flow which has 4 quarters) and 4 years of annual figures. All the rows are also present by comparing a scrape to excel with the figures for Y, which does getFin(Y) without a problem. I was hoping that someone who knows a lot more about scraping then I do could look into this. Best wishes to all, --John Sparks __ 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] Libraries issue
Hi Ben, I could be completely off target (corrections welcome if I am), but I think the semicolon in the environment variable is making two separate paths and maybe R chooses the first? It should be easy to try changing. HTH, Josh (and sorry for the wild goose hunt if my memory is shoddy) On Sat, Mar 19, 2011 at 9:37 AM, Ben Ward benjamin.w...@bathspa.org wrote: Hi, I've just discovered R keeps installing my packages into C:\Users\Ben instead of C:\\Users\\Ben;/R/win-library/2.12 which is what is returned by running Sys.getenv(R_LIBS_USER). I've tried setting environment variables in windows control panel of R_LIBS. But nothing seems to be working, it still wants to fill my user folder, I've tried uninstalling and re-installing but it still does the same thing. Does anybody know how I can fix this? Thanks, Ben W. [[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. -- Joshua Wiley Ph.D. Student, Health Psychology University of California, Los Angeles http://www.joshuawiley.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] GAMLSS Question
Dear All: I have succeeded in fitting a GAMLSS.dist model to growth data I am working with it. My aim is to create a matrix of predicted percentiles and the corresponding the fitted model's sigma mu nu by agebins. Q: How do it generate these parameters as in L M S per Cole and Green 1992? Here are my working codes. Name of fitted model is gamlssfit Agebin-seq(6,36,6) centmatx -centiles.pred(gamlssfit,xname=agemos,xvalues=Agebin,cent=c(10,25,50,75,90)) Although I got matrix of the percentiles by agebins, I want to obtain the L M S/sigma mu nu corresponding to the same agebins. Any help here will be appreciated. Thanks, Y Addo -- View this message in context: http://r.789695.n4.nabble.com/GAMLSS-Question-tp3389986p3389986.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] Plotting graph problem!!
Thanks a lot for teaching me!!! By the way,one more question,how do i plot a boxplot of that?? On 19/03/11 15:04, Allan Engelhardt wrote: You should probably tell us which part of a- read.csv(http://r.789695.n4.nabble.com/file/n3389613/Life_Expectancies_2008.csv;) hist(a) Should be hist(a$Life.Expectancies.at.Birth), of course. Sorry. -- View this message in context: http://r.789695.n4.nabble.com/Plotting-graph-problem-tp3389613p3390021.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 would you avoid loops in this simple example?
I'm trying to code more R-like and avoid loops. Here is an example I'm having
a hard time getting away from loops with, and the real matrices are rather
large, and the computation is too time-consuming.
### Dimensions
N - 2
M - 3
P - 4
### Array and Matrices
nu - array(NA,dim=c(N,M,P))
Lambda - matrix(1:12,P,M)
F - matrix(1:8,N,P)
### Loop to avoid
for (i in 1:N) {for (m in 1:M) {for (p in 1:P) {
nu[i,m,p] - Lambda[p,m] * F[i,p]
}}}
Any help is appreciated. Thanks.
--
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[R] Output a table formatted with standard deviations below means
Is it in bad form to double post to StackOverflow and R-help? Apologies if so. Here's my task: I've got a matrix of means like so means-matrix(1:10,nrow=2) colnames(means)-c(a,b,c,d,e) and a matrix of standard deviations like so sds-matrix(seq(0.1,1,by=0.1),nrow=2) colnames(sds)-c(a,b,c,d,e) and I want to output a Latex (or HTML) table where the standard deviations appear in parens just below the corresponding means. Something like this: a b c d e \\ 1 3 5 7 9 \\ (0.1)(0.3) (0.5) (0.7) (0.9) \\ 2 4 6 8 10 \\ (0.2)(0.4) (0.6) (0.8) (1.0) \\ except in proper Latex (or HTML). How can I do this from R? Someone mentioned the apsrtable package but that seems to require my having a model object. Thanks in advance folks. [[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] Output a table formatted with standard deviations below means
Hi Nathan,
Do not know a direct way, but the following seems to work:
# data
means - matrix(1:10,nrow=2)
sds - matrix(seq(0.1,1,by=0.1),nrow=2)
colnames(means) - colnames(sds) - c(a,b,c,d,e)
# adding ( ) to the SDs
sdsn - t(apply(sds, 1, function(x) paste('(', x, ')', sep = )))
# formatting
res - do.call(rbind, lapply(1:nrow(means), function(i) rbind(means[i, ],
sdsn[i, ])))
res
# LaTeX
require(xtable)
xtable(res)
*HTH,*
*Jorge*
*
*
On Sat, Mar 19, 2011 at 12:13 PM, Nathan Torrance wrote:
Is it in bad form to double post to StackOverflow and R-help? Apologies if
so. Here's my task:
I've got a matrix of means like so
means-matrix(1:10,nrow=2)
colnames(means)-c(a,b,c,d,e)
and a matrix of standard deviations like so
sds-matrix(seq(0.1,1,by=0.1),nrow=2)
colnames(sds)-c(a,b,c,d,e)
and I want to output a Latex (or HTML) table where the standard deviations
appear in parens just below the corresponding means.
Something like this:
a b c d e \\
1 3 5 7 9 \\
(0.1)(0.3) (0.5) (0.7) (0.9) \\
2 4 6 8 10 \\
(0.2)(0.4) (0.6) (0.8) (1.0) \\
except in proper Latex (or HTML).
How can I do this from R?
Someone mentioned the apsrtable package but that seems to require my
having a model object.
Thanks in advance folks.
[[alternative HTML version deleted]]
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http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Output a table formatted with standard deviations below means
On Mar 19, 2011, at 12:13 PM, Nathan Torrance wrote: Is it in bad form to double post to StackOverflow and R-help? Apologies if so. Here's my task: I've got a matrix of means like so means-matrix(1:10,nrow=2) colnames(means)-c(a,b,c,d,e) and a matrix of standard deviations like so sds-matrix(seq(0.1,1,by=0.1),nrow=2) colnames(sds)-c(a,b,c,d,e) and I want to output a Latex (or HTML) table where the standard deviations appear in parens just below the corresponding means. require(Hmisc) mtx - matrix(c( means[1,], paste((,sds[1,],)), means[2,], paste((,sds[2,],))), nrow=4, byrow=TRUE) colnames(mtx)-colnames(means) latex(mtx) -- David Something like this: a b c d e \\ 1 3 5 7 9 \\ (0.1)(0.3) (0.5) (0.7) (0.9) \\ 2 4 6 8 10 \\ (0.2)(0.4) (0.6) (0.8) (1.0) \\ except in proper Latex (or HTML). How can I do this from R? Someone mentioned the apsrtable package but that seems to require my having a model object. Thanks in advance folks. [[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. 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] How would you avoid loops in this simple example?
Hi,
You are basically just doing matrix multiplication, which R has some
built in, optimized functions for. You can see the documentation at
?matmult
This gets you part of the way there. I suspect you can even avoid the
last loop if you know enough about linear algebra and how to use some
clever transposition and inner or outer multiplication (?outer ?t
?matmult).
## alternate nu
nu2 - array(NA,dim=c(N,M,P))
## avoiding much of that loop
for(i in 1:P) {
nu2[,, i] - F[, i, drop = FALSE] %*% Lambda[i, ]
}
HTH,
Josh
On Sat, Mar 19, 2011 at 10:27 AM, zerfetzen
paul.heinrich.dietr...@gmail.com wrote:
I'm trying to code more R-like and avoid loops. Here is an example I'm having
a hard time getting away from loops with, and the real matrices are rather
large, and the computation is too time-consuming.
### Dimensions
N - 2
M - 3
P - 4
### Array and Matrices
nu - array(NA,dim=c(N,M,P))
Lambda - matrix(1:12,P,M)
F - matrix(1:8,N,P)
### Loop to avoid
for (i in 1:N) {for (m in 1:M) {for (p in 1:P) {
nu[i,m,p] - Lambda[p,m] * F[i,p]
}}}
Any help is appreciated. Thanks.
--
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Joshua Wiley
Ph.D. Student, Health Psychology
University of California, Los Angeles
http://www.joshuawiley.com/
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Re: [R] Libraries issue
On Mar 19, 2011, at 17:37 , Ben Ward wrote: Hi, I've just discovered R keeps installing my packages into C:\Users\Ben instead of C:\\Users\\Ben;/R/win-library/2.12 which is what is returned by running Sys.getenv(R_LIBS_USER). Er, I'm rusty on Windows, but that's what it is supposed to do, isn't it? It's a path with two semicolon separated directories. -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@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] som package: the code of som.train (what is it?)
Hi to all, I am new in the forum, and also in using R (with Rkward in Kubuntu). I have a little problem with the som package: I do the first steps (som.init and som), but when I have to do the train [ som.train(data, code, xdim, ydim, alpha=NULL, alphaType=inverse, neigh=gaussian, topol=rect, radius=NULL, rlen=NULL, err.radius=1, inv.alp.c=NULL) ] I cannot understand what I have to write in the place of code. I'm sorry if my doubt seems non comprehensible to someone, but I am not an expert in maths, nor in programming. Thanks to all for the help. -- View this message in context: http://r.789695.n4.nabble.com/som-package-the-code-of-som-train-what-is-it-tp3390108p3390108.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 running a function
Dear people,
I'm trying to do some analysis of a data using the models by Royle Donazio
in their fantastic book, particular the following function:
http://www.mbr-pwrc.usgs.gov/pubanalysis/roylebook/panel4pt1.fn
that applied to my data and in the console is as follows:
`desman.y` - structure(c(3L,4L,3L,2L,1L), .Names = c(1, 2, 3, 4,
5))
RN-function(y=desman.y,J=5,nsites=39,Nmax=100){
+
+ lik-function(parms){
+ r-expit(parms[1])
+ lambda-exp(parms[2])
+ pvec-1-(1-r)^(0:Nmax)
+ gN-dpois(0:Nmax,lambda)
+ gN-gN/sum(gN)
+ lik-rep(NA,nsites)
+ for(i in 1:nsites){
+ lik[i]-sum(dbinom(y[i],J,pvec)*gN)
+ }
+ -1*sum(log(lik))
+}
+
+
+ tmp-nlm(lik,c(0,0),hessian=TRUE)
+ ests-tmp$estimate
+ aic-tmp$minimum*2 + 2*length(ests)
+ se- sqrt(diag(solve(tmp$hessian)))
+ list(ests=ests,se=se,aic=aic)
+ }
but when I try to see the results (i.e., the list in the function), I've the
follow errors:
summary(RN)
Error in object[[i]] : object of type 'closure' is not subsettable
or obtains something like:
print(RN)
function(y=desman.y,J=5,nsites=39,Nmax=100){
lik-function(parms){
r-expit(parms[1])
lambda-exp(parms[2])
pvec-1-(1-r)^(0:Nmax)
gN-dpois(0:Nmax,lambda)
gN-gN/sum(gN)
lik-rep(NA,nsites)
for(i in 1:nsites){
lik[i]-sum(dbinom(y[i],J,pvec)*gN)
}
-1*sum(log(lik))
}
tmp-nlm(lik,c(0,0),hessian=TRUE)
ests-tmp$estimate
aic-tmp$minimum*2 + 2*length(ests)
se- sqrt(diag(solve(tmp$hessian)))
list(ests=ests,se=se,aic=aic)
}
this second one seems like the analyses are not done at all.
Any suggestion? Many thanks,
Pablo
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Re: [R] Problem in installing and starting Rattle
On Mon, Mar 7, 2011 at 6:57 AM, nerice neil.r...@plymouth.ac.uk wrote: CHECK FOR CONFLICTS IN YOUR PATH !!! I had a related problem when trying to use library RGtk2 for the first time. My problem was that when loading the library R was looking for the file zlib1.dll but couldn't find the procedure to launch RGtk2. I was getting an Entry Point not found error from Rgui.exe. The reason was because I had another package in my PATH environment variable (C:\program files\Intel\WiFi\bin) which had a CONFLICTING version of the zlib1.dll - and it was looking in this file and not the zlib1.dll which came with GTK+. Removed this conflict from the PATH and all was ok. I also had a related problem trying to use libary RGtk2 under Windows XP. I kept getting the message unable to load shared object C:\R\site-library\RGtk2\libs\i386\RGtk2.dll Uninstalling and reinstalling various versions of GTK2, both through R and outside R, many times, did not help. With the help of Neil Rice's comment, I found that there was another version of zlib1.dll in a directory on my PATH. Removing that directory from the path (inside R) fixed the problem and RGtk2 runs fine now. Here's an R expression to look for other copies on zlib1.dll on the path: with(list(x=file.path(strsplit(Sys.getenv(PATH), ;)$PATH, zlib1.dll)), x[file.exists(x)]) [1] C:\\R\\GTK2-Runtime\\bin/zlib1.dll There are many ways to modify the PATH. To set PATH inside R: Sys.setenv(PATH=paste(grep(UNWANTEDPATH, strsplit(Sys.getenv(PATH), ;)[[1]], value=T, invert=T), collapse=;)) (substitute some pattern that matches the unwanted directory for UNWANTEDPATH, remembering to use four backslashes to match one). -- Tony Plate __ 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] Libraries issue
Hi. On Sat, Mar 19, 2011 at 12:17 PM, peter dalgaard pda...@gmail.com wrote: On Mar 19, 2011, at 17:37 , Ben Ward wrote: Hi, I've just discovered R keeps installing my packages into C:\Users\Ben instead of C:\\Users\\Ben;/R/win-library/2.12 which is what is returned by running Sys.getenv(R_LIBS_USER). Er, I'm rusty on Windows, but that's what it is supposed to do, isn't it? It's a path with two semicolon separated directories. Unless explicitly requested to be so, most likely it is indeed meant to be without the semicolon, i.e. C:\\Users\\Ben/R/win-library/2.12 (or normalized C:\\Users\\Ben\R\win-library\2.12, but that doesn't matter here). This is in line with what is said in help(.libPaths): By default R_LIBS is unset, and R_LIBS_USER is set to subdirectory ‘R/win-library/x.y’ of the home directory, for R x.y.z. Here are my Windows environment variables: Sys.getenv(R_LIBS_USER) R_LIBS_USER C:\\Users\\hb/R/win-library/2.12 Sys.getenv(HOME) HOME C:\\Users\\hb There should certainly not be any semicolons in the latter. If you set HOME to C:\\Users\\hb; before starting R, you do get: Sys.getenv(R_LIBS_USER) R_LIBS_USER C:\\Users\\hb;/R/win-library/2.12 My $.02 /henrik -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@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-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 newbie: how to replace string/regular expression
I would read up on the 'gsub' command in R help. It does what you would like. -- View this message in context: http://r.789695.n4.nabble.com/R-newbie-how-to-replace-string-regular-expression-tp873169p3390170.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] problem running a function
Try
RN()
- Phil Spector
Statistical Computing Facility
Department of Statistics
UC Berkeley
spec...@stat.berkeley.edu
On Sat, 19 Mar 2011, garciap wrote:
Dear people,
I'm trying to do some analysis of a data using the models by Royle Donazio
in their fantastic book, particular the following function:
http://www.mbr-pwrc.usgs.gov/pubanalysis/roylebook/panel4pt1.fn
that applied to my data and in the console is as follows:
`desman.y` - structure(c(3L,4L,3L,2L,1L), .Names = c(1, 2, 3, 4,
5))
RN-function(y=desman.y,J=5,nsites=39,Nmax=100){
+
+ lik-function(parms){
+ r-expit(parms[1])
+ lambda-exp(parms[2])
+ pvec-1-(1-r)^(0:Nmax)
+ gN-dpois(0:Nmax,lambda)
+ gN-gN/sum(gN)
+ lik-rep(NA,nsites)
+ for(i in 1:nsites){
+ lik[i]-sum(dbinom(y[i],J,pvec)*gN)
+ }
+ -1*sum(log(lik))
+}
+
+
+ tmp-nlm(lik,c(0,0),hessian=TRUE)
+ ests-tmp$estimate
+ aic-tmp$minimum*2 + 2*length(ests)
+ se- sqrt(diag(solve(tmp$hessian)))
+ list(ests=ests,se=se,aic=aic)
+ }
but when I try to see the results (i.e., the list in the function), I've the
follow errors:
summary(RN)
Error in object[[i]] : object of type 'closure' is not subsettable
or obtains something like:
print(RN)
function(y=desman.y,J=5,nsites=39,Nmax=100){
lik-function(parms){
r-expit(parms[1])
lambda-exp(parms[2])
pvec-1-(1-r)^(0:Nmax)
gN-dpois(0:Nmax,lambda)
gN-gN/sum(gN)
lik-rep(NA,nsites)
for(i in 1:nsites){
lik[i]-sum(dbinom(y[i],J,pvec)*gN)
}
-1*sum(log(lik))
}
tmp-nlm(lik,c(0,0),hessian=TRUE)
ests-tmp$estimate
aic-tmp$minimum*2 + 2*length(ests)
se- sqrt(diag(solve(tmp$hessian)))
list(ests=ests,se=se,aic=aic)
}
this second one seems like the analyses are not done at all.
Any suggestion? Many thanks,
Pablo
--
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Re: [R] How would you avoid loops in this simple example?
On Sat, Mar 19, 2011 at 10:27:11AM -0700, zerfetzen wrote:
I'm trying to code more R-like and avoid loops. Here is an example I'm having
a hard time getting away from loops with, and the real matrices are rather
large, and the computation is too time-consuming.
### Dimensions
N - 2
M - 3
P - 4
### Array and Matrices
nu - array(NA,dim=c(N,M,P))
Lambda - matrix(1:12,P,M)
F - matrix(1:8,N,P)
### Loop to avoid
for (i in 1:N) {for (m in 1:M) {for (p in 1:P) {
nu[i,m,p] - Lambda[p,m] * F[i,p]
}}}
Try the following
Lambda1 - aperm(array(Lambda, dim=c(P, M, N)), perm=c(3, 2, 1))
F1 - aperm(array(F, dim=c(N, P, M)), perm=c(1, 3, 2))
nu1 - Lambda1 * F1
identical(nu, nu1)
[1] TRUE
The function array() recycles its first argument, if the
required dimension of the output is larger. The function
aperm() then puts the indices to the required order.
Hope this helps.
Petr Savicky.
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Re: [R] GAMLSS Question
Hi, predictAll should do what you want. See ?predict.gamlss. HTH, Denes Dear All: I have succeeded in fitting a GAMLSS.dist model to growth data I am working with it. My aim is to create a matrix of predicted percentiles and the corresponding the fitted model's sigma mu nu by agebins. Q: How do it generate these parameters as in L M S per Cole and Green 1992? Here are my working codes. Name of fitted model is gamlssfit Agebin-seq(6,36,6) centmatx -centiles.pred(gamlssfit,xname=agemos,xvalues=Agebin,cent=c(10,25,50,75,90)) Although I got matrix of the percentiles by agebins, I want to obtain the L M S/sigma mu nu corresponding to the same agebins. Any help here will be appreciated. Thanks, Y Addo -- View this message in context: http://r.789695.n4.nabble.com/GAMLSS-Question-tp3389986p3389986.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] Libraries issue
Hi, Got it fixed now, thanks everyone, still confused as to why it's never done that before, but at least it's fine now. Ben W. On 19/03/2011 19:38, Henrik Bengtsson wrote: Hi. On Sat, Mar 19, 2011 at 12:17 PM, peter dalgaardpda...@gmail.com wrote: On Mar 19, 2011, at 17:37 , Ben Ward wrote: Hi, I've just discovered R keeps installing my packages into C:\Users\Ben instead of C:\\Users\\Ben;/R/win-library/2.12 which is what is returned by running Sys.getenv(R_LIBS_USER). Er, I'm rusty on Windows, but that's what it is supposed to do, isn't it? It's a path with two semicolon separated directories. Unless explicitly requested to be so, most likely it is indeed meant to be without the semicolon, i.e. C:\\Users\\Ben/R/win-library/2.12 (or normalized C:\\Users\\Ben\R\win-library\2.12, but that doesn't matter here). This is in line with what is said in help(.libPaths): By default R_LIBS is unset, and R_LIBS_USER is set to subdirectory ‘R/win-library/x.y’ of the home directory, for R x.y.z. Here are my Windows environment variables: Sys.getenv(R_LIBS_USER) R_LIBS_USER C:\\Users\\hb/R/win-library/2.12 Sys.getenv(HOME) HOME C:\\Users\\hb There should certainly not be any semicolons in the latter. If you set HOME to C:\\Users\\hb; before starting R, you do get: Sys.getenv(R_LIBS_USER) R_LIBS_USER C:\\Users\\hb;/R/win-library/2.12 My $.02 /henrik -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@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-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 running a function
garciap garciap at usal.es writes:
Dear people,
I'm trying to do some analysis of a data using the models by Royle Donazio
in their fantastic book, particular the following function:
http://www.mbr-pwrc.usgs.gov/pubanalysis/roylebook/panel4pt1.fn
[snip]
I'm guessing you're fairly new to R, because you seem confused about
how functions work. You don't need to redefine the function with
your particular data: instead, you 'call' the function with your
data inserted in the call.
Below I've taken the definition of RN from the URL you provided;
I change the 'expit' function to 'plogis', which is an
equivalent function already built into R; and tried to run the RN()
function on your data. I ran into some trouble running the function
before I realized that you had specified 'nsites' different from
the length of your y vector; I don't know under what circumstances
that would ever make sense, since the function is trying to
calculate values from each element of y between 1 and nsites ...
Then the function did run, although it gave lots of warnings
and couldn't compute the standard error for lambda. It also gave
a very small value for r and a very large value for lambda; I suspect
you don't have enough data to do a very good job estimating in this
case ...
RN-function(y,J=11,nsites=length(y),Nmax=100,old=TRUE){
lik-function(parms){
r-plogis(parms[1])
lambda-exp(parms[2])
pvec-1-(1-r)^(0:Nmax)
gN-dpois(0:Nmax,lambda)
gN-gN/sum(gN)
if (old) {
likvec - numeric(nsites)
for(i in 1:nsites){
likvec[i]-sum(dbinom(y[i],J,pvec)*gN)
}
} else {
likvec - rowSums(sweep(outer(y,pvec,dbinom,size=J),2,
gN,*))
}
res - -sum(log(likvec))
res
}
tmp-nlm(f=lik,
p=c(0,0),
hessian=TRUE)
ests-tmp$estimate
aic-tmp$minimum*2 + 2*length(ests)
se- sqrt(diag(solve(tmp$hessian)))
list(ests=ests,se=se,aic=aic)
}
desman - RN(y=c(3,4,3,2,1),J=5)
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[R] Problems using NLS in conjunction with non-parameteric bootstrapping
Hello,
I have been successfully using nls to fit a non-linear, self-limiting
function to several sets of data collected in 2010 (example found below).
To generate confidence intervals for parameter estimates, I've been
attempting to bootstrap my sample. Unfortunately, I have meet with
singularity gradients and failures to converge. I have altered maxiter and
minFactor statements, used several different starting parameters, and the
plinear and port algorithm to no avail. I used this same approach on a 2009
data set with no problems.
I'm assuming that one or more of my bootstrap samples is causing the
problem. If this is the case, are there any suggestions on how I can proceed
with bootstrapping to generate CI?
Thank you in advance,
Mark
y - c(3.46,1.00,2.0,2.23,4.24,1.00,4.58,
4.69,3.00,5.10,2.83,3.46,1.73,2.46,1.41,2.24,3.00,1.73)
x - c(0.39,0.05,0.10,0.20,0.53,0.17,0.61,
0.40,0.30,0.40,0.42,0.35,0.28,0.40,0.12,0.25,0.71,0.15)
mydata - data.frame(x,y)
names(mydata) - c(x,y) # variable names
%x=Trap success; proportion of total trap nights where at least one deer was
photographed
%y=Square root transformation of total number of deer photographed
#asymptotic equation y = (a*x)/(b+x)
NlMFunc1 - function(x, a, b) {(a*x)/(b+x)}
NlMFunc1 - nls(y ~ NlMFunc1(x, alpha, beta),
data = RPOvTS, start = list(alpha = 10, beta = 1), control = list(maxiter =
1, minFactor=1/20048),
trace = T)
summary(NlMFunc1)
logLik(NlMFunc1)
#Generate non-parametric bootstrap estimates of alpha and beta
#using bootstrapping
BootF=function (data,i){
# take a random sample of size 18 from a SqRtFemPhoto
# sample with replacement
d - data[i,]
NlmResampF- function(x, a, b) {(a*x)/(b+x)}
NlmResampF - nls(y ~ NlmResampF (x, alpha, beta),
data = d, start = list(alpha = 10, beta = 1),
control = list(maxiter = 1, minFactor=1/20048,
trace = T))
c(logLik(NlmResampF ), coef(NlmResampF )) }
#summary(NlmResampF )
#logLik(NlmResampF )
library(boot)
Female.boot-boot(data=mydata, statistic=BootF,
R=1000)
Female.boot$t
--
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[R] create a matrix with values from data.frame
Hello, I'm trying to create a matrix (95x55) with data from a data.frame pop: xloc yloc go indEne totW 123 20 516 1 0.02 20.21 223 20 1143 1 0.02 20.21 323 20 250 1 0.02 20.21 422 15 251 1 0.02 18.69 522 15 598 1 0.02 18.69 621 19 250 1 0.02 20.21 722 20 251 1 0.02 18.69 822 20 598 1 0.02 18.69 where xloc is the x dimension, yloc the y dimension, and totW the values for each cell (xloc,yloc) in my matrix (55x95): I'm trying: Bio=with(pop, (table(factor(totW, levels = 1:55), factor(totW, levels = 1:95 But I don't get what I want. Hints? Thanks! Nic __ 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] persuade tabulate function to count NAs in a data frame
On 03/20/2011 01:58 AM, Bodnar Laszlo EB_HU wrote: Hi, I'd like to ask you a question again. It is basically about data frames, NAs and tabulate function. Hi Bodnar, The freq function in the prettyR package might do what you want. 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] create a matrix with values from data.frame
On Mar 19, 2011, at 5:29 PM, Nicolas Gutierrez wrote: Hello, I'm trying to create a matrix (95x55) with data from a data.frame pop: xloc yloc go indEne totW 123 20 516 1 0.02 20.21 223 20 1143 1 0.02 20.21 323 20 250 1 0.02 20.21 422 15 251 1 0.02 18.69 522 15 598 1 0.02 18.69 621 19 250 1 0.02 20.21 722 20 251 1 0.02 18.69 822 20 598 1 0.02 18.69 where xloc is the x dimension, yloc the y dimension, and totW the values for each cell (xloc,yloc) in my matrix (55x95): I'm trying: Bio=with(pop, (table(factor(totW, levels = 1:55), factor(totW, levels = 1:95 You probably should be using `cut` rather than `factor`. (Both will create factor-class variables.) Factor will give you a different level at each unique value while it appears that you want integer valued cuts. It's also unclear why you would be applying these cuts to totW twice You have three rows with identical (23,20) x,y coordinates and two each for (22,15) and (22,20), although the go values are different. But I don't get what I want. Hints? Thanks! Better advice might follow if you said what you were really trying to do and what the final answer should look like. Nic __ 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] create a matrix with values from data.frame
Here is one way to fill in the value using indexing; it appears that you data has the same xloc/yloc values x xloc yloc go ind Ene totW 1 23 20 516 1 0.02 20.21 2 23 20 1143 1 0.02 20.21 3 23 20 250 1 0.02 20.21 4 22 15 251 1 0.02 18.69 5 22 15 598 1 0.02 18.69 6 21 19 250 1 0.02 20.21 7 22 20 251 1 0.02 18.69 8 22 20 598 1 0.02 18.69 x.mat - matrix(NA, 95, 55) # create matrix x.mat[cbind(x$xloc, x$yloc)] - x$totW which(!is.na(x.mat), arr.ind =TRUE) row col [1,] 22 15 [2,] 21 19 [3,] 22 20 [4,] 23 20 On Sat, Mar 19, 2011 at 5:29 PM, Nicolas Gutierrez nicol...@uw.edu wrote: Hello, I'm trying to create a matrix (95x55) with data from a data.frame pop: xloc yloc go ind Ene totW 1 23 20 516 1 0.02 20.21 2 23 20 1143 1 0.02 20.21 3 23 20 250 1 0.02 20.21 4 22 15 251 1 0.02 18.69 5 22 15 598 1 0.02 18.69 6 21 19 250 1 0.02 20.21 7 22 20 251 1 0.02 18.69 8 22 20 598 1 0.02 18.69 where xloc is the x dimension, yloc the y dimension, and totW the values for each cell (xloc,yloc) in my matrix (55x95): I'm trying: Bio=with(pop, (table(factor(totW, levels = 1:55), factor(totW, levels = 1:95 But I don't get what I want. Hints? Thanks! Nic __ 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? __ 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] Plotting graph problem!!
On 03/20/2011 04:33 AM, andrew456 wrote: Thanks a lot for teaching me!!! By the way,one more question,how do i plot a boxplot of that?? Hi Andrew, As you seem to be an R newbie and some of the replies may have been cryptic to a newbie, try this: boxplot(a$Life.Expectancies.at.Birth) To explain the above a little bit, when reading in a text file, R does some silent substitutions, like sticking full stops (.) in where there were spaces in the field labels. The dollar sign operator means return the list element of a - a data frame column in this case - that has the name after the dollar sign. That gives the boxplot function a vector of numeric values and it knows what to do. These things are so familiar to most of us that we don't bother to explain them. You will probably encounter more of these little mysteries as you progress with R. Good luck. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] create a matrix with values from data.frame
Thanks Jim and David.. that was easy! Nic On 3/19/2011 3:00 PM, jim holtman wrote: x.mat- matrix(NA, 95, 55) # create matrix x.mat[cbind(x$xloc, x$yloc)]- x$totW which(!is.na(x.mat), arr.ind =TRUE) __ 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] I want to create an object to use for the plot command
I'm using the TSA package (along with all prerequisites) to do some GARCH work and for some reason, something which used to work for me has decided to up and stop. The code is as follows, after loading the package: gs - garch.sim(alpha=c(1.9,0.1), beta=c(0.71, -0.083, -0.016),rnd = rnorm, n = 400, ntrans=500) gs1 - garch.sim(alpha=c(1.9,0.1), beta=c(0.7, -0.08, -0.016),rnd = rnorm, n = 400, ntrans=500) gts=ts(gs) gts1=ts(gs1) dgts=gts1-gts test - garch(dgts, order=c(0,0)) plot(test) However, I get the following error: Error in plot(test) : object 'test' not found What's extra annoying is that I had been using this type of code before and it was working fine, I honestly don't know what the problem is, I've used R reasonable extensively before but never with these packages so I'm not sure what I might have done wrong. If anyone could take the time to help me out, I'd really appreciate it. Yours etc, Aodhán -- View this message in context: http://r.789695.n4.nabble.com/I-want-to-create-an-object-to-use-for-the-plot-command-tp3390383p3390383.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] Referring to objects themselves
Is it possible to refer to an object from within a method, as in *this *in Java? I can't find anything about this in the documentation. Sorry if I missed it. Thanks. *-- Russ Abbott* *_* *** Professor, Computer Science* * California State University, Los Angeles* * Google voice: 747-*999-5105 * blog: *http://russabbott.blogspot.com/ vita: http://sites.google.com/site/russabbott/ *_* [[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] I want to create an object to use for the plot command
On Mar 19, 2011, at 7:02 PM, AOLeary wrote: I'm using the TSA package (along with all prerequisites) to do some GARCH work and for some reason, something which used to work for me has decided to up and stop. The code is as follows, after loading the package: gs - garch.sim(alpha=c(1.9,0.1), beta=c(0.71, -0.083, -0.016),rnd = rnorm, n = 400, ntrans=500) gs1 - garch.sim(alpha=c(1.9,0.1), beta=c(0.7, -0.08, -0.016),rnd = rnorm, n = 400, ntrans=500) gts=ts(gs) gts1=ts(gs1) dgts=gts1-gts test - garch(dgts, order=c(0,0)) plot(test) However, I get the following error: Actually you failed to note that you got an earlier error from the garch() function: Error in sigt[1:max(order[1], order[2])] - rep.int(NA, max(order[1], : replacement has length zero Which raises the question... what does it mean to specify a GARCH model of order c(0,0)? -- David. Error in plot(test) : object 'test' not found What's extra annoying is that I had been using this type of code before and it was working fine, I honestly don't know what the problem is, I've used R reasonable extensively before but never with these packages so I'm not sure what I might have done wrong. If anyone could take the time to help me out, I'd really appreciate it. Yours etc, Aodhán -- View this message in context: http://r.789695.n4.nabble.com/I-want-to-create-an-object-to-use-for-the-plot-command-tp3390383p3390383.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. 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] Referring to objects themselves
On Sat, Mar 19, 2011 at 6:34 PM, Russ Abbott russ.abb...@gmail.com wrote: Is it possible to refer to an object from within a method, as in *this *in Java? I can't find anything about this in the documentation. Sorry if I missed it. Assuming you are referring to S3, the first argument to a method is the object (unless specified otherwise in the UseMethod call but that is rarely done). -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at 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.
Re: [R] I want to create an object to use for the plot command
Hm, thank you David, that is a good point. I'm trying to model it as a white noise model, essentially. Now that I think of it there's probably an easier way to do this that I haven't thought of yet. I was trying it this way based on something I'd remembered reading from Engle's original paper on ARCH models where an ARCH(0,0) model would correspond to a white noise process. It may be that the GARCH implementation in R has a different specification. In any case, thank you for pointing that out. A simple error I hadn't noticed at all. Yours etc, Aodhán -- View this message in context: http://r.789695.n4.nabble.com/I-want-to-create-an-object-to-use-for-the-plot-command-tp3390383p3390444.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] Referring to objects themselves
Actually, I guess I'm not really talking about objects. I was looking
through the scoping demo. It uses this function.
open.account - function(total) {
+
+ list(
+deposit = function(amount) {
+if(amount = 0)
+stop(Deposits must be positive!\n)
+total - total + amount
+cat(amount,deposited. Your balance is, total, \n\n)
+},
+withdraw = function(amount) {
+if(amount total)
+stop(You don't have that much money!\n)
+total - total - amount
+cat(amount,withdrawn. Your balance is, total, \n\n)
+},
+balance = function() {
+cat(Your balance is, total, \n\n)
+}
+)
+ }
I wanted to re-write the function so that instead of referring to *total *in
*deposit *and *withdraw *I could refer to *balance*. Something like this,
withdraw = function(amount) {
+if(amount total)
+stop(You don't have that much money!\n)
+total - total - amount
+cat(amount,withdrawn. Your balance is, *this,balance()*,
\n\n)
But that doesn't work. Is it possible to do this?
Thanks.
*-- Russ Abbott*
*_*
*** Professor, Computer Science*
* California State University, Los Angeles*
* Google voice: 747-*999-5105
* blog: *http://russabbott.blogspot.com/
vita: http://sites.google.com/site/russabbott/
*_*
On Sat, Mar 19, 2011 at 4:40 PM, Gabor Grothendieck ggrothendi...@gmail.com
wrote:
On Sat, Mar 19, 2011 at 6:34 PM, Russ Abbott russ.abb...@gmail.com
wrote:
Is it possible to refer to an object from within a method, as in *this
*in
Java? I can't find anything about this in the documentation. Sorry if I
missed it.
Assuming you are referring to S3, the first argument to a method is
the object (unless specified otherwise in the UseMethod call but that
is rarely done).
--
Statistics Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.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] How to draw a map of Europe?
Hi R users, I need to draw a map of select European countries with country names shown on the map. Does anyone know how to do this in R? Also, is it possible to draw a historical map of European countries using R? Thanks a lot for your help. Maomao [[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] Referring to objects themselves
You might want to check out Reference Classes (?SetRefClass). The object itself is stored in '.self' and can be referenced that way. HTH, Janko -Ursprüngliche Nachricht- Von: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Im Auftrag von Russ Abbott Gesendet: Samstag, 19. März 2011 23:35 An: r-help@r-project.org Betreff: [R] Referring to objects themselves Is it possible to refer to an object from within a method, as in *this *in Java? I can't find anything about this in the documentation. Sorry if I missed it. Thanks. *-- Russ Abbott* *_* *** Professor, Computer Science* * California State University, Los Angeles* * Google voice: 747-*999-5105 * blog: *http://russabbott.blogspot.com/ vita: http://sites.google.com/site/russabbott/ *_* [[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] Referring to objects themselves
On Sat, Mar 19, 2011 at 8:02 PM, Russ Abbott russ.abb...@gmail.com wrote:
Actually, I guess I'm not really talking about objects. I was looking
through the scoping demo. It uses this function.
open.account - function(total) {
+
+ list(
+ deposit = function(amount) {
+ if(amount = 0)
+ stop(Deposits must be positive!\n)
+ total - total + amount
+ cat(amount,deposited. Your balance is, total, \n\n)
+ },
+ withdraw = function(amount) {
+ if(amount total)
+ stop(You don't have that much money!\n)
+ total - total - amount
+ cat(amount,withdrawn. Your balance is, total, \n\n)
+ },
+ balance = function() {
+ cat(Your balance is, total, \n\n)
+ }
+ )
+ }
I wanted to re-write the function so that instead of referring to total in
deposit and withdraw I could refer to balance. Something like this,
withdraw = function(amount) {
+ if(amount total)
+ stop(You don't have that much money!\n)
+ total - total - amount
+ cat(amount,withdrawn. Your balance is, this,balance(),
\n\n)
But that doesn't work. Is it possible to do this?
Thanks.
Try this:
open.account - function(total) {
this - environment()
list(...same list as before...)
}
Now within the body of any of the methods in the list, this$total
refers to the balance.
--
Statistics Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Referring to objects themselves
You could (in addition to the other suggestions) try package proto (. refers
to self but see also the package's vignette)
account - proto(
deposit = function(., amount) {
if(amount = 0) stop(Deposits must be positive!\n)
.$total - .$total + amount
cat(amount,deposited. )
.$balance()
},
withdraw = function(., amount) {
if(amount .$total) stop(You don't have that much money!\n)
.$total - .$total - amount
cat(amount,withdrawn. )
.$balance()
},
balance = function(.) {
cat(Your balance is, .$total, \n\n)
},
new = function(., total) .$proto(total = total)
)
a - account$new(10)
a$withdraw(10)
a$balance()
On Sun, Mar 20, 2011 at 2:02 AM, Russ Abbott russ.abb...@gmail.com wrote:
Actually, I guess I'm not really talking about objects. I was looking
through the scoping demo. It uses this function.
open.account - function(total) {
+
+ list(
+deposit = function(amount) {
+if(amount = 0)
+stop(Deposits must be positive!\n)
+total - total + amount
+cat(amount,deposited. Your balance is, total, \n\n)
+},
+withdraw = function(amount) {
+if(amount total)
+stop(You don't have that much money!\n)
+total - total - amount
+cat(amount,withdrawn. Your balance is, total, \n\n)
+},
+balance = function() {
+cat(Your balance is, total, \n\n)
+}
+)
+ }
I wanted to re-write the function so that instead of referring to *total
*in
*deposit *and *withdraw *I could refer to *balance*. Something like this,
withdraw = function(amount) {
+if(amount total)
+stop(You don't have that much money!\n)
+total - total - amount
+cat(amount,withdrawn. Your balance is, *this,balance()*,
\n\n)
But that doesn't work. Is it possible to do this?
Thanks.
*-- Russ Abbott*
*_*
*** Professor, Computer Science*
* California State University, Los Angeles*
* Google voice: 747-*999-5105
* blog: *http://russabbott.blogspot.com/
vita: http://sites.google.com/site/russabbott/
*_*
On Sat, Mar 19, 2011 at 4:40 PM, Gabor Grothendieck
ggrothendi...@gmail.com
wrote:
On Sat, Mar 19, 2011 at 6:34 PM, Russ Abbott russ.abb...@gmail.com
wrote:
Is it possible to refer to an object from within a method, as in *this
*in
Java? I can't find anything about this in the documentation. Sorry if
I
missed it.
Assuming you are referring to S3, the first argument to a method is
the object (unless specified otherwise in the UseMethod call but that
is rarely done).
--
Statistics Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.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.
[[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 draw a map of Europe?
Date: Sat, 19 Mar 2011 19:32:43 -0500 From: shali...@gmail.com To: r-help@r-project.org Subject: [R] How to draw a map of Europe? Hi R users, I need to draw a map of select European countries with country names shown on the map. Does anyone know how to do this in R? Also, is it possible to draw a historical map of European countries using R? This came up on this list a while ago and I was just using that example for some work I'm doing but I have only copied what was posted and added minor things to it. I can't give you actual answer but you are probably just a few key words away from a google searhc. The term you are probably looking for is shapefile. Try that on google. For example, http://www.google.com/#sclient=psyhl=enq=shapefile+cran+europe turns up things that may help. Thanks a lot for your help. Maomao __ 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] Problems with package npmc
Hi there, I am having a problem with package npmc. If I use the included datasets (brain, kronen) everything is fine, but if I try and use my dataset I receive an error message: Error in probval.GenzBretz(algorithm, n, df, lower, upper, infin, corr, : NAs in foreign function call (arg 2) In addition: Warning message: In probval.GenzBretz(algorithm, n, df, lower, upper, infin, corr, : NAs introduced by coercion I couldn't solve the problem. C. -- View this message in context: http://r.789695.n4.nabble.com/Problems-with-package-npmc-tp3390472p3390472.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] Referring to objects themselves
See also the proto package, I believe. -- Bert On Sat, Mar 19, 2011 at 5:51 PM, Janko Thyson janko.thyson.rst...@googlemail.com wrote: You might want to check out Reference Classes (?SetRefClass). The object itself is stored in '.self' and can be referenced that way. HTH, Janko -Ursprüngliche Nachricht- Von: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Im Auftrag von Russ Abbott Gesendet: Samstag, 19. März 2011 23:35 An: r-help@r-project.org Betreff: [R] Referring to objects themselves Is it possible to refer to an object from within a method, as in *this *in Java? I can't find anything about this in the documentation. Sorry if I missed it. Thanks. *-- Russ Abbott* *_* *** Professor, Computer Science* * California State University, Los Angeles* * Google voice: 747-*999-5105 * blog: *http://russabbott.blogspot.com/ vita: http://sites.google.com/site/russabbott/ *_* [[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. -- Bert Gunter Genentech Nonclinical Biostatistics __ 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] Referring to objects themselves
Thanks for all the suggestions. I realize that this isn't the most important
thing in the world -- and as a newcomer to R I gather it's not the way most
people use R anyway.
But I tried to do what looked like the simplest suggestion.
open.account.2 - function(total) {
this - environment()
list(
deposit = function(amount) {
if(amount = 0)
stop(Deposits must be positive!\n)
total - total + amount
cat(amount, deposited. Your balance is, this$balance(),
\n\n)
},
withdraw = function(amount) {
if(amount total)
stop(You don't have that much money!\n)
total - total - amount
cat(amount, withdrawn. Your balance is, this$balance(),
\n\n)
},
balance = function() {
cat(Your balance is, this$total, \n\n)
}
)
}
When I ran it, this is what happened.
x - open.account.2(100)
x$balance()
Your balance is 100
OK so far. But
x$deposit(50)
Error in cat(amount, deposited. Your balance is, this$balance(), \n\n)
:
attempt to apply non-function
Am I doing this the wrong way?
Thanks for your interest.
*-- Russ *
On Sat, Mar 19, 2011 at 6:33 PM, Bert Gunter gunter.ber...@gene.com wrote:
See also the proto package, I believe.
-- Bert
On Sat, Mar 19, 2011 at 5:51 PM, Janko Thyson
janko.thyson.rst...@googlemail.com wrote:
You might want to check out Reference Classes (?SetRefClass). The object
itself is stored in '.self' and can be referenced that way.
HTH,
Janko
-Ursprüngliche Nachricht-
Von: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
Im
Auftrag von Russ Abbott
Gesendet: Samstag, 19. März 2011 23:35
An: r-help@r-project.org
Betreff: [R] Referring to objects themselves
Is it possible to refer to an object from within a method, as in *this
*in
Java? I can't find anything about this in the documentation. Sorry if I
missed it.
Thanks.
*-- Russ Abbott*
*_*
*** Professor, Computer Science*
* California State University, Los Angeles*
* Google voice: 747-*999-5105
* blog: *http://russabbott.blogspot.com/
vita: http://sites.google.com/site/russabbott/
*_*
[[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.
--
Bert Gunter
Genentech Nonclinical Biostatistics
[[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 draw a map of Europe?
On Mar 19, 2011, at 8:32 PM, Sally Luo wrote: Hi R users, I need to draw a map of select European countries with country names shown on the map. Does anyone know how to do this in R? Adding a tiny bit to the material produced from a search and finding something from Roger Bivand in response to Rense Nieuwenhuis: http://finzi.psych.upenn.edu/R/Rhelp02/archive/85586.html require(maps) country2001 - c(Austria, Belgium, Switzerland, Czechoslovakia, Germany, Denmark, Spain, Finland, France, UK, Greece, Hungary, Ireland, Israel, Italy, Luxembourg, Netherlands, Norway, Poland, Portugal, Sweden, Slovenia) color2001 - c(green, yellow,red,red, red, red, red, red, green, red, red, red, red, red, red, red, red, blue, red, red, red, orange) europe$names[grep(Sicily, europe$names)] - Italy:Sicily europe$names[grep(Sardinia, europe$names)] - Italy:Sardinia match - match.map(europe,country2001) color - color2001[match] map(database=world, fill=TRUE, col=color, xlim=c(-25,70),ylim=c(35,71)) text(0, 45, France) Also, is it possible to draw a historical map of European countries using R? Thanks a lot for your help. Maomao [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Referring to objects themselves
you can omit the list and do the following:
open.account.2 - function(total) {
deposit - function(amount) {
if(amount = 0)
stop(Deposits must be positive!\n)
total - total + amount
cat(amount, deposited. Your balance is, this$balance(),\n\n)
}
withdraw - function(amount) {
if(amount total)
stop(You don't have that much money!\n)
total - total - amount
cat(amount, withdrawn. Your balance is, this$balance(),\n\n)
}
balance - function() {
cat(Your balance is, this$total, \n\n)
}
this - environment()
}
But notice that the function balance returns nothing (because of the cat)
and balance message will be printed (cat'ed) doubly - this is easy to fix.
(but you don't really need this in this case as you can use balance
instead of this$balance)
The last row does two things: invisibly returns the environment (necessary
for things like x$balance()) and assigns it to this
Regards,
Kenn
On Sun, Mar 20, 2011 at 3:45 AM, Russ Abbott russ.abb...@gmail.com wrote:
Thanks for all the suggestions. I realize that this isn't the most
important
thing in the world -- and as a newcomer to R I gather it's not the way most
people use R anyway.
But I tried to do what looked like the simplest suggestion.
open.account.2 - function(total) {
this - environment()
list(
deposit = function(amount) {
if(amount = 0)
stop(Deposits must be positive!\n)
total - total + amount
cat(amount, deposited. Your balance is, this$balance(),
\n\n)
},
withdraw = function(amount) {
if(amount total)
stop(You don't have that much money!\n)
total - total - amount
cat(amount, withdrawn. Your balance is, this$balance(),
\n\n)
},
balance = function() {
cat(Your balance is, this$total, \n\n)
}
)
}
When I ran it, this is what happened.
x - open.account.2(100)
x$balance()
Your balance is 100
OK so far. But
x$deposit(50)
Error in cat(amount, deposited. Your balance is, this$balance(), \n\n)
:
attempt to apply non-function
Am I doing this the wrong way?
Thanks for your interest.
*-- Russ *
On Sat, Mar 19, 2011 at 6:33 PM, Bert Gunter gunter.ber...@gene.com
wrote:
See also the proto package, I believe.
-- Bert
On Sat, Mar 19, 2011 at 5:51 PM, Janko Thyson
janko.thyson.rst...@googlemail.com wrote:
You might want to check out Reference Classes (?SetRefClass). The
object
itself is stored in '.self' and can be referenced that way.
HTH,
Janko
-Ursprüngliche Nachricht-
Von: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org
]
Im
Auftrag von Russ Abbott
Gesendet: Samstag, 19. März 2011 23:35
An: r-help@r-project.org
Betreff: [R] Referring to objects themselves
Is it possible to refer to an object from within a method, as in *this
*in
Java? I can't find anything about this in the documentation. Sorry if
I
missed it.
Thanks.
*-- Russ Abbott*
*_*
*** Professor, Computer Science*
* California State University, Los Angeles*
* Google voice: 747-*999-5105
* blog: *http://russabbott.blogspot.com/
vita: http://sites.google.com/site/russabbott/
*_*
[[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.
--
Bert Gunter
Genentech Nonclinical Biostatistics
[[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] Part of a density plot
Suupose I have y - rbeta(1, 2, 5) and I only want to see only the density plot from x = 0 to x = 1 How do I do this? -- Thanks, Jim. [[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] Referring to objects themselves
On Sun, Mar 20, 2011 at 4:13 AM, Kenn Konstabel lebats...@gmail.com wrote: you can omit the list and do the following: /.../ (but you don't really need this in this case as you can use balance instead of this$balance) P.S. using this would make some difference in one case: instead of total - total + amount # need - here you can have this$total - this$total + amount # can use - [[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 would you avoid loops in this simple example?
Thanks for the help, and now I have some functions to learn. Both suggestions work great, really appreciate it. -- View this message in context: http://r.789695.n4.nabble.com/How-would-you-avoid-loops-in-this-simple-example-tp3390017p3390549.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 draw a map of Europe?
I've created historical maps using R, but it required careful research, translating the boundaries into longitude and latitude shape files, then plotting them, similar to the example that David just provided. It seemed to be the easiest way I knew to produce the desired result, but it still took a moderate level of effort. Hope this helps. Spencer Graves On 3/19/2011 6:51 PM, David Winsemius wrote: On Mar 19, 2011, at 8:32 PM, Sally Luo wrote: Hi R users, I need to draw a map of select European countries with country names shown on the map. Does anyone know how to do this in R? Adding a tiny bit to the material produced from a search and finding something from Roger Bivand in response to Rense Nieuwenhuis: http://finzi.psych.upenn.edu/R/Rhelp02/archive/85586.html require(maps) country2001 - c(Austria, Belgium, Switzerland, Czechoslovakia, Germany, Denmark, Spain, Finland, France, UK, Greece, Hungary, Ireland, Israel, Italy, Luxembourg, Netherlands, Norway, Poland, Portugal, Sweden, Slovenia) color2001 - c(green, yellow,red,red, red, red, red, red, green, red, red, red, red, red, red, red, red, blue, red, red, red, orange) europe$names[grep(Sicily, europe$names)] - Italy:Sicily europe$names[grep(Sardinia, europe$names)] - Italy:Sardinia match - match.map(europe,country2001) color - color2001[match] map(database=world, fill=TRUE, col=color, xlim=c(-25,70),ylim=c(35,71)) text(0, 45, France) Also, is it possible to draw a historical map of European countries using R? Thanks a lot for your help. Maomao [[alternative HTML version deleted]] 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] Part of a density plot
Take a look at pvladens() function in bootruin package. Ravi. Ravi Varadhan, Ph.D. Assistant Professor, Division of Geriatric Medicine and Gerontology School of Medicine Johns Hopkins University Ph. (410) 502-2619 email: rvarad...@jhmi.edu - Original Message - From: Jim Silverton jim.silver...@gmail.com Date: Saturday, March 19, 2011 10:16 pm Subject: Re: [R] Part of a density plot To: r-help@r-project.org Suupose I have y - rbeta(1, 2, 5) and I only want to see only the density plot from x = 0 to x = 1 How do I do this? -- Thanks, Jim. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list PLEASE do read the posting guide 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] Part of a density plot
On 2011-03-19 19:15, Jim Silverton wrote: Suupose I have y- rbeta(1, 2, 5) and I only want to see only the density plot from x = 0 to x = 1 How do I do this? I'm not quite sure what you want, but this may be it: plot(density(y), xlim = c(0, 1), xaxs = 'i') Peter Ehlers __ 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] Referring to objects themselves
Wonderful! Thanks. I think I've got it. You can even put this - environment() at the top as long as this is returned at the end. I gather that the environment keeps accumulating elements even though it is assigned to 'this' at the beginning. I had thought that $ worked only on lists, but I guess it works on environment objects also. typeof(x) [1] environment is.list(x) [1] FALSE *-- Russ * *_* *** Professor, Computer Science* * California State University, Los Angeles* * Google voice: 747-*999-5105 * blog: *http://russabbott.blogspot.com/ vita: http://sites.google.com/site/russabbott/ *_* On Sat, Mar 19, 2011 at 7:21 PM, Kenn Konstabel lebats...@gmail.com wrote: On Sun, Mar 20, 2011 at 4:13 AM, Kenn Konstabel lebats...@gmail.comwrote: you can omit the list and do the following: /.../ (but you don't really need this in this case as you can use balance instead of this$balance) P.S. using this would make some difference in one case: instead of total - total + amount # need - here you can have this$total - this$total + amount # can use - [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Referring to objects themselves
On Sat, Mar 19, 2011 at 9:45 PM, Russ Abbott russ.abb...@gmail.com wrote:
Thanks for all the suggestions. I realize that this isn't the most important
thing in the world -- and as a newcomer to R I gather it's not the way most
people use R anyway.
But I tried to do what looked like the simplest suggestion.
open.account.2 - function(total) {
this - environment()
list(
deposit = function(amount) {
if(amount = 0)
stop(Deposits must be positive!\n)
total - total + amount
cat(amount, deposited. Your balance is, this$balance(),
\n\n)
},
withdraw = function(amount) {
if(amount total)
stop(You don't have that much money!\n)
total - total - amount
cat(amount, withdrawn. Your balance is, this$balance(),
\n\n)
},
balance = function() {
cat(Your balance is, this$total, \n\n)
}
)
}
When I ran it, this is what happened.
x - open.account.2(100)
x$balance()
Your balance is 100
OK so far. But
x$deposit(50)
Error in cat(amount, deposited. Your balance is, this$balance(), \n\n)
:
attempt to apply non-function
Am I doing this the wrong way?
Thanks for your interest.
balance is a component of the list. Its not directly a component of
this. If you name the list you can refer to it as
this$methods$balance
open.account.2 - function(total) {
this - environment()
methods - list(...whatever...)
}
--
Statistics Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problems with package npmc
On 2011-03-19 17:27, carloskij wrote: Hi there, I am having a problem with package npmc. If I use the included datasets (brain, kronen) everything is fine, but if I try and use my dataset I receive an error message: So somehow your own dataset does not comply with the requirements of npmc. Since we don't have your data, only you can tell what's wrong. Error in probval.GenzBretz(algorithm, n, df, lower, upper, infin, corr, : NAs in foreign function call (arg 2) In addition: Warning message: In probval.GenzBretz(algorithm, n, df, lower, upper, infin, corr, : NAs introduced by coercion The error msg comes from mvtnorm. Obviously, it's not happy with the arguments it's getting. Provide more details as per the posting guide. A *minimal* reproducible example (i.e. data + code) would be best. Peter Ehlers I couldn't solve the problem. C. -- View this message in context: http://r.789695.n4.nabble.com/Problems-with-package-npmc-tp3390472p3390472.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] Referring to objects themselves
For most standard things we do in R, one do not need this feature. R
is a functional language. Everything is passed around as
pass-by-value (but in a smart way so that under the hood you get
pass-by-reference in most cases). Reference variables become useful
first when you for instance have more complex and larger objects, and
also when you work toward external resources, e.g. data bases,
persistent memory, web sites etc.
If you need true pass-by-reference, it is possible to obtain this in R
at a low-resolution granularity, which means, you can do it for basic
R data types (vectors, lists, ...) but not (really) for single
elements of such data types. In R the 'environment' data type acts as
a container for other data types. You can update the objects inside
the environment and pass it around as if it was a reference variable.
As already suggested, the proto and the R.oo packages utilize
environment. Recently Reference Classes joined and is now part of
core R. (There are other difference between these too.)
So, if you're new to R and don't really need reference variables (most
people don't), rethink how you think of classes and objects in R (=
think functional language). Though, you would learn lots by playing
around with environments and scopes and R's method dispatching
mechanisms.
/Henrik
On Sat, Mar 19, 2011 at 6:45 PM, Russ Abbott russ.abb...@gmail.com wrote:
Thanks for all the suggestions. I realize that this isn't the most important
thing in the world -- and as a newcomer to R I gather it's not the way most
people use R anyway.
But I tried to do what looked like the simplest suggestion.
open.account.2 - function(total) {
this - environment()
list(
deposit = function(amount) {
if(amount = 0)
stop(Deposits must be positive!\n)
total - total + amount
cat(amount, deposited. Your balance is, this$balance(),
\n\n)
},
withdraw = function(amount) {
if(amount total)
stop(You don't have that much money!\n)
total - total - amount
cat(amount, withdrawn. Your balance is, this$balance(),
\n\n)
},
balance = function() {
cat(Your balance is, this$total, \n\n)
}
)
}
When I ran it, this is what happened.
x - open.account.2(100)
x$balance()
Your balance is 100
OK so far. But
x$deposit(50)
Error in cat(amount, deposited. Your balance is, this$balance(), \n\n)
:
attempt to apply non-function
Am I doing this the wrong way?
Thanks for your interest.
*-- Russ *
On Sat, Mar 19, 2011 at 6:33 PM, Bert Gunter gunter.ber...@gene.com wrote:
See also the proto package, I believe.
-- Bert
On Sat, Mar 19, 2011 at 5:51 PM, Janko Thyson
janko.thyson.rst...@googlemail.com wrote:
You might want to check out Reference Classes (?SetRefClass). The object
itself is stored in '.self' and can be referenced that way.
HTH,
Janko
-Ursprüngliche Nachricht-
Von: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
Im
Auftrag von Russ Abbott
Gesendet: Samstag, 19. März 2011 23:35
An: r-help@r-project.org
Betreff: [R] Referring to objects themselves
Is it possible to refer to an object from within a method, as in *this
*in
Java? I can't find anything about this in the documentation. Sorry if
I
missed it.
Thanks.
*-- Russ Abbott*
*_*
*** Professor, Computer Science*
* California State University, Los Angeles*
* Google voice: 747-*999-5105
* blog: *http://russabbott.blogspot.com/
vita: http://sites.google.com/site/russabbott/
*_*
[[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.
--
Bert Gunter
Genentech Nonclinical Biostatistics
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented,
Re: [R] Referring to objects themselves
Actually I'm a big Haskell fan. So I think of functional programming very
positively. However, the environment() function doesn't seem to be treated
functionally. If I write
this - environment()
at the top of the previous example, the other functions and the variables
they are bound to are inserted into the environment which had already been
bound to 'this' afterwards.
In fact, even when it is left at the end that line inserts 'this' into the
environment, which strictly speaking it shouldn't do. So there seem to be
some not-quite-functional processes going on.
*-- Russ*
On Sat, Mar 19, 2011 at 8:56 PM, Henrik Bengtsson h...@biostat.ucsf.eduwrote:
For most standard things we do in R, one do not need this feature. R
is a functional language. Everything is passed around as
pass-by-value (but in a smart way so that under the hood you get
pass-by-reference in most cases). Reference variables become useful
first when you for instance have more complex and larger objects, and
also when you work toward external resources, e.g. data bases,
persistent memory, web sites etc.
If you need true pass-by-reference, it is possible to obtain this in R
at a low-resolution granularity, which means, you can do it for basic
R data types (vectors, lists, ...) but not (really) for single
elements of such data types. In R the 'environment' data type acts as
a container for other data types. You can update the objects inside
the environment and pass it around as if it was a reference variable.
As already suggested, the proto and the R.oo packages utilize
environment. Recently Reference Classes joined and is now part of
core R. (There are other difference between these too.)
So, if you're new to R and don't really need reference variables (most
people don't), rethink how you think of classes and objects in R (=
think functional language). Though, you would learn lots by playing
around with environments and scopes and R's method dispatching
mechanisms.
/Henrik
On Sat, Mar 19, 2011 at 6:45 PM, Russ Abbott russ.abb...@gmail.com
wrote:
Thanks for all the suggestions. I realize that this isn't the most
important
thing in the world -- and as a newcomer to R I gather it's not the way
most
people use R anyway.
But I tried to do what looked like the simplest suggestion.
open.account.2 - function(total) {
this - environment()
list(
deposit = function(amount) {
if(amount = 0)
stop(Deposits must be positive!\n)
total - total + amount
cat(amount, deposited. Your balance is, this$balance(),
\n\n)
},
withdraw = function(amount) {
if(amount total)
stop(You don't have that much money!\n)
total - total - amount
cat(amount, withdrawn. Your balance is, this$balance(),
\n\n)
},
balance = function() {
cat(Your balance is, this$total, \n\n)
}
)
}
When I ran it, this is what happened.
x - open.account.2(100)
x$balance()
Your balance is 100
OK so far. But
x$deposit(50)
Error in cat(amount, deposited. Your balance is, this$balance(),
\n\n)
:
attempt to apply non-function
Am I doing this the wrong way?
Thanks for your interest.
*-- Russ *
On Sat, Mar 19, 2011 at 6:33 PM, Bert Gunter gunter.ber...@gene.com
wrote:
See also the proto package, I believe.
-- Bert
On Sat, Mar 19, 2011 at 5:51 PM, Janko Thyson
janko.thyson.rst...@googlemail.com wrote:
You might want to check out Reference Classes (?SetRefClass). The
object
itself is stored in '.self' and can be referenced that way.
HTH,
Janko
-Ursprüngliche Nachricht-
Von: r-help-boun...@r-project.org [mailto:
r-help-boun...@r-project.org]
Im
Auftrag von Russ Abbott
Gesendet: Samstag, 19. März 2011 23:35
An: r-help@r-project.org
Betreff: [R] Referring to objects themselves
Is it possible to refer to an object from within a method, as in *this
*in
Java? I can't find anything about this in the documentation. Sorry
if
I
missed it.
Thanks.
*-- Russ Abbott*
*_*
*** Professor, Computer Science*
* California State University, Los Angeles*
* Google voice: 747-*999-5105
* blog: *http://russabbott.blogspot.com/
vita: http://sites.google.com/site/russabbott/
*_*
[[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
Re: [R] Referring to objects themselves
On Sun, Mar 20, 2011 at 12:10 AM, Russ Abbott russ.abb...@gmail.com wrote: Actually I'm a big Haskell fan. So I think of functional programming very positively. However, the environment() function doesn't seem to be treated functionally. If I write this - environment() at the top of the previous example, the other functions and the variables they are bound to are inserted into the environment which had already been bound to 'this' afterwards. In fact, even when it is left at the end that line inserts 'this' into the environment, which strictly speaking it shouldn't do. So there seem to be some not-quite-functional processes going on. this - environment() does not create an environment. It merely allows this to refer to the environment that was already there and is what holds the variables created during the execution of the function. -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at 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] R as a non-functional language
I'm reading Torgo (2010) *Data Mining with
R*http://www.liaad.up.pt/~ltorgo/DataMiningWithR/code.htmlin
preparation for a class I'll be teaching next quarter. Here's an
example
that is very non-functional.
pH - c(4.5,7,7.3,8.2,6.3)
names(pH) - c('area1','area2','mud','dam','middle')
pH
area1 area2muddam middle
4.57.07.38.26.3
This sort of thing seems to be quite common in R.
*-- Russ *
[[alternative HTML version deleted]]
__
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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 as a non-functional language
On Sun, Mar 20, 2011 at 12:20 AM, Russ Abbott russ.abb...@gmail.com wrote:
I'm reading Torgo (2010) *Data Mining with
R*http://www.liaad.up.pt/~ltorgo/DataMiningWithR/code.htmlin
preparation for a class I'll be teaching next quarter. Here's an
example
that is very non-functional.
pH - c(4.5,7,7.3,8.2,6.3)
names(pH) - c('area1','area2','mud','dam','middle')
pH
area1 area2 mud dam middle
4.5 7.0 7.3 8.2 6.3
This sort of thing seems to be quite common in R.
Try this:
pH - setNames(c(4.5,7,7.3,8.2,6.3), c('area1','area2','mud','dam','middle'))
--
Statistics Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at 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.
Re: [R] R as a non-functional language
The idiom I prefer is
pH - structure(c(4.5,7,7.3,8.2,6.3),
names = c('area1','area2','mud','dam','middle'))
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Gabor Grothendieck
Sent: Sunday, 20 March 2011 2:33 PM
To: russ.abb...@gmail.com
Cc: r-help@r-project.org
Subject: Re: [R] R as a non-functional language
On Sun, Mar 20, 2011 at 12:20 AM, Russ Abbott russ.abb...@gmail.com wrote:
I'm reading Torgo (2010) *Data Mining with
R*http://www.liaad.up.pt/~ltorgo/DataMiningWithR/code.htmlin
preparation for a class I'll be teaching next quarter. Here's an
example
that is very non-functional.
pH - c(4.5,7,7.3,8.2,6.3)
names(pH) - c('area1','area2','mud','dam','middle')
pH
area1 area2 mud dam middle
4.5 7.0 7.3 8.2 6.3
This sort of thing seems to be quite common in R.
Try this:
pH - setNames(c(4.5,7,7.3,8.2,6.3), c('area1','area2','mud','dam','middle'))
--
Statistics Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at 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-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 as a non-functional language
I'm afraid I disagree. As a number of people have shown, it's certainly
possible to get the end result
pH - c(4.5,7,7.3,8.2,6.3)
names(pH) - c('area1','area2','mud','dam','middle')
pH
area1 area2muddam middle
4.57.07.38.26.3
using a single expression. But what makes this non-functional is that the
names() function operates on a reference to the pH object/entity/element. In
other words, the names() function has a side effect, which is not permitted
in strictly functional programming.
I don't know if R has threads. But imagine it did and that one ran
names(pH) - c('area1','area2','mud','dam','middle')
and
names(pH) - c('areaA','areaB','dirt','blockage','center')
in simultaneous threads. Since they are both operating on the same pH
element, it is uncertain what the result would be. That's one of the things
that functional programming prevents.
*-- Russ *
On Sat, Mar 19, 2011 at 10:22 PM, bill.venab...@csiro.au wrote:
PS the form
names(p) - c(...)
is still functional, of course. It is just a bit of syntactic sugar for
the clumsier
p - `names-`(p, c(...))
e.g.
pH - `names-`(pH, letters[1:5])
pH
a b c d e
4.5 7.0 7.3 8.2 6.3
-Original Message-
From: Venables, Bill (CMIS, Dutton Park)
Sent: Sunday, 20 March 2011 3:09 PM
To: 'Gabor Grothendieck'; 'russ.abb...@gmail.com'
Cc: 'r-help@r-project.org'
Subject: RE: [R] R as a non-functional language
The idiom I prefer is
pH - structure(c(4.5,7,7.3,8.2,6.3),
names = c('area1','area2','mud','dam','middle'))
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf Of Gabor Grothendieck
Sent: Sunday, 20 March 2011 2:33 PM
To: russ.abb...@gmail.com
Cc: r-help@r-project.org
Subject: Re: [R] R as a non-functional language
On Sun, Mar 20, 2011 at 12:20 AM, Russ Abbott russ.abb...@gmail.com
wrote:
I'm reading Torgo (2010) *Data Mining with
R*http://www.liaad.up.pt/~ltorgo/DataMiningWithR/code.htmlin
preparation for a class I'll be teaching next quarter. Here's an
example
that is very non-functional.
pH - c(4.5,7,7.3,8.2,6.3)
names(pH) - c('area1','area2','mud','dam','middle')
pH
area1 area2muddam middle
4.57.07.38.26.3
This sort of thing seems to be quite common in R.
Try this:
pH - setNames(c(4.5,7,7.3,8.2,6.3),
c('area1','area2','mud','dam','middle'))
--
Statistics Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at 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.
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Using the Mahalanobis Function
Hello all, I am a 2 month newbie to R and am stumped. I have a data set that I've run multivariate stats on using the manova function (I included the data set). Now it comes time for a table of effect sizes with significance. The univariate tests are easy. Where I run into trouble filling in the table of effect sizes is the Mahalanobis D as an effect size. I've included the table so you can see what group's I'm comparing. I know there's a great function for filling in ?1 and ?2 : mahalanobis(x, center, cov, inverted=FALSE, ...) The problem is I lack the knowledge around cluster analysis of what goes into the function for [x, center, cov.] I have only a basic understanding of this topic (a picture of a measured distance between two clusters on a graph). Could someone please use my data set or a similar one (a multivariate with at least 3 outcome variables) and actually run this function (mahalanobis). Then please send me your output from [R] starting from the data set all the way to the statistic. PS I know the Mahalanobis D should be ?1=3.93 ?2=3.04. The Y,M,O in the data set stands for young, middle, old. I am running the latest version of R on a windows 7 machine. Effect Sizes Contrasts Dependent Variables Friends Parents Strangers All Young-Middle -1.8768797* -3.2842941* -1.1094004* ?1 Middle-Old 1.34900725* 1.54919532* -2.0107882* ?2 Gender Age Friend.Agression Parent.Agression Stranger.Agression 1 f y87 8 2 f y56 8 3 f y63 7 4 f y55 7 5 f m 15 13 10 6 f m 13 11 9 7 f m 12 12 9 8 f m 18 10 7 9 f o 11 11 10 10 f o 104 12 11 f o 129 12 12 f o98 14 13 m y 137 7 14 m y95 10 15 m y 114 4 16 m y 153 4 17 m m 14 12 8 18 m m 10 15 11 19 m m 12 11 8 20 m m 109 9 21 m o 108 11 22 m o 13 11 13 23 m o98 12 24 m o79 16 [[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.
