[R] Cochran-Armitage
Hello, Which package allows to use Cochrana-Armitage trend test? I tried to search for but I found only package coin in which there is no explicit function. Best, RobMac __ 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] Complex integration in R
Hi Borja
library(elliptic)
?myintegrate
HTH
rksh
Borja Soto Varela wrote:
Dear R-user
I need a function to approximate a complex integration. My function is:
aprox2=function(s,x,rate){
dexp(x,rate)*exp(-s*x)
}
where argument s is a complex number. I can't use the integrate function
because it's only used with numeric arguments
Does anyone know some function to approximate complex integrals?
Thanks
Borja
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Re: [R] The end of Matlab
Duncan Murdoch wrote: On 11/12/2008 9:45 PM, Mike Rowe wrote: Greetings! I come to R by way of Matlab. One feature in Matlab I miss is its end keyword. When you put end inside an indexing expression, it is interpreted as the length of the variable along the dimension being indexed. For example, if the same feature were implemented in R: my.vector[5:end] would be equivalent to: my.vector[5:length(my.vector)] And if my.vector is of length less than 5? or: this.matrix[3:end,end] would be equivalent to: this.matrix[3:nrow(this.matrix),ncol(this.matrix)] # or this.matrix[3:dim(this.matrix)[1],dim(this.matrix)[2]] As you can see, the R version requires more typing, and I am a lousy typist. It doesn't save typing, but a more readable version would be rows - nrow(this.matrix) cols - ncol(this.matrix) this.matrix[3:rows, cols] and if nrow(this.matrix) is less than 3? With this in mind, I wanted to try to implement something like this in R. It seems like that in order to be able to do this, I would have to be able to access the parse tree of the expression currently being evaluated by the interpreter from within my End function-- is this possible? Since the [ and [[ operators are primitive I can't see their arguments via the call stack functions... Anyone got a workaround? Would anybody else like to see this feature added to R? I like the general rule that subexpressions have values that can be evaluated independent of context, so I don't think this is a good idea. but this 'general rule' is not really adhered to in r! one example already discussed here at length is subset: subset(data.frame(...), select=a) what will be selected? column named a, or columns named by the components of the vector a? this is an example of how you can't say what an expression means in a context-independent manner. and this is an ubiquitous problem in r. vQ __ 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 graph library: how can generates a fully connected graph from a similarity matrix
On Fri, Dec 12, 2008 at 2:10 AM, dinesh kumar baru...@gmail.com wrote: Dear R users I have a similarity matrix 100X100. I used this matrix as adjacency matrix to generate igraph graph object. Its a fully connected graph. The similarity score is the weight of the edge. Now I want to remove all possible lowest scores (edges) but I want to get back a fully connected graph (dont want any isolated vertex).How can I do it? Actually your matrix is only 87x87. If you mean that you want a graph with 87 vertices, and some edge weights being zero, then you can simply do (assuming there are no negative edge weights) G - graph.adjacency(adjmat+1, mode=undirected, weighted=TRUE) E(G)$weight - E(G)$weight - 1 If you mean that you want to remove isolate vertices after creating the graph, that would be: G - graph.adjacency(adjmat, mode=undirected, weighted=TRUE) G - remove.vertices(G, V(G)[ degree(G)==0 ]) (For your data nothing really happens, there are no isolate vertices.) Also is there any possibility that I can remove the edges which dont pass a threshold (below 70% similarity score). You can remove it initially, from the matrix: adjmat2 - adjmat adjmat2[ adjmat2 0.7 ] - 0 G - graph.adjacency(adjmat2, mode=undirected, weighted=TRUE) or after, from the graph itself: G - graph.adjacency(adjmat+1, mode=undirected, weighted=TRUE) E(G)$weight - E(G)$weight - 1 G2 - delete.edges(G, E(G)[ weight 0.7 ]) Gabor ps. there is also an igraph mailing list, you can find it from the igraph homepage. Just in case I miss your messages here. I attached the similarity matrix. I would appreciate the reply Thanks in advance Dinesh -- Dinesh Kumar Barupal Junior Specialist Metabolomics Fiehn Lab UCD Genome Center 451 East Health Science Drive GBSF Builidng University of California DAVIS 95616 http://fiehnlab.ucdavis.edu/staff/kumar __ 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. -- Gabor Csardi gabor.csa...@unil.ch UNIL DGM __ 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] The end of Matlab
On Fri, 12 Dec 2008, Duncan Murdoch wrote: On 11/12/2008 9:45 PM, Mike Rowe wrote: Greetings! I come to R by way of Matlab. One feature in Matlab I miss is its end keyword. When you put end inside an indexing expression, it is interpreted as the length of the variable along the dimension being indexed. For example, if the same feature were implemented in R: my.vector[5:end] would be equivalent to: my.vector[5:length(my.vector)] And if my.vector is of length less than 5? Also consider my.vector[-(1:4)] or: this.matrix[3:end,end] would be equivalent to: this.matrix[3:nrow(this.matrix),ncol(this.matrix)] # or this.matrix[3:dim(this.matrix)[1],dim(this.matrix)[2]] As you can see, the R version requires more typing, and I am a lousy typist. It doesn't save typing, but a more readable version would be rows - nrow(this.matrix) cols - ncol(this.matrix) this.matrix[3:rows, cols] I would have used this.matrix[-(1:2), ncol(this.matrix)] which I find much clearer as to its intentions. With this in mind, I wanted to try to implement something like this in R. It seems like that in order to be able to do this, I would have to be able to access the parse tree of the expression currently being evaluated by the interpreter from within my End function-- is this possible? Since the [ and [[ operators are primitive I can't see their arguments via the call stack functions... Anyone got a workaround? Would anybody else like to see this feature added to R? Learning to use the power of R's indexing and functios like head() and tail() (which are just syntactic sugar) will probably lead you not to miss this. I like the general rule that subexpressions have values that can be evaluated independent of context, so I don't think this is a good idea. Also, '[' is generic, so it would need to be done in such a way that it applied to all methods. As arguments other than the first are passed unevaluated to the methods, I don't think this is really possible (you don't even know if the third argument to `[` is a dimension for a method). Also, this would effectively make 'end' a reserved word, or 3:end is ambiguous (or at best context-dependent). -- 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] The end of Matlab
On 12/12/2008 3:41 AM, Wacek Kusnierczyk wrote: Duncan Murdoch wrote: On 11/12/2008 9:45 PM, Mike Rowe wrote: Greetings! I come to R by way of Matlab. One feature in Matlab I miss is its end keyword. When you put end inside an indexing expression, it is interpreted as the length of the variable along the dimension being indexed. For example, if the same feature were implemented in R: my.vector[5:end] would be equivalent to: my.vector[5:length(my.vector)] And if my.vector is of length less than 5? or: this.matrix[3:end,end] would be equivalent to: this.matrix[3:nrow(this.matrix),ncol(this.matrix)] # or this.matrix[3:dim(this.matrix)[1],dim(this.matrix)[2]] As you can see, the R version requires more typing, and I am a lousy typist. It doesn't save typing, but a more readable version would be rows - nrow(this.matrix) cols - ncol(this.matrix) this.matrix[3:rows, cols] and if nrow(this.matrix) is less than 3? With this in mind, I wanted to try to implement something like this in R. It seems like that in order to be able to do this, I would have to be able to access the parse tree of the expression currently being evaluated by the interpreter from within my End function-- is this possible? Since the [ and [[ operators are primitive I can't see their arguments via the call stack functions... Anyone got a workaround? Would anybody else like to see this feature added to R? I like the general rule that subexpressions have values that can be evaluated independent of context, so I don't think this is a good idea. but this 'general rule' is not really adhered to in r! one example already discussed here at length is subset: subset(data.frame(...), select=a) what will be selected? column named a, or columns named by the components of the vector a? this is an example of how you can't say what an expression means in a context-independent manner. From which you might conclude that I don't like the design of subset, and you'd be right. However, I don't think this is a counterexample to my general rule. In the subset function, the select argument is treated as an unevaluated expression, and then there are rules about what to do with it. (I.e. try to look up name `a` in the data frame, if that fails, ...) For the requested behaviour to similarly fall within the general rule, we'd have to treat all indices to all kinds of things (vectors, matrices, dataframes, etc.) as unevaluated expressions, with special handling for the particular symbol `end`. But Mike wanted an End function, so presumably he wanted the old behaviour of indexing, but to have a function whose value depended on where it was called from. We do have those (e.g. the functions for examining the stack that Mike wanted to make use of), and they're needed for debugging and a few special cases, but as a general rule they should be avoided. and this is an ubiquitous problem in r. I don't think so. 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] problem with legend
valeria pedrina wrote: hi all, I want to do a plot and put the legend on the left of y axis this is my code: x-seq(1980,2005,1) plot(x,tfa_ita,type=l,col=1,xlim=c(1979,2005),ylim=c(0.2,1.7),xlab=,ylab=,main=Totale Attivita` Finanziarie) lines(x,tfa_spa,type=l,col=2) lines(x,tfa_aus,type=l,col=3) lines(x,tfa_uk,type=l,col=4) lines(x,tfa_ger,type=l,col=5) lines(x,tfa_usa,type=l,col=1,lty=4) lines(x,tfa_jap,type=l,col=2,lty=4) lines(x,tfa_can,type=l,col=3,lty=4) lines(x,tfa_fra,type=l,col=4,lty=4) legend(locator[1],c(ita,spa,aus,uk,ger,usa,jap,can,fra),col=c(1,2,3,4,5,1,2,3,4),lty=c(1,1,1,1,1,4,4,4,4)) when I touch the graphics to put the legend, R puts it on my lines and not on the left of y axis Hi Valeria, The legend command should start with locator(1) using parentheses and not square brackets. This is probably just a typo in your email, or you wouldn't have gotten a legend at all. By default, the legend is placed with the upper left corner at the user coordinates specified. If you want to place it partly outside the plot, use par(xpd=TRUE) and box.col=(parbg). Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] recursive List extraction question
Dear all, I've got a list L - list(L1 = list (foo = bar , SL = NULL ) , L2 = list ( foo = bar , SL = list (SSL1 = list (DF = data.frame(val = 21, foo = bar) , DFOO = list(foo = foo, bar = bar) ) , SSL2 = list (DF = data.frame(val = 22, foo = bar) , DFOO = list(foo = foo, bar = bar) ) ) ) , L3 = list ( foo = bar , SL = list (SSL1 = list (DF = data.frame(val=31, foo=bar) , DFOO = list(foo=foo, bar=bar) ) ) ) ) from which I'ld like to extract the values 21,22 and 31. lapply( lapply( lapply( lapply(L, [[,SL) ,[[,1) ,[[,DF) ,[[,val) gives me 21 and 31. Because of lapply(...,[[,1), it searches through the first element of each SL, which are the SSL1. It misses SSL2. Is there a way to replace the ,[[,1), with a regex or the like to get the job done? Does anybody now any other solution? Thanks and regards, Dominik -- Andreas Dominik Cullmann Forstliche Versuchs- und Forschungsanstalt Wonnhalde 4 79100 Freiburg Tel. +49 761 4018 204 Email: dominik.cullm...@forst.bwl.de mailto:dominik.cullm...@forst.bwl.de Homepage: www.fva-bw.de http://www.fva-bw.de __ 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] snowfall sfInit error
Thanks On Thu, Dec 11, 2008 at 10:19 AM, Jochen Knaus j...@imbi.uni-freiburg.dewrote: Dear Mr. Ripley, indeed that it true. sfInit() currently have a bug on Windows depending on the usage of the Linux tools and the broken Exceptionhandling. Too bad I never tested it accordingly on Windows (as we do not have any Windows machines in our institute). snowfall 1.62 is in the pipe with many other fixes (e.g. NetWorkSpaces usage) and I will include a Windows workaround in it. It will go out for testing at the beginning of the week and should be on CRAN end of the week. Best regards, Jochen Knaus On Sat, 6 Dec 2008, chi...@gmail.com wrote: Dear all, I am trying to execute the simple example in snowfall http://cran.r-project.org/web/packages/snowfall/vignettes/snowfall.pdf... require(snow) require(snowfall) sfInit( parallel=TRUE, cpus=2 ) sfLapply( 1:10, exp ) sfStop() I have installed the snow and snowfall packages in R on a machine with windows xp, however, after running the sfInit( parallel=TRUE, cpus=2 ) line I get an error ... Error in system(whoami, intern = TRUE, ignore.stderr = TRUE) : whoami not found Error in paste(sep = _, R, uname, format(Sys.time(), %H%M%S_%m%d%y)) : object uname not found I am the only (administrator) user of the computer. It has a dual core processor, and is not networked. I would be greatful if someone could tell me how to proceed. Follow the posting guide (see the footer of this message) and talk to the maintainer of 'snowfall'. Most likely it is not intended to be used on Windows, but has not declared that. 'whoami' and 'uname' are Unix programs, not Windows ones, but R's Sys.info() provides equivalent information. Kind regards Chibisi [[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.
[R] repeated two ways anova
Hi there, I have a question regarding a data set that looks like the following: 8 repeated measurements for 3 dosage levels. However, the measurements for each dosage levels are taken on a different group of subjects. example: subject time dosage measure 11 1 1 154 11 2 1 150 : : : : 11 8 1 158 12 1 1 154 12 2 1 150 : : : : 12 8 1 158 21 1 2 138 21 3 2 130 : : : : 21 8 2 145 22 1 2 138 22 3 2 130 : : : : 22 8 2 145 31 1 3 148 31 3 3 150 : : : : 31 8 3 155 32 1 3 148 32 3 3 150 : : : : 32 8 3 155 Should I analyze this using repeated two ways anova? And what is the function to do this? Thank you. Cecilia [[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] Concordance Index - interpretation
Hello everyone. This is a question regarding generation of the concordance index (c index) in R using the function rcorr.cens. In particular about interpretation of its direction and form of the 'predictor'. One of the arguments is a numeric predictor variable ( presumably this is just a *single* predictor variable). Say this variable takes numeric values Am I correct in thinking that if the c index is 0.5 (with Somers D positive) then this tells us that the higher the numeric values of the 'predictor', the greater the survival probability and similarly if the c index is 0.5 (with Somers D negative) then this tells us that the higher the numeric values of the 'predictor' the lower the survival probability ? The c index estimates the probability of concordance between predicted and observed responsesHarrel et al (1996) says in predicting time until death, concordance is calculated by considering all possible pairs of patients, at least one of whom has died. If the *predicted* survival time (probability) is larger for the patient who (actually) lived longer, the predictions for that pair are said to be concordant with the (actual) outcomes. . I have read that the c index is defined by the proportion of all usable patients in which the predictions and outcomes are concordant. Now, secondly, I'd like to ask what form the predictor can take. Presumably if the predictor was a continuous-type variable e.g. 'age' then predicted survival probability (calculated internally via Cox regression?) would be compared with actual survival time for each specific age to get the c index? Now, if the predictor was an *ordinal categorical variable* where 1=worst group and 5=best group - I presume that the c index would be calculated similarly but this time there would be many ties in the predictor (as regards predicted survival probability) - hence if I wanted to count all ties in such a case I would keep the default argument outx=FALSE? Does anyone have a clear reference which gives the formula used to generate the concordance index (with worked examples)? Many thanks for your help on these interpretations Kind Regards, Kim __ 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] The end of Matlab
Dear list, Learning to use the power of R's indexing and functios like head() and tail() (which are just syntactic sugar) will probably lead you not to miss this. However, how do I exclude the last columns of a data.frame or matrix (or, in general, head and tail for given dimensions of an array)? I.e. something nicer than t (head (t (x), -n)) for excluding the last n columns of matrix x THX, Claudia -- Claudia Beleites Dipartimento dei Materiali e delle Risorse Naturali Università degli Studi di Trieste Via Alfonso Valerio 6/a I-34127 Trieste phone: +39 (0 40) 5 58-34 47 email: cbelei...@units.it __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] recursive List extraction question
Try this: rapply(L, c)[grep(\\.val$, names(rapply(L, c)))] On Fri, Dec 12, 2008 at 7:55 AM, dominik.cullm...@forst.bwl.de wrote: Dear all, I've got a list L - list(L1 = list (foo = bar , SL = NULL ) , L2 = list ( foo = bar , SL = list (SSL1 = list (DF = data.frame(val = 21, foo = bar) , DFOO = list(foo = foo, bar = bar) ) , SSL2 = list (DF = data.frame(val = 22, foo = bar) , DFOO = list(foo = foo, bar = bar) ) ) ) , L3 = list ( foo = bar , SL = list (SSL1 = list (DF = data.frame(val=31, foo=bar) , DFOO = list(foo=foo, bar=bar) ) ) ) ) from which I'ld like to extract the values 21,22 and 31. lapply( lapply( lapply( lapply(L, [[,SL) ,[[,1) ,[[,DF) ,[[,val) gives me 21 and 31. Because of lapply(...,[[,1), it searches through the first element of each SL, which are the SSL1. It misses SSL2. Is there a way to replace the ,[[,1), with a regex or the like to get the job done? Does anybody now any other solution? Thanks and regards, Dominik -- Andreas Dominik Cullmann Forstliche Versuchs- und Forschungsanstalt Wonnhalde 4 79100 Freiburg Tel. +49 761 4018 204 Email: dominik.cullm...@forst.bwl.de mailto:dominik.cullm...@forst.bwl.de Homepage: www.fva-bw.de http://www.fva-bw.de __ 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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[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] Downloading Reuters data from R
Thank you very much for this. But since I don't know much of DLL, I am
kind of a stuck with how to proceed with 'reuters_ts1.zip'. This zip
file contains the 'reuters_ts.dll' file.
dyn.load(reuters_ts.dll) generates the error,
dyn.load(Z:\\reuters_ts1\\package\\reuters_ts.dll)
Error in inDL(x, as.logical(local), as.logical(now), ...) :
unable to load shared library 'C:/Documents and
Settings/shubhak/reuters_ts1/package/reuters_ts.dll':
LoadLibrary failure: This application has failed to start because the
application configuration is incorrect. Reinstalling the application may
fix this problem.
Where should the 'reuters_ts1.zip' to be stored? And how can I access
'reuters_ts.dll' file for my use? Even checked ?dyn.load, but a bit
confused. How do we use this?
I am sorry, if this troubles. Mine is a Windows XP Config.
Thanks again,
Shubha
-Original Message-
From: rory.wins...@rbs.com [mailto:rory.wins...@rbs.com]
Sent: Thursday, December 11, 2008 9:44 PM
To: Shubha Vishwanath Karanth; r-h...@stat.math.ethz.ch
Subject: RE: Downloading Reuters data from R
Hi Shubha
I have created an extension DLL for downloading time series data from
Reuters. You can download it from here:
http://www.theresearchkitchen.com/blog/archives/287
There is also a short manual available at the same location:
http://www.theresearchkitchen.com/blog/wp-content/uploads/2008/12/intro.
pdf
I am currently in the process of uploading a separate extension DLL for
retrieval of real-time data from Reuters.
Thanks
Rory
Rory Winston
RBS Global Banking Markets
Office: +44 20 7085 4476
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf Of Shubha Vishwanath Karanth
Sent: 11 December 2008 07:41
To: r-h...@stat.math.ethz.ch
Subject: [R] Downloading Reuters data from R
Hi R,
Can we download Reuters (3000 Xtra) data from R? Does ODBC package help
me in this? Or otherwise, is there a way to extract daily closing prices
data of Reuters from R?
Thank you very much,
Shubha
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Downloading Reuters data from R
Shubha
I suspect it may be because it cannot find a dependent DLL. I'll email you
off-list and we can work through it.
Cheers
Rory
Rory Winston
RBS Global Banking Markets
Office: +44 20 7085 4476
-Original Message-
From: Shubha Vishwanath Karanth [mailto:shub...@ambaresearch.com]
Sent: 12 December 2008 11:29
To: WINSTON, Rory, GBM; r-h...@stat.math.ethz.ch
Subject: RE: Downloading Reuters data from R
Thank you very much for this. But since I don't know much of DLL, I am kind of
a stuck with how to proceed with 'reuters_ts1.zip'. This zip file contains the
'reuters_ts.dll' file.
dyn.load(reuters_ts.dll) generates the error,
dyn.load(Z:\\reuters_ts1\\package\\reuters_ts.dll)
Error in inDL(x, as.logical(local), as.logical(now), ...) :
unable to load shared library 'C:/Documents and
Settings/shubhak/reuters_ts1/package/reuters_ts.dll':
LoadLibrary failure: This application has failed to start because the
application configuration is incorrect. Reinstalling the application may fix
this problem.
Where should the 'reuters_ts1.zip' to be stored? And how can I access
'reuters_ts.dll' file for my use? Even checked ?dyn.load, but a bit confused.
How do we use this?
I am sorry, if this troubles. Mine is a Windows XP Config.
Thanks again,
Shubha
-Original Message-
From: rory.wins...@rbs.com [mailto:rory.wins...@rbs.com]
Sent: Thursday, December 11, 2008 9:44 PM
To: Shubha Vishwanath Karanth; r-h...@stat.math.ethz.ch
Subject: RE: Downloading Reuters data from R
Hi Shubha
I have created an extension DLL for downloading time series data from Reuters.
You can download it from here:
http://www.theresearchkitchen.com/blog/archives/287
There is also a short manual available at the same location:
http://www.theresearchkitchen.com/blog/wp-content/uploads/2008/12/intro.
pdf
I am currently in the process of uploading a separate extension DLL for
retrieval of real-time data from Reuters.
Thanks
Rory
Rory Winston
RBS Global Banking Markets
Office: +44 20 7085 4476
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf Of Shubha Vishwanath Karanth
Sent: 11 December 2008 07:41
To: r-h...@stat.math.ethz.ch
Subject: [R] Downloading Reuters data from R
Hi R,
Can we download Reuters (3000 Xtra) data from R? Does ODBC package help me in
this? Or otherwise, is there a way to extract daily closing prices data of
Reuters from R?
Thank you very much,
Shubha
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Re: [R] Cochran-Armitage
On 12/12/2008 3:29 AM, robert-mcfad...@o2.pl wrote: Hello, Which package allows to use Cochrana-Armitage trend test? I tried to search for but I found only package coin in which there is no explicit function. But there is this example in coin: ### Cochran-Armitage trend test for proportions ### Lung tumors in female mice exposed to 1,2-dichloroethane ### Encyclopedia of Biostatistics (Armitage Colton, 1998), ### Chapter Trend Test for Counts and Proportions, page 4578, Table 2 lungtumor - data.frame(dose = rep(c(0, 1, 2), c(40, 50, 48)), tumor = c(rep(c(0, 1), c(38, 2)), rep(c(0, 1), c(43, 7)), rep(c(0, 1), c(33, 15 table(lungtumor$dose, lungtumor$tumor) ### Cochran-Armitage test (permutation equivalent to correlation ### between dose and tumor), cf. Table 2 for results independence_test(tumor ~ dose, data = lungtumor, teststat = quad) See the following: http://finzi.psych.upenn.edu/R/library/coin/html/ContingencyTests.html There also is an implementation in the GeneticsBase package (Bioconductor). Best, RobMac __ 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. -- Chuck Cleland, Ph.D. NDRI, Inc. (www.ndri.org) 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894 __ 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] ref card for data manipulation?
On Thu, Dec 11, 2008 at 1:38 PM, Vitalie Spinu vitosm...@rambler.ru wrote: Tom Short's card is an excellent one but it does not cover high level packages like plyr, reshape, DoBy, and a few base data.manip functions are not there as well. I'm not sure whether this can (partially) fill the gap, but Quick-R [1] has a decent overview of data manipulation, and is essentially a reference card. The maintainer of the Web site is open to improvements, so it might make sense to contribute relevant documentation to those pages. Regards, Liviu [1] http://www.statmethods.net/ -- Do you know how to read? http://www.alienetworks.com/srtest.cfm Do you know how to write? http://garbl.home.comcast.net/~garbl/stylemanual/e.htm#e-mail __ 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] save as ascii
Hello r-help I want to save my dataframe as an ascii file. a bit of my data frame: vmsrina[1:100,] CKRDYRNR CHRNR cowno dek lakt flow peakflow 1 3596600182 35966 182 9383 3.0527442 3.18 2 3596600182 35966 182 9393 1.8978755 3.06 3 3596600182 35966 182 9403 2.1215936 2.79 4 3596600182 35966 182 9413 1.2411489 2.79 5 3596600182 35966 182 9423 2.1456878 2.85 6 3596600182 35966 182 9433 2.0810122 3.03 7 3596600182 35966 182 9443 1.8588443 3.12 8 3596600182 35966 182 9453 1.8986586 2.82 9 3596600182 35966 182 9463 2.2081765 1.29 10 3596600182 35966 182 9473 1.7747261 2.85 11 3596600182 35966 182 9483 1.7764401 2.73 I would like to have it out as an ascii file, with no colnames or rownames. Just a simple flat file only containing the data. Something like this: 3596600182 35966 182 938 3 3.0527442 3.18 3596600182 35966 182 939 3 1.8978755 3.06 3596600182 35966 182 940 3 2.1215936 2.79 3596600182 35966 182 941 3 1.2411489 2.79 3596600182 35966 182 942 3 2.1456878 2.85 3596600182 35966 182 943 3 2.0810122 3.03 Does anyone have an idea which function i should use? I have tried write.table(), save(), dput(), drop() with no succes for what i want. thanks Rina [[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] The end of Matlab
How about: x[, -seq(to=ncol(x), length=n)] Patrick Burns patr...@burns-stat.com +44 (0)20 8525 0696 http://www.burns-stat.com (home of S Poetry and A Guide for the Unwilling S User) Claudia Beleites wrote: Dear list, Learning to use the power of R's indexing and functios like head() and tail() (which are just syntactic sugar) will probably lead you not to miss this. However, how do I exclude the last columns of a data.frame or matrix (or, in general, head and tail for given dimensions of an array)? I.e. something nicer than t (head (t (x), -n)) for excluding the last n columns of matrix x THX, Claudia __ 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] 1st Call for Papers - 2nd International Symposium on Distributed Computing and Artificial Intelligence (DCAI'09)
To the R users community: (We apologize for multiples copies) (Please distribute) --- 1st Call for Papers - 2nd International Symposium on Distributed Computing and Artificial Intelligence (DCAI'09) June 10th - 12th , 2009 - Salamanca - Spain http://dcai.usal.es/ The International Symposium on Distributed Computing and Artificial Intelligence 2009 is an annual forum that will bring together ideas, projects, lessons, etc. associated with distributed computing, artificial intelligence and its applications in different themes. This meeting will be held at the University of Salamanca in June 10-12th, 2009. This symposium will be organized by the Biomedicine, Intelligent System and Educational Technology Research Group (http://bisite.usal.es/) of the University of Salamanca. The technology transfer in this field is still a challenge and for that reason this type of contributions will be specially considered in this symposium. This conference is the forum in which to present application of innovative techniques to complex problems. The workshop will be organized into the 10th International Work-Conference on Artificial Neural Networks (IWANN2009). (http://iwann.usal.es/) SUBMISSION INSTRUCTIONS --- Everyone interested in participating and presenting his/her work in this workshop may do it by sending a contribution. The papers should be written in English. There are three possibilities: 1- Long papers: A maximum length of 8 pages. They must consist of original, relevant and previously unpublished sound research results related to any of the topics of the conference. 2- Short papers: A maximum length of 4 pages. They can be project report, a summary of a PhD thesis, or work in progress. 3- Doctoral consortium: PhD students are invited to present the topic and progress of their research, in order to obtain feedback from a panel of experts. The length of these papers should be no longer than 8 pages. - Papers Format Papers must be prepared according to the LNCS template of Springer (MS-WORD or LaTex format) without page numbers. - Publication All papers accepted will be published in an special volume of IWANN in Lecture Notes in Computer Science ( LNCS Springer Verlag) . IWANN is included in the ranking of the best conferences established by the Computer Science Conference Ranking based on the Estimated Impact of Conference (EIC), concretely in position 55 among 620 considered (in the Artificial Intelligence field). Therefore the papers will be indexed by CiteSeer.IST , and by the organization Computing Research and Education Association (CORE) . - Submitting papers In order to submit a paper you must register as an author at DCAI 2009 conference management system http://gsii.usal.es/conftoolDCAI. All papers for DCAI 2009 must be submitted in electronic form (PDF format, original document word or latex and images). IMPORTANT DATES --- - Paper submission deadline: 14th February, 2009 - Acceptance notification: 2nd March, 2009 - Final version submission, March 16th, 2009 - (DCAI'09 celebration: 10th-12th June, 2009 TOPICS --- Distributed applications ICTs: trade, medicine, industry, the Internet, etc.. Implementation of the AI Bioinformatics Implementation of the AI Biotechnology Implementation of AI in the development of mobile devices Networks Intelligence Environment distributed Algorithms Computer GRID Distributed databases Systems multimedia and animation distributed Distributed Operating Systems Real Time Systems Trade and Electronic Business Systems and fault-tolerant real-time systems Distributed Architectures Multiagent Systems High-performance Computing Languages, Compilers, planning, load balancing E-learning Technology for Internet Middleware Systems mobile and wireless Security Parallel Computing Software Engineering and Formal Methods Distributed Intelligent Information Systems Robotics and Control Satisfaction of restrictions Search heuristics Reasoning based on models Reasoning not monotonic Planning and scheduling tasks Qualitative Reasoning Reasoning with uncertainty Reasoning temporal and spatial Other models reasoning Reasoning based on cases Data Analysis Evolutionary Computation Networks of neurons Learning through reinforcement Other models of learning Applications of AI (TTIA) Logic Systems support for the decision Intelligent Interaction Knowledge Management Knowledge Representation Ontologies and semantic web Natural Language Processing Perception (vision, speech recognition,â¦) Other items (creativity, games,â¦) GENERAL CO-CHAIRS --- Sigeru Omatu - Osaka Prefecture University, Japan (Chairman)
Re: [R] save as ascii
On 12/12/2008 6:58 AM, Rina Oldager Miehs wrote: Hello r-help I want to save my dataframe as an ascii file. a bit of my data frame: vmsrina[1:100,] CKRDYRNR CHRNR cowno dek lakt flow peakflow 1 3596600182 35966 182 9383 3.0527442 3.18 2 3596600182 35966 182 9393 1.8978755 3.06 3 3596600182 35966 182 9403 2.1215936 2.79 4 3596600182 35966 182 9413 1.2411489 2.79 5 3596600182 35966 182 9423 2.1456878 2.85 6 3596600182 35966 182 9433 2.0810122 3.03 7 3596600182 35966 182 9443 1.8588443 3.12 8 3596600182 35966 182 9453 1.8986586 2.82 9 3596600182 35966 182 9463 2.2081765 1.29 10 3596600182 35966 182 9473 1.7747261 2.85 11 3596600182 35966 182 9483 1.7764401 2.73 I would like to have it out as an ascii file, with no colnames or rownames. Just a simple flat file only containing the data. Something like this: 3596600182 35966 182 938 3 3.0527442 3.18 3596600182 35966 182 939 3 1.8978755 3.06 3596600182 35966 182 940 3 2.1215936 2.79 3596600182 35966 182 941 3 1.2411489 2.79 3596600182 35966 182 942 3 2.1456878 2.85 3596600182 35966 182 943 3 2.0810122 3.03 Does anyone have an idea which function i should use? I have tried write.table(), save(), dput(), drop() with no succes for what i want. You want write.table. For example: test - data.frame(letters=letters[1:5], numbers=1:5) write.table(test,col.names=FALSE,row.names=FALSE,quote=FALSE) a 1 b 2 c 3 d 4 e 5 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] The end of Matlab
Duncan Murdoch wrote: On 12/12/2008 3:41 AM, Wacek Kusnierczyk wrote: but this 'general rule' is not really adhered to in r! one example already discussed here at length is subset: subset(data.frame(...), select=a) what will be selected? column named a, or columns named by the components of the vector a? this is an example of how you can't say what an expression means in a context-independent manner. From which you might conclude that I don't like the design of subset, and you'd be right. However, I don't think this is a counterexample to my general rule. In the subset function, the select argument is treated as an unevaluated expression, and then there are rules about what to do with it. (I.e. try to look up name `a` in the data frame, if that fails, ...) For the requested behaviour to similarly fall within the general rule, we'd have to treat all indices to all kinds of things (vectors, matrices, dataframes, etc.) as unevaluated expressions, with special handling for the particular symbol `end`. But Mike wanted an End function, so presumably he wanted the old behaviour of indexing, but to have a function whose value depended on where it was called from. We do have those (e.g. the functions for examining the stack that Mike wanted to make use of), and they're needed for debugging and a few special cases, but as a general rule they should be avoided. and this is an ubiquitous problem in r. I don't think so. i'd think that neither the 'evaluate' nor the 'deparse' approaches to establishing the values of arguments are particularly rare in r. vQ __ 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] The end of Matlab
Duncan Murdoch wrote: On 11/12/2008 9:45 PM, Mike Rowe wrote: this.matrix[3:end,end] would be equivalent to: this.matrix[3:nrow(this.matrix),ncol(this.matrix)] # or this.matrix[3:dim(this.matrix)[1],dim(this.matrix)[2]] As you can see, the R version requires more typing, and I am a lousy typist. It doesn't save typing, but a more readable version would be rows - nrow(this.matrix) cols - ncol(this.matrix) this.matrix[3:rows, cols] With this in mind, I wanted to try to implement something like this in R. It seems like that in order to be able to do this, I would have to be able to access the parse tree of the expression currently being evaluated by the interpreter from within my End function-- is this possible? Since the [ and [[ operators are primitive I can't see their arguments via the call stack functions... Anyone got a workaround? Would anybody else like to see this feature added to R? I like the general rule that subexpressions have values that can be evaluated independent of context, so I don't think this is a good idea. if 'end' poses a problem to the general rule of context-free establishment of the values of expressions, the python way might be another option: x[3:] instead of x[3:length(x)] x[3:end] (modulo 0-based indexing in python) could this be considered? laziness seems to be considered a virtue here, and r is stuffed with 'features' designed by lazy programmers to avoid, e.g., typing quotes; why would not having to type 'length(...)' or 'nrows(...)' etc. be considered annoying? vQ __ 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] The end of Matlab
From which you might conclude that I don't like the design of subset, and you'd be right. However, I don't think this is a counterexample to my general rule. In the subset function, the select argument is treated as an unevaluated expression, and then there are rules about what to do with it. (I.e. try to look up name `a` in the data frame, if that fails, ...) For the requested behaviour to similarly fall within the general rule, we'd have to treat all indices to all kinds of things (vectors, matrices, dataframes, etc.) as unevaluated expressions, with special handling for the particular symbol `end`. Except you wouldn't have to necessarily change indexing - you could change seq instead. Then 5:end could produce some kind of special data structure (maybe an iterator) that was recognised by the various indexing functions. This would still be a lot of work for not a lot of payoff, but it would be a logically consistent way of adding this behaviour to indexing, and the basic work would make it possible to develop other sorts of indexing, eg df[evens(), ], or df[last(5), last(3)]. Hadley -- http://had.co.nz/ __ 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] Extracting the name of an object into a character string and vice versa
I am still struggling to map a character string to an object name and vice versa in R. I thought the as.name() function might work, but observe the following behaviour ... attach(warpbreaks) levels(tension) [1] L M H levels(as.name(tension)) NULL objectname-as.name(tension) objectname tension levels(objectname) NULL So even though it sets up a symbol, this symbol isn't recognised as an object name by functions such as levels(). I need 2 functions, call them A and B such that A(tension) yields the object name tension which is recognised by functions and B(tension) yields the character result tension. Any suggestions would be greatly appreciated, Philip This message should be regarded as confidential. If you have received this email in error please notify the sender and destroy it immediately. Statements of intent shall only become binding when confirmed in hard copy by an authorised signatory. The contents of this email may relate to dealings with other companies within the Detica Group plc group of companies. Detica Limited is registered in England under No: 1337451. Registered offices: Surrey Research Park, Guildford, Surrey, GU2 7YP, England. [[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] Extracting the name of an object into a character string and vice versa
Its a FAQ: http://cran.r-project.org/doc/FAQ/R-FAQ.html#How-can-I-turn-a-string-into-a-variable_003f On Fri, Dec 12, 2008 at 8:30 AM, Philip Whittall philip.whitt...@detica.com wrote: I am still struggling to map a character string to an object name and vice versa in R. I thought the as.name() function might work, but observe the following behaviour ... attach(warpbreaks) levels(tension) [1] L M H levels(as.name(tension)) NULL objectname-as.name(tension) objectname tension levels(objectname) NULL So even though it sets up a symbol, this symbol isn't recognised as an object name by functions such as levels(). I need 2 functions, call them A and B such that A(tension) yields the object name tension which is recognised by functions and B(tension) yields the character result tension. Any suggestions would be greatly appreciated, Philip This message should be regarded as confidential. If you have received this email in error please notify the sender and destroy it immediately. Statements of intent shall only become binding when confirmed in hard copy by an authorised signatory. The contents of this email may relate to dealings with other companies within the Detica Group plc group of companies. Detica Limited is registered in England under No: 1337451. Registered offices: Surrey Research Park, Guildford, Surrey, GU2 7YP, England. [[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] Cochran-Armitage
Chuck Cleland wrote: On 12/12/2008 3:29 AM, robert-mcfad...@o2.pl wrote: Hello, Which package allows to use Cochrana-Armitage trend test? I tried to search for but I found only package coin in which there is no explicit function. But there is this example in coin: ### Cochran-Armitage trend test for proportions ### Lung tumors in female mice exposed to 1,2-dichloroethane ### Encyclopedia of Biostatistics (Armitage Colton, 1998), ### Chapter Trend Test for Counts and Proportions, page 4578, Table 2 lungtumor - data.frame(dose = rep(c(0, 1, 2), c(40, 50, 48)), tumor = c(rep(c(0, 1), c(38, 2)), rep(c(0, 1), c(43, 7)), rep(c(0, 1), c(33, 15 table(lungtumor$dose, lungtumor$tumor) ### Cochran-Armitage test (permutation equivalent to correlation ### between dose and tumor), cf. Table 2 for results independence_test(tumor ~ dose, data = lungtumor, teststat = quad) See the following: http://finzi.psych.upenn.edu/R/library/coin/html/ContingencyTests.html Also prop.trend.test(). There seems to be a subtle difference, though: independence_test(tumor ~ dose, data = lungtumor, teststat = quad) Asymptotic General Independence Test data: tumor by dose chi-squared = 10.6381, df = 1, p-value = 0.001108 tt - table(lungtumor$dose, lungtumor$tumor) prop.trend.test(tt[,2],rowSums(tt)) Chi-squared Test for Trend in Proportions data: tt[, 2] out of rowSums(tt) , using scores: 1 2 3 X-squared = 10.7157, df = 1, p-value = 0.001062 Anyone have a guess at what the difference is? (Just curious.) -pd There also is an implementation in the GeneticsBase package (Bioconductor). Best, RobMac __ 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. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 __ 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] Functions in R like lincom and nlcom of Stata
Hello all, Does anyone know if there exists any function in R that resembles the lincom and nlcom of STATA?. These functions computes point estimates, standard errors, significance levels, confidence intervals, etc. for linear and non linear combinations of previous estimated parameters. Down here you've got links to descriptions of the functions of STATA nlcom: http://www.stata.com/help.cgi?nlcom lincom: http://www.stata.com/help.cgi?lincom Thank you, Marc [[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] The end of Matlab
Am Freitag 12 Dezember 2008 13:10:20 schrieb Patrick Burns:
How about:
x[, -seq(to=ncol(x), length=n)]
Doing it is not my problem. I just agree with Mike in that I would like if I
could do shorter than:
x[, 1 : (ncol(x) - n)]
which I btw prefer to your solution.
Also, I don't have a problem writing generalized versions of head and tail to
work along other/more dimensions. Or a combined function, taking first and last
arguments.
Still, they would not be as convenient to use as matlab's:
3 : end - 4
which btw. also does not need parentheses.
I guess the general problem is that there is only one thing with integers that
can easily be (ab)used as a flag: the negative sign.
But there are (at least) 2 possibly useful special ways of indexing:
- exclusion (as in R)
- using -n for end - n (as in perl)
Now we enjoy having a shortcut for exclusion (at least I do), but still feel
that marking from the end would be useful.
As no other signs (in the sense of flag) are available for integers, we won't
be able to stop typing somewhat more in R.
Wacek:
x[3:]
instead of
x[3:length(x)]
x[3:end]
I don't think that would help:
what to use for end - 3 within the convention that negative values mean
exclusion?
--- now I start dreaming ---
However, it is possible to define new binary operators (operators are great for
lazy typing...).
Let's say %:% should be a new operator to generate proper indexing sequences
to be used inside [ :
e.g. an.array [ 1:3, -2 %:% -5, ...]
If we now find an.array which is x inside [ (and also inside [[) - which is
possible but maybe a bit fiddly
and if we can also find out which of the indices is actually evaluated (which I
don't know how to do)
then we could use something* as a flag for from the end and calculate the
proper sequence.
something* could e.g. be
either an attribute to the operators (convenient if we can define an unary
operator that allows setting it, e.g. § 3 [§ is the easy-to-type sign on my
keyboard that is not yet used...])
or i (the imaginary one) if there is no other convenient unary operator e.g.
3i
=
easy part of the solution:
make.index - function (x, along.dim = 1, from, to){
if (is.null (dim (x)))
dim - length (x)
else
dim - dim (x)[along.dim]
if (is.complex (from)){
from - dim - from # 0i means end
## warning if re (from) != 0 ?
}
if (is.complex (to)){
to - dim - to # 0i means end
## warning if re (to) != 0 ?
}
from : to
}
%:% - function (e1, e2) ## using a new operator does not mess up :
make.index (x = find.x (), along.dim = find.dim (), e1, e2)
now, the heavy part are the still missing find.x () and find.dim () functions...
I'm not sure whether this would be worth the work, but maybe someone is around
who just knows how to do this.
Claudia
--
Claudia Beleites
Dipartimento dei Materiali e delle Risorse Naturali
Università degli Studi di Trieste
Via Alfonso Valerio 6/a
I-34127 Trieste
phone: +39 (0 40) 5 58-34 47
email: cbelei...@units.it
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] setting the R_Libs gives warning message from Rgui.exe
Daren Tan wrote: Hi, I keep getting the error message and a pop-up window for selecting CRAN mirror server from Rgui.exe after setting the R_Libs Warning in install.packages(necessary[!installed], dep = T) : argument 'lib' is missing: using 'D:/Program Files/R/R-2.8.0.libs' This is a warning that R chooses the first library in the current list, and this is obviously the one you intended, isn't it? --- Please select a CRAN mirror for use in this session --- Error in contrib.url(repos, type) : This is the more interesting error. What is the whole message? You may have chosen a non-working mirror or your internet connectrion is broken, or ...or... or ... Uwe Ligges I set the command for Rgui.exe to be D:\Program Files\R\R-2.8.0\bin\Rgui.exe --no-restore --no-save --max-mem-size 2000MB R_LIBS=D:/Program Files/R/R-2.8.0.libs sessionInfo() R version 2.8.0 (2008-10-20) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] qvalue_1.1 loaded via a namespace (and not attached): [1] tools_2.8.0 _ [[elided Hotmail spam]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Fwd: Re: The end of Matlab (sorry, I messed up a sentence)
-- Weitergeleitete Nachricht --
Betreff: Re: [R] The end of Matlab
Datum: Freitag 12 Dezember 2008
Von: Claudia Beleites cbelei...@units.it
An: r-help@r-project.org
Am Freitag 12 Dezember 2008 13:10:20 schrieb Patrick Burns:
How about:
x[, -seq(to=ncol(x), length=n)]
Doing it is not my problem. I just agree with Mike in that I would like if I
could do shorter than:
x[, 1 : (ncol(x) - n)]
which I btw prefer to your solution.
Also, I don't have a problem writing generalized versions of head and tail to
work along other/more dimensions. Or a combined function, taking head-n and
tail-n arguments.
Still, they would not be as convenient to use as matlab's:
3 : end - 4
which btw. also does not need parentheses.
I guess the general problem is that there is only one thing with integers that
can easily be (ab)used as a flag: the negative sign.
But there are (at least) 2 possibly useful special ways of indexing:
- exclusion (as in R)
- using -n for end - n (as in perl)
Now we enjoy having a shortcut for exclusion (at least I do), but still feel
that marking from the end would be useful.
As no other signs (in the sense of flag) are available for integers, we won't
be able to stop typing somewhat more in R.
Wacek:
x[3:]
instead of
x[3:length(x)]
x[3:end]
I don't think that would help:
what to use for end - 3 within the convention that negative values mean
exclusion?
--- now I start dreaming ---
However, it is possible to define new binary operators (operators are great for
lazy typing...).
Let's say %:% should be a new operator to generate proper indexing sequences
to be used inside [ :
e.g. an.array [ 1:3, -2 %:% -5, ...]
If we now find an.array which is x inside [ (and also inside [[) - which is
possible but maybe a bit fiddly
and if we can also find out which of the indices is actually evaluated (which I
don't know how to do)
then we could use something* as a flag for from the end and calculate the
proper sequence.
something* could e.g. be
either an attribute to the operators (convenient if we can define an unary
operator that allows setting it, e.g. § 3 [§ is the easy-to-type sign on my
keyboard that is not yet used...])
or i (the imaginary one) if there is no other convenient unary operator e.g.
3i
=
easy part of the solution:
make.index - function (x, along.dim = 1, from, to){
if (is.null (dim (x)))
dim - length (x)
else
dim - dim (x)[along.dim]
if (is.complex (from)){
from - dim - from # 0i means end
## warning if re (from) != 0 ?
}
if (is.complex (to)){
to - dim - to # 0i means end
## warning if re (to) != 0 ?
}
from : to
}
%:% - function (e1, e2) ## using a new operator does not mess up :
make.index (x = find.x (), along.dim = find.dim (), e1, e2)
now, the heavy part are the still missing find.x () and find.dim () functions...
I'm not sure whether this would be worth the work, but maybe someone is around
who just knows how to do this.
Claudia
--
Claudia Beleites
Dipartimento dei Materiali e delle Risorse Naturali
Università degli Studi di Trieste
Via Alfonso Valerio 6/a
I-34127 Trieste
phone: +39 (0 40) 5 58-34 47
email: cbelei...@units.it
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---
--
Claudia Beleites
Dipartimento dei Materiali e delle Risorse Naturali
Università degli Studi di Trieste
Via Alfonso Valerio 6/a
I-34127 Trieste
phone: +39 (0 40) 5 58-34 47
email: cbelei...@units.it
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[R] Error message when starting TINN-R
When R starts I get the following error message
Warning message:
In grep(paste([{]TclEval , topic, [}], sep = ), tclvalue(.Tcl(dde
services TclEval {})), :
argument 'useBytes = TRUE' will be ignored
Has anyone else run into this issue and is there any way to can fix this?
Thanks,
Patrick
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Re: [R] The end of Matlab
Claudia Beleites wrote: Am Freitag 12 Dezember 2008 13:10:20 schrieb Patrick Burns: How about: x[, -seq(to=ncol(x), length=n)] Doing it is not my problem. I just agree with Mike in that I would like if I could do shorter than: x[, 1 : (ncol(x) - n)] which I btw prefer to your solution. Also, I don't have a problem writing generalized versions of head and tail to work along other/more dimensions. Or a combined function, taking first and last arguments. Still, they would not be as convenient to use as matlab's: 3 : end - 4 which btw. also does not need parentheses. I guess the general problem is that there is only one thing with integers that can easily be (ab)used as a flag: the negative sign. But there are (at least) 2 possibly useful special ways of indexing: - exclusion (as in R) - using -n for end - n (as in perl) Now we enjoy having a shortcut for exclusion (at least I do), but still feel that marking from the end would be useful. As no other signs (in the sense of flag) are available for integers, we won't be able to stop typing somewhat more in R. Wacek: x[3:] instead of x[3:length(x)] x[3:end] I don't think that would help: what to use for end - 3 within the convention that negative values mean exclusion? might seem tricky, but not impossible: x[-2] # could mean 'all except for 2nd', as it is now x[1:-2] # could mean 'from start to the 2nd backwards from the end' since r disallows mixing positive and negative indexing, the above would not be ambiguous. worse with x[-3:-1] which could mean both 'except for 3rd, 2nd, and 1st' and 'from the 3rd to the 1st from the end', and so would be ambiguous. in this context, indeed, having explicit 'end' could help avoid the ambiguity. vQ __ 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] Error message when starting TINN-R
I have asked the maintainer for a fix and didn't get a reply, which is why I
posted to the list to see if there were any other ideas.
Sorry to bother. . . with my warning message.
Patrick
-Original Message-
From: Prof Brian Ripley [mailto:rip...@stats.ox.ac.uk]
Sent: Friday, December 12, 2008 9:34 AM
To: Richardson, Patrick
Cc: 'r-help@r-project.org'
Subject: Re: [R] Error message when starting TINN-R
And the *Error* message was (that was a warning)?
The warning comes from some contributed code, probably in Tinn-R. Please
find out where it is and ask the maintainer for a fix. But it looks
harmless enough.
On Fri, 12 Dec 2008, Richardson, Patrick wrote:
When R starts I get the following error message
Warning message:
In grep(paste([{]TclEval , topic, [}], sep = ), tclvalue(.Tcl(dde
services TclEval {})), :
argument 'useBytes = TRUE' will be ignored
Has anyone else run into this issue and is there any way to can fix this?
Thanks,
Patrick
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Re: [R] The end of Matlab
On 12/12/2008 8:25 AM, hadley wickham wrote:
From which you might conclude that I don't like the design of subset, and
you'd be right. However, I don't think this is a counterexample to my
general rule. In the subset function, the select argument is treated as an
unevaluated expression, and then there are rules about what to do with it.
(I.e. try to look up name `a` in the data frame, if that fails, ...)
For the requested behaviour to similarly fall within the general rule, we'd
have to treat all indices to all kinds of things (vectors, matrices,
dataframes, etc.) as unevaluated expressions, with special handling for the
particular symbol `end`.
Except you wouldn't have to necessarily change indexing - you could
change seq instead. Then 5:end could produce some kind of special
data structure (maybe an iterator) that was recognised by the various
indexing functions.
Ummm, doesn't that require changes to *both* indexing and seq?
This would still be a lot of work for not a lot
of payoff, but it would be a logically consistent way of adding this
behaviour to indexing, and the basic work would make it possible to
develop other sorts of indexing, eg df[evens(), ], or df[last(5),
last(3)].
I agree: it would be a nice addition, but a fair bit of work. I think
it would be quite doable for the indexable things in the base packages,
but there are a lot of contributed packages that define [ methods, and
those methods would all need to be modified too.
(Just to be clear, when I say doable, I'm thinking that your iterators
return functions that compute subsets of index ranges. For example,
evens() might be implemented as
evens - function() {
result - function(indices) {
indices[indices %% 2 == 0]
}
class(result) - iterator
return(result)
}
and then `[` in v[evens()] would recognize that it had been passed an
iterator, and would pass 1:length(v) to the iterator to get the subset
of even indices. Is that what you had in mind?)
Duncan
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Re: [R] assign()ing within apply
Any tips?
DaveT.
-Original Message-
From: Thompson, David (MNR)
Sent: December 9, 2008 04:03 PM
To: 'r-help@r-project.org'
Subject: assign()ing within apply
Hello,
I'm trying to convert a character column in several dataframes
to lower case.
###
#
# Sample data and 'spp' column summaries:
# dput(ban.ovs.1993[sample(row.names(ban.ovs.1993), 20), 1:4])
ban.ovs.93 - structure(list(oplt = c(43L, 43L, 38L, 26L, 35L,
8L, 39L, 1L,
34L, 50L, 10L, 29L, 31L, 24L, 18L, 12L, 27L, 49L, 28L, 51L),
rplt = c(NA_integer_, NA_integer_, NA_integer_, NA_integer_,
NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_,
NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_,
NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_,
NA_integer_), tree = c(427L, 410L, 639L, 494L, 649L, 166L,
735L, 163L, 120L, 755L, 612L, 174L, 129L, 331L, 269L, 152L,
552L, 227L, 243L, 96L), spp = c(MH, MST, MH, HE,
BE, MH, MH, MH, MH, Or, IW, Or, MH, MH,
BY, MH, MH, BE, MH, MR)), .Names = c(oplt,
rplt, tree, spp), row.names = c(4587L, 4570L, 3947L, 2761L,
3653L, 652L, 4136L, 64L, 3567L, 5318L, 838L, 3091L, 3366L, 2423L,
1775L, 1061L, 2893L, 5161L, 2967L, 5395L), class = data.frame)
# dput(pem.ovs.1994[sample(row.names(pem.ovs.1994), 20), 1:4])
pem.ovs.94 - structure(list(oplt = c(8L, 17L, 36L, 9L, 31L,
11L, 35L, 51L,
51L, 49L, 40L, 1L, 9L, 17L, 4L, 42L, 6L, 3L, 39L, 25L), tree = c(531L,
557L, 546L, 261L, 592L, 134L, 695L, 933L, 945L, 114L, 34L, 54L,
549L, 574L, 193L, 96L, 70L, 4L, 546L, 789L), spp = c(MH, MH,
MH, BF, BF, MH, IW, OR, OR, BF, MH, IW, OR,
MH, SM, BE, BE, BE, OR, OR), oaz = c(38L, 205L,
140L, 277L, 329L, 209L, 222L, 24L, 67L, 187L, 156L, 181L, 174L,
248L, 42L, 279L, 273L, 357L, 160L, 183L)), .Names = c(oplt,
tree, spp, oaz), row.names = c(1204L, 2943L, 5790L, 1616L,
5063L, 2013L, 5691L, 8188L, 8200L, 7822L, 6302L, 54L, 1698L,
2960L, 421L, 6690L, 775L, 245L, 6205L, 4121L), class = data.frame)
# count per spp
invisible(lapply(ls(pat='ovs'), function(y) { cat(y, \n) ;
print(summary.factor(get(y)[,'spp'])) ; cat(\n) } ) )
ban.ovs.93
BE BY HE IW MH MR MST Or
2 1 1 1 11 1 1 2
pem.ovs.94
BE BF IW MH OR SM
3 3 2 6 5 1
#
###
I have tried variants on the following and cannot remember how
to have the result assign()ed back to the original dataframes.
lapply(ls(pat='ovs'), function(y) { assign(paste(y,
[,'spp'], sep=), tolower(get(y)[,'spp'])) } )
I *do* get the expected results:
[[1]]
[1] mh mst mh he be mh mh mh mh
or iw or mh mh by mh mh be mh mr
[[2]]
[1] mh mh mh bf bf mh iw or or bf mh
iw or mh sm be be be or or
, I just can't remember how to get them back into the original
dataframe objects. Suggestions?
Thanx, DaveT.
*
Silviculture Data Analyst
Ontario Forest Research Institute
Ontario Ministry of Natural Resources
david.john.thomp...@ontario.ca
http://ontario.ca/ofri
*
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Re: [R] The end of Matlab
Wacek: x[3:] instead of x[3:length(x)] x[3:end] I don't think that would help: what to use for end - 3 within the convention that negative values mean exclusion? might seem tricky, but not impossible: x[-2] # could mean 'all except for 2nd', as it is now x[1:-2] # could mean 'from start to the 2nd backwards from the end' since r disallows mixing positive and negative indexing, the above would not be ambiguous. worse with x[-3:-1] which could mean both 'except for 3rd, 2nd, and 1st' and 'from the 3rd to the 1st from the end', and so would be ambiguous. in this context, indeed, having explicit 'end' could help avoid the ambiguity. on the other hand, another possible solution would be to have ':' mean, inside range selection expressions, not the usual sequence generation, but rather specification of start and end indices: x[1:2] # from 1st to 2nd, inclusive x[seq(1,2)] # same as above x[c(1,2)] # same as above x[1:-2] # from 1st to 2nd from the end, not x[c(1,0,-1,-2)] x[seq(1,-2)] # no way, mixed indices x[-2:-1] # from 2nd to 1st, both from the end, not x[c(-2,-1)] x[length(x) + -1:0] # same as above x[seq(-2,-1)] # except for 2nd and 1st x[c(-2,-1)] # same as above x[2:] # from 2nd up x[seq(2, max(2, length(x)))] # same as above (would not be without max) x[:3] # up to 3rd x[seq(1,3)] # same as above x[:-3] # up to 3rd from the end x[seq(1, length(x)-2)] # same as above with additional specifications for the behaviour in case of invalid indices and decreasing indices: x[2:1] # from the 2nd to the 1st, in reverse order # or nothing, invalid indexing which can be easily done with the unambiguous x[seq(2,1)] or x[c(2,1)] this is daydreaming, of course, because such modifications would break much old code, and the benefit may not outweigh the effort. vQ __ 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] Please help me in Converting this from C# to R [C1]
Please, can you tell me if you know how can i use the library Igraph in C#
?
Thanks
Nadifi Taoufik
*
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[R] How-To capture and handle errors with R
The following error occurs every now and then by calling a function of wmTSA package: Error in `row.names-.data.frame`(`*tmp*`, value = c(1, 0)) : invalid 'row.names' length I would greatly appreciate some guidelines about how to catch such an error upon its occurrence and have it handled by my own routine rather than letting R stop the currently run script. I had a look a the R on-line documentation about errors handler and also ran some provided examples that confused my mind. The error is in textual form. I do not know whether I have to pass the whole message to the handler. When such an exception occurs the execution control is not transferred to my routine. I would like to see a working example. Thank you so much, Maura Alice Messenger ;-) chatti anche con gli amici di Windows Live Messenger e tutti i telefonini TIM! Vai su http://maileservizi.alice.it/alice_messenger/index.html?pmk=footer [[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] Row order in plot
Thanks very much for the replies. Both suggestions worked perfectly. That's one more step towards understanding R. Thanks again. -- View this message in context: http://www.nabble.com/Row-order-in-plot-tp20962774p20974800.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] preprocessCore
Bonjour! Je suis en train de faire un projet utilisant Affymatrix mais j'ai un problème à télécharger un package depuis R: une fois que je télécharge le package et je demande de faire rma ca sort l'erreur suivante et je n'ai aucune idée de comment je pourrais faire. library(preprocessCore) plac.rma - rma(plac.new) Background correcting Normalizing Calculating Expression Errore in rma(plac.new) : function 'R_subColSummarize_medianpolish_log' not provided by package 'preprocessCore' Est-ce que vous avez un conseil à me donner? J'ai un projet à finir et je suis complètement bloquée :( Merci d'avance, Irene Vicari __ 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] Eror handling with R
Is there any way to handle errors retuened by R functions ... something like the exception handling in C++ ? Thank you so much, Maura Alice Messenger ;-) chatti anche con gli amici di Windows Live Messenger e tutti i telefonini TIM! Vai su http://maileservizi.alice.it/alice_messenger/index.html?pmk=footer [[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 generate a prediction equation for a stratified survival model that was fitted by cph() in Design package
Dear Dr. Harrell,
Thanks for response so quickly. Here is example code to illustrate the
problem.
n - 1000
set.seed(731)
age - 50 + 12*rnorm(n)
label(age) - Age
sex - factor(sample(c('Male','Female'), n,
+ rep=TRUE, prob=c(.6, .4)))
cens - 15*runif(n)
h - .02*exp(.04*(age-50)+.8*(sex=='Female'))
dt - -log(runif(n))/h
label(dt) - 'Follow-up Time'
e - ifelse(dt = cens,1,0)
dt - pmin(dt, cens)
units(dt) - Year
dat - data.frame(dt,e,age,sex)
dd - datadist(dat)
options(datadist='dd')
f1 - cph( Surv(dt,e) ~ rcs(age,4) + sex, data=dat,x=TRUE, y=TRUE,
surv=TRUE)
f2 - cph( Surv(dt,e)~ age + strat(sex), data=dat, x=TRUE,
y=TRUE,surv=TRUE)
Function(f1) # works well
function(age = 48.800654,sex = Male) {0.28612987-0.017321951*
age+0.00012586581*pmax(age-29.600456,0)^3-0.00046285671*pmax(age-44.2731
98,0)^3+0.00042111763*pmax(age-53.769262,0)^3-8.4126731e-05*pmax(age-69.
855597,0)^3-0.64448916*(sex==Male) }
environment: 0x02c2aef4
Function(f2)
Error in Nam[[i]] : subscript out of bounds
I am using Windows R ( version 2.6.0 2007-10-03).
Best regards,
Changhong Yu
-Original Message-
From: Frank E Harrell Jr [mailto:f.harr...@vanderbilt.edu]
Sent: Thursday, December 11, 2008 6:58 PM
To: Yu, Changhong
Cc: r-help@r-project.org
Subject: Re: [R] How to generate a prediction equation for a stratified
survival model that was fitted by cph() in Design package
Yu, Changhong wrote:
Dear all,
I used cph() function from Frank harrell's Design package to create a
survival model, then used functions 'Function' and 'sascode' to
generate
prediction equation based on the saved survival model. But it failed.
I
included a stratified variable in the model. If I removed the
stratification, they were working well. Does that mean that function
'Function' doesn't accept a stratified model?
It is supposed to work for that case. Please send trivial example code
with data defined in the code that replicates the problem you are
seeing, and I'll debug.
Frank
Any thoughts on this will be appreciated. Thanks.
Changhong
===
P Please consider the environment before printing this e-mail
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--
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Department of Biostatistics Vanderbilt
University
P Please consider the environment before printing this e-mail
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Re: [R] setting the R_Libs gives warning message from Rgui.exe
I have managed to get rid the two warning messages simply by uninstalling and installing again R. Very likely that I disrupted the installation of a large package. Date: Fri, 12 Dec 2008 15:07:38 +0100 From: lig...@statistik.tu-dortmund.de To: dare...@hotmail.com CC: r-h...@stat.math.ethz.ch Subject: Re: [R] setting the R_Libs gives warning message from Rgui.exe Daren Tan wrote: Hi, I keep getting the error message and a pop-up window for selecting CRAN mirror server from Rgui.exe after setting the R_Libs Warning in install.packages(necessary[!installed], dep = T) : argument 'lib' is missing: using 'D:/Program Files/R/R-2.8.0.libs' This is a warning that R chooses the first library in the current list, and this is obviously the one you intended, isn't it? --- Please select a CRAN mirror for use in this session --- Error in contrib.url(repos, type) : This is the more interesting error. What is the whole message? You may have chosen a non-working mirror or your internet connectrion is broken, or ...or... or ... Uwe Ligges I set the command for Rgui.exe to be D:\Program Files\R\R-2.8.0\bin\Rgui.exe --no-restore --no-save --max-mem-size 2000MB R_LIBS=D:/Program Files/R/R-2.8.0.libs sessionInfo() R version 2.8.0 (2008-10-20) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] qvalue_1.1 loaded via a namespace (and not attached): [1] tools_2.8.0 _ [[elided Hotmail spam]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] DSC 2009: Now open for registration and abstract submission
Re. Workshop on Directions in Statistical Computing, Copenhagen 13-14 July 2009. http://www.r-project.org/dsc-2009 The web interface for registration and submission of abstracts is now open. (The site is still under construction in a number of respects. In particular, we haven't negotiated discounts with any of the hotels yet.) -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 ___ r-annou...@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-announce __ 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] Eror handling with R
Is try() what you're looking for? Sarah On Fri, Dec 12, 2008 at 5:43 AM, mau...@alice.it wrote: Is there any way to handle errors retuened by R functions ... something like the exception handling in C++ ? Thank you so much, Maura Alice Messenger ;-) chatti anche con gli amici di Windows Live Messenger e tutti i telefonini TIM! Vai su http://maileservizi.alice.it/alice_messenger/index.html?pmk=footer -- Sarah Goslee http://www.functionaldiversity.org __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] The end of Matlab
Here is how to emulate matlab end in R in the case of matrices.
Rather than redefine the matrix class (which would be a bit intrusive) we
just define a subclass of matrix called matrix2. Note in the examples that
matrix2 survives some operations such as + but not others such as crossprod
so in those one would have to coerce back to matrix2 using as.matrix2.
as.matrix2 - function(x, ...) UseMethod(as.matrix2)
as.matrix2.default - function(x, ...) {
do.call(structure, list(x, ...,
class = c(matrix2, setdiff(class(x), matrix2
}
matrix2 - function(data, ...) as.matrix2(matrix(data, ...))
[.matrix2 - function(x, i, j, ...) {
i - if (missing(i)) TRUE
else eval.parent(do.call(substitute, list(substitute(i), list(end =
nrow(x)
j - if (missing(j)) TRUE
else eval.parent(do.call(substitute, list(substitute(j), list(end =
ncol(x)
.subset(x, i, j, ...)
}
# test
m - matrix2(1:12, 3, 4)
# matrix2 survives the + operation
class(m+2)
[1] matrix2 matrix
# but not crossprod
class(crossprod(m))
[1] matrix
# coercing back
as.matrix2(crossprod(m))
[,1] [,2] [,3] [,4]
[1,] 14 32 50 68
[2,] 32 77 122 167
[3,] 50 122 194 266
[4,] 68 167 266 365
attr(,class)
[1] matrix2 matrix
# example of using end
m[2:end, 2:end]
[,1] [,2] [,3]
[1,]58 11
[2,]69 12
On Thu, Dec 11, 2008 at 9:45 PM, Mike Rowe mwr...@gmail.com wrote:
Greetings!
I come to R by way of Matlab. One feature in Matlab I miss is its
end keyword. When you put end inside an indexing expression, it
is interpreted as the length of the variable along the dimension being
indexed. For example, if the same feature were implemented in R:
my.vector[5:end]
would be equivalent to:
my.vector[5:length(my.vector)]
or:
this.matrix[3:end,end]
would be equivalent to:
this.matrix[3:nrow(this.matrix),ncol(this.matrix)] # or
this.matrix[3:dim(this.matrix)[1],dim(this.matrix)[2]]
As you can see, the R version requires more typing, and I am a lousy
typist.
With this in mind, I wanted to try to implement something like this in
R. It seems like that in order to be able to do this, I would have to
be able to access the parse tree of the expression currently being
evaluated by the interpreter from within my End function-- is this
possible? Since the [ and [[ operators are primitive I can't see
their arguments via the call stack functions...
Anyone got a workaround? Would anybody else like to see this feature
added to R?
Thanks,
Mike
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[R] character count
Dear list, I have a variable that consists of typed responses. I wish to compute a variable equal to the number of characters in the original variable. For example: x - c(convert this to 32 because it has 32 characters, this one has 22 characters, 12 characters) [Some magic function here] x [1] 32 22 12 Any ideas? __ 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] The end of Matlab
I just realized that my idea of doing something without going into the extraction functions itself won't work :-( it was a nice dream, though. The reason is that there is no general way to find out what the needed length is: At least I'm just writing a class where 2 kinds of columns are involved. I don't give a dim attribute, though. But I could, and then: how to know how it should be interpreted? on the other hand, another possible solution would be to have ':' mean, inside range selection expressions, not the usual sequence generation, but rather specification of start and end indices: ... this is daydreaming, of course, because such modifications would break much old code, nothing would break if some other sign instead of : would be used. Maybe something like end... and the benefit may not outweigh the effort. This might be true in any case. If I only think of how many lines of nrow, ncol, length Co I could have written instead of posting wrong proposals Claudia -- Claudia Beleites Dipartimento dei Materiali e delle Risorse Naturali Università degli Studi di Trieste Via Alfonso Valerio 6/a I-34127 Trieste phone: +39 (0 40) 5 58-34 47 email: cbelei...@units.it __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] character count
nchar (c(convert this to 47 because it has 47 characters, this one has 26 characters, 13 characters)) HTH Claudia -- Claudia Beleites Dipartimento dei Materiali e delle Risorse Naturali Università degli Studi di Trieste Via Alfonso Valerio 6/a I-34127 Trieste phone: +39 (0 40) 5 58-34 47 email: cbelei...@units.it __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] The end of Matlab
Claudia Beleites wrote: Wacek: x[3:] instead of x[3:length(x)] x[3:end] I don't think that would help: what to use for end - 3 within the convention that negative values mean exclusion? might seem tricky, but not impossible: x[-2] # could mean 'all except for 2nd', as it is now x[1:-2] # could mean 'from start to the 2nd backwards from the end' I know you get thus far. You might even think to decide whether exclusion or 'from the end' is meant from ascending ./. descending order of the sequence, but this messes around with returning the reverse order. that's a design issue. one simple solution is to have this sort of indexing return always in ascending order. thus, x = 1:5 x[1:-1] # 1 2 3 4 5 x[5:-5] # NULL rather than 5 4 3 2 1 -- as in matlab or python x[seq(5,1)] # 5 4 3 2 1 that is, the ':'-based indexing can be made not to mess with the order. for reversing the order, why not use: x[5:-1:1] # 5 4 3 2 1 x[-3:-1:-5] # 3 2 1 rather than x[c(-3,-4,-5)], which would be 1 2 since r disallows mixing positive and negative indexing, the above would not be ambiguous. worse with x[-3:-1] which could mean both 'except for 3rd, 2nd, and 1st' and 'from the 3rd to the 1st from the end', and so would be ambiguous. in this context, indeed, having explicit 'end' could help avoid the ambiguity. that's the problem. also: how would 'except from the 5th last to the 3rd last' be expressed? for exclusions you'd need to use negative indices anyway: x[seq(-5,-3)] now, neither x[-5:-3] nor x[-3:-5] would do the job they do now, but the above is not particularly longer, while selecting the 5th-to3rd-from-the-end columns is simply x[-5:-3] (which could be made to fail on out-of-range indices) instead of something like x[length(x) - 4:2] (which will silently do the wrong thing if length(x) 4, and thus requires extra care). this is a rather loose idea, and unrealistic in the context of r, but i do not see much problem with it on the conceptual level. vQ __ 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] Odp: character count
Hi r-help-boun...@r-project.org napsal dne 12.12.2008 16:31:10: Dear list, I have a variable that consists of typed responses. I wish to compute a variable equal to the number of characters in the original variable. For example: x - c(convert this to 32 because it has 32 characters, this one has 22 characters, 12 characters) [Some magic function here] If you consider space as a character then nchar(x) gives you the result. If not so such construction can do it unlist(lapply(lapply(strsplit(x, ), paste, collapse=), nchar)) Regards Petr x [1] 32 22 12 Any ideas? __ 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] Odp: character count
On Fri, Dec 12, 2008 at 11:00 AM, Petr PIKAL petr.pi...@precheza.cz wrote: Hi r-help-boun...@r-project.org napsal dne 12.12.2008 16:31:10: Dear list, I have a variable that consists of typed responses. I wish to compute a variable equal to the number of characters in the original variable. For example: x - c(convert this to 32 because it has 32 characters, this one has 22 characters, 12 characters) [Some magic function here] If you consider space as a character then nchar(x) gives you the result. If not so such construction can do it unlist(lapply(lapply(strsplit(x, ), paste, collapse=), nchar)) or perhaps: x - abc def nchar(gsub( , , x)) # 6 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Odp: character count
Or : nchar(gsub([[:space:]], , x)) On Fri, Dec 12, 2008 at 2:00 PM, Petr PIKAL petr.pi...@precheza.cz wrote: Hi r-help-boun...@r-project.org napsal dne 12.12.2008 16:31:10: Dear list, I have a variable that consists of typed responses. I wish to compute a variable equal to the number of characters in the original variable. For example: x - c(convert this to 32 because it has 32 characters, this one has 22 characters, 12 characters) [Some magic function here] If you consider space as a character then nchar(x) gives you the result. If not so such construction can do it unlist(lapply(lapply(strsplit(x, ), paste, collapse=), nchar)) Regards Petr x [1] 32 22 12 Any ideas? __ 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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[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] character count
Thanks to everyone who responded. This turns out to be amazingly easy. To count characters including spaces: nchar(x) To count characters excluding spaces: nchar(gsub( *,,x)) Thanks! On Fri, Dec 12, 2008 at 11:00 AM, Petr PIKAL petr.pi...@precheza.cz wrote: Hi r-help-boun...@r-project.org napsal dne 12.12.2008 16:31:10: Dear list, I have a variable that consists of typed responses. I wish to compute a variable equal to the number of characters in the original variable. For example: x - c(convert this to 32 because it has 32 characters, this one has 22 characters, 12 characters) [Some magic function here] If you consider space as a character then nchar(x) gives you the result. If not so such construction can do it unlist(lapply(lapply(strsplit(x, ), paste, collapse=), nchar)) Regards Petr x [1] 32 22 12 Any ideas? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] What packages have impute method ?
Besides the impute package, are there others that have alternative impute approaches ? I hope to compare their performances. Thanks __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Functions in R like lincom and nlcom of Stata
Hello all, Does anyone know if there exists any function in R that resembles the lincom and nlcom of STATA?. These functions computes point estimates, standard errors, significance levels, confidence intervals, etc. for linear and non linear combinations of previous estimated parameters. Down here you've got links to descriptions of the functions of STATA nlcom: http://www.stata.com/help.cgi?nlcom lincom: http://www.stata.com/help.cgi?lincom Thank you, Marc __ 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] mixed model nested ANOVA
Hi, I'm working on leaf characteristics of trees. Each tree is characterised by about 10 leaf traits. The trees were sampled at 9 different locations (about 20 to 30 trees/location, NOT balanced), grouped in 3 different climatic zones (Sahelian, Soudanian and Guinean) (NOT balanced). Further, each tree is characterised by some degree of human pressure (mutilation degree), in total 4 different degrees were defined (NOT balanced). In the dryer zones, the trees are under a much higher human pressure than in the more humid climatic zones, zone and mutilation degree are thus strongly correlated. I want to know how zones (fixed effects, climate interests me) and locations (nested in zones, random effects, location doesn't interests me) are influencing the leaf traits (say for example SLA). Further, also human pressure is affecting leaf traits so I want to characterise the influence of mutilation degree (fixed effects) on SLA. I found some interesting information, but still, I am not be able to analyse the data properly. I think I have to use the function lme() or lme(). Can anyone tell me which function and command I have to use? And how I can produce an ANOVA table? Thanks in advance, Sebpe De Smedt [[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] character count
On Fri, Dec 12, 2008 at 11:05 AM, Ista Zahn iz...@psych.rochester.edu wrote: Thanks to everyone who responded. This turns out to be amazingly easy. To count characters including spaces: nchar(x) To count characters excluding spaces: nchar(gsub( *,,x)) The * is unnecessary. Thanks! On Fri, Dec 12, 2008 at 11:00 AM, Petr PIKAL petr.pi...@precheza.cz wrote: Hi r-help-boun...@r-project.org napsal dne 12.12.2008 16:31:10: Dear list, I have a variable that consists of typed responses. I wish to compute a variable equal to the number of characters in the original variable. For example: x - c(convert this to 32 because it has 32 characters, this one has 22 characters, 12 characters) [Some magic function here] If you consider space as a character then nchar(x) gives you the result. If not so such construction can do it unlist(lapply(lapply(strsplit(x, ), paste, collapse=), nchar)) Regards Petr x [1] 32 22 12 Any ideas? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] converting multiple columns from POSIX* to Date
Something strange. The lapply only processed the first row and then wrote that value to every row of the original dataframe. It is as if the lapply is indeed processing every item on the list, namely each column, but the ifelse or the as.Date is getting messed up. Not only is it only processing the first row but it is also returning the value as numbers rather than dates. I am now playing around with Hadley Wickham's plyr package. So far looking good but still need to work out a few things. Farrel Buchinsky GrandCentral Tel: (412) 567-7870 On Wed, Dec 10, 2008 at 19:08, Marc Schwartz marc_schwa...@comcast.netwrote: Use inherits() then rather than class(): DF[] - lapply(DF, function(x) ifelse(inherits(x, POSIXt), as.Date(x), x)) That should hopefully work better than my first attempt. HTH, Marc Schwartz on 12/10/2008 05:47 PM Farrel Buchinsky wrote: I will try that but I am somewhat skeptical since when I go class(date.of.birth) I get not just one word but two: POSIXt POSIXct. Will that not mess up the logical test When I tried the following: lapply(as.list(dataframename),class)==POSIXt every item was false Farrel Buchinsky GrandCentral Tel: (412) 567-7870 Dear Farrel, Determine the class of each column and apply as.Date() just to those which class is POSIX. For more details see ?class. Here is an example assuming that you're data is named mydata: apply(mydata, 2, function(x) ifelse( class(x)==POSIXt | class(x)==POSIXlt , as.Date(x) , x ) ) HTH, Jorge On Wed, Dec 10, 2008 at 6:26 PM, Farrel Buchinsky fjb...@gmail.com wrote: converting a POSIX class variable to a date class is easy. dates-as.Date(x) #where X is of class POSIX How does one do that to all columns in a data frame that are of POSIX class and leave all the other columns (integers, factors) as is. Feel free to reply with just one or two buzzwords that I could then search for to find how to do it. Farrel Buchinsky __ 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. [[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] The end of Matlab
Just to muddy the waters a bit further. Currently we can do things like:
pascal.tri - numeric(0)
class(pascal.tri) - 'pasctri'
`[.pasctri` - function(x, ...) {
+ dots - list(...)
+ n - dots[[1]]
+ row - choose(n, 0:n)
+ if(length(dots) 1) {
+ row - row[ dots[[2]] ]
+ }
+ row
+ }
pascal.tri[4]
[1] 1 4 6 4 1
pascal.tri[4,2]
[1] 4
Now whether that is clever or abusive, I'm not sure (probably not clever).
But what would we expect:
pascal.tri[end]
to return?
Also if we can access the last element of a vector as:
x[end]
(which I am not opposed to, just don't know if it is worth the effort) then how
long will it be before someone wants to be able to do:
x[end+1] - new.value
and put that in a loop, which would lead to very poor programming practice (but
so easy it would tempt many).
Just my $0.015 worth,
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
project.org] On Behalf Of Wacek Kusnierczyk
Sent: Friday, December 12, 2008 8:57 AM
To: claudia.belei...@gmx.de
Cc: R help
Subject: Re: [R] The end of Matlab
Claudia Beleites wrote:
Wacek:
x[3:]
instead of
x[3:length(x)]
x[3:end]
I don't think that would help:
what to use for end - 3 within the convention that negative values
mean
exclusion?
might seem tricky, but not impossible:
x[-2]
# could mean 'all except for 2nd', as it is now
x[1:-2]
# could mean 'from start to the 2nd backwards from the end'
I know you get thus far. You might even think to decide whether
exclusion or
'from the end' is meant from ascending ./. descending order of the
sequence,
but this messes around with returning the reverse order.
that's a design issue. one simple solution is to have this sort of
indexing return always in ascending order. thus,
x = 1:5
x[1:-1]
# 1 2 3 4 5
x[5:-5]
# NULL rather than 5 4 3 2 1 -- as in matlab or python
x[seq(5,1)]
# 5 4 3 2 1
that is, the ':'-based indexing can be made not to mess with the order.
for reversing the order, why not use:
x[5:-1:1]
# 5 4 3 2 1
x[-3:-1:-5]
# 3 2 1 rather than x[c(-3,-4,-5)], which would be 1 2
since r disallows mixing positive and negative indexing, the above
would
not be ambiguous. worse with
x[-3:-1]
which could mean both 'except for 3rd, 2nd, and 1st' and 'from the
3rd
to the 1st from the end', and so would be ambiguous. in this
context,
indeed, having explicit 'end' could help avoid the ambiguity.
that's the problem.
also: how would 'except from the 5th last to the 3rd last' be
expressed?
for exclusions you'd need to use negative indices anyway:
x[seq(-5,-3)]
now, neither x[-5:-3] nor x[-3:-5] would do the job they do now, but
the
above is not particularly longer, while selecting the
5th-to3rd-from-the-end columns is simply x[-5:-3] (which could be made
to fail on out-of-range indices) instead of something like x[length(x)
-
4:2] (which will silently do the wrong thing if length(x) 4, and thus
requires extra care).
this is a rather loose idea, and unrealistic in the context of r, but i
do not see much problem with it on the conceptual level.
vQ
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Re: [R] The end of Matlab
On Fri, Dec 12, 2008 at 8:41 AM, Duncan Murdoch murd...@stats.uwo.ca wrote:
On 12/12/2008 8:25 AM, hadley wickham wrote:
From which you might conclude that I don't like the design of subset, and
you'd be right. However, I don't think this is a counterexample to my
general rule. In the subset function, the select argument is treated as
an
unevaluated expression, and then there are rules about what to do with
it.
(I.e. try to look up name `a` in the data frame, if that fails, ...)
For the requested behaviour to similarly fall within the general rule,
we'd
have to treat all indices to all kinds of things (vectors, matrices,
dataframes, etc.) as unevaluated expressions, with special handling for
the
particular symbol `end`.
Except you wouldn't have to necessarily change indexing - you could
change seq instead. Then 5:end could produce some kind of special
data structure (maybe an iterator) that was recognised by the various
indexing functions.
Ummm, doesn't that require changes to *both* indexing and seq?
Ooops, yes. I meant it wouldn't require indexing to use unevaluated
expression.
This would still be a lot of work for not a lot
of payoff, but it would be a logically consistent way of adding this
behaviour to indexing, and the basic work would make it possible to
develop other sorts of indexing, eg df[evens(), ], or df[last(5),
last(3)].
I agree: it would be a nice addition, but a fair bit of work. I think it
would be quite doable for the indexable things in the base packages, but
there are a lot of contributed packages that define [ methods, and those
methods would all need to be modified too.
That's true, although I suspect many contributed [.methods eventually
delegate to base methods and might work without further modification.
(Just to be clear, when I say doable, I'm thinking that your iterators
return functions that compute subsets of index ranges. For example, evens()
might be implemented as
evens - function() {
result - function(indices) {
indices[indices %% 2 == 0]
}
class(result) - iterator
return(result)
}
and then `[` in v[evens()] would recognize that it had been passed an
iterator, and would pass 1:length(v) to the iterator to get the subset of
even indices. Is that what you had in mind?)
Yes, that's exactly what I was thinking, although you'd have to put
some thought into the conventions - would it be better to pass in the
length of the vector instead of a vector of indices? Should all
iterators return logical vectors? That way you could do x[evens()
last(5)] to get the even indices out of the last 5, as opposed to
x[evens()][last(5)] which would return the last 5 even indices.
You could also imagine similar iterators for random sampling, like
samp(0.2) to choose 20% of the indices, or boot(0.8) to choose 80%
with replacement. first(n) could also be useful, selecting the first
min(n, length(vector)) observations. An iterator version of rev()
would also be handy.
Maybe selector would be a better name than iterator though, as these
don't have the same feel as iterators in other languages.
Hadley
--
http://had.co.nz/
__
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] The end of Matlab
On Fri, 12 Dec 2008 17:38:13 +0100, hadley wickham h.wick...@gmail.com wrote: You could also imagine similar iterators for random sampling, like samp(0.2) to choose 20% of the indices, or boot(0.8) to choose 80% with replacement. first(n) could also be useful, selecting the first min(n, length(vector)) observations. An iterator version of rev() would also be handy. Maybe selector would be a better name than iterator though, as these don't have the same feel as iterators in other languages. That is really something!! Real high level language!! Selectors could depend on named variables in data frame as well: mtcars[sel(cyl3)last(5)] mtcars[sel(cyl3)boot(80%)] or may be just mtcars[cyl3last(20)] or this is already too far? VS. __ 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 mimic select.list using RGtk2/gWidgetsRGtk2?
I want to write a function mimic the function of select.list(), here
is my preliminary version.
select - function(x,multiple=TRUE,...){
ans-new.env()
g - gwindow(title=title,wid=200,heigh=500)
x1-ggroup(FALSE,con=g)
x2-gtable(x,multiple=multiple,con=x1,expand=TRUE)
gbutton(OK,con=x1,handler=function(h,...){
value - svalue(x2)
if (length(value)==0) value=
assign(selected,value,env=h$action$env)
dispose(x1)
},action=list(env=ans))
ans
}
However, it doesn't behave as what I want. What I want is that: for
{select(c(a,b)); foo()}, foo() only runs after I have clicked the
OK button of select(). Any hints?
Thanks.
--
HUANG Ronggui, Wincent
Tel: (00852) 3442 3832
PhD Candidate, City University of Hong Kong
Website: http://ronggui.huang.googlepages.com/
RQDA project: http://rqda.r-forge.r-project.org/
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] The end of Matlab
On 12/12/2008 11:38 AM, hadley wickham wrote:
On Fri, Dec 12, 2008 at 8:41 AM, Duncan Murdoch murd...@stats.uwo.ca wrote:
On 12/12/2008 8:25 AM, hadley wickham wrote:
From which you might conclude that I don't like the design of subset, and
you'd be right. However, I don't think this is a counterexample to my
general rule. In the subset function, the select argument is treated as
an
unevaluated expression, and then there are rules about what to do with
it.
(I.e. try to look up name `a` in the data frame, if that fails, ...)
For the requested behaviour to similarly fall within the general rule,
we'd
have to treat all indices to all kinds of things (vectors, matrices,
dataframes, etc.) as unevaluated expressions, with special handling for
the
particular symbol `end`.
Except you wouldn't have to necessarily change indexing - you could
change seq instead. Then 5:end could produce some kind of special
data structure (maybe an iterator) that was recognised by the various
indexing functions.
Ummm, doesn't that require changes to *both* indexing and seq?
Ooops, yes. I meant it wouldn't require indexing to use unevaluated
expression.
This would still be a lot of work for not a lot
of payoff, but it would be a logically consistent way of adding this
behaviour to indexing, and the basic work would make it possible to
develop other sorts of indexing, eg df[evens(), ], or df[last(5),
last(3)].
I agree: it would be a nice addition, but a fair bit of work. I think it
would be quite doable for the indexable things in the base packages, but
there are a lot of contributed packages that define [ methods, and those
methods would all need to be modified too.
That's true, although I suspect many contributed [.methods eventually
delegate to base methods and might work without further modification.
(Just to be clear, when I say doable, I'm thinking that your iterators
return functions that compute subsets of index ranges. For example, evens()
might be implemented as
evens - function() {
result - function(indices) {
indices[indices %% 2 == 0]
}
class(result) - iterator
return(result)
}
and then `[` in v[evens()] would recognize that it had been passed an
iterator, and would pass 1:length(v) to the iterator to get the subset of
even indices. Is that what you had in mind?)
Yes, that's exactly what I was thinking, although you'd have to put
some thought into the conventions - would it be better to pass in the
length of the vector instead of a vector of indices? Should all
iterators return logical vectors? That way you could do x[evens()
last(5)] to get the even indices out of the last 5, as opposed to
x[evens()][last(5)] which would return the last 5 even indices.
Actually, I don't think so. evens() last(5) would fail to evaluate,
because you're trying to do a logical combination of two functions, not
of two logical vectors. Or are we going to extend the logical operators
to work on iterators/selectors too?
Duncan Murdoch
You could also imagine similar iterators for random sampling, like
samp(0.2) to choose 20% of the indices, or boot(0.8) to choose 80%
with replacement. first(n) could also be useful, selecting the first
min(n, length(vector)) observations. An iterator version of rev()
would also be handy.
Maybe selector would be a better name than iterator though, as these
don't have the same feel as iterators in other languages.
Hadley
__
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] The end of Matlab
On Fri, Dec 12, 2008 at 11:18 AM, Duncan Murdoch murd...@stats.uwo.ca wrote:
On 12/12/2008 11:38 AM, hadley wickham wrote:
On Fri, Dec 12, 2008 at 8:41 AM, Duncan Murdoch murd...@stats.uwo.ca
wrote:
On 12/12/2008 8:25 AM, hadley wickham wrote:
From which you might conclude that I don't like the design of subset,
and
you'd be right. However, I don't think this is a counterexample to my
general rule. In the subset function, the select argument is treated
as
an
unevaluated expression, and then there are rules about what to do with
it.
(I.e. try to look up name `a` in the data frame, if that fails, ...)
For the requested behaviour to similarly fall within the general rule,
we'd
have to treat all indices to all kinds of things (vectors, matrices,
dataframes, etc.) as unevaluated expressions, with special handling for
the
particular symbol `end`.
Except you wouldn't have to necessarily change indexing - you could
change seq instead. Then 5:end could produce some kind of special
data structure (maybe an iterator) that was recognised by the various
indexing functions.
Ummm, doesn't that require changes to *both* indexing and seq?
Ooops, yes. I meant it wouldn't require indexing to use unevaluated
expression.
This would still be a lot of work for not a lot
of payoff, but it would be a logically consistent way of adding this
behaviour to indexing, and the basic work would make it possible to
develop other sorts of indexing, eg df[evens(), ], or df[last(5),
last(3)].
I agree: it would be a nice addition, but a fair bit of work. I think
it
would be quite doable for the indexable things in the base packages, but
there are a lot of contributed packages that define [ methods, and those
methods would all need to be modified too.
That's true, although I suspect many contributed [.methods eventually
delegate to base methods and might work without further modification.
(Just to be clear, when I say doable, I'm thinking that your iterators
return functions that compute subsets of index ranges. For example,
evens()
might be implemented as
evens - function() {
result - function(indices) {
indices[indices %% 2 == 0]
}
class(result) - iterator
return(result)
}
and then `[` in v[evens()] would recognize that it had been passed an
iterator, and would pass 1:length(v) to the iterator to get the subset of
even indices. Is that what you had in mind?)
Yes, that's exactly what I was thinking, although you'd have to put
some thought into the conventions - would it be better to pass in the
length of the vector instead of a vector of indices? Should all
iterators return logical vectors? That way you could do x[evens()
last(5)] to get the even indices out of the last 5, as opposed to
x[evens()][last(5)] which would return the last 5 even indices.
Actually, I don't think so. evens() last(5) would fail to evaluate,
because you're trying to do a logical combination of two functions, not of
two logical vectors. Or are we going to extend the logical operators to
work on iterators/selectors too?
Oh yes, that's a good point. But wouldn't the following do the job?
.selector - function(a, b) {
function(n) a(n) b(n)
}
or
.selector - function(a, b) {
function(n) intersect(a(n), b(n))
}
depending on whether selectors return logical or numeric vectors.
Writing functions for | and ! would be similarly easy. Or am I
missing something?
Hadley
--
http://had.co.nz/
__
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] The end of Matlab
On Fri, Dec 12, 2008 at 11:11 AM, Vitalie Spinu vitosm...@rambler.ru wrote: On Fri, 12 Dec 2008 17:38:13 +0100, hadley wickham h.wick...@gmail.com wrote: You could also imagine similar iterators for random sampling, like samp(0.2) to choose 20% of the indices, or boot(0.8) to choose 80% with replacement. first(n) could also be useful, selecting the first min(n, length(vector)) observations. An iterator version of rev() would also be handy. Maybe selector would be a better name than iterator though, as these don't have the same feel as iterators in other languages. That is really something!! Real high level language!! Selectors could depend on named variables in data frame as well: mtcars[sel(cyl3)last(5)] mtcars[sel(cyl3)boot(80%)] or may be just mtcars[cyl3last(20)] or this is already too far? This would be a considerable extension because then the selector would need to know about all other variables in the dataset, and you'd need someway of combining selectors with logical vectors. So it would be a huge increase in complexity for not much gain, given that with just the interface we have described you could do: mtcars[mtcars$cyl 3, ][last(20), ] # or subset(mtcars, cyl 3)[last(20), ] The main idea of selectors is that they would be independent of the data structure that they are being used with. Hadley -- http://had.co.nz/ __ 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] spatial AR and ARIMA
Erin Hodgess erinm.hodgess at gmail.com writes: Dear R People: Are there functions for spatial AR and ARIMA models in R, please? Would looking at the Spatial task view on your CRAN mirror help? If by AR you mean simultaneous or conditional autoregressive models using spatial weights (or moving average, but not SAR and SMA at the same time), see spautolm() in spdep. Note that with corSpatial(), you can fit a selection of relevant mixed effects models using nlme and similar packages - is this what you are looking for? Roger Bivand Thanks, Sincerely, Erin __ 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] The end of Matlab
On Fri, Dec 12, 2008 at 12:11 PM, Vitalie Spinu vitosm...@rambler.ru wrote: On Fri, 12 Dec 2008 17:38:13 +0100, hadley wickham h.wick...@gmail.com wrote: You could also imagine similar iterators for random sampling, like samp(0.2) to choose 20% of the indices, or boot(0.8) to choose 80% with replacement. first(n) could also be useful, selecting the first min(n, length(vector)) observations. An iterator version of rev() would also be handy. Maybe selector would be a better name than iterator though, as these don't have the same feel as iterators in other languages. That is really something!! Real high level language!! Selectors could depend on named variables in data frame as well: mtcars[sel(cyl3)last(5)] mtcars[sel(cyl3)boot(80%)] or may be just mtcars[cyl3last(20)] You can do this (and quite a bit more) in data.table: library(data.table) mtcars.dt - as.data.table(mtcars) tail(mtcars.dt[cyl 5], 4) mpg cyl disp hp dratwt qsec vs am gear carb [1,] 27.3 4 79.0 66 4.08 1.935 18.9 1 141 [2,] 26.0 4 120.3 91 4.43 2.140 16.7 0 152 [3,] 30.4 4 95.1 113 3.77 1.513 16.9 1 152 [4,] 21.4 4 121.0 109 4.11 2.780 18.6 1 142 __ 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] The end of Matlab
On 12/12/2008 12:23 PM, hadley wickham wrote:
On Fri, Dec 12, 2008 at 11:18 AM, Duncan Murdoch murd...@stats.uwo.ca wrote:
On 12/12/2008 11:38 AM, hadley wickham wrote:
On Fri, Dec 12, 2008 at 8:41 AM, Duncan Murdoch murd...@stats.uwo.ca
wrote:
On 12/12/2008 8:25 AM, hadley wickham wrote:
From which you might conclude that I don't like the design of subset,
and
you'd be right. However, I don't think this is a counterexample to my
general rule. In the subset function, the select argument is treated
as
an
unevaluated expression, and then there are rules about what to do with
it.
(I.e. try to look up name `a` in the data frame, if that fails, ...)
For the requested behaviour to similarly fall within the general rule,
we'd
have to treat all indices to all kinds of things (vectors, matrices,
dataframes, etc.) as unevaluated expressions, with special handling for
the
particular symbol `end`.
Except you wouldn't have to necessarily change indexing - you could
change seq instead. Then 5:end could produce some kind of special
data structure (maybe an iterator) that was recognised by the various
indexing functions.
Ummm, doesn't that require changes to *both* indexing and seq?
Ooops, yes. I meant it wouldn't require indexing to use unevaluated
expression.
This would still be a lot of work for not a lot
of payoff, but it would be a logically consistent way of adding this
behaviour to indexing, and the basic work would make it possible to
develop other sorts of indexing, eg df[evens(), ], or df[last(5),
last(3)].
I agree: it would be a nice addition, but a fair bit of work. I think
it
would be quite doable for the indexable things in the base packages, but
there are a lot of contributed packages that define [ methods, and those
methods would all need to be modified too.
That's true, although I suspect many contributed [.methods eventually
delegate to base methods and might work without further modification.
(Just to be clear, when I say doable, I'm thinking that your iterators
return functions that compute subsets of index ranges. For example,
evens()
might be implemented as
evens - function() {
result - function(indices) {
indices[indices %% 2 == 0]
}
class(result) - iterator
return(result)
}
and then `[` in v[evens()] would recognize that it had been passed an
iterator, and would pass 1:length(v) to the iterator to get the subset of
even indices. Is that what you had in mind?)
Yes, that's exactly what I was thinking, although you'd have to put
some thought into the conventions - would it be better to pass in the
length of the vector instead of a vector of indices? Should all
iterators return logical vectors? That way you could do x[evens()
last(5)] to get the even indices out of the last 5, as opposed to
x[evens()][last(5)] which would return the last 5 even indices.
Actually, I don't think so. evens() last(5) would fail to evaluate,
because you're trying to do a logical combination of two functions, not of
two logical vectors. Or are we going to extend the logical operators to
work on iterators/selectors too?
Oh yes, that's a good point. But wouldn't the following do the job?
.selector - function(a, b) {
function(n) a(n) b(n)
}
or
.selector - function(a, b) {
function(n) intersect(a(n), b(n))
}
depending on whether selectors return logical or numeric vectors.
Writing functions for | and ! would be similarly easy. Or am I
missing something?
No, I think those definitions would be fine, but I'd be concerned about
speed issues if we start messing with primitives.
While we're at it, we might as well do the same sort of thing for :, and
define a selector named end, and then 3:end would give a selector from 3
to the end, which brings us back to the original question. So it's not
nearly as intrusive as I thought it would be.
Duncan Murdoch
__
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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] Make installed packages available to new R version
After installing a new version of R, how do I make the packages that I have already installed and use on the old version available to the new version? Thank you, Roy Robertson __ 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] The end of Matlab
Oh yes, that's a good point. But wouldn't the following do the job?
.selector - function(a, b) {
function(n) a(n) b(n)
}
or
.selector - function(a, b) {
function(n) intersect(a(n), b(n))
}
depending on whether selectors return logical or numeric vectors.
Writing functions for | and ! would be similarly easy. Or am I
missing something?
No, I think those definitions would be fine, but I'd be concerned about
speed issues if we start messing with primitives.
Speed or expressiveness: pick one? ;) People could always use the
regular subsetting mechanisms if they want the best speed - any
changes to support selectors wouldn't affect the speed of the other
methods of subsetting, would they?
While we're at it, we might as well do the same sort of thing for :, and
define a selector named end, and then 3:end would give a selector from 3 to
the end, which brings us back to the original question. So it's not nearly
as intrusive as I thought it would be.
3:end() do you mean? Or do you mean extending seq so that it uses
unevaluted input?
Hadley
--
http://had.co.nz/
__
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] Make installed packages available to new R version
Have a look at this http://thread.gmane.org/gmane.comp.lang.r.general/87014/focus=133050 it is safer to have all you packages reinstalled once you have updated R. HTH. On Fri, 12 Dec 2008 18:47:33 +0100, Roy Robertson jroyrobert...@comcast.net wrote: After installing a new version of R, how do I make the packages that I have already installed and use on the old version available to the new version? Thank you, Roy Robertson __ 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] candisc plotting
Dear Michael, You haven't told us what your data is, and we can only surmise -- not very helpful for you and annoying for those who try to help. Apologies, I am brand new to R and this mailing list. Will try to be more concise. Here is my data a NEW verion of my data: Curvature Diameter Quality 1 2.95 6.63Passed 2 2.53 7.79Passed 3 3.57 5.65Passed 4 3.16 5.47Passed 5 2.58 4.46 NotPassed 6 2.16 6.22 NotPassed 7 3.27 3.52 NotPassed What I am trying to get from the candisc method is a 1 dimensional scatterplot that separates my two groups Passed and NotPassed On this data I do a do.mod - lm(cbind(Diameter, Curvature) ~ Quality, data=do) do.mod produces Coefficients: Diameter Curvature (Intercept)4.73332.6700 QualityPassed 1.65170.3825 I then run the candisc method: do.can - candisc(do.mod, data=do) this produces: Canonical Discriminant Analysis for Quality: CanRsq Eigenvalue Difference Percent Cumulative 1 0.91354 10.566100100 Test of H0: The canonical correlations in the current row and all that follow are zero LR test stat approx F num Df den Df Pr( F) 10.086 52.831 1 5 0.0007706 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 What I think I would like to plot is the discriminant function of each sample 1-7. Here is an example of what I am trying to do with candisc. http://people.revoledu.com/kardi/tutorial/LDA/Numerical%20Example.html Thanks On Thu, Dec 11, 2008 at 3:36 PM, Michael Friendly frien...@yorku.ca wrote: Dear Pete, You haven't told us what your data is, and we can only surmise -- not very helpful for you and annoying for those who try to help. Pete Shepard wrote: Hello, I have a file with two dependent variables (three and five) and one independent variable. I do i.mod - lm(cbind(three, five) ~ species, data=i.txt) and get the following output: Coefficients: three five (Intercept) 9.949 9.586 species -1.166 -1.156 From this, it seems that species is numeric variable, not a factor. If so, canonical discriminant analysis in not appropriate, so all following bets are off. That's likely why you end up with only one canonical dimension. I do a i.can-candisc(i.mod,data=i): Is data=i the same as data=i.txt? and get the following output: Canonical Discriminant Analysis for species: CanRsq Eigenvalue Difference Percent Cumulative 1 0.0965060.10681100100 Test of H0: The canonical correlations in the current row and all that follow are zero LR test stat approx F num Df den Df Pr( F) 10.903 63.875 1598 6.859e-15 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 this is different than the output I get with SAS: What was your SAS code? Was the data the same? Eigenvalue Difference Proportion Cumulative Ratio F Value Num DF Den DF Pr F 1 0.10681. 1. 0.90349416 31.88 2597 .0001 I am also wondering how to plot the can1*can1 like it is done in SAS. proc plot; plot can1*can1=species; format species spechar.; title2 'Plot of Constits_vs_cassettes'; run; If you want to compare plots for canonical analysis in SAS and R, see my macros, canplot and hecan at http://www.math.yorku.ca/SCS/sasmac/ But in general, if all you have is 1 canonical dimension, a dotplot or boxplot of the canonical scores would be more useful than a scatterplot plot of can1 * can1. The plot method for candisc objects in the candisc package has some code to handle the 1 can-D case. hope this helps -Michael Thanks [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele Streethttp://www.math.yorku.ca/SCS/friendly.html Toronto, ONT M3J 1P3 CANADA [[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] The end of Matlab
On 12/12/2008 1:06 PM, hadley wickham wrote:
Oh yes, that's a good point. But wouldn't the following do the job?
.selector - function(a, b) {
function(n) a(n) b(n)
}
or
.selector - function(a, b) {
function(n) intersect(a(n), b(n))
}
depending on whether selectors return logical or numeric vectors.
Writing functions for | and ! would be similarly easy. Or am I
missing something?
No, I think those definitions would be fine, but I'd be concerned about
speed issues if we start messing with primitives.
Speed or expressiveness: pick one? ;) People could always use the
regular subsetting mechanisms if they want the best speed - any
changes to support selectors wouldn't affect the speed of the other
methods of subsetting, would they?
While we're at it, we might as well do the same sort of thing for :, and
define a selector named end, and then 3:end would give a selector from 3 to
the end, which brings us back to the original question. So it's not nearly
as intrusive as I thought it would be.
3:end() do you mean? Or do you mean extending seq so that it uses
unevaluted input?
My end would be the output of your end(). If there are no args and no
local context, I don't see the need for it to be a function call. It
would just be defined as something like
end - structure( function(n) c(rep(FALSE, n-1), TRUE), class=selector)
I'm not sure what the definition of : should be if one of the args is a
selector.
Duncan
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Re: [R] The end of Matlab
evens() last(5) wouldn't x[evens()][last(5)] do the already? or is different, though. Claudia -- Claudia Beleites Dipartimento dei Materiali e delle Risorse Naturali Università degli Studi di Trieste Via Alfonso Valerio 6/a I-34127 Trieste phone: +39 (0 40) 5 58-34 47 email: cbelei...@units.it __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Make installed packages available to new R version
Roy Robertson jroyrobert...@comcast.net wrote: After installing a new version of R, how do I make the packages that I have already installed and use on the old version available to the new version? Here is my solution. It has worked over many releases of R, though it will probably require one initial re-installation of packages. Set environment variable R_LIBS to some permanent directory before installing a version of R. (That is, NOT a directory under the tree of your current R version.) When you subsequently install packages, they will go into that location and won't need re-installation with each new version of R. It's still necessary to run update.packages() periodically -- such as after installing a new R version -- to keep the installed packages current. -- Mike Prager, NOAA, Beaufort, NC * Opinions expressed are personal and not represented otherwise. * Any use of tradenames does not constitute a NOAA endorsement. __ 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] The end of Matlab
That depends on what you want evens() last(5) to mean. Does that mean the last 5 evens (returning 5 values) or the values in the last 5 that are also even items (returning either 2 or 3 values depending on if the structure has an odd or even number of elements). It could be interpreted either way. Your subset below does the first, the other examples do the 2nd. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Claudia Beleites Sent: Friday, December 12, 2008 11:38 AM To: r-help@r-project.org Subject: Re: [R] The end of Matlab evens() last(5) wouldn't x[evens()][last(5)] do the already? or is different, though. Claudia -- Claudia Beleites Dipartimento dei Materiali e delle Risorse Naturali Università degli Studi di Trieste Via Alfonso Valerio 6/a I-34127 Trieste phone: +39 (0 40) 5 58-34 47 email: cbelei...@units.it __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-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] loop with dates
Hello,
I am trying to do a loop with dates, but when I try to use the index is not
a date.
Fcorte - as.Date('2008/11/30',format = %Y/%m/%d)
fini - Fcorte + 1
ffin - seq(fini,by='months',length=2)[2] - 1
for (i in seq(fini,to = ffin, by='days'))
print (weekdays(i)) # i doesn't a date
How can I do a loop with dates and get the index of each date? are there a
method to convert the index i to date?
Thanks in advance.
[[alternative HTML version deleted]]
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Re: [R] The end of Matlab
My end would be the output of your end(). If there are no args and no local context, I don't see the need for it to be a function call. It would just be defined as something like end - structure( function(n) c(rep(FALSE, n-1), TRUE), class=selector) Oh, I see what you mean. I'm not sure what the definition of : should be if one of the args is a selector. Alternatively you could use !first(2), and only use end/last when you want to select the last n observations. Of course !first(2) would be the equivalent to -(1:2) so there's not much savings there. Hadley -- http://had.co.nz/ __ 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] loop with dates
Try this:
weekdays(seq(fini,to = ffin, by='days'))
or in a loop:
sapply(as.character(seq(fini,to = ffin, by='days')),
function(d)weekdays(as.Date(d)))
On Fri, Dec 12, 2008 at 4:55 PM, Fernando Bizuet fbiz...@gmail.com wrote:
Hello,
I am trying to do a loop with dates, but when I try to use the index is not
a date.
Fcorte - as.Date('2008/11/30',format = %Y/%m/%d)
fini - Fcorte + 1
ffin - seq(fini,by='months',length=2)[2] - 1
for (i in seq(fini,to = ffin, by='days'))
print (weekdays(i)) # i doesn't a date
How can I do a loop with dates and get the index of each date? are there a
method to convert the index i to date?
Thanks in advance.
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
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Re: [R] loop with dates
Try iterating over the index rather than the value of
each component:
s - seq(fini,to = ffin, by='days')
for (i in seq_along(s)) print(s[[i]])
On Fri, Dec 12, 2008 at 1:55 PM, Fernando Bizuet fbiz...@gmail.com wrote:
Hello,
I am trying to do a loop with dates, but when I try to use the index is not
a date.
Fcorte - as.Date('2008/11/30',format = %Y/%m/%d)
fini - Fcorte + 1
ffin - seq(fini,by='months',length=2)[2] - 1
for (i in seq(fini,to = ffin, by='days'))
print (weekdays(i)) # i doesn't a date
How can I do a loop with dates and get the index of each date? are there a
method to convert the index i to date?
Thanks in advance.
[[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.
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Re: [R] Odp: character count
Ok, I knew somebody come with regex solution. My regex skills are limited so I do not use it very often. Regards Petr r-help-boun...@r-project.org napsal dne 12.12.2008 17:03:38: On Fri, Dec 12, 2008 at 11:00 AM, Petr PIKAL petr.pi...@precheza.cz wrote: Hi r-help-boun...@r-project.org napsal dne 12.12.2008 16:31:10: Dear list, I have a variable that consists of typed responses. I wish to compute a variable equal to the number of characters in the original variable. For example: x - c(convert this to 32 because it has 32 characters, this one has 22 characters, 12 characters) [Some magic function here] If you consider space as a character then nchar(x) gives you the result. If not so such construction can do it unlist(lapply(lapply(strsplit(x, ), paste, collapse=), nchar)) or perhaps: x - abc def nchar(gsub( , , x)) # 6 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ 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] prevalence ratio and confidence intervals
Hi everybody, I would like to estimate prevalence ratio and confidence intervals. I tried to do a log-binomial regression, but there was a failure of convergence. Now, I would like to learn how to do a poisson regression with robust variance. I am trying to estimate coefficients with poisson regression and then get standard errors that are adjusted for heteroskedasticity. glm22- svyglm(y~x1+x2+x3+offset(log(x4)), data = banco, family = poisson, design= design_tarv) # Y has a binomial distribution (0/1) # X1, X2, X3 e X4 are categorical variables. #I am using the library(survey) because it is an analysis of Complex Sample Survey Data . summary(glm22) Call: svyglm(y~x1+x2+x3+ offset(log(x4)),data = banco, family = poisson, design = design_tarv) Survey design: svydesign(ids = ~conglomerado, strata = ~estrato, data = banco, weights = ~peso) Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) -5.612240.07223 -77.699 2e-16 *** x1 0.338470.07428 4.557 0.000155 *** x2 0.177450.07059 2.514 0.019765 * x3 0.335080.09447 3.547 0.001808 ** x4 0.243820.08808 2.768 0.011217 * --- Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 (Dispersion parameter for poisson family taken to be 0.7535822) Number of Fisher Scoring iterations: 5 # Using family=quasipoisson, I found the same values. library(sandwich) vcovHAC(glm22) (Intercept)x1 x2 x3x4 (Intercept)1.060857e-12-1.306035e-13-5.139155e-13 -9.788354e-13 -3.428080e-13 x1 -1.306035e-13 7.237868e-13 -3.263182e-13 -1.620593e-13 1.704392e-13 x2 -5.139155e-13 -3.263182e-13 1.250564e-12 7.207572e-13 -9.350062e-13 x3 -9.788354e-13 -1.620593e-13 7.207572e-13 1.707176e-12 -2.244859e-13 x4 -3.428080e-13 1.704392e-13 -9.350062e-13 -2.244859e-13 2.031640e-12 sqrt(diag(vcovHAC(glm22))) (Intercept) x1x2x3 x4 1.029979e-06 8.507566e-07 1.118286e-06 1.306589e-06 1.425356e-06 I think these standards errors are very small. Is this the correct form to do poisson regression with robust variance? Thank you for the help, Roberta. __ 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] Make installed packages available to new R version
You have not told us your OS (despite the posting guide). For Windows this is covered in the rw-FAQ. Similar advice would apply on a Unix-alike. For Mac OS X, see the recent archives of the R-sig-mac list. E.g. the strangely titled threads (look in a threaded view) around https://stat.ethz.ch/pipermail/r-sig-mac/2008-November/005565.html (probably using the Package Installer). On Fri, 12 Dec 2008, Roy Robertson wrote: After installing a new version of R, how do I make the packages that I have already installed and use on the old version available to the new version? Thank you, Roy Robertson __ 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] loop with dates
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Fernando Bizuet
Sent: Friday, December 12, 2008 12:55 PM
To: r-help@r-project.org
Subject: [R] loop with dates
Hello,
I am trying to do a loop with dates, but when I try to use
the index is not
a date.
See ?for. That help page mentions the following which can clarify what
to expect
... The variable 'var' has the same type as 'seq' ...
Small illustration,
fac - gl(5,1,labels=letters[1:5])
fac
[1] a b c d e
Levels: a b c d e
typeof(fac)
[1] integer
for(i in fac) print(i)
[1] 1
[1] 2
[1] 3
[1] 4
[1] 5
Fcorte - as.Date('2008/11/30',format = %Y/%m/%d)
fini - Fcorte + 1
ffin - seq(fini,by='months',length=2)[2] - 1
for (i in seq(fini,to = ffin, by='days'))
print (weekdays(i)) # i doesn't a date
typeof(ffin)
[1] double
As your index is no longer of class 'Date', you will get
Error in UseMethod(weekdays) : no applicable method for weekdays
How can I do a loop with dates and get the index of each
date? are there a
method to convert the index i to date?
Here's one way
dd - seq(fini,to = ffin, by='days')
for (i in seq_along(dd)) print(dd[i])
Thanks in advance.
[[alternative HTML version deleted]]
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Re: [R] assign()ing within apply
Thanks Jorge,
I am aware of the method you suggest, however, it's not quite what I was
asking for.
I was attempting to do this change on 56 dataframes, so I attempted to
do so with a list of all rather than each individually.
Thanks, DaveT.
From: Jorge Ivan Velez [mailto:jorgeivanve...@gmail.com]
Sent: December 12, 2008 11:11 AM
To: Thompson, David (MNR)
Subject: Re: [R] assign()ing within apply
Dear David,
Try this:
ban.ovs.93[,'spp']-tolower(ban.ovs.93[,'spp'])
ban.ovs.93
pem.ovs.94[,'spp']-tolower(pem.ovs.94[,'spp'])
pem.ovs.94
HTH,
Jorge
On Fri, Dec 12, 2008 at 9:51 AM, Thompson, David (MNR)
david.john.thomp...@ontario.ca wrote:
Any tips?
DaveT.
-Original Message-
From: Thompson, David (MNR)
Sent: December 9, 2008 04:03 PM
To: 'r-help@r-project.org'
Subject: assign()ing within apply
Hello,
I'm trying to convert a character column in several
dataframes
to lower case.
###
#
# Sample data and 'spp' column summaries:
# dput(ban.ovs.1993[sample(row.names(ban.ovs.1993),
20), 1:4])
ban.ovs.93 - structure(list(oplt = c(43L, 43L, 38L,
26L, 35L,
8L, 39L, 1L,
34L, 50L, 10L, 29L, 31L, 24L, 18L, 12L, 27L, 49L, 28L,
51L),
rplt = c(NA_integer_, NA_integer_, NA_integer_,
NA_integer_,
NA_integer_, NA_integer_, NA_integer_, NA_integer_,
NA_integer_,
NA_integer_, NA_integer_, NA_integer_, NA_integer_,
NA_integer_,
NA_integer_, NA_integer_, NA_integer_, NA_integer_,
NA_integer_,
NA_integer_), tree = c(427L, 410L, 639L, 494L,
649L, 166L,
735L, 163L, 120L, 755L, 612L, 174L, 129L, 331L,
269L, 152L,
552L, 227L, 243L, 96L), spp = c(MH, MST, MH,
HE,
BE, MH, MH, MH, MH, Or, IW, Or,
MH, MH,
BY, MH, MH, BE, MH, MR)), .Names =
c(oplt,
rplt, tree, spp), row.names = c(4587L, 4570L,
3947L, 2761L,
3653L, 652L, 4136L, 64L, 3567L, 5318L, 838L, 3091L,
3366L, 2423L,
1775L, 1061L, 2893L, 5161L, 2967L, 5395L), class =
data.frame)
# dput(pem.ovs.1994[sample(row.names(pem.ovs.1994),
20), 1:4])
pem.ovs.94 - structure(list(oplt = c(8L, 17L, 36L, 9L,
31L,
11L, 35L, 51L,
51L, 49L, 40L, 1L, 9L, 17L, 4L, 42L, 6L, 3L, 39L, 25L),
tree = c(531L,
557L, 546L, 261L, 592L, 134L, 695L, 933L, 945L, 114L,
34L, 54L,
549L, 574L, 193L, 96L, 70L, 4L, 546L, 789L), spp =
c(MH, MH,
MH, BF, BF, MH, IW, OR, OR, BF, MH,
IW, OR,
MH, SM, BE, BE, BE, OR, OR), oaz = c(38L,
205L,
140L, 277L, 329L, 209L, 222L, 24L, 67L, 187L, 156L,
181L, 174L,
248L, 42L, 279L, 273L, 357L, 160L, 183L)), .Names =
c(oplt,
tree, spp, oaz), row.names = c(1204L, 2943L,
5790L, 1616L,
5063L, 2013L, 5691L, 8188L, 8200L, 7822L, 6302L, 54L,
1698L,
2960L, 421L, 6690L, 775L, 245L, 6205L, 4121L), class =
data.frame)
# count per spp
invisible(lapply(ls(pat='ovs'), function(y) { cat(y,
\n) ;
print(summary.factor(get(y)[,'spp'])) ; cat(\n) } ) )
ban.ovs.93
BE BY HE IW MH MR MST Or
2 1 1 1 11 1 1 2
pem.ovs.94
BE BF IW MH OR SM
3 3 2 6 5 1
#
###
I have tried variants on the following and cannot
remember how
to have the result assign()ed back to the original
dataframes.
lapply(ls(pat='ovs'), function(y) { assign(paste(y,
[,'spp'], sep=), tolower(get(y)[,'spp'])) } )
I *do* get the expected results:
[[1]]
[1] mh mst mh he be mh mh mh
mh
or iw or mh mh by mh mh be
mh mr
[[2]]
[1] mh mh mh bf bf mh iw or or bf
mh
iw or mh sm be be be or or
, I just can't remember how to get them back into the
original
dataframe objects. Suggestions?
Thanx, DaveT.
*
Silviculture Data Analyst
[R] ANNOUNCE: 2009 John M. Chambers Statistical Software Award
John M. Chambers Statistical Software Award - 2009
Statistical Computing Section
American Statistical Association
The Statistical Computing Section of the American Statistical
Association announces the competition for the John M. Chambers
Statistical Software Award. In 1998 the Association for Computing
Machinery presented its Software System Award to John Chambers for the
design and development of S. Dr. Chambers generously donated his award
to the Statistical Computing Section to endow an annual prize for
statistical software written by an undergraduate or graduate student.
The prize carries with it a cash award of $1000, plus a substantial
allowance for travel to the annual Joint Statistical Meetings where
the award will be presented.
Teams of up to 3 people can participate in the competition, with the
cash award being split among team members. The travel allowance will
be given to just one individual in the team, who will be presented the
award at JSM. To be eligible, the team must have designed and
implemented a piece of statistical software. The individual within
the team indicated to receive the travel allowance must have begun the
development while a student, and must either currently be a student,
or have completed all requirements for her/his last degree after
January 1, 2007. To apply for the award, teams must provide the
following materials:
Current CV's of all team members.
A letter from a faculty mentor at the academic institution of the
individual indicated to receive the travel award. The letter
should confirm that the individual had substantial participation in
the development of the software, certify her/his student status
when the software began to be developed (and either the current
student status or the date of degree completion), and briefly
discuss the importance of the software to statistical practice.
A brief, one to two page description of the software, summarizing
what it does, how it does it, and why it is an important
contribution. If the team member competing for the travel
allowance has continued developing the software after finishing
her/his studies, the description should indicate what was developed
when the individual was a student and what has been added since.
Access to the software by the award committee for their use on
inputs of their choosing. Access to the software can consist of an
executable file, Web-based access, macro code, or other appropriate
form. Access should be accompanied by enough information to allow
the judges to effectively use and evaluate the software (including
its design considerations.) This information can be provided in a
variety of ways, including but not limited to a user manual (paper
or electronic), a paper, a URL, online help to the system, and
source code. In particular, the entrant must be prepared to
provide complete source code for inspection by the committee if
requested.
All materials must be in English. We prefer that electronic text be
submitted in Postscript or PDF. The entries will be judged on a
variety of dimensions, including the importance and relevance for
statistical practice of the tasks performed by the software, ease of
use, clarity of description, elegance and availability for use by the
statistical community. Preference will be given to those entries that
are grounded in software design rather than calculation. The decision
of the award committee is final.
All application materials must be received by 5:00pm EST, Monday,
February 23, 2009 at the address below. The winner will be announced
in May and the award will be given at the 2009 Joint Statistical
Meetings.
Information on the competition can also be accessed on the website of
the Statistical Computing Section (www.statcomputing.org or see the
ASA website, www.amstat.org for a pointer), including the names and
contributions of previous winners. Inquiries and application
materials should be emailed or mailed to:
Chambers Software Award
c/o J.R. Lockwood
The RAND Corporation
4570 Fifth Avenue, Suite 600
Pittsburgh, PA 15213
lockw...@rand.org
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Re: [R] The end of Matlab
On Fri, 12 Dec 2008 18:27:02 +0100, hadley wickham h.wick...@gmail.com wrote: or may be just mtcars[cyl3last(20)] or this is already too far? This would be a considerable extension because then the selector would need to know about all other variables in the dataset, and you'd need someway of combining selectors with logical vectors. If selector returns a logical vector then I really don't see where is the problem. Probably I am mistaken but implementing mtcars[cyl3] is not such a big deal. Just an operator `[.` start searching for cyl from inside the x frame and not from parent.frame as it does now. It is just like putting with inside '[', or not? When started with R I was really disappointed that such a natural and intuitive subsetting is not allowed, but instead lengthy and ackward mtcars[mtcars$syl3] is required. R is an interactive language for 99% of the users and features like that(and selectors indeed) would make a tremendous difference. Regards, SV. __ 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] mixed model nested ANOVA
Hi Sebpe, the analysis of the data that you describe could be a complex and lengthy process, in which decisions that you are confronted by are affected by previous decisions that you have made. I recommend obtaining the assistance of a statistician, preferably a local one whose door you can knock on. If you are unable to do so then I suggest that you borrow/buy a copy of the Pinheiro and Bates book, which documents lme() and its friends, and study it carefully, especially the worked examples. Good luck! Andrew On Fri, Dec 12, 2008 at 03:13:06PM +, Sebpe De Smedt wrote: Hi, I'm working on leaf characteristics of trees. Each tree is characterised by about 10 leaf traits. The trees were sampled at 9 different locations (about 20 to 30 trees/location, NOT balanced), grouped in 3 different climatic zones (Sahelian, Soudanian and Guinean) (NOT balanced). Further, each tree is characterised by some degree of human pressure (mutilation degree), in total 4 different degrees were defined (NOT balanced). In the dryer zones, the trees are under a much higher human pressure than in the more humid climatic zones, zone and mutilation degree are thus strongly correlated. I want to know how zones (fixed effects, climate interests me) and locations (nested in zones, random effects, location doesn't interests me) are influencing the leaf traits (say for example SLA). Further, also human pressure is affecting leaf traits so I want to characterise the influence of mutilation degree (fixed effects) on SLA. I found some interesting information, but still, I am not be able to analyse the data properly. I think I have to use the function lme() or lme(). Can anyone tell me which function and command I have to use? And how I can produce an ANOVA table? Thanks in advance, Sebpe De Smedt [[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. -- Andrew Robinson Department of Mathematics and StatisticsTel: +61-3-8344-6410 University of Melbourne, VIC 3010 Australia Fax: +61-3-8344-4599 http://www.ms.unimelb.edu.au/~andrewpr http://blogs.mbs.edu/fishing-in-the-bay/ __ 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] Avoiding multiple outputs using RODBC package
I am using R as a data manipulation tool for a SQL database. So in some of my R scripts I use the RODBC package to retreive data, then run analysis, and use the sqlSave function in the RODBC package to store the results in a database. There are two problems I want to avoid, and they are highly related: (1) having R rerun analysis which has already been done and saved into output database table, and (2) ending up with more than one identical row in my output database table. - The analysis I am running allows the user to input a large number of variables, for example: date, version, a, b, c, d, e, f, g, ... After R completes its analysis, I write the results to a database table in the format: Value, date, version, a, b, c, d, e, f, g, ... where Value is the result of the R analysis, and the rest of the columns are the criteria that was used to get that value. -- Can anyone think of a way to address these problems? The only thing I can think of so far is to run an sqlQuery to get a table of all the variable combinations that are saved at the start, and then simply avoid computing and re-outputing those results. However, my results database table currently has over 200K rows (and will grow very quickly as I keep going with this project), so I think that would not be the most expeditious answer as I think just the SQL query to download 200K rows x 10+ columns is going to be time consuming in and of itself. I know this is kindof a weird problem, and am open to all sorts of ideas... Thanks! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Help with a permutation test
Hello List and thanks in advance for all of your help,
I am trying implement a permutation test of a multinomial logistic
regression ('multinom' within the nnet package). In the end I want to
compare the parameter estimate from my data to the distribution of
randomized parameter estimates.
I have figured out how to permute my dependent variable (MNNUM) x number of
times, apply multinomial logistic regression, to each permutation, and save
the results in a list. Where I am stuck is figuring out how to take the
mean and SD of the coefficients from my list of regressions. I know that
the coefficients are stored in the $wts slot of the model.
Below is what I have so far. I am sure there are nicer ways to do this and
if you feel so inclined please suggest them.
#this is a function to permute the MNNUM column once
rand- function(DF){
new.DF-DF
new.DF$MNNUM-sample(new.DF$MNNUM)
new.DF
}
#this function does one model I am interested in.
modeltree-function(DF){
MLM.plot - multinom(MN_fact ~ Canpy + mean_dbh + num_beechoak +
num_class5 + prop_hard , data=hfdata, trace=FALSE)
MLM.plot
}
# this replicates the 'rand' function and applies a model
resamp.funct-function(DF,funct, n){
list-replicate(n,rand(DF), simplify = FALSE)
sapply(list, funct, simplify = FALSE)
}
#So if I paste below:
l-resamp.funct(hfdata, modeltree, 3)
# I get
l-resamp.funct(hfdata, modltree, 3)
l
[[1]]
Call:
multinom(formula = MN_fact ~ Canpy + mean_dbh + num_beechoak +
num_class5 + prop_hard, data = hfdata, trace = FALSE)
Coefficients:
(Intercept) Canpymean_dbh num_beechoak num_class5
prop_hard
none -11.1845028 0.063880939 0.08440340 -0.7050239 -0.0998379
6.894522
sabrinus -10.6848488 0.055157318 0.19276777 -0.6441996 0.1219245
3.325704
volans-0.2481854 0.004410597 -0.02710102 -0.1061700 -0.1858376
2.495856
Residual Deviance: 163.7211
AIC: 199.7211
[[2]]
Call:
multinom(formula = MN_fact ~ Canpy + mean_dbh + num_beechoak +
num_class5 + prop_hard, data = hfdata, trace = FALSE)
Coefficients:
(Intercept) Canpymean_dbh num_beechoak num_class5
prop_hard
none -11.1845028 0.063880939 0.08440340 -0.7050239 -0.0998379
6.894522
sabrinus -10.6848488 0.055157318 0.19276777 -0.6441996 0.1219245
3.325704
volans-0.2481854 0.004410597 -0.02710102 -0.1061700 -0.1858376
2.495856
Residual Deviance: 163.7211
AIC: 199.7211
[[3]]
Call:
multinom(formula = MN_fact ~ Canpy + mean_dbh + num_beechoak +
num_class5 + prop_hard, data = hfdata, trace = FALSE)
Coefficients:
(Intercept) Canpymean_dbh num_beechoak num_class5
prop_hard
none -11.1845028 0.063880939 0.08440340 -0.7050239 -0.0998379
6.894522
sabrinus -10.6848488 0.055157318 0.19276777 -0.6441996 0.1219245
3.325704
volans-0.2481854 0.004410597 -0.02710102 -0.1061700 -0.1858376
2.495856
Residual Deviance: 163.7211
AIC: 199.7211
[[alternative HTML version deleted]]
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Re: [R] character count
Hi Ista,
one way could be:
ncharacters-unlist(lapply(x,function(x)nchar(gsub(' ','',x
ncharacters
From: Ista Zahn iz...@psych.rochester.edu
To: r-help@r-project.org
Sent: Friday, December 12, 2008 10:31:10 AM
Subject: [R] character count
Dear list,
I have a variable that consists of typed responses. I wish to compute
a variable equal to the number of characters in the original variable.
For example:
x - c(convert this to 32 because it has 32 characters, this one has 22
characters, 12 characters)
[Some magic function here]
x
[1] 32 22 12
Any ideas?
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[R] Trellis margins settings so that they are like a base graphic with no figure region when printed to png file?
Dear R-experts, I want to produce a very small png file (35 x 18 px) that contains a histogram without a figure region or margins, only the pure heights. In the base graphic this was easy: png(filename = hist.png, res = 72, width=35, height=18) par(mar=c(0,0,0,0), oma=c(0,0,0,0)) hist(rnorm(100), main=) dev.off() Now I want a grid graphics output as I need the graphic as an object. I tried several trellis.par settings but I was not able to figure it out (PROBLEM (1)). Up to now it looks like this: myHistogram - histogram(rnorm(100), xlab=, ylab=, par.settings=list( axis.line=list(col=transparent), xlab.text=list(col=transparent), ylab.text=list(col=transparent), axis.text=list(col=transparent) ) ) This looks acceptable although I would like smaller margins, that is to say no margins at all. PROBLEM (2) now is, that when it is printed to the png file, the graphic almost consist of margins only. The main part of the plot shrinks to some tiny points. I don't know how to change the settings, so I that I get the same as in the base system. Does anyone know? TIA Mark __ 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 can we predict differences in a slope, given that the random component was significant?
Dear R users, Using R lme function, I found that both fixed and random effects of variable A on variable B are significant. Now, I'd like to analyze what variables are predicting differences in the slope. In other words, I'd like to know what variables (e.g., variable C) are predicting individual differences in the effects of A on B. I have many data points for A and B for each individual, whereas I have only one data point for C. I'd appreciate if anyone could answer the question. Thank you for your attention. [[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] aggregate and median
Hello R-experts, I have a simple question: how do I aggregate data using the median function with na.rm = TRUE, i.e. aggregate(x, list(x$y, x$z), FUN = '') I have tried 'median(x, na.rm = TRUE)' but that doesn't help. Any suggestions are very much appreciated, Thorsten __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] aggregate and median
aggregate(x, list(x$y, x$a), FUN=median, na.rm=TRUE) On Fri, Dec 12, 2008 at 2:13 PM, t.r...@med2.uni-kiel.de wrote: Hello R-experts, I have a simple question: how do I aggregate data using the median function with na.rm = TRUE, i.e. aggregate(x, list(x$y, x$z), FUN = '') I have tried 'median(x, na.rm = TRUE)' but that doesn't help. Any suggestions are very much appreciated, Thorsten __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] The end of Matlab
On Fri, Dec 12, 2008 at 3:08 PM, Vitalie Spinu vitosm...@rambler.ru wrote: On Fri, 12 Dec 2008 18:27:02 +0100, hadley wickham h.wick...@gmail.com wrote: or may be just mtcars[cyl3last(20)] or this is already too far? This would be a considerable extension because then the selector would need to know about all other variables in the dataset, and you'd need someway of combining selectors with logical vectors. If selector returns a logical vector then I really don't see where is the problem. Probably I am mistaken but implementing mtcars[cyl3] is not such a big deal. Just an operator `[.` start searching for cyl from inside the x frame and not from parent.frame as it does now. It is just like putting with inside '[', or not? And that's a big change to the current behaviour! I think there are a few good reasons why this shouldn't be the default: * You could no longer do: cyl - 4; mtcars[mtcars$cyl == cyl, ] (which is very useful when writing function) * If you want that behaviour, then just use subset * It only makes sense for variables of data frames, not for all the other types of subsets * Generally it's better to be explicit than not When started with R I was really disappointed that such a natural and intuitive subsetting is not allowed, but instead lengthy and ackward mtcars[mtcars$syl3] is required. R is an interactive language for 99% of the users and features like that(and selectors indeed) would make a tremendous difference. Regards, SV. -- http://had.co.nz/ __ 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] [Rd] gregexpr - match overlap mishandled (PR#13391)
Greg Snow wrote:
Where do you get should and expect from? All the regular expression
tools that I am familiar with only match non-overlapping patterns unless you
do extra to specify otherwise. One of the standard references for regular
expressions if you really want to understand what is going on is Mastering
Regular Expressions by Jeffrey Friedl. You should really read through that
book before passing judgment on the correctness of an implementation.
If you want the overlaps, you need to come up with a regular expression that
will match without consuming all of the string. Here is one way to do it
with your example:
gregexpr(1122(?=1122), paste(rep(1122, 10), collapse=), perl=TRUE)
[[1]]
[1] 1 5 9 13 17 21 25 29 33
attr(,match.length)
[1] 4 4 4 4 4 4 4 4 4
another option would be to move the anchor backwards after each match,
but i'm not sure if the problem really needs it and if it could be done
from within r.
greg (and another person who answered this post earlier):
while your frustration is understandable, i think reid (and possibly
other users as well) would benefit from a brief explanation instead of
your emotional reactions. you ought to be more patient and less
arrogant with newbies who will often think there is a bug in r when
there isn't.
reid:
when matching is performed, there is a pointer moved through the
string. in global matching, after a match is found the pointer is just
behind the matched substring, and further matching proceeds from there.
for example example, suppose you match aaa (the string) with aa (the
pattern) globally. after the first successful match, the position
pointer is *behind the second a* in the string, and no further match can
be found from there.in this context, 'global' does not mean that all
possible matches are found, rather that matching is performed iteratively.
the above is probably a solution to your problem, though the matches
have length 4, not 8. in perl, you could manually move back the anchor
after each match, e.g.:
$string = 1122 x 10;
$n = length($string)/2;
@matches = ();
$string =~ /11221122(??{push @matches [$-[0], $]; pos($s) -= $n})/g;
now @matches has 9 elements, each a ref to an array with the starting
position and the content (of length 8) of the respective match:
@matches = ([0, 11221122], [4, 11221122], ...)
not sure if you can do this within r. not sure if you'll ever need it.
for more complex cases when you need overlapping matches and you need
their content, greg's solution might not do, but in general that's the
solution.
vQ
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Re: [R] mixed exponential distribution
On Dec 10, 2008, at 10:36 AM, Fazekas, Jacob wrote: Good morning, Is there anyway to do Mixed Exponential Distribution in R? require(fortunes) fortune(109) I am trying to load some lag-weighted empirical survival distribution into R and run a mixed exponential on that data. You might want see whether the worked examples on pp 12-13 are helpful: http://cran.r-project.org/web/packages/actuar/vignettes/risk.pdf The actuar package implements much of the classic Loss Models tome. -- David Winsemius, MD, MPH Heritage Labs Thanks, Jacob Fazekas Jacob Fazekas Assistant Actuary Auto-Owners Insurance Company 517-703-2543 fazekas.ja...@aoins.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
