[R] error using lapply with oneway_test (coin package)
Dear expeRts, I would like to use a oneway_test (from package coin) to test whether two groups differ on various variables. The variables are encoded within a data frame. Unfortunately, I obtained an error, that I don't understand. Could you please help me ? Example: library(coin) y - as.data.frame(matrix(rnorm(200), ncol=2)) group - as.factor(unif(100)) lapply(y, function(var) oneway_test(var ~ group)) Error message is: (in French, my locale) Erreur dans eval(expr, envir, enclos) : objet 'var' introuvable (my personal translation in English) Error in eval(expr, envir, enclos) : object 'var' not found Thank you, Matthieu Matthieu Dubois Post-doctoral fellow Psychology and NeuroCognition Lab (CNRS UMR 5105) Université Pierre Mendès-France BP47 --- 38040 Grenoble Cedex 9 --- France Email: matthieu.dub...@upmf-grenoble.fr Gmail: matth...@gmail.com http://web.upmf-grenoble.fr/LPNC/membre_matthieu_dubois [[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] error using lapply with oneway_test (coin package)
On 07/05/2009 6:11 AM, Matthieu Dubois wrote: Dear expeRts, I would like to use a oneway_test (from package coin) to test whether two groups differ on various variables. The variables are encoded within a data frame. Unfortunately, I obtained an error, that I don't understand. Could you please help me ? Example: library(coin) y - as.data.frame(matrix(rnorm(200), ncol=2)) group - as.factor(unif(100)) lapply(y, function(var) oneway_test(var ~ group)) Error message is: (in French, my locale) Erreur dans eval(expr, envir, enclos) : objet 'var' introuvable (my personal translation in English) Error in eval(expr, envir, enclos) : object 'var' not found That's a scoping problem, I think a bug in oneway_test. Because the formula var ~ group is created with the anonymous function within lapply, its environment should be the evaluation frame of that function call and var should be visible. If I replace oneway_test() with lm() it works. I think a workaround is to construct the data argument explicitly, i.e. lapply(y, function(var) oneway_test(var ~ group, data.frame(var=var, group=group))) I've cc'd Torsten Hothorn, the maintainer of coin. Duncan Murdoch Thank you, Matthieu Matthieu Dubois Post-doctoral fellow Psychology and NeuroCognition Lab (CNRS UMR 5105) Université Pierre Mendès-France BP47 --- 38040 Grenoble Cedex 9 --- France Email: matthieu.dub...@upmf-grenoble.fr Gmail: matth...@gmail.com http://web.upmf-grenoble.fr/LPNC/membre_matthieu_dubois [[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] error using lapply with oneway_test (coin package)
That's a scoping problem, I think a bug in oneway_test. Because the formula var ~ group is created with the anonymous function within lapply, its environment should be the evaluation frame of that function call and var should be visible. If I replace oneway_test() with lm() it works. I think a workaround is to construct the data argument explicitly, i.e. lapply(y, function(var) oneway_test(var ~ group, data.frame(var=var, group=group))) yes, that would be the fix: R lapply(y, function(var) oneway_test(var ~ group, data = data.frame(var = var, group = group))) $V1 Asymptotic 2-Sample Permutation Test data: var by group (1, 2) Z = -1.2054, p-value = 0.2280 alternative hypothesis: true mu is not equal to 0 $V2 Asymptotic 2-Sample Permutation Test data: var by group (1, 2) Z = 0.5672, p-value = 0.5706 alternative hypothesis: true mu is not equal to 0 Thanks, Duncan. Torsten I've cc'd Torsten Hothorn, the maintainer of coin. Duncan Murdoch Thank you, Matthieu Matthieu Dubois Post-doctoral fellow Psychology and NeuroCognition Lab (CNRS UMR 5105) Université Pierre Mendès-France BP47 --- 38040 Grenoble Cedex 9 --- France Email: matthieu.dub...@upmf-grenoble.fr Gmail: matth...@gmail.com http://web.upmf-grenoble.fr/LPNC/membre_matthieu_dubois [[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] Error with lapply [addirional clarification needed]
I need one more clarification here : Here I did : fn - function(i) return(list(i, i^2)) ss = sapply(1:4, fn) Here the object ss should be a matrix object : is.matrix(ss) However I feel it lacks some the matrix object properties. For example the syntax min(ss[1,]) generates an error : Error in min(ss[1, ]) : invalid 'type' (list) of argument. What should be the way out? Am I missing something ? Regards, baptiste auguie-2 wrote: Hi, you are feeding lapply i as an optional argument, which is passed to fn() and causes an error. Just use lapply(1:4, fn), or better yet, sapply, fn - function(i) return(i^2) sapply(1:4, fn) [1] 1 4 9 16 Hope this helps, baptiste On 20 Nov 2008, at 16:31, megh wrote: I have written following codes, with intention to get a list with values 1,2,9,16 : fn - function(i) return(i^2) lapply(1:4, fn, i) However I got following error : Error in FUN(1:4[[1L]], ...) : unused argument(s) (1) Can anyone please tell me what will be the correct code here? Regards, -- View this message in context: http://www.nabble.com/Error-with-lapply-tp20605066p20605066.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. _ Baptiste Auguié School of Physics University of Exeter Stocker Road, Exeter, Devon, EX4 4QL, UK Phone: +44 1392 264187 http://newton.ex.ac.uk/research/emag __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://www.nabble.com/Error-with-lapply-tp20605066p20634821.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error with lapply [addirional clarification needed]
megh wrote: I need one more clarification here : Here I did : fn - function(i) return(list(i, i^2)) ss = sapply(1:4, fn) Here the object ss should be a matrix object : is.matrix(ss) However I feel it lacks some the matrix object properties. For example the syntax min(ss[1,]) generates an error : Error in min(ss[1, ]) : invalid 'type' (list) of argument. What should be the way out? Am I missing something ? ss is a dim'ed list object, because fn returns a list. This appears to be a feature, although rarely used. One point is that you can do fn - function(i) return(list(as.character(i), i^2)) ss - sapply(1:4, fn) ss [,1] [,2] [,3] [,4] [1,] 1 2 3 4 [2,] 14916 ss[,1] [[1]] [1] 1 [[2]] [1] 1 I.e., the rows can be of different mode. The easiest way out is just not to do that, i.e. return a vectore c(i, i^2) instead. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 with lapply [addirional clarification needed]
Try str(ss) to see what it really looks like. You probably want: fn - function(i) c(i, i^2) On Sat, Nov 22, 2008 at 4:54 AM, megh [EMAIL PROTECTED] wrote: I need one more clarification here : Here I did : fn - function(i) return(list(i, i^2)) ss = sapply(1:4, fn) Here the object ss should be a matrix object : is.matrix(ss) However I feel it lacks some the matrix object properties. For example the syntax min(ss[1,]) generates an error : Error in min(ss[1, ]) : invalid 'type' (list) of argument. What should be the way out? Am I missing something ? Regards, baptiste auguie-2 wrote: Hi, you are feeding lapply i as an optional argument, which is passed to fn() and causes an error. Just use lapply(1:4, fn), or better yet, sapply, fn - function(i) return(i^2) sapply(1:4, fn) [1] 1 4 9 16 Hope this helps, baptiste On 20 Nov 2008, at 16:31, megh wrote: I have written following codes, with intention to get a list with values 1,2,9,16 : fn - function(i) return(i^2) lapply(1:4, fn, i) However I got following error : Error in FUN(1:4[[1L]], ...) : unused argument(s) (1) Can anyone please tell me what will be the correct code here? Regards, -- View this message in context: http://www.nabble.com/Error-with-lapply-tp20605066p20605066.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. _ Baptiste Auguié School of Physics University of Exeter Stocker Road, Exeter, Devon, EX4 4QL, UK Phone: +44 1392 264187 http://newton.ex.ac.uk/research/emag __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://www.nabble.com/Error-with-lapply-tp20605066p20634821.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Error with lapply
I have written following codes, with intention to get a list with values 1,2,9,16 : fn - function(i) return(i^2) lapply(1:4, fn, i) However I got following error : Error in FUN(1:4[[1L]], ...) : unused argument(s) (1) Can anyone please tell me what will be the correct code here? Regards, -- View this message in context: http://www.nabble.com/Error-with-lapply-tp20605066p20605066.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error with lapply
Hi, you are feeding lapply i as an optional argument, which is passed to fn() and causes an error. Just use lapply(1:4, fn), or better yet, sapply, fn - function(i) return(i^2) sapply(1:4, fn) [1] 1 4 9 16 Hope this helps, baptiste On 20 Nov 2008, at 16:31, megh wrote: I have written following codes, with intention to get a list with values 1,2,9,16 : fn - function(i) return(i^2) lapply(1:4, fn, i) However I got following error : Error in FUN(1:4[[1L]], ...) : unused argument(s) (1) Can anyone please tell me what will be the correct code here? Regards, -- View this message in context: http://www.nabble.com/Error-with-lapply-tp20605066p20605066.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. _ Baptiste Auguié School of Physics University of Exeter Stocker Road, Exeter, Devon, EX4 4QL, UK Phone: +44 1392 264187 http://newton.ex.ac.uk/research/emag __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 with lapply
on 11/20/2008 10:31 AM megh wrote: I have written following codes, with intention to get a list with values 1,2,9,16 : fn - function(i) return(i^2) lapply(1:4, fn, i) However I got following error : Error in FUN(1:4[[1L]], ...) : unused argument(s) (1) Can anyone please tell me what will be the correct code here? Regards, Try this: fn - function(i) i^2 lapply(1:4, fn) [[1]] [1] 1 [[2]] [1] 4 [[3]] [1] 9 [[4]] [1] 16 The error message indicates that the argument 'i' that you have in your initial attempt to use lappply() is unused, because the values 1:4 are passed to the function's first argument by default already. Thus, specifying 'i' again is an error, since there is not a second argument in your function fn(). Note also that 'return()' is not needed, as per the Details in ?return: If the end of a function is reached without calling return, the value of the last evaluated expression is returned. Note also, that since lapply() effectively uses an internal loop, a faster vectorized approach would be: as.list((1:4) ^ 2) [[1]] [1] 1 [[2]] [1] 4 [[3]] [1] 9 [[4]] [1] 16 For example, using 100,000 instead of 4: system.time(x1 - lapply(1:10, fn)) user system elapsed 0.500 0.015 0.600 system.time(x2 - as.list((1:10) ^ 2)) user system elapsed 0.018 0.004 0.039 identical(x1, x2) [1] TRUE HTH, Marc Schwartz __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 with lapply
lapply already passes the first arg to fn and by specifying the i (which is undefined -- its only defined within fn) it would be trying to to pass a second arg to fn yet fn takes only takes one arg. Try these: lapply(1:4, fn) lapply(1:4, ^, 2) On Thu, Nov 20, 2008 at 11:31 AM, megh [EMAIL PROTECTED] wrote: I have written following codes, with intention to get a list with values 1,2,9,16 : fn - function(i) return(i^2) lapply(1:4, fn, i) However I got following error : Error in FUN(1:4[[1L]], ...) : unused argument(s) (1) Can anyone please tell me what will be the correct code here? Regards, -- View this message in context: http://www.nabble.com/Error-with-lapply-tp20605066p20605066.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error with lapply
To be clear, the problem is not the return statement in your function, but the extra argument, i, in your lapply statement: lapply(1:4,fn) works just fine with your original function. You need to read ?lapply more carefully: fn receives the values of the first argument (1:4) in turn automatically; other arguments in lapply are passed in as **additional** arguments to fn, of which there are none here. Compare: fn - function(i,a)i^2+a lapply(1:4,fn) ## error lapply(1:4,fn,5) Cheers, Bert Bert Gunter Genentech -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Marc Schwartz Sent: Thursday, November 20, 2008 8:50 AM To: megh Cc: r-help@r-project.org Subject: Re: [R] Error with lapply on 11/20/2008 10:31 AM megh wrote: I have written following codes, with intention to get a list with values 1,2,9,16 : fn - function(i) return(i^2) lapply(1:4, fn, i) However I got following error : Error in FUN(1:4[[1L]], ...) : unused argument(s) (1) Can anyone please tell me what will be the correct code here? Regards, Try this: fn - function(i) i^2 lapply(1:4, fn) [[1]] [1] 1 [[2]] [1] 4 [[3]] [1] 9 [[4]] [1] 16 The error message indicates that the argument 'i' that you have in your initial attempt to use lappply() is unused, because the values 1:4 are passed to the function's first argument by default already. Thus, specifying 'i' again is an error, since there is not a second argument in your function fn(). Note also that 'return()' is not needed, as per the Details in ?return: If the end of a function is reached without calling return, the value of the last evaluated expression is returned. Note also, that since lapply() effectively uses an internal loop, a faster vectorized approach would be: as.list((1:4) ^ 2) [[1]] [1] 1 [[2]] [1] 4 [[3]] [1] 9 [[4]] [1] 16 For example, using 100,000 instead of 4: system.time(x1 - lapply(1:10, fn)) user system elapsed 0.500 0.015 0.600 system.time(x2 - as.list((1:10) ^ 2)) user system elapsed 0.018 0.004 0.039 identical(x1, x2) [1] TRUE HTH, Marc Schwartz __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] error in lapply
Dear all,
I am getting a error while using lapply to generate plots. The variable
.name is used to identify each plot in the main variable. The method
worked once but afterwards seems to throw up an error when used in a
different case. The input ...
dataOut - lapply(names(dataIn), FUN =
function(.name){anotherplotFun(dataIn[[.name]], numb = .name)} )
Throws up the error ...
Error in testFun(corrData[[.name]], numb = .name) :
promise already under evaluation: recursive default argument reference or
earlier problems?
Thanks
Chibisi
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__
R-help@r-project.org mailing list
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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] error in lapply (sorry error in last e-mail)
Dear all,
I am getting a error while using lapply to generate plots. The variable
.name is used to identify each plot in the main variable. The method
worked once but afterwards seems to throw up an error when used in a
different case. The input ...
dataOut - lapply(names(dataIn), FUN = function(.name){
anotherplotFun(dataIn[[.name]], numb = .name)} )
Throws up the error ...
Error in anotherplotFun(dataIn[[.name]], numb = .name) :
promise already under evaluation: recursive default argument reference or
earlier problems?
Thanks
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.
